Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.

PubMed

Kole, Chittaranjan; Muthamilarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J; Cockram, James; de Oliveira, Antonio Costa; De Pace, Ciro; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W; Iorizzo, Massimo; Ismail, Abdelbagi M; Marshall, Athole; Mayes, Sean; Nguyen, Henry T; Ogbonnaya, Francis C; Ortiz, Rodomiro; Paterson, Andrew H; Simon, Philipp W; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K; Wullschleger, Stan D; Yano, Masahiro; Prasad, Manoj

2015-01-01

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

PubMed Central

2012-01-01

Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking. PMID:22448748

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

PubMed

Uwimana, Brigitte; Smulders, Marinus J M; Hooftman, Danny A P; Hartman, Yorike; van Tienderen, Peter H; Jansen, Johannes; McHale, Leah K; Michelmore, Richard W; Visser, Richard G F; van de Wiel, Clemens C M

2012-03-26

After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.

A scalable satellite-based crop yield mapper: Integrating satellites and crop models for field-scale estimation in India

NASA Astrophysics Data System (ADS)

Jain, M.; Singh, B.; Srivastava, A.; Lobell, D. B.

2015-12-01

Food security will be challenged over the upcoming decades due to increased food demand, natural resource degradation, and climate change. In order to identify potential solutions to increase food security in the face of these changes, tools that can rapidly and accurately assess farm productivity are needed. With this aim, we have developed generalizable methods to map crop yields at the field scale using a combination of satellite imagery and crop models, and implement this approach within Google Earth Engine. We use these methods to examine wheat yield trends in Northern India, which provides over 15% of the global wheat supply and where over 80% of farmers rely on wheat as a staple food source. In addition, we identify the extent to which farmers are shifting sow date in response to heat stress, and how well shifting sow date reduces the negative impacts of heat stress on yield. To identify local-level decision-making, we map wheat sow date and yield at a high spatial resolution (30 m) using Landsat satellite imagery from 1980 to the present. This unique dataset allows us to examine sow date decisions at the field scale over 30 years, and by relating these decisions to weather experienced over the same time period, we can identify how farmers learn and adapt cropping decisions based on weather through time.

Analysis of physiological and morphological traits associated with thermal stress acclimation in cotton

USDA-ARS?s Scientific Manuscript database

Management strategies to reduce water withdrawals for irrigation and maintain agriculture industry viability and vitality of the Southern Ogallala Aquifer Region include developing crop cultivars that produce economic returns with less water. Knowledge to identify and develop profitable crop cultiv...

A study of the early detection of insect infestations and density/distribution of host plants. [Rio Grande

NASA Technical Reports Server (NTRS)

Hart, W. G. (Principal Investigator); Ingle, S. J.; Davis, M. R.

1975-01-01

The author has identified the following significant results. With comparative observations of film types and seasonal influences on reflectance characteristics, many crop varieties can be identified. This study shows that citrus, sugar cane, brush, some winter vegetables, and grain crops could be identified. Vegetative patterns in border areas can be detected. This information can be useful in detecting avenues of entry of pest species and areas of stress that require vigilance in stopping the spread of destructive species. Influence of some environmental factors on crops that may be confused with pest injury, or related factors, can be detected and identified with Skylab data (S-190B).

Corn response to climate stress detected with satellite-based NDVI time series

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ruoyu; Cherkauer, Keith; Bowling, Laura

Corn growth conditions and yield are closely dependent on climate variability. Leaf growth, measured as the leaf area index, can be used to identify changes in crop growth in response to climate stress. This research was conducted to capture patterns of spatial and temporal corn leaf growth under climate stress for the St. Joseph River watershed, in northeastern Indiana. Leaf growth is represented by the Normalized Difference Vegetative Index (NDVI) retrieved from multiple years (2000–2010) of Landsat 5 TM images. By comparing NDVI values for individual image dates with the derived normal curve, the response of crop growth to environmentalmore » factors is quantified as NDVI residuals. Regression analysis revealed a significant relationship between yield and NDVI residual during the pre-silking period, indicating that NDVI residuals reflect crop stress in the early growing period that impacts yield. Both the mean NDVI residuals and the percentage of image pixels where corn was under stress (risky pixel rate) are significantly correlated with water stress. Dry weather is prone to hamper potential crop growth, with stress affecting most of the observed corn pixels in the area. Oversupply of rainfall at the end of the growing season was not found to have a measurable effect on crop growth, while above normal precipitation earlier in the growing season reduces the risk of yield loss at the watershed scale. Furthermore, the spatial extent of stress is much lower when precipitation is above normal than under dry conditions, masking the impact of small areas of yield loss at the watershed scale.« less

Corn response to climate stress detected with satellite-based NDVI time series

DOE PAGES

Wang, Ruoyu; Cherkauer, Keith; Bowling, Laura

2016-03-23

Corn growth conditions and yield are closely dependent on climate variability. Leaf growth, measured as the leaf area index, can be used to identify changes in crop growth in response to climate stress. This research was conducted to capture patterns of spatial and temporal corn leaf growth under climate stress for the St. Joseph River watershed, in northeastern Indiana. Leaf growth is represented by the Normalized Difference Vegetative Index (NDVI) retrieved from multiple years (2000–2010) of Landsat 5 TM images. By comparing NDVI values for individual image dates with the derived normal curve, the response of crop growth to environmentalmore » factors is quantified as NDVI residuals. Regression analysis revealed a significant relationship between yield and NDVI residual during the pre-silking period, indicating that NDVI residuals reflect crop stress in the early growing period that impacts yield. Both the mean NDVI residuals and the percentage of image pixels where corn was under stress (risky pixel rate) are significantly correlated with water stress. Dry weather is prone to hamper potential crop growth, with stress affecting most of the observed corn pixels in the area. Oversupply of rainfall at the end of the growing season was not found to have a measurable effect on crop growth, while above normal precipitation earlier in the growing season reduces the risk of yield loss at the watershed scale. Furthermore, the spatial extent of stress is much lower when precipitation is above normal than under dry conditions, masking the impact of small areas of yield loss at the watershed scale.« less

Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman-Derr, Devin; Tringe, Susannah G.

The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attemptedmore » to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here in this paper, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions« less

How can we improve crop genotypes to increase stress resilience and productivity in a future climate? A new crop screening method based on productivity and resistance to abiotic stress

PubMed Central

Thiry, Arnauld A.; Chavez Dulanto, Perla N.; Reynolds, Matthew P.; Davies, William J.

2016-01-01

The need to accelerate the selection of crop genotypes that are both resistant to and productive under abiotic stress is enhanced by global warming and the increase in demand for food by a growing world population. In this paper, we propose a new method for evaluation of wheat genotypes in terms of their resilience to stress and their production capacity. The method quantifies the components of a new index related to yield under abiotic stress based on previously developed stress indices, namely the stress susceptibility index, the stress tolerance index, the mean production index, the geometric mean production index, and the tolerance index, which were created originally to evaluate drought adaptation. The method, based on a scoring scale, offers simple and easy visualization and identification of resilient, productive and/or contrasting genotypes according to grain yield. This new selection method could help breeders and researchers by defining clear and strong criteria to identify genotypes with high resilience and high productivity and provide a clear visualization of contrasts in terms of grain yield production under stress. It is also expected that this methodology will reduce the time required for first selection and the number of first-selected genotypes for further evaluation by breeders and provide a basis for appropriate comparisons of genotypes that would help reveal the biology behind high stress productivity of crops. PMID:27677299

Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

DOE PAGES

Kole, Chittaranjan; Muthamiliarasan, Mehanathan; Henry, Robert; ...

2015-08-11

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful inmore » enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.« less

Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kole, Chittaranjan; Muthamiliarasan, Mehanathan; Henry, Robert

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful inmore » enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.« less

Temperature stress and plant sexual reproduction: uncovering the weakest links.

PubMed

Zinn, Kelly E; Tunc-Ozdemir, Meral; Harper, Jeffrey F

2010-04-01

The reproductive (gametophytic) phase in flowering plants is often highly sensitive to hot or cold temperature stresses, with even a single hot day or cold night sometimes being fatal to reproductive success. This review describes studies of temperature stress on several crop plants, which suggest that pollen development and fertilization may often be the most sensitive reproductive stage. Transcriptome and proteomic studies on several plant species are beginning to identify stress response pathways that function during pollen development. An example is provided here of genotypic differences in the reproductive stress tolerance between two ecotypes of Arabidopsis thaliana Columbia (Col) and Hilversum (Hi-0), when reproducing under conditions of hot days and cold nights. Hi-0 exhibited a more severe reduction in seed set, correlated with a reduction in pollen tube growth potential and tropism defects. Hi-0 thus provides an Arabidopsis model to investigate strategies for improved stress tolerance in pollen. Understanding how different plants cope with stress during reproductive development offers the potential to identify genetic traits that could be manipulated to improve temperature tolerance in selected crop species being cultivated in marginal climates.

Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

PubMed Central

Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; Schranz, M Eric; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; Michelmore, Richard W; van Tienderen, Peter H

2014-01-01

The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. PMID:25360276

microRNAs Associated with Drought Response in the Bioenergy Crop Sugarcane (Saccharum spp.)

PubMed Central

Vilela, Romel Duarte; Costa, Gustavo Gilson Lacerda; Dias, Lara Isys; Endres, Laurício; Menossi, Marcelo

2012-01-01

Sugarcane (Saccharum spp.) is one of the most important crops in the world. Drought stress is a major abiotic stress factor that significantly reduces sugarcane yields. However the gene network that mediates plant responses to water stress remains largely unknown in several crop species. Although several microRNAs that mediate post-transcriptional regulation during water stress have been described in other species, the role of the sugarcane microRNAs during drought stress has not been studied. The objective of this work was to identify sugarcane miRNAs that are differentially expressed under drought stress and to correlate this expression with the behavior of two sugarcane cultivars with different drought tolerances. The sugarcane cultivars RB867515 (higher drought tolerance) and RB855536 (lower drought tolerance) were cultivated in a greenhouse for three months and then subjected to drought for 2, 4, 6 or 8 days. By deep sequencing of small RNAs, we were able to identify 18 miRNA families. Among all of the miRNAs thus identified, seven were differentially expressed during drought. Six of these miRNAs were differentially expressed at two days of stress, and five miRNAs were differentially expressed at four days. The expression levels of five miRNAs (ssp-miR164, ssp-miR394, ssp-miR397, ssp-miR399-seq 1 and miR528) were validated by RT-qPCR (quantitative reverse transcriptase PCR). Six precursors and the targets of the differentially expressed miRNA were predicted using an in silico approach and validated by RT-qPCR; many of these targets may play important roles in drought tolerance. These findings constitute a significant increase in the number of identified miRNAs in sugarcane and contribute to the elucidation of the complex regulatory network that is activated by drought stress. PMID:23071617

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

PubMed Central

Dwivedi, Sangam L.; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

2017-01-01

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses. PMID:28900432

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes.

PubMed

Dwivedi, Sangam L; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

2017-01-01

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.

Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum).

PubMed

Dash, Prasanta K; Cao, Yongguo; Jailani, Abdul K; Gupta, Payal; Venglat, Prakash; Xiang, Daoquan; Rai, Rhitu; Sharma, Rinku; Thirunavukkarasu, Nepolean; Abdin, Malik Z; Yadava, Devendra K; Singh, Nagendra K; Singh, Jas; Selvaraj, Gopalan; Deyholos, Mike; Kumar, Polumetla Ananda; Datla, Raju

2014-01-01

A robust phenotypic plasticity to ward off adverse environmental conditions determines performance and productivity in crop plants. Flax (linseed), is an important cash crop produced for natural textile fiber (linen) or oilseed with many health promoting products. This crop is prone to drought stress and yield losses in many parts of the world. Despite recent advances in drought research in a number of important crops, related progress in flax is very limited. Since, response of this plant to drought stress has not been addressed at the molecular level; we conducted microarray analysis to capture transcriptome associated with induced drought in flax. This study identified 183 differentially expressed genes (DEGs) associated with diverse cellular, biophysical and metabolic programs in flax. The analysis also revealed especially the altered regulation of cellular and metabolic pathways governing photosynthesis. Additionally, comparative transcriptome analysis identified a plethora of genes that displayed differential regulation both spatially and temporally. These results revealed co-regulated expression of 26 genes in both shoot and root tissues with implications for drought stress response. Furthermore, the data also showed that more genes are upregulated in roots compared to shoots, suggesting that roots may play important and additional roles in response to drought in flax. With prolonged drought treatment, the number of DEGs increased in both tissue types. Differential expression of selected genes was confirmed by qRT-PCR, thus supporting the suggested functional association of these intrinsic genes in maintaining growth and homeostasis in response to imminent drought stress in flax. Together the present study has developed foundational and new transcriptome data sets for drought stress in flax.

A multimodal image sensor system for identifying water stress in grapevines

NASA Astrophysics Data System (ADS)

Zhao, Yong; Zhang, Qin; Li, Minzan; Shao, Yongni; Zhou, Jianfeng; Sun, Hong

2012-11-01

Water stress is one of the most common limitations of fruit growth. Water is the most limiting resource for crop growth. In grapevines, as well as in other fruit crops, fruit quality benefits from a certain level of water deficit which facilitates to balance vegetative and reproductive growth and the flow of carbohydrates to reproductive structures. A multi-modal sensor system was designed to measure the reflectance signature of grape plant surfaces and identify different water stress levels in this paper. The multi-modal sensor system was equipped with one 3CCD camera (three channels in R, G, and IR). The multi-modal sensor can capture and analyze grape canopy from its reflectance features, and identify the different water stress levels. This research aims at solving the aforementioned problems. The core technology of this multi-modal sensor system could further be used as a decision support system that combines multi-modal sensory data to improve plant stress detection and identify the causes of stress. The images were taken by multi-modal sensor which could output images in spectral bands of near-infrared, green and red channel. Based on the analysis of the acquired images, color features based on color space and reflectance features based on image process method were calculated. The results showed that these parameters had the potential as water stress indicators. More experiments and analysis are needed to validate the conclusion.

Emerging trends in the functional genomics of the abiotic stress response in crop plants.

PubMed

Vij, Shubha; Tyagi, Akhilesh K

2007-05-01

Plants are exposed to different abiotic stresses, such as water deficit, high temperature, salinity, cold, heavy metals and mechanical wounding, under field conditions. It is estimated that such stress conditions can potentially reduce the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms developed during evolution to mitigate against stress by plants. Before the advent of the genomics era, researchers primarily used a gene-by-gene approach to decipher the function of the genes involved in the abiotic stress response. However, abiotic stress tolerance is a complex trait and, although large numbers of genes have been identified to be involved in the abiotic stress response, there remain large gaps in our understanding of the trait. The availability of the genome sequences of certain important plant species has enabled the use of strategies, such as genome-wide expression profiling, to identify the genes associated with the stress response, followed by the verification of gene function by the analysis of mutants and transgenics. Certain components of both abscisic acid-dependent and -independent cascades involved in the stress response have already been identified. Information originating from the genome-wide analysis of abiotic stress tolerance will help to provide an insight into the stress-responsive network(s), and may allow the modification of this network to reduce the loss caused by stress and to increase agricultural productivity.

Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

PubMed Central

Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

2015-01-01

Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. PMID:26340626

Food Allergy - Basic Mechanisms and Applications to Identifying Risks Associated with Plant Incorporated Pesticides and Other Genetically Modified Crops

EPA Science Inventory

Food allergy is a relatively new concern for toxicologists as a result of the incorporation of novel proteins into food crops in order to promote resistance to pests and other stresses, improve nutrition, or otherwise modify the phenotype. Food allergy can manifest as inflammatio...

Increased yield stability of field-grown winter barley (Hordeum vulgare L.) varietal mixtures through ecological processes

PubMed Central

Creissen, Henry E.; Jorgensen, Tove H.; Brown, James K.M.

2016-01-01

Crop variety mixtures have the potential to increase yield stability in highly variable and unpredictable environments, yet knowledge of the specific mechanisms underlying enhanced yield stability has been limited. Ecological processes in genetically diverse crops were investigated by conducting field trials with winter barley varieties (Hordeum vulgare), grown as monocultures or as three-way mixtures in fungicide treated and untreated plots at three sites. Mixtures achieved yields comparable to the best performing monocultures whilst enhancing yield stability despite being subject to multiple predicted and unpredicted abiotic and biotic stresses including brown rust (Puccinia hordei) and lodging. There was compensation through competitive release because the most competitive variety overyielded in mixtures thereby compensating for less competitive varieties. Facilitation was also identified as an important ecological process within mixtures by reducing lodging. This study indicates that crop varietal mixtures have the capacity to stabilise productivity even when environmental conditions and stresses are not predicted in advance. Varietal mixtures provide a means of increasing crop genetic diversity without the need for extensive breeding efforts. They may confer enhanced resilience to environmental stresses and thus be a desirable component of future cropping systems for sustainable arable farming. PMID:27375312

Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress.

PubMed

Lata, Charu; Sahu, Pranav Pankaj; Prasad, Manoj

2010-03-19

Dehydration stress is one of the most important abiotic stresses that adversely influence crop growth and productivity. With the aim to understand the molecular mechanisms underlying dehydration stress tolerance in foxtail millet (Setaria italica L.), a drought tolerant crop, we examined its transcriptome changes at two time points (early and late) of dehydration stress. Two suppression subtractive hybridization (SSH) forward libraries were constructed from 21-day old seedlings of tolerant cv. Prasad at 0.5 and 6h PEG-induced dehydration stress. A total of 327 unique ESTs were identified from both libraries and were classified into 11 different categories according to their putative functions. The plant response against dehydration stress was complex, representing major transcripts involved in metabolism, stress, signaling, transcription regulation, translation and proteolysis. By Reverse Northern (RN) technique we identified the differential expression pattern of 327 transcripts, 86 (about 26%) of which showed > or = 1.7-fold induction. Further the obtained results were validated by quantitative real-time PCR (qRT-PCR) to have a comparative expression profiling of randomly chosen 9 up-regulated transcripts (> or =2.5 fold induction) between cv. Prasad (tolerant) and cv. Lepakshi (sensitive) upon dehydration stress. These transcripts showed a differential expression pattern in both cultivars at different time points of stress treatment as analyzed by qRT-PCR. The possible relationship of the identified transcripts with dehydration tolerance mechanism is discussed. Copyright 2010 Elsevier Inc. All rights reserved.

A meteorologically driven grain sorghum stress indicator model

NASA Technical Reports Server (NTRS)

Taylor, T. W.; Ravet, F. W. (Principal Investigator)

1981-01-01

A grain sorghum soil moisture and temperature stress model is described. It was developed to serve as a meteorological data filter to alert commodity analysts to potential stress conditions and crop phenology in selected grain sorghum production areas. The model also identifies optimum conditions on a daily basis and planting/harvest problems associated with poor tractability.

Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea.

PubMed

Bhardwaj, Ankur R; Joshi, Gopal; Kukreja, Bharti; Malik, Vidhi; Arora, Priyanka; Pandey, Ritu; Shukla, Rohit N; Bankar, Kiran G; Katiyar-Agarwal, Surekha; Goel, Shailendra; Jagannath, Arun; Kumar, Amar; Agarwal, Manu

2015-01-21

Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses. We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resource generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.

Large Area Crop Inventory Experiment (LACIE). Detecting and monitoring agricultural vegetative water stress over large areas using LANDSAT digital data. [Great Plains

NASA Technical Reports Server (NTRS)

Thompson, D. R.; Wehmanen, O. A. (Principal Investigator)

1978-01-01

The author has identified the following significant results. The Green Number Index technique which uses LANDSAT digital data from 5X6 nautical mile sampling frames was expanded to evaluate its usefulness in detecting and monitoring vegetative water stress over the Great Plains. At known growth stages for wheat, segments were classified as drought or non drought. Good agreement was found between the 18 day remotely sensed data and a weekly ground-based crop moisture index. Operational monitoring of the 1977 U.S.S.R. and Australian wheat crops indicated drought conditions. Drought isoline maps produced by the Green Number Index technique were in good agreement with conventional sources.

Evaluation and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) Under Drought Stress Conditions

PubMed Central

Sinha, Pallavi; Singh, Vikas K.; Suryanarayana, V.; Krishnamurthy, L.; Saxena, Rachit K.; Varshney, Rajeev K.

2015-01-01

Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions. PMID:25849964

Evaluation and validation of housekeeping genes as reference for gene expression studies in pigeonpea (Cajanus cajan) under drought stress conditions.

PubMed

Sinha, Pallavi; Singh, Vikas K; Suryanarayana, V; Krishnamurthy, L; Saxena, Rachit K; Varshney, Rajeev K

2015-01-01

Gene expression analysis using quantitative real-time PCR (qRT-PCR) is a very sensitive technique and its sensitivity depends on the stable performance of reference gene(s) used in the study. A number of housekeeping genes have been used in various expression studies in many crops however, their expression were found to be inconsistent under different stress conditions. As a result, species specific housekeeping genes have been recommended for different expression studies in several crop species. However, such specific housekeeping genes have not been reported in the case of pigeonpea (Cajanus cajan) despite the fact that genome sequence has become available for the crop. To identify the stable housekeeping genes in pigeonpea for expression analysis under drought stress conditions, the relative expression variations of 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18SrRNA, 25SrRNA, TUB6, ACT1, IF4α, UBC and HSP90) were studied on root, stem and leaves tissues of Asha (ICPL 87119). Three statistical algorithms geNorm, NormFinder and BestKeeper were used to define the stability of candidate genes. geNorm analysis identified IF4α and TUB6 as the most stable housekeeping genes however, NormFinder analysis determined IF4α and HSP90 as the most stable housekeeping genes under drought stress conditions. Subsequently validation of the identified candidate genes was undertaken in qRT-PCR based gene expression analysis of uspA gene which plays an important role for drought stress conditions in pigeonpea. The relative quantification of the uspA gene varied according to the internal controls (stable and least stable genes), thus highlighting the importance of the choice of as well as validation of internal controls in such experiments. The identified stable and validated housekeeping genes will facilitate gene expression studies in pigeonpea especially under drought stress conditions.

Sonora exploratory study for the detection of wheat-leaf rust

NASA Technical Reports Server (NTRS)

Payne, R. W. (Principal Investigator)

1980-01-01

The applicability of LANDSAT remote sensing technology to the detection of a wheat-leaf-rust epidemic in Sonora, Mexico, during 1977 was investigated. LANDSAT data acquired during crop years 1975-76 and 1976-77 were clustered, classified, and analyzed in order to detect agricultural changes. Analysis of 1977 data indicates a significant proportion of the identified wheat is stressed (potentially rust-infected). Additional analyses show a significant increase in fallowing during the year, as well as a substantial decrease in reservoir levels in the Sonora agricultural region. Ground observations are required to substantiate these analyses. The possibility exists that heat-rust is not LANDSAT detectable and that the clusters identified as containing stressed signatures represent different varieties of wheat or perhaps nonwheat crops.

Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress.

PubMed

Singh, Roshan Kumar; Jaishankar, Jananee; Muthamilarasan, Mehanathan; Shweta, Shweta; Dangi, Anand; Prasad, Manoj

2016-09-02

Heat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.

Environment characterization as an aid to wheat improvement: interpreting genotype-environment interactions by modelling water-deficit patterns in North-Eastern Australia.

PubMed

Chenu, K; Cooper, M; Hammer, G L; Mathews, K L; Dreccer, M F; Chapman, S C

2011-03-01

Genotype-environment interactions (GEI) limit genetic gain for complex traits such as tolerance to drought. Characterization of the crop environment is an important step in understanding GEI. A modelling approach is proposed here to characterize broadly (large geographic area, long-term period) and locally (field experiment) drought-related environmental stresses, which enables breeders to analyse their experimental trials with regard to the broad population of environments that they target. Water-deficit patterns experienced by wheat crops were determined for drought-prone north-eastern Australia, using the APSIM crop model to account for the interactions of crops with their environment (e.g. feedback of plant growth on water depletion). Simulations based on more than 100 years of historical climate data were conducted for representative locations, soils, and management systems, for a check cultivar, Hartog. The three main environment types identified differed in their patterns of simulated water stress around flowering and during grain-filling. Over the entire region, the terminal drought-stress pattern was most common (50% of production environments) followed by a flowering stress (24%), although the frequencies of occurrence of the three types varied greatly across regions, years, and management. This environment classification was applied to 16 trials relevant to late stages testing of a breeding programme. The incorporation of the independently-determined environment types in a statistical analysis assisted interpretation of the GEI for yield among the 18 representative genotypes by reducing the relative effect of GEI compared with genotypic variance, and helped to identify opportunities to improve breeding and germplasm-testing strategies for this region.

Advanced methodology to determine plant stresses using in-situ spectral data

NASA Astrophysics Data System (ADS)

Polinova, Maria; Brook, Anna; Housh, Mashor

2017-04-01

Fluorescence method in remote sensing has long been a traditional method estimating plant state. Vegetation indices (VIs) are tool for assessment plants' state based on its spectral characteristics. During the last half-century, in this domain were developed many vegetation indices and even more modifications of these indices. Nowadays, visible range across electromagnetic waves allows assessing plants' health and calculating its physical parameters. One of the VI's capabilities is detecting stress in plants. This approach has application in different areas. For discerning external environment (unnatural) stress from features of plant's development most of VIs have border values for greenness and health. This is the reason for these methods to be superficial and insufficient detecting and estimating stresses on the early stages. This limits plays especial importance in agriculture. Late stress detection leads to irreversible damage in crops and yield loss. We propose new principle of VI analysis for determination unnatural stress on early stages. Novelty of this method is common consideration several VIs related to plant's pigmentation: chlorophyll, carotenoids and anthocyanins. We have tasted this method on two agriculture fields: tomatoes and cotton. The goal of study was to determinate water crop stress at its beginning. A single VI shows reactions on emergence growth stage, fruit producing and ripening phase. It was hard to isolate crops' reaction on water from reaction on growth changes. Nevertheless, we have noted that there is correlation between chlorophyll VIs and carotenoid VIs. The correlation strength was depended on stress type. Based on common VIs analysis we were able to identify dryness and over irrigation stress. In addition, we have determine reaction on fertilizers input. Common VIs analysis can improve existing fluorescence method of remote sensing monitoring. It can find application in areas where the early plant's stress detection is very impotent (e.g. agriculture). Another advantage of this method is identifying stress type. It can increase the role of spectral data for design making.

Phytohormones and Beneficial Microbes: Essential Components for Plants to Balance Stress and Fitness

PubMed Central

Egamberdieva, Dilfuza; Wirth, Stephan J.; Alqarawi, Abdulaziz A.; Abd_Allah, Elsayed F.; Hashem, Abeer

2017-01-01

Plants are subjected to various abiotic stresses, such as drought, extreme temperature, salinity, and heavy metals. Abiotic stresses have negative impact on the physiology and morphology of plants through defects in the genetic regulation of cellular pathways. Plants employ several tolerance mechanisms and pathways to avert the effects of stresses that are triggered whenever alterations in metabolism are encountered. Phytohormones are among the most important growth regulators; they are known for having a prominent impact on plant metabolism, and additionally, they play a vital role in the stimulation of plant defense response mechanisms against stresses. Exogenous phytohormone supplementation has been adopted to improve growth and metabolism under stress conditions. Recent investigations have shown that phytohormones produced by root-associated microbes may prove to be important metabolic engineering targets for inducing host tolerance to abiotic stresses. Phytohormone biosynthetic pathways have been identified using several genetic and biochemical methods, and numerous reviews are currently available on this topic. Here, we review current knowledge on the function of phytohormones involved in the improvement of abiotic stress tolerance and defense response in plants exposed to different stressors. We focus on recent successes in identifying the roles of microbial phytohormones that induce stress tolerance, especially in crop plants. In doing so, this review highlights important plant morpho-physiological traits that can be exploited to identify the positive effects of phytohormones on stress tolerance. This review will therefore be helpful to plant physiologists and agricultural microbiologists in designing strategies and tools for the development of broad spectrum microbial inoculants supporting sustainable crop production under hostile environments. PMID:29163398

Towards Establishment of a Rice Stress Response Interactome

PubMed Central

Seo, Young-Su; Chern, Mawsheng; Bartley, Laura E.; Han, Muho; Jung, Ki-Hong; Lee, Insuk; Walia, Harkamal; Richter, Todd; Xu, Xia; Cao, Peijian; Bai, Wei; Ramanan, Rajeshwari; Amonpant, Fawn; Arul, Loganathan; Canlas, Patrick E.; Ruan, Randy; Park, Chang-Jin; Chen, Xuewei; Hwang, Sohyun; Jeon, Jong-Seong; Ronald, Pamela C.

2011-01-01

Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance. PMID:21533176

Microarray and growth analyses identify differences and similarities of early corn response to weeds, shade, and nitrogen stress

USDA-ARS?s Scientific Manuscript database

Weed interference with crop growth is often attributed to water, nutrient, or light competition; however, specific physiological responses to these stresses are not well described. This study’s objective was to compare growth, yield, and gene expression responses of corn to nitrogen (N), low light (...

Drought-responsive protein profiles reveal diverse defense pathways in corn kernels under field drought atress

USDA-ARS?s Scientific Manuscript database

Drought stress is a major factor which contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two lines (B73 and Lo964) with contrasting drought sensitivity were...

Using observed warming to identify hazards to Mozambique maize production

USGS Publications Warehouse

Funk, Christopher C.; Harrison, Laura; Eilerts, Gary

2011-01-01

New Perspectives on Crop Yield Constraints because of Climate Change. Climate change impact assessments usually focus on changes to precipitation because most global food production is from rainfed cropping systems; however, other aspects of climate change may affect crop growth and potential yields.A recent (2011) study by the University of California, Santa Barbara (UCSB) Climate Hazards Group, determined that climate change may be affecting Mozambique's primary food crop in a usually overlooked, but potentially significant way (Harrison and others, 2011). The study focused on the direct relation between maize crop development and growing season temperature. It determined that warming during the past three decades in Mozambique may be causing more frequent crop stress and yield reductions in that country's maize crop, independent of any changes occurring in rainfall. This report summarizes the findings and conclusions of that study.

Hyperspectral imaging to identify salt-tolerant wheat lines

USDA-ARS?s Scientific Manuscript database

In order to address the worldwide growing demand for food, agriculture is facing certain challenges and limitations. One of the important threats limiting crop productivity is salinity. Identifying salt tolerate varieties is crucial to mitigate the negative effects of this abiotic stress in agricult...

Characterizing drought stress and trait influence on maize yield under current and future conditions.

PubMed

Harrison, Matthew T; Tardieu, François; Dong, Zhanshan; Messina, Carlos D; Hammer, Graeme L

2014-03-01

Global climate change is predicted to increase temperatures, alter geographical patterns of rainfall and increase the frequency of extreme climatic events. Such changes are likely to alter the timing and magnitude of drought stresses experienced by crops. This study used new developments in the classification of crop water stress to first characterize the typology and frequency of drought-stress patterns experienced by European maize crops and their associated distributions of grain yield, and second determine the influence of the breeding traits anthesis-silking synchrony, maturity and kernel number on yield in different drought-stress scenarios, under current and future climates. Under historical conditions, a low-stress scenario occurred most frequently (ca. 40%), and three other stress types exposing crops to late-season stresses each occurred in ca. 20% of cases. A key revelation shown was that the four patterns will also be the most dominant stress patterns under 2050 conditions. Future frequencies of low drought stress were reduced by ca. 15%, and those of severe water deficit during grain filling increased from 18% to 25%. Despite this, effects of elevated CO2 on crop growth moderated detrimental effects of climate change on yield. Increasing anthesis-silking synchrony had the greatest effect on yield in low drought-stress seasonal patterns, whereas earlier maturity had the greatest effect in crops exposed to severe early-terminal drought stress. Segregating drought-stress patterns into key groups allowed greater insight into the effects of trait perturbation on crop yield under different weather conditions. We demonstrate that for crops exposed to the same drought-stress pattern, trait perturbation under current climates will have a similar impact on yield as that expected in future, even though the frequencies of severe drought stress will increase in future. These results have important ramifications for breeding of maize and have implications for studies examining genetic and physiological crop responses to environmental stresses. © 2013 John Wiley & Sons Ltd.

Genetic and Computational Approaches for Studying Plant Development and Abiotic Stress Responses Using Image-Based Phenotyping

NASA Astrophysics Data System (ADS)

Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.

2017-12-01

The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.

Stomatal density and metabolic determinants mediate salt stress adaptation and water use efficiency in basil (Ocimum basilicum L.).

PubMed

Barbieri, Giancarlo; Vallone, Simona; Orsini, Francesco; Paradiso, Roberta; De Pascale, Stefania; Negre-Zakharov, Florence; Maggio, Albino

2012-11-15

Increasing salinity tolerance and water-use efficiency in crop plants are two major challenges that agriculture must face in the next decades. Many physiological mechanisms and molecular components mediating crop response to environmental stresses have been identified. However, the functional inter-links between stress adaptation responses have not been completely understood. Using two basil cultivars (Napoletano and Genovese) with contrasting ability to respond to salt stress, here we demonstrate that reduced stomatal density, high ascorbate level and polyphenol oxidase (PPO) activity coordinately contribute to improve basil adaptation and water use efficiency (WUE) in saline environment. The constitutively reduced stomatal density was associated with a "delayed" accumulation of stress molecules (and growth inhibiting signals) such as abscisic acid (ABA) and proline, in the more tolerant Genovese. Leaf volatile profiling also revealed cultivar-specific patterns, which may suggest a role for the volatile phenylpropanoid eugenol and monoterpenes in conferring stress tolerance via antioxidant and signalling functions. Copyright © 2012 Elsevier GmbH. All rights reserved.

Role of redox homeostasis in thermo-tolerance under a climate change scenario

PubMed Central

de Pinto, Maria Concetta; Locato, Vittoria; Paradiso, Annalisa; De Gara, Laura

2015-01-01

Background Climate change predictions indicate a progressive increase in average temperatures and an increase in the frequency of heatwaves, which will have a negative impact on crop productivity. Over the last decade, a number of studies have addressed the question of how model plants or specific crops modify their metabolism when exposed to heat stress. Scope This review provides an overview of the redox pathways that contribute to how plants cope with heat stress. The focus is on the role of reactive oxygen species (ROS), redox metabolites and enzymes in the signalling pathways leading to the activation of defence responses. Additional attention is paid to the regulating mechanisms that lead to an increase in specific ROS-scavenging systems during heat stress, which have been studied in different model systems. Finally, increasing thermo-tolerance in model and crop plants by exposing them to heat acclimation or to exogenous treatments is discussed. Conclusions Although there is clear evidence that several strategies are specifically activated according to the intensity and the duration of heat stress, as well as the capacity of the different species or genotypes to overcome stress, an alteration in redox homeostasis seems to be a common event. Different mechanisms that act to enhance redox systems enable crops to overcome heat stress more effectively. Knowledge of thermo-tolerance within agronomic biodiversity is thus of key importance to enable researchers to identify new strategies for overcoming the impacts of climate change, and for decision-makers in planning for an uncertain future with new choices and options open to them. PMID:26034009

Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives

PubMed Central

Landi, Simone; Hausman, Jean-Francois; Guerriero, Gea; Esposito, Sergio

2017-01-01

Poaceae represent the most important group of crops susceptible to abiotic stress. This large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), and barley (Hordeum vulgare). These crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, while barley presents a natural drought and salt tolerance. During the green revolution (1940–1960), cereal breeding was very successful in developing high-yield crops varieties; however, these cultivars were maximized for highest yield under optimal conditions, and did not present suitable traits for tolerance under unfavorable conditions. The improvement of crop abiotic stress tolerance requires a deep knowledge of the phenomena underlying tolerance, to devise novel approaches and decipher the key components of agricultural production systems. Approaches to improve food production combining both enhanced water use efficiency (WUE) and acceptable yields are critical to create a sustainable agriculture in the future. This paper analyzes the latest results on abiotic stress tolerance in Poaceae. In particular, the focus will be directed toward various aspects of water deprivation and salinity response efficiency in Poaceae. Aspects related to cell wall metabolism will be covered, given the importance of the plant cell wall in sensing environmental constraints and in mediating a response; the role of silicon (Si), an important element for monocots' normal growth and development, will also be discussed, since it activates a broad-spectrum response to different exogenous stresses. Perspectives valorizing studies on landraces conclude the survey, as they help identify key traits for breeding purposes. PMID:28744298

Solar-Induced Fluorescence of Maize Across A Water Stress Gradient in the Midwestern USA

NASA Astrophysics Data System (ADS)

Miao, G.; Guan, K.; Suyker, A.; Yang, X.; Benarcchi, C. J.; Gamon, J. A.; Berry, J. A.; DeLucia, E.; Franz, T.; Arkebauer, T. J.; Zygielbaum, A. I.; Walter-Shea, E. A.; Moore, C.; Zhang, Y.; Kim, H.; Hmimina, G.

2017-12-01

In the coming decades, agricultural ecosystems will be challenged by rising temperatures, changing rainfall patterns, and increasing extreme weather. Understanding how crops respond to weather variability and how humans manage agriculture to mitigate and adapt to climate change is critical for improving agricultural sustainability and supporting increasing global food demands. Accurately estimating gross primary productivity (GPP) of crops is of importance to evaluate their sustainability and capability but remains a challenge. The recent development of solar-induced fluorescence (SIF) technology is stimulating studies to use SIF to approximate GPP. It has been observed that agricultural lands have remarkably high SIF and the SIF signal could be used as an indicator of vegetation stress, which is particularly valuable for improved monitoring of crop productivity and stress. To investigate the applicability of SIF for detecting maize stress and estimating GPP, we deployed three FluoSpec2 systems in 2017 at three long-term eddy covariance flux sites across the US Corn Belt, a rain-fed maize field (AmeriFlux sites US-NE3) and an irrigated maize field (US-NE2) at Mead, Nebraska and a rain-fed maize field at Urbana, Illinois. Together these form a water stress gradient. Variations in GPP, SIF, photosynthetic efficiency (LUE), SIF yield (SIFy), and relationships between GPP and SIF, LUE and SIFy will be compared as indications of the difference in maize growth across the water stress gradient. More importantly, differences in GPP and SIF signals will be examined over multiple growth stages to assess the potential of SIF in identifying the growth stages that are mostly affected by water stress and the ones that play the most important roles on the crop yield.

An explainable deep machine vision framework for plant stress phenotyping.

PubMed

Ghosal, Sambuddha; Blystone, David; Singh, Asheesh K; Ganapathysubramanian, Baskar; Singh, Arti; Sarkar, Soumik

2018-05-01

Current approaches for accurate identification, classification, and quantification of biotic and abiotic stresses in crop research and production are predominantly visual and require specialized training. However, such techniques are hindered by subjectivity resulting from inter- and intrarater cognitive variability. This translates to erroneous decisions and a significant waste of resources. Here, we demonstrate a machine learning framework's ability to identify and classify a diverse set of foliar stresses in soybean [ Glycine max (L.) Merr.] with remarkable accuracy. We also present an explanation mechanism, using the top-K high-resolution feature maps that isolate the visual symptoms used to make predictions. This unsupervised identification of visual symptoms provides a quantitative measure of stress severity, allowing for identification (type of foliar stress), classification (low, medium, or high stress), and quantification (stress severity) in a single framework without detailed symptom annotation by experts. We reliably identified and classified several biotic (bacterial and fungal diseases) and abiotic (chemical injury and nutrient deficiency) stresses by learning from over 25,000 images. The learned model is robust to input image perturbations, demonstrating viability for high-throughput deployment. We also noticed that the learned model appears to be agnostic to species, seemingly demonstrating an ability of transfer learning. The availability of an explainable model that can consistently, rapidly, and accurately identify and quantify foliar stresses would have significant implications in scientific research, plant breeding, and crop production. The trained model could be deployed in mobile platforms (e.g., unmanned air vehicles and automated ground scouts) for rapid, large-scale scouting or as a mobile application for real-time detection of stress by farmers and researchers. Copyright © 2018 the Author(s). Published by PNAS.

Extraction of Rice Phenological Differences under Heavy Metal Stress Using EVI Time-Series from HJ-1A/B Data.

PubMed

Liu, Shuyuan; Liu, Xiangnan; Liu, Meiling; Wu, Ling; Ding, Chao; Huang, Zhi

2017-05-30

An effective method to monitor heavy metal stress in crops is of critical importance to assure agricultural production and food security. Phenology, as a sensitive indicator of environmental change, can respond to heavy metal stress in crops and remote sensing is an effective method to detect plant phenological changes. This study focused on identifying the rice phenological differences under varied heavy metal stress using EVI (enhanced vegetation index) time-series, which was obtained from HJ-1A/B CCD images and fitted with asymmetric Gaussian model functions. We extracted three phenological periods using first derivative analysis: the tillering period, heading period, and maturation period; and constructed two kinds of metrics with phenological characteristics: date-intervals and time-integrated EVI, to explore the rice phenological differences under mild and severe stress levels. Results indicated that under severe stress the values of the metrics for presenting rice phenological differences in the experimental areas of heavy metal stress were smaller than the ones under mild stress. This finding represents a new method for monitoring heavy metal contamination through rice phenology.

Optimizing Land and Water Resources for Agriculture in the Krishna River Basin, India

NASA Astrophysics Data System (ADS)

Jain Figueroa, A.; McLaughlin, D.

2017-12-01

Many estimates suggest that the world needs a 50% increase in food production to meet the demands of the 2050 global population. Cropland expansion and yield improvements are unlikely to be sufficient and could have adverse environmental impacts. This work focuses on reallocating limited land and water resources to improve efficiency and increase benefits. We accomplish this by combining optimization methods, global data sources, and hydrologic modeling to identify opportunities for increasing crop production of subsistence and/or cash crops, subject to sustainability contraints. Our approach identifies the tradeoffs between the population that can be fed with local resources, revenue from crop exports, and environmental benefit from riparian flows. We focus our case study on India's Krishna river basin, a semi-arid region with a high proportion of subsistence farmers, a diverse crop mix, and increasing stress on water resources.

Assessing corn water stress using spectral reflectance

NASA Astrophysics Data System (ADS)

Mefford, Brenna S.

Multiple remote sensing techniques have been developed to identify crop water stress, but some methods may be difficult for farmers to apply. Unlike most techniques, shortwave vegetation indices can be calculated using satellite, aerial, or ground imagery from the green (525-600 nm), red (625-700 nm), and near infrared (750-900 nm) spectral bands. If vegetation indices can be used to monitor crop water stress, growers could use this information as a quick low-cost guideline for irrigation management, thus helping save water by preventing over irrigating. This study occurred in the 2013 growing season near Greeley, CO, where pressurized drip irrigation was used to irrigate twelve corn ( Zea mays L.) treatments of varying water deficit. Multispectral data was collected and four different vegetation indices were evaluated: Normalized Difference Vegetation Index (NDVI), Optimized Soil-Adjusted Vegetation Index (OSAVI), Green Normalized Difference Vegetation Index (GNDVI), and the Wide Dynamic Range Vegetation Index (WDRVI). The four vegetation indices were compared to corn water stress as indicated by the stress coefficient (Ks) and water deficit in the root zone, calculated by using a water balance that monitors crop evapotranspiration (ET), irrigation events, precipitation events, and deep percolation. ET for the water balance was calculated using two different methods for comparison purposes: (1) calculation of the stress coefficient (Ks) using FAO-56 standard procedures; (2) use of canopy temperature ratio (Tc ratio) of a stressed crop to a non-stressed crop to calculate Ks. It was found that obtaining Ks from Tc ratio is a viable option, and requires less data to obtain than Ks from FAO-56. In order to compare the indices to Ks, vegetation ratios were developed in the process of normalization. Vegetation ratios are defined as the non-stressed vegetation index divided by the stressed vegetation index. Results showed that vegetation ratios were sensitive to water stress as indicated by good R2 values (Nratio = 0.53, G ratio=0.46, Oratio=0.49) and low RMSE values (Nratio = 0.076, Gratio=0.062, Oratio=0.076) when compared to Ks. Therefore it can be concluded that corn spectral reflectance is sensitive to water stress. In order to use spectral reflectance to manage crop water stress an irrigation trigger point of 0.93 for the vegetation ratios was determined. These results were validated using data collected by a MSR5 multispectral sensor in an adjacent field (SWIIM Field). The results from the second field proved better than in the main field giving higher R 2 values (Nratio = 0.66, Gratio = 0.63, Oratio = 0.66), and lower RMSE values (Nratio = 0.043, Gratio = 0.036, Oratio = 0.043) between Ks and the vegetation indices. SWIIM field further validated the results that spectral reflectance can be used to monitor corn water stress.

The yield difference between wild-type cotton and transgenic cotton that expresses IPT depends on when water-deficit stress is applied

USDA-ARS?s Scientific Manuscript database

Drought is the No. 1 factor that limits agricultural production in the world, thus, making crops more drought tolerant is a major goal in agriculture. Many genes with functions in abiotic stress tolerance were identified, and overexpression of these genes confers increased drought tolerance in trans...

Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

PubMed Central

Li, Man-Wah; Qi, Xinpeng; Ni, Meng; Lam, Hon-Ming

2013-01-01

Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the “-omics” studies, with an emphasis on their possible impacts on crop stress research and crop improvement. PMID:23759993

Extraction of Rice Heavy Metal Stress Signal Features Based on Long Time Series Leaf Area Index Data Using Ensemble Empirical Mode Decomposition

PubMed Central

Liu, Xiangnan; Zhang, Biyao; Liu, Ming; Wu, Ling

2017-01-01

The use of remote sensing technology to diagnose heavy metal stress in crops is of great significance for environmental protection and food security. However, in the natural farmland ecosystem, various stressors could have a similar influence on crop growth, therefore making heavy metal stress difficult to identify accurately, so this is still not a well resolved scientific problem and a hot topic in the field of agricultural remote sensing. This study proposes a method that uses Ensemble Empirical Mode Decomposition (EEMD) to obtain the heavy metal stress signal features on a long time scale. The method operates based on the Leaf Area Index (LAI) simulated by the Enhanced World Food Studies (WOFOST) model, assimilated with remotely sensed data. The following results were obtained: (i) the use of EEMD was effective in the extraction of heavy metal stress signals by eliminating the intra-annual and annual components; (ii) LAIdf (The first derivative of the sum of the interannual component and residual) can preferably reflect the stable feature responses to rice heavy metal stress. LAIdf showed stability with an R2 of greater than 0.9 in three growing stages, and the stability is optimal in June. This study combines the spectral characteristics of the stress effect with the time characteristics, and confirms the potential of long-term remotely sensed data for improving the accuracy of crop heavy metal stress identification. PMID:28878147

A greenhouse experiment for the identification of spectral indices for crop water and nitrogen status assessment

NASA Astrophysics Data System (ADS)

Marino Gallina, Pietro; Bechini, Luca; Cabassi, Giovanni; Cavalli, Daniele; Chiaradia, Enrico Antonio; Corti, Martina; Ferrante, Antonio; Martinetti, Livia; Masseroni, Daniele; Morgutti, Silvia; Nocito, Fabio Francesco; Facchi, Arianna

2015-04-01

Improvements in crop production depend on the correct adoption of agronomic and irrigation management strategies. The use of high spatial and temporal resolution monitoring methods may be used in precision agriculture to improve the efficiency in water and nutrient input management, guaranteeing the environmental sustainability of agricultural productions. In the last decades, many indices for the monitoring of water or nitrogen status of crops were developed by using multispectral images and, more recently, hyperspectral and thermal images acquired by satellite of airborne platforms. To date, however, comprehensive studies aimed at identifying indices as independent as possible for the management of the two types of stress are still scarce in the literature. Moreover, the chemometric approach for the statistical analysis of the acquired images is not yet widely experienced in this research area. In this context, this work presents the set-up of a greenhouse experiment that will start in February 2015 in Milan (Northern Italy), which aims to the objectives described above. The experiment will be carried out on two crops with a different canopy geometry (rice and spinach) subjected to four nitrogen treatments, for a total of 96 pots. Hyperspectral scanner and thermal images will be acquired at four phenological stages. At each phenological phase, acquisitions will be conducted on one-fourth of the pots, in the first instance in good water conditions and, subsequently, at different time steps after the cessation of irrigation. During the acquisitions, measurements of leaf area index and biomass, chlorophyll and nitrogen content in the plants, soil water content, stomatal conductance and leaf water potential will be performed. Moreover, on leaf samples, destructive biochemical analysis will be conducted to evaluate the physiological stress status of crops in the light of different irrigation and nutrient levels. Multivariate regression analysis between the acquired spectra and the chemical-physical properties of the crop determined with standard methods will be used to identify suitable models for the estimation of crop water and nitrogen status. The most significant wavelengths for the detection of water and nitrogen stress could be the subject of a future experimentation in open field conditions using multispectral systems.

Identification and expression analysis of cold and freezing stress responsive genes of Brassica oleracea.

PubMed

Ahmed, Nasar Uddin; Jung, Hee-Jeong; Park, Jong-In; Cho, Yong-Gu; Hur, Yoonkang; Nou, Ill-Sup

2015-01-10

Cold and freezing stress is a major environmental constraint to the production of Brassica crops. Enhancement of tolerance by exploiting cold and freezing tolerance related genes offers the most efficient approach to address this problem. Cold-induced transcriptional profiling is a promising approach to the identification of potential genes related to cold and freezing stress tolerance. In this study, 99 highly expressed genes were identified from a whole genome microarray dataset of Brassica rapa. Blast search analysis of the Brassica oleracea database revealed the corresponding homologous genes. To validate their expression, pre-selected cold tolerant and susceptible cabbage lines were analyzed. Out of 99 BoCRGs, 43 were differentially expressed in response to varying degrees of cold and freezing stress in the contrasting cabbage lines. Among the differentially expressed genes, 18 were highly up-regulated in the tolerant lines, which is consistent with their microarray expression. Additionally, 12 BoCRGs were expressed differentially after cold stress treatment in two contrasting cabbage lines, and BoCRG54, 56, 59, 62, 70, 72 and 99 were predicted to be involved in cold regulatory pathways. Taken together, the cold-responsive genes identified in this study provide additional direction for elucidating the regulatory network of low temperature stress tolerance and developing cold and freezing stress resistant Brassica crops. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhancing Adoption of Irrigation Scheduling to Sustain the Viability of Fruit and Nut Crops in California

NASA Astrophysics Data System (ADS)

Fulton, A.; Snyder, R.; Hillyer, C.; English, M.; Sanden, B.; Munk, D.

2012-04-01

Enhancing Adoption of Irrigation Scheduling to Sustain the Viability of Fruit and Nut Crops in California Allan Fulton, Richard Snyder, Charles Hillyer, Marshall English, Blake Sanden, and Dan Munk Adoption of scientific methods to decide when to irrigate and how much water to apply to a crop has increased over the last three decades in California. In 1988, less than 4.3 percent of US farmers employed some type of science-based technique to assist in making irrigation scheduling decisions (USDA, 1995). An ongoing survey in California, representing an industry irrigating nearly 0.4 million planted almond hectares, indicates adoption rates ranging from 38 to 55 percent of either crop evapotranspiration (ETc), soil moisture monitoring, plant water status, or some combination of these irrigation scheduling techniques to assist with making irrigation management decisions (California Almond Board, 2011). High capital investment to establish fruit and nut crops, sensitivity to over and under-irrigation on crop performance and longevity, and increasing costs and competition for water have all contributed to increased adoption of scientific irrigation scheduling methods. These trends in adoption are encouraging and more opportunities exist to develop improved irrigation scheduling tools, especially computer decision-making models. In 2009 and 2010, an "On-line Irrigation Scheduling Advisory Service" (OISO, 2012), also referred to as Online Irrigation Management (IMO), was used and evaluated in commercial walnut, almond, and French prune orchards in the northern Sacramento Valley of California. This specific model has many features described as the "Next Generation of Irrigation Schedulers" (Hillyer, 2010). While conventional irrigation management involves simply irrigating as needed to avoid crop stress, this IMO is designed to control crop stress, which requires: (i) precise control of crop water availability (rather than controlling applied water); (ii) quantifying crop stress in order to manage it in heterogeneous fields; and (iii) predicting crop responses to water stress. The capacities of this IMO include: 1. Modeling of the disposition of applied water in spatially variable fields; 2. Conjunctive scheduling for multiple fields, rather than scheduling each field independently; 3. Long range forecasting of crop water requirements to better utilize limited water or limited delivery system capacity: and 4. Explicit modeling of the uncertainties of water use and crop yield. This was one of the first efforts to employ a "Next Generation" type computer irrigation scheduling advisory model or IMO in orchard crops. This paper discusses experiences with introducing this model to fruit and nut growers of various size and scale in the northern Sacramento Valley of California and the accuracy of its forecasts of irrigation needs in fruit and nut crops. Strengths and opportunities to forge ahead in the development of a "Next Generation" irrigation scheduler were identified from this on-farm evaluation.

Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.)

PubMed Central

Kantar, Michael B.; Sosa, Chrystian C.; Khoury, Colin K.; Castañeda-Álvarez, Nora P.; Achicanoy, Harold A.; Bernau, Vivian; Kane, Nolan C.; Marek, Laura; Seiler, Gerald; Rieseberg, Loren H.

2015-01-01

Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation. PMID:26500675

Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.).

PubMed

Kantar, Michael B; Sosa, Chrystian C; Khoury, Colin K; Castañeda-Álvarez, Nora P; Achicanoy, Harold A; Bernau, Vivian; Kane, Nolan C; Marek, Laura; Seiler, Gerald; Rieseberg, Loren H

2015-01-01

Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation.

The use of infrared thermal imaging as a non-destructive screening tool for identifying drought-tolerant lentil genotypes.

PubMed

Biju, Sajitha; Fuentes, Sigfredo; Gupta, Dorin

2018-06-01

Lentil (Lens culinaris, Medik.) is an important legume crop, which often experience drought stress especially at the flowering and grain filling phenological stages. The availability of efficient and robust screening tools based on relevant non-destructive quantifiable traits would facilitate research on crop improvement for drought tolerance. The objective of this study was to evaluate the drought tolerance of 37 lentil genotypes using infrared thermal imaging (IRTI), drought tolerance parameters and multivariate data analysis. Potted plants were kept in a completely randomized design in a growth chamber with five replicates. Plants were subjected to three different drought treatments: 100, 50 and 20% of field capacity at the onset of reproductive period. The relative drought stress tolerance was determined based on a set of morpho-physiological parameters including non-destructive measures based on IRTI, such as: canopy temperature (Tc), canopy temperature depression (CTD) and crop water stress index (CWSI) during the growing period and destructive measures at harvest, such as: dry root-shoot ratio (RS ratio), relative water content (RWC) and harvest index (HI). The drought tolerance indices used were drought susceptibility index (DSI) and drought tolerance efficiency (DTE). Results showed that drought stress treatments significantly reduced the RWC, HI, CTD and DSI, whereas, the values of Tc, CWSI, RS ratio and DTE significantly increased for all the genotypes. The cluster analysis from morpho-physiological parameters clustered genotypes in three distinctive groups as per the level of drought stress tolerance. The genotypes with higher values of RS ratio, RWC, HI, DTE and CTD and lower values of DSI, Tc and CWSI were identified as drought-tolerant genotypes. Based on this preliminary screening, the genotypes Digger, Cumra, Indianhead, ILL 5588, ILL 6002 and ILL 5582 were identified as promising drought-tolerant genotypes. It can be concluded that the IRTI analysis is a high-throughput constructive screening tool along with RS ratio, RWC, HI and other drought tolerance indices to define the drought stress tolerance variability within lentil plants. These results provide a foundation for future research directed at identifying powerful drought assessment traits using rapid and non-destructive techniques, such as IRTI along with the yield traits, and understanding the biochemical and molecular mechanisms underlying lentil tolerance to drought stress. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.).

PubMed

Pandey, Garima; Yadav, Chandra Bhan; Sahu, Pranav Pankaj; Muthamilarasan, Mehanathan; Prasad, Manoj

2017-05-01

Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

PubMed Central

Ramalingam, Abirami; Kudapa, Himabindu; Pazhamala, Lekha T.; Weckwerth, Wolfram; Varshney, Rajeev K.

2015-01-01

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these “omics” approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs. PMID:26734026

Drought stress and aflatoxin contamination: Transcriptional responses of Aspergillus flavus to oxidative stress are related to stress tolerance and aflatoxin production capability

USDA-ARS?s Scientific Manuscript database

Oilseed crops such as maize and peanut are staple food crops which are vital for global food security. The contamination of these crops with carcinogenic aflatoxins during infection by Aspergillus flavus under drought stress conditions is a serious threat to the safety of these commodities. In order...

Heat and drought stresses in crops and approaches for their mitigation

NASA Astrophysics Data System (ADS)

Lamaoui, Mouna; Jemo, Martin; Datla, Raju; Bekkaoui, Faouzi

2018-02-01

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavourable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

Heat and Drought Stresses in Crops and Approaches for Their Mitigation.

PubMed

Lamaoui, Mouna; Jemo, Martin; Datla, Raju; Bekkaoui, Faouzi

2018-01-01

Drought and heat are major abiotic stresses that reduce crop productivity and weaken global food security, especially given the current and growing impacts of climate change and increases in the occurrence and severity of both stress factors. Plants have developed dynamic responses at the morphological, physiological and biochemical levels allowing them to escape and/or adapt to unfavorable environmental conditions. Nevertheless, even the mildest heat and drought stress negatively affects crop yield. Further, several independent studies have shown that increased temperature and drought can reduce crop yields by as much as 50%. Response to stress is complex and involves several factors including signaling, transcription factors, hormones, and secondary metabolites. The reproductive phase of development, leading to the grain production is shown to be more sensitive to heat stress in several crops. Advances coming from biotechnology including progress in genomics and information technology may mitigate the detrimental effects of heat and drought through the use of agronomic management practices and the development of crop varieties with increased productivity under stress. This review presents recent progress in key areas relevant to plant drought and heat tolerance. Furthermore, an overview and implications of physiological, biochemical and genetic aspects in the context of heat and drought are presented. Potential strategies to improve crop productivity are discussed.

Hop (Humulus lupulus L.) response mechanisms in drought stress: Proteomic analysis with physiology.

PubMed

Kolenc, Zala; Vodnik, Dominik; Mandelc, Stanislav; Javornik, Branka; Kastelec, Damijana; Čerenak, Andreja

2016-08-01

Drought is one of the major environmental devastating stressors that impair the growth and productivity of crop plants. Despite the relevance of drought stress, changes in physiology and resistance mechanisms are not completely understood for certain crops, including hop (Humulus lupulus L.). In this research the drought response of hop was studied using a conventional physiological approach (gas exchange techniques, fluorescence, relative water content measurements) and proteomic analysis (2D-DIGE). Plants of two cultivars (Aurora and Savinjski golding) were exposed to progressive drought in a pot experiment and analysed at different stress stages (mild, moderate and severe). Measurements of relative water content revealed a hydrostable water balance of hop. Photosynthesis was decreased due to stomatal and non-stomatal limitation to the same extent in both cultivars. Of 28 identified differentially abundant proteins, the majority were down regulated and included in photosynthetic (41%) and sugar metabolism (33%). Fifteen % of identified proteins were classified into the nitrogen metabolism, 4% were related to a ROS related pathway and 7% to other functions. Copyright © 2016. Published by Elsevier Masson SAS.

Modelling shifts in agroclimate and crop cultivar response under climate change.

PubMed

Rötter, Reimund P; Höhn, Jukka; Trnka, Mirek; Fronzek, Stefan; Carter, Timothy R; Kahiluoto, Helena

2013-10-01

(i) to identify at national scale areas where crop yield formation is currently most prone to climate-induced stresses, (ii) to evaluate how the severity of these stresses is likely to develop in time and space, and (iii) to appraise and quantify the performance of two strategies for adapting crop cultivation to a wide range of (uncertain) climate change projections. To this end we made use of extensive climate, crop, and soil data, and of two modelling tools: N-AgriCLIM and the WOFOST crop simulation model. N-AgriCLIM was developed for the automatic generation of indicators describing basic agroclimatic conditions and was applied over the whole of Finland. WOFOST was used to simulate detailed crop responses at four representative locations. N-AgriCLIM calculations have been performed nationally for 3829 grid boxes at a 10 × 10 km resolution and for 32 climate scenarios. Ranges of projected shifts in indicator values for heat, drought and other crop-relevant stresses across the scenarios vary widely - so do the spatial patterns of change. Overall, under reference climate the most risk-prone areas for spring cereals are found in south-west Finland, shifting to south-east Finland towards the end of this century. Conditions for grass are likely to improve. WOFOST simulation results suggest that CO2 fertilization and adjusted sowing combined can lead to small yield increases of current barley cultivars under most climate scenarios on favourable soils, but not under extreme climate scenarios and poor soils. This information can be valuable for appraising alternative adaptation strategies. It facilitates the identification of regions in which climatic changes might be rapid or otherwise notable for crop production, requiring a more detailed evaluation of adaptation measures. The results also suggest that utilizing the diversity of cultivar responses seems beneficial given the high uncertainty in climate change projections.

Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling.

PubMed

Yadav, Amita; Khan, Yusuf; Prasad, Manoj

2016-03-01

A set of novel and known dehydration-responsive miRNAs have been identified in foxtail millet. These findings provide new insights into understanding the functional role of miRNAs and their respective targets in regulating plant response to dehydration stress. MicroRNAs perform significant regulatory roles in growth, development and stress response of plants. Though the miRNA-mediated gene regulatory networks under dehydration stress remain largely unexplored in plant including foxtail millet (Setaria italica), which is a natural abiotic stress tolerant crop. To find out the dehydration-responsive miRNAs at the global level, four small RNA libraries were constructed from control and dehydration stress treated seedlings of two foxtail millet cultivars showing contrasting tolerance behavior towards dehydration stress. Using Illumina sequencing technology, 55 known and 136 novel miRNAs were identified, representing 22 and 48 miRNA families, respectively. Eighteen known and 33 novel miRNAs were differentially expressed during dehydration stress. After the stress treatment, 32 dehydration-responsive miRNAs were up-regulated in tolerant cultivar and 22 miRNAs were down-regulated in sensitive cultivar, suggesting that miRNA-mediated molecular regulation might play important roles in providing contrasting characteristics to these cultivars. Predicted targets of identified miRNAs were found to encode various transcription factors and functional enzymes, indicating their involvement in broad spectrum regulatory functions and biological processes. Further, differential expression patterns of seven known miRNAs were validated by northern blot and expression of ten novel dehydration-responsive miRNAs were confirmed by SL-qRT PCR. Differential expression behavior of five miRNA-target genes was verified under dehydration stress treatment and two of them also validated by RLM RACE. Overall, the present study highlights the importance of dehydration stress-associated post-transcriptional regulation governed by miRNAs and their targets in a naturally stress-tolerant model crop.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

Simulating canopy temperature for modelling heat stress in cereals

USDA-ARS?s Scientific Manuscript database

Crop models must be improved to account for the large effects of heat stress effects on crop yields. To date, most approaches in crop models use air temperature despite evidence that crop canopy temperature better explains yield reductions associated with high temperature events. This study presents...

SWAPDT: A method for Short-time Withering Assessment of Probability for Drought Tolerance in Camellia sinensis validated by targeted metabolomics.

PubMed

Nyarukowa, Christopher; Koech, Robert; Loots, Theodor; Apostolides, Zeno

2016-07-01

Climate change is causing droughts affecting crop production on a global scale. Classical breeding and selection strategies for drought-tolerant cultivars will help prevent crop losses. Plant breeders, for all crops, need a simple and reliable method to identify drought-tolerant cultivars, but such a method is missing. Plant metabolism is often disrupted by abiotic stress conditions. To survive drought, plants reconfigure their metabolic pathways. Studies have documented the importance of metabolic regulation, i.e. osmolyte accumulation such as polyols and sugars (mannitol, sorbitol); amino acids (proline) during drought. This study identified and quantified metabolites in drought tolerant and drought susceptible Camellia sinensis cultivars under wet and drought stress conditions. For analyses, GC-MS and LC-MS were employed for metabolomics analysis.%RWC results show how the two drought tolerant and two drought susceptible cultivars differed significantly (p≤0.05) from one another; the drought susceptible exhibited rapid water loss compared to the drought tolerant. There was a significant variation (p<0.05) in metabolite content (amino acid, sugars) between drought tolerant and drought susceptible tea cultivars after short-time withering conditions. These metabolite changes were similar to those seen in other plant species under drought conditions, thus validating this method. The Short-time Withering Assessment of Probability for Drought Tolerance (SWAPDT) method presented here provides an easy method to identify drought tolerant tea cultivars that will mitigate the effects of drought due to climate change on crop losses. Copyright © 2016. Published by Elsevier GmbH.

Research advances in major cereal crops for adaptation to abiotic stresses

PubMed Central

Maiti, RK; Satya, Pratik

2014-01-01

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers’ fields. PMID:25523172

Research advances in major cereal crops for adaptation to abiotic stresses.

PubMed

Maiti, R K; Satya, Pratik

2014-01-01

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers' fields.

Transcriptome analysis of hexaploid hulless oat in response to salinity stress

PubMed Central

Wu, Bin; Hu, Yani; Huo, Pengjie; Zhang, Qian; Chen, Xin; Zhang, Zongwen

2017-01-01

Background Oat is a cereal crop of global importance used for food, feed, and forage. Understanding salinity stress tolerance mechanisms in plants is an important step towards generating crop varieties that can cope with environmental stresses. To date, little is known about the salt tolerance of oat at the molecular level. To better understand the molecular mechanisms underlying salt tolerance in oat, we investigated the transcriptomes of control and salt-treated oat using RNA-Seq. Results Using Illumina HiSeq 4000 platform, we generated 72,291,032 and 356,891,432 reads from non-stressed control and salt-stressed oat, respectively. Assembly of 64 Gb raw sequence data yielded 128,414 putative unique transcripts with an average length of 1,189 bp. Analysis of the assembled unigenes from the salt stressed and control libraries indicated that about 65,000 unigenes were differentially expressed at different stages. Functional annotation showed that ABC transporters, plant hormone signal transduction, plant-pathogen interactions, starch and sucrose metabolism, arginine and proline metabolism, and other secondary metabolite pathways were enriched under salt stress. Based on the RPKM values of assembled unigenes, 24 differentially expressed genes under salt stress were selected for quantitative RT-PCR validation, which successfully confirmed the results of RNA-Seq. Furthermore, we identified 18,039 simple sequence repeats, which may help further elucidate salt tolerance mechanisms in oat. Conclusions Our global survey of transcriptome profiles of oat plants in response to salt stress provides useful insights into the molecular mechanisms underlying salt tolerance in this crop. These findings also represent a rich resource for further analysis of salt tolerance and for breeding oat with improved salt tolerance through the use of salt-related genes. PMID:28192458

Drought coping strategies in cotton: increased crop per drop.

PubMed

Ullah, Abid; Sun, Heng; Yang, Xiyan; Zhang, Xianlong

2017-03-01

The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought specific as well as general morpho-physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production and reactive oxygen species (ROS) scavenging, have been identified by researchers. Drought stress induces the expression of stress-related transcription factors and genes, such as ROS scavenging, ABA or mitogen-activated protein kinases (MAPK) signalling genes, which activate various drought-related pathways to induce tolerance in the plant. It is crucial to elucidate and induce drought-tolerant traits via quantitative trait loci (QTL) analysis, transgenic approaches and exogenous application of substances. The current review article highlights the natural as well as engineered drought tolerance strategies in cotton. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Crop and medicinal plants proteomics in response to salt stress

PubMed Central

Aghaei, Keyvan; Komatsu, Setsuko

2013-01-01

Increasing of world population marks a serious need to create new crop cultivars and medicinal plants with high growth and production at any environmental situations. Among the environmental unfavorable conditions, salinity is the most widespread in the world. Crop production and growth severely decreases under salt stress; however, some crop cultivars show significant tolerance against the negative effects of salinity. Among salt stress responses of crops, proteomic responses play a pivotal role in their ability to cope with it and have become the main center of notification. Many physiological responses are detectable in terms of protein increase and decrease even before physiological responses take place. Thus proteomic approach makes a short cut in the way of inferring how crops response to salt stress. Nowadays many salt-responsive proteins such as heat shock proteins, pathogen-related proteins, protein kinases, ascorbate peroxidase, osmotin, ornithine decarboxylase, and some transcription factors, have been detected in some major crops which are thought to give them the ability of withstanding against salt stress. Proteomic analysis of medicinal plants also revealed that alkaloid biosynthesis related proteins such as tryptophan synthase, codeinone reductase, strictosidine synthase, and 12-oxophytodienoate reductase might have major role in production of secondary metabolites. In this review we are comparing some different or similar proteomic responses of several crops and medicinal plants to salt stress and discuss about the future prospects. PMID:23386857

Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress

PubMed Central

Gu, Junfei; Yin, Xinyou; Zhang, Chengwei; Wang, Huaqi; Struik, Paul C.

2014-01-01

Background and Aims Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. Methods Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameters were estimated from additive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. Key Results To account for genotypic yield differences, it was necessary to parameterize the model for differences in an additional trait ‘total crop nitrogen uptake’ (Nmax) among the ILs. Genetic variation in Nmax had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10–36 % more yield than those based on markers for yield per se. Conclusions This study outlines a genotype-to-phenotype approach that exploits the potential value of marker-based crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions. PMID:24984712

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

PubMed Central

Djami-Tchatchou, Arnaud T.; Sanan-Mishra, Neeti; Ntushelo, Khayalethu; Dubery, Ian A.

2017-01-01

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic—or abiotic origin. PMID:28382044

Predicting optimum crop designs using crop models and seasonal climate forecasts.

PubMed

Rodriguez, D; de Voil, P; Hudson, D; Brown, J N; Hayman, P; Marrou, H; Meinke, H

2018-02-02

Expected increases in food demand and the need to limit the incorporation of new lands into agriculture to curtail emissions, highlight the urgency to bridge productivity gaps, increase farmers profits and manage risks in dryland cropping. A way to bridge those gaps is to identify optimum combination of genetics (G), and agronomic managements (M) i.e. crop designs (GxM), for the prevailing and expected growing environment (E). Our understanding of crop stress physiology indicates that in hindsight, those optimum crop designs should be known, while the main problem is to predict relevant attributes of the E, at the time of sowing, so that optimum GxM combinations could be informed. Here we test our capacity to inform that "hindsight", by linking a tested crop model (APSIM) with a skillful seasonal climate forecasting system, to answer "What is the value of the skill in seasonal climate forecasting, to inform crop designs?" Results showed that the GCM POAMA-2 was reliable and skillful, and that when linked with APSIM, optimum crop designs could be informed. We conclude that reliable and skillful GCMs that are easily interfaced with crop simulation models, can be used to inform optimum crop designs, increase farmers profits and reduce risks.

Characterizing tradeoffs between water and food under different climate regimes across the United States

NASA Astrophysics Data System (ADS)

Troy, T.; Zhu, X.; Kipgen, C.; Li, X.; Pal, I.

2015-12-01

As water demand approaches or exceeds the available water supply in many regions of the globe, water stress will become increasingly prevalent with potentially necessary tradeoffs required between water prioritization amongst sectors. Agriculture is the largest consumptive water user in the US, and irrigation plays a vital role in ensuring a stable food supply by buffering against climate extremes. However, it also plays a negative role in inducing water stress in many regions. Much research has focused on reducing agricultural water use, but this needs to be complemented by better quantifying the benefit of irrigation on crop yields under a range of climate conditions. Regions are identified with significant irrigation benefits with and without water stress to parse apart the role of climate, crop choice, and water usage to then evaluate tradeoffs with food production in a climate-water-food nexus.

The response of transgenic Brassica species to salt stress: a review.

PubMed

Shah, Nadil; Anwar, Sumera; Xu, Jingjing; Hou, Zhaoke; Salah, Akram; Khan, Shahbaz; Gong, Jianfang; Shang, Zhengwei; Qian, Li; Zhang, Chunyu

2018-06-01

Salt stress is considered one of the main abiotic factors to limit crop growth and productivity by affecting morpho-physiological and biochemical processes. Genetically, a number of salt tolerant Brassica varieties have been developed and introduced, but breeding of such varieties is time consuming. Therefore, current focus is on transgenic technology, which plays an important role in the development of salt tolerant varieties. Various salt tolerant genes have been characterized and incorporated into Brassica. Therefore, such genetic transformation of Brassica species is a significant step for improvement of crops, as well as conferring salt stress resistance qualities to Brassica species. Complete genome sequencing has made the task of genetically transforming Brassica species easier, by identifying desired candidate genes. The present review discusses relevant information about the principles which should be employed to develop transgenic Brassica species, and also will recommend tools for improved tolerance to salinity.

Plant salt-tolerance mechanisms

DOE PAGES

Deinlein, Ulrich; Stephan, Aaron B.; Horie, Tomoaki; ...

2014-06-01

Crop performance is severely affected by high salt concentrations in soils. To engineer more salt-tolerant plants it is crucial to unravel the key components of the plant salt-tolerance network. Here we review our understanding of the core salt-tolerance mechanisms in plants. Recent studies have shown that stress sensing and signaling components can play important roles in regulating the plant salinity stress response. We also review key Na+ transport and detoxification pathways and the impact of epigenetic chromatin modifications on salinity tolerance. In addition, we discuss the progress that has been made towards engineering salt tolerance in crops, including marker-assisted selectionmore » and gene stacking techniques. We also identify key open questions that remain to be addressed in the future.« less

Abiotic stresses affect Trichoderma harzianum T39-induced resistance to downy mildew in grapevine.

PubMed

Roatti, Benedetta; Perazzolli, Michele; Gessler, Cesare; Pertot, Ilaria

2013-12-01

Enhancement of plant defense through the application of resistance inducers seems a promising alternative to chemical fungicides for controlling crop diseases but the efficacy can be affected by abiotic factors in the field. Plants respond to abiotic stresses with hormonal signals that may interfere with the mechanisms of induced systemic resistance (ISR) to pathogens. In this study, we exposed grapevines to heat, drought, or both to investigate the effects of abiotic stresses on grapevine resistance induced by Trichoderma harzianum T39 (T39) to downy mildew. Whereas the efficacy of T39-induced resistance was not affected by exposure to heat or drought, it was significantly reduced by combined abiotic stresses. Decrease of leaf water potential and upregulation of heat-stress markers confirmed that plants reacted to abiotic stresses. Basal expression of defense-related genes and their upregulation during T39-induced resistance were attenuated by abiotic stresses, in agreement with the reduced efficacy of T39. The evidence reported here suggests that exposure of crops to abiotic stress should be carefully considered to optimize the use of resistance inducers, especially in view of future global climate changes. Expression analysis of ISR marker genes could be helpful to identify when plants are responding to abiotic stresses, in order to optimize treatments with resistance inducers in field.

Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

PubMed Central

Ghatak, Arindam; Chaturvedi, Palak; Weckwerth, Wolfram

2017-01-01

Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet. PMID:28626463

Remote sensing leaf water stress in coffee (Coffea arabica) using secondary effects of water absorption and random forests

NASA Astrophysics Data System (ADS)

Chemura, Abel; Mutanga, Onisimo; Dube, Timothy

2017-08-01

Water management is an important component in agriculture, particularly for perennial tree crops such as coffee. Proper detection and monitoring of water stress therefore plays an important role not only in mitigating the associated adverse impacts on crop growth and productivity but also in reducing expensive and environmentally unsustainable irrigation practices. Current methods for water stress detection in coffee production mainly involve monitoring plant physiological characteristics and soil conditions. In this study, we tested the ability of selected wavebands in the VIS/NIR range to predict plant water content (PWC) in coffee using the random forest algorithm. An experiment was set up such that coffee plants were exposed to different levels of water stress and reflectance and plant water content measured. In selecting appropriate parameters, cross-correlation identified 11 wavebands, reflectance difference identified 16 and reflectance sensitivity identified 22 variables related to PWC. Only three wavebands (485 nm, 670 nm and 885 nm) were identified by at least two methods as significant. The selected wavebands were trained (n = 36) and tested on independent data (n = 24) after being integrated into the random forest algorithm to predict coffee PWC. The results showed that the reflectance sensitivity selected bands performed the best in water stress detection (r = 0.87, RMSE = 4.91% and pBias = 0.9%), when compared to reflectance difference (r = 0.79, RMSE = 6.19 and pBias = 2.5%) and cross-correlation selected wavebands (r = 0.75, RMSE = 6.52 and pBias = 1.6). These results indicate that it is possible to reliably predict PWC using wavebands in the VIS/NIR range that correspond with many of the available multispectral scanners using random forests and further research at field and landscape scale is required to operationalize these findings.

The beginnings of crop phosphoproteomics: exploring early warning systems of stress

PubMed Central

Rampitsch, Christof; Bykova, Natalia V.

2012-01-01

This review examines why a knowledge of plant protein phosphorylation events is important in devising strategies to protect crops from both biotic and abiotic stresses, and why proteomics should be included when studying stress pathways. Most of the achievements in elucidating phospho-signaling pathways in biotic and abiotic stress are reported from model systems: while these are discussed, this review attempts mainly to focus on work done with crops, with examples of achievements reported from rice, maize, wheat, grape, Brassica, tomato, and soy bean after cold acclimation, hormonal and oxidative hydrogen peroxide treatment, salt stress, mechanical wounding, or pathogen challenge. The challenges that remain to transfer this information into a format that can be used to protect crops against biotic and abiotic stresses are enormous. The tremendous increase in the speed and ease of DNA sequencing is poised to reveal the whole genomes of many crop species in the near future, which will facilitate phosphoproteomics and phosphogenomics research. PMID:22783265

Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.).

PubMed

Yue, Hong; Wang, Meng; Liu, Siyan; Du, Xianghong; Song, Weining; Nie, Xiaojun

2016-05-10

WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown. A total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes. This was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop.

Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response.

PubMed

Barua, Pragya; Lande, Nilesh Vikram; Subba, Pratigya; Gayen, Dipak; Pinto, Sneha; Prasad, T S Keshav; Chakraborty, Subhra; Chakraborty, Niranjan

2018-05-10

Non-availability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NP) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration and nuclear proteins were extracted from unstressed control as well as from 72 and 144 h stressed tissues. We identified 4832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases and transcription factors, besides 660 uncharacterised proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops. This article is protected by copyright. All rights reserved.

Automatic Detection of Regions in Spinach Canopies Responding to Soil Moisture Deficit Using Combined Visible and Thermal Imagery

PubMed Central

Raza, Shan-e-Ahmed; Smith, Hazel K.; Clarkson, Graham J. J.; Taylor, Gail; Thompson, Andrew J.; Clarkson, John; Rajpoot, Nasir M.

2014-01-01

Thermal imaging has been used in the past for remote detection of regions of canopy showing symptoms of stress, including water deficit stress. Stress indices derived from thermal images have been used as an indicator of canopy water status, but these depend on the choice of reference surfaces and environmental conditions and can be confounded by variations in complex canopy structure. Therefore, in this work, instead of using stress indices, information from thermal and visible light imagery was combined along with machine learning techniques to identify regions of canopy showing a response to soil water deficit. Thermal and visible light images of a spinach canopy with different levels of soil moisture were captured. Statistical measurements from these images were extracted and used to classify between canopies growing in well-watered soil or under soil moisture deficit using Support Vector Machines (SVM) and Gaussian Processes Classifier (GPC) and a combination of both the classifiers. The classification results show a high correlation with soil moisture. We demonstrate that regions of a spinach crop responding to soil water deficit can be identified by using machine learning techniques with a high accuracy of 97%. This method could, in principle, be applied to any crop at a range of scales. PMID:24892284

Major Energy Plants and Their Potential for Bioenergy Development in China

NASA Astrophysics Data System (ADS)

Li, Xiaofeng; Hou, Shenglin; Su, Man; Yang, Mingfeng; Shen, Shihua; Jiang, Gaoming; Qi, Dongmei; Chen, Shuangyan; Liu, Gongshe

2010-10-01

China is rich in energy plant resources. In this article, 64 plant species are identified as potential energy plants in China. The energy plant species include 38 oilseed crops, 5 starch-producing crops, 3 sugar-producing crops and 18 species for lignocellulosic biomass. The species were evaluated on the basis of their production capacity and their resistance to salt, drought, and/or low temperature stress. Ten plant species have high production and/or stress resistance and can be potentially developed as the candidate energy plants. Of these, four species could be the primary energy plants in China: Barbados nut ( Jatropha curcas L.), Jerusalem artichoke ( Helianthus tuberosus L.), sweet sorghum ( Sorghum bicolor L.) and Chinese silvergrass ( Miscanthus sinensis Anderss.). We discuss the use of biotechnological techniques such as genome sequencing, molecular markers, and genetic transformation to improve energy plants. These techniques are being used to develop new cultivars and to analyze and manipulate genetic variation to improve attributes of energy plants in China.

Meteorological risks and impacts on crop production systems in Belgium

NASA Astrophysics Data System (ADS)

Gobin, Anne

2013-04-01

Extreme weather events such as droughts, heat stress, rain storms and floods can have devastating effects on cropping systems. The perspective of rising risk-exposure is exacerbated further by projected increases of extreme events with climate change. More limits to aid received for agricultural damage and an overall reduction of direct income support to farmers further impacts farmers' resilience. Based on insurance claims, potatoes and rapeseed are the most vulnerable crops, followed by cereals and sugar beets. Damages due to adverse meteorological events are strongly dependent on crop type, crop stage and soil type. Current knowledge gaps exist in the response of arable crops to the occurrence of extreme events. The degree of temporal overlap between extreme weather events and the sensitive periods of the farming calendar requires a modelling approach to capture the mixture of non-linear interactions between the crop and its environment. The regional crop model REGCROP (Gobin, 2010) enabled to examine the likely frequency and magnitude of drought, heat stress and waterlogging in relation to the cropping season and crop sensitive stages of six arable crops: winter wheat, winter barley, winter rapeseed, potato, sugar beet and maize. Since crop development is driven by thermal time, crops matured earlier during the warmer 1988-2008 period than during the 1947-1987 period. Drought and heat stress, in particular during the sensitive crop stages, occur at different times in the cropping season and significantly differ between two climatic periods, 1947-1987 and 1988-2008. Soil moisture deficit increases towards harvesting, such that earlier maturing winter crops may avoid drought stress that occurs in late spring and summer. This is reflected in a decrease both in magnitude and frequency of soil moisture deficit around the sensitive stages during the 1988-2008 period when atmospheric drought may be compensated for with soil moisture. The risk of drought spells during the sensitive stages of summer crops increases and may be further aggravated by atmospheric moisture deficits and heat stress. Summer crops may therefore benefit from earlier planting dates and beneficial moisture conditions during early canopy development, but will suffer from increased drought and heat stress during crop maturity. During the harvesting stages, the number of waterlogged days increases in particular for tuber crops. Physically based crop models assist in understanding the links between different factors causing crop damage. The approach allows for assessing the meteorological impacts on crop growth due to the sensitive stages occurring earlier during the growing season and due to extreme weather events. Though average yields have risen continuously between 1947 and 2008 mainly due to technological advances, there is no evidence that relative tolerance to adverse weather conditions such as atmospheric moisture deficit and temperature extremes has changed.

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress

PubMed Central

Khan, Faraz; Chai, Hui Hui; Ajmera, Ishan; Hodgman, Charlie; Mayes, Sean; Lu, Chungui

2017-01-01

The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome. PMID:28420201

Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.)

PubMed Central

Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath; B., Venkata Suresh; Parida, Swarup Kumar; Prasad, Manoj

2013-01-01

The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants. PMID:23691254

Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.).

PubMed

Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath; B, Venkata Suresh; Parida, Swarup Kumar; Prasad, Manoj

2013-01-01

The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.

On the interactions among tropospheric ozone levels and typical environmental stresses challenging Mediterranean crops.

PubMed

Fagnano, Massimo; Maggio, Albino

2018-03-01

The main environmental stresses of Italian croplands are discussed in relation to their interactions with ozone effects on crops. Water deficit and salinization are frequent in Mediterranean environments during spring-summer causing a decrease of soil water potential and water uptake by roots and consequently stomatal closure. These stresses also stimulate secondary metabolism and antioxidant accumulation, which also serves as a stress protection mechanism. High concentrations of tropospheric ozone are common all over Italy during the spring-summer season. Ozone injuries to vegetation are related to its penetration into plant tissues, mostly via stomatal uptake, rather than to tropospheric concentrations per se. In several crops, closure of stomata due to drought/salinization reduces ozone entering into leaf tissues and counteracts possible ozone damages. Furthermore, the stimulation of antioxidant synthesis as a response to environmental stresses can represent a further protection factor from ozone injuries for Mediterranean crops.The co-existence of stress-induced stomatal closure and high ozone levels during spring-summer in Mediterranean environments implies that models that do not take into account physiological responses of crops to drought and salinity stress may overestimate ozone damages when stress responses overlap with seasonal ozone peaks. The shift from concentration-based to flux-based approaches has improved the accuracy of models to assess ozone effects on agricultural crops. It is, however, necessary to further refine the flux concept with respect to the plant abiotic stress defense capacity that can differ among genotypes, climatic conditions, and physiological states.

Improving adaptation to drought stress in white pea bean (Phaseolus vulgaris L): genotypic effects on grain yield, yield components and pod harvest index

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris L.) is the most important food legume crop in Africa and Latin America where rainfall pattern is unpredictable. The objectives were to identify better yielding common bean lines with good canning quality under drought, and to identify traits that could be used as sele...

Genome-wide analysis of the Hsp70 family genes in pepper (Capsicum annuum L.) and functional identification of CaHsp70-2 involvement in heat stress.

PubMed

Guo, Meng; Liu, Jin-Hong; Ma, Xiao; Zhai, Yu-Fei; Gong, Zhen-Hui; Lu, Ming-Hui

2016-11-01

Hsp70s function as molecular chaperones and are encoded by a multi-gene family whose members play a crucial role in plant response to stress conditions, and in plant growth and development. Pepper (Capsicum annuum L.) is an important vegetable crop whose genome has been sequenced. Nonetheless, no overall analysis of the Hsp70 gene family is reported in this crop plant to date. To assess the functionality of Capsicum annuum Hsp70 (CaHsp70) genes, pepper genome database was analyzed in this research. A total of 21 CaHsp70 genes were identified and their characteristics were also described. The promoter and transcript expression analysis revealed that CaHsp70s were involved in pepper growth and development, and heat stress response. Ectopic expression of a cytosolic gene, CaHsp70-2, regulated expression of stress-related genes and conferred increased thermotolerance in transgenic Arabidopsis. Taken together, our results provide the basis for further studied to dissect CaHsp70s' function in response to heat stress as well as other environmental stresses. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Circadian redox signaling in plant immunity and abiotic stress.

PubMed

Spoel, Steven H; van Ooijen, Gerben

2014-06-20

Plant crops are critically important to provide quality food and bio-energy to sustain a growing human population. Circadian clocks have been shown to deliver an adaptive advantage to plants, vastly increasing biomass production by efficient anticipation to the solar cycle. Plant stress, on the other hand, whether biotic or abiotic, prevents crops from reaching maximum productivity. Stress is associated with fluctuations in cellular redox and increased phytohormone signaling. Recently, direct links between circadian timekeeping, redox fluctuations, and hormone signaling have been identified. A direct implication is that circadian control of cellular redox homeostasis influences how plants negate stress to ensure growth and reproduction. Complex cellular biochemistry leads from perception of stress via hormone signals and formation of reactive oxygen intermediates to a physiological response. Circadian clocks and metabolic pathways intertwine to form a confusing biochemical labyrinth. Here, we aim to find order in this complex matter by reviewing current advances in our understanding of the interface between these networks. Although the link is now clearly defined, at present a key question remains as to what extent the circadian clock modulates redox, and vice versa. Furthermore, the mechanistic basis by which the circadian clock gates redox- and hormone-mediated stress responses remains largely elusive.

Regional-scale yield simulations using crop and climate models: assessing uncertainties, sensitivity to temperature and adaptation options

NASA Astrophysics Data System (ADS)

Challinor, A. J.

2010-12-01

Recent progress in assessing the impacts of climate variability and change on crops using multiple regional-scale simulations of crop and climate (i.e. ensembles) is presented. Simulations for India and China used perturbed responses to elevated carbon dioxide constrained using observations from FACE studies and controlled environments. Simulations with crop parameter sets representing existing and potential future adapted varieties were also carried out. The results for India are compared to sensitivity tests on two other crop models. For China, a parallel approach used socio-economic data to account for autonomous farmer adaptation. Results for the USA analysed cardinal temperatures under a range of local warming scenarios for 2711 varieties of spring wheat. The results are as follows: 1. Quantifying and reducing uncertainty. The relative contribution of uncertainty in crop and climate simulation to the total uncertainty in projected yield changes is examined. The observational constraints from FACE and controlled environment studies are shown to be the likely critical factor in maintaining relatively low crop parameter uncertainty. Without these constraints, crop simulation uncertainty in a doubled CO2 environment would likely be greater than uncertainty in simulating climate. However, consensus across crop models in India varied across different biophysical processes. 2. The response of yield to changes in local mean temperature was examined and compared to that found in the literature. No consistent response to temperature change was found across studies. 3. Implications for adaptation. China. The simulations of spring wheat in China show the relative importance of tolerance to water and heat stress in avoiding future crop failures. The greatest potential for reducing the number of harvests less than one standard deviation below the baseline mean yield value comes from alleviating water stress; the greatest potential for reducing harvests less than two standard deviations below the mean comes from alleviation of heat stress. The socio-economic analysis suggests that adaptation is also possible through measures such as greater investment. India. The simulations of groundnut in India identified regions where heat stress will play an increasing role in limiting crop yields, and other regions where crops with greater thermal time requirement will be needed. The simulations were used, together with an observed dataset and a simple analysis of crop cardinal temperatures and thermal time, to estimate the potential for adaptation using existing cultivars. USA. Analysis of spring wheat in the USA showed that at +2oC of local warming, 87% of the 2711 varieties examined, and all of the five most common varieties, could be used to maintain the crop duration of the current climate (i.e. successful adaptation to mean warming). At +4o this fell to 54% of all varieties, and two of the top five. 4. Future research. The results, and the limitations of the study, suggest directions for research to link climate and crop models, socio-economic analyses and crop variety trial data in order to prioritise adaptation options such as capacity building, plant breeding and biotechnology.

Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance

PubMed Central

Koevoets, Iko T.; Venema, Jan Henk; Elzenga, J. Theo. M.; Testerink, Christa

2016-01-01

To face future challenges in crop production dictated by global climate changes, breeders and plant researchers collaborate to develop productive crops that are able to withstand a wide range of biotic and abiotic stresses. However, crop selection is often focused on shoot performance alone, as observation of root properties is more complex and asks for artificial and extensive phenotyping platforms. In addition, most root research focuses on development, while a direct link to the functionality of plasticity in root development for tolerance is often lacking. In this paper we review the currently known root system architecture (RSA) responses in Arabidopsis and a number of crop species to a range of abiotic stresses, including nutrient limitation, drought, salinity, flooding, and extreme temperatures. For each of these stresses, the key molecular and cellular mechanisms underlying the RSA response are highlighted. To explore the relevance for crop selection, we especially review and discuss studies linking root architectural responses to stress tolerance. This will provide a first step toward understanding the relevance of adaptive root development for a plant’s response to its environment. We suggest that functional evidence on the role of root plasticity will support breeders in their efforts to include root properties in their current selection pipeline for abiotic stress tolerance, aimed to improve the robustness of crops. PMID:27630659

Using leaf optical properties to detect ozone effects on foliar biochemistry

USDA-ARS?s Scientific Manuscript database

Efficient methods for accurate and meaningful high-throughput plant phenotyping are limiting the development and breeding of stress-tolerant crops. A number of emerging techniques, specifically remote sensing methods, have been identified as promising tools for plant phenotyping. These remote-sensin...

Future crop production threatened by extreme heat

NASA Astrophysics Data System (ADS)

Siebert, Stefan; Ewert, Frank

2014-04-01

Heat is considered to be a major stress limiting crop growth and yields. While important findings on the impact of heat on crop yield have been made based on experiments in controlled environments, little is known about the effects under field conditions at larger scales. The study of Deryng et al (2014 Global crop yield response to extreme heat stress under multiple climate change futures Environ. Res. Lett. 9 034011), analysing the impact of heat stress on maize, spring wheat and soya bean under climate change, represents an important contribution to this emerging research field. Uncertainties in the occurrence of heat stress under field conditions, plant responses to heat and appropriate adaptation measures still need further investigation.

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

PubMed Central

2011-01-01

Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. Results We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress. Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. Conclusions This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE. PMID:21320317

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.

PubMed

Molina, Carlos; Zaman-Allah, Mainassara; Khan, Faheema; Fatnassi, Nadia; Horres, Ralf; Rotter, Björn; Steinhauer, Diana; Amenc, Laurie; Drevon, Jean-Jacques; Winter, Peter; Kahl, Günter

2011-02-14

The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Heat stress regimes for the investigation of pollen thermotolerance in crop plants.

PubMed

Mesihovic, Anida; Iannacone, Rina; Firon, Nurit; Fragkostefanakis, Sotirios

2016-06-01

Pollen thermotolerance. Global warming is predicted to increase the frequency and severity of extreme weather phenomena such as heat waves thereby posing a major threat for crop productivity and food security. The yield in case of most crop species is dependent on the success of reproductive development. Pollen development has been shown to be highly sensitive to elevated temperatures while the development of the female gametophyte as well as sporophytic tissues might also be disturbed under mild or severe heat stress conditions. Therefore, assessing pollen thermotolerance is currently of high interest for geneticists, plant biologists and breeders. A key aspect in pollen thermotolerance studies is the selection of the appropriate heat stress regime, the developmental stage that the stress is applied to, as well as the method of application. Literature search reveals a rather high variability in heat stress treatments mainly due to the lack of standardized protocols for different plant species. In this review, we summarize and discuss experimental approaches that have been used in various crops, with special focus on tomato, rice and wheat, as the best studied crops regarding pollen thermotolerance. The overview of stress treatments and the major outcomes of each study aim to provide guidelines for similar research in other crops.

Applications of UAVs in row-crop agriculture: advantages and limitations

NASA Astrophysics Data System (ADS)

Basso, B.; Putnam, G.; Price, R.; Zhang, J.

2016-12-01

The application of Unmanned Aerial Vehicles (UAV) to monitor agricultural fields has increased over the last few years due to advances in the technology, sensors, post-processing software for image analysis, along with more favorable regulations that allowed UAVs to be flown for commercial use. UAV have several capabilities depending on the type of sensors that are mounted onboard. The most widely used application remains crop scouting to identify areas within fields where the crops underperform for various reasons (nutritional status and water stress, presence of weeds, poor stands etc). In this talk, we present the preliminary results of UAVs field based research to better understand spatial and temporal variability of crop yield. Their advantage in providing timely information is critical, but adaptive management requires a system approach to account for the interactions occurring between genetics, environment and management.

Silicon in vascular plants: uptake, transport and its influence on mineral stress under acidic conditions.

PubMed

Pontigo, Sofía; Ribera, Alejandra; Gianfreda, Liliana; de la Luz Mora, María; Nikolic, Miroslav; Cartes, Paula

2015-07-01

So far, considerable advances have been achieved in understanding the mechanisms of Si uptake and transport in vascular plants. This review presents a comprehensive update about this issue, but also provides the new insights into the role of Si against mineral stresses that occur in acid soils. Such information could be helpful to understand both the differential Si uptake ability as well as the benefits of this mineral element on plants grown under acidic conditions. Silicon (Si) has been widely recognized as a beneficial element for many plant species, especially under stress conditions. In the last few years, great efforts have been made to elucidate the mechanisms involved in uptake and transport of Si by vascular plants and recently, different Si transporters have been identified. Several researches indicate that Si can alleviate various mineral stresses in plants growing under acidic conditions, including aluminium (Al) and manganese (Mn) toxicities as well as phosphorus (P) deficiency all of which are highly detrimental to crop production. This review presents recent findings concerning the influence of uptake and transport of Si on mineral stress under acidic conditions because a knowledge of this interaction provides the basis for understanding the role of Si in mitigating mineral stress in acid soils. Currently, only four Si transporters have been identified and there is little information concerning the response of Si transporters under stress conditions. More investigations are therefore needed to establish whether there is a relationship between Si transporters and the benefits of Si to plants subjected to mineral stress. Evidence presented suggests that Si supply and its subsequent accumulation in plant tissues could be exploited as a strategy to improve crop productivity on acid soils.

Estimating maize water stress by standard deviation of canopy temperature in thermal imagery

USDA-ARS?s Scientific Manuscript database

A new crop water stress index using standard deviation of canopy temperature as an input was developed to monitor crop water status. In this study, thermal imagery was taken from maize under various levels of deficit irrigation treatments in different crop growing stages. The Expectation-Maximizatio...

Evaluation of thermal remote sensing indices to estimate crop evapotranspiration coefficients

USDA-ARS?s Scientific Manuscript database

Remotely sensed data such as spectral reflectance and infrared canopy temperature can be used to quantify crop canopy cover and/or crop water stress, often through the use of vegetation indices calculated from the near-infrared and red bands, and stress indices calculated from the thermal wavelength...

Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress.

PubMed

Gu, Junfei; Yin, Xinyou; Zhang, Chengwei; Wang, Huaqi; Struik, Paul C

2014-09-01

Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameters were estimated from additive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. To account for genotypic yield differences, it was necessary to parameterize the model for differences in an additional trait 'total crop nitrogen uptake' (Nmax) among the ILs. Genetic variation in Nmax had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10-36 % more yield than those based on markers for yield per se. This study outlines a genotype-to-phenotype approach that exploits the potential value of marker-based crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome-wide association mapping of canopy wilting in diverse soybean genotypes

USDA-ARS?s Scientific Manuscript database

Drought stress is a major global constraint for crop production, and slow canopy wilting has been shown to be a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and confirm those loci with previously reported can...

GLOBAL EXPRESSION PROFILING AS A TOOL TO DEVELOP MOLECULAR MARKERS LINKED TO HERBICIDE STRESS IN ARABIDOPSIS

EPA Science Inventory

Herbicide drift (unintentional physical movement from target to off-target plants) is a cause of crop loss in US. Low-dose, high-potency herbicides that have short environmental persistence times constrain efforts to develop or identify metabolite or biochemical markers of exposu...

Comparison of Gene Expressions of Maize Kernel Pathogenesis-Related Proteins in Different Maize Genotypes

USDA-ARS?s Scientific Manuscript database

Aflatoxins are carcinogenic mycotoxins produced by the fungus Aspergillus flavus during infection of various grain crops including maize (Zea mays). Contamination of maize with aflatoxins has been shown to be exasperated by late season drought stress. Previous studies have identified numerous resist...

Genomic regions associated with freezing tolerance and snow mold tolerance in winter wheat

USDA-ARS?s Scientific Manuscript database

Crops grown through the winter are subject to selective pressures that vary with each year’s unique conditions, necessitating tolerance of numerous stress factors. The objective of this study was to identify molecular markers in winter wheat (Triticum aestivum L. em Thell) associated with tolerance...

Metabolomic analysis to evaluate the effects of drought stress on selected African eggplant accessions

USDA-ARS?s Scientific Manuscript database

Drought stress is one of the main abiotic stresses that affect crops. It leads to biochemical changes that can have adverse effects on plant growth, development and productivity. African eggplants are important vegetable and fruit crops reported to adapt and thrive well under drought stress. The div...

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants.

PubMed

Tripathi, Prateek; Rabara, Roel C; Rushton, Paul J

2014-02-01

Drought is one of the major challenges affecting crop productivity and yield. However, water stress responses are notoriously multigenic and quantitative with strong environmental effects on phenotypes. It is also clear that water stress often does not occur alone under field conditions but rather in conjunction with other abiotic stresses such as high temperature and high light intensities. A multidisciplinary approach with successful integration of a whole range of -omics technologies will not only define the system, but also provide new gene targets for both transgenic approaches and marker-assisted selection. Transcription factors are major players in water stress signaling and some constitute major hubs in the signaling webs. The main transcription factors in this network include MYB, bHLH, bZIP, ERF, NAC, and WRKY transcription factors. The role of WRKY transcription factors in abiotic stress signaling networks is just becoming apparent and systems biology approaches are starting to define their places in the signaling network. Using systems biology approaches, there are now many transcriptomic analyses and promoter analyses that concern WRKY transcription factors. In addition, reports on nuclear proteomics have identified WRKY proteins that are up-regulated at the protein level by water stress. Interactomics has started to identify different classes of WRKY-interacting proteins. What are often lacking are connections between metabolomics, WRKY transcription factors, promoters, biosynthetic pathways, fluxes and downstream responses. As more levels of the system are characterized, a more detailed understanding of the roles of WRKY transcription factors in drought responses in crops will be obtained.

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

PubMed

Moschen, Sebastián; Di Rienzo, Julio A; Higgins, Janet; Tohge, Takayuki; Watanabe, Mutsumi; González, Sergio; Rivarola, Máximo; García-García, Francisco; Dopazo, Joaquin; Hopp, H Esteban; Hoefgen, Rainer; Fernie, Alisdair R; Paniego, Norma; Fernández, Paula; Heinz, Ruth A

2017-07-01

By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach. Our results showed a delay in plant senescence with an increase in the expression level of photosynthesis related genes as well as higher levels of sugars, osmoprotectant amino acids and ionic nutrients under drought conditions. In addition, we identified transcription factors that were upregulated during drought conditions and that may act as hubs in the transcriptional network. Many of these transcription factors belong to families implicated in the drought response in model species. The integration of transcriptomic and metabolomic data in this study, together with physiological measurements, has improved our understanding of the biological responses during droughts and contributes to elucidate the molecular mechanisms involved under this environmental condition. These findings will provide useful biotechnological tools to improve stress tolerance while maintaining crop yield under restricted water availability.

'Omics' techniques for identifying flooding-response mechanisms in soybean.

PubMed

Komatsu, Setsuko; Shirasaka, Naoki; Sakata, Katsumi

2013-11-20

Plant growth and productivity are adversely influenced by various environmental stresses, which often lead to reduced seedling growth and decreased crop yields. Plants respond to stressful conditions through changes in 'omics' profiles, including transcriptomics, proteomics, and metabolomics. Linking plant phenotype to gene expression patterns, protein abundance, and metabolite accumulation is one of the main challenges for improving agricultural production. 'Omics' approaches may shed insight into the mechanisms that function in soybean in response to environmental stresses, particularly flooding by frequent rain, which occurs worldwide due to changes in global climate. Flooding causes significant reductions in the growth and yield of several crops, especially soybean. The application of 'omics' techniques may facilitate the development of flood-tolerant cultivars of soybean. In this review, the use of 'omics' techniques towards understanding the flooding-responsive mechanisms of soybeans is discussed, as the findings from these studies are expected to have applications in both breeding and agronomy. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

Genetic engineering strategies for biotic and abiotic stress tolerance and quality enhancement in horticultural crops: a comprehensive review.

PubMed

Parmar, Nehanjali; Singh, Kunwar Harendra; Sharma, Deepika; Singh, Lal; Kumar, Pankaj; Nanjundan, J; Khan, Yasin Jeshima; Chauhan, Devendra Kumar; Thakur, Ajay Kumar

2017-08-01

Genetic engineering technique offers myriads of applications in improvement of horticultural crops for biotic and abiotic stress tolerance, and produce quality enhancement. During last two decades, a large number of transgenic horticultural crops has been developed and more are underway. A number of genes including natural and synthetic Cry genes, protease inhibitors, trypsin inhibitors and cystatin genes have been used to incorporate insect and nematode resistance. For providing protection against fungal and bacterial diseases, various genes like chitinase, glucanase, osmotin, defensin and pathogenesis-related genes are being transferred to many horticultural crops world over. RNAi technique has been found quite successful in inducing virus resistance in horticultural crops in addition to coat protein genes. Abiotic stresses such as drought, heat and salinity adversely affect production and productivity of horticultural crops and a number of genes encoding for biosynthesis of stress protecting compounds including mannitol, glycine betaine and heat shock proteins have been employed for abiotic stress tolerance besides various transcription factors like DREB1, MAPK, WRKY, etc. Antisense gene and RNAi technologies have revolutionized the pace of improvement of horticultural crops, particularly ornamentals for color modification, increasing shelf-life and reducing post-harvest losses. Precise genome editing tools, particularly CRISPR/Cas9, have been efficiently applied in tomato, petunia, citrus, grape, potato and apple for gene mutation, repression, activation and epigenome editing. This review provides comprehensive overview to draw the attention of researchers for better understanding of genetic engineering advancements in imparting biotic and abiotic stress tolerance as well as on improving various traits related to quality, texture, plant architecture modification, increasing shelf-life, etc. in different horticultural crops.

Genetic Analysis of Ca 2+ Priming in Arabidopsis Guard Cell Stomatal Closure in Response to the Drought Hormone Abscisic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephan, Aaron B.

2014-11-01

A primary objective of modern agriculture and biofuel production is to utilize arable land to its fullest potential. However, sub-optimal growing conditions—arising from abiotic stresses such as drought, soil salinity, low humidity, cold, and heat—reduce crop yield and quality. Optimal yield under both stressed and non-stressed conditions requires the plant to activate coping mechanisms at a level commensurate with the severity of the drought stress. The osmotic sensors and associated regulatory mechanisms that initiate drought- and salt-tolerance responses in plants are largely unknown. This research aimed to identify and characterize these initial sensory components.

Use of remote sensing for land use policy formulation

NASA Technical Reports Server (NTRS)

1981-01-01

Progress in studies for using remotely sensed data for assessing crop stress and in crop estimation is reported. The estimation of acreage of small forested areas in the southern lower peninsula of Michigan using LANDSAT data is evaluated. Damage to small grains caused by the cereal leaf beetle was assessed through remote sensing. The remote detection of X-disease of peach and cherry trees and of fire blight of pear and apple trees was investigated. The reliability of improving on standard methods of crop production estimation was demonstrated. Areas of virus infestation in vineyards and blueberry fields in western and southwestern Michigan were identified. The installation and systems integration of a microcomputer system for processing and making available remotely sensed data are described.

Adverse weather impacts on arable cropping systems

NASA Astrophysics Data System (ADS)

Gobin, Anne

2016-04-01

Damages due to extreme or adverse weather strongly depend on crop type, crop stage, soil conditions and management. The impact is largest during the sensitive periods of the farming calendar, and requires a modelling approach to capture the interactions between the crop, its environment and the occurrence of the meteorological event. The hypothesis is that extreme and adverse weather events can be quantified and subsequently incorporated in current crop models. Since crop development is driven by thermal time and photoperiod, a regional crop model was used to examine the likely frequency, magnitude and impacts of frost, drought, heat stress and waterlogging in relation to the cropping season and crop sensitive stages. Risk profiles and associated return levels were obtained by fitting generalized extreme value distributions to block maxima for air humidity, water balance and temperature variables. The risk profiles were subsequently confronted with yields and yield losses for the major arable crops in Belgium, notably winter wheat, winter barley, winter oilseed rape, sugar beet, potato and maize at the field (farm records) to regional scale (statistics). The average daily vapour pressure deficit (VPD) and reference evapotranspiration (ET0) during the growing season is significantly lower (p < 0.001) and has a higher variability before 1988 than after 1988. Distribution patterns of VPD and ET0 have relevant impacts on crop yields. The response to rising temperatures depends on the crop's capability to condition its microenvironment. Crops short of water close their stomata, lose their evaporative cooling potential and ultimately become susceptible to heat stress. Effects of heat stress therefore have to be combined with moisture availability such as the precipitation deficit or the soil water balance. Risks of combined heat and moisture deficit stress appear during the summer. These risks are subsequently related to crop damage. The methodology of defining meteorological risks and subsequently relating the risk to the cropping calendar will be demonstrated for major arable crops in Belgium. Physically based crop models assist in understanding the links between adverse weather events, sensitive crop stages and crop damage. Financial support was obtained from Belspo under research contract SD/RI/03A.

Suitability of non-lethal marker and marker-free systems for development of transgenic crop plants: present status and future prospects.

PubMed

Manimaran, P; Ramkumar, G; Sakthivel, K; Sundaram, R M; Madhav, M S; Balachandran, S M

2011-01-01

Genetically modified crops are one of the prudent options for enhancing the production and productivity of crop plants by safeguarding from the losses due to biotic and abiotic stresses. Agrobacterium-mediated and biolistic transformation methods are used to develop transgenic crop plants in which selectable marker genes (SMG) are generally deployed to identify 'true' transformants. The commonly used SMG obtained from prokaryotic sources when employed in transgenic plants pose risks due to their lethal nature during selection process. In the recent past, some non-lethal SMGs have been identified and used for selection of transformants with increased precision and high selection efficiency. Considering the concerns related to bio-safety of the environment, it is desirable to remove the SMG in order to maximize the commercial success through wide adoption and public acceptance of genetically modified (GM) food crops. In this review, we examine the availability, and the suitability of wide range of non-lethal selection markers and elimination of SMG methods to develop marker-free transgenics for achieving global food security. As the strategies for marker-free plants are still in proof-of-concept stage, adaptation of new genomics tools for identification of novel non-lethal marker systems and its application for developing marker-free transgenics would further strengthen the crop improvement program. Copyright © 2011 Elsevier Inc. All rights reserved.

Using eddy covariance and flux partitioning to assess basal, soil, and stress coefficients for crop evapotranspiration models

USDA-ARS?s Scientific Manuscript database

Current approaches to scheduling crop irrigation using reference evapotranspiration (ET0) recommend using a dual-coefficient approach using basal (Kcb) and soil (Ke) coefficients along with a stress coefficient (Ks) to model crop evapotranspiration (ETc), [e.g. ETc=(Ks*Kcb+Ke)*ET0]. However, indepe...

Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress.

PubMed

Khan, Sardar-Ali; Li, Meng-Zhan; Wang, Suo-Min; Yin, Hong-Ju

2018-05-31

Owing to diverse abiotic stresses and global climate deterioration, the agricultural production worldwide is suffering serious losses. Breeding stress-resilient crops with higher quality and yield against multiple environmental stresses via application of transgenic technologies is currently the most promising approach. Deciphering molecular principles and mining stress-associate genes that govern plant responses against abiotic stresses is one of the prerequisites to develop stress-resistant crop varieties. As molecular switches in controlling stress-responsive genes expression, transcription factors (TFs) play crucial roles in regulating various abiotic stress responses. Hence, functional analysis of TFs and their interaction partners during abiotic stresses is crucial to perceive their role in diverse signaling cascades that many researchers have continued to undertake. Here, we review current developments in understanding TFs, with particular emphasis on their functions in orchestrating plant abiotic stress responses. Further, we discuss novel molecular mechanisms of their action under abiotic stress conditions. This will provide valuable information for understanding regulatory mechanisms to engineer stress-tolerant crops.

A Method of High Throughput Monitoring Crop Physiology Using Chlorophyll Fluorescence and Multispectral Imaging.

PubMed

Wang, Heng; Qian, Xiangjie; Zhang, Lan; Xu, Sailong; Li, Haifeng; Xia, Xiaojian; Dai, Liankui; Xu, Liang; Yu, Jingquan; Liu, Xu

2018-01-01

We present a high throughput crop physiology condition monitoring system and corresponding monitoring method. The monitoring system can perform large-area chlorophyll fluorescence imaging and multispectral imaging. The monitoring method can determine the crop current condition continuously and non-destructively. We choose chlorophyll fluorescence parameters and relative reflectance of multispectral as the indicators of crop physiological status. Using tomato as experiment subject, the typical crop physiological stress, such as drought, nutrition deficiency and plant disease can be distinguished by the monitoring method. Furthermore, we have studied the correlation between the physiological indicators and the degree of stress. Besides realizing the continuous monitoring of crop physiology, the monitoring system and method provide the possibility of machine automatic diagnosis of the plant physiology. Highlights: A newly designed high throughput crop physiology monitoring system and the corresponding monitoring method are described in this study. Different types of stress can induce distinct fluorescence and spectral characteristics, which can be used to evaluate the physiological status of plants.

Early warning and crop condition assessment research

NASA Technical Reports Server (NTRS)

Boatwright, G. O.; Whitehead, V. S.

1986-01-01

The Early Warning Crop Condition Assessment Project of AgRISTARS was a multiagency and multidisciplinary effort. Its mission and objectives were centered around development and testing of remote-sensing techniques that enhance operational methodologies for global crop-condition assessments. The project developed crop stress indicators models that provide data filter and alert capabilities for monitoring global agricultural conditions. The project developed a technique for using NOAA-n satellite advanced very-high-resolution radiometer (AVHRR) data for operational crop-condition assessments. This technology was transferred to the Foreign Agricultural Service of the USDA. The project developed a U.S. Great Plains data base that contains various meteorological parameters and vegetative index numbers (VIN) derived from AVHRR satellite data. It developed cloud screening techniques and scan angle correction models for AVHRR data. It also developed technology for using remotely acquired thermal data for crop water stress indicator modeling. The project provided basic technology including spectral characteristics of soils, water, stressed and nonstressed crop and range vegetation, solar zenith angle, and atmospheric and canopy structure effects.

Induction of abiotic stress tolerance in plants by endophytic microbes.

PubMed

Lata, R; Chowdhury, S; Gond, S K; White, J F

2018-04-01

Endophytes are micro-organisms including bacteria and fungi that survive within healthy plant tissues and promote plant growth under stress. This review focuses on the potential of endophytic microbes that induce abiotic stress tolerance in plants. How endophytes promote plant growth under stressful conditions, like drought and heat, high salinity and poor nutrient availability will be discussed. The molecular mechanisms for increasing stress tolerance in plants by endophytes include induction of plant stress genes as well as biomolecules like reactive oxygen species scavengers. This review may help in the development of biotechnological applications of endophytic microbes in plant growth promotion and crop improvement under abiotic stress conditions. Increasing human populations demand more crop yield for food security while crop production is adversely affected by abiotic stresses like drought, salinity and high temperature. Development of stress tolerance in plants is a strategy to cope with the negative effects of adverse environmental conditions. Endophytes are well recognized for plant growth promotion and production of natural compounds. The property of endophytes to induce stress tolerance in plants can be applied to increase crop yields. With this review, we intend to promote application of endophytes in biotechnology and genetic engineering for the development of stress-tolerant plants. © 2018 The Society for Applied Microbiology.

Improving plot- and regional-scale crop models for simulating impacts of climate variability and extremes

NASA Astrophysics Data System (ADS)

Tao, F.; Rötter, R.

2013-12-01

Many studies on global climate report that climate variability is increasing with more frequent and intense extreme events1. There are quite large uncertainties from both the plot- and regional-scale models in simulating impacts of climate variability and extremes on crop development, growth and productivity2,3. One key to reducing the uncertainties is better exploitation of experimental data to eliminate crop model deficiencies and develop better algorithms that more adequately capture the impacts of extreme events, such as high temperature and drought, on crop performance4,5. In the present study, in a first step, the inter-annual variability in wheat yield and climate from 1971 to 2012 in Finland was investigated. Using statistical approaches the impacts of climate variability and extremes on wheat growth and productivity were quantified. In a second step, a plot-scale model, WOFOST6, and a regional-scale crop model, MCWLA7, were calibrated and validated, and applied to simulate wheat growth and yield variability from 1971-2012. Next, the estimated impacts of high temperature stress, cold damage, and drought stress on crop growth and productivity based on the statistical approaches, and on crop simulation models WOFOST and MCWLA were compared. Then, the impact mechanisms of climate extremes on crop growth and productivity in the WOFOST model and MCWLA model were identified, and subsequently, the various algorithm and impact functions were fitted against the long-term crop trial data. Finally, the impact mechanisms, algorithms and functions in WOFOST model and MCWLA model were improved to better simulate the impacts of climate variability and extremes, particularly high temperature stress, cold damage and drought stress for location-specific and large area climate impact assessments. Our studies provide a good example of how to improve, in parallel, the plot- and regional-scale models for simulating impacts of climate variability and extremes, as needed for better informed decision-making on adaptation strategies. References 1. Coumou, D. & Rahmstorf, S. A decade of extremes. Nature Clim. Change, 2, 491-496 (2012). 2. Rötter, R. P., Carter, T. R., Olesen, J. E. & Porter, J. R. Crop-climate models need an overhaul. Nature Clim. Change, 1, 175-177 (2011). 3. Asseng, S. et al., Uncertainty in simulating wheat yields under climate change. Nature Clim. Change. 10.1038/nclimate1916. (2013). 4. Porter, J.R., & Semenov, M., Crop responses to climatic variation . Trans. R. Soc. B., 360, 2021-2035 (2005). 5. Porter, J.R. & Christensen, S. Deconstructing crop processes and models via identities. Plant, Cell and Environment . doi: 10.1111/pce.12107 (2013). 6. Boogaard, H.L., van Diepen C.A., Rötter R.P., Cabrera J.M. & van Laar H.H. User's guide for the WOFOST 7.1 crop growth simulation model and Control Center 1.5, Alterra, Wageningen, The Netherlands. (1998) 7. Tao, F. & Zhang, Z. Climate change, wheat productivity and water use in the North China Plain: a new super-ensemble-based probabilistic projection. Agric. Forest Meteorol., 170, 146-165. (2013).

Finger Millet: A "Certain" Crop for an "Uncertain" Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments.

PubMed

Gupta, Sanjay Mohan; Arora, Sandeep; Mirza, Neelofar; Pande, Anjali; Lata, Charu; Puranik, Swati; Kumar, J; Kumar, Anil

2017-01-01

Crop growth and productivity has largely been vulnerable to various abiotic and biotic stresses that are only set to be compounded due to global climate change. Therefore developing improved varieties and designing newer approaches for crop improvement against stress tolerance have become a priority now-a-days. However, most of the crop improvement strategies are directed toward staple cereals such as rice, wheat, maize etc., whereas attention on minor cereals such as finger millet [ Eleusine coracana (L.) Gaertn.] lags far behind. It is an important staple in several semi-arid and tropical regions of the world with excellent nutraceutical properties as well as ensuring food security in these areas even during harsh environment. This review highlights the importance of finger millet as a model nutraceutical crop. Progress and prospects in genetic manipulation for the development of abiotic and biotic stress tolerant varieties is also discussed. Although limited studies have been conducted for genetic improvement of finger millets, its nutritional significance in providing minerals, calories and protein makes it an ideal model for nutrition-agriculture research. Therefore, improved genetic manipulation of finger millets for resistance to both abiotic and biotic stresses, as well as for enhancing nutrient content will be very effective in millet improvement. Key message: Apart from the excellent nutraceutical value of finger millet, its ability to tolerate various abiotic stresses and resist pathogens make it an excellent model for exploring vast genetic and genomic potential of this crop, which provide us a wide choice for developing strategies for making climate resilient staple crops.

Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: Case study in tomato.

PubMed

Zsögön, Agustin; Cermak, Tomas; Voytas, Dan; Peres, Lázaro Eustáquio Pereira

2017-03-01

The ideotype is a theoretical model of an archetypal cultivated plant. Recent progress in genome editing is aiding the pursuit of this ideal in crop breeding. Breeding is relatively straightforward when the traits in question are monogenic in nature and show Mendelian inheritance. Conversely, traits with a diffuse, polygenic basis such as abiotic stress resistance are more difficult to harness. In recent years, many genes have been identified that are important for plant domestication and act by increasing yield, grain or fruit size or altering plant architecture. Here, we propose that (a) key monogenic traits whose physiology has been unveiled can be molecularly tailored to achieve the ideotype; and (b) wild relatives of crops harboring polygenic stress resistance genes or other traits of interest could be de novo domesticated by manipulating monogenic yield-related traits through state-of-the-art gene editing techniques. An overview of the genomic and physiological challenges in the world's main staple crops is provided. We focus on tomato and its wild Solanum (section Lycopersicon) relatives as a suitable model for molecular design in the pursuit of the ideotype for elite cultivars and to test de novo domestication of wild relatives. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Seeing is believing I: The use of thermal sensing from satellite imagery to predict crop yield

NASA Astrophysics Data System (ADS)

B, Potgieter A.; D, Rodriguez; B, Power; J, Mclean; P, Davis

2014-02-01

Volatility in crop production has been part of the Australian environment since cropping began with the arrival of the first European settlers. Climate variability is the main factor affecting crop production at national, state and local scales. At field level spatial patterns on yield production are also determined by spatially changing soil properties in interaction with seasonal climate conditions and weather patterns at critical stages in the crop development. Here we used a combination of field level weather records, canopy characteristics, and satellite information to determine the spatial performance of a large field of wheat. The main objective of this research is to determine the ability of remote sensing technologies to capture yield losses due to water stress at the canopy level. The yield, canopy characteristics (i.e. canopy temperature and ground cover) and seasonal conditions of a field of wheat (~1400ha) (-29.402° South and 149.508°, New South Wales, Australia) were continuously monitored during the winter of 2011. Weather and crop variables were continuously monitored by installing three automatic weather stations in a transect covering different positions and soils in the landscape. Weather variables included rainfall, minimum and maximum temperatures and relative humidity, and crop characteristics included ground cover and canopy temperature. Satellite imagery Landsat TM 5 and 7 was collected at five different stages in the crop cycle. Weather variables and crop characteristics were used to calculate a crop stress index (CSI) at point and field scale (39 fields). Field data was used to validate a spatial satellite image derived index. Spatial yield data was downloaded from the harvester at the different locations in the field. We used the thermal band (land surface temperature, LST) and enhanced vegetation index (EVI) bands from the MODIS (250 m for visible bands and 1km for thermal band) and a derived EVI from Landsat TM 7 (25 m for visible and 90m for thermal) satellite platforms. Results showed that spatial variations in crop yield were related to a satellite derived canopy stress index (CSIsat) and a moisture stress index (MSIsat). A weather station level canopy stress index (CSIws) calculated at midday was correlated to the CSIsat at late morning. In addition, a strong linear relationship was observed between EVI and LST at point scale throughout the crop growth period. Differences were smallest at anthesis when the canopy closure was highest. This suggests that LST imagery data around flowering could be used to calculate crop stress over large areas of the crop. The harvested yield was related (R2 = 0.67) to CSIsat using a fix date across all fields. This relationship improved (R2 = 0.92) using both indices from all five dates across all fields during the crop growth period. Here we successfully showed that satellite derived crop attributes (CSIsat and MSIsat) can account for most of the variability in final crop yield and that they can be used to predict crop yield at field scales. Applications of these results could enhance the ability of producers to hedge their financial on -farm crop production losses due to in-season water stress by taking crop insurance. This is likely to further improve their adaptive capacity and thus strengthening the long-term viability of the industry domestically and elsewhere.

Redox Strategies for Crop Improvement.

PubMed

Kerchev, Pavel; De Smet, Barbara; Waszczak, Cezary; Messens, Joris; Van Breusegem, Frank

2015-11-10

Recently, the agro-biotech industry has been driven by overcoming the limitations imposed by fluctuating environmental stress conditions on crop productivity. A common theme among (a)biotic stresses is the perturbation of the redox homeostasis. As a strategy to engineer stress-tolerant crops, many approaches have been centered on restricting the negative impact of reactive oxygen species (ROS) accumulation. In this study, we discuss the scientific background of the existing redox-based strategies to improve crop performance and quality. In this respect, a special focus goes to summarizing the current patent landscape because this aspect is very often ignored, despite constituting the forefront of applied research. The current increased understanding of ROS acting as signaling molecules has opened new avenues to exploit redox biology for crop improvement required for sustainable food security.

Viticulture microzoning: a functional approach aiming to grape and wine qualities

NASA Astrophysics Data System (ADS)

Bonfante, A.; Agrillo, A.; Albrizio, R.; Basile, A.; Buonomo, R.; De Mascellis, R.; Gambuti, A.; Giorio, P.; Guida, G.; Langella, G.; Manna, P.; Minieri, L.; Moio, L.; Siani, T.; Terribile, F.

2014-12-01

This paper aims to test a new physically oriented approach to viticulture zoning at the farm scale, strongly rooted on hydropedology and aiming to achieve a better use of environmental features with respect to plant requirement and wine production. The physics of our approach is defined by the use of soil-plant-atmosphere simulation models which applies physically-based equations to describe the soil hydrological processes and solves soil-plant water status. This study (ZOVISA project) was conducted in a farm devoted to high quality wines production (Aglianico DOC), located in South Italy (Campania region, Mirabella Eclano-AV). The soil spatial distribution was obtained after standard soil survey informed by geophysical survey. Two Homogenous Zones (HZs) were identified; in each one of those a physically based model was applied to solve the soil water balance and estimate the soil functional behaviour (crop water stress index, CWSI) defining the functional Homogeneous Zones (fHzs). In these last, experimental plots were established and monitored for investigating soil-plant water status, crop development (biometric and physiological parameters) and daily climate variables (temperature, solar radiation, rainfall, wind). The effects of crop water status on crop response over must and wine quality were then evaluated in the fHZs. This was performed by comparing crop water stress with (i) crop physiological measurement (leaf gas exchange, chlorophyll a fluorescence, leaf water potential, chlorophyll content, LAI measurement), (ii) grape bunches measurements (berry weight, sugar content, titratable acidity, etc.) and (iii) wine quality (aromatic response). Eventually this experiment has proved the usefulness of the physical based approach also in the case of mapping viticulture microzoning.

[Natural nucleotide polymorphism of the Srlk gene that determines salt stress tolerance in alfalfa (Medicago sativa L)].

PubMed

Vishnevskaia, M S; Pavlov, A V; Dziubenko, E A; Dziubenko, N I; Potokina, E K

2014-04-01

Based on legume genome syntheny, the nucleotide sequence of Srlk gene, key role of which in response to salt stress was demonstrated for the model species Medicago truncatula, was identified in the major forage and siderate crop alfalfa (Medicago sativa). In twelve alfalfa samples originating from regions with contrasting growing conditions, 19 SNPs were revealed in the Srlk gene. For two nonsynonymous SNPs, molecular markers were designed that could be further used to analyze the association between Srlk gene nucleotide polymorphism and the variability in salt stress tolerance among alfalfa cultivars.

Using Landsat digital data to detect moisture stress in corn-soybean growing regions

NASA Technical Reports Server (NTRS)

Thompson, D. R.; Wehmanen, O. A.

1980-01-01

As a part of a follow-on study to the moisture stress detection effort conducted in the Large Area Crop Inventory Experiment (LACIE), a technique utilizing transformed Landsat digital data was evaluated for detecting moisture stress in humid growing regions using sample segments from Iowa, Illinois, and Indiana. At known growth stages of corn and soybeans, segments were classified as undergoing moisture stress or not undergoing stress. The remote-sensing-based information was compared to a weekly ground-based index (Crop Moisture Index). This comparison demonstrated that the remote sensing technique could be used to monitor the growing conditions within a region where corn and soybeans are the major crop.

AgroClimate: Simulating and Monitoring the Risk of Extreme Weather Events from a Crop Phenology Perspective

NASA Astrophysics Data System (ADS)

Fraisse, C.; Pequeno, D.; Staub, C. G.; Perry, C.

2016-12-01

Climate variability, particularly the occurrence of extreme weather conditions such as dry spells and heat stress during sensitive crop developmental phases can substantially increase the prospect of reduced crop yields. Yield losses or crop failure risk due to stressful weather conditions vary mainly due to stress severity and exposure time and duration. The magnitude of stress effects is also crop specific, differing in terms of thresholds and adaptation to environmental conditions. To help producers in the Southeast USA mitigate and monitor the risk of crop losses due to extreme weather events we developed a web-based tool that evaluates the risk of extreme weather events during the season taking into account the crop development stages. Producers can enter their plans for the upcoming season in a given field (e.g. crop, variety, planting date, acreage etc.), select or not a specific El Nino Southern Oscillation (ENSO) phase, and will be presented with the probabilities (ranging from 0 -100%) of extreme weather events occurring during sensitive phases of the growing season for the selected conditions. The DSSAT models CERES-Maize, CROPGRO-Soybean, CROPGRO-Cotton, and N-Wheat phenology models have been translated from FORTRAN to a standalone versions in R language. These models have been tested in collaboration with Extension faculty and producers during the 2016 season and their usefulness for risk mitigation and monitoring evaluated. A companion AgroClimate app was also developed to help producers track and monitor phenology development during the cropping season.

Genome editing using CRISPR/Cas9-targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses.

PubMed

Abdelrahman, Mostafa; Al-Sadi, Abdullah M; Pour-Aboughadareh, Alireza; Burritt, David J; Tran, Lam-Son Phan

2018-03-12

Developing more crops able to sustainably produce high yields when grown under biotic/abiotic stresses is an important goal, if crop production and food security are to be guaranteed in the face of ever-increasing human population and unpredictable global climatic conditions. However, conventional crop improvement, through random mutagenesis or genetic recombination, is time-consuming and cannot keep pace with increasing food demands. Targeted genome editing (GE) technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR)/(CRISPR)-associated protein 9 (Cas9), have great potential to aid in the breeding of crops that are able to produce high yields under conditions of biotic/abiotic stress. This is due to their high efficiency, accuracy and low risk of off-target effects, compared with conventional random mutagenesis methods. The use of CRISPR/Cas9 system has grown very rapidly in recent years with numerous examples of targeted mutagenesis in crop plants, including gene knockouts, modifications, and the activation and repression of target genes. The potential of the GE approach for crop improvement has been clearly demonstrated. However, the regulation and social acceptance of GE crops still remain a challenge. In this review, we evaluate the recent applications of the CRISPR/Cas9-mediated GE, as a means to produce crop plants with greater resilience to the stressors they encounter when grown under increasing stressful environmental conditions. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava (Manihot esculenta Crantz).

PubMed

Ou, Wenjun; Mao, Xiang; Huang, Chao; Tie, Weiwei; Yan, Yan; Ding, Zehong; Wu, Chunlai; Xia, Zhiqiang; Wang, Wenquan; Zhou, Shiyi; Li, Kaimian; Hu, Wei

2018-01-01

KT/HAK/KUP (KUP) family is responsible for potassium ion (K + ) transport, which plays a vital role in the response of plants to abiotic stress by maintaining osmotic balance. However, our understanding of the functions of the KUP family in the drought-resistant crop cassava ( Manihot esculenta Crantz) is limited. In the present study, 21 cassava KUP genes ( MeKUPs ) were identified and classified into four clusters based on phylogenetic relationships, conserved motifs, and gene structure analyses. Transcriptome analysis revealed the expression diversity of cassava KUPs in various tissues of three genotypes. Comparative transcriptome analysis showed that the activation of MeKUP genes by drought was more in roots than that in leaves of Arg7 and W14 genotypes, whereas less in roots than that in leaves of SC124 variety. These findings indicate that different cassava genotypes utilize various drought resistance mechanism mediated by KUP genes. Specific KUP genes showed broad upregulation after exposure to salt, osmotic, cold, H 2 O 2 , and abscisic acid (ABA) treatments. Taken together, this study provides insights into the KUP -mediated drought response of cassava at transcription levels and identifies candidate genes that may be utilized in improving crop tolerance to abiotic stress.

Evaluation of neural network modeling to predict non-water-stressed leaf temperature in wine grape for calculation of crop water stress index

USDA-ARS?s Scientific Manuscript database

Precision irrigation management in wine grape production is hindered by the lack of a reliable method to easily quantify and monitor vine water status. Mild to moderate water stress is desirable in wine grape for controlling vine vigor and optimizing fruit yield and quality. A crop water stress ind...

Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef).

PubMed

Cannarozzi, Gina; Plaza-Wüthrich, Sonia; Esfeld, Korinna; Larti, Stéphanie; Wilson, Yi Song; Girma, Dejene; de Castro, Edouard; Chanyalew, Solomon; Blösch, Regula; Farinelli, Laurent; Lyons, Eric; Schneider, Michel; Falquet, Laurent; Kuhlemeier, Cris; Assefa, Kebebew; Tadele, Zerihun

2014-07-09

Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

Morphological and physiological evaluations of seedling quality

Treesearch

Diane L. Haase

2007-01-01

Seedling quality and subsequent field performance can be influenced by various stress factors. Measuring seedling quality can help to identify possible crop problems in order to make informed decisions for culturing, lifting, storing, and planting. In addition, seedling quality data can help seedling growers and users to better understand annual patterns among species...

GLOBAL TRANSCRIPTION PROFILING REVEALS DIFFERENTIAL RESPONSES TO CHRONIC NITROGEN STRESS AND PUTATIVE NITROGEN REGULATORY COMPONENTS IN ARABIDOPSIS

EPA Science Inventory

Background: A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and to identifying N-responsive gen...

Sensitivity analysis of the Aquacrop and SAFYE crop models for the assessment of water limited winter wheat yield in regional scale applications.

PubMed

Silvestro, Paolo Cosmo; Pignatti, Stefano; Yang, Hao; Yang, Guijun; Pascucci, Simone; Castaldi, Fabio; Casa, Raffaele

2017-01-01

Process-based models can be usefully employed for the assessment of field and regional-scale impact of drought on crop yields. However, in many instances, especially when they are used at the regional scale, it is necessary to identify the parameters and input variables that most influence the outputs and to assess how their influence varies when climatic and environmental conditions change. In this work, two different crop models, able to represent yield response to water, Aquacrop and SAFYE, were compared, with the aim to quantify their complexity and plasticity through Global Sensitivity Analysis (GSA), using Morris and EFAST (Extended Fourier Amplitude Sensitivity Test) techniques, for moderate to strong water limited climate scenarios. Although the rankings of the sensitivity indices was influenced by the scenarios used, the correlation among the rankings, higher for SAFYE than for Aquacrop, assessed by the top-down correlation coefficient (TDCC), revealed clear patterns. Parameters and input variables related to phenology and to water stress physiological processes were found to be the most influential for Aquacrop. For SAFYE, it was found that the water stress could be inferred indirectly from the processes regulating leaf growth, described in the original SAFY model. SAFYE has a lower complexity and plasticity than Aquacrop, making it more suitable to less data demanding regional scale applications, in case the only objective is the assessment of crop yield and no detailed information is sought on the mechanisms of the stress factors affecting its limitations.

Sensitivity analysis of the Aquacrop and SAFYE crop models for the assessment of water limited winter wheat yield in regional scale applications

PubMed Central

Pignatti, Stefano; Yang, Hao; Yang, Guijun; Pascucci, Simone; Castaldi, Fabio

2017-01-01

Process-based models can be usefully employed for the assessment of field and regional-scale impact of drought on crop yields. However, in many instances, especially when they are used at the regional scale, it is necessary to identify the parameters and input variables that most influence the outputs and to assess how their influence varies when climatic and environmental conditions change. In this work, two different crop models, able to represent yield response to water, Aquacrop and SAFYE, were compared, with the aim to quantify their complexity and plasticity through Global Sensitivity Analysis (GSA), using Morris and EFAST (Extended Fourier Amplitude Sensitivity Test) techniques, for moderate to strong water limited climate scenarios. Although the rankings of the sensitivity indices was influenced by the scenarios used, the correlation among the rankings, higher for SAFYE than for Aquacrop, assessed by the top-down correlation coefficient (TDCC), revealed clear patterns. Parameters and input variables related to phenology and to water stress physiological processes were found to be the most influential for Aquacrop. For SAFYE, it was found that the water stress could be inferred indirectly from the processes regulating leaf growth, described in the original SAFY model. SAFYE has a lower complexity and plasticity than Aquacrop, making it more suitable to less data demanding regional scale applications, in case the only objective is the assessment of crop yield and no detailed information is sought on the mechanisms of the stress factors affecting its limitations. PMID:29107963

Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield

PubMed Central

Choe, Eunsoo; Drnevich, Jenny; Williams, Martin M.

2016-01-01

Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The objectives were to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network. PMID:26796516

Learning from halophytes: physiological basis and strategies to improve abiotic stress tolerance in crops

PubMed Central

Shabala, Sergey

2013-01-01

Background Global annual losses in agricultural production from salt-affected land are in excess of US$12 billion and rising. At the same time, a significant amount of arable land is becoming lost to urban sprawl, forcing agricultural production into marginal areas. Consequently, there is a need for a major breakthrough in crop breeding for salinity tolerance. Given the limited range of genetic diversity in this trait within traditional crops, stress tolerance genes and mechanisms must be identified in extremophiles and then introduced into traditional crops. Scope and Conclusions This review argues that learning from halophytes may be a promising way of achieving this goal. The paper is focused around two central questions: what are the key physiological mechanisms conferring salinity tolerance in halophytes that can be introduced into non-halophyte crop species to improve their performance under saline conditions and what specific genes need to be targeted to achieve this goal? The specific traits that are discussed and advocated include: manipulation of trichome shape, size and density to enable their use for external Na+ sequestration; increasing the efficiency of internal Na+ sequestration in vacuoles by the orchestrated regulation of tonoplast NHX exchangers and slow and fast vacuolar channels, combined with greater cytosolic K+ retention; controlling stomata aperture and optimizing water use efficiency by reducing stomatal density; and efficient control of xylem ion loading, enabling rapid shoot osmotic adjustment while preventing prolonged Na+ transport to the shoot. PMID:24085482

Finger Millet: A “Certain” Crop for an “Uncertain” Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments

PubMed Central

Gupta, Sanjay Mohan; Arora, Sandeep; Mirza, Neelofar; Pande, Anjali; Lata, Charu; Puranik, Swati; Kumar, J.; Kumar, Anil

2017-01-01

Crop growth and productivity has largely been vulnerable to various abiotic and biotic stresses that are only set to be compounded due to global climate change. Therefore developing improved varieties and designing newer approaches for crop improvement against stress tolerance have become a priority now-a-days. However, most of the crop improvement strategies are directed toward staple cereals such as rice, wheat, maize etc., whereas attention on minor cereals such as finger millet [Eleusine coracana (L.) Gaertn.] lags far behind. It is an important staple in several semi-arid and tropical regions of the world with excellent nutraceutical properties as well as ensuring food security in these areas even during harsh environment. This review highlights the importance of finger millet as a model nutraceutical crop. Progress and prospects in genetic manipulation for the development of abiotic and biotic stress tolerant varieties is also discussed. Although limited studies have been conducted for genetic improvement of finger millets, its nutritional significance in providing minerals, calories and protein makes it an ideal model for nutrition-agriculture research. Therefore, improved genetic manipulation of finger millets for resistance to both abiotic and biotic stresses, as well as for enhancing nutrient content will be very effective in millet improvement. Key message: Apart from the excellent nutraceutical value of finger millet, its ability to tolerate various abiotic stresses and resist pathogens make it an excellent model for exploring vast genetic and genomic potential of this crop, which provide us a wide choice for developing strategies for making climate resilient staple crops. PMID:28487720

Are GM Crops for Yield and Resilience Possible?

PubMed

Paul, Matthew J; Nuccio, Michael L; Basu, Shib Sankar

2018-01-01

Crop yield improvements need to accelerate to avoid future food insecurity. Outside Europe, genetically modified (GM) crops for herbicide- and insect-resistance have been transformative in agriculture; other traits have also come to market. However, GM of yield potential and stress resilience has yet to impact on food security. Genes have been identified for yield such as grain number, size, leaf growth, resource allocation, and signaling for drought tolerance, but there is only one commercialized drought-tolerant GM variety. For GM and genome editing to impact on yield and resilience there is a need to understand yield-determining processes in a cell and developmental context combined with evaluation in the grower environment. We highlight a sugar signaling mechanism as a paradigm for this approach. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prioritizing stream types according to their potential risk to receive crop plant material--A GIS-based procedure to assist in the risk assessment of genetically modified crops and systemic insecticide residues.

PubMed

Bundschuh, Rebecca; Kuhn, Ulrike; Bundschuh, Mirco; Naegele, Caroline; Elsaesser, David; Schlechtriemen, Ulrich; Oehen, Bernadette; Hilbeck, Angelika; Otto, Mathias; Schulz, Ralf; Hofmann, Frieder

2016-03-15

Crop plant residues may enter aquatic ecosystems via wind deposition or surface runoff. In the case of genetically modified crops or crops treated with systemic pesticides, these materials may contain insecticidal Bt toxins or pesticides that potentially affect aquatic life. However, the particular exposure pattern of aquatic ecosystems (i.e., via plant material) is not properly reflected in current risk assessment schemes, which primarily focus on waterborne toxicity and not on plant material as the route of uptake. To assist in risk assessment, the present study proposes a prioritization procedure of stream types based on the freshwater network and crop-specific cultivation data using maize in Germany as a model system. To identify stream types with a high probability of receiving crop materials, we developed a formalized, criteria-based and thus transparent procedure that considers the exposure-related parameters, ecological status--an estimate of the diversity and potential vulnerability of local communities towards anthropogenic stress--and availability of uncontaminated reference sections. By applying the procedure to maize, ten stream types out of 38 are expected to be the most relevant if the ecological effects from plant-incorporated pesticides need to be evaluated. This information is an important first step to identifying habitats within these stream types with a high probability of receiving crop plant material at a more local scale, including accumulation areas. Moreover, the prioritization procedure developed in the present study may support the selection of aquatic species for ecotoxicological testing based on their probability of occurrence in stream types having a higher chance of exposure. Finally, this procedure can be adapted to any geographical region or crop of interest and is, therefore, a valuable tool for a site-specific risk assessment of crop plants carrying systemic pesticides or novel proteins, such as insecticidal Bt toxins, expressed in genetically modified crops. Copyright © 2015 Elsevier B.V. All rights reserved.

Differential proteomic analysis reveals sequential heat stress-responsive regulatory network in radish (Raphanus sativus L.) taproot.

PubMed

Wang, Ronghua; Mei, Yi; Xu, Liang; Zhu, Xianwen; Wang, Yan; Guo, Jun; Liu, Liwang

2018-05-01

Differential abundance protein species (DAPS) involved in reducing damage and enhancing thermotolerance in radish were firstly identified. Proteomic analysis and omics association analysis revealed a HS-responsive regulatory network in radish. Heat stress (HS) is a major destructive factor influencing radish production and supply in summer, for radish is a cool season vegetable crop being susceptible to high temperature. In this study, the proteome changes of radish taproots under 40 °C treatment at 0 h (Control), 12 h (Heat12) and 24 h (Heat24) were analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification) approach. In total, 2258 DAPS representing 1542 differentially accumulated uniprotein species which respond to HS were identified. A total of 604, 910 and 744 DAPS was detected in comparison of Control vs. Heat12, Control vs. Heat24, and Heat12 vs. Heat24, respectively. Gene ontology and pathway analysis showed that annexin, ubiquitin-conjugating enzyme, ATP synthase, heat shock protein (HSP) and other stress-related proteins were predominately enriched in signal transduction, stress and defense pathways, photosynthesis and energy metabolic pathways, working cooperatively to reduce stress-induced damage in radish. Based on iTRAQ combined with the transcriptomics analysis, a schematic model of a sequential HS-responsive regulatory network was proposed. The initial sensing of HS occurred at the plasma membrane, and then key components of stress signal transduction triggered heat-responsive genes in the plant protective metabolism to re-establish homeostasis and enhance thermotolerance. These results provide new insights into characteristics of HS-responsive DAPS and facilitate dissecting the molecular mechanisms underlying heat tolerance in radish and other root crops.

The Dynamic Changes of the Plasma Membrane Proteins and the Protective Roles of Nitric Oxide in Rice Subjected to Heavy Metal Cadmium Stress

PubMed Central

Yang, Liming; Ji, Jianhui; Harris-Shultz, Karen R.; Wang, Hui; Wang, Hongliang; Abd-Allah, Elsayed F.; Luo, Yuming; Hu, Xiangyang

2016-01-01

The heavy metal cadmium is a common environmental contaminant in soils and has adverse effects on crop growth and development. The signaling processes in plants that initiate cellular responses to environmental stress have been shown to be located in the plasma membrane (PM). A better understanding of the PM proteome in response to environmental stress might provide new insights for improving stress-tolerant crops. Nitric oxide (NO) is reported to be involved in the plant response to cadmium (Cd) stress. To further investigate how NO modulates protein changes in the plasma membrane during Cd stress, a quantitative proteomics approach based on isobaric tags for relative and absolute quantification (iTRAQ) was used to identify differentially regulated proteins from the rice plasma membrane after Cd or Cd and NO treatment. Sixty-six differentially expressed proteins were identified, of which, many function as transporters, ATPases, kinases, metabolic enzymes, phosphatases, and phospholipases. Among these, the abundance of phospholipase D (PLD) was altered substantially after the treatment of Cd or Cd and NO. Transient expression of the PLD fused with green fluorescent peptide (GFP) in rice protoplasts showed that the Cd and NO treatment promoted the accumulation of PLD in the plasma membrane. Addition of NO also enhanced Cd-induced PLD activity and the accumulation of phosphatidic acid (PA) produced through PLD activity. Meanwhile, NO elevated the activities of antioxidant enzymes and caused the accumulation of glutathione, both which function to reduce Cd-induced H2O2 accumulation. Taken together, we suggest that NO signaling is associated with the accumulation of antioxidant enzymes, glutathione and PA which increases cadmium tolerance in rice via the antioxidant defense system. PMID:26955374

UPLC-QTOF analysis reveals metabolomic changes in the flag leaf of wheat (Triticum aestivum L.) under low-nitrogen stress.

PubMed

Zhang, Yang; Ma, Xin-Ming; Wang, Xiao-Chun; Liu, Ji-Hong; Huang, Bing-Yan; Guo, Xiao-Yang; Xiong, Shu-Ping; La, Gui-Xiao

2017-02-01

Wheat is one of the most important grain crop plants worldwide. Nitrogen (N) is an essential macronutrient for the growth and development of wheat and exerts a marked influence on its metabolites. To investigate the influence of low nitrogen stress on various metabolites of the flag leaf of wheat (Triticum aestivum L.), a metabolomic analysis of two wheat cultivars under different induced nitrogen levels was conducted during two important growth periods based on large-scale untargeted metabolomic analysis using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF). Multivariate analyses-such as principle components analysis (PCA) and orthogonal partial least square discriminant analysis (OPLS-DA)-were used for data analysis. PCA yielded distinctive clustering information among the samples, classifying the wheat flag samples into two categories: those under normal N treatment and low N treatment. By processing OPLS-DA, eleven secondary metabolites were shown to be responsible for classifying the two groups. The secondary metabolites may be considered potential biomarkers of low nitrogen stress. Chemical analyses showed that most of the identified secondary metabolites were flavonoids and their related derivatives, such as iso-vitexin, iso-orientin and methylisoorientin-2″-O-rhamnoside, etc. This study confirmed the effect of low nitrogen stress on the metabolism of wheat, and revealed that the accumulation of secondary metabolites is a response to abiotic stresses. Meanwhile, we aimed to identify markers which could be used to monitor the nitrogen status of wheat crops, presumably to guide appropriate fertilization regimens. Furthermore, the UPLC-QTOF metabolic platform technology can be used to study metabolomic variations of wheat under abiotic stresses. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Mining Halophytes for Plant Growth-Promoting Halotolerant Bacteria to Enhance the Salinity Tolerance of Non-halophytic Crops

PubMed Central

Etesami, Hassan; Beattie, Gwyn A.

2018-01-01

Salinity stress is one of the major abiotic stresses limiting crop production in arid and semi-arid regions. Interest is increasing in the application of PGPRs (plant growth promoting rhizobacteria) to ameliorate stresses such as salinity stress in crop production. The identification of salt-tolerant, or halophilic, PGPRs has the potential to promote saline soil-based agriculture. Halophytes are a useful reservoir of halotolerant bacteria with plant growth-promoting capabilities. Here, we review recent studies on the use of halophilic PGPRs to stimulate plant growth and increase the tolerance of non-halophytic crops to salinity. These studies illustrate that halophilic PGPRs from the rhizosphere of halophytic species can be effective bio-inoculants for promoting the production of non-halophytic species in saline soils. These studies support the viability of bioinoculation with halophilic PGPRs as a strategy for the sustainable enhancement of non-halophytic crop growth. The potential of this strategy is discussed within the context of ensuring sustainable food production for a world with an increasing population and continuing climate change. We also explore future research needs for using halotolerant PGPRs under salinity stress. PMID:29472908

Nitrogen fertility and abiotic stresses management in cotton crop: a review.

PubMed

Khan, Aziz; Tan, Daniel Kean Yuen; Afridi, Muhammad Zahir; Luo, Honghai; Tung, Shahbaz Atta; Ajab, Mir; Fahad, Shah

2017-06-01

This review outlines nitrogen (N) responses in crop production and potential management decisions to ameliorate abiotic stresses for better crop production. N is a primary constituent of the nucleotides and proteins that are essential for life. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. Therefore, increasing plant N use efficiency (NUE) is important for the development of sustainable agriculture. NUE has a key role in crop yield and can be enhanced by controlling loss of fertilizers by application of humic acid and natural polymers (hydrogels), having high water-holding capacity which can improve plant performance under field conditions. Abiotic stresses such as waterlogging, drought, heat, and salinity are the major limitations for successful crop production. Therefore, integrated management approaches such as addition of aminoethoxyvinylglycine (AVG), the film antitranspirant (di-1-p-menthene and pinolene) nutrients, hydrogels, and phytohormones may provide novel approaches to improve plant tolerance against abiotic stress-induced damage. Moreover, for plant breeders and molecular biologists, it is a challenge to develop cotton cultivars that can tolerate plant abiotic stresses while having high potential NUE for the future.

Drought-related vulnerability and risk assessment of groundwater in Belgium: estimation of the groundwater recharge and crop yield vulnerability with the B-CGMS

NASA Astrophysics Data System (ADS)

Jacquemin, Ingrid; Verbeiren, Boud; Vanderhaegen, Sven; Canters, Frank; Vermeiren, Karolien; Engelen, Guy; Huysmans, Marijke; Batelaan, Okke; Tychon, Bernard

2016-04-01

Due to common belief that regions under temperate climate are not affected by (meteorological and groundwater) drought, these events and their impacts remain poorly studied: in the GroWaDRISK, we propose to take stock of this question. We aim at providing a better understanding of the influencing factors (land use and land cover changes, water demand and climate) and the drought-related impacts on the environment, water supply and agriculture. The study area is located in the North-East of Belgium, corresponding approximatively to the Dijle and Demer catchments. To establish an overview of the groundwater situation, we assess the system input: the recharge. To achieve this goal, two models, B-CGMS and WetSpass are used to evaluate the recharge, respectively, over agricultural land and over the remaining areas, as a function of climate and for various land uses and land covers. B-CGMS, which is an adapted version for Belgium of the European Crop Growth Monitoring System, is used for assessing water recharge at a daily timestep and under different agricultural lands: arable land (winter wheat, maize...), orchards, horticulture and floriculture and for grassland. B-CGMS is designed to foresee crop yield and obviously it studies the impact of drought on crop yield and raises issues for the potential need of irrigation. For both yields and water requirements, the model proposes a potential mode, driven by temperature and solar radiation, and a water-limited mode for which water availability can limit crop growth. By this way, we can identify where and when water consumption and yield are not optimal, in addition to the Crop Water Stress Index. This index is calculated for a given crop, as the number of days affected by water stress during the growth sensitive period. Both recharge and crop yield are assessed for the current situation (1980 - 2012), taking into account the changing land use/land cover, in terms of areas and localization of the agricultural land and where the proportion of the different crops had considerably evolved through time (e.g., increase of grain maize and potatoes while winter cereals decrease). The preliminary results of the recharge lead to an average value in the area showing a significant negative trend, in both simulations with fixed (base = 1980) and changing land cover. In the same time, we could observe an increasing number of water stress periods, especially for maize, one of the main crops in the area. Finally, a preliminary test will be presented for the horizon 2040, for which we use meteorological time series (for high and low hydrologic impacts) given by the CCI-HYDR Perturbation Tool (Ntegeka V. and Willems P., 2009). This preliminary test aims to (1) evaluate the amplitude of the potential recharge deficit and, (2) especially, to define vulnerability zones, affected by frequent water stress, in connection with irrigation needs which could possibly increase the groundwater extraction.

A UAS-based remote sensing platform for crop water stress detection

NASA Astrophysics Data System (ADS)

Zhang, H.; Wang, D.; Ayars, J. E.

2014-12-01

The remote detection of water stress in a biofuel crop field was investigated using canopy temperature measurements. An experimental trial was set up in the central valley of Maui, Hawaii, comprising different sugarcane varieties and irrigation regimes. An unmanned aerial system (UAS) was equipped with a FLIR A615 thermal camera to acquire canopy temperature imagery. Images were mosaicked and processed to show spatial temperature difference of entire field. A weather station was installed in a full irrigation plot to collect meteorological parameters. The sensitivity of canopy to air temperature difference and crop water stress index were investigated on detecting cop water stress levels. The results showed that low irrigation level treatment plots resulted in higher canopy temperatures compared to the high irrigation level treatment plots. Canopy temperatures also showed differences in water stress in different sugarcane varieties. The study demonstrated the feasibility of UAS-based thermal method to quantify plant water status of sugar canes used for biofuel crops.

Crosstalk between Two bZIP Signaling Pathways Orchestrates Salt-Induced Metabolic Reprogramming in Arabidopsis Roots

PubMed Central

Hartmann, Laura; Pedrotti, Lorenzo; Weiste, Christoph; Fekete, Agnes; Schierstaedt, Jasper; Göttler, Jasmin; Kempa, Stefan; Krischke, Markus; Dietrich, Katrin; Mueller, Martin J.; Vicente-Carbajosa, Jesus; Hanson, Johannes; Dröge-Laser, Wolfgang

2015-01-01

Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity. PMID:26276836

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array.

PubMed

Ps, Shanmugavadivel; Sv, Amitha Mithra; Prakash, Chandra; Mk, Ramkumar; Tiwari, Ratan; Mohapatra, Trilochan; Singh, Nagendra Kumar

2017-12-01

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F 8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance. To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively. The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

Linking groundwater use and stress to specific crops using the groundwater footprint in the Central Valley and High Plains aquifer systems, U.S.

NASA Astrophysics Data System (ADS)

Esnault, Laurent; Gleeson, Tom; Wada, Yoshihide; Heinke, Jens; Gerten, Dieter; Flanary, Elizabeth; Bierkens, Marc F. P.; van Beek, Ludovicus P. H.

2014-06-01

A number of aquifers worldwide are being depleted, mainly by agricultural activities, yet groundwater stress has not been explicitly linked to specific agricultural crops. Using the newly developed concept of the groundwater footprint (the area required to sustain groundwater use and groundwater-dependent ecosystem services), we develop a methodology to derive crop-specific groundwater footprints. We illustrate this method by calculating high-resolution groundwater footprint estimates of crops in two heavily used aquifer systems: the Central Valley and High Plains, U.S. In both aquifer systems, hay and haylage, corn, and cotton have the largest groundwater footprints, which highlights that most of the groundwater stress is induced by crops meant for cattle feed. Our results are coherent with other studies in the High Plains but suggest lower groundwater stress in the Central Valley, likely due to artificial recharge from surface water diversions which were not taken into account in previous estimates. Uncertainties of recharge and irrigation application efficiency contribute the most to the total relative uncertainty of the groundwater footprint to aquifer area ratios. Our results and methodology will be useful for hydrologists, water resource managers, and policy makers concerned with which crops are causing the well-documented groundwater stress in semiarid to arid agricultural regions around the world.

Linking Groundwater Use and Stress to Specific Crops Using the Groundwater Footprint in the Central Valley and High Plains Aquifer Systems, U.S.

NASA Astrophysics Data System (ADS)

Wada, Y.; Esnault, L.; Gleeson, T.; Heinke, J.; Gerten, D.; Flanary, E.; Bierkens, M. F.; Van Beek, L. P.

2014-12-01

A number of aquifers worldwide are being depleted, mainly by agricultural activities, yet groundwater stress has not been explicitly linked to specific agricultural crops. Using the newly-developed concept of the groundwater footprint (the area required to sustain groundwater use and groundwater-dependent ecosystem services), we develop a methodology to derive crop-specific groundwater footprints. We illustrate this method by calculating high resolution groundwater footprint estimates of crops in two heavily used aquifer systems: the Central Valley and High Plains, U.S. In both aquifer systems, hay and haylage, corn and cotton have the largest groundwater footprints, which highlights that most of the groundwater stress is induced by crops meant for cattle feed. Our results are coherent with other studies in the High Plains but suggest lower groundwater stress in the Central Valley, likely due to artificial recharge from surface water diversions which were not taken into account in previous estimates. Uncertainties of recharge and irrigation application efficiency contribute the most to the total relative uncertainty of the groundwater footprint to aquifer area ratios. Our results and methodology will be useful for hydrologists, water resource managers, and policy makers concerned with which crops are causing the well-documented groundwater stress in semiarid to arid agricultural regions around the world.

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

PubMed Central

Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

2016-01-01

As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality. PMID:27258266

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science.

PubMed

Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

2016-06-01

As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.

Genome-Wide Analysis of miRNA targets in Brachypodium and Biomass Energy Crops

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, Pamela J.

2015-08-11

MicroRNAs (miRNAs) contribute to the control of numerous biological processes through the regulation of specific target mRNAs. Although the identities of these targets are essential to elucidate miRNA function, the targets are much more difficult to identify than the small RNAs themselves. Before this work, we pioneered the genome-wide identification of the targets of Arabidopsis miRNAs using an approach called PARE (German et al., Nature Biotech. 2008; Nature Protocols, 2009). Under this project, we applied PARE to Brachypodium distachyon (Brachypodium), a model plant in the Poaceae family, which includes the major food grain and bioenergy crops. Through in-depth global analysismore » and examination of specific examples, this research greatly expanded our knowledge of miRNAs and target RNAs of Brachypodium. New regulation in response to environmental stress or tissue type was found, and many new miRNAs were discovered. More than 260 targets of new and known miRNAs with PARE sequences at the precise sites of miRNA-guided cleavage were identified and characterized. Combining PARE data with the small RNA data also identified the miRNAs responsible for initiating approximately 500 phased loci, including one of the novel miRNAs. PARE analysis also revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. The project included generation of small RNA and PARE resources for bioenergy crops, to facilitate ongoing discovery of conserved miRNA-target RNA regulation. By associating specific miRNA-target RNA pairs with known physiological functions, the research provides insights about gene regulation in different tissues and in response to environmental stress. This, and release of new PARE and small RNA data sets should contribute basic knowledge to enhance breeding and may suggest new strategies for improvement of biomass energy crops.« less

The Reference Genome of the Halophytic Plant Eutrema salsugineum

PubMed Central

Yang, Ruolin; Jarvis, David E.; Chen, Hao; Beilstein, Mark A.; Grimwood, Jane; Jenkins, Jerry; Shu, ShengQiang; Prochnik, Simon; Xin, Mingming; Ma, Chuang; Schmutz, Jeremy; Wing, Rod A.; Mitchell-Olds, Thomas; Schumaker, Karen S.; Wang, Xiangfeng

2013-01-01

Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8× coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species. PMID:23518688

Morphological plasticity of root growth under mild water stress increases water use efficiency without reducing yield in maize

NASA Astrophysics Data System (ADS)

Cai, Qian; Zhang, Yulong; Sun, Zhanxiang; Zheng, Jiaming; Bai, Wei; Zhang, Yue; Liu, Yang; Feng, Liangshan; Feng, Chen; Zhang, Zhe; Yang, Ning; Evers, Jochem B.; Zhang, Lizhen

2017-08-01

A large yield gap exists in rain-fed maize (Zea mays L.) production in semi-arid regions, mainly caused by frequent droughts halfway through the crop-growing period due to uneven distribution of rainfall. It is questionable whether irrigation systems are economically required in such a region since the total amount of rainfall does generally meet crop requirements. This study aimed to quantitatively determine the effects of water stress from jointing to grain filling on root and shoot growth and the consequences for maize grain yield, above- and below-ground dry matter, water uptake (WU) and water use efficiency (WUE). Pot experiments were conducted in 2014 and 2015 with a mobile rain shelter to achieve conditions of no, mild or severe water stress. Maize yield was not affected by mild water stress over 2 years, while severe stress reduced yield by 56 %. Both water stress levels decreased root biomass slightly but shoot biomass substantially. Mild water stress decreased root length but increased root diameter, resulting in no effect on root surface area. Due to the morphological plasticity in root growth and the increase in root / shoot ratio, WU under water stress was decreased, and overall WUE for both above-ground dry matter and grain yield increased. Our results demonstrate that an irrigation system might be not economically and ecologically necessary because the frequently occurring mild water stress did not reduce crop yield much. The study helps us to understand crop responses to water stress during a critical water-sensitive period (middle of the crop-growing season) and to mitigate drought risk in dry-land agriculture.

Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage.

PubMed

Chidambaranathan, Parameswaran; Jagannadham, Prasanth Tej Kumar; Satheesh, Viswanathan; Kohli, Deshika; Basavarajappa, Santosh Halasabala; Chellapilla, Bharadwaj; Kumar, Jitendra; Jain, Pradeep Kumar; Srinivasan, R

2018-05-01

The heat stress transcription factors (Hsfs) play a prominent role in thermotolerance and eliciting the heat stress response in plants. Identification and expression analysis of Hsfs gene family members in chickpea would provide valuable information on heat stress responsive Hsfs. A genome-wide analysis of Hsfs gene family resulted in the identification of 22 Hsf genes in chickpea in both desi and kabuli genome. Phylogenetic analysis distinctly separated 12 A, 9 B, and 1 C class Hsfs, respectively. An analysis of cis-regulatory elements in the upstream region of the genes identified many stress responsive elements such as heat stress elements (HSE), abscisic acid responsive element (ABRE) etc. In silico expression analysis showed nine and three Hsfs were also expressed in drought and salinity stresses, respectively. Q-PCR expression analysis of Hsfs under heat stress at pod development and at 15 days old seedling stage showed that CarHsfA2, A6, and B2 were significantly upregulated in both the stages of crop growth and other four Hsfs (CarHsfA2, A6a, A6c, B2a) showed early transcriptional upregulation for heat stress at seedling stage of chickpea. These subclasses of Hsfs identified in this study can be further evaluated as candidate genes in the characterization of heat stress response in chickpea.

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

PubMed Central

Shriram, Varsha; Kumar, Vinay; Devarumath, Rachayya M.; Khare, Tushar S.; Wani, Shabir H.

2016-01-01

The microRNAs (miRNAs) are small (20–24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed. PMID:27379117

Intensity of heat stress in winter wheat—phenology compensates for the adverse effect of global warming

NASA Astrophysics Data System (ADS)

Eyshi Rezaei, Ehsan; Siebert, Stefan; Ewert, Frank

2015-02-01

Higher temperatures during the growing season are likely to reduce crop yields with implications for crop production and food security. The negative impact of heat stress has also been predicted to increase even further for cereals such as wheat under climate change. Previous empirical modeling studies have focused on the magnitude and frequency of extreme events during the growth period but did not consider the effect of higher temperature on crop phenology. Based on an extensive set of climate and phenology observations for Germany and period 1951-2009, interpolated to 1 × 1 km resolution and provided as supplementary data to this article (available at stacks.iop.org/ERL/10/024012/mmedia), we demonstrate a strong relationship between the mean temperature in spring and the day of heading (DOH) of winter wheat. We show that the cooling effect due to the 14 days earlier DOH almost fully compensates for the adverse effect of global warming on frequency and magnitude of crop heat stress. Earlier heading caused by the warmer spring period can prevent exposure to extreme heat events around anthesis, which is the most sensitive growth stage to heat stress. Consequently, the intensity of heat stress around anthesis in winter crops cultivated in Germany may not increase under climate change even if the number and duration of extreme heat waves increase. However, this does not mean that global warning would not harm crop production because of other impacts, e.g. shortening of the grain filling period. Based on the trends for the last 34 years in Germany, heat stress (stress thermal time) around anthesis would be 59% higher in year 2009 if the effect of high temperatures on accelerating wheat phenology were ignored. We conclude that climate impact assessments need to consider both the effect of high temperature on grain set at anthesis but also on crop phenology.

Uncertainty in future agro-climate projections in the United States and benefits of greenhouse gas mitigation

DOE PAGES

Monier, Erwan; Xu, Liyi; Snyder, Richard

2016-04-26

Scientific challenges exist on how to extract information from the wide range of projected impacts simulated by crop models driven by climate ensembles. A stronger focus is required to understand and identify the mechanisms and drivers of projected changes in crop yield. In this study, we investigate the robustness of future projections of five metrics relevant to agriculture stakeholders (accumulated frost days, dry days, growing season length, plant heat stress and start of field operations). We use a large ensemble of climate simulations by the MIT IGSM-CAM integrated assessment model that accounts for the uncertainty associated with different emissions scenarios,more » climate sensitivities, and representations of natural variability. By the end of the century, the US is projected to experience fewer frosts, a longer growing season, more heat stress and an earlier start of field operations-although the magnitude and even the sign of these changes vary greatly by regions. Projected changes in dry days are shown not to be robust. We highlight the important role of natural variability, in particular for changes in dry days (a precipitation-related index) and heat stress (a threshold index). The wide range of our projections compares well the CMIP5 multi-model ensemble, especially for temperature-related indices. This suggests that using a single climate model that accounts for key sources of uncertainty can provide an efficient and complementary framework to the more common approach of multi-model ensembles. We also show that greenhouse gas mitigation has the potential to significantly reduce adverse effects (heat stress, risks of pest and disease) of climate change on agriculture, while also curtailing potentially beneficial impacts (earlier planting, possibility for multiple cropping). A major benefit of climate mitigation is potentially preventing changes in several indices to emerge from the noise of natural variability, even by 2100. This has major implications considering that any significant climate change impacts on crop yield would result in nation-wide changes in the agriculture sector. Lastly, we argue that the analysis of agro-climate indices should more often complement crop model projections, as they can provide valuable information to better understand the drivers of changes in crop yield and production and thus better inform adaptation decisions.« less

Uncertainty in future agro-climate projections in the United States and benefits of greenhouse gas mitigation

NASA Astrophysics Data System (ADS)

Monier, Erwan; Xu, Liyi; Snyder, Richard

2016-05-01

Scientific challenges exist on how to extract information from the wide range of projected impacts simulated by crop models driven by climate ensembles. A stronger focus is required to understand and identify the mechanisms and drivers of projected changes in crop yield. In this study, we investigate the robustness of future projections of five metrics relevant to agriculture stakeholders (accumulated frost days, dry days, growing season length, plant heat stress and start of field operations). We use a large ensemble of climate simulations by the MIT IGSM-CAM integrated assessment model that accounts for the uncertainty associated with different emissions scenarios, climate sensitivities, and representations of natural variability. By the end of the century, the US is projected to experience fewer frosts, a longer growing season, more heat stress and an earlier start of field operations—although the magnitude and even the sign of these changes vary greatly by regions. Projected changes in dry days are shown not to be robust. We highlight the important role of natural variability, in particular for changes in dry days (a precipitation-related index) and heat stress (a threshold index). The wide range of our projections compares well the CMIP5 multi-model ensemble, especially for temperature-related indices. This suggests that using a single climate model that accounts for key sources of uncertainty can provide an efficient and complementary framework to the more common approach of multi-model ensembles. We also show that greenhouse gas mitigation has the potential to significantly reduce adverse effects (heat stress, risks of pest and disease) of climate change on agriculture, while also curtailing potentially beneficial impacts (earlier planting, possibility for multiple cropping). A major benefit of climate mitigation is potentially preventing changes in several indices to emerge from the noise of natural variability, even by 2100. This has major implications considering that any significant climate change impacts on crop yield would result in nation-wide changes in the agriculture sector. Finally, we argue that the analysis of agro-climate indices should more often complement crop model projections, as they can provide valuable information to better understand the drivers of changes in crop yield and production and thus better inform adaptation decisions.

Uncertainty in future agro-climate projections in the United States and benefits of greenhouse gas mitigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Monier, Erwan; Xu, Liyi; Snyder, Richard

Scientific challenges exist on how to extract information from the wide range of projected impacts simulated by crop models driven by climate ensembles. A stronger focus is required to understand and identify the mechanisms and drivers of projected changes in crop yield. In this study, we investigate the robustness of future projections of five metrics relevant to agriculture stakeholders (accumulated frost days, dry days, growing season length, plant heat stress and start of field operations). We use a large ensemble of climate simulations by the MIT IGSM-CAM integrated assessment model that accounts for the uncertainty associated with different emissions scenarios,more » climate sensitivities, and representations of natural variability. By the end of the century, the US is projected to experience fewer frosts, a longer growing season, more heat stress and an earlier start of field operations-although the magnitude and even the sign of these changes vary greatly by regions. Projected changes in dry days are shown not to be robust. We highlight the important role of natural variability, in particular for changes in dry days (a precipitation-related index) and heat stress (a threshold index). The wide range of our projections compares well the CMIP5 multi-model ensemble, especially for temperature-related indices. This suggests that using a single climate model that accounts for key sources of uncertainty can provide an efficient and complementary framework to the more common approach of multi-model ensembles. We also show that greenhouse gas mitigation has the potential to significantly reduce adverse effects (heat stress, risks of pest and disease) of climate change on agriculture, while also curtailing potentially beneficial impacts (earlier planting, possibility for multiple cropping). A major benefit of climate mitigation is potentially preventing changes in several indices to emerge from the noise of natural variability, even by 2100. This has major implications considering that any significant climate change impacts on crop yield would result in nation-wide changes in the agriculture sector. Lastly, we argue that the analysis of agro-climate indices should more often complement crop model projections, as they can provide valuable information to better understand the drivers of changes in crop yield and production and thus better inform adaptation decisions.« less

Responsive Proteins in Wheat Cultivars with Contrasting Nitrogen Efficiencies under the Combined Stress of High Temperature and Low Nitrogen

PubMed Central

Abd_Allah, Elsayed Fathi; Nauman, Mohd; Asif, Ambreen; Hashem, Abeer; Alqarawi, Abdulaziz A.

2017-01-01

Productivity of wheat (Triticum aestivum) is markedly affected by high temperature and nitrogen deficiency. Identifying the functional proteins produced in response to these multiple stresses acting in a coordinated manner can help in developing tolerance in the crop. In this study, two wheat cultivars with contrasting nitrogen efficiencies (N-efficient VL616 and N-inefficient UP2382) were grown in control conditions, and under a combined stress of high temperature (32 °C) and low nitrogen (4 mM), and their leaf proteins were analysed in order to identify the responsive proteins. Two-dimensional electrophoresis unravelled sixty-one proteins, which varied in their expression in wheat, and were homologous to known functional proteins involved in biosynthesis, carbohydrate metabolism, energy metabolism, photosynthesis, protein folding, transcription, signalling, oxidative stress, water stress, lipid metabolism, heat stress tolerance, nitrogen metabolism, and protein synthesis. When exposed to high temperature in combination with low nitrogen, wheat plants altered their protein expression as an adaptive means to maintain growth. This response varied with cultivars. Nitrogen-efficient cultivars showed a higher potential of redox homeostasis, protein stability, osmoprotection, and regulation of nitrogen levels. The identified stress-responsive proteins can pave the way for enhancing the multiple-stress tolerance in wheat and developing a better understanding of its mechanism. PMID:29186028

Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume.

PubMed

Yang, Shuyi; Grall, Aurélie; Chapman, Mark A

2018-05-01

For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop. © 2018 Botanical Society of America.

Identification of Suitable Water Harvesting Zones Based on Geomorphic Resources for Drought Areas: A Case Study of Una District, Himachal Pradesh, India.

NASA Astrophysics Data System (ADS)

Prakasam, D. C., Jr.; Zaman, B.

2014-12-01

Water is one of the most vital natural resource and its availability and quality determine ecosystem productivity, both for agricultural and natural systems. Una district is one of the major potential agricultural districts in Himachal Pradesh, India. More than 70% of the population of this district is engaged in agriculture and allied sectors and major crops grown are maize, wheat, rice, sugarcane, pulses and vegetables. The region faces drought every year and about 90 per cent of the area is water stressed. This has resulted in crop loss and shortage of food and fodder. The sources of drinking water, small ponds and bowlies dry-up during summer season resulting in scarcity of drinking water. Una district receives rainfall during monsoons from June to September and also during non-monsoon period (winter). The annual average rainfall in the area is about 1040 mm with 55 average rainy days. But due to heavy surface run-off the farmers not able to cultivate the crops more than once in a year. Past research indicate that the geomorphology of the Una district might be responsible for such droughts as it controls the surface as well as ground water resources. The research proposes to develop a water stress model for Una district using the geomorphic parameters, water resource and land use land cover data of the study area. Using Survey of India topographical maps (1:50000), the geomorphic parameters are extracted. The spatial layers of these parameters i.e. drainage density, slope, relative relief, ruggedness index, surface water body's frequency are created in GIS. A time series of normalized remotely sensed data of the study area is used for land use land cover classification and analyses. Based on the results from the water stress model, the drought/water stress areas and water harvesting zones are identified and documented. The results of this research will help the general population in resolving the drinking water problem to a certain extent and also the cultivators to water the crops more than twice per year which might increase the crop yield in Una district.

Testing the responses of four wheat crop models to heat stress at anthesis and grain filling.

PubMed

Liu, Bing; Asseng, Senthold; Liu, Leilei; Tang, Liang; Cao, Weixing; Zhu, Yan

2016-05-01

Higher temperatures caused by future climate change will bring more frequent heat stress events and pose an increasing risk to global wheat production. Crop models have been widely used to simulate future crop productivity but are rarely tested with observed heat stress experimental datasets. Four wheat models (DSSAT-CERES-Wheat, DSSAT-Nwheat, APSIM-Wheat, and WheatGrow) were evaluated with 4 years of environment-controlled phytotron experimental datasets with two wheat cultivars under heat stress at anthesis and grain filling stages. Heat stress at anthesis reduced observed grain numbers per unit area and individual grain size, while heat stress during grain filling mainly decreased the size of the individual grains. The observed impact of heat stress on grain filling duration, total aboveground biomass, grain yield, and grain protein concentration (GPC) varied depending on cultivar and accumulated heat stress. For every unit increase of heat degree days (HDD, degree days over 30 °C), grain filling duration was reduced by 0.30-0.60%, total aboveground biomass was reduced by 0.37-0.43%, and grain yield was reduced by 1.0-1.6%, but GPC was increased by 0.50% for cv Yangmai16 and 0.80% for cv Xumai30. The tested crop simulation models could reproduce some of the observed reductions in grain filling duration, final total aboveground biomass, and grain yield, as well as the observed increase in GPC due to heat stress. Most of the crop models tended to reproduce heat stress impacts better during grain filling than at anthesis. Some of the tested models require improvements in the response to heat stress during grain filling, but all models need improvements in simulating heat stress effects on grain set during anthesis. The observed significant genetic variability in the response of wheat to heat stress needs to be considered through cultivar parameters in future simulation studies. © 2016 John Wiley & Sons Ltd.

Expression profiling of Crambe abyssinica under arsenate stress identifies genes and gene networks involved in arsenic metabolism and detoxification

PubMed Central

2010-01-01

Background Arsenic contamination is widespread throughout the world and this toxic metalloid is known to cause cancers of organs such as liver, kidney, skin, and lung in human. In spite of a recent surge in arsenic related studies, we are still far from a comprehensive understanding of arsenic uptake, detoxification, and sequestration in plants. Crambe abyssinica, commonly known as 'abyssinian mustard', is a non-food, high biomass oil seed crop that is naturally tolerant to heavy metals. Moreover, it accumulates significantly higher levels of arsenic as compared to other species of the Brassicaceae family. Thus, C. abyssinica has great potential to be utilized as an ideal inedible crop for phytoremediation of heavy metals and metalloids. However, the mechanism of arsenic metabolism in higher plants, including C. abyssinica, remains elusive. Results To identify the differentially expressed transcripts and the pathways involved in arsenic metabolism and detoxification, C. abyssinica plants were subjected to arsenate stress and a PCR-Select Suppression Subtraction Hybridization (SSH) approach was employed. A total of 105 differentially expressed subtracted cDNAs were sequenced which were found to represent 38 genes. Those genes encode proteins functioning as antioxidants, metal transporters, reductases, enzymes involved in the protein degradation pathway, and several novel uncharacterized proteins. The transcripts corresponding to the subtracted cDNAs showed strong upregulation by arsenate stress as confirmed by the semi-quantitative RT-PCR. Conclusions Our study revealed novel insights into the plant defense mechanisms and the regulation of genes and gene networks in response to arsenate toxicity. The differential expression of transcripts encoding glutathione-S-transferases, antioxidants, sulfur metabolism, heat-shock proteins, metal transporters, and enzymes in the ubiquitination pathway of protein degradation as well as several unknown novel proteins serve as molecular evidence for the physiological responses to arsenate stress in plants. Additionally, many of these cDNA clones showing strong upregulation due to arsenate stress could be used as valuable markers. Further characterization of these differentially expressed genes would be useful to develop novel strategies for efficient phytoremediation as well as for engineering arsenic tolerant crops with reduced arsenic translocation to the edible parts of plants. PMID:20546591

Development of remote sensing techniques for assessment of salinity induced plant stresses

NASA Astrophysics Data System (ADS)

Stong, Matthew Harold

Salinity has been shown to reduce vegetative growth, crop quality, and yield in agricultural crops. Remote sensing is capable of providing data about large areas. This project was designed to induce salinity stress in a crop, pak choi, and thereafter monitor the response of the crop as expressed by its spectral reflectances. The project was conducted in the National Taiwan University Phytotron, and spectral data was collected using a GER 2600. Yield and soil salinity (ECe) were also measured. After three seasons of data were collected, wavelengths sensitive to salinity were selected. These wavelengths, which are within the spectral response of biochemicals produced by plants as a response to soil salinity, were used to create two indices, the Salinity Stress Index (SSI) and the Normalized Salinity Stress Index (NSSI). After creating the indices tests were conducted to determine the efficacy of these indices in detecting salinity and drought stresses as compared to existing indices (SRVI and NDVI). This project induced salinity and drought stress in a crop, pak choi, and thereafter monitored the response of the crop as expressed by its spectral reflectances. The SSI and NSSI correlated well to both ECe and marketable yield. Additionally the SSI and NSSI were found to provide statistical differences between salinity stressed treatments and the control treatment. Drought stress was not detected well by any of the indices reviewed although the SSI and NSSI indices tended to increase with drought stress and decrease with salinity stress. As a final test, specific ion toxicities of sodium and chloride were tested against the developed indices (SSI and NSSI) and existing indices (NDVI, SRVI, and NDWI). There were no differences in SSI and NSSI responses to specific ion concentration in the high salinity treatments. These results indicated that the SSI and NSSI are not sensitive to the specific ion concentration in irrigation water. However, the SSI and NSSI were higher for the sodium water than the choride water in the low salinity treatments. It is likely that this difference was caused by the fact that the high SAR water decreased infiltration and caused water stress.

Functional homogeneous zones (fHZs) in viticultural zoning procedure: an Italian case study on Aglianico vine

NASA Astrophysics Data System (ADS)

Bonfante, A.; Agrillo, A.; Albrizio, R.; Basile, A.; Buonomo, R.; De Mascellis, R.; Gambuti, A.; Giorio, P.; Guida, G.; Langella, G.; Manna, P.; Minieri, L.; Moio, L.; Siani, T.; Terribile, F.

2015-06-01

This paper aims to test a new physically oriented approach to viticulture zoning at farm scale that is strongly rooted in hydropedology and aims to achieve a better use of environmental features with respect to plant requirements and wine production. The physics of our approach are defined by the use of soil-plant-atmosphere simulation models, applying physically based equations to describe the soil hydrological processes and solve soil-plant water status. This study (part of the ZOVISA project) was conducted on a farm devoted to production of high-quality wines (Aglianico DOC), located in southern Italy (Campania region, Mirabella Eclano, AV). The soil spatial distribution was obtained after standard soil survey informed by geophysical survey. Two homogeneous zones (HZs) were identified; in each one a physically based model was applied to solve the soil water balance and estimate the soil functional behaviour (crop water stress index, CWSI) defining the functional homogeneous zones (fHZs). For the second process, experimental plots were established and monitored for investigating soil-plant water status, crop development (biometric and physiological parameters) and daily climate variables (temperature, solar radiation, rainfall, wind). The effects of crop water status on crop response over must and wine quality were then evaluated in the fHZs. This was performed by comparing crop water stress with (i) crop physiological measurement (leaf gas exchange, chlorophyll a fluorescence, leaf water potential, chlorophyll content, leaf area index (LAI) measurement), (ii) grape bunches measurements (berry weight, sugar content, titratable acidity, etc.) and (iii) wine quality (aromatic response). This experiment proved the usefulness of the physically based approach, also in the case of mapping viticulture microzoning.

Redox systems are a potential link between drought stress susceptibility and the exacerbation of aflatoxin contamination in crops

USDA-ARS?s Scientific Manuscript database

Drought stress aggravates Aspergillus flavus infection and aflatoxin contamination in oilseed crops such as peanut and maize. Reactive oxygen species (ROS) are produced in plants in response to abiotic and biotic stresses as a means of defense. In the host plant-A. flavus interaction under drought c...

Cassava biology and physiology.

PubMed

El-Sharkawy, Mabrouk A

2004-11-01

Cassava or manioc (Manihot esculenta Crantz), a perennial shrub of the New World, currently is the sixth world food crop for more than 500 million people in tropical and sub-tropical Africa, Asia and Latin America. It is cultivated mainly by resource-limited small farmers for its starchy roots, which are used as human food either fresh when low in cyanogens or in many processed forms and products, mostly starch, flour, and for animal feed. Because of its inherent tolerance to stressful environments, where other food crops would fail, it is often considered a food-security source against famine, requiring minimal care. Under optimal environmental conditions, it compares favorably in production of energy with most other major staple food crops due to its high yield potential. Recent research at the Centro Internacional de Agricultura Tropical (CIAT) in Colombia has demonstrated the ability of cassava to assimilate carbon at very high rates under high levels of humidity, temperature and solar radiation,which correlates with productivity across all environments whether dry or humid. When grown on very poor soils under prolonged drought for more than 6 months, the crop reduce both its leaf canopy and transpiration water loss, but its attached leaves remain photosynthetically active, though at greatly reduced rates. The main physiological mechanism underlying such a remarkable tolerance to drought was rapid stomatal closure under both atmospheric and edaphic water stress, protecting the leaf against dehydration while the plant depletes available soil water slowly during long dry periods. This drought tolerance mechanism leads to high crop water use efficiency values. Although the cassava fine root system is sparse, compared to other crops, it can penetrate below 2 m soil,thus enabling the crop to exploit deep water if available. Leaves of cassava and wild Manihot possess elevated activities of the C4 enzyme PEP carboxylase but lack the leaf Kranz anatomy typical of C4 species, pointing to the need for further research on cultivated and wild Manihot to further improve its photosynthetic potential and yield,particularly under stressful environments. Moreover, a wide range in values of Km (CO2) for the C3 photosynthetic enzyme Rubisco was found among cassava cultivars indicating the possibility of selection for higher affinity to CO2, and consequently higher leaf photosynthesis. Several plant traits that may be of value in crop breeding and improvement have been identified, such as an extensive fine root system, long leaf life, strong root sink and high leaf photosynthesis. Selection of parental materials for tolerance to drought and infertile soils under representative field conditions have resulted in developing improved cultivars that have high yields in favorable environments while producing reasonable and stable yields under stress.

Rainfall and crop modeling-based water stress assessment for rainfed maize cultivation in peninsular India

NASA Astrophysics Data System (ADS)

Manivasagam, V. S.; Nagarajan, R.

2018-04-01

Water stress due to uneven rainfall distribution causes a significant impact on the agricultural production of monsoon-dependent peninsular India. In the present study, water stress assessment for rainfed maize crop is carried out for kharif (June-October) and rabi (October-February) cropping seasons which coincide with two major Indian monsoons. Rainfall analysis (1976-2010) shows that the kharif season receives sufficient weekly rainfall (28 ± 32 mm) during 26th-39th standard meteorological weeks (SMWs) from southwest monsoon, whereas the rabi season experiences a major portion of its weekly rainfall due to northeast monsoon between the 42nd and 51st SMW (31 ± 42 mm). The later weeks experience minimal rainfall (5.5 ± 15 mm) and thus expose the late sown maize crops to a severe water stress during its maturity stage. Wet and dry spell analyses reveal a substantial increase in the rainfall intensity over the last few decades. However, the distribution of rainfall shows a striking decrease in the number of wet spells, with prolonged dry spells in both seasons. Weekly rainfall classification shows that the flowering and maturity stages of kharif maize (33rd-39th SMWs) can suffer around 30-40% of the total water stress. In the case of rabi maize, the analysis reveals that a shift in the sowing time from the existing 42nd SMW (16-22 October) to the 40th SMW (1-7 October) can avoid terminal water stress. Further, AquaCrop modeling results show that one or two minimal irrigations during the flowering and maturity stages (33rd-39th SMWs) of kharif maize positively avoid the mild water stress exposure. Similarly, rabi maize requires an additional two or three lifesaving irrigations during its flowering and maturity stages (48th-53rd SMWs) to improve productivity. Effective crop planning with appropriate sowing time, short duration crop, and high yielding drought-resistant varieties will allow for better utilization of the monsoon rain, thus reducing water stress with an increase in rainfed maize productivity.

Crop Production under Drought and Heat Stress: Plant Responses and Management Options

PubMed Central

Fahad, Shah; Bajwa, Ali A.; Nazir, Usman; Anjum, Shakeel A.; Farooq, Ayesha; Zohaib, Ali; Sadia, Sehrish; Nasim, Wajid; Adkins, Steve; Saud, Shah; Ihsan, Muhammad Z.; Alharby, Hesham; Wu, Chao; Wang, Depeng; Huang, Jianliang

2017-01-01

Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future. PMID:28706531

Heavy metal-induced stress in rice crops detected using multi-temporal Sentinel-2 satellite images.

PubMed

Liu, Meiling; Wang, Tiejun; Skidmore, Andrew K; Liu, Xiangnan

2018-05-05

Regional-level information on heavy metal pollution in agro-ecosystems is essential for food security because excessive levels of heavy metals in crops may pose risks to humans. However, collecting this information over large areas is inherently costly. This paper investigates the possibility of applying multi-temporal Sentinel-2 satellite images to detect heavy metal-induced stress (i.e., Cd stress) in rice crops in four study areas in Zhuzhou City, Hunan Province, China. For this purpose, we compared seven Sentinel-2 images acquired in 2016 and 2017 with in situ measured hyper-spectral data, chlorophyll content, rice leaf area index, and heavy metal concentrations in soil collected from 2014 to 2017. Vegetation indices (VIs) related to red edge bands were referred to as the sensitive indicators for screening stressed rice from unstressed rice. The coefficients of spatio-temporal variation (CSTV) derived from the VIs allowed us to discriminate crops exposed to pollution from heavy metals as well as environmental stressors. The results indicate that (i) the red edge chlorophyll index, the red edge position index, and the normalized difference red edge 2 index derived from multi-temporal Sentinel-2 images were good indicators for screening stressed rice from unstressed rice; (ii) Rice under Cd stress remained stable with lower CSTV values of VIs overall growth stages in the experimental region, whereas rice under other stressors (i.e., pests and disease) showed abrupt changes at some growth stages and presented "hot spots" with greater CSTV values; and (iii) the proposed spatio-temporal anomaly detection method was successful at detecting rice under Cd stress; and CSTVs of rice VIs stabilized regardless of whether they were applied to consecutive growth stages or to two different crop years. This study suggests that regional heavy metal stress may be accurately detected using multi-temporal Sentinel-2 images, using VIs sensitive to the spatio-temporal characteristics of crops. Copyright © 2018 Elsevier B.V. All rights reserved.

Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdés-López, Oswaldo; Batek, Josef; Gomez-Hernandez, Nicolas

2016-04-25

Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Roots provide support, water and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined the response of these plant organs to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to whole roots. We identified 2,013 genes differentially regulated in root hairsmore » in response to heat stress. Our gene regulatory module analysis identified ten, key modules that controlled the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from roots and root hairs. These experiments identified a variety of proteins whose expression changed within 3 hours of application of heat stress. Most of these proteins were predicted to play a role in thermotolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.« less

Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

PubMed

Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K

2013-12-01

The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

Hormonal regulation of reproductive growth under normal and heat-stress conditions in legume and other model crop species.

PubMed

Ozga, Jocelyn A; Kaur, Harleen; Savada, Raghavendra P; Reinecke, Dennis M

2017-04-01

Legume crops are grown throughout the world and provide an excellent food source of digestible protein and starch, as well as dietary fibre, vitamins, minerals, and flavonoids. Fruit and seeds from legumes are also an important source of vegetables for a well-balanced diet. A trend in elevated temperature as a result of climate change increases the risk of a heat stress-induced reduction in legume crop yield. High temperatures during the crop reproductive development phase are particularly detrimental to fruit/seed production because the growth and development of the reproductive tissues are sensitive to small changes in temperature. Hormones are signalling molecules that play important roles in a plant's ability to integrate different environmental inputs and modify their developmental processes to optimize growth, survival, and reproduction. This review focuses on the hormonal regulation of reproductive development and heat stress-induced alteration of this regulation during (i) pollination, (ii) early fruit set, and (iii) seed development that affects fruit/seed yield in legume and other model crops. Further understanding of hormone-regulated reproductive growth under non-stress and heat-stress conditions can aid in trait selection and the development of gene modification strategies and cultural practices to improve heat tolerance in legume crops contributing to improved food security. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Impacts of extreme heat and drought on crop yields in China: an assessment by using the DLEM-AG2 model

NASA Astrophysics Data System (ADS)

Zhang, J.; Yang, J.; Pan, S.; Tian, H.

2016-12-01

China is not only one of the major agricultural production countries with the largest population in the world, but it is also the most susceptible to climate change and extreme events. Much concern has been raised about how extreme climate has affected crop yield, which is crucial for China's food supply security. However, the quantitative assessment of extreme heat and drought impacts on crop yield in China has rarely been investigated. By using the Dynamic Land Ecosystem Model (DLEM-AG2), a highly integrated process-based ecosystem model with crop-specific simulation, here we quantified spatial and temporal patterns of extreme climatic heat and drought stress and their impacts on the yields of major food crops (rice, wheat, maize, and soybean) across China during 1981-2015, and further investigated the underlying mechanisms. Simulated results showed that extreme heat and drought stress significantly reduced national cereal production and increased the yield gaps between potential yield and rain-fed yield. The drought stress was the primary factor to reduce crop yields in the semi-arid and arid regions, and extreme heat stress slightly aggravated the yield loss. The yield gap between potential yield and rain-fed yield was larger at locations with lower precipitation. Our results suggest that a large exploitable yield gap in response to extreme climatic heat-drought stress offers an opportunity to increase productivity in China by optimizing agronomic practices, such as irrigation, fertilizer use, sowing density, and sowing date.

Expression patterns of members of the ethylene signaling-related gene families in response to dehydration stresses in cassava.

PubMed

Ren, Meng Yun; Feng, Ren Jun; Shi, Hou Rui; Lu, Li Fang; Yun, Tian Yan; Peng, Ming; Guan, Xiao; Zhang, Heng; Wang, Jing Yi; Zhang, Xi Yan; Li, Cheng Liang; Chen, Yan Jun; He, Peng; Zhang, Yin Dong; Xie, Jiang Hui

2017-01-01

Drought is the one of the most important environment stresses that restricts crop yield worldwide. Cassava (Manihot esculenta Crantz) is an important food and energy crop that has many desirable traits such as drought, heat and low nutrients tolerance. However, the mechanisms underlying drought tolerance in cassava are unclear. Ethylene signaling pathway, from the upstream receptors to the downstream transcription factors, plays important roles in environmental stress responses during plant growth and development. In this study, we used bioinformatics approaches to identify and characterize candidate Manihot esculenta ethylene receptor genes and transcription factor genes. Using computational methods, we localized these genes on cassava chromosomes, constructed phylogenetic trees and identified stress-responsive cis-elements within their 5' upstream regions. Additionally, we measured the trehalose and proline contents in cassava fresh leaves after drought, osmotic, and salt stress treatments, and then it was found that the regulation patterns of contents of proline and trehalose in response to various dehydration stresses were differential, or even the opposite, which shows that plant may take different coping strategies to deal with different stresses, when stresses come. Furthermore, expression profiles of these genes in different organs and tissues under non-stress and abiotic stress were investigated through quantitative real-time PCR (qRT-PCR) analyses in cassava. Expression profiles exhibited clear differences among different tissues under non-stress and various dehydration stress conditions. We found that the leaf and tuberous root tissues had the greatest and least responses, respectively, to drought stress through the ethylene signaling pathway in cassava. Moreover, tuber and root tissues had the greatest and least reponses to osmotic and salt stresses through ethylene signaling in cassava, respectively. These results show that these plant tissues had differential expression levels of genes involved in ethylene signaling in response to the stresses tested. Moreover, after several gene duplication events, the spatiotemporally differential expression pattern of homologous genes in response to abiotic and biotic stresses may imply their functional diversity as a mechanism for adapting to the environment. Our data provide a framework for further research on the molecular mechanisms of cassava resistance to drought stress and provide a foundation for breeding drought-resistant new cultivars.

Expression patterns of members of the ethylene signaling–related gene families in response to dehydration stresses in cassava

PubMed Central

Shi, Hou Rui; Lu, Li Fang; Yun, Tian Yan; Peng, Ming; Guan, Xiao; Zhang, Heng; Wang, Jing Yi; Zhang, Xi Yan; Li, Cheng Liang; Chen, Yan Jun; He, Peng; Zhang, Yin Dong; Xie, Jiang Hui

2017-01-01

Drought is the one of the most important environment stresses that restricts crop yield worldwide. Cassava (Manihot esculenta Crantz) is an important food and energy crop that has many desirable traits such as drought, heat and low nutrients tolerance. However, the mechanisms underlying drought tolerance in cassava are unclear. Ethylene signaling pathway, from the upstream receptors to the downstream transcription factors, plays important roles in environmental stress responses during plant growth and development. In this study, we used bioinformatics approaches to identify and characterize candidate Manihot esculenta ethylene receptor genes and transcription factor genes. Using computational methods, we localized these genes on cassava chromosomes, constructed phylogenetic trees and identified stress-responsive cis-elements within their 5’ upstream regions. Additionally, we measured the trehalose and proline contents in cassava fresh leaves after drought, osmotic, and salt stress treatments, and then it was found that the regulation patterns of contents of proline and trehalose in response to various dehydration stresses were differential, or even the opposite, which shows that plant may take different coping strategies to deal with different stresses, when stresses come. Furthermore, expression profiles of these genes in different organs and tissues under non-stress and abiotic stress were investigated through quantitative real-time PCR (qRT-PCR) analyses in cassava. Expression profiles exhibited clear differences among different tissues under non-stress and various dehydration stress conditions. We found that the leaf and tuberous root tissues had the greatest and least responses, respectively, to drought stress through the ethylene signaling pathway in cassava. Moreover, tuber and root tissues had the greatest and least reponses to osmotic and salt stresses through ethylene signaling in cassava, respectively. These results show that these plant tissues had differential expression levels of genes involved in ethylene signaling in response to the stresses tested. Moreover, after several gene duplication events, the spatiotemporally differential expression pattern of homologous genes in response to abiotic and biotic stresses may imply their functional diversity as a mechanism for adapting to the environment. Our data provide a framework for further research on the molecular mechanisms of cassava resistance to drought stress and provide a foundation for breeding drought-resistant new cultivars. PMID:28542282

Ectopic expression of TaOEP16-2-5B, a wheat plastid outer envelope protein gene, enhances heat and drought stress tolerance in transgenic Arabidopsis plants.

PubMed

Zang, Xinshan; Geng, Xiaoli; Liu, Kelu; Wang, Fei; Liu, Zhenshan; Zhang, Liyuan; Zhao, Yue; Tian, Xuejun; Hu, Zhaorong; Yao, Yingyin; Ni, Zhongfu; Xin, Mingming; Sun, Qixin; Peng, Huiru

2017-05-01

Abiotic stresses, such as heat and drought, are major environmental factors restricting crop productivity and quality worldwide. A plastid outer envelope protein gene, TaOEP16-2, was identified from our previous transcriptome analysis [1,2]. In this study, the isolation and functional characterization of the TaOEP16-2 gene was reported. Three homoeologous sequences of TaOEP16-2 were isolated from hexaploid wheat, which were localized on the chromosomes 5A, 5B and 5D, respectively. These three homoeologues exhibited different expression patterns under heat stress conditions, TaOEP16-2-5B was the dominant one, and TaOEP16-2-5B was selected for further analysis. Compared with wild type (WT) plants, transgenic Arabidopsis plants overexpressing the TaOEP16-2-5B gene exhibited enhanced tolerance to heat stress, which was supported by improved survival rate, strengthened cell membrane stability and increased sucrose content. It was also found that TaOEP16-2 was induced by drought stress and involved in drought stress tolerance. TaOEP16-2-5B has the same function in ABA-controlled seed germination as AtOEP16-2. Our results suggest that TaOEP16-2-5B plays an important role in heat and drought stress tolerance, and could be utilized in transgenic breeding of wheat and other crop plants. Copyright © 2017 Elsevier B.V. All rights reserved.

Abiotic Stress Signaling in Wheat – An Inclusive Overview of Hormonal Interactions During Abiotic Stress Responses in Wheat

PubMed Central

Abhinandan, Kumar; Skori, Logan; Stanic, Matija; Hickerson, Neil M. N.; Jamshed, Muhammad; Samuel, Marcus A.

2018-01-01

Rapid global warming directly impacts agricultural productivity and poses a major challenge to the present-day agriculture. Recent climate change models predict severe losses in crop production worldwide due to the changing environment, and in wheat, this can be as large as 42 Mt/°C rise in temperature. Although wheat occupies the largest total harvested area (38.8%) among the cereals including rice and maize, its total productivity remains the lowest. The major production losses in wheat are caused more by abiotic stresses such as drought, salinity, and high temperature than by biotic insults. Thus, understanding the effects of these stresses becomes indispensable for wheat improvement programs which have depended mainly on the genetic variations present in the wheat genome through conventional breeding. Notably, recent biotechnological breakthroughs in the understanding of gene functions and access to whole genome sequences have opened new avenues for crop improvement. Despite the availability of such resources in wheat, progress is still limited to the understanding of the stress signaling mechanisms using model plants such as Arabidopsis, rice and Brachypodium and not directly using wheat as the model organism. This review presents an inclusive overview of the phenotypic and physiological changes in wheat due to various abiotic stresses followed by the current state of knowledge on the identified mechanisms of perception and signal transduction in wheat. Specifically, this review provides an in-depth analysis of different hormonal interactions and signaling observed during abiotic stress signaling in wheat. PMID:29942321

Development of transgenic crops based on photo-biotechnology.

PubMed

Ganesan, Markkandan; Lee, Hyo-Yeon; Kim, Jeong-Il; Song, Pill-Soon

2017-11-01

The phenotypes associated with plant photomorphogenesis such as the suppressed shade avoidance response and de-etiolation offer the potential for significant enhancement of crop yields. Of many light signal transducers and transcription factors involved in the photomorphogenic responses of plants, this review focuses on the transgenic overexpression of the photoreceptor genes at the uppermost stream of the signalling events, particularly phytochromes, crytochromes and phototropins as the transgenes for the genetic engineering of crops with improved harvest yields. In promoting the harvest yields of crops, the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the tolerance to abiotic stresses such as drought, salinity and heavy metal ions. As a genetic engineering approach, the term photo-biotechnology has been coined to convey the idea that the greater the photosynthetic efficiency that crop plants can be engineered to possess, the stronger the resistance to biotic and abiotic stresses. Development of GM crops based on photoreceptor transgenes (mainly phytochromes, crytochromes and phototropins) is reviewed with the proposal of photo-biotechnology that the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the added benefits of crops' tolerance to environmental stresses. © 2016 John Wiley & Sons Ltd.

Hyperspectral remote sensing of vegetation

USGS Publications Warehouse

Thenkabail, Prasad S.; Lyon, John G.; Huete, Alfredo

2011-01-01

Hyperspectral narrow-band (or imaging spectroscopy) spectral data are fast emerging as practical solutions in modeling and mapping vegetation. Recent research has demonstrated the advances in and merit of hyperspectral data in a range of applications including quantifying agricultural crops, modeling forest canopy biochemical properties, detecting crop stress and disease, mapping leaf chlorophyll content as it influences crop production, identifying plants affected by contaminants such as arsenic, demonstrating sensitivity to plant nitrogen content, classifying vegetation species and type, characterizing wetlands, and mapping invasive species. The need for significant improvements in quantifying, modeling, and mapping plant chemical, physical, and water properties is more critical than ever before to reduce uncertainties in our understanding of the Earth and to better sustain it. There is also a need for a synthesis of the vast knowledge spread throughout the literature from more than 40 years of research.

Endophytic fungal diversity of Fragaria vesca, a crop wild relative of strawberry, along environmental gradients within a small geographical area

PubMed Central

Yokoya, Kazutomo; Postel, Sarah; Fang, Rui

2017-01-01

Background Fungal endophytes are highly diverse ubiquitous asymptomatic microorganisms, some of which appear to be symbiotic. Depending on abiotic conditions and genotype of the plant, the diversity of endophytes may confer fitness benefits to plant communities. Methods We studied a crop wild relative (CWR) of strawberry, along environmental gradients with a view to understand the cultivable root-derived endophytic fungi that can be evaluated for promoting growth and tolerating stress in selected plant groups. The main objectives were to understand whether: (a) suboptimal soil types are drivers for fungal distribution and diversity; (b) high pH and poor nutrient availability lead to fungal-plant associations that help deliver fitness benefits; and (c) novel fungi can be identified for their use in improving plant growth, and alleviate stress in diverse crops. Results The study revealed that habitats with high pH and low nutrient availability have higher fungal diversity, with more rare fungi isolated from locations with chalky soil. Plants from location G were the healthiest even though soil from this location was the poorest in nutrients. Study of environmental gradients, especially extreme habitat types, may help understand the root zone fungal diversity of different functional classes. Two small in vitro pilot studies conducted with two isolates showed that endophytic fungi from suboptimal habitats can promote plant growth and fitness benefits in selected plant groups. Discussion Targeting native plants and crop wild relatives for research offers opportunities to unearth diverse functional groups of root-derived endophytic fungi that are beneficial for crops. PMID:28168102

Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.).

PubMed

Patanun, Onsaya; Lertpanyasampatha, Manassawe; Sojikul, Punchapat; Viboonjun, Unchera; Narangajavana, Jarunya

2013-03-01

MicroRNAs (miRNAs) are a newly discovered class of noncoding endogenous small RNAs involved in plant growth and development as well as response to environmental stresses. miRNAs have been extensively studied in various plant species, however, only few information are available in cassava, which serves as one of the staple food crops, a biofuel crop, animal feed and industrial raw materials. In this study, the 169 potential cassava miRNAs belonging to 34 miRNA families were identified by computational approach. Interestingly, mes-miR319b was represented as the first putative mirtron demonstrated in cassava. A total of 15 miRNA clusters involving 7 miRNA families, and 12 pairs of sense and antisense strand cassava miRNAs belonging to six different miRNA families were discovered. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. The cis-regulatory elements relevant to drought stress and plant hormone response were identified in the promoter regions of those miRNA genes. The results provided a foundation for further investigation of the functional role of known transcription factors in the regulation of cassava miRNAs. The better understandings of the complexity of miRNA-mediated genes network in cassava would unravel cassava complex biology in storage root development and in coping with environmental stresses, thus providing more insights for future exploitation in cassava improvement.

High temperature combined with drought affect rainfed spring wheat and barley in South-Eastern Russia: I. Phenology and growth

PubMed Central

Hossain, Akbar; Teixeira da Silva, Jaime A.; Lozovskaya, Marina Viacheslavovna; Zvolinsky, Vacheslav Petrovich

2012-01-01

Heat stress, when combined with drought, is one of the major limitations to food production worldwide, especially in areas that use rainfed agriculture. As the world population continues to grow, and water resources for the crop production decline and temperature increases, so the development of heat- and drought-tolerant cultivars is an issue of global concern. In this context, four barley and two wheat genotypes were evaluated in south-eastern Russia to identify heat- and drought-tolerant genotypes for future breeding programmes by identifying suitable sowing times for specific genotypes. High temperature stress, when combined with drought during late sowing, decreased the days to visible awns, days to heading and days to ripe harvest, finally negatively affecting the growth and development of plants and resulting in a lower plant population m−2, tillers plant−1, plant height and dry matter production m−2. On the other hand, low temperature in combination with early sowing increased the number of days to germination, reduced seedling stand establishment and tillering capacity, finally affecting the growth and development of the crops. Compared to overall performance and optimum sowing date, barley genotypes ‘Zernograd.770’ and ‘Nutans’, and wheat genotype ‘Line4’ performed best in both late (high temperature with drought) and early (low temperature) stress conditions. PMID:23961209

Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses).

PubMed

Tang, Sha; Li, Lin; Wang, Yongqiang; Chen, Qiannan; Zhang, Wenying; Jia, Guanqing; Zhi, Hui; Zhao, Baohua; Diao, Xianmin

2017-08-30

Understanding drought-tolerance mechanisms and identifying genetic dominance are important for crop improvement. Setaria italica, which is extremely drought-tolerant, has been regarded as a model plant for studying stress biology. Moreover, different genotypes of S. italica have evolved various drought-tolerance/avoidance mechanisms that should be elucidated. Physiological and transcriptomic comparisons between drought-tolerant S. italica cultivar 'Yugu1' and drought-sensitive 'An04' were conducted. 'An04' had higher yields and more efficient photosystem activities than 'Yugu1' under well-watered conditions, and this was accompanied by positive brassinosteroid regulatory actions. However, 'An04's growth advantage was severely repressed by drought, while 'Yugu1' maintained normal growth under a water deficiency. High-throughput sequencing suggested that the S. italica transcriptome was severely remodelled by genotype × environment interactions. Expression profiles of genes related to phytohormone metabolism and signalling, transcription factors, detoxification, and other stress-related proteins were characterised, revealing genotype-dependent and -independent drought responses in different S. italica genotypes. Combining our data with drought-tolerance-related QTLs, we identified 20 candidate genes that contributed to germination and early seedling' drought tolerance in S. italica. Our analysis provides a comprehensive picture of how different S. italica genotypes respond to drought, and may be used for the genetic improvement of drought tolerance in Poaceae crops.

Development of a multispectral sensor for crop canopy temperature measurement

USDA-ARS?s Scientific Manuscript database

Quantifying spatial and temporal variability in plant stress has precision agriculture applications in controlling variable rate irrigation and variable rate nutrient application. One approach to plant stress detection is crop canopy temperature measurement by the use of thermographic or radiometric...

Weather based risks and insurances for crop production in Belgium

NASA Astrophysics Data System (ADS)

Gobin, Anne

2014-05-01

Extreme weather events such as late frosts, droughts, heat waves and rain storms can have devastating effects on cropping systems. Damages due to extreme events are strongly dependent on crop type, crop stage, soil type and soil conditions. The perspective of rising risk-exposure is exacerbated further by limited aid received for agricultural damage, an overall reduction of direct income support to farmers and projected intensification of weather extremes with climate change. According to both the agriculture and finance sectors, a risk assessment of extreme weather events and their impact on cropping systems is needed. The impact of extreme weather events particularly during the sensitive periods of the farming calendar requires a modelling approach to capture the mixture of non-linear interactions between the crop, its environment and the occurrence of the meteorological event. The risk of soil moisture deficit increases towards harvesting, such that drought stress occurs in spring and summer. Conversely, waterlogging occurs mostly during early spring and autumn. Risks of temperature stress appear during winter and spring for chilling and during summer for heat. Since crop development is driven by thermal time and photoperiod, the regional crop model REGCROP (Gobin, 2010) enabled to examine the likely frequency, magnitude and impacts of frost, drought, heat stress and waterlogging in relation to the cropping season and crop sensitive stages. The risk profiles were subsequently confronted with yields, yield losses and insurance claims for different crops. Physically based crop models such as REGCROP assist in understanding the links between different factors causing crop damage as demonstrated for cropping systems in Belgium. Extreme weather events have already precipitated contraction of insurance coverage in some markets (e.g. hail insurance), and the process can be expected to continue if the losses or damages from such events increase in the future. Climate change will stress this further and impacts on crop growth are expected to be twofold, owing to the sensitive stages occurring earlier during the growing season and to the changes in return period of extreme weather events. Though average yields have risen continuously due to technological advances, there is no evidence that relative tolerance to adverse weather events has improved. The research is funded by the Belgian Science Policy Organisation (Belspo) under contract nr SD/RI/03A.

Genetic regulation of salt stress tolerance revealed by RNA-Seq in cotton diploid wild species, Gossypium davidsonii

PubMed Central

Zhang, Feng; Zhu, Guozhong; Du, Lei; Shang, Xiaoguang; Cheng, Chaoze; Yang, Bing; Hu, Yan; Cai, Caiping; Guo, Wangzhen

2016-01-01

Cotton is an economically important crop throughout the world, and is a pioneer crop in salt stress tolerance research. Investigation of the genetic regulation of salinity tolerance will provide information for salt stress-resistant breeding. Here, we employed next-generation RNA-Seq technology to elucidate the salt-tolerant mechanisms in cotton using the diploid cotton species Gossypium davidsonii which has superior stress tolerance. A total of 4744 and 5337 differentially expressed genes (DEGs) were found to be involved in salt stress tolerance in roots and leaves, respectively. Gene function annotation elucidated salt overly sensitive (SOS) and reactive oxygen species (ROS) signaling pathways. Furthermore, we found that photosynthesis pathways and metabolism play important roles in ion homeostasis and oxidation balance. Moreover, our studies revealed that alternative splicing also contributes to salt-stress responses at the posttranscriptional level, implying its functional role in response to salinity stress. This study not only provides a valuable resource for understanding the genetic control of salt stress in cotton, but also lays a substantial foundation for the genetic improvement of crop resistance to salt stress. PMID:26838812

Genetic regulation of salt stress tolerance revealed by RNA-Seq in cotton diploid wild species, Gossypium davidsonii.

PubMed

Zhang, Feng; Zhu, Guozhong; Du, Lei; Shang, Xiaoguang; Cheng, Chaoze; Yang, Bing; Hu, Yan; Cai, Caiping; Guo, Wangzhen

2016-02-03

Cotton is an economically important crop throughout the world, and is a pioneer crop in salt stress tolerance research. Investigation of the genetic regulation of salinity tolerance will provide information for salt stress-resistant breeding. Here, we employed next-generation RNA-Seq technology to elucidate the salt-tolerant mechanisms in cotton using the diploid cotton species Gossypium davidsonii which has superior stress tolerance. A total of 4744 and 5337 differentially expressed genes (DEGs) were found to be involved in salt stress tolerance in roots and leaves, respectively. Gene function annotation elucidated salt overly sensitive (SOS) and reactive oxygen species (ROS) signaling pathways. Furthermore, we found that photosynthesis pathways and metabolism play important roles in ion homeostasis and oxidation balance. Moreover, our studies revealed that alternative splicing also contributes to salt-stress responses at the posttranscriptional level, implying its functional role in response to salinity stress. This study not only provides a valuable resource for understanding the genetic control of salt stress in cotton, but also lays a substantial foundation for the genetic improvement of crop resistance to salt stress.

A database of annotated tentative orthologs from crop abiotic stress transcripts.

PubMed

Balaji, Jayashree; Crouch, Jonathan H; Petite, Prasad V N S; Hoisington, David A

2006-10-07

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

PubMed Central

Cui, Licao; Feng, Kewei; Liu, Fuyan; Du, Xianghong; Tong, Wei; Nie, Xiaojun; Ji, Wanquan; Weining, Song

2015-01-01

Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops. PMID:26372557

Is current irrigation sustainable in the United States? An integrated assessment of climate change impact on water resources and irrigated crop yields

NASA Astrophysics Data System (ADS)

Blanc, Elodie; Caron, Justin; Fant, Charles; Monier, Erwan

2017-08-01

While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U.S. as well as subsequent impacts on crop yields by 2050, while accounting for climate change projection uncertainty. We find that climate and socioeconomic changes will increase water shortages and strongly reduce irrigated yields for specific crops (i.e., cotton and forage), or in specific regions (i.e., the Southwest) where irrigation is not sustainable. Crop modeling studies that do not represent changes in irrigation availability can thus be misleading. Yet, since the most water-stressed basins represent a relatively small share of U.S. irrigated areas, the overall reduction in U.S. crop yields is small. The response of crop yields to climate change and water stress also suggests that some level of adaptation will be feasible, like relocating croplands to regions with sustainable irrigation or switching to less irrigation intensive crops. Finally, additional simulations show that greenhouse gas (GHG) mitigation can alleviate the effect of water stress on irrigated crop yields, enough to offset the reduced CO2 fertilization effect compared to an unconstrained GHG emission scenario.

Is current irrigation sustainable in the United States? An integrated assessment of climate change impact on water resources and irrigated crop yields.

PubMed

Blanc, Elodie; Caron, Justin; Fant, Charles; Monier, Erwan

2017-08-01

While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U.S. as well as subsequent impacts on crop yields by 2050, while accounting for climate change projection uncertainty. We find that climate and socioeconomic changes will increase water shortages and strongly reduce irrigated yields for specific crops (i.e., cotton and forage), or in specific regions (i.e., the Southwest) where irrigation is not sustainable. Crop modeling studies that do not represent changes in irrigation availability can thus be misleading. Yet, since the most water-stressed basins represent a relatively small share of U.S. irrigated areas, the overall reduction in U.S. crop yields is small. The response of crop yields to climate change and water stress also suggests that some level of adaptation will be feasible, like relocating croplands to regions with sustainable irrigation or switching to less irrigation intensive crops. Finally, additional simulations show that greenhouse gas (GHG) mitigation can alleviate the effect of water stress on irrigated crop yields, enough to offset the reduced CO 2 fertilization effect compared to an unconstrained GHG emission scenario.

Soybean Salt Tolerance 1 (GmST1) Reduces ROS Production, Enhances ABA Sensitivity, and Abiotic Stress Tolerance in Arabidopsis thaliana.

PubMed

Ren, Shuxin; Lyle, Chimera; Jiang, Guo-Liang; Penumala, Abhishek

2016-01-01

Abiotic stresses, including high soil salinity, significantly reduce crop production worldwide. Salt tolerance in plants is a complex trait and is regulated by multiple mechanisms. Understanding the mechanisms and dissecting the components on their regulatory pathways will provide new insights, leading to novel strategies for the improvement of salt tolerance in agricultural and economic crops of importance. Here we report that soybean salt tolerance 1, named GmST1, exhibited strong tolerance to salt stress in the Arabidopsis transgenic lines. The GmST1-overexpressed Arabidopsis also increased sensitivity to ABA and decreased production of reactive oxygen species under salt stress. In addition, GmST1 significantly improved drought tolerance in Arabidopsis transgenic lines. GmST1 belongs to a 3-prime part of Glyma.03g171600 gene in the current version of soybean genome sequence annotation. However, comparative reverse transcription-polymerase chain reaction analysis around Glyma.03g171600 genomic region confirmed that GmST1 might serve as an intact gene in soybean leaf tissues. Unlike Glyma.03g171600 which was not expressed in leaves, GmST1 was strongly induced by salt treatment in the leaf tissues. By promoter analysis, a TATA box was detected to be positioned close to GmST1 start codon and a putative ABRE and a DRE cis-acting elements were identified at about 1 kb upstream of GmST1 gene. The data also indicated that GmST1-transgenic lines survived under drought stress and showed a significantly lower water loss than non-transgenic lines. In summary, our results suggest that overexpression of GmST1 significantly improves Arabidopsis tolerance to both salt and drought stresses and the gene may be a potential candidate for genetic engineering of salt- and drought-tolerant crops.

Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

PubMed

Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

2017-03-01

Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.

Genome-Wide Analysis of the GRF Family Reveals Their Involvement in Abiotic Stress Response in Cassava.

PubMed

Shang, Sang; Wu, Chunlai; Huang, Chao; Tie, Weiwei; Yan, Yan; Ding, Zehong; Xia, Zhiqiang; Wang, Wenquan; Peng, Ming; Tian, Libo; Hu, Wei

2018-02-20

GENERAL REGULATORY FACTOR (GRF) proteins play vital roles in the regulation of plant growth, development, and response to abiotic stress. However, little information is known for this gene family in cassava ( Manihot esculenta ). In this study, 15 MeGRFs were identified from the cassava genome and were clustered into the ε and the non-ε groups according to phylogenetic, conserved motif, and gene structure analyses. Transcriptomic analyses showed eleven Me GRFs with constitutively high expression in stems, leaves, and storage roots of two cassava genotypes. Expression analyses revealed that the majority of GRFs showed transcriptional changes under cold, osmotic, salt, abscisic acid (ABA), and H₂O₂ treatments. Six Me GRFs were found to be commonly upregulated by abiotic stress, ABA, and H₂O₂ treatments, which may be the converging points of multiple signaling pathways. Interaction network analysis identified 18 possible interactors of MeGRFs. Taken together, this study elucidates the transcriptional control of Me GRFs in tissue development and the responses of abiotic stress and related signaling in cassava. Some constitutively expressed, tissue-specific, and abiotic stress-responsive candidate MeGRF genes were identified for the further genetic improvement of crops.

Bell pepper rootstock response to Phytophthora capsici under salinity stress

USDA-ARS?s Scientific Manuscript database

Vegetable grafting is currently used as an eco-friendly technology to increase crop productivity and overcome several biotic and abiotic stress conditions that affect Cucurbitaceae and Solanaceae vegetable crops. In recent years, researchers with breeding programs and seed companies have selected ro...

Evaluation of AIS Data for Agronomic and Rangeland Vegetation: Preliminary Results for August 1984 Flight over Nebraska Sandhills Agricultural Laboratory

NASA Technical Reports Server (NTRS)

Blad, B. L.; Starks, P. J.; Hays, C.; Gardner, B. R.

1985-01-01

Since 1978 scientists from the Center for Agricultural Meteorology and Climatology at the University of Nebraska have been conducting research at the Sandhills Agricultural Laboratory on the effects of water stress on crop growth, development and yield using remote sensing techniques. We have been working to develop techniques, both remote and ground-based, to monitor water stress, phenological development, leaf area, phytomass production and grain yields of corn, soybeans and sorghum. Because of the sandy soils and relatively low rainfall at the site it is an excellent location to study water stress without the necessity of installing expensive rainout shelters. The primary objectives of research with the airborne imaging spectrometer (AIS) data collected during an August 1984 flight over the Sandhills Agricultural Laboratory are to evaluate the potential of using AIS to: (1) discriminate crop type; (2) to detect subtle architectural differences that exist among different cultivars or hybrids of agronomic crops; (3) to detect and quantify, if possible, the level of water stress imposed on the crops; and (4) to evaluate leaf area and biomass differences for different crops.

Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress

PubMed Central

dos Reis, Sávio Pinho; Lima, Aline Medeiros; de Souza, Cláudia Regina Batista

2012-01-01

Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. PMID:22942725

Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination.

PubMed

Ma, Qiaoli; Kang, Junmei; Long, Ruicai; Zhang, Tiejun; Xiong, Junbo; Zhang, Kun; Wang, Tenghua; Yang, Qingchuan; Sun, Yan

2017-07-01

Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L -1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.

Bacillus: A Biological Tool for Crop Improvement through Bio-Molecular Changes in Adverse Environments

PubMed Central

Radhakrishnan, Ramalingam; Hashem, Abeer; Abd_Allah, Elsayed F.

2017-01-01

Crop productivity is affected by environmental and genetic factors. Microbes that are beneficial to plants are used to enhance the crop yield and are alternatives to chemical fertilizers and pesticides. Pseudomonas and Bacillus species are the predominant plant growth-promoting bacteria. The spore-forming ability of Bacillus is distinguished from that of Pseudomonas. Members of this genus also survive for a long time under unfavorable environmental conditions. Bacillus spp. secrete several metabolites that trigger plant growth and prevent pathogen infection. Limited studies have been conducted to understand the physiological changes that occur in crops in response to Bacillus spp. to provide protection against adverse environmental conditions. This review describes the current understanding of Bacillus-induced physiological changes in plants as an adaptation to abiotic and biotic stresses. During water scarcity, salinity and heavy metal accumulate in soil, Bacillus spp. produce exopolysaccharides and siderophores, which prevent the movement of toxic ions and adjust the ionic balance and water transport in plant tissues while controlling the pathogenic microbial population. In addition, the synthesis of indole-3-acetic acid, gibberellic acid and1-aminocyclopropane-1-carboxylate (ACC) deaminase by Bacillus regulates the intracellular phytohormone metabolism and increases plant stress tolerance. Cell-wall-degrading substances, such as chitosanase, protease, cellulase, glucanase, lipopeptides and hydrogen cyanide from Bacillus spp. damage the pathogenic bacteria, fungi, nematodes, viruses and pests to control their populations in plants and agricultural lands. The normal plant metabolism is affected by unfavorable environmental stimuli, which suppress crop growth and yield. Abiotic and biotic stress factors that have detrimental effects on crops are mitigated by Bacillus-induced physiological changes, including the regulation of water transport, nutrient up-take and the activation of the antioxidant and defense systems. Bacillus association stimulates plant immunity against stresses by altering stress-responsive genes, proteins, phytohormones and related metabolites. This review describes the beneficial effect of Bacillus spp. on crop plants, which improves plant productivity under unfavorable climatic conditions, and the current understanding of the mitigation mechanism of Bacillus spp. in stress-tolerant and/or stress-resistant plants. PMID:28932199

Bacillus: A Biological Tool for Crop Improvement through Bio-Molecular Changes in Adverse Environments.

PubMed

Radhakrishnan, Ramalingam; Hashem, Abeer; Abd Allah, Elsayed F

2017-01-01

Crop productivity is affected by environmental and genetic factors. Microbes that are beneficial to plants are used to enhance the crop yield and are alternatives to chemical fertilizers and pesticides. Pseudomonas and Bacillus species are the predominant plant growth-promoting bacteria. The spore-forming ability of Bacillus is distinguished from that of Pseudomonas . Members of this genus also survive for a long time under unfavorable environmental conditions. Bacillus spp. secrete several metabolites that trigger plant growth and prevent pathogen infection. Limited studies have been conducted to understand the physiological changes that occur in crops in response to Bacillus spp. to provide protection against adverse environmental conditions. This review describes the current understanding of Bacillus -induced physiological changes in plants as an adaptation to abiotic and biotic stresses. During water scarcity, salinity and heavy metal accumulate in soil, Bacillus spp. produce exopolysaccharides and siderophores, which prevent the movement of toxic ions and adjust the ionic balance and water transport in plant tissues while controlling the pathogenic microbial population. In addition, the synthesis of indole-3-acetic acid, gibberellic acid and1-aminocyclopropane-1-carboxylate (ACC) deaminase by Bacillus regulates the intracellular phytohormone metabolism and increases plant stress tolerance. Cell-wall-degrading substances, such as chitosanase, protease, cellulase, glucanase, lipopeptides and hydrogen cyanide from Bacillus spp. damage the pathogenic bacteria, fungi, nematodes, viruses and pests to control their populations in plants and agricultural lands. The normal plant metabolism is affected by unfavorable environmental stimuli, which suppress crop growth and yield. Abiotic and biotic stress factors that have detrimental effects on crops are mitigated by Bacillus -induced physiological changes, including the regulation of water transport, nutrient up-take and the activation of the antioxidant and defense systems. Bacillus association stimulates plant immunity against stresses by altering stress-responsive genes, proteins, phytohormones and related metabolites. This review describes the beneficial effect of Bacillus spp. on crop plants, which improves plant productivity under unfavorable climatic conditions, and the current understanding of the mitigation mechanism of Bacillus spp. in stress-tolerant and/or stress-resistant plants.

OsASR5 enhances drought tolerance through a stomatal closure pathway associated with ABA and H2 O2 signalling in rice.

PubMed

Li, Jinjie; Li, Yang; Yin, Zhigang; Jiang, Jihong; Zhang, Minghui; Guo, Xiao; Ye, Zhujia; Zhao, Yan; Xiong, Haiyan; Zhang, Zhanying; Shao, Yujie; Jiang, Conghui; Zhang, Hongliang; An, Gynheung; Paek, Nam-Chon; Ali, Jauhar; Li, Zichao

2017-02-01

Drought is one of the major abiotic stresses that directly implicate plant growth and crop productivity. Although many genes in response to drought stress have been identified, genetic improvement to drought resistance especially in food crops is showing relatively slow progress worldwide. Here, we reported the isolation of abscisic acid, stress and ripening (ASR) genes from upland rice variety, IRAT109 (Oryza sativa L. ssp. japonica), and demonstrated that overexpression of OsASR5 enhanced osmotic tolerance in Escherichia coli and drought tolerance in Arabidopsis and rice by regulating leaf water status under drought stress conditions. Moreover, overexpression of OsASR5 in rice increased endogenous ABA level and showed hypersensitive to exogenous ABA treatment at both germination and postgermination stages. The production of H 2 O 2 , a second messenger for the induction of stomatal closure in response to ABA, was activated in overexpression plants under drought stress conditions, consequently, increased stomatal closure and decreased stomatal conductance. In contrast, the loss-of-function mutant, osasr5, showed sensitivity to drought stress with lower relative water content under drought stress conditions. Further studies demonstrated that OsASR5 functioned as chaperone-like protein and interacted with stress-related HSP40 and 2OG-Fe (II) oxygenase domain containing proteins in yeast and plants. Taken together, we suggest that OsASR5 plays multiple roles in response to drought stress by regulating ABA biosynthesis, promoting stomatal closure, as well as acting as chaperone-like protein that possibly prevents drought stress-related proteins from inactivation. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Anireddy; Ben-Hur, Asa

Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites ofmore » ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.« less

Common bean proteomics: Present status and future strategies.

PubMed

Zargar, Sajad Majeed; Mahajan, Reetika; Nazir, Muslima; Nagar, Preeti; Kim, Sun Tae; Rai, Vandna; Masi, Antonio; Ahmad, Syed Mudasir; Shah, Riaz Ahmad; Ganai, Nazir Ahmad; Agrawal, Ganesh K; Rakwal, Randeep

2017-10-03

Common bean (Phaseolus vulgaris L.) is a legume of appreciable importance and usefulness worldwide to the human population providing food and feed. It is rich in high-quality protein, energy, fiber and micronutrients especially iron, zinc, and pro-vitamin A; and possesses potentially disease-preventing and health-promoting compounds. The recently published genome sequence of common bean is an important landmark in common bean research, opening new avenues for understanding its genetics in depth. This legume crop is affected by diverse biotic and abiotic stresses severely limiting its productivity. Looking at the trend of increasing world population and the need for food crops best suited to the health of humankind, the legumes will be in great demand, including the common bean mostly for its nutritive values. Hence the need for new research in understanding the biology of this crop brings us to utilize and apply high-throughput omics approaches. In this mini-review our focus will be on the need for proteomics studies in common bean, potential of proteomics for understanding genetic regulation under abiotic and biotic stresses and how proteogenomics will lead to nutritional improvement. We will also discuss future proteomics-based strategies that must be adopted to mine new genomic resources by identifying molecular switches regulating various biological processes. Common bean is regarded as "grain of hope" for the poor, being rich in high-quality protein, energy, fiber and micronutrients (iron, zinc, pro-vitamin A); and possesses potentially disease-preventing and health-promoting compounds. Increasing world population and the need for food crops best suited to the health of humankind, puts legumes into great demand, which includes the common bean mostly. An important landmark in common bean research was the recent publication of its genome sequence, opening new avenues for understanding its genetics in depth. This legume crop is affected by diverse biotic and abiotic stresses severely limiting its productivity. Therefore, the need for new research in understanding the biology of this crop brings us to utilize and apply high-throughput omics approaches. Proteomics can be used to track all the candidate proteins/genes responsible for a biological process under specific conditions in a particular tissue. The potential of proteomics will not only help in determining the functions of a large number of genes in a single experiment but will also be a useful tool to mine new genes that can provide solution to various problems (abiotic stress, biotic stress, nutritional improvement, etc). We believe that a combined approach including breeding along with omics tools will lead towards attaining sustainability in legumes, including common bean. Copyright © 2017 Elsevier B.V. All rights reserved.

AGPase: its role in crop productivity with emphasis on heat tolerance in cereals.

PubMed

Saripalli, Gautam; Gupta, Pushpendra Kumar

2015-10-01

AGPase, a key enzyme of starch biosynthetic pathway, has a significant role in crop productivity. Thermotolerant variants of AGPase in cereals may be used for developing cultivars, which may enhance productivity under heat stress. Improvement of crop productivity has always been the major goal of plant breeders to meet the global demand for food. However, crop productivity itself is influenced in a large measure by a number of abiotic stresses including heat, which causes major losses in crop productivity. In cereals, crop productivity in terms of grain yield mainly depends upon the seed starch content so that starch biosynthesis and the enzymes involved in this process have been a major area of investigation for plant physiologists and plant breeders alike. Considerable work has been done on AGPase and its role in crop productivity, particularly under heat stress, because this enzyme is one of the major enzymes, which catalyses the rate-limiting first committed key enzymatic step of starch biosynthesis. Keeping the above in view, this review focuses on the basic features of AGPase including its structure, regulatory mechanisms involving allosteric regulators, its sub-cellular localization and its genetics. Major emphasis, however, has been laid on the genetics of AGPases and its manipulation for developing high yielding cultivars that will have comparable productivity under heat stress. Some important thermotolerant variants of AGPase, which mainly involve specific amino acid substitutions, have been highlighted, and the prospects of using these thermotolerant variants of AGPase in developing cultivars for heat prone areas have been discussed. The review also includes a brief account on transgenics for AGPase, which have been developed for basic studies and crop improvement.

Overview and highlights of Early Warning and Crop Condition Assessment project

NASA Technical Reports Server (NTRS)

Boatwright, G. O.; Whitehead, V. S.

1985-01-01

Work of the Early Warning and Crop Condition Assessment (EW/CCA) project, one of eight projects in the Agriculture and Resources Inventory Surveys Through Aerospace Remote Sensing (AgRISTARS), is reviewed. Its mission, to develop and test remote sensing techniques that enhance operational methodologies for crop condition assessment, was in response to initiatives issued by the Secretary of Agriculture. Meteorologically driven crop stress indicator models have been developed or modified for wheat, maize, grain sorghum, and soybeans. These models provide early warning alerts of potential or actual crop stresses due to water deficits, adverse temperatures, and water excess that could delay planting or harvesting operations. Recommendations are given for future research involving vegetative index numbers and the NOAA and Landsat satellites.

Big agronomic data validates an oxymoron: Sustainable intensification under climate change

USDA-ARS?s Scientific Manuscript database

Crop science is increasingly embracing big data to reconcile the apparent rift between intensification of food production and sustainability of a steadily stressed production base. A strategy based on long-term agroecosystem research and modeling simulation of crops, crop rotations and cropping sys...

Silicon Regulates Antioxidant Activities of Crop Plants under Abiotic-Induced Oxidative Stress: A Review

PubMed Central

Kim, Yoon-Ha; Khan, Abdul L.; Waqas, Muhammad; Lee, In-Jung

2017-01-01

Silicon (Si) is the second most abundant element in soil, where its availability to plants can exhilarate to 10% of total dry weight of the plant. Si accumulation/transport occurs in the upward direction, and has been identified in several crop plants. Si application has been known to ameliorate plant growth and development during normal and stressful conditions over past two-decades. During abiotic (salinity, drought, thermal, and heavy metal etc) stress, one of the immediate responses by plant is the generation of reactive oxygen species (ROS), such as singlet oxygen (1O2), superoxide (O2−), hydrogen peroxide (H2O2), and hydroxyl radicals (OH), which cause severe damage to the cell structure, organelles, and functions. To alleviate and repair this damage, plants have developed a complex antioxidant system to maintain homeostasis through non-enzymatic (carotenoids, tocopherols, ascorbate, and glutathione) and enzymatic antioxidants [superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX)]. To this end, the exogenous application of Si has been found to induce stress tolerance by regulating the generation of ROS, reducing electrolytic leakage, and malondialdehyde (MDA) contents, and immobilizing and reducing the uptake of toxic ions like Na, under stressful conditions. However, the interaction of Si and plant antioxidant enzyme system remains poorly understood, and further in-depth analyses at the transcriptomic level are needed to understand the mechanisms responsible for the Si-mediated regulation of stress responses. PMID:28428797

Silicon Regulates Antioxidant Activities of Crop Plants under Abiotic-Induced Oxidative Stress: A Review.

PubMed

Kim, Yoon-Ha; Khan, Abdul L; Waqas, Muhammad; Lee, In-Jung

2017-01-01

Silicon (Si) is the second most abundant element in soil, where its availability to plants can exhilarate to 10% of total dry weight of the plant. Si accumulation/transport occurs in the upward direction, and has been identified in several crop plants. Si application has been known to ameliorate plant growth and development during normal and stressful conditions over past two-decades. During abiotic (salinity, drought, thermal, and heavy metal etc) stress, one of the immediate responses by plant is the generation of reactive oxygen species (ROS), such as singlet oxygen ( 1 O 2 ), superoxide ([Formula: see text]), hydrogen peroxide (H 2 O 2 ), and hydroxyl radicals (OH), which cause severe damage to the cell structure, organelles, and functions. To alleviate and repair this damage, plants have developed a complex antioxidant system to maintain homeostasis through non-enzymatic (carotenoids, tocopherols, ascorbate, and glutathione) and enzymatic antioxidants [superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX)]. To this end, the exogenous application of Si has been found to induce stress tolerance by regulating the generation of ROS, reducing electrolytic leakage, and malondialdehyde (MDA) contents, and immobilizing and reducing the uptake of toxic ions like Na, under stressful conditions. However, the interaction of Si and plant antioxidant enzyme system remains poorly understood, and further in-depth analyses at the transcriptomic level are needed to understand the mechanisms responsible for the Si-mediated regulation of stress responses.

Transcript Profiling Reveals the Presence of Abiotic Stress and Developmental Stage Specific Ascorbate Oxidase Genes in Plants

PubMed Central

Batth, Rituraj; Singh, Kapil; Kumari, Sumita; Mustafiz, Ananda

2017-01-01

Abiotic stress and climate change is the major concern for plant growth and crop yield. Abiotic stresses lead to enhanced accumulation of reactive oxygen species (ROS) consequently resulting in cellular damage and major losses in crop yield. One of the major scavengers of ROS is ascorbate (AA) which acts as first line of defense against external oxidants. An enzyme named ascorbate oxidase (AAO) is known to oxidize AA and deleteriously affect the plant system in response to stress. Genome-wide analysis of AAO gene family has led to the identification of five, three, seven, four, and six AAO genes in Oryza sativa, Arabidopsis, Glycine max, Zea mays, and Sorghum bicolor genomes, respectively. Expression profiling of these genes was carried out in response to various abiotic stresses and during various stages of vegetative and reproductive development using publicly available microarray database. Expression analysis in Oryza sativa revealed tissue specific expression of AAO genes wherein few members were exclusively expressed in either root or shoot. These genes were found to be regulated by both developmental cues as well as diverse stress conditions. The qRT-PCR analysis in response to salinity and drought stress in rice shoots revealed OsAAO2 to be the most stress responsive gene. On the other hand, OsAAO3 and OsAAO4 genes showed enhanced expression in roots under salinity/drought stresses. This study provides lead about important stress responsive AAO genes in various crop plants, which could be used to engineer climate resilient crop plants. PMID:28261251

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice.

PubMed

Barrera-Figueroa, Blanca E; Gao, Lei; Wu, Zhigang; Zhou, Xuefeng; Zhu, Jianhua; Jin, Hailing; Liu, Renyi; Zhu, Jian-Kang

2012-08-03

MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulated miRNAs have been identified in vegetative tissues in several plants, they are not well studied in reproductive tissues such as inflorescences. We used Illumina deep sequencing technology to sequence four small RNA libraries that were constructed from the inflorescences of rice plants that were grown under control condition and drought, cold, or salt stress. We identified 227 miRNAs that belong to 127 families, including 70 miRNAs that are not present in the miRBase. We validated 62 miRNAs (including 10 novel miRNAs) using published small RNA expression data in DCL1, DCL3, and RDR2 RNAi lines and confirmed 210 targets from 86 miRNAs using published degradome data. By comparing the expression levels of miRNAs, we identified 18, 15, and 10 miRNAs that were regulated by drought, cold and salt stress conditions, respectively. In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs). We discovered novel miRNAs and stress-regulated miRNAs that may play critical roles in stress response in rice inflorescences. Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination.

Is current irrigation sustainable in the United States? An integrated assessment of climate change impact on water resources and irrigated crop yields

DOE PAGES

Blanc, Elodie; Caron, Justin; Fant, Charles; ...

2017-06-27

While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U.S. as well as subsequent impacts on crop yields by 2050, while accounting for climatemore » change projection uncertainty. We find that climate and socioeconomic changes will increase water shortages and strongly reduce irrigated yields for specific crops (i.e., cotton and forage), or in specific regions (i.e., the Southwest) where irrigation is not sustainable. Crop modeling studies that do not represent changes in irrigation availability can thus be misleading. Yet, since the most water-stressed basins represent a relatively small share of U.S. irrigated areas, the overall reduction in U.S. crop yields is small. The response of crop yields to climate change and water stress also suggests that some level of adaptation will be feasible, like relocating croplands to regions with sustainable irrigation or switching to less irrigation intensive crops. Finally, additional simulations show that greenhouse gas (GHG) mitigation can alleviate the effect of water stress on irrigated crop yields, enough to offset the reduced CO 2 fertilization effect compared to an unconstrained GHG emission scenario.« less

Is current irrigation sustainable in the United States? An integrated assessment of climate change impact on water resources and irrigated crop yields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blanc, Elodie; Caron, Justin; Fant, Charles

While climate change impacts on crop yields has been extensively studied, estimating the impact of water shortages on irrigated crop yields is challenging because the water resources management system is complex. To investigate this issue, we integrate a crop yield reduction module and a water resources model into the MIT Integrated Global System Modeling framework, an integrated assessment model linking a global economic model to an Earth system model. We assess the effects of climate and socioeconomic changes on water availability for irrigation in the U.S. as well as subsequent impacts on crop yields by 2050, while accounting for climatemore » change projection uncertainty. We find that climate and socioeconomic changes will increase water shortages and strongly reduce irrigated yields for specific crops (i.e., cotton and forage), or in specific regions (i.e., the Southwest) where irrigation is not sustainable. Crop modeling studies that do not represent changes in irrigation availability can thus be misleading. Yet, since the most water-stressed basins represent a relatively small share of U.S. irrigated areas, the overall reduction in U.S. crop yields is small. The response of crop yields to climate change and water stress also suggests that some level of adaptation will be feasible, like relocating croplands to regions with sustainable irrigation or switching to less irrigation intensive crops. Finally, additional simulations show that greenhouse gas (GHG) mitigation can alleviate the effect of water stress on irrigated crop yields, enough to offset the reduced CO 2 fertilization effect compared to an unconstrained GHG emission scenario.« less

Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa.

PubMed

Hiremath, Pavana J; Farmer, Andrew; Cannon, Steven B; Woodward, Jimmy; Kudapa, Himabindu; Tuteja, Reetu; Kumar, Ashish; Bhanuprakash, Amindala; Mulaosmanovic, Benjamin; Gujaria, Neha; Krishnamurthy, Laxmanan; Gaur, Pooran M; Kavikishor, Polavarapu B; Shah, Trushar; Srinivasan, Ramamurthy; Lohse, Marc; Xiao, Yongli; Town, Christopher D; Cook, Douglas R; May, Gregory D; Varshney, Rajeev K

2011-10-01

Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103,215 tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20,634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42,141 aligned TUSs with putative gene structures (including 39,281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44,639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd. No claim to original US government works.

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress

USDA-ARS?s Scientific Manuscript database

Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms...

Minimizing instrumentation requirement for estimating crop water stress index and transpiration of maize

USDA-ARS?s Scientific Manuscript database

Research was conducted in northern Colorado in 2011 to estimate the Crop Water Stress Index (CWSI) and actual water transpiration (Ta) of maize under a range of irrigation regimes. The main goal was to obtain these parameters with minimum instrumentation and measurements. The results confirmed that ...

Deficit irrigation: Arriving at the crop water stress index via gas exchange measurements

USDA-ARS?s Scientific Manuscript database

Plant gas exchange provides a highly sensitive measure of the degree of drought stress. Canopy temperature (Tc) provides a much easier to acquire indication of crop water deficit that has been used in irrigation scheduling systems, but interpretation of this measurement has proven difficult. Our goa...

Infrared thermometry of water-stressed crops - emerging methods and technologies

USDA-ARS?s Scientific Manuscript database

Infrared thermometry has shown potential to quantify water stress in crop canopy. This presentation will outline the limited irrigation experiments by the USDA-ARS in northern Colorado, which is used for a framework to evaluate canopy temperature. Recent methods have been introduced that may be accu...

Investigation of LANDSAT follow-on thematic mapper spatial, radiometric and spectral resolution

NASA Technical Reports Server (NTRS)

Nalepka, R. F. (Principal Investigator); Morgenstern, J. P.; Kent, E. R.; Erickson, J. D.

1976-01-01

The author has identified the following significant results. Fine resolution M7 multispectral scanner data collected during the Corn Blight Watch Experiment in 1971 served as the basis for this study. Different locations and times of year were studied. Definite improvement using 30-40 meter spatial resolution over present LANDSAT 1 resolution and over 50-60 meter resolution was observed, using crop area mensuration as the measure. Simulation studies carried out to extrapolate the empirical results to a range of field size distributions confirmed this effect, showing the improvement to be most pronounced for field sizes of 1-4 hectares. Radiometric sensitivity study showed significant degradation of crop classification accuracy immediately upon relaxation from the nominally specified values of 0.5% noise equivalent reflectance. This was especially the case for data which were spectrally similar such as that collected early in the growing season and also when attempting to accomplish crop stress detection.

A one-layer satellite surface energy balance for estimating evapotranspiration rates and crop water stress indexes.

PubMed

Barbagallo, Salvatore; Consoli, Simona; Russo, Alfonso

2009-01-01

Daily evapotranspiration fluxes over the semi-arid Catania Plain area (Eastern Sicily, Italy) were evaluated using remotely sensed data from Landsat Thematic Mapper TM5 images. A one-source parameterization of the surface sensible heat flux exchange using satellite surface temperature has been used. The transfer of sensible and latent heat is described by aerodynamic resistance and surface resistance. Required model inputs are brightness, temperature, fractional vegetation cover or leaf area index, albedo, crop height, roughness lengths, net radiation, air temperature, air humidity and wind speed. The aerodynamic resistance (r(ah)) is formulated on the basis of the Monin-Obukhov surface layer similarity theory and the surface resistance (r(s)) is evaluated from the energy balance equation. The instantaneous surface flux values were converted into evaporative fraction (EF) over the heterogeneous land surface to derive daily evapotranspiration values. Remote sensing-based assessments of crop water stress (CWSI) were also made in order to identify local irrigation requirements. Evapotranspiration data and crop coefficient values obtained from the approach were compared with: (i) data from the semi-empirical approach "K(c) reflectance-based", which integrates satellite data in the visible and NIR regions of the electromagnetic spectrum with ground-based measurements and (ii) surface energy flux measurements collected from a micrometeorological tower located in the experiment area. The expected variability associated with ET flux measurements suggests that the approach-derived surface fluxes were in acceptable agreement with the observations.

Characterization of expressed sequence tags (ESTs) of pigeonpea (Cajanus cajan L.) and functional validation of selected genes for abiotic stress tolerance in Arabidopsis thaliana.

PubMed

Priyanka, B; Sekhar, K; Sunita, T; Reddy, V D; Rao, Khareedu Venkateswara

2010-03-01

Pigeonpea, a major grain legume crop with remarkable drought tolerance traits, has been used for the isolation of stress-responsive genes. Herein, we report generation of ESTs, transcript profiles of selected genes and validation of candidate genes obtained from the subtracted cDNA libraries of pigeonpea plants subjected to PEG/water-deficit stress conditions. Cluster analysis of 124 selected ESTs yielded 75 high-quality ESTs. Homology searches disclosed that 55 ESTs share significant similarity with the known/putative proteins or ESTs available in the databases. These ESTs were characterized and genes relevant to the specific physiological processes were identified. Of the 75 ESTs obtained from the cDNA libraries of drought-stressed plants, 20 ESTs proved to be unique to the pigeonpea. These sequences are envisaged to serve as a potential source of stress-inducible genes of the drought stress-response transcriptome, and hence may be used for deciphering the mechanism of drought tolerance of the pigeonpea. Expression profiles of selected genes revealed increased levels of m-RNA transcripts in pigeonpea plants subjected to different abiotic stresses. Transgenic Arabidopsis lines, expressing Cajanus cajan hybrid-proline-rich protein (CcHyPRP), C. cajan cyclophilin (CcCYP) and C. cajan cold and drought regulatory (CcCDR) genes, exhibited marked tolerance, increased plant biomass and enhanced photosynthetic rates under PEG/NaCl/cold/heat stress conditions. This study represents the first report dealing with the isolation of drought-specific ESTs, transcriptome analysis and functional validation of drought-responsive genes of the pigeonpea. These genes, as such, hold promise for engineering crop plants bestowed with tolerance to major abiotic stresses.

Physical robustness of canopy temperature models for crop heat stress simulation across environments and production conditions

USDA-ARS?s Scientific Manuscript database

Despite widespread application in studying climate change impacts, most crop models ignore complex interactions among air temperature, crop and soil water status, CO2 concentration and atmospheric conditions that influence crop canopy temperature. The current study extended previous studies by evalu...

Effects of abiotic stress and crop management on cereal grain composition: implications for food quality and safety.

PubMed

Halford, Nigel G; Curtis, Tanya Y; Chen, Zhiwei; Huang, Jianhua

2015-03-01

The effects of abiotic stresses and crop management on cereal grain composition are reviewed, focusing on phytochemicals, vitamins, fibre, protein, free amino acids, sugars, and oils. These effects are discussed in the context of nutritional and processing quality and the potential for formation of processing contaminants, such as acrylamide, furan, hydroxymethylfurfuryl, and trans fatty acids. The implications of climate change for cereal grain quality and food safety are considered. It is concluded that the identification of specific environmental stresses that affect grain composition in ways that have implications for food quality and safety and how these stresses interact with genetic factors and will be affected by climate change needs more investigation. Plant researchers and breeders are encouraged to address the issue of processing contaminants or risk appearing out of touch with major end-users in the food industry, and not to overlook the effects of environmental stresses and crop management on crop composition, quality, and safety as they strive to increase yield. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Breeding implications of drought stress under future climate for upland rice in Brazil.

PubMed

Ramirez-Villegas, Julian; Heinemann, Alexandre B; Pereira de Castro, Adriano; Breseghello, Flávio; Navarro-Racines, Carlos; Li, Tao; Rebolledo, Maria C; Challinor, Andrew J

2018-05-01

Rice is the most important food crop in the developing world. For rice production systems to address the challenges of increasing demand and climate change, potential and on-farm yield increases must be increased. Breeding is one of the main strategies toward such aim. Here, we hypothesize that climatic and atmospheric changes for the upland rice growing period in central Brazil are likely to alter environment groupings and drought stress patterns by 2050, leading to changing breeding targets during the 21st century. As a result of changes in drought stress frequency and intensity, we found reductions in productivity in the range of 200-600 kg/ha (up to 20%) and reductions in yield stability throughout virtually the entire upland rice growing area (except for the southeast). In the face of these changes, our crop simulation analysis suggests that the current strategy of the breeding program, which aims at achieving wide adaptation, should be adjusted. Based on the results for current and future climates, a weighted selection strategy for the three environmental groups that characterize the region is suggested. For the highly favorable environment (HFE, 36%-41% growing area, depending on RCP), selection should be done under both stress-free and terminal stress conditions; for the favorable environment (FE, 27%-40%), selection should aim at testing under reproductive and terminal stress, and for the least favorable environment (LFE, 23%-27%), selection should be conducted for response to reproductive stress only and for the joint occurrence of reproductive and terminal stress. Even though there are differences in timing, it is noteworthy that stress levels are similar across environments, with 40%-60% of crop water demand unsatisfied. Efficient crop improvement targeted toward adaptive traits for drought tolerance will enhance upland rice crop system resilience under climate change. © 2018 John Wiley & Sons Ltd.

Omics Approach to Identify Factors Involved in Brassica Disease Resistance.

PubMed

Francisco, Marta; Soengas, Pilar; Velasco, Pablo; Bhadauria, Vijai; Cartea, Maria E; Rodríguez, Victor M

2016-01-01

Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, forage and ornamental. Damage caused by pathogens attack affects negatively various aspects of plant growth, development, and crop productivity. Over the last few decades, advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to biotic stress conditions. In this regard, various 'omics' technologies enable qualitative and quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. In this review, we have described advances in 'omic' tools (genomics, transcriptomics, proteomics and metabolomics) in the view of conventional and modern approaches being used to elucidate the molecular mechanisms that underlie Brassica disease resistance.

Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet

PubMed Central

Shivhare, Radha; Lata, Charu

2017-01-01

Pearl millet is one of the most important small-grained C4 Panicoid crops with a large genome size (∼2352 Mb), short life cycle and outbreeding nature. It is highly resilient to areas with scanty rain and high temperature. Pearl millet is a nutritionally superior staple crop for people inhabiting hot, drought-prone arid and semi-arid regions of South Asia and Africa where it is widely grown and used for food, hay, silage, bird feed, building material, and fuel. Having excellent nutrient composition and exceptional buffering capacity against variable climatic conditions and pathogen attack makes pearl millet a wonderful model crop for stress tolerance studies. Pearl millet germplasm show a large range of genotypic and phenotypic variations including tolerance to abiotic and biotic stresses. Conventional breeding for enhancing abiotic and biotic stress resistance in pearl millet have met with considerable success, however, in last few years various novel approaches including functional genomics and molecular breeding have been attempted in this crop for augmenting yield under adverse environmental conditions, and there is still a lot of scope for further improvement using genomic tools. Discovery and use of various DNA-based markers such as EST-SSRs, DArT, CISP, and SSCP-SNP in pearl millet not only help in determining population structure and genetic diversity but also prove to be important for developing strategies for crop improvement at a faster rate and greater precision. Molecular marker-based genetic linkage maps and identification of genomic regions determining yield under abiotic stresses particularly terminal drought have paved way for marker-assisted selection and breeding of pearl millet cultivars. Reference collections and marker-assisted backcrossing have also been used to improve biotic stress resistance in pearl millet specifically to downy mildew. Whole genome sequencing of pearl millet genome will give new insights for processing of functional genes and assist in crop improvement programs through molecular breeding approaches. This review thus summarizes the exploration of pearl millet genetic and genomic resources for improving abiotic and biotic stress resistance and development of cultivars superior in stress tolerance. PMID:28167949

Detecting crop yield reduction due to irrigation-induced soil salinization in South-West Russia

NASA Astrophysics Data System (ADS)

Argaman, E.; Beets, W.; Croes, J.; Keesstra, S.; Verzandvoort, S.; Zeiliguer, A.

2012-04-01

The South-European part of the Russian Federation has experienced serious land degradation in the form of soil salinization since the 1960s. This land degradation was caused by intensive, large-scale irrigation on reclaimed land in combination with the salt-rich nature of the substrate. Alkaline soil salinity is believed to be an important factor decreasing crop yield in this area. A large research effort has been directed to the effects of soil salinity on crops, there is a need for simple, easily determinable indicators of crop health and soil salinity in irrigated systems, that can help to detect crop water stress in an early stage. The objectives of this research were to study the effects of soil salinity and vegetation water stress on the performance of alfalfa crop yield and physiological crop properties, and to study the possibility to measure soil salinity and alkalinity and the crop water stress index at plot level using a thermal gun and a regular digital camera. The study area was located in Saratov District, in the South-West part of Russia. Variables on the surface energy balance, crop properties, soil properties and visible reflectance were measured on plots with alfalfa cultures in two fields with and without signs of alkaline soil salinity, and with and without irrigation in July 2009. The research showed no clear adverse effects of soil salinity and soil alkalinity on crop yield and physiological crop properties. Soil salinity, as reflected by the electric conductivity, positively affected the root biomass of alfalfa in the range of 0.15 to 1.52 dS/m . This was a result of EC levels being below the documented threshold to negatively affect Alfalfa, as would be the case in truly saline soils. The soil pH also showed a positive correlation with root biomass within the range of pH 6.2 and 8.5 . From the literature these pH values are generally believed to be too high to exhibit a positive relationship with root biomass. No relationship was found between EC and pH on the one hand , and soil moisture content on the other. However, soil moisture content in the topsoil appeared to have a major influence on the crop water stress index, which on its turn affected the leaf area index, the fresh biomass and the mean plant height. The crop leaf color as detected by a regular digital camera appeared to be correlated with pH and EC properties of the soil. The visible light band ratios red/green and blue/green correlated well with the crop water stress index. More research is necessary to prove if this relation is applicable in different environments, and for different crops. A confirmation of these findings would offer scope to increase the spatial support of this technique using satellite images.

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

PubMed Central

Francis, Aleena; Dhaka, Namrata; Bakshi, Mohit; Jung, Ki-Hong; Sharma, Manoj K.; Sharma, Rita

2016-01-01

Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance. PMID:27917941

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum.

PubMed

Francis, Aleena; Dhaka, Namrata; Bakshi, Mohit; Jung, Ki-Hong; Sharma, Manoj K; Sharma, Rita

2016-12-05

Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.

Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency.

PubMed

Kulkarni, Manoj; Soolanayakanahally, Raju; Ogawa, Satoshi; Uga, Yusaku; Selvaraj, Michael G; Kagale, Sateesh

2017-01-01

Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.

[Nitrogen stress measurement of canola based on multi-spectral charged coupled device imaging sensor].

PubMed

Feng, Lei; Fang, Hui; Zhou, Wei-Jun; Huang, Min; He, Yong

2006-09-01

Site-specific variable nitrogen application is one of the major precision crop production management operations. Obtaining sufficient crop nitrogen stress information is essential for achieving effective site-specific nitrogen applications. The present paper describes the development of a multi-spectral nitrogen deficiency sensor, which uses three channels (green, red, near-infrared) of crop images to determine the nitrogen level of canola. This sensor assesses the nitrogen stress by means of estimated SPAD value of the canola based on canola canopy reflectance sensed using three channels (green, red, near-infrared) of the multi-spectral camera. The core of this investigation is the calibration methods between the multi-spectral references and the nitrogen levels in crops measured using a SPAD 502 chlorophyll meter. Based on the results obtained from this study, it can be concluded that a multi-spectral CCD camera can provide sufficient information to perform reasonable SPAD values estimation during field operations.

Quantitative proteomic analysis of the Salmonella-lettuce interaction

PubMed Central

Zhang, Yuping; Nandakumar, Renu; Bartelt-Hunt, Shannon L; Snow, Daniel D; Hodges, Laurie; Li, Xu

2014-01-01

Human pathogens can internalize food crops through root and surface uptake and persist inside crop plants. The goal of the study was to elucidate the global modulation of bacteria and plant protein expression after Salmonella internalizes lettuce. A quantitative proteomic approach was used to analyse the protein expression of Salmonella enterica serovar Infantis and lettuce cultivar Green Salad Bowl 24 h after infiltrating S. Infantis into lettuce leaves. Among the 50 differentially expressed proteins identified by comparing internalized S. Infantis against S. Infantis grown in Luria Broth, proteins involved in glycolysis were down-regulated, while one protein involved in ascorbate uptake was up-regulated. Stress response proteins, especially antioxidant proteins, were up-regulated. The modulation in protein expression suggested that internalized S. Infantis might utilize ascorbate as a carbon source and require multiple stress response proteins to cope with stresses encountered in plants. On the other hand, among the 20 differentially expressed lettuce proteins, proteins involved in defense response to bacteria were up-regulated. Moreover, the secreted effector PipB2 of S. Infantis and R proteins of lettuce were induced after bacterial internalization into lettuce leaves, indicating human pathogen S. Infantis triggered the defense mechanisms of lettuce, which normally responds to plant pathogens. PMID:24512637

Operation of agricultural test fields for study of stressed crops by remote sensing

NASA Technical Reports Server (NTRS)

Toler, R. W.

1974-01-01

A test site for the study of winter wheat development and collection of ERTS data was established in September of 1973. The test site is a 10 mile square area located 12.5 miles west of Amarillo, Texas on Interstate Hwy. 40, in Randall and Potter counties. The center of the area is the Southwestern Great Plains Research Center at Bushland, Texas. Within the test area all wheat fields were identified by ground truth and designated irrigated or dryland. The fields in the test area other than wheat were identified as to pasture or the crop that was grown. A ground truth area of hard red winter wheat was established west of Hale Center, Texas. Maps showing the location of winter wheat fields in excess of 40 acres in size within a 10 mile radius were supplied NASA. Satellite data was collected for this test site (ERTS-1).

Development of a Wireless Computer Vision Instrument to Detect Biotic Stress in Wheat

PubMed Central

Casanova, Joaquin J.; O'Shaughnessy, Susan A.; Evett, Steven R.; Rush, Charles M.

2014-01-01

Knowledge of crop abiotic and biotic stress is important for optimal irrigation management. While spectral reflectance and infrared thermometry provide a means to quantify crop stress remotely, these measurements can be cumbersome. Computer vision offers an inexpensive way to remotely detect crop stress independent of vegetation cover. This paper presents a technique using computer vision to detect disease stress in wheat. Digital images of differentially stressed wheat were segmented into soil and vegetation pixels using expectation maximization (EM). In the first season, the algorithm to segment vegetation from soil and distinguish between healthy and stressed wheat was developed and tested using digital images taken in the field and later processed on a desktop computer. In the second season, a wireless camera with near real-time computer vision capabilities was tested in conjunction with the conventional camera and desktop computer. For wheat irrigated at different levels and inoculated with wheat streak mosaic virus (WSMV), vegetation hue determined by the EM algorithm showed significant effects from irrigation level and infection. Unstressed wheat had a higher hue (118.32) than stressed wheat (111.34). In the second season, the hue and cover measured by the wireless computer vision sensor showed significant effects from infection (p = 0.0014), as did the conventional camera (p < 0.0001). Vegetation hue obtained through a wireless computer vision system in this study is a viable option for determining biotic crop stress in irrigation scheduling. Such a low-cost system could be suitable for use in the field in automated irrigation scheduling applications. PMID:25251410

TaHsfA6f is a transcriptional activator that regulates a suite of heat stress protection genes in wheat (Triticum aestivum L.) including previously unknown Hsf targets

PubMed Central

Xue, Gang-Ping; Drenth, Janneke; McIntyre, C. Lynne

2015-01-01

Heat stress is a significant environmental factor adversely affecting crop yield. Crop adaptation to high-temperature environments requires transcriptional reprogramming of a suite of genes involved in heat stress protection. This study investigated the role of TaHsfA6f, a member of the A6 subclass of heat shock transcription factors, in the regulation of heat stress protection genes in Triticum aestivum (bread wheat), a poorly understood phenomenon in this crop species. Expression analysis showed that TaHsfA6f was expressed constitutively in green organs but was markedly up-regulated during heat stress. Overexpression of TaHsfA6f in transgenic wheat using a drought-inducible promoter resulted in up-regulation of heat shock proteins (HSPs) and a number of other heat stress protection genes that included some previously unknown Hsf target genes such as Golgi anti-apoptotic protein (GAAP) and the large isoform of Rubisco activase. Transgenic wheat plants overexpressing TaHsfA6f showed improved thermotolerance. Transactivation assays showed that TaHsfA6f activated the expression of reporter genes driven by the promoters of several HSP genes (TaHSP16.8, TaHSP17, TaHSP17.3, and TaHSP90.1-A1) as well as TaGAAP and TaRof1 (a co-chaperone) under non-stress conditions. DNA binding analysis revealed the presence of high-affinity TaHsfA6f-binding heat shock element-like motifs in the promoters of these six genes. Promoter truncation and mutagenesis analyses identified TaHsfA6f-binding elements that were responsible for transactivation of TaHSP90.1-A1 and TaGAAP by TaHsfA6f. These data suggest that TaHsfA6f is a transcriptional activator that directly regulates TaHSP, TaGAAP, and TaRof1 genes in wheat and its gene regulatory network has a positive impact on thermotolerance. PMID:25428996

TaHsfA6f is a transcriptional activator that regulates a suite of heat stress protection genes in wheat (Triticum aestivum L.) including previously unknown Hsf targets.

PubMed

Xue, Gang-Ping; Drenth, Janneke; McIntyre, C Lynne

2015-02-01

Heat stress is a significant environmental factor adversely affecting crop yield. Crop adaptation to high-temperature environments requires transcriptional reprogramming of a suite of genes involved in heat stress protection. This study investigated the role of TaHsfA6f, a member of the A6 subclass of heat shock transcription factors, in the regulation of heat stress protection genes in Triticum aestivum (bread wheat), a poorly understood phenomenon in this crop species. Expression analysis showed that TaHsfA6f was expressed constitutively in green organs but was markedly up-regulated during heat stress. Overexpression of TaHsfA6f in transgenic wheat using a drought-inducible promoter resulted in up-regulation of heat shock proteins (HSPs) and a number of other heat stress protection genes that included some previously unknown Hsf target genes such as Golgi anti-apoptotic protein (GAAP) and the large isoform of Rubisco activase. Transgenic wheat plants overexpressing TaHsfA6f showed improved thermotolerance. Transactivation assays showed that TaHsfA6f activated the expression of reporter genes driven by the promoters of several HSP genes (TaHSP16.8, TaHSP17, TaHSP17.3, and TaHSP90.1-A1) as well as TaGAAP and TaRof1 (a co-chaperone) under non-stress conditions. DNA binding analysis revealed the presence of high-affinity TaHsfA6f-binding heat shock element-like motifs in the promoters of these six genes. Promoter truncation and mutagenesis analyses identified TaHsfA6f-binding elements that were responsible for transactivation of TaHSP90.1-A1 and TaGAAP by TaHsfA6f. These data suggest that TaHsfA6f is a transcriptional activator that directly regulates TaHSP, TaGAAP, and TaRof1 genes in wheat and its gene regulatory network has a positive impact on thermotolerance. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

PubMed Central

Wang, Yan; Xu, Liang; Chen, Yinglong; Shen, Hong; Gong, Yiqin; Limera, Cecilia; Liu, Liwang

2013-01-01

Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops. PMID:23840502

Pre-sowing Seed Treatments in Direct-seeded Early Rice: Consequences for Emergence, Seedling Growth and Associated Metabolic Events under Chilling Stress

NASA Astrophysics Data System (ADS)

Wang, Weiqin; Chen, Qian; Hussain, Saddam; Mei, Junhao; Dong, Huanglin; Peng, Shaobing; Huang, Jianliang; Cui, Kehui; Nie, Lixiao

2016-01-01

Double direct-seeding for double rice cropping is a simplified, labor saving, and efficient cropping system to improve multiple-crop index and total rice production in central China. However, poor crop establishment of direct-seeded early rice due to chilling stress is the main obstacle to wide spread of this system. A series of experiments were conducted to unravel the effects of pre-sowing seed treatments on emergence, seedling growth and associated metabolic events of direct-seeded early rice under chilling stress. Two seed priming treatments and two seed coating treatments were used in all the experiments. A non-treated control treatment was also maintained for comparison. In both the field and growth chamber studies, seed priming with selenium or salicylic acid significantly enhanced the emergence and seedling growth of rice compared with non-treated control. Nevertheless, such positive effects were not apparent for seed coating treatments. Better emergence and vigorous seedling growth of rice after seed priming was associated with enhanced α-amylase activity, higher soluble sugars contents, and greater respiration rate in primed rice seedlings under chilling stress. Taking together, these findings may provide new avenues for understanding and advancing priming-induced chilling tolerance in direct-seeded early rice in double rice cropping system.

Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops

PubMed Central

Bita, Craita E.; Gerats, Tom

2013-01-01

Global warming is predicted to have a general negative effect on plant growth due to the damaging effect of high temperatures on plant development. The increasing threat of climatological extremes including very high temperatures might lead to catastrophic loss of crop productivity and result in wide spread famine. In this review, we assess the impact of global climate change on the agricultural crop production. There is a differential effect of climate change both in terms of geographic location and the crops that will likely show the most extreme reductions in yield as a result of expected extreme fluctuations in temperature and global warming in general. High temperature stress has a wide range of effects on plants in terms of physiology, biochemistry and gene regulation pathways. However, strategies exist to crop improvement for heat stress tolerance. In this review, we present recent advances of research on all these levels of investigation and focus on potential leads that may help to understand more fully the mechanisms that make plants tolerant or susceptible to heat stress. Finally, we review possible procedures and methods which could lead to the generation of new varieties with sustainable yield production, in a world likely to be challenged both by increasing population, higher average temperatures and larger temperature fluctuations. PMID:23914193

Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops.

PubMed

Bita, Craita E; Gerats, Tom

2013-01-01

Global warming is predicted to have a general negative effect on plant growth due to the damaging effect of high temperatures on plant development. The increasing threat of climatological extremes including very high temperatures might lead to catastrophic loss of crop productivity and result in wide spread famine. In this review, we assess the impact of global climate change on the agricultural crop production. There is a differential effect of climate change both in terms of geographic location and the crops that will likely show the most extreme reductions in yield as a result of expected extreme fluctuations in temperature and global warming in general. High temperature stress has a wide range of effects on plants in terms of physiology, biochemistry and gene regulation pathways. However, strategies exist to crop improvement for heat stress tolerance. In this review, we present recent advances of research on all these levels of investigation and focus on potential leads that may help to understand more fully the mechanisms that make plants tolerant or susceptible to heat stress. Finally, we review possible procedures and methods which could lead to the generation of new varieties with sustainable yield production, in a world likely to be challenged both by increasing population, higher average temperatures and larger temperature fluctuations.

Mapping Crop Yield and Sow Date Using High Resolution Imagery

NASA Astrophysics Data System (ADS)

Royal, K.

2015-12-01

Keitasha Royal, Meha Jain, Ph.D., David Lobell, Ph.D Mapping Crop Yield and Sow Date Using High Resolution ImageryThe use of satellite imagery in agriculture is becoming increasingly more significant and valuable. Due to the emergence of new satellites, such as Skybox, these satellites provide higher resolution imagery (e.g 1m) therefore improving the ability to map smallholder agriculture. For the smallholder farm dominated area of northern India, Skybox high-resolution satellite imagery can aid in understanding how to improve farm yields. In particular, we are interested in mapping winter wheat in India, as this region produces approximately 80% of the country's wheat crop, which is important given that wheat is a staple crop that provides approximately 20% of household calories. In northeast India, the combination of increased heat stress, limited irrigation access, and the difficulty for farmers to access advanced farming technologies results in farmers only producing about 50% of their potential crop yield. The use of satellite imagery can aid in understanding wheat yields through time and help identify ways to increase crop yields in the wheat belt of India. To translate Skybox satellite data into meaningful information about wheat fields, we examine vegetation indices, such as the normalized difference vegetation index (NDVI), to measure the "greenness" of plants to help determine the health of the crops. We test our ability to predict crop characteristics, like sow date and yield, using vegetation indices of 59 fields for which we have field data in Bihar, India.

Remote sensing in precision farming: real-time monitoring of water and fertilizer requirements of agricultural crops

NASA Astrophysics Data System (ADS)

Zilberman, Arkadi; Ben Asher, Jiftah; Kopeika, Norman S.

2016-10-01

The advancements in remote sensing in combination with sensor technology (both passive and active) enable growers to analyze an entire crop field as well as its local features. In particular, changes of actual evapo-transpiration (ET) as a function of water availability can be measured remotely with infrared radiometers. Detection of crop water stress and ET and combining it with the soil water flow model enable rational irrigation timing and application amounts. Nutrient deficiency, and in particular nitrogen deficiency, causes substantial crop losses. This deficiency needs to be identified immediately. A faster the detection and correction, a lesser the damage to the crop yield. In the present work, to retrieve ET a novel deterministic approach was used which is based on the remote sensing data. The algorithm can automatically provide timely valuable information on plant and soil water status, which can improve the management of irrigated crops. The solution is capable of bridging between Penman-Monteith ET model and Richards soil water flow model. This bridging can serve as a preliminary tool for expert irrigation system. To support decisions regarding fertilizers the greenness of plant canopies is assessed and quantified by using the spectral reflectance sensors and digital color imaging. Fertilization management can be provided on the basis of sampling and monitoring of crop nitrogen conditions using RS technique and translating measured N concentration in crop to kg/ha N application in the field.

Agricultural biotechnology for crop improvement in a variable climate: hope or hype?

PubMed

Varshney, Rajeev K; Bansal, Kailash C; Aggarwal, Pramod K; Datta, Swapan K; Craufurd, Peter Q

2011-07-01

Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dynamic Succession of Soil Bacterial Community during Continuous Cropping of Peanut (Arachis hypogaea L.)

PubMed Central

Chen, Mingna; Li, Xiao; Yang, Qingli; Chi, Xiaoyuan; Pan, Lijuan; Chen, Na; Yang, Zhen; Wang, Tong; Wang, Mian; Yu, Shanlin

2014-01-01

Plant health and soil fertility are affected by plant–microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including Acidobacteriales, Burkholderiales, Bdellovibrionales, and so on, also were affected by plant age. PMID:25010658

Development of an irrigation scheduling software based on model predicted crop water stress

USDA-ARS?s Scientific Manuscript database

Modern irrigation scheduling methods are generally based on sensor-monitored soil moisture regimes rather than crop water stress which is difficult to measure in real-time, but can be computed using agricultural system models. In this study, an irrigation scheduling software based on RZWQM2 model pr...

Leaf temperature of maize and crop water stress index with variable irrigation and nitrogen supply

USDA-ARS?s Scientific Manuscript database

Water scarcity due to changing climate, population growth, and economic development is a major threat to the sustainability of irrigated agriculture in the Western United States and other regions around the world. Water stress indices based on crop canopy temperature can be useful for assessing plan...

The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

PubMed Central

Tripathi, Prateek

2014-01-01

Abstract Drought is one of the major constraints in crop production and has an effect on a global scale. In order to improve crop production, it is necessary to understand how plants respond to stress. A good understanding of regulatory mechanisms involved in plant responses during drought will enable researchers to explore and manipulate key regulatory points in order to enhance stress tolerance in crops. Transcription factors (TFs) have played an important role in crop improvement from the dawn of agriculture. TFs are therefore good candidates for genetic engineering to improve crop tolerance to drought because of their role as master regulators of clusters of genes. Many families of TFs, such as CCAAT, homeodomain, bHLH, NAC, AP2/ERF, bZIP, and WRKY have members that may have the potential to be tools for improving crop tolerance to drought. In this review, the roles of TFs as tools to improve drought tolerance in crops are discussed. The review also focuses on current strategies in the use of TFs, with emphasis on several major TF families in improving drought tolerance of major crops. Finally, many promising transgenic lines that may have improved drought responses have been poorly characterized and consequently their usefulness in the field is uncertain. New advances in high-throughput phenotyping, both greenhouse and field based, should facilitate improved phenomics of transgenic lines. Systems biology approaches should then define the underlying changes that result in higher yields under water stress conditions. These new technologies should help show whether manipulating TFs can have effects on yield under field conditions. PMID:25118806

The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress.

PubMed

Ye, Jianqiu; Yang, Hai; Shi, Haitao; Wei, Yunxie; Tie, Weiwei; Ding, Zehong; Yan, Yan; Luo, Ying; Xia, Zhiqiang; Wang, Wenquan; Peng, Ming; Li, Kaimian; Zhang, He; Hu, Wei

2017-11-02

Mitogen-activated protein kinase kinase kinases (MAPKKKs), an important unit of MAPK cascade, play crucial roles in plant development and response to various stresses. However, little is known concerning the MAPKKK family in the important subtropical and tropical crop cassava. In this study, 62 MAPKKK genes were identified in the cassava genome, and were classified into 3 subfamilies based on phylogenetic analysis. Most of MAPKKKs in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis showed that MAPKKK genes participated in tissue development and response to drought stress. Comparative expression profiles revealed that many MAPKKK genes were activated in cultivated varieties SC124 and Arg7 and the function of MeMAPKKKs in drought resistance may be different between SC124/Arg7 and W14. Expression analyses of the 7 selected MeMAPKKK genes showed that most of them were significantly upregulated by osmotic, salt and ABA treatments, whereas slightly induced by H 2 O 2 and cold stresses. Taken together, this study identified candidate MeMAPKKK genes for genetic improvement of abiotic stress resistance and provided new insights into MAPKKK -mediated cassava resistance to drought stress.

Unraveling the role of fungal symbionts in plant abiotic stress tolerance

PubMed Central

Singh, Lamabam Peter

2011-01-01

Fungal symbionts have been found to be associated with every plant studied in the natural ecosystem, where they colonize and reside entirely or partially in the internal tissues of their host plant. Fungal endophytes can express/form a range of different lifestyle/relationships with different host including symbiotic, mutualistic, commensalistic and parasitic in response to host genotype and environmental factors. In mutualistic association fungal endophyte can enhance growth, increase reproductive success and confer biotic and abiotic stress tolerance to its host plant. Since abiotic stress such as, drought, high soil salinity, heat, cold, oxidative stress and heavy metal toxicity is the common adverse environmental conditions that affect and limit crop productivity worldwide. It may be a promising alternative strategy to exploit fungal endophytes to overcome the limitations to crop production brought by abiotic stress. There is an increasing interest in developing the potential biotechnological applications of fungal endophytes for improving plant stress tolerance and sustainable production of food crops. Here we have described the fungal symbioses, fungal symbionts and their role in abiotic stress tolerance. A putative mechanism of stress tolerance by symbionts has also been covered. PMID:21512319

A roadmap for breeding orphan leafy vegetable species: a case study of Gynandropsis gynandra (Cleomaceae).

PubMed

Sogbohossou, E O Deedi; Achigan-Dako, Enoch G; Maundu, Patrick; Solberg, Svein; Deguenon, Edgar M S; Mumm, Rita H; Hale, Iago; Van Deynze, Allen; Schranz, M Eric

2018-01-01

Despite an increasing awareness of the potential of "orphan" or unimproved crops to contribute to food security and enhanced livelihoods for farmers, coordinated research agendas to facilitate production and use of orphan crops by local communities are generally lacking. We provide an overview of the current knowledge on leafy vegetables with a focus on Gynandropsis gynandra , a highly nutritious species used in Africa and Asia, and highlight general and species-specific guidelines for participatory, genomics-assisted breeding of orphan crops. Key steps in genome-enabled orphan leafy vegetables improvement are identified and discussed in the context of Gynandropsis gynandra breeding, including: (1) germplasm collection and management; (2) product target definition and refinement; (3) characterization of the genetic control of key traits; (4) design of the 'process' for cultivar development; (5) integration of genomic data to optimize that 'process'; (6) multi-environmental participatory testing and end-user evaluation; and (7) crop value chain development. The review discusses each step in detail, with emphasis on improving leaf yield, phytonutrient content, organoleptic quality, resistance to biotic and abiotic stresses and post-harvest management.

Gene Expression Changes in Phosphorus Deficient Potato (Solanum tuberosum L.) Leaves and the Potential for Diagnostic Gene Expression Markers

PubMed Central

Hammond, John P.; Broadley, Martin R.; Bowen, Helen C.; Spracklen, William P.; Hayden, Rory M.; White, Philip J.

2011-01-01

Background There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. Results We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. Conclusions This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture. PMID:21935429

Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum.

PubMed

Fan, Xinqi; Guo, Qi; Xu, Peng; Gong, YuanYong; Shu, Hongmei; Yang, Yang; Ni, Wanchao; Zhang, Xianggui; Shen, Xinlian

2015-01-01

WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.

Physiological genomics of response to soil drying in diverse Arabidopsis accessions.

PubMed

Des Marais, David L; McKay, John K; Richards, James H; Sen, Saunak; Wayne, Tierney; Juenger, Thomas E

2012-03-01

Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural mutant screen to determine gene function. Here, we document physiological and transcriptomic response to soil drying in 17 natural accessions of Arabidopsis. By imposing ecologically realistic stress conditions, we found that acclimation in Arabidopsis involved a strong signature of increased investment in photosynthesis, carbohydrate turnover, and root growth. Our results extend previous work in the Columbia accession suggesting that abscisic acid signaling pathways play an important role in drought stress response. We also identified several mechanisms, including an increase in leaf nitrogen concentration and upregulation of two-component signaling relays, that were common to most natural accessions but had not been identified in studies using only the Columbia accession. Principal component analysis reveals strong correlations between suites of genes and specific physiological responses to stress. The functional variants we identified may represent adaptive mutations in natural habitats and useful variants for agronomic improvement of crop species.

Physiological Genomics of Response to Soil Drying in Diverse Arabidopsis Accessions[W][OA

PubMed Central

Des Marais, David L.; McKay, John K.; Richards, James H.; Sen, Saunak; Wayne, Tierney; Juenger, Thomas E.

2012-01-01

Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural mutant screen to determine gene function. Here, we document physiological and transcriptomic response to soil drying in 17 natural accessions of Arabidopsis. By imposing ecologically realistic stress conditions, we found that acclimation in Arabidopsis involved a strong signature of increased investment in photosynthesis, carbohydrate turnover, and root growth. Our results extend previous work in the Columbia accession suggesting that abscisic acid signaling pathways play an important role in drought stress response. We also identified several mechanisms, including an increase in leaf nitrogen concentration and upregulation of two-component signaling relays, that were common to most natural accessions but had not been identified in studies using only the Columbia accession. Principal component analysis reveals strong correlations between suites of genes and specific physiological responses to stress. The functional variants we identified may represent adaptive mutations in natural habitats and useful variants for agronomic improvement of crop species. PMID:22408074

A scheme for the uniform mapping and monitoring of earth resources and environmental complexes: An assessment of natural vegetation, environmental, and crop analogs. [Sierra-Lahontan and Colorado Plateaus, Northern Great Valley (CA), and Louisiana Coastal Plain

NASA Technical Reports Server (NTRS)

Poulton, C. E.; Welch, R. I. (Principal Investigator)

1975-01-01

The author has identified the following significant results. A study was performed to develop and test a procedure for the uniform mapping and monitoring of natural ecosystems in the semi-arid and wood regions of the Sierra-Lahontan and Colorado Plateau areas, and for the estimating of rice crop production in the Northern Great Valley (Ca.) and the Louisiana Coastal Plain. ERTS-1 and high flight and low flight aerial photos were used in a visual photointerpretation scheme to identify vegetation complexes, map acreages, and evaluate crop vigor and stress. Results indicated that the vegetation analog concept is valid; that depending on the kind of vegetation and its density, analogs are interpretable at different levels in the hierarchical classification from second to the fourth level. The second level uses physiognomic growth form-structural criteria, and the fourth level uses floristic or taxonomic criteria, usually at generic level. It is recommended that analog comparisons should be made in relatively small test areas where large homogeneous examples can be found of each analog.

Breeding for sustainable production in a changing climate – understanding the physiological basis of genetic by environmental interactions

USDA-ARS?s Scientific Manuscript database

Abiotic stresses (drought, cold, heat, excess, water, salinity) result in loses in yield and quality of crops. In addition, these stresses limit the areas that can be cultivated because of yield instability and crop loss. Global warming models predict erratic weather patterns making the impact of th...

HKT transporters mediate salt stress resistance in plants: from structure and function to the field

DOE PAGES

Hamamoto, Shin; Horie, Tomoaki; Hauser, Felix; ...

2014-12-18

Plant cells are sensitive to salinity stress and do not require sodium as an essential element for their growth and development. Saline soils reduce crop yields and limit available land. The research shows that HKT transporters provide a potent mechanism for mediating salt tolerance in plants. Knowledge of the molecular ion transport and regulation mechanisms and the control of HKT gene expression are crucial for understanding the mechanisms by which HKT transporters enhance crop performance under salinity stress. Our review focuses on HKT transporters in monocot plants and in Arabidopsis as a dicot plant, as a guide to efforts towardmore » improving salt tolerance of plants for increasing the production of crops and bioenergy feedstocks.« less

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes

PubMed Central

Bhawna; Bonthala, V.S.; Gajula, MNV Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely. Database URL: http://www.multiomics.in/PvTFDB/ PMID:27465131

African Orphan Crops under Abiotic Stresses: Challenges and Opportunities.

PubMed

Tadele, Zerihun

2018-01-01

A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as "orphan crops") including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented.

Hyperspectral imaging to identify salt-tolerant wheat lines

NASA Astrophysics Data System (ADS)

Moghimi, Ali; Yang, Ce; Miller, Marisa E.; Kianian, Shahryar; Marchetto, Peter

2017-05-01

In order to address the worldwide growing demand for food, agriculture is facing certain challenges and limitations. One of the important threats limiting crop productivity is salinity. Identifying salt tolerate varieties is crucial to mitigate the negative effects of this abiotic stress in agricultural production systems. Traditional measurement methods of this stress, such as biomass retention, are labor intensive, environmentally influenced, and often poorly correlated to salinity stress alone. In this study, hyperspectral imaging, as a non-destructive and rapid method, was utilized to expedite the process of identifying relatively the most salt tolerant line among four wheat lines including Triticum aestivum var. Kharchia, T. aestivum var. Chinese Spring, (Ae. columnaris) T. aestivum var. Chinese Spring, and (Ae. speltoides) T. aestivum var. Chinese Spring. To examine the possibility of early detection of a salt tolerant line, image acquisition was started one day after stress induction and continued on three, seven, and 12 days after adding salt. Simplex volume maximization (SiVM) method was deployed to detect superior wheat lines in response to salt stress. The results of analyzing images taken as soon as one day after salt induction revealed that Kharchia and (columnaris)Chinese Spring are the most tolerant wheat lines, while (speltoides) Chinese Spring was a moderately susceptible, and Chinese Spring was a relatively susceptible line to salt stress. These results were confirmed with the measuring biomass performed several weeks later.

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii

PubMed Central

He, Qiuling; Jones, Don C.; Li, Wei; Xie, Fuliang; Ma, Jun; Sun, Runrun; Wang, Qinglian; Zhu, Shuijin; Zhang, Baohong

2016-01-01

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement. PMID:27009386

Decision Support Systems To Manage Water Resources At Irrigation District Level In Southern Italy Using Remote Sensing Information. An Integrated Project (AQUATER)

NASA Astrophysics Data System (ADS)

Rinaldi, M.; Castrignanò, A.; Mastrorilli, M.; Rana, G.; Ventrella, D.; Acutis, M.; D'Urso, G.; Mattia, F.

2006-08-01

An efficient management of water resources is crucial point for Italy and in particular for southern areas characterized by Mediterranean climate in order to improve the economical and environmental sustainability of the agricultural activity. A three-year Project (2005-2008) has been funded by the Italian Ministry of Agriculture and Forestry Policies; it involves four Italian research institutions: the Agricultural Research Council (ISA, Bari), the National Research Council (ISSIA, Bari) and two Universities (Federico II-Naples and Milan). It is focused on the remote sensing, the plant and the climate and, for interdisciplinary relationships, the project working group consists of agronomists, engineers and physicists. The aims of the Project are: a) to produce a Decision Support System (DSS) combining remote sensing information, spatial data and simulation models to manage water resources in irrigation districts; b) to simulate irrigation scenarios to evaluate the effects of water stress on crop yield using agro-ecological indicators; c) to identify the most sensitive areas to drought risk in Southern Italy. The tools used in this Project will be: 1. Remote sensing images, topographic maps, soil and land use maps; 2. Geographic Information Systems; 3. Geostatistic methodologies; 4. Ground truth measurements (land use, canopy and soil temperatures, soil and plant water status, Normalized Difference Vegetation Index, Crop Water Stress Index, Leaf Area Index, actual evapotranspiration, crop coefficients, crop yield, agro-ecological indicators); 5. Crop simulation models. The Project is structured in four work packages with specific objectives, high degree of interaction and information exchange: 1) Remote Sensing and Image Analysis; 2) Cropping Systems; 3) Modelling and Softwares Development; 4) Stakeholders. The final product will be a DSS with the purpose of integrating remote sensing images, to estimate crop and soil variables related to drought, to assimilate these variables into a simulation model at district scale and, finally, to estimate evapotranspiration, plant water status and drought indicators. A project Web home page, a technical course about DSS for the employers of irrigation authorities and dissemination of results (meetings, publications, reports), are also planned.

Plant MYB Transcription Factors: Their Role in Drought Response Mechanisms

PubMed Central

Baldoni, Elena; Genga, Annamaria; Cominelli, Eleonora

2015-01-01

Water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. Several molecular networks involved in stress perception, signal transduction and stress responses in plants have been elucidated so far. Transcription factors are major players in water stress signaling. In recent years, different MYB transcription factors, mainly in Arabidopsis thaliana (L.) Heynh. but also in some crops, have been characterized for their involvement in drought response. For some of them there is evidence supporting a specific role in response to water stress, such as the regulation of stomatal movement, the control of suberin and cuticular waxes synthesis and the regulation of flower development. Moreover, some of these genes have also been characterized for their involvement in other abiotic or biotic stresses, an important feature considering that in nature, plants are often simultaneously subjected to multiple rather than single environmental perturbations. This review summarizes recent studies highlighting the role of the MYB family of transcription factors in the adaptive responses to drought stress. The practical application value of MYBs in crop improvement, such as stress tolerance engineering, is also discussed. PMID:26184177

Plant MYB Transcription Factors: Their Role in Drought Response Mechanisms.

PubMed

Baldoni, Elena; Genga, Annamaria; Cominelli, Eleonora

2015-07-13

Water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. Several molecular networks involved in stress perception, signal transduction and stress responses in plants have been elucidated so far. Transcription factors are major players in water stress signaling. In recent years, different MYB transcription factors, mainly in Arabidopsis thaliana (L.) Heynh. but also in some crops, have been characterized for their involvement in drought response. For some of them there is evidence supporting a specific role in response to water stress, such as the regulation of stomatal movement, the control of suberin and cuticular waxes synthesis and the regulation of flower development. Moreover, some of these genes have also been characterized for their involvement in other abiotic or biotic stresses, an important feature considering that in nature, plants are often simultaneously subjected to multiple rather than single environmental perturbations. This review summarizes recent studies highlighting the role of the MYB family of transcription factors in the adaptive responses to drought stress. The practical application value of MYBs in crop improvement, such as stress tolerance engineering, is also discussed.

Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing.

PubMed

Liu, Minmin; Yu, Huiyang; Zhao, Gangjun; Huang, Qiufeng; Lu, Yongen; Ouyang, Bo

2017-06-26

Abiotic stresses cause severe loss of crop production. Among them, drought is one of the most frequent environmental stresses, which limits crop growth, development and productivity. Plant drought tolerance is fine-tuned by a complex gene regulatory network. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success to improve plant yield and quality. Recent studies have demonstrated that microRNAs play critical roles in plant drought tolerance. However, little is known about the microRNA in drought response of the model plant tomato. Here, we described the profiling of drought-responsive microRNA and mRNA in tomato using high-throughput next-generation sequencing. Drought stress was applied on the seedlings of M82, a drought-sensitive cultivated tomato genotype, and IL9-1, a drought-tolerant introgression line derived from the stress-resistant wild species Solanum pennellii LA0716 and M82. Under drought, IL9-1 performed superior than M82 regarding survival rate, H 2 O 2 elimination and leaf turgor maintenance. A total of four small RNA and eight mRNA libraries were constructed and sequenced using Illumina sequencing technology. 105 conserved and 179 novel microRNAs were identified, among them, 54 and 98 were differentially expressed upon drought stress, respectively. The majority of the differentially-expressed conserved microRNAs was up-regulated in IL9-1 whereas down-regulated in M82. Under drought stress, 2714 and 1161 genes were found to be differentially expressed in M82 and IL9-1, respectively, and many of their homologues are involved in plant stress, such as genes encoding transcription factor and protein kinase. Various pathways involved in abiotic stress were revealed by Gene Ontology and pathway analysis. The mRNA sequencing results indicated that most of the target genes were regulated by their corresponding microRNAs, which suggested that microRNAs may play essential roles in the drought tolerance of tomato. In this study, numerous microRNAs and mRNAs involved in the drought response of tomato were identified using high-throughput sequencing, which will provide new insights into the complex regulatory network of plant adaption to drought stress. This work will also help to exploit new players functioning in plant drought-stress tolerance.

The CROSTVOC project - an integrated approach to study the effect of stress on BVOC exchange between agricultural crops and grassland ecosystems and the atmosphere

NASA Astrophysics Data System (ADS)

Amelynck, Crist; Heinesch, Bernard; Aubinet, Marc; Bachy, Aurélie; Delaplace, Pierre; Digrado, Anthony; du Jardin, Patrick; Fauconnier, Marie-Laure; Mozaffar, Ahsan; Schoon, Niels

2015-04-01

Global changes in atmospheric composition and climate are expected to affect BVOC exchange between terrestrial vegetation and the atmosphere through changes in the drivers of constitutive BVOC emissions and by increases in frequency and intensity of biotic or abiotic stress episodes. Indeed, several studies indicate changes in the emission patterns of constitutive BVOCs and emission of stress-induced BVOCs following heat, drought and oxidative stress, amongst others. Relating changes in BVOC emissions to the occurrence of one or multiple stressors in natural environmental conditions is not straightforward and only few field studies have dealt with it, especially for agricultural crop and grassland ecosystems. The CROSTVOC project aims to contribute in filling this knowledge gap in three ways. Firstly, it aims at performing long-term BVOC emission field measurements from maize (Zea mays L.) and wheat (Triticum aestivum L.), two important crop species on the global scale, and from grassland. This should lead to a better characterization of (mainly oxygenated) BVOC emissions from these understudied ecosystems, allowing a better representation of those emissions in air quality and atmospheric chemistry and transport models. BVOC fluxes are obtained by the Disjunct Eddy Covariance by mass scanning (DEC-MS) technique, using a hs-PTR-MS instrument for BVOC analysis. Secondly, the eddy covariance BVOC flux measurements (especially at the grassland site) will be accompanied by ozone flux, chlorophyll fluorescence, photosynthesis and soil moisture measurements, amongst others, to allow linking alterations in BVOC emissions to stress episodes. Simultaneously, automated dynamic enclosures will be deployed in order to detect specific abiotic and biotic stress markers by PTR-MS and identify them unambiguously by GC-MS. Thirdly, the field measurements will be accompanied by laboratory BVOC flux measurements in an environmental chamber in order to better disentangle the responses of the BVOC emissions to driving factors that co-occur in field conditions and to determine the influence of single abiotic stressors on BVOC emissions. Next to a general presentation, some preliminary results of the project will be shown.

Drought-responsive WRKY transcription factor genes TaWRKY1 and TaWRKY33 from wheat confer drought and/or heat resistance in Arabidopsis.

PubMed

He, Guan-Hua; Xu, Ji-Yuan; Wang, Yan-Xia; Liu, Jia-Ming; Li, Pan-Song; Chen, Ming; Ma, You-Zhi; Xu, Zhao-Shi

2016-05-23

Drought stress is one of the major causes of crop loss. WRKY transcription factors, as one of the largest transcription factor families, play important roles in regulation of many plant processes, including drought stress response. However, far less information is available on drought-responsive WRKY genes in wheat (Triticum aestivum L.), one of the three staple food crops. Forty eight putative drought-induced WRKY genes were identified from a comparison between de novo transcriptome sequencing data of wheat without or with drought treatment. TaWRKY1 and TaWRKY33 from WRKY Groups III and II, respectively, were selected for further investigation. Subcellular localization assays revealed that TaWRKY1 and TaWRKY33 were localized in the nuclei in wheat mesophyll protoplasts. Various abiotic stress-related cis-acting elements were observed in the promoters of TaWRKY1 and TaWRKY33. Quantitative real-time PCR (qRT-PCR) analysis showed that TaWRKY1 was slightly up-regulated by high-temperature and abscisic acid (ABA), and down-regulated by low-temperature. TaWRKY33 was involved in high responses to high-temperature, low-temperature, ABA and jasmonic acid methylester (MeJA). Overexpression of TaWRKY1 and TaWRKY33 activated several stress-related downstream genes, increased germination rates, and promoted root growth in Arabidopsis under various stresses. TaWRKY33 transgenic Arabidopsis lines showed lower rates of water loss than TaWRKY1 transgenic Arabidopsis lines and wild type plants during dehydration. Most importantly, TaWRKY33 transgenic lines exhibited enhanced tolerance to heat stress. The functional roles highlight the importance of WRKYs in stress response.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.).

PubMed

Shi, Weiping; Cheng, Jingye; Wen, Xiaojie; Wang, Jixiang; Shi, Guanyan; Yao, Jiayan; Hou, Liyuan; Sun, Qian; Xiang, Peng; Yuan, Xiangyang; Dong, Shuqi; Guo, Pingyi; Guo, Jie

2018-01-01

Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet ( Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F 1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.

Is genetically modified crop the answer for the next green revolution?

PubMed

Basu, Saikat Kumar; Dutta, Madhuleema; Goyal, Aakash; Bhowmik, Pankaj Kumar; Kumar, Jitendra; Nandy, Sanjib; Scagliusi, Sandra Mansun; Prasad, Rajib

2010-01-01

Post-green revolution advances made in biotechnology paved the way of cultivating the high-yielding, stress and disease resistant genetically modified (GM) varieties of wheat, rice, maize cotton and several other crops. The recent rapid commercialization of the genetically modified crops in Asia, Americas and Australia indicates the potentiality of this new technology. GM crops give higher yields and are rich in nutritional values containing vitamins and minerals and can thus can help to alleviate hunger and malnutrition of the growing population in the under developed and developing countries. It could also be possible to develop more biotic and abiotic stress resistant genotypes in these crops where it was difficult to develop due to the unavailability of genes of resistance in the crossing germplasms. However, further research and investigations are needed to popularize the cultivation of these crops in different parts of the world. This review provides an insight of the impact of GM crops on contemporary agriculture across the past few decades, traces its' history across time, highlights new achievements and breakthroughs and discusses the future implication of this powerful technology in the coming few decades.

Crop stress and aflatoxin contamination: perspectives and prevention strategies.

USDA-ARS?s Scientific Manuscript database

The fungal metabolites called aflatoxins are potent naturally occurring carcinogens, produced primarily by Aspergillus flavus and A. parasiticus. A. flavus affects many agricultural crops such as maize, cotton, peanuts, and tree nuts. It can contaminate these crops with aflatoxins in the field befor...

Translating knowledge about abiotic stress tolerance to breeding programmes.

PubMed

Gilliham, Matthew; Able, Jason A; Roy, Stuart J

2017-06-01

Plant breeding and improvements in agronomic practice are making a consistent contribution to increasing global crop production year upon year. However, the rate of yield improvement currently lags behind the targets set to produce enough food to meet the demands of the predicted global population in 2050. Furthermore, crops that are exposed to harmful abiotic environmental factors (abiotic stresses, e.g. water limitation, salinity, extreme temperature) are prone to reduced yields. Here, we briefly describe the processes undertaken in conventional breeding programmes, which are usually designed to improve yields in near-optimal conditions rather than specifically breeding for improved crop yield stability under stressed conditions. While there is extensive fundamental research activity that examines mechanisms of plant stress tolerance, there are few examples that apply this research to improving commercial crop yields. There are notable exceptions, and we highlight some of these to demonstrate the magnitude of yield gains that could be made by translating agronomic, phenological and genetic solutions focused on improving or mitigating the effect of abiotic stress in the field; in particular, we focus on improvements in crop water-use efficiency and salinity tolerance. We speculate upon the reasons for the disconnect between research and research translation. We conclude that to realise untapped rapid gains towards food security targets new funding structures need to be embraced. Such funding needs to serve both the core and collaborative activities of the fundamental, pre-breeding and breeding research communities in order to expedite the translation of innovative research into the fields of primary producers. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Progress and challenges for abiotic stress proteomics of crop plants.

PubMed

Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar

2013-06-01

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low altitude remote sensing technologies for crop stress monitoring: a case study on spatial and temporal monitoring of irrigated pinto bean

USDA-ARS?s Scientific Manuscript database

Site-specific crop management is a promising approach to maximize crop yield with optimal use of rapidly depleting natural resources. Availability of high resolution crop data at critical growth stages is a key for real-time data-driven decisions during the production season. The goal of this study ...

Use of thermal infrared and colour infrared imagery to detect crop moisture stress. [Alberta, Canada

NASA Technical Reports Server (NTRS)

Mckenzie, R. C.; Clark, N. F.; Cihlar, J. (Principal Investigator)

1979-01-01

The author has identified the following significant results. In the presence of variable plant cover (primarily percent cover) and variable available water content, the remotely sensed apparent temperatures correlate closely with plant cover and poorly with soil water. To the extent that plant cover is not systematically related to available soil water, available water in the root zone values may not be reliably predicted from the thermal infrared data. On the other hand, if plant cover is uniform and the soil surface is shown in a minor way, the thermal data indicate plant stress and consequently available water in the soil profile.

Identification of ecogeographical gaps in the Spanish Aegilops collections with potential tolerance to drought and salinity

PubMed Central

Parra-Quijano, Mauricio; Iriondo, Jose María

2017-01-01

Drought, one of the most important abiotic stress factors limiting biomass, significantly reduces crop productivity. Salinization also affects the productivity of both irrigated and rain-fed wheat crops. Species of genus Aegilops can be considered crop wild relatives (CWR) of wheat and have been widely used as gene sources in wheat breeding, especially in providing resistance to pests and diseases. Five species (Ae. biuncialis, Ae. geniculata, Ae. neglecta, Ae. triuncialis and Ae. ventricosa) are included in the Spanish National Inventory of CWRs. This study aimed to identify ecogeographic gaps in the Spanish Network on Plant Genetic Resources for Food and Agriculture (PGRFA) with potential tolerance to drought and salinity. Data on the Spanish populations of the target species collected and conserved in genebanks of the Spanish Network on PGRFA and data on other population occurrences in Spain were compiled and assessed for their geo-referencing quality. The records with the best geo-referencing quality values were used to identify the ecogeographical variables that might be important for Aegilops distribution in Spain. These variables were then used to produce ecogeographic land characterization maps for each species, allowing us to identify populations from low and non-represented ecogeographical categories in ex situ collections. Predictive characterization strategy was used to identify 45 Aegilops populations in these ecogeographical gaps with potential tolerance to drought and salinity conditions. Further efforts are being made to collect and evaluate these populations. PMID:28761779

Unravelling chemical priming machinery in plants: the role of reactive oxygen-nitrogen-sulfur species in abiotic stress tolerance enhancement.

PubMed

Antoniou, Chrystalla; Savvides, Andreas; Christou, Anastasis; Fotopoulos, Vasileios

2016-10-01

Abiotic stresses severely limit crop yield and their detrimental effects are aggravated by climate change. Chemical priming is an emerging field in crop stress management. The exogenous application of specific chemical agents before stress events results in tolerance enhancement and reduction of stress impacts on plant physiology and growth. However, the molecular mechanisms underlying the remarkable effects of chemical priming on plant physiology remain to be elucidated. Reactive oxygen, nitrogen and sulfur species (RONSS) are molecules playing a vital role in the stress acclimation of plants. When applied as priming agents, RONSS improve stress tolerance. This review summarizes the recent knowledge on the role of RONSS in cell signalling and gene regulation contributing to abiotic stress tolerance enhancement. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress.

PubMed

Wu, Chunlai; Hu, Wei; Yan, Yan; Tie, Weiwei; Ding, Zehong; Guo, Jianchun; He, Guangyuan

2018-05-17

Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection. Transcriptomic analysis showed the expression profiles of MeLEAs in different tissues of stem, leaves, and storage roots of three accessions. Comparative transcriptomic analysis revealed that the function of MeLEAs in response to drought may be differentiated in different accessions. Compared with the wild subspecies W14, more MeLEA genes were activated in cultivated varieties Arg7 and SC124 after drought treatment. Several MeLEA genes showed induction under various stresses and related signaling treatments. Taken together, this study demonstrates the transcriptional control of MeLEAs in tissue development and the responses to abiotic stress in cassava and identifies candidate genes for improving crop resistance to abiotic stress.

Quantifying the effect of Tmax extreme events on local adaptation to climate change of maize crop in Andalusia for the 21st century

NASA Astrophysics Data System (ADS)

Gabaldon, Clara; Lorite, Ignacio J.; Ines Minguez, M.; Lizaso, Jon; Dosio, Alessandro; Sanchez, Enrique; Ruiz-Ramos, Margarita

2015-04-01

Extreme events of Tmax can threaten maize production on Andalusia (Ruiz-Ramos et al., 2011). The objective of this work is to attempt a quantification of the effects of Tmax extreme events on the previously identified (Gabaldón et al., 2013) local adaptation strategies to climate change of irrigated maize crop in Andalusia for the first half of the 21st century. This study is focused on five Andalusia locations. Local adaptation strategies identified consisted on combinations of changes on sowing dates and choice of cultivar (Gabaldón et al., 2013). Modified cultivar features were the duration of phenological phases and the grain filling rate. The phenological and yield simulations with the adaptative changes were obtained from a modelling chain: current simulated climate and future climate scenarios (2013-2050) were taken from a group of regional climate models at high resolution (25 km) from the European Project ENSEMBLES (http://www.ensembles-eu.org/). After bias correcting these data for temperature and precipitation (Dosio and Paruolo, 2011; Dosio et al., 2012) crop simulations were generated by the CERES-maize model (Jones and Kiniry, 1986) under DSSAT platform, previously calibrated and validated. Quantification of the effects of extreme Tmax on maize yield was computed for different phenological stages following Teixeira et al. (2013). A heat stress index was computed; this index assumes that yield-damage intensity due to heat stress increases linearly from 0.0 at a critical temperature to a maximum of 1.0 at a limit temperature. The decrease of crop yield is then computed by a normalized production damage index which combines attainable yield and heat stress index for each location. Selection of the most suitable adaptation strategy will be reviewed and discussed in light of the quantified effect on crop yield of the projected change of Tmax extreme events. This study will contribute to MACSUR knowledge Hub within the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE - JPI) of EU and is financed by MULCLIVAR project (CGL2012-38923-C02-02) and IFAPA project AGR6126 from Junta de Andalucía, Spain. References Dosio A. and Paruolo P., 2011. Bias correction of the ENSEMBLES high-resolution climate change projections for use by impact models: Evaluation on the present climate. Journal of Geophysical Research, VOL. 116, D16106, doi:10.1029/2011JD015934 Dosio A., Paruolo P. and Rojas R., 2012. Bias correction of the ENSEMBLES high resolution climate change projections for use by impact models: Analysis of the climate change signal. Journal of Geophysical Research, Volume 117, D17, doi: 0.1029/2012JD017968 Gabaldón C, Lorite IJ, Mínguez MI, Dosio A, Sánchez-Sánchez E and Ruiz-Ramos M, 2013. Evaluation of local adaptation strategies to climate change of maize crop in Andalusia for the first half of 21st century. Geophysical Research Abstracts. Vol. 15, EGU2013-13625, 2013. EGU General Assembly 2013, April 2013, Vienna, Austria. Jones C.A. and J.R. Kiniry. 1986. CERES-Maize: A simulation model of maize growth and development. Texas A&M Univ. Press, College Station. Ruiz-Ramos M., E. Sanchez, C. Galllardo, and M.I. Minguez. 2011. Impacts of projected maximum temperature extremes for C21 by an ensemble of regional climate models on cereal cropping systems in the Iberian Peninsula. Natural Hazards and Earth System Science 11: 3275-3291. Teixeira EI, Fischer G, van Velthuizen H, Walter C, Ewert F. Global hotspots of heat stress on agricultural crops due to climate change. Agric For Meteorol. 2013;170(15):206-215.

African Orphan Crops under Abiotic Stresses: Challenges and Opportunities

PubMed Central

2018-01-01

A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as “orphan crops”) including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented. PMID:29623231

HKT transporters mediate salt stress resistance in plants: from structure and function to the field.

PubMed

Hamamoto, Shin; Horie, Tomoaki; Hauser, Felix; Deinlein, Ulrich; Schroeder, Julian I; Uozumi, Nobuyuki

2015-04-01

Plant cells are sensitive to salinity stress and do not require sodium as an essential element for their growth and development. Saline soils reduce crop yields and limit available land. Research shows that HKT transporters provide a potent mechanism for mediating salt tolerance in plants. Knowledge of the molecular ion transport and regulation mechanisms and the control of HKT gene expression are crucial for understanding the mechanisms by which HKT transporters enhance crop performance under salinity stress. This review focuses on HKT transporters in monocot plants and in Arabidopsis as a dicot plant, as a guide to efforts toward improving salt tolerance of plants for increasing the production of crops and bioenergy feedstocks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions

PubMed Central

2013-01-01

Background Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes. Results Two soybean genotypes—drought-tolerant Jindou21 and drought-sensitive Zhongdou33—were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000–33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes— Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000—are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points. Conclusions Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean. PMID:24093224

Proteomic analysis of Metarhizium anisopliae secretion in the presence of the insect pest Callosobruchus maculatus.

PubMed

Murad, André M; Noronha, Eliane F; Miller, Robert N G; Costa, Fabio T; Pereira, Caroline D; Mehta, Angela; Caldas, Ruy A; Franco, Octávio L

2008-12-01

Crop improvement in agriculture generally focuses on yield, seed quality and nutritional characteristics, as opposed to resistance to biotic stresses. Consequently, natural antifeedant toxins are often rare in seed material, with commercial crops being prone to insect pest predation. In the specific case of cowpea (Vigna unguiculata), smallholder cropping is affected by insect pests that reproduce inside the stored seeds. Entomopathogenic organisms can offer an alternative to conventional pesticides for pest control, producing hydrolases that degrade insect exoskeleton. In this study, protein secretions of the ascomycete Metarhizium anisopliae, which conferred bioinsecticidal activity against Callosobruchus maculatus, were characterized via 2D electrophoresis and mass spectrometry. Proteases, reductases and acetyltransferase enzymes were detected. These may be involved in degradation and nutrient uptake from dehydrated C. maculatus. Proteins identified in this work allowed description of metabolic pathways. Their potential applications in biotechnology include both novel compound development and production of genetically modified plants resistant to insect pests.

Significance of Genetic, Environmental, and Pre- and Postharvest Factors Affecting Carotenoid Contents in Crops: A Review.

PubMed

Saini, Ramesh Kumar; Keum, Young-Soo

2018-05-30

Carotenoids are a diverse group of tetraterpenoid pigments that play indispensable roles in plants and animals. The biosynthesis of carotenoids in plants is strictly regulated at the transcriptional and post-transcriptional levels in accordance with inherited genetic signals and developmental requirements and in response to external environmental stimulants. The alteration in the biosynthesis of carotenoids under the influence of external environmental stimulants, such as high light, drought, salinity, and chilling stresses, has been shown to significantly influence the nutritional value of crop plants. In addition to these stimulants, several pre- and postharvesting cultivation practices significantly influence carotenoid compositions and contents. Thus, this review discusses how various environmental stimulants and pre- and postharvesting factors can be positively modulated for the enhanced biosynthesis and accumulation of carotenoids in the edible parts of crop plants, such as the leaves, roots, tubers, flowers, fruit, and seeds. In addition, future research directions in this context are identified.

Genetic and management approaches to boost UK wheat yields by ameliorating water deficits.

PubMed

Dodd, Ian C; Whalley, W R; Ober, Eric S; Parry, M A J

2011-11-01

Faced with the challenge of increasing global food production, there is the need to exploit all approaches to increasing crop yields. A major obstacle to boosting yields of wheat (an important staple in many parts of the world) is the availability and efficient use of water, since there is increasing stress on water resources used for agriculture globally, and also in parts of the UK. Improved soil and crop management and the development of new genotypes may increase wheat yields when water is limiting. Technical and scientific issues concerning management options such as irrigation and the use of growth-promoting rhizobacteria are explored, since these may allow the more efficient use of irrigation. Fundamental understanding of how crops sense and respond to multiple abiotic stresses can help improve the effective use of irrigation water. Experiments are needed to test the hypothesis that modifying wheat root system architecture (by increasing root proliferation deep in the soil profile) will allow greater soil water extraction thereby benefiting productivity and yield stability. Furthermore, better knowledge of plant and soil interactions and how below-ground and above-ground processes communicate within the plant can help identify traits and ultimately genes (or alleles) that will define genotypes that yield better under dry conditions. Developing new genotypes will take time and, therefore, these challenges need to be addressed now.

Toxicity and tolerance of aluminum in plants: tailoring plants to suit to acid soils.

PubMed

Sade, Hemalatha; Meriga, Balaji; Surapu, Varalakshmi; Gadi, Jogeswar; Sunita, M S L; Suravajhala, Prashanth; Kavi Kishor, P B

2016-04-01

Aluminum (Al) stress is one of the serious limiting factors in plant productivity in acidic soils, which constitute about 50 % of the world's potentially arable lands and causes anywhere between 25 and 80 % of yield losses depending upon the species. The mechanism of Al toxicity and tolerance has been examined in plants, which is vital for crop improvement and enhanced food production in the future. Two mechanisms that facilitate Al tolerance in plants are Al exclusion from the roots and the ability to tolerate Al in the symplast or both. Although efforts have been made to unravel Al-resistant factors, many aspects remain unclear. Certain gene families such as MATE, ALMT, ASR, and ABC transporters have been implicated in some plants for resistance to Al which would enhance the opportunities for creating crop plants suitable to grow in acidic soils. Though QTLs have been identified related to Al-tolerance, no crop plant that is tolerant to Al has been evolved so far using breeding or molecular approaches. The remarkable changes that plants experience at the physiological, biochemical and molecular level under Al stress, the vast array of genes involved in Al toxicity-tolerance, the underlying signaling events and the holistic image of the molecular regulation, and the possibility of creating transgenics for Al tolerance are discussed in this review.

Use of thermal and visible imagery for estimating crop water status of irrigated grapevine.

PubMed

Möller, M; Alchanatis, V; Cohen, Y; Meron, M; Tsipris, J; Naor, A; Ostrovsky, V; Sprintsin, M; Cohen, S

2007-01-01

Achieving high quality wine grapes depends on the ability to maintain mild to moderate levels of water stress in the crop during the growing season. This study investigates the use of thermal imaging for monitoring water stress. Experiments were conducted on a wine-grape (Vitis vinifera cv. Merlot) vineyard in northern Israel. Irrigation treatments included mild, moderate, and severe stress. Thermal and visible (RGB) images of the crop were taken on four days at midday with a FLIR thermal imaging system and a digital camera, respectively, both mounted on a truck-crane 15 m above the canopy. Aluminium crosses were used to match visible and thermal images in post-processing and an artificial wet surface was used to estimate the reference wet temperature (T(wet)). Monitored crop parameters included stem water potential (Psi(stem)), leaf conductance (g(L)), and leaf area index (LAI). Meteorological parameters were measured at 2 m height. CWSI was highly correlated with g(L) and moderately correlated with Psi(stem). The CWSI-g(L) relationship was very stable throughout the season, but for that of CWSI-Psi(stem) both intercept and slope varied considerably. The latter presumably reflects the non-direct nature of the physiological relationship between CWSI and Psi(stem). The highest R(2) for the CWSI to g(L) relationship, 0.91 (n=12), was obtained when CWSI was computed using temperatures from the centre of the canopy, T(wet) from the artificial wet surface, and reference dry temperature from air temperature plus 5 degrees C. Using T(wet) calculated from the inverted Penman-Monteith equation and estimated from an artificially wetted part of the canopy also yielded crop water-stress estimates highly correlated with g(L) (R(2)=0.89 and 0.82, respectively), while a crop water-stress index using 'theoretical' reference temperatures computed from climate data showed significant deviations in the late season. Parameter variability and robustness of the different CWSI estimates are discussed. Future research should aim at developing thermal imaging into an irrigation scheduling tool applicable to different crops.

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions1[OPEN

PubMed Central

Sandhu, Nitika; Raman, K. Anitha; Torres, Rolando O.; Audebert, Alain; Dardou, Audrey; Kumar, Arvind; Henry, Amelia

2016-01-01

Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity. PMID:27342311

High Resolution Modelling of Crop Response to Climate Change

NASA Astrophysics Data System (ADS)

Mirmasoudi, S. S.; Byrne, J. M.; MacDonald, R. J.; Lewis, D.

2014-12-01

Crop production is one of the most vulnerable sectors to climatic variability and change. Increasing atmospheric CO2 concentration and other greenhouse gases are causing increases in global temperature. In western North America, water supply is largely derived from mountain snowmelt. Climate change will have a significant impact on mountain snowpack and subsequently, the snow-derived water supply. This will strain water supplies and increase water demand in areas with substantial irrigation agriculture. Increasing temperatures may create heat stress for some crops regardless of soil water supply, and increasing surface O3 and other pollutants may damage crops and ecosystems. CO2 fertilization may or may not be an advantage in future. This work is part of a larger study that will address a series of questions based on a range of future climate scenarios for several watersheds in western North America. The key questions are: (1) how will snowmelt and rainfall runoff vary in future; (2) how will seasonal and inter-annual soil water supply vary, and how might that impacts food supplies; (3) how might heat stress impact (some) crops even with adequate soil water; (4) will CO2 fertilization alter crop yields; and (5) will pollution loads, particularly O3, cause meaningful changes to crop yields? The Generate Earth Systems Science (GENESYS) Spatial Hydrometeorological Model is an innovative, efficient, high-resolution model designed to assess climate driven changes in mountain snowpack derived water supplies. We will link GENESYS to the CROPWAT crop model system to assess climate driven changes in water requirement and associated crop productivity for a range of future climate scenarios. Literature bases studies will be utilised to develop approximate crop response functions for heat stress, CO2 fertilization and for O3 damages. The overall objective is to create modeling systems that allows meaningful assessment of agricultural productivity at a watershed scale under a range of climate scenarios.

An energy balance approach for mapping crop waterstress and yield impacts over the Czech Republic

USDA-ARS?s Scientific Manuscript database

There is a growing demand for timely, spatially distributed information regarding crop condition and water use to inform agricultural decision making and yield forecasting efforts. Remote sensing of land-surface temperature has proven valuable for mapping evapotranspiration (ET) and crop stress from...

A low-cost microcontroller-based system to monitor crop temperature and water status

USDA-ARS?s Scientific Manuscript database

A prototype microcontroller-based system was developed to automate the measurement and recording of soil-moisture status and canopy-, air-, and soil-temperature levels in cropped fields. Measurements of these conditions within the cropping system are often used to assess plant stress, and can assis...

Assessing FAO-56 dual crop coefficients using eddy covariance flux partitioning

USDA-ARS?s Scientific Manuscript database

Current approaches to scheduling crop irrigation using reference evapotranspiration (ET0) recommend using a dual-coefficient approach using basal (Kcb) and soil (Ke) coefficients along with a stress coefficient (Ks) to model crop evapotranspiration (ETc), [e.g. ETc=(Ks*Kcb+Ke)*ET0]. However, determi...

Soil water improvements with the long-term use of a winter rye cover crop

USDA-ARS?s Scientific Manuscript database

The Midwestern United States is projected to experience increasing rainfall variability. One approach to mitigate climate impacts is to utilize crop and soil management practices that enhance soil water storage, reducing the risks of flooding as well as drought-induced crop water stress. While some ...

Tuber and inulin production of Jerusalem artichoke (Helianthus tuberosus, L.) under salinity stress

USDA-ARS?s Scientific Manuscript database

Salinization of soils and irrigation waters has increased soil salinity worldwide, and threaten to reduce crop yield. In the semiarid regions, fresh water scarcity demands salt- and drought-tolerant crops. Jerusalem artichoke (cv. Stampede), a North American crop with inulin-rich tubers, is a carb...

Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics.

PubMed

Sanchez, Diego H; Pieckenstain, Fernando L; Szymanski, Jedrzey; Erban, Alexander; Bromke, Mariusz; Hannah, Matthew A; Kraemer, Ute; Kopka, Joachim; Udvardi, Michael K

2011-02-14

One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl(-) correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, 'triangulation' from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species.

Metabolite profiling of barley flag leaves under drought and combined heat and drought stress reveals metabolic QTLs for metabolites associated with antioxidant defense

PubMed Central

Templer, Sven Eduard; Ammon, Alexandra; Pscheidt, David; Ciobotea, Otilia; Schuy, Christian; McCollum, Christopher; Sonnewald, Uwe; Hanemann, Anja; Förster, Jutta; Ordon, Frank; von Korff, Maria

2017-01-01

Abstract Barley (Hordeum vulgare L.) is among the most stress-tolerant crops; however, not much is known about the genetic and environmental control of metabolic adaptation of barley to abiotic stresses. We have subjected a genetically diverse set of 81 barley accessions, consisting of Mediterranean landrace genotypes and German elite breeding lines, to drought and combined heat and drought stress at anthesis. Our aim was to (i) investigate potential differences in morphological, physiological, and metabolic adaptation to the two stress scenarios between the Mediterranean and German barley genotypes and (ii) identify metabolic quantitative trait loci (mQTLs). To this end, we have genotyped the investigated barley lines with an Illumina iSelect 9K array and analyzed a set of 57 metabolites from the primary C and N as well as antioxidant metabolism in flag leaves under control and stress conditions. We found that drought-adapted genotypes attenuate leaf carbon metabolism much more strongly than elite lines during drought stress adaptation. Furthermore, we identified mQTLs for flag leaf γ-tocopherol, glutathione, and succinate content by association genetics that co-localize with genes encoding enzymes of the pathways producing these antioxidant metabolites. Our results provide the molecular basis for breeding barley cultivars with improved abiotic stress tolerance. PMID:28338908

Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

DOE PAGES

Valdés-López, Oswaldo; Batek, Josef; Gomez-Hernandez, Nicolas; ...

2016-04-25

Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. Here in this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identifiedmore » 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. In conclusion, the data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.« less

Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress

PubMed Central

Prasad, Kasavajhala V. S. K.; Abdel-Hameed, Amira A. E.; Xing, Denghui; Reddy, Anireddy S. N.

2016-01-01

Abiotic and biotic stresses cause significant yield losses in all crops. Acquisition of stress tolerance in plants requires rapid reprogramming of gene expression. SR1/CAMTA3, a member of signal responsive transcription factors (TFs), functions both as a positive and a negative regulator of biotic stress responses and as a positive regulator of cold stress-induced gene expression. Using high throughput RNA-seq, we identified ~3000 SR1-regulated genes. Promoters of about 60% of the differentially expressed genes have a known DNA binding site for SR1, suggesting that they are likely direct targets. Gene ontology analysis of SR1-regulated genes confirmed previously known functions of SR1 and uncovered a potential role for this TF in salt stress. Our results showed that SR1 mutant is more tolerant to salt stress than the wild type and complemented line. Improved tolerance of sr1 seedlings to salt is accompanied with the induction of salt-responsive genes. Furthermore, ChIP-PCR results showed that SR1 binds to promoters of several salt-responsive genes. These results suggest that SR1 acts as a negative regulator of salt tolerance by directly repressing the expression of salt-responsive genes. Overall, this study identified SR1-regulated genes globally and uncovered a previously uncharacterized role for SR1 in salt stress response. PMID:27251464

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

PubMed Central

Penmetsa, R. V.; Dutta, S.; Kulwal, P. L.; Saxena, R. K.; Datta, S.; Sharma, T. R.; Rosen, B.; Carrasquilla-Garcia, N.; Farmer, A. D.; Dubey, A.; Saxena, K. B.; Gao, J.; Fakrudin, B.; Singh, M. N.; Singh, B. P.; Wanjari, K. B.; Yuan, M.; Srivastava, R. K.; Kilian, A.; Upadhyaya, H. D.; Mallikarjuna, N.; Town, C. D.; Bruening, G. E.; He, G.; May, G. D.; McCombie, R.; Jackson, S. A.; Singh, N. K.; Cook, D. R.

2009-01-01

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop’ to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine. PMID:20976284

Effects, tolerance mechanisms and management of salt stress in grain legumes.

PubMed

Farooq, Muhammad; Gogoi, Nirmali; Hussain, Mubshar; Barthakur, Sharmistha; Paul, Sreyashi; Bharadwaj, Nandita; Migdadi, Hussein M; Alghamdi, Salem S; Siddique, Kadambot H M

2017-09-01

Salt stress is an ever-present threat to crop yields, especially in countries with irrigated agriculture. Efforts to improve salt tolerance in crop plants are vital for sustainable crop production on marginal lands to ensure future food supplies. Grain legumes are a fascinating group of plants due to their high grain protein contents and ability to fix biological nitrogen. However, the accumulation of excessive salts in soil and the use of saline groundwater are threatening legume production worldwide. Salt stress disturbs photosynthesis and hormonal regulation and causes nutritional imbalance, specific ion toxicity and osmotic effects in legumes to reduce grain yield and quality. Understanding the responses of grain legumes to salt stress and the associated tolerance mechanisms, as well as assessing management options, may help in the development of strategies to improve the performance of grain legumes under salt stress. In this manuscript, we discuss the effects, tolerance mechanisms and management of salt stress in grain legumes. The principal inferences of the review are: (i) salt stress reduces seed germination (by up to more than 50%) either by inhibiting water uptake and/or the toxic effect of ions in the embryo, (ii) salt stress reduces growth (by more than 70%), mineral uptake, and yield (by 12-100%) due to ion toxicity and reduced photosynthesis, (iii) apoplastic acidification is a good indicator of salt stress tolerance, (iv) tolerance to salt stress in grain legumes may develop through excretion and/or compartmentalization of toxic ions, increased antioxidant capacity, accumulation of compatible osmolytes, and/or hormonal regulation, (v) seed priming and nutrient management may improve salt tolerance in grain legumes, (vi) plant growth promoting rhizobacteria and arbuscular mycorrhizal fungi may help to improve salt tolerance due to better plant nutrient availability, and (vii) the integration of screening, innovative breeding, and the development of transgenics and crop management strategies may enhance salt tolerance and yield in grain legumes on salt-affected soils. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Interspecies and Intraspecies Analysis of Trehalose Contents and the Biosynthesis Pathway Gene Family Reveals Crucial Roles of Trehalose in Osmotic-Stress Tolerance in Cassava

PubMed Central

Han, Bingying; Fu, Lili; Zhang, Dan; He, Xiuquan; Chen, Qiang; Peng, Ming; Zhang, Jiaming

2016-01-01

Trehalose is a nonreducing α,α-1,1-disaccharide in a wide range of organisms, and has diverse biological functions that range from serving as an energy source to acting as a protective/signal sugar. However, significant amounts of trehalose have rarely been detected in higher plants, and the function of trehalose in the drought-tolerant crop cassava (Manihot esculenta Crantz) is unclear. We measured soluble sugar concentrations of nine plant species with differing levels of drought tolerance and 41 cassava varieties using high-performance liquid chromatography with evaporative light-scattering detector (HPLC-ELSD). Significantly high amounts of trehalose were identified in drought-tolerant crops cassava, Jatropha curcas, and castor bean (Ricinus communis). All cassava varieties tested contained high amounts of trehalose, although their concentrations varied from 0.23 to 1.29 mg·g−1 fresh weight (FW), and the trehalose level was highly correlated with dehydration stress tolerance of detached leaves of the varieties. Moreover, the trehalose concentrations in cassava leaves increased 2.3–5.5 folds in response to osmotic stress simulated by 20% PEG 6000. Through database mining, 24 trehalose pathway genes, including 12 trehalose-6-phosphate synthases (TPS), 10 trehalose-6-phosphate phosphatases (TPP), and two trehalases were identified in cassava. Phylogenetic analysis indicated that there were four cassava TPS genes (MeTPS1–4) that were orthologous to the solely active TPS gene (AtTPS1 and OsTPS1) in Arabidopsis and rice, and a new TPP subfamily was identified in cassava, suggesting that the trehalose biosynthesis activities in cassava had potentially been enhanced in evolutionary history. RNA-seq analysis indicated that MeTPS1 was expressed at constitutionally high level before and after osmotic stress, while other trehalose pathway genes were either up-regulated or down-regulated, which may explain why cassava accumulated high level of trehalose under normal conditions. MeTPS1 was then transformed into tobacco (Nicotiana benthamiana). Results indicated that transgenic tobacco lines accumulated significant level of trehalose and possessed improved drought stress tolerance. In conclusion, cassava accumulated significantly high amount of trehalose under normal conditions due to multiplied trehalose biosynthesis gene families and constant expression of the active MeTPS1 gene. High levels of trehalose subsequently contributed to high drought stress tolerance. PMID:27420056

Supporting Climatic Trends of Corn and Soybean Production in the USA

NASA Astrophysics Data System (ADS)

Mishra, V.; Cherkauer, K. A.; Verdin, J. P.

2010-12-01

The United States of America (USA) is a major source of corn and soybeans, producing about 39 percent of the world’s corn and 50 percent of world’s soybean supply. The north central states, including parts of the Midwestern US and the Great Plains form what is commonly described as the “Corn Belt” and consist of the most productive grain growing region in the United States. Changes in climate, including precipitation and temperature, are being observed throughout the world, and the Corn Belt region of the US is not immune posing a potential threat to global food security. We conducted a retrospective analysis of observed climate variables and crop production statistics to evaluate if observed climatic trends are having a positive or negative effect on corn and soybean production in the US. We selected climate indices based on gridded daily precipitation, maximum and minimum air temperature data from the National Climatic Data Center (NCDC) for the period of 1920-2009 and for 13 states in the Corn Belt region. We used the standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI) for different periods overlapping the important seasons for crop growths, such as the planting (April-May), grain-filling (June-August), and harvesting (September -October) seasons. We estimated the seasonal average of maximum and minimum daily temperatures to identify the historic trends and variability in air temperature during the key crop-growth seasons. Extreme warm temperatures can affect crop growth and yields adversely; therefore, cumulative maximum air temperature above the 90th percentiles (e.g. Cumulative Heat Index) was estimated for each growing period. We evaluated historic trends and variability of areal extents of severe or extreme droughts along with the areal extents facing the high cumulative heat stress. Our results showed that climatic extremes (e.g. droughts and heat stress) that occurred during the period of June - August (JJA), affected the yields of corn and soybeans most severely. High moisture and low heat stress during the JJA period favored crop yields, while low moisture and high heat conditions during the planting season (April-May) increased yields. Results also indicated that this part of the US is trending towards lower heat stress and drought extents, and higher moisture conditions during the JJA period. Therefore, in future, if the present trends persist, we expect the climate will more supportive of increased corn and soybean yields.

Plant responses to environmental stresses-from gene to biotechnology.

PubMed

Ahanger, Mohammad Abass; Akram, Nudrat Aisha; Ashraf, Muhammad; Alyemeni, Mohammed Nasser; Wijaya, Leonard; Ahmad, Parvaiz

2017-07-01

Increasing global population, urbanization and industrialization are increasing the rate of conversion of arable land into wasteland. Supplying food to an ever-increasing population is one of the biggest challenges that agriculturalists and plant scientists are currently confronting. Environmental stresses make this situation even graver. Despite the induction of several tolerance mechanisms, sensitive plants often fail to survive under environmental extremes. New technological approaches are imperative. Conventional breeding methods have a limited potential to improve plant genomes against environmental stress. Recently, genetic engineering has contributed enormously to the development of genetically modified varieties of different crops such as cotton, maize, rice, canola and soybean. The identification of stress-responsive genes and their subsequent introgression or overexpression within sensitive crop species are now being widely carried out by plant scientists. Engineering of important tolerance pathways, like antioxidant enzymes, osmolyte accumulation, membrane-localized transporters for efficient compartmentation of deleterious ions and accumulation of essential elements and resistance against pests or pathogens is also an area that has been intensively researched. In this review, the role of biotechnology and its successes, prospects and challenges in developing stress-tolerant crop cultivars are discussed.

Alfalfa Cellulose Synthase Gene Expression under Abiotic Stress: A Hitchhiker’s Guide to RT-qPCR Normalization

PubMed Central

Guerriero, Gea; Legay, Sylvain; Hausman, Jean-Francois

2014-01-01

Abiotic stress represents a serious threat affecting both plant fitness and productivity. One of the promptest responses that plants trigger following abiotic stress is the differential expression of key genes, which enable to face the adverse conditions. It is accepted and shown that the cell wall senses and broadcasts the stress signal to the interior of the cell, by triggering a cascade of reactions leading to resistance. Therefore the study of wall-related genes is particularly relevant to understand the metabolic remodeling triggered by plants in response to exogenous stresses. Despite the agricultural and economical relevance of alfalfa (Medicago sativa L.), no study, to our knowledge, has addressed specifically the wall-related gene expression changes in response to exogenous stresses in this important crop, by monitoring the dynamics of wall biosynthetic gene expression. We here identify and analyze the expression profiles of nine cellulose synthases, together with other wall-related genes, in stems of alfalfa plants subjected to different abiotic stresses (cold, heat, salt stress) at various time points (e.g. 0, 24, 72 and 96 h). We identify 2 main responses for specific groups of genes, i.e. a salt/heat-induced and a cold/heat-repressed group of genes. Prior to this analysis we identified appropriate reference genes for expression analyses in alfalfa, by evaluating the stability of 10 candidates across different tissues (namely leaves, stems, roots), under the different abiotic stresses and time points chosen. The results obtained confirm an active role played by the cell wall in response to exogenous stimuli and constitute a step forward in delineating the complex pathways regulating the response of plants to abiotic stresses. PMID:25084115

Deriving the Characteristic Scale for Effectively Monitoring Heavy Metal Stress in Rice by Assimilation of GF-1 Data with the WOFOST Model

PubMed Central

Huang, Zhi; Liu, Xiangnan; Jin, Ming; Ding, Chao; Jiang, Jiale; Wu, Ling

2016-01-01

Accurate monitoring of heavy metal stress in crops is of great importance to assure agricultural productivity and food security, and remote sensing is an effective tool to address this problem. However, given that Earth observation instruments provide data at multiple scales, the choice of scale for use in such monitoring is challenging. This study focused on identifying the characteristic scale for effectively monitoring heavy metal stress in rice using the dry weight of roots (WRT) as the representative characteristic, which was obtained by assimilation of GF-1 data with the World Food Studies (WOFOST) model. We explored and quantified the effect of the important state variable LAI (leaf area index) at various spatial scales on the simulated rice WRT to find the critical scale for heavy metal stress monitoring using the statistical characteristics. Furthermore, a ratio analysis based on the varied heavy metal stress levels was conducted to identify the characteristic scale. Results indicated that the critical threshold for investigating the rice WRT in monitoring studies of heavy metal stress was larger than 64 m but smaller than 256 m. This finding represents a useful guideline for choosing the most appropriate imagery. PMID:26959033

Increasing Crop Yields in Water Stressed Countries by Combining Operations of Freshwater Reservoir and Wastewater Reclamation Plant

NASA Astrophysics Data System (ADS)

Bhushan, R.; Ng, T. L.

2015-12-01

Freshwater resources around the world are increasing in scarcity due to population growth, industrialization and climate change. This is a serious concern for water stressed countries, including those in Asia and North Africa where future food production is expected to be negatively affected by this. To address this problem, we investigate the potential of combining freshwater reservoir and wastewater reclamation operations. Reservoir water is the cheaper source of irrigation, but is often limited and climate sensitive. Treated wastewater is a more reliable alternative for irrigation, but often requires extensive further treatment which can be expensive. We propose combining the operations of a reservoir and a wastewater reclamation plant (WWRP) to augment the supply from the reservoir with reclaimed water for increasing crop yields in water stressed regions. The joint system of reservoir and WWRP is modeled as a multi-objective optimization problem with the double objective of maximizing the crop yield and minimizing total cost, subject to constraints on reservoir storage, spill and release, and capacity of the WWRP. We use the crop growth model Aquacrop, supported by The Food and Agriculture Organization of the United Nations (FAO), to model crop growth in response to water use. Aquacrop considers the effects of water deficit on crop growth stages, and from there estimates crop yield. We generate results comparing total crop yield under irrigation with water from just the reservoir (which is limited and often interrupted), and yield with water from the joint system (which has the potential of higher supply and greater reliability). We will present results for locations in India and Africa to evaluate the potential of the joint operations for improving food security in those areas for different budgets.

Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk

PubMed Central

Kissoudis, Christos; van de Wiel, Clemens; Visser, Richard G. F.; van der Linden, Gerard

2014-01-01

Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops. PMID:24904607

Some Like It Hot, Some Like It Warm: Phenotyping to Explore Thermotolerance Diversity

PubMed Central

Yeh, Ching-Hui; Kaplinsky, Nicholas J.; Hu, Catherine; Charng, Yee-yung

2012-01-01

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This thermotolerance diversity’ means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables differentiate thermotolerance assays: 1) the heat stress regime used, 2) the developmental stage of the plants being studied, and 3) the actual phenotype which is scored. Consideration of these variables will be essential for deepening our understanding of the molecular genetics of plant thermotolerance. PMID:22920995

Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress

PubMed Central

Ambavaram, Madana M. R.; Basu, Supratim; Krishnan, Arjun; Ramegowda, Venkategowda; Batlang, Utlwang; Rahman, Lutfor; Baisakh, Niranjan; Pereira, Andy

2014-01-01

Plants capture solar energy and atmospheric carbon dioxide (CO2) through photosynthesis, which is the primary component of crop yield, and needs to be increased considerably to meet the growing global demand for food. Environmental stresses, which are increasing with climate change, adversely affect photosynthetic carbon metabolism (PCM) and limit yield of cereals such as rice (Oryza sativa) that feeds half the world. To study the regulation of photosynthesis, we developed a rice gene regulatory network and identified a transcription factor HYR (HIGHER YIELD RICE) associated with PCM, which on expression in rice enhances photosynthesis under multiple environmental conditions, determining a morpho-physiological programme leading to higher grain yield under normal, drought and high-temperature stress conditions. We show HYR is a master regulator, directly activating photosynthesis genes, cascades of transcription factors and other downstream genes involved in PCM and yield stability under drought and high-temperature environmental stress conditions. PMID:25358745

Label-free Proteomic Reveals that Cowpea Severe Mosaic Virus Transiently Suppresses the Host Leaf Protein Accumulation During the Compatible Interaction with Cowpea (Vigna unguiculata [L.] Walp.).

PubMed

Paiva, Ana L S; Oliveira, Jose T A; de Souza, Gustavo A; Vasconcelos, Ilka M

2016-12-02

Viruses are important plant pathogens that threaten diverse crops worldwide. Diseases caused by Cowpea severe mosaic virus (CPSMV) have drawn attention because of the serious damages they cause to economically important crops including cowpea. This work was undertaken to quantify and identify the responsive proteins of a susceptible cowpea genotype infected with CPSMV, in comparison with mock-inoculated controls, using label-free quantitative proteomics and databanks, aiming at providing insights on the molecular basis of this compatible interaction. Cowpea leaves were mock- or CPSMV-inoculated and 2 and 6 days later proteins were extracted and analyzed. More than 3000 proteins were identified (data available via ProteomeXchange, identifier PXD005025) and 75 and 55 of them differentially accumulated in response to CPSMV, at 2 and 6 DAI, respectively. At 2 DAI, 76% of the proteins decreased in amount and 24% increased. However, at 6 DAI, 100% of the identified proteins increased. Thus, CPSMV transiently suppresses the synthesis of proteins involved particularly in the redox homeostasis, protein synthesis, defense, stress, RNA/DNA metabolism, signaling, and other functions, allowing viral invasion and spread in cowpea tissues.

[Transgenic rice breeding for abiotic stress tolerance--present and future].

PubMed

Zhao, Feng-Yun; Zhang, Hui

2007-01-01

Environmental stresses and the continuing deterioration of arable land, along with an explosive increase in world population, pose serious threats to global agricultural production and food security. Improving the tolerance of the major crop plants to abiotic stresses has been a main goal in agriculture for a long time. As rice is considered one of the major crops, the development of new cultivars with enhanced abiotic stress-tolerance will undoubtedly have an important effect on global food production. The transgenic approach offers an attractive alternative to conventional techniques for the genetic improvement of rice cultivars. In recent years, an array of stress-related genes has already been transferred to rice to improve its resistance against abiotic stresses. Many transgenic rice plants with enhanced abiotic stress-tolerance have been obtained. This article focuses on the progress in the study of abiotic stress tolerance in transgenic rice breeding.

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

PubMed Central

Gehan, Malia A; Mockler, Todd C; Weinig, Cynthia; Ewers, Brent E

2017-01-01

The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought. PMID:28826479

Leaf proteome alterations in the context of physiological and morphological responses to drought and heat stress in barley (Hordeum vulgare L.)

PubMed Central

von Korff, M.

2013-01-01

The objective of this study was to identify barley leaf proteins differentially regulated in response to drought and heat and the combined stresses in context of the morphological and physiological changes that also occur. The Syrian landrace Arta and the Australian cultivar Keel were subjected to drought, high temperature, or a combination of both treatments starting at heading. Changes in the leaf proteome were identified using differential gel electrophoresis and mass spectrometry. The drought treatment caused strong reductions of biomass and yield, while photosynthetic performance and the proteome were not significantly changed. In contrast, the heat treatment and the combination of heat and drought reduced photosynthetic performance and caused changes of the leaf proteome. The proteomic analysis identified 99 protein spots differentially regulated in response to heat treatment, 14 of which were regulated in a genotype-specific manner. Differentially regulated proteins predominantly had functions in photosynthesis, but also in detoxification, energy metabolism, and protein biosynthesis. The analysis indicated that de novo protein biosynthesis, protein quality control mediated by chaperones and proteases, and the use of alternative energy resources, i.e. glycolysis, play important roles in adaptation to heat stress. In addition, genetic variation identified in the proteome, in plant growth and photosynthetic performance in response to drought and heat represent stress adaption mechanisms to be exploited in future crop breeding efforts. PMID:23918963

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.

PubMed

Bhawna; Bonthala, V S; Gajula, Mnv Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely.Database URL: http://www.multiomics.in/PvTFDB/. © The Author(s) 2016. Published by Oxford University Press.

Expression of Arabidopsis glycine-rich RNA-binding protein AtGRP2 or AtGRP7 improves grain yield of rice (Oryza sativa) under drought stress conditions.

PubMed

Yang, Deok Hee; Kwak, Kyung Jin; Kim, Min Kyung; Park, Su Jung; Yang, Kwang-Yeol; Kang, Hunseung

2014-01-01

Although posttranscriptional regulation of RNA metabolism is increasingly recognized as a key regulatory process in plant response to environmental stresses, reports demonstrating the importance of RNA metabolism control in crop improvement under adverse environmental stresses are severely limited. To investigate the potential use of RNA-binding proteins (RBPs) in developing stress-tolerant transgenic crops, we generated transgenic rice plants (Oryza sativa) that express Arabidopsis thaliana glycine-rich RBP (AtGRP) 2 or 7, which have been determined to harbor RNA chaperone activity and confer stress tolerance in Arabidopsis, and analyzed the response of the transgenic rice plants to abiotic stresses. AtGRP2- or AtGRP7-expressing transgenic rice plants displayed similar phenotypes comparable with the wild-type plants under high salt or cold stress conditions. By contrast, AtGRP2- or AtGRP7-expressing transgenic rice plants showed much higher recovery rates and grain yields compared with the wild-type plants under drought stress conditions. The higher grain yield of the transgenic rice plants was due to the increases in filled grain numbers per panicle. Collectively, the present results show the importance of posttranscriptional regulation of RNA metabolism in plant response to environmental stress and suggest that GRPs can be utilized to improve the yield potential of crops under stress conditions. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Hormone balance and abiotic stress tolerance in crop plants.

PubMed

Peleg, Zvi; Blumwald, Eduardo

2011-06-01

Plant hormones play central roles in the ability of plants to adapt to changing environments, by mediating growth, development, nutrient allocation, and source/sink transitions. Although ABA is the most studied stress-responsive hormone, the role of cytokinins, brassinosteroids, and auxins during environmental stress is emerging. Recent evidence indicated that plant hormones are involved in multiple processes. Cross-talk between the different plant hormones results in synergetic or antagonic interactions that play crucial roles in response of plants to abiotic stress. The characterization of the molecular mechanisms regulating hormone synthesis, signaling, and action are facilitating the modification of hormone biosynthetic pathways for the generation of transgenic crop plants with enhanced abiotic stress tolerance. Copyright © 2011 Elsevier Ltd. All rights reserved.

Agricultural production and water use scenarios in Cyprus under global change

NASA Astrophysics Data System (ADS)

Bruggeman, Adriana; Zoumides, Christos; Camera, Corrado; Pashiardis, Stelios; Zomeni, Zomenia

2014-05-01

In many countries of the world, food demand exceeds the total agricultural production. In semi-arid countries, agricultural water demand often also exceeds the sustainable supply of water resources. These water-stressed countries are expected to become even drier, as a result of global climate change. This will have a significant impact on the future of the agricultural sector and on food security. The aim of the AGWATER project consortium is to provide recommendations for climate change adaptation for the agricultural sector in Cyprus and the wider Mediterranean region. Gridded climate data sets, with 1-km horizontal resolution were prepared for Cyprus for 1980-2010. Regional Climate Model results were statistically downscaled, with the help of spatial weather generators. A new soil map was prepared using a predictive modelling and mapping technique and a large spatial database with soil and environmental parameters. Stakeholder meetings with agriculture and water stakeholders were held to develop future water prices, based on energy scenarios and to identify climate resilient production systems. Green houses, including also hydroponic systems, grapes, potatoes, cactus pears and carob trees were the more frequently identified production systems. The green-blue-water model, based on the FAO-56 dual crop coefficient approach, has been set up to compute agricultural water demand and yields for all crop fields in Cyprus under selected future scenarios. A set of agricultural production and water use performance indicators are computed by the model, including green and blue water use, crop yield, crop water productivity, net value of crop production and economic water productivity. This work is part of the AGWATER project - AEIFORIA/GEOGRO/0311(BIE)/06 - co-financed by the European Regional Development Fund and the Republic of Cyprus through the Research Promotion Foundation.

Sustainable Agriculture - Enhancing environmental benefits, food nutritional quality and building crop resilience to abiotic and biotic stresses

USDA-ARS?s Scientific Manuscript database

Feeding nutrition-dense food to future world populations presents agriculture with enormous challenges as estimates indicate that crop production must as much as double. Crop production cannot be increased to meet this challenge simply by increasing land acreage or using past agricultural intensific...

Satellite-based mapping of field-scale stress indicators for crop yield forecasting: an application over Mead, NE

USDA-ARS?s Scientific Manuscript database

In global agricultural regions, water is one of the most widely limiting factors of crop performance and production. Evapotranspiration (ET) describes crop water use through transpiration and water lost through direct soil evaporation, which makes it a good indicator of soil moisture availability an...

Continental-Scale Evaluation of Assimilated Soil Moisture Retrievals From the Advanced Microwave Scanning Radiometer

USDA-ARS?s Scientific Manuscript database

Soil moisture is a fundamental data source used in crop growth stage and crop stress models developed by the USDA Foreign Agriculture Service for global crop estimation. USDA’s International Production Assessment Division (IPAD) of the Office of Global Analysis (OGA). Currently, the PECAD DSS utiliz...

Understanding the weather signal in national crop-yield variability

NASA Astrophysics Data System (ADS)

Frieler, Katja; Schauberger, Bernhard; Arneth, Almut; Balkovič, Juraj; Chryssanthacopoulos, James; Deryng, Delphine; Elliott, Joshua; Folberth, Christian; Khabarov, Nikolay; Müller, Christoph; Olin, Stefan; Pugh, Thomas A. M.; Schaphoff, Sibyll; Schewe, Jacob; Schmid, Erwin; Warszawski, Lila; Levermann, Anders

2017-06-01

Year-to-year variations in crop yields can have major impacts on the livelihoods of subsistence farmers and may trigger significant global price fluctuations, with severe consequences for people in developing countries. Fluctuations can be induced by weather conditions, management decisions, weeds, diseases, and pests. Although an explicit quantification and deeper understanding of weather-induced crop-yield variability is essential for adaptation strategies, so far it has only been addressed by empirical models. Here, we provide conservative estimates of the fraction of reported national yield variabilities that can be attributed to weather by state-of-the-art, process-based crop model simulations. We find that observed weather variations can explain more than 50% of the variability in wheat yields in Australia, Canada, Spain, Hungary, and Romania. For maize, weather sensitivities exceed 50% in seven countries, including the United States. The explained variance exceeds 50% for rice in Japan and South Korea and for soy in Argentina. Avoiding water stress by simulating yields assuming full irrigation shows that water limitation is a major driver of the observed variations in most of these countries. Identifying the mechanisms leading to crop-yield fluctuations is not only fundamental for dampening fluctuations, but is also important in the context of the debate on the attribution of loss and damage to climate change. Since process-based crop models not only account for weather influences on crop yields, but also provide options to represent human-management measures, they could become essential tools for differentiating these drivers, and for exploring options to reduce future yield fluctuations.

Rice Phospholipase A Superfamily: Organization, Phylogenetic and Expression Analysis during Abiotic Stresses and Development

PubMed Central

Singh, Amarjeet; Baranwal, Vinay; Shankar, Alka; Kanwar, Poonam; Ranjan, Rajeev; Yadav, Sandeep; Pandey, Amita; Kapoor, Sanjay; Pandey, Girdhar K.

2012-01-01

Background Phospholipase A (PLA) is an important group of enzymes responsible for phospholipid hydrolysis in lipid signaling. PLAs have been implicated in abiotic stress signaling and developmental events in various plants species. Genome-wide analysis of PLA superfamily has been carried out in dicot plant Arabidopsis. A comprehensive genome-wide analysis of PLAs has not been presented yet in crop plant rice. Methodology/Principal Findings A comprehensive bioinformatics analysis identified a total of 31 PLA encoding genes in the rice genome, which are divided into three classes; phospholipase A1 (PLA1), patatin like phospholipases (pPLA) and low molecular weight secretory phospholipase A2 (sPLA2) based on their sequences and phylogeny. A subset of 10 rice PLAs exhibited chromosomal duplication, emphasizing the role of duplication in the expansion of this gene family in rice. Microarray expression profiling revealed a number of PLA members expressing differentially and significantly under abiotic stresses and reproductive development. Comparative expression analysis with Arabidopsis PLAs revealed a high degree of functional conservation between the orthologs in two plant species, which also indicated the vital role of PLAs in stress signaling and plant development across different plant species. Moreover, sub-cellular localization of a few candidates suggests their differential localization and functional role in the lipid signaling. Conclusion/Significance The comprehensive analysis and expression profiling would provide a critical platform for the functional characterization of the candidate PLA genes in crop plants. PMID:22363522

Biotechnological advancement in genetic improvement of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, Dinesh Kumar

2016-07-01

With the advent of molecular biotechnology, plant genetic engineering techniques have opened an avenue for the genetic improvement of important vegetable crops. Vegetable crop productivity and quality are seriously affected by various biotic and abiotic stresses which destabilize rural economies in many countries. Moreover, absence of proper post-harvest storage and processing facilities leads to qualitative and quantitative losses. In the past four decades, conventional breeding has significantly contributed to the improvement of vegetable yields, quality, post-harvest life, and resistance to biotic and abiotic stresses. However, there are many constraints in conventional breeding, which can only be overcome by advancements made in modern biology. Broccoli (Brassica oleracea L. var. italica) is an important vegetable crop, of the family Brassicaceae; however, various biotic and abiotic stresses cause enormous crop yield losses during the commercial cultivation of broccoli. Thus, genetic engineering can be used as a tool to add specific characteristics to existing cultivars. However, a pre-requisite for transferring genes into plants is the availability of efficient regeneration and transformation techniques. Recent advances in plant genetic engineering provide an opportunity to improve broccoli in many aspects. The goal of this review is to summarize genetic transformation studies on broccoli to draw the attention of researchers and scientists for its further genetic advancement.

Proteomic Analysis of Pigeonpea (Cajanus cajan) Seeds Reveals the Accumulation of Numerous Stress-Related Proteins.

PubMed

Krishnan, Hari B; Natarajan, Savithiry S; Oehrle, Nathan W; Garrett, Wesley M; Darwish, Omar

2017-06-14

Pigeonpea is one of the major sources of dietary protein for more than a billion people living in South Asia. This hardy legume is often grown in low-input and risk-prone marginal environments. Considerable research effort has been devoted by a global research consortium to develop genomic resources for the improvement of this legume crop. These efforts have resulted in the elucidation of the complete genome sequence of pigeonpea. Despite these developments, little is known about the seed proteome of this important crop. Here, we report the proteome of pigeonpea seed. To enable the isolation of maximum number of seed proteins, including those that are present in very low amounts, three different protein fractions were obtained by employing different extraction media. High-resolution two-dimensional (2-D) electrophoresis followed by MALDI-TOF-TOF-MS/MS analysis of these protein fractions resulted in the identification of 373 pigeonpea seed proteins. Consistent with the reported high degree of synteny between the pigeonpea and soybean genomes, a large number of pigeonpea seed proteins exhibited significant amino acid homology with soybean seed proteins. Our proteomic analysis identified a large number of stress-related proteins, presumably due to its adaptation to drought-prone environments. The availability of a pigeonpea seed proteome reference map should shed light on the roles of these identified proteins in various biological processes and facilitate the improvement of seed composition.

Characterisation of the willow phenylalanine ammonia-lyase (PAL) gene family reveals expression differences compared with poplar

PubMed Central

de Jong, Femke; Hanley, Steven J.; Beale, Michael H.; Karp, Angela

2015-01-01

Willow is an important biomass crop for the bioenergy industry, and therefore optimal growth with minimal effects of biotic and abiotic stress is essential. The phenylpropanoid pathway is responsible for the biosynthesis of not only lignin but also of flavonoids, condensed tannins, benzenoids and phenolic glycosides which all have a role in protecting the plant against biotic and abiotic stress. All products of the phenylpropanoid pathway are important for the healthy growth of short rotation cropping species such as willow. However, the phenylpropanoid pathway in willow remains largely uncharacterised. In the current study we identified and characterised five willow phenylalanine ammonia-lyase (PAL) genes, which encode enzymes that catalyse the deamination of l-phenylalanine to form trans-cinnamic acid, the entry point into the phenylpropanoid pathway. Willow PAL1, PAL2, PAL3 and PAL4 genes were orthologous to the poplar genes. However no orthologue of PAL5 appears to be present in willow. Moreover, two tandemly repeated PAL2 orthologues were identified in a single contig. Willow PALs show similar sub-cellular localisation to the poplar genes. However, the enzyme kinetics and gene expression of the willow PAL genes differed slightly, with willow PAL2 being more widely expressed than its poplar orthologues implying a wider role for PALs in the production of flavonoids, condensed tannins, benzenoids, and phenolic glycosides, in willow. PMID:26070140

Agricultural Productivity Forecasts for Improved Drought Monitoring

NASA Technical Reports Server (NTRS)

Limaye, Ashutosh; McNider, Richard; Moss, Donald; Alhamdan, Mohammad

2010-01-01

Water stresses on agricultural crops during critical phases of crop phenology (such as grain filling) has higher impact on the eventual yield than at other times of crop growth. Therefore farmers are more concerned about water stresses in the context of crop phenology than the meteorological droughts. However the drought estimates currently produced do not account for the crop phenology. US Department of Agriculture (USDA) and National Oceanic and Atmospheric Administration (NOAA) have developed a drought monitoring decision support tool: The U.S. Drought Monitor, which currently uses meteorological droughts to delineate and categorize drought severity. Output from the Drought Monitor is used by the States to make disaster declarations. More importantly, USDA uses the Drought Monitor to make estimates of crop yield to help the commodities market. Accurate estimation of corn yield is especially critical given the recent trend towards diversion of corn to produce ethanol. Ethanol is fast becoming a standard 10% ethanol additive to petroleum products, the largest traded commodity. Thus the impact of large-scale drought will have dramatic impact on the petroleum prices as well as on food prices. USDA's World Agricultural Outlook Board (WAOB) serves as a focal point for economic intelligence and the commodity outlook for U.S. WAOB depends on Drought Monitor and has emphatically stated that accurate and timely data are needed in operational agrometeorological services to generate reliable projections for agricultural decision makers. Thus, improvements in the prediction of drought will reflect in early and accurate assessment of crop yields, which in turn will improve commodity projections. We have developed a drought assessment tool, which accounts for the water stress in the context of crop phenology. The crop modeling component is done using various crop modules within Decision Support System for Agrotechnology Transfer (DSSAT). DSSAT is an agricultural crop simulation system, which integrates the effects of soil, crop phenotype, weather, and management options. It has been in use for more than 15 years by researchers, growers and has become a de-facto standard in crop modeling communities spanning over 100 countries. The meteorological forcings to DSSAT are provided by NASA s National Land Data Assimilation System (NLDAS) datasets. NLDAS is a framework that incorporates atmospheric forcing and land parameter values along with land surface models to diagnose and predict the state of the land surface.

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress

PubMed Central

Li, Qingye; Chang, Rong; Sun, Yijun; Li, Bosheng

2016-01-01

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance. PMID:27902743

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress.

PubMed

Li, Qingye; Chang, Rong; Sun, Yijun; Li, Bosheng

2016-01-01

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance.

Global Adoption of Genetically Modified (GM) Crops: Challenges for the Public Sector.

PubMed

Huesing, Joseph E; Andres, David; Braverman, Michael P; Burns, Andrea; Felsot, Allan S; Harrigan, George G; Hellmich, Richard L; Reynolds, Alan; Shelton, Anthony M; Jansen van Rijssen, Wilna; Morris, E Jane; Eloff, Jacobus N

2016-01-20

Advances in biotechnology continue to drive the development of a wide range of insect-protected, herbicide-tolerant, stress-tolerant, and nutritionally enhanced genetically modified (GM) crops, yet societal and public policy considerations may slow their commercialization. Such restrictions may disproportionately affect developing countries, as well as smaller entrepreneurial and public sector initiatives. The 2014 IUPAC International Congress of Pesticide Chemistry (San Francisco, CA, USA; August 2014) included a symposium on "Challenges Associated with Global Adoption of Agricultural Biotechnology" to review current obstacles in promoting GM crops. Challenges identified by symposium presenters included (i) poor public understanding of GM technology and the need for enhanced communication strategies, (ii) nonharmonized and prescriptive regulatory requirements, and (iii) limited experience with regulations and product development within some public sector programs. The need for holistic resistance management programs to enable the most effective use of insect-protected crops was also a point of emphasis. This paper provides details on the symposium discussion and provides background information that can be used in support of further adoption of beneficial GM crops. Overall, it emphasizes that global adoption of modern agricultural biotechnology has not only provided benefits to growers and consumers but has great potential to provide solutions to an increasing global population and diminishing agricultural land. This potential will be realized by continued scientific innovation, harmonized regulatory systems, and broader communication of the benefits of the high-yielding, disease-resistant, and nutritionally enhanced crops attainable through modern biotechnology.

Increasing crop diversity mitigates weather variations and improves yield stability.

PubMed

Gaudin, Amélie C M; Tolhurst, Tor N; Ker, Alan P; Janovicek, Ken; Tortora, Cristina; Martin, Ralph C; Deen, William

2015-01-01

Cropping sequence diversification provides a systems approach to reduce yield variations and improve resilience to multiple environmental stresses. Yield advantages of more diverse crop rotations and their synergistic effects with reduced tillage are well documented, but few studies have quantified the impact of these management practices on yields and their stability when soil moisture is limiting or in excess. Using yield and weather data obtained from a 31-year long term rotation and tillage trial in Ontario, we tested whether crop rotation diversity is associated with greater yield stability when abnormal weather conditions occur. We used parametric and non-parametric approaches to quantify the impact of rotation diversity (monocrop, 2-crops, 3-crops without or with one or two legume cover crops) and tillage (conventional or reduced tillage) on yield probabilities and the benefits of crop diversity under different soil moisture and temperature scenarios. Although the magnitude of rotation benefits varied with crops, weather patterns and tillage, yield stability significantly increased when corn and soybean were integrated into more diverse rotations. Introducing small grains into short corn-soybean rotation was enough to provide substantial benefits on long-term soybean yields and their stability while the effects on corn were mostly associated with the temporal niche provided by small grains for underseeded red clover or alfalfa. Crop diversification strategies increased the probability of harnessing favorable growing conditions while decreasing the risk of crop failure. In hot and dry years, diversification of corn-soybean rotations and reduced tillage increased yield by 7% and 22% for corn and soybean respectively. Given the additional advantages associated with cropping system diversification, such a strategy provides a more comprehensive approach to lowering yield variability and improving the resilience of cropping systems to multiple environmental stresses. This could help to sustain future yield levels in challenging production environments.

Shared and novel molecular responses of mandarin to drought.

PubMed

Gimeno, Jacinta; Gadea, José; Forment, Javier; Pérez-Valle, Jorge; Santiago, Julia; Martínez-Godoy, María A; Yenush, Lynne; Bellés, José M; Brumós, Javier; Colmenero-Flores, José M; Talón, Manuel; Serrano, Ramón

2009-07-01

Drought is the most important stress experienced by citrus crops. A citrus cDNA microarray of about 6.000 genes has been utilized to identify transcriptomic responses of mandarin to water stress. As observed in other plant species challenged with drought stress, key genes for lysine catabolism, proline and raffinose synthesis, hydrogen peroxide reduction, vacuolar malate transport, RCI2 proteolipids and defence proteins such as osmotin, dehydrins and heat-shock proteins are induced in mandarin. Also, some aquaporin genes are repressed. The osmolyte raffinose could be detected in stressed roots while the dehydrin COR15 protein only accumulated in stressed leaves but not in roots. Novel drought responses in mandarin include the induction of genes encoding a new miraculin isoform, chloroplast beta-carotene hydroxylase, oleoyl desaturase, ribosomal protein RPS13A and protein kinase CTR1. These results suggest that drought tolerance in citrus may benefit from inhibition of proteolysis, activation of zeaxanthin and linolenoyl synthesis, reinforcement of ribosomal structure and down-regulation of the ethylene response.

Drought response in wheat: key genes and regulatory mechanisms controlling root system architecture and transpiration efficiency

NASA Astrophysics Data System (ADS)

Kulkarni, Manoj; Soolanayakanahally, Raju; Ogawa, Satoshi; Uga, Yusaku; Selvaraj, Michael G.; Kagale, Sateesh

2017-12-01

Abiotic stresses such as drought, heat, salinity and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize and/or Arabidopsis. The overall aim of this review was to provide an overview of candidate genes that have been tested as regulators of drought response in plants. The lack of a reference genome sequence for wheat and nontransgenic approaches for manipulation of gene functions in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerance cultivars.

Airborne monitoring of crop canopy temperatures for irrigation scheduling and yield prediction

NASA Technical Reports Server (NTRS)

Millard, J. P.; Jackson, R. D.; Goettelman, R. C.; Reginato, R. J.; Idso, S. B.; Lapado, R. L.

1977-01-01

Airborne and ground measurements were made on April 1 and 29, 1976, over a USDA test site consisting mostly of wheat in various stages of water stress, but also including alfalfa and bare soil. These measurements were made to evaluate the feasibility of measuring crop temperatures from aircraft so that a parameter termed stress degree day, SDD, could be computed. Ground studies have shown that SDD is a valuable indicator of a crop's water needs, and that it can be related to irrigation scheduling and yield. The aircraft measurement program required predawn and afternoon flights coincident with minimum and maximum crop temperatures. Airborne measurements were made with an infrared line scanner and with color IR photography. The scanner data were registered, subtracted, and color-coded to yield pseudo-colored temperature-difference images. Pseudo-colored images reading directly in daily SDD increments were also produced. These maps enable a user to assess plant water status and thus determine irrigation needs and crop yield potentials.

Estimating crop yields and crop evapotranspiration distributions from remote sensing and geospatial agricultural data

NASA Astrophysics Data System (ADS)

Smith, T.; McLaughlin, D.

2017-12-01

Growing more crops to provide a secure food supply to an increasing global population will further stress land and water resources that have already been significantly altered by agriculture. The connection between production and resource use depends on crop yields and unit evapotranspiration (UET) rates that vary greatly, over both time and space. For regional and global analyses of food security it is appropriate to treat yield and UET as uncertain variables conditioned on climatic and soil properties. This study describes how probability distributions of these variables can be estimated by combining remotely sensed land use and evapotranspiration data with in situ agronomic and soils data, all available at different resolutions and coverages. The results reveal the influence of water and temperature stress on crop yield at large spatial scales. They also provide a basis for stochastic modeling and optimization procedures that explicitly account for uncertainty in the environmental factors that affect food production.

Abscisic acid and abiotic stress tolerance in crop plants

USDA-ARS?s Scientific Manuscript database

biotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the ...

Water Stress Detection using Temperature, Emissivity, and Reflectance

NASA Astrophysics Data System (ADS)

Gerhards, Max; Rock, Gilles; Schlerf, Martin; Udelhoven, Thomas

2017-04-01

Water stress is one of the most critical abiotic stressors limiting crop development. The main imaging and non-imaging remote sensing based techniques for the detection of plant stress (water stress and other types of stress) are thermography, visible (VIS), near- and shortwave infrared (NIR/SWIR) reflectance, and fluorescence. Just very recently, in addition to broadband thermography, narrowband (hyperspectral) thermal imaging has become available, which even facilitates the retrieval of spectral emissivity as an additional measure of plant stress. It is, however, still unclear at what stage plant stress is detectable with the various techniques. During summer 2014 a water treatment experiment was run on 60 potato plants (Solanum tuberosum L. Cilena) with one half of the plants watered and the other half stressed. Crop response was measured using broadband and hyperspectral thermal cameras and a VNIR/SWIR spectrometer. Stomatal conductance was measured using a leaf porometer. Various measures and indices were computed and analysed for their sensitivity towards water stress (Crop Water Stress Index (CWSI), Moisture Stress Index (MSI), Photochemical Reflectance Index (PRI), and spectral emissivity, amongst others). The results show that water stress as measured through stomatal conductance started on day 2 after watering was stopped. The fastest reacting, i.e., starting on day 7, indices were temperature based measures (e.g., CWSI) and NIR/SWIR reflectance based indices related to plant water content (e.g., MSI). Spectral emissivity reacted equally fast. Contrarily, visual indices (e.g., PRI) either did not respond at all or responded in an inconsistent manner. This experiment shows that pre-visual water stress detection is feasible using indices depicting leaf temperature, leaf water content and spectral emissivity.

Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome.

PubMed

Liu, Hongzhan; Zhang, Gaisheng; Wang, Junsheng; Li, Jingjing; Song, Yulong; Qiao, Lin; Niu, Na; Wang, Junwei; Ma, Shoucai; Li, Lili

2018-01-05

Heterosis is widely used to increase the yield of many crops. However, as wheat is a self-pollinating crop, hybrid breeding is not so successful in this organism. Even though male sterility induced by chemical hybridizing agents is an important aspect of crossbreeding, the mechanisms by which these agents induce male sterility in wheat is not well understood. We performed proteomic analyses using the wheat Triticum aestivum L.to identify those proteins involved in physiological male sterility (PHYMS) induced by the chemical hybridizing agent CHA SQ-1. A total of 103 differentially expressed proteins were found by 2D-PAGE and subsequently identified by MALDI-TOF/TOF MS/MS. In general, these proteins had obvious functional tendencies implicated in carbohydrate metabolism, oxidative stress and resistance, protein metabolism, photosynthesis, and cytoskeleton and cell structure. In combination with phenotypic, tissue section, and bioinformatics analyses, the identified differentially expressed proteins revealed a complex network behind the regulation of PHYMS and pollen development. Accordingly, we constructed a protein network of male sterility in wheat, drawing relationships between the 103 differentially expressed proteins and their annotated biological pathways. To further validate our proposed protein network, we determined relevant physiological values and performed real-time PCR assays. Our proteomics based approach has enabled us to identify certain tendencies in PHYMS anthers. Anomalies in carbohydrate metabolism and oxidative stress, together with premature tapetum degradation, may be the cause behind carbohydrate starvation and male sterility in CHA SQ-1 treated plants. Here, we provide important insight into the mechanisms underlying CHA SQ-1-induced male sterility. Our findings have practical implications for the application of hybrid breeding in wheat.

Genome-wide association studies to identify rice salt-tolerance markers.

PubMed

Patishtan, Juan; Hartley, Tom N; Fonseca de Carvalho, Raquel; Maathuis, Frans J M

2018-05-01

Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance. © 2017 John Wiley & Sons Ltd.

Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism.

PubMed

George, Iniga S; Pascovici, Dana; Mirzaei, Mehdi; Haynes, Paul A

2015-09-01

Grapes (Vitis vinifera) are a valuable fruit crop and wine production is a major industry. Global warming and expanded range of cultivation will expose grapes to more temperature stresses in future. Our study investigated protein level responses to abiotic stresses, with particular reference to proteomic changes induced by the impact of four different temperature stress regimes, including both hot and cold temperatures, on cultured grape cells. Cabernet Sauvignon cell suspension cultures grown at 26°C were subjected to 14 h of exposure to 34 and 42°C for heat stress, and 18 and 10°C for cold stress. Cells from the five temperatures were harvested in biological triplicates and label-free quantitative shotgun proteomic analysis was performed. A total of 2042 non-redundant proteins were identified from the five temperature points. Fifty-five proteins were only detected in extreme heat stress conditions (42°C) and 53 proteins were only detected at extreme cold stress conditions (10°C). Gene Ontology (GO) annotations of differentially expressed proteins provided insights into the metabolic pathways that are involved in temperature stress in grape cells. Sugar metabolism displayed switching between alternative and classical pathways during temperature stresses. Additionally, nine proteins involved in the phenylpropanoid pathway were greatly increased in abundance at extreme cold stress, and were thus found to be cold-responsive proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD000977 (http://proteomecentral.proteomexchange.org/dataset/PXD000977). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A wheat salinity-induced WRKY transcription factor TaWRKY93 confers multiple abiotic stress tolerance in Arabidopsis thaliana.

PubMed

Qin, Yuxiang; Tian, Yanchen; Liu, Xiuzhi

2015-08-21

Wheat is an important crop in the world. But most of the cultivars are salt sensitive, and often adversely affected by salt stress. WRKY transcription factors play a major role in plant responses to salt stress, but the effective salinity regulatory WRKYs identified in bread wheat are limited and the mechanism of salt stress tolerance is also not well explored. Here, we identified a salt (NaCl) induced class II WRKY transcription factor TaWRKY93. Its transcript level was strongly induced by salt (NaCl) and exogenous abscisic acid (ABA). Over-expression of TaWRKY93 in Arabidopsis thaliana enhanced salt (NaCl), drought, low temperature and osmotic (mannitol) stress tolerance, mainly demonstrated by transgenic plants forming longer primary roots or more lateral roots on MS plates supplemented with NaCl and mannitol individually, higher survival rate under drought and low temperature stress. Further, transgenic plants maintained a more proline content, higher relative water content and less electrolyte leakage than the wild type plants. The transcript abundance of a series of abiotic stress-related genes was up-regulated in the TaWRKY93 transgenic plants. In summary, TaWRKY93 is a new positive regulator of abiotic stress, it may increase salinity, drought and low temperature stress tolerance through enhancing osmotic adjustment, maintaining membrane stability and increasing transcription of stress related genes, and contribute to the superior agricultural traits of SR3 through promoting root development. It can be used as a candidate gene for wheat transgenic engineering breeding against abiotic stress. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantifying agricultural drought impacts using soil moisture model and drought indices in South Korea

NASA Astrophysics Data System (ADS)

Nam, W. H.; Bang, N.; Hong, E. M.; Pachepsky, Y. A.; Han, K. H.; Cho, H.; Ok, J.; Hong, S. Y.

2017-12-01

Agricultural drought is defined as a combination of abnormal deficiency of precipitation, increased crop evapotranspiration demands from high-temperature anomalies, and soil moisture deficits during the crop growth period. Soil moisture variability and their spatio-temporal trends is a key component of the hydrological balance, which determines the crop production and drought stresses in the context of agriculture. In 2017, South Korea has identified the extreme drought event, the worst in one hundred years according to the South Korean government. The objective of this study is to quantify agricultural drought impacts using observed and simulated soil moisture, and various drought indices. A soil water balance model is used to simulate the soil water content in the crop root zone under rain-fed (no irrigation) conditions. The model used includes physical process using estimated effective rainfall, infiltration, redistribution in soil water zone, and plant water uptake in the form of actual crop evapotranspiration. Three widely used drought indices, including the Standardized Precipitation Index (SPI), the Standardized Precipitation Evapotranspiration Index (SPEI), and the Self-Calibrated Palmer Drought Severity Index (SC-PDSI) are compared with the observed and simulated soil moisture in the context of agricultural drought impacts. These results demonstrated that the soil moisture model could be an effective tool to provide improved spatial and temporal drought monitoring for drought policy.

Proteome Characterization of Leaves in Common Bean

PubMed Central

Robison, Faith M.; Heuberger, Adam L.; Brick, Mark A.; Prenni, Jessica E.

2015-01-01

Dry edible bean (Phaseolus vulgaris L.) is a globally relevant food crop. The bean genome was recently sequenced and annotated allowing for proteomics investigations aimed at characterization of leaf phenotypes important to agriculture. The objective of this study was to utilize a shotgun proteomics approach to characterize the leaf proteome and to identify protein abundance differences between two bean lines with known variation in their physiological resistance to biotic stresses. Overall, 640 proteins were confidently identified. Among these are proteins known to be involved in a variety of molecular functions including oxidoreductase activity, binding peroxidase activity, and hydrolase activity. Twenty nine proteins were found to significantly vary in abundance (p-value < 0.05) between the two bean lines, including proteins associated with biotic stress. To our knowledge, this work represents the first large scale shotgun proteomic analysis of beans and our results lay the groundwork for future studies designed to investigate the molecular mechanisms involved in pathogen resistance. PMID:28248269

Piriformospora indica: Potential and Significance in Plant Stress Tolerance

PubMed Central

Gill, Sarvajeet S.; Gill, Ritu; Trivedi, Dipesh K.; Anjum, Naser A.; Sharma, Krishna K.; Ansari, Mohammed W.; Ansari, Abid A.; Johri, Atul K.; Prasad, Ram; Pereira, Eduarda; Varma, Ajit; Tuteja, Narendra

2016-01-01

Owing to its exceptional ability to efficiently promote plant growth, protection and stress tolerance, a mycorrhiza like endophytic Agaricomycetes fungus Piriformospora indica has received a great attention over the last few decades. P. indica is an axenically cultiviable fungus which exhibits its versatility for colonizing/hosting a broad range of plant species through directly manipulating plant hormone-signaling pathway during the course of mutualism. P. indica-root colonization leads to a better plant performance in all respect, including enhanced root proliferation by indole-3-acetic acid production which in turn results into better nutrient-acquisition and subsequently to improved crop growth and productivity. Additionally, P. indica can induce both local and systemic resistance to fungal and viral plant diseases through signal transduction. P. indica-mediated stimulation in antioxidant defense system components and expressing stress-related genes can confer crop/plant stress tolerance. Therefore, P. indica can biotize micropropagated plantlets and also help these plants to overcome transplantation shock. Nevertheless, it can also be involved in a more complex symbiotic relationship, such as tripartite symbiosis and can enhance population dynamic of plant growth promoting rhizobacteria. In brief, P. indica can be utilized as a plant promoter, bio-fertilizer, bioprotector, bioregulator, and biotization agent. The outcome of the recent literature appraised herein will help us to understand the physiological and molecular bases of mechanisms underlying P. indica-crop plant mutual relationship. Together, the discussion will be functional to comprehend the usefulness of crop plant-P. indica association in both achieving new insights into crop protection/improvement as well as in sustainable agriculture production. PMID:27047458

Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions

PubMed Central

Joshi, Rohit; Wani, Shabir H.; Singh, Balwant; Bohra, Abhishek; Dar, Zahoor A.; Lone, Ajaz A.; Pareek, Ashwani; Singla-Pareek, Sneh L.

2016-01-01

Increasing vulnerability of plants to a variety of stresses such as drought, salt and extreme temperatures poses a global threat to sustained growth and productivity of major crops. Of these stresses, drought represents a considerable threat to plant growth and development. In view of this, developing staple food cultivars with improved drought tolerance emerges as the most sustainable solution toward improving crop productivity in a scenario of climate change. In parallel, unraveling the genetic architecture and the targeted identification of molecular networks using modern “OMICS” analyses, that can underpin drought tolerance mechanisms, is urgently required. Importantly, integrated studies intending to elucidate complex mechanisms can bridge the gap existing in our current knowledge about drought stress tolerance in plants. It is now well established that drought tolerance is regulated by several genes, including transcription factors (TFs) that enable plants to withstand unfavorable conditions, and these remain potential genomic candidates for their wide application in crop breeding. These TFs represent the key molecular switches orchestrating the regulation of plant developmental processes in response to a variety of stresses. The current review aims to offer a deeper understanding of TFs engaged in regulating plant’s response under drought stress and to devise potential strategies to improve plant tolerance against drought. PMID:27471513

Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance

PubMed Central

Sita, Kumari; Sehgal, Akanksha; HanumanthaRao, Bindumadhava; Nair, Ramakrishnan M.; Vara Prasad, P. V.; Kumar, Shiv; Gaur, Pooran M.; Farooq, Muhammad; Siddique, Kadambot H. M.; Varshney, Rajeev K.; Nayyar, Harsh

2017-01-01

Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress. PMID:29123532

Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance.

PubMed

Sita, Kumari; Sehgal, Akanksha; HanumanthaRao, Bindumadhava; Nair, Ramakrishnan M; Vara Prasad, P V; Kumar, Shiv; Gaur, Pooran M; Farooq, Muhammad; Siddique, Kadambot H M; Varshney, Rajeev K; Nayyar, Harsh

2017-01-01

Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.

Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land.

PubMed

Fan, Yangyang; Wang, Qian; Kang, Lifang; Liu, Wei; Xu, Qin; Xing, Shilai; Tao, Chengcheng; Song, Zhihong; Zhu, Caiyun; Lin, Cong; Yan, Juan; Li, Jianqiang; Sang, Tao

2015-10-01

Understanding the genetic basis of water use efficiency (WUE) and its roles in plant adaptation to a drought environment is essential for the production of second-generation energy crops in water-deficit marginal land. In this study, RNA-Seq and WUE measurements were performed for 78 individuals of Miscanthus lutarioriparius grown in two common gardens, one located in warm and wet Central China near the native habitats of the species and the other located in the semiarid Loess Plateau, the domestication site of the energy crop. The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location. A matrix correlation analysis was conducted between gene expression levels and WUE to identify candidate genes involved in the improvement of WUE from the native to the domestication site. A total of 48 candidate genes were identified and assigned to functional categories, including photosynthesis, stomatal regulation, protein metabolism, and abiotic stress responses. Of these genes, nearly 73% were up-regulated in the semiarid site. It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation. The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Genome-Wide Identification, Expression Diversication of Dehydrin Gene Family and Characterization of CaDHN3 in Pepper (Capsicum annuum L.).

PubMed

Jing, Hua; Li, Chao; Ma, Fang; Ma, Ji-Hui; Khan, Abid; Wang, Xiao; Zhao, Li-Yang; Gong, Zhen-Hui; Chen, Ru-Gang

2016-01-01

Dehydrins (DHNs) play a crucial role in enhancing abiotic stress tolerance in plants. Although DHNs have been identified and characterized in many plants, there is little known about Capsicum annuum L., one of the economically important vegetable crops. In this study, seven CaDHNs in the pepper genome were identified, which could be divided into two classes: YnSKn- and SKn-type, based on their highly conserved domains. Quantitative real-time PCR (qRT-PCR) results showed that the seven DHN genes were expressed in all tissues and might be involved in the growth and development of pepper. The gene expression profiles analysis suggested that most of the CaDHN genes were induced by various stresses (low temperature, salt and mannitol) and signaling molecules (ABA, SA and MeJA). Furthermore, the CaDHN3 (YSK2)-silenced pepper plants showed obvious lower resistance to abiotic stresses (cold, salt and mannitol) than the control plants (TRV2:00). So the CaDHN3 might act as a positive role in resisting abiotic stresses. This study lays the foundation for further studies into the regulation of their expression under various conditions.

Genome-Wide Identification, Expression Diversication of Dehydrin Gene Family and Characterization of CaDHN3 in Pepper (Capsicum annuum L.)

PubMed Central

Ma, Ji-Hui; Khan, Abid; Wang, Xiao; Zhao, Li-Yang; Gong, Zhen-Hui; Chen, Ru-Gang

2016-01-01

Dehydrins (DHNs) play a crucial role in enhancing abiotic stress tolerance in plants. Although DHNs have been identified and characterized in many plants, there is little known about Capsicum annuum L., one of the economically important vegetable crops. In this study, seven CaDHNs in the pepper genome were identified, which could be divided into two classes: YnSKn- and SKn-type, based on their highly conserved domains. Quantitative real-time PCR (qRT-PCR) results showed that the seven DHN genes were expressed in all tissues and might be involved in the growth and development of pepper. The gene expression profiles analysis suggested that most of the CaDHN genes were induced by various stresses (low temperature, salt and mannitol) and signaling molecules (ABA, SA and MeJA). Furthermore, the CaDHN3 (YSK2)-silenced pepper plants showed obvious lower resistance to abiotic stresses (cold, salt and mannitol) than the control plants (TRV2:00). So the CaDHN3 might act as a positive role in resisting abiotic stresses. This study lays the foundation for further studies into the regulation of their expression under various conditions. PMID:27551973

The Wheat NAC Transcription Factor TaNAC2L Is Regulated at the Transcriptional and Post-Translational Levels and Promotes Heat Stress Tolerance in Transgenic Arabidopsis.

PubMed

Guo, Weiwei; Zhang, Jinxia; Zhang, Ning; Xin, Mingming; Peng, Huiru; Hu, Zhaorong; Ni, Zhongfu; Du, Jinkun

2015-01-01

Heat stress poses a serious threat to global crop production. In efforts that aim to mitigate the adverse effects of heat stress on crops, a variety of genetic tools are being used to develop plants with improved thermotolerance. The characterization of important regulators of heat stress tolerance provides essential information for this aim. In this study, we examine the wheat (Triticum aestivum) NAC transcription factor gene TaNAC2L. High temperature induced TaNAC2L expression in wheat and overexpression of TaNAC2L in Arabidopsis thaliana enhanced acquired heat tolerance without causing obvious alterations in phenotype compared with wild type under normal conditions. TaNAC2L overexpression also activated the expression of heat-related genes in the transgenic Arabidopsis plants, suggesting that TaNAC2L may improve heat tolerance by regulating the expression of stress-responsive genes. Notably, TaNAC2L is also regulated at the post-translational level and might be degraded via a proteasome-mediated pathway. Thus, this wheat transcription factor may have potential uses in enhancing thermotolerance in crops.

Proteomics of contrasting rice genotypes: Identification of potential targets for raising crops for saline environment.

PubMed

Lakra, Nita; Kaur, Charanpreet; Anwar, Khalid; Singla-Pareek, Sneh Lata; Pareek, Ashwani

2018-05-01

High salinity is one of the major problems in crop productivity, affecting seed germination as well as yield. In order to enhance tolerance of crops towards salinity, it is essential to understand the underlying physiological and molecular mechanisms. In this endeavor, study of contrasting genotypes of the same species differing in their response towards salinity stress can be very useful. In the present study, we have investigated temporal differences in morphological, physiological and proteome profiles of two contrasting genotypes of rice to understand the basis of salt tolerance. When compared to IR64 rice, Pokkali, the salt-tolerant wild genotype, has enhanced capacity to cope with stress, better growth rate and possesses efficient antioxidant system, as well as better photosynthetic machinery. Our proteome studies revealed a higher and an early abundance of proteins involved in stress tolerance and photosynthesis in Pokkali in comparison with IR64, which, in contrast, showed greater changes in metabolic machinery even during early duration of stress. Our findings suggest important differences in physicochemical and proteome profiles of the two genotypes, which may be the basis of observed stress tolerance in the salt-tolerant Pokkali. © 2017 John Wiley & Sons Ltd.

Soil Modification by Native Shrubs Boosts Crop Productivity in Sudano-Sahelian Agroforestry System

NASA Astrophysics Data System (ADS)

Bogie, N. A.; Bayala, R.; Diedhiou, I.; Ghezzehei, T. A.; Dick, R.

2014-12-01

A changing climate along with human and animal population pressure can have a devastating effect on crop yields and food security in the Sudano-Sahel. Agricultural solutions to address soil degradation and crop water stress are needed to combat this increasingly difficult situation. Significant differences in crop success have been observed in peanut and millet grown in association with two native evergreen shrubs Piliostigma reticulatum, and Guiera senegalensis at the sites of Nioro du Rip and Keur Matar, respectively.We investigate how farmers can increase crop productivity by capitalizing on the evolutionary adaptation of native shrubs to the harsh Sudano-Sahelian environment as well as the physical mechanisms at work in the system that can lead to more robust yields. Soil moisture and water potential data were collected during a dry season millet irrigation experiment where stress was imposed in the intercropped system. Despite lower soil moisture content, crops grown in association with shrubs have increased biomass production and a faster development cycle. Hydraulic redistribution is thought to exist in this system and we found diurnal fluctuations in water potential within the intercropped system that increased in magnitude of to 0.4 Mpa per day as the soil dried below 1.0 Mpa during the stress treatment. An isotopic tracer study investigating hydraulic redistribution was carried out by injecting labeled water into shrub roots and sampling shrubs and nearby crops for isotopic analysis of plant water. These findings build on work that was completed in 2004 at the site, but point to lower overall magnitude of diurnal soil water potential fluctuations in dry soils. Using even the limited resources that farmers possess, this agroforestry technique can be expanded over wide swaths of the Sahel.

Multi-year strongest California drought from 500 m SNPP/VIIRS

NASA Astrophysics Data System (ADS)

Guo, W.; Kogan, F.

2016-12-01

Starting in 2006, the western United States was affected by a 10-year long mega-drought. Among 17 western states, California was the most severely drought-affected, especially in 2012-2015, when the area of stronger than moderate vegetation stress reached 70%. This drought had considerable impacts on California's environmental, economy and society. Currently, drought in the USA is monitored by the US Drought Monitor (USDM), which estimates drought area and intensity on an area with an effective resolution of around 30-by-30 km. California produces more than 90% of US fruits, vegetables, berries and nuts, which are grown on relatively small areas (200-500 acres, or 0.5 to 2 km²). Since most of these crops are irrigated, it is important to estimate crop conditions on the area comparable to the size of the planted crop. This paper demonstrates how the new 0.5-by-0.5 km Vegetation health (VH) technology (VH-500) developed from the data collected by the Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi National Polar-orbiting Partnership (SNPP) satellite launched in 2011, monitors the current mega-drought in California, distinguishing drought-affected area with and without irrigation and estimating drought start/end, intensity, duration and impacts. The VH-500 method and data showed that California's vegetation was under medium-to-exceptional stress, especially in 2013 and 2014. However, in the middle of such intensive stress, in some of the 500-m areas of the Central Valley where principal crops are growing, vegetation experienced favorable conditions because some of these crops were irrigated. The VH-500 drought estimates showed general similarities with the assessed economic drought impacts (crop fallowing, employment loss and crop revenue change) in California.

Assessment of winter wheat loss risk impacted by climate change from 1982 to 2011

NASA Astrophysics Data System (ADS)

Du, Xin

2017-04-01

The world's farmers will face increasing pressure to grow more food on less land in succeeding few decades, because it seems that the continuous population growth and agricultural products turning to biofuels would extend several decades into the future. Therefore, the increased demand for food supply worldwide calls for improved accuracy of crop productivity estimation and assessment of grain production loss risk. Extensive studies have been launched to evaluate the impacts of climate change on crop production based on various crop models drove with global or regional climate model (GCM/RCM) output. However, assessment of climate change impacts on agriculture productivity is plagued with uncertainties of the future climate change scenarios and complexity of crop model. Therefore, given uncertain climate conditions and a lack of model parameters, these methods are strictly limited in application. In this study, an empirical assessment approach for crop loss risk impacted by water stress has been established and used to evaluate the risk of winter wheat loss in China, United States, Germany, France and United Kingdom. The average value of winter wheat loss risk impacted by water stress for the three countries of Europe is about -931kg/ha, which is obviously higher in contrast with that in China (-570kg/ha) and in United States (-367kg/ha). Our study has important implications for further application of operational assessment of crop loss risk at a country or region scale. Future studies should focus on using higher spatial resolution remote sensing data, combining actual evapo-transpiration to estimate water stress, improving the method for downscaling of statistic crop yield data, and establishing much more rational and elaborate zoning method.

A meteorologically-driven yield reduction model for spring and winter wheat

NASA Technical Reports Server (NTRS)

Ravet, F. W.; Cremins, W. J.; Taylor, T. W.; Ashburn, P.; Smika, D.; Aaronson, A. (Principal Investigator)

1983-01-01

A yield reduction model for spring and winter wheat was developed for large-area crop condition assessment. Reductions are expressed in percentage from a base yield and are calculated on a daily basis. The algorithm contains two integral components: a two-layer soil water budget model and a crop calendar routine. Yield reductions associated with hot, dry winds (Sukhovey) and soil moisture stress are determined. Input variables include evapotranspiration, maximum temperature and precipitation; subsequently crop-stage, available water holding percentage and stress duration are evaluated. No specific base yield is required and may be selected by the user; however, it may be generally characterized as the maximum likely to be produced commercially at a location.

Crop water-stress assessment using an airborne thermal scanner

NASA Technical Reports Server (NTRS)

Millard, J. P.; Jackson, R. D.; Reginato, R. J.; Idso, S. B.; Goettelman, R. C.

1978-01-01

An airborne thermal scanner was used to measure the temperature of a wheat crop canopy in Phoenix, Arizona. The results indicate that canopy temperatures acquired about an hour and a half past solar noon were well correlated with presunrise plant water tension, a parameter directly related to plant growth and development. Pseudo-colored thermal images reading directly in stress degree days, a unit indicative of crop irrigation needs and yield potential, were produced. The aircraft data showed significant within-field canopy temperature variability, indicating the superiority of the synoptic view provided by aircraft over localized ground measurements. The standard deviation between airborne and ground-acquired canopy temperatures was 2 C or less.

Large area application of a corn hazard model. [Soviet Union

NASA Technical Reports Server (NTRS)

Ashburn, P.; Taylor, T. W. (Principal Investigator)

1981-01-01

An application test of the crop calendar portion of a corn (maize) stress indicator model developed by the early warning, crop condition assessment component of AgRISTARS was performed over the corn for grain producing regions of the U.S.S.R. during the 1980 crop year using real data. Performance of the crop calendar submodel was favorable; efficiency gains in meteorological data analysis time were on a magnitude of 85 to 90 percent.

Abscisic Acid and Abiotic Stress Tolerance in Crop Plants

PubMed Central

Sah, Saroj K.; Reddy, Kambham R.; Li, Jiaxu

2016-01-01

Abiotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the magnitude of stress challenges, although that is not enough to protect them. Therefore, many strategies have been used to produce abiotic stress tolerance crop plants, among them, abscisic acid (ABA) phytohormone engineering could be one of the methods of choice. ABA is an isoprenoid phytohormone, which regulates various physiological processes ranging from stomatal opening to protein storage and provides adaptation to many stresses like drought, salt, and cold stresses. ABA is also called an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to different environmental stress conditions. In this review, we will discuss the role of ABA in response to abiotic stress at the molecular level and ABA signaling. The review also deals with the effect of ABA in respect to gene expression. PMID:27200044

Comment on 'Shang S. 2012. Calculating actual crop evapotranspiration under soil water stress conditions with appropriate numerical methods and time step. Hydrological Processes 26: 3338-3343. DOI: 10.1002/hyp.8405'

NASA Technical Reports Server (NTRS)

Yatheendradas, Soni; Narapusetty, Balachandrudu; Peters-Lidard, Christa; Funk, Christopher; Verdin, James

2014-01-01

A previous study analyzed errors in the numerical calculation of actual crop evapotranspiration (ET(sub a)) under soil water stress. Assuming no irrigation or precipitation, it constructed equations for ET(sub a) over limited soil-water ranges in a root zone drying out due to evapotranspiration. It then used a single crop-soil composite to provide recommendations about the appropriate usage of numerical methods under different values of the time step and the maximum crop evapotranspiration (ET(sub c)). This comment reformulates those ET(sub a) equations for applicability over the full range of soil water values, revealing a dependence of the relative error in numerical ET(sub a) on the initial soil water that was not seen in the previous study. It is shown that the recommendations based on a single crop-soil composite can be invalid for other crop-soil composites. Finally, a consideration of the numerical error in the time-cumulative value of ET(sub a) is discussed besides the existing consideration of that error over individual time steps as done in the previous study. This cumulative ET(sub a) is more relevant to the final crop yield.

Ectopic Expression of Pumpkin NAC Transcription Factor CmNAC1 Improves Multiple Abiotic Stress Tolerance in Arabidopsis

PubMed Central

Cao, Haishun; Wang, Li; Nawaz, Muhammad A.; Niu, Mengliang; Sun, Jingyu; Xie, Junjun; Kong, Qiusheng; Huang, Yuan; Cheng, Fei; Bie, Zhilong

2017-01-01

Drought, cold and salinity are the major environmental stresses that limit agricultural productivity. NAC transcription factors regulate the stress response in plants. Pumpkin (Cucurbita moschata) is an important cucurbit vegetable crop and it has strong resistance to abiotic stress; however, the biological functions of stress-related NAC genes in this crop are largely unknown. This study reports the function of CmNAC1, a stress-responsive pumpkin NAC domain protein. The CmNAC1-GFP fusion protein was transiently expressed in tobacco leaves for subcellular localization analysis, and we found that CmNAC1 is localized in the nucleus. Transactivation assay in yeast cells revealed that CmNAC1 functions as a transcription activator, and its transactivation domain is located in the C-terminus. CmNAC1 was ubiquitously expressed in different organs, and its transcript was induced by salinity, cold, dehydration, H2O2, and abscisic acid (ABA) treatment. Furthermore, the ectopic expression (EE) of CmNAC1 in Arabidopsis led to ABA hypersensitivity and enhanced tolerance to salinity, drought and cold stress. In addition, five ABA-responsive elements were enriched in CmNAC1 promoter. The CmNAC1-EE plants exhibited different root architecture, leaf morphology, and significantly high concentration of ABA compared with WT Arabidopsis under normal conditions. Our results indicated that CmNAC1 is a critical factor in ABA signaling pathways and it can be utilized in transgenic breeding to improve the abiotic stress tolerance of crops. PMID:29234347

Unmanned aircraft system-derived crop height and normalized difference vegetation index metrics for sorghum yield and aphid stress assessment

NASA Astrophysics Data System (ADS)

Stanton, Carly; Starek, Michael J.; Elliott, Norman; Brewer, Michael; Maeda, Murilo M.; Chu, Tianxing

2017-04-01

A small, fixed-wing unmanned aircraft system (UAS) was used to survey a replicated small plot field experiment designed to estimate sorghum damage caused by an invasive aphid. Plant stress varied among 40 plots through manipulation of aphid densities. Equipped with a consumer-grade near-infrared camera, the UAS was flown on a recurring basis over the growing season. The raw imagery was processed using structure-from-motion to generate normalized difference vegetation index (NDVI) maps of the fields and three-dimensional point clouds. NDVI and plant height metrics were averaged on a per plot basis and evaluated for their ability to identify aphid-induced plant stress. Experimental soil signal filtering was performed on both metrics, and a method filtering low near-infrared values before NDVI calculation was found to be the most effective. UAS NDVI was compared with NDVI from sensors onboard a manned aircraft and a tractor. The correlation results showed dependence on the growth stage. Plot averages of NDVI and canopy height values were compared with per-plot yield at 14% moisture and aphid density. The UAS measures of plant height and NDVI were correlated to plot averages of yield and insect density. Negative correlations between aphid density and NDVI were seen near the end of the season in the most damaged crops.

Rationalising vitamin B6 biofortification in crop plants.

PubMed

Fudge, Jared; Mangel, Nathalie; Gruissem, Wilhelm; Vanderschuren, Hervé; Fitzpatrick, Teresa B

2017-04-01

Vitamin B 6 encompasses a group of related compounds (vitamers) that can only be biosynthesised de novo by plants and microorganisms. Enzymatic cofactor and antioxidant functions for vitamin B 6 are established in all kingdoms. Human vitamin B 6 dietary insufficiency or genetic defects in B 6 vitamer interconversion result in various neurological and inflammatory pathologies with several populations at-risk or marginal for vitamin B 6 status. Three (rice, wheat and cassava) of the world's top five staple crops do not meet the recommended dietary allowance for vitamin B 6 , when consumed as a major proportion of the diet. In addition, controlled enhancement of the appropriate B 6 vitamer in crops has the potential to confer stress resistance. Thus, crop biofortification strategies represent an opportunity to reduce the risk of deficiency in populations with limited diet diversity and quality, as well as improving stress tolerance. Copyright © 2016 Elsevier Ltd. All rights reserved.

From genomics to functional markers in the era of next-generation sequencing.

PubMed

Salgotra, R K; Gupta, B B; Stewart, C N

2014-03-01

The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of "perfect" markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress.

PubMed

Jha, Uday Chand; Bohra, Abhishek; Jha, Rintu

2017-01-01

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

Effects of climate change on crops and weeds: scope for developing cultivars better adapted to both abiotic stress and an ability to suppress weeds

USDA-ARS?s Scientific Manuscript database

The challenges of climate change on agricultural production are multifaceted. The parameters most likely to affect the performance of crops and weeds are increased CO2 levels, increases in temperature, and extended periods of drought. It is likely that increased CO2 concentration will benefit crops ...

Are we on the right track: Can our understanding of abscission in model systems promote or derail making improvements in less studied crops

USDA-ARS?s Scientific Manuscript database

As the world population grows and resources and climate conditions change, crop improvement continues to be one of the most important challenges for agriculturalists. The yield and quality of many crops is affected by abscission or shattering, and environmental stresses often hasten or alter the abs...

Spatio-Temporal Dynamics of Maize Yield Water Constraints under Climate Change in Spain

PubMed Central

Ferrero, Rosana; Lima, Mauricio; Gonzalez-Andujar, Jose Luis

2014-01-01

Many studies have analyzed the impact of climate change on crop productivity, but comparing the performance of water management systems has rarely been explored. Because water supply and crop demand in agro-systems may be affected by global climate change in shaping the spatial patterns of agricultural production, we should evaluate how and where irrigation practices are effective in mitigating climate change effects. Here we have constructed simple, general models, based on biological mechanisms and a theoretical framework, which could be useful in explaining and predicting crop productivity dynamics. We have studied maize in irrigated and rain-fed systems at a provincial scale, from 1996 to 2009 in Spain, one of the most prominent “hot-spots” in future climate change projections. Our new approach allowed us to: (1) evaluate new structural properties such as the stability of crop yield dynamics, (2) detect nonlinear responses to climate change (thresholds and discontinuities), challenging the usual linear way of thinking, and (3) examine spatial patterns of yield losses due to water constraints and identify clusters of provinces that have been negatively affected by warming. We have reduced the uncertainty associated with climate change impacts on maize productivity by improving the understanding of the relative contributions of individual factors and providing a better spatial comprehension of the key processes. We have identified water stress and water management systems as being key causes of the yield gap, and detected vulnerable regions where efforts in research and policy should be prioritized in order to increase maize productivity. PMID:24878747

Spatio-temporal dynamics of maize yield water constraints under climate change in Spain.

PubMed

Ferrero, Rosana; Lima, Mauricio; Gonzalez-Andujar, Jose Luis

2014-01-01

Many studies have analyzed the impact of climate change on crop productivity, but comparing the performance of water management systems has rarely been explored. Because water supply and crop demand in agro-systems may be affected by global climate change in shaping the spatial patterns of agricultural production, we should evaluate how and where irrigation practices are effective in mitigating climate change effects. Here we have constructed simple, general models, based on biological mechanisms and a theoretical framework, which could be useful in explaining and predicting crop productivity dynamics. We have studied maize in irrigated and rain-fed systems at a provincial scale, from 1996 to 2009 in Spain, one of the most prominent "hot-spots" in future climate change projections. Our new approach allowed us to: (1) evaluate new structural properties such as the stability of crop yield dynamics, (2) detect nonlinear responses to climate change (thresholds and discontinuities), challenging the usual linear way of thinking, and (3) examine spatial patterns of yield losses due to water constraints and identify clusters of provinces that have been negatively affected by warming. We have reduced the uncertainty associated with climate change impacts on maize productivity by improving the understanding of the relative contributions of individual factors and providing a better spatial comprehension of the key processes. We have identified water stress and water management systems as being key causes of the yield gap, and detected vulnerable regions where efforts in research and policy should be prioritized in order to increase maize productivity.

Strategies for soil-based precision agriculture in cotton

NASA Astrophysics Data System (ADS)

Neely, Haly L.; Morgan, Cristine L. S.; Stanislav, Scott; Rouze, Gregory; Shi, Yeyin; Thomasson, J. Alex; Valasek, John; Olsenholler, Jeff

2016-05-01

The goal of precision agriculture is to increase crop yield while maximizing the use efficiency of farm resources. In this application, UAV-based systems are presenting agricultural researchers with an opportunity to study crop response to environmental and management factors in real-time without disturbing the crop. The spatial variability soil properties, which drive crop yield and quality, cannot be changed and thus keen agronomic choices with soil variability in mind have the potential to increase profits. Additionally, measuring crop stress over time and in response to management and environmental conditions may enable agronomists and plant breeders to make more informed decisions about variety selection than the traditional end-of-season yield and quality measurements. In a previous study, seed-cotton yield was measured over 4 years and compared with soil variability as mapped by a proximal soil sensor. It was found that soil properties had a significant effect on seed-cotton yield and the effect was not consistent across years due to different precipitation conditions. However, when seed-cotton yield was compared to the normalized difference vegetation index (NDVI), as measured using a multispectral camera from a UAV, predictions improved. Further improvement was seen when soil-only pixels were removed from the analysis. On-going studies are using UAV-based data to uncover the thresholds for stress and yield potential. Long-term goals of this research include detecting stress before yield is reduced and selecting better adapted varieties.

Analysis of Environmental Stress Factors Using an Artificial Growth System and Plant Fitness Optimization

PubMed Central

Lee, Meonghun; Yoe, Hyun

2015-01-01

The environment promotes evolution. Evolutionary processes represent environmental adaptations over long time scales; evolution of crop genomes is not inducible within the relatively short time span of a human generation. Extreme environmental conditions can accelerate evolution, but such conditions are often stress inducing and disruptive. Artificial growth systems can be used to induce and select genomic variation by changing external environmental conditions, thus, accelerating evolution. By using cloud computing and big-data analysis, we analyzed environmental stress factors for Pleurotus ostreatus by assessing, evaluating, and predicting information of the growth environment. Through the indexing of environmental stress, the growth environment can be precisely controlled and developed into a technology for improving crop quality and production. PMID:25874206

Weather based risks and insurances for agricultural production

NASA Astrophysics Data System (ADS)

Gobin, Anne

2015-04-01

Extreme weather events such as frost, drought, heat waves and rain storms can have devastating effects on cropping systems. According to both the agriculture and finance sectors, a risk assessment of extreme weather events and their impact on cropping systems is needed. The principle of return periods or frequencies of natural hazards is adopted in many countries as the basis of eligibility for the compensation of associated losses. For adequate risk management and eligibility, hazard maps for events with a 20-year return period are often used. Damages due to extreme events are strongly dependent on crop type, crop stage, soil type and soil conditions. The impact of extreme weather events particularly during the sensitive periods of the farming calendar therefore requires a modelling approach to capture the mixture of non-linear interactions between the crop, its environment and the occurrence of the meteorological event in the farming calendar. Physically based crop models such as REGCROP (Gobin, 2010) assist in understanding the links between different factors causing crop damage. Subsequent examination of the frequency, magnitude and impacts of frost, drought, heat stress and soil moisture stress in relation to the cropping season and crop sensitive stages allows for risk profiles to be confronted with yields, yield losses and insurance claims. The methodology is demonstrated for arable food crops, bio-energy crops and fruit. The perspective of rising risk-exposure is exacerbated further by limited aid received for agricultural damage, an overall reduction of direct income support to farmers and projected intensification of weather extremes with climate change. Though average yields have risen continuously due to technological advances, there is no evidence that relative tolerance to adverse weather events has improved. The research is funded by the Belgian Science Policy Organisation (Belspo) under contract nr SD/RI/03A.

Assessment of water use in the Spanish irrigation district "Río Adaja"

NASA Astrophysics Data System (ADS)

Naroua, Illiassou; Rodriguez-Sinobas, Leonor; Sánchez Calvo, Raúl

2013-04-01

Intensive agricultural practices combined with the increasing pressure of urbanization and the changing lifestyles, have strengthened the problems of competing users over limited water resources in a fragile and already stressed environment. Sustainable irrigated agriculture is prescribed as a policy approach that maximizes economic benefits while maintaining environmental quality. Within this framework a proper management of irrigation systems saving water is required. On the other hand, crops with high tolerance to water stress and deficit irrigation are recommended. However, crop yield, among other factors, is very sensitive to water Thus, studies addressing the relations among crop water requirements, irrigation depth and crop yield are necessary. This type of study has been carried out in the Spanish irrigation District "Río Adaja" in the year 2010-2011 with the crops: wheat, barley, sugarbeet, corn, onion, potato, sunflower, clover and carrot. A soil hydrology balance model was applied taking into account climatic data for the nearby weather station and soil characteristics. Effective precipitation was calculated by the index curve number. Crop water requirements were calculated by the FAO Penman-Monteith with the application of the dual crop coefficient. Likewise, productivity was measured by the following indexes: annual relative irrigation supply (ARIS), relative water supply (RWS), relative rainfall supply (RS) and water productivity (WP). Results show that water applied with the irrigation of clover, sugarbeet, corn and onion was less than their water requirements There was a 35 % difference between the amount of water simulated with the model and the gross amount applied during the irrigation period by the irrigation district. WP values differed among crops depending, mainly, on the crop`s market price and the amount of irrigation water. The highest values corresponded to potato and onion crops.

Effects of arsenic toxicity on morphological characters in blackgram (Vigna mungo L.) during early growth stage.

PubMed

Shamim, M Z; Pandey, A

2017-07-31

Blackgram is an important pulse crop of the tropic and sub-tropic area and has been identified as a potential crop in many countries. In the south-East Asia arsenic toxicity in soil and water is one of the most environmental problems. Crop productivity is highly affected by cultivation in arsenic polluted soil or irrigation through arsenic polluted water. The present study was conducted to evaluate the effect of arsenic (As) on fresh shoot length, fresh shoot weight, fresh root length, fresh shoot weight and total fresh biomass, The results indicate that root length is more affected than shoot length due to arsenic toxicity. The fresh shoot weight observed was more affected than fresh root weight. This study indicates that arsenic toxicity causes the deleterious effect on blackgram growth. The toxic effect of blackgram depends on the genotypic variability. Some blackgram genotypes show very less toxic effect of arsenic due to its genetic makeup. Experimental findings of study indicate that longer root length and more shoot weight in arsenic stress condition may be tolerant blackgram genotype to arsenic toxicity.

Use of Unmanned Aerial Vehicles for Improving Farm Scale Agricultural Water Management in Agriculture at a Farm Scale. A case study for field crops in the California's Central Valley

NASA Astrophysics Data System (ADS)

Medellin-Azuara, J.; Morande, J. A.; Jin, Y.; Chen, Y.; Paw U, K. T.; Viers, J. H.

2016-12-01

Traditional methods for estimating consumptive water use as evapotranspiration (ET) for agriculture in areas with water limitations such as California have always been a challenge for farmers, water managers, researchers and government agencies. Direct measurement of evapotranspiration (ET) and crop water stress in agriculture can be a cumbersome and costly task. Furthermore, spatial variability of applied water and irrigation and stress level in crops, due to inherent heterogeneity in soil conditions, topography, management practices, and lack of uniformity in water applications may affect estimates water use efficiency and water balances. This situation difficult long-term management of agroecosystems. This paper presents a case study for various areas in California's Central Valley using Unmanned Aerial Vehicles (UAVs) for a late portion of the 2016 irrigation season These estimates are compared those obtained by direct measurement (from previously deployed stations), and energy balance approaches with remotely sensed data in a selection of field crop parcels. This research improves information on water use and site conditions in agriculture by enhancing remote sensing-based estimations through the use of higher resolution multi-spectral and thermal imagery captured by UAV. We assess whether more frequent information at higher spatial resolution from UAVs can improve estimations of overall ET through energy balance and imagery. Stress levels and ET are characterized spatially to examine irrigation practices and their performance to improve water use in the agroecosystem. Ground based data such as air and crop temperature and stem water potential is collected to validate UAV aerial measurements. Preliminary results show the potential of UAV technology to improve timing, resolution and accuracy in the ET estimation and assessment of crop stress at a farm scales. Side to side comparison with ground level stations employing surface renewal, eddy covariance and energy balance provides a testbed to improve understanding of consumptive use and crop water management in water scarce irrigated agriculture regions. Keywords. California Central Valley, Agricultural Water Use, Remote Sensing, Energy Balance, Evapotranspiration, Water management,

Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield.

PubMed

Guo, Mei; Rupe, Mary A; Wei, Jun; Winkler, Chris; Goncalves-Butruille, Marymar; Weers, Ben P; Cerwick, Sharon F; Dieter, Jo Ann; Duncan, Keith E; Howard, Richard J; Hou, Zhenglin; Löffler, Carlos M; Cooper, Mark; Simmons, Carl R

2014-01-01

Crop improvement for yield and drought tolerance is challenging due to the complex genetic nature of these traits and environmental dependencies. This study reports that transgenic over-expression of Zea mays AR GOS1 (ZAR1) enhanced maize organ growth, grain yield, and drought-stress tolerance. The ZAR1 transgene exhibited environmental interactions, with yield increase under Temperate Dry and yield reduction under Temperate Humid or High Latitude environments. Native ZAR1 allele variation associated with drought-stress tolerance. Two founder alleles identified in the mid-maturity germplasm of North America now predominate in Pioneer's modern breeding programme, and have distinct proteins, promoters and expression patterns. These two major alleles show heterotic group partitioning, with one predominant in Pioneer's female and the other in the male heterotic groups, respectively. These two alleles also associate with favourable crop performance when heterozygous. Allele-specific transgene testing showed that, of the two alleles discussed here, each allele differed in their impact on yield and environmental interactions. Moreover, when transgenically stacked together the allelic pair showed yield and environmental performance advantages over either single allele, resembling heterosis effects. This work demonstrates differences in transgenic efficacy of native alleles and the differences reflect their association with hybrid breeding performance.

Dehydration-induced WRKY genes from tobacco and soybean respond to jasmonic acid treatments in BY-2 cell culture.

PubMed

Rabara, Roel C; Tripathi, Prateek; Lin, Jun; Rushton, Paul J

2013-02-15

Drought is one of the important environmental factors affecting crop production worldwide and therefore understanding the molecular response of plant to stress is an important step in crop improvement. WRKY transcription factors are one of the 10 largest transcription factor families across the green lineage. In this study, highly upregulated dehydration-induced WRKY and enzyme-coding genes from tobacco and soybean were selected from microarray data for promoter analyses. Putative stress-related cis-regulatory elements such as TGACG motif, ABRE-like elements; W and G-like sequences were identified by an in silico analyses of promoter region of the selected genes. GFP quantification of transgenic BY-2 cell culture showed these promoters direct higher expression in-response to 100 μM JA treatment compared to 100 μM ABA, 10% PEG and 85 mM NaCl treatments. Thus promoter activity upon JA treatment and enrichment of MeJA-responsive elements in the promoter of the selected genes provides insights for these genes to be jasmonic acid responsive with potential of mediating cross-talk during dehydration responses. Copyright © 2013 Elsevier Inc. All rights reserved.

Integration of environmental and spectral data for sunflower stress determination. [Red River Valley, Minnesota

NASA Technical Reports Server (NTRS)

Lillesand, T.; Seeley, M.

1983-01-01

Stress in sunflowers was assessed in western and northwestern Minnesota. Weekly ground observations (acquired in 1980 and 1981) were analyzed in concert with large scale aerial photography and concurrent LANDSAT data. Using multidate supervised and unsupervised classification procedures, it was found that all crops grown in association with sunflowers in the study area are spectrally separable from one another. Under conditions of extreme drought, severely stressed plants were differentiable from those not severely stressed, but between-crop separation was not possible. Initial regression analyses to estimate sunflower seed yield showed a sensitivity to environmental stress during the flowering and seed development stages. One of the most important biological factors related to sunflower production in the Red River Valley area was found to be the extent and severity of insect infestations.

IrrE, a Global Regulator of Extreme Radiation Resistance in Deinococcus radiodurans, Enhances Salt Tolerance in Escherichia coli and Brassica napus

PubMed Central

Zhou, Zhengfu; Yan, Yongliang; Zhang, Wei; Lu, Wei; Ping, Shuzhen; Dai, Qilin; Yuan, Menglong; Feng, Bin; Hou, Xiaoguang; Zhang, Ying; Ruiqiang; Liu, Tingting; Feng, Lu; Wang, Lei; Chen, Ming; Lin, Min

2009-01-01

Background Globally, about 20% of cultivated land is now affected by salinity. Salt tolerance is a trait of importance to all crops in saline soils. Previous efforts to improve salt tolerance in crop plants have met with only limited success. Bacteria of the genus Deinococcus are known for their ability to survive highly stressful conditions, and therefore possess a unique pool of genes conferring extreme resistance. In Deinococcus radiodurans, the irrE gene encodes a global regulator responsible for extreme radioresistance. Methodology/Principal Findings Using plate assays, we showed that IrrE protected E. coli cells against salt shock and other abiotic stresses such as oxidative, osmotic and thermal shocks. Comparative proteomic analysis revealed that IrrE functions as a switch to regulate different sets of proteins such as stress responsive proteins, protein kinases, glycerol-degrading enzymes, detoxification proteins, and growth-related proteins in E. coli. We also used quantitative RT-PCR to investigate expression of nine selected stress-responsive genes in transgenic and wild-type Brassica napus plants. Transgenic B. napus plants expressing the IrrE protein can tolerate 350 mM NaCl, a concentration that inhibits the growth of almost all crop plants. Conclusions Expression of IrrE, a global regulator for extreme radiation resistance in D. radiodurans, confers significantly enhanced salt tolerance in both E. coli and B. napus. We thus propose that the irrE gene might be used as a potentially promising transgene to improve abiotic stress tolerances in crop plants. PMID:19204796

RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance.

PubMed

Badhan, Sapna; Kole, Pravas; Ball, Andrew; Mantri, Nitin

2018-06-13

Chickpea (Cicer arietinum L.) is the second most important winter crop which is consumed globally due to its high nutritional value. Chickpea as one of the leguminous crop is important in crop rotation with cereal crops like wheat and barley. The main constraints for chickpea production are abiotic stresses such as drought, salinity, and heat. Among these, drought is a major cause of the decline in chickpea production in worldwide. Studies conducted so far have provided a limited insight into different genetic pathways associated with drought tolerance/response. In this study, the leaf tissue from shoots apical meristem stage of drought tolerant (ICC8261) and drought sensitive (ICC283) genotypes were analysed using RNA sequencing to identify genes/pathways associated with drought tolerance/sensitivity in both genotypes. It was observed that genes related to ethylene response, MYB-related protein, xyloglucan endotransglycosylase, alkane hydroxylase MAH-like, BON-1 associated, peroxidase 3, cysteine-rich and transmembrane domain, vignain and mitochondrial uncoupling were specifically up-regulated in the tolerant genotype whereas, same genes were down-regulated in sensitive genotype. The crosstalk between the different hormones and transcriptional factors involved in drought tolerance and sensitivity in both genotypes make them great candidates for future research. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Characterization of agricultural drought risk by a two-dimensional copula

NASA Astrophysics Data System (ADS)

Vergni, Lorenzo; Todisco, Francesca; Mannocchi, Francesco

2015-04-01

In this work, the joint probability distribution of two agricultural drought characteristics (Relative Severity, RS, and Onset, O) has been modeled by a two-dimensional copula. The application is illustrated with reference to a single-station case study (Perugia, Central Italy) and to the crop sunflower, widely grown in Central Italy, usually under rainfed conditions. The 86-year time series of daily precipitation and maximum and minimum temperature from the Perugia station (Central Italy) were used to simulate the soil water dynamics in the root-zone of sunflower. For each year, single seasonal values of RS and O have been quantified by applying the theory of runs to the soil water volume dynamics, with a threshold equal to the crop critical point. RS derives from the summation of the severities (i.e. total water stress) of the drought runs occurred during the growing season. The attribute 'relative' is here used because the severity value is corrected taking into account both the available water capacity of the soil and the growing season length. Thus, RS is a non-dimensional value ranging between 0 (no water stress) and 1 (maximum theoretical water stress for a given growing season length). The characteristic O describes the water stress temporal position (with respect to the growing season length) and it derives from a weighted average of the times of occurrence of the different drought runs (run severities being the weights). O is a non-dimensional value that expresses the temporal position of water stress as percentage of residual growing season, and it ranges between 0 (drought location at harvest) and 1 (drought location at seeding). The information provided by this characteristic can be considered particularly useful in agricultural drought risk management, because, as it is known, the drought impact on crop yield (being equal the severity) can vary substantially with the sensitivity of the growth stages affected by water stress conditions. The analysis showed that the best-fitting marginal distribution for both drought onset and relative severity is a truncated Gumbel distribution. The distribution parameters, estimated by a maximum log-likelihood algorithm are α=0.385 and β=0.091 for O and α=0.183 and β=0.076 for RS. The dependence structure of O and RS was investigated by several graphical and analytical techniques. Among these, the Genest-Rémillard goodness-of-fit test based on the Cramer-Von Mises statistic, has been applied. It was found that a Student copula, (with parameter 0.924 and 18 degrees of freedom) is able to adequately reproduce both the overall dependence structure and the upper tail dependence among variables. The Student copula has been finally used to obtain joint probabilities and bivariate return periods of drought onset and relative severity. To check the reliability of the drought risk assessment provided by the identified copula model, the bivariate return period of each pair (RSi, Oi) was compared with the univariate return period of the corresponding yield value, estimated for each year by means of a crop growth model, specifically calibrated and validated for sunflower in Central Italy. This comparison, taking into account the uncertainty and the complexity of the phenomenon, led to satisfactory results and enabled to identify the combinations of O and RS values that can be considered critical for sunflower in Perugia.

Monsoon variability, crop water requirement, and crop planning for kharif rice in Sagar Island, India.

PubMed

Mandal, S; Choudhury, B U; Satpati, L N

2015-12-01

In the Sagar Island of Bay of Bengal, rainfed lowland rice is the major crop, grown solely depending on erratic distribution of southwest monsoon (SM) rainfall. Lack of information on SM rainfall variability and absence of crop scheduling accordingly results in frequent occurrence of intermittent water stress and occasional crop failure. In the present study, we analyzed long period (1982-2010) SM rainfall behavior (onset, withdrawal, rainfall and wetness indices, dry and wet spells), crop water requirement (CWR, by Food and Agriculture Organization (FAO) 56), and probability of weekly rainfall occurrence (by two-parameter gamma distribution) to assess the variability and impact on water availability, CWR, and rice productivity. Finally, crop planning was suggested to overcome monsoon uncertainties on water availability and rice productivity. Study revealed that the normal onset and withdrawal weeks for SM rainfall were 22nd ± 1 and 43rd ± 2 meteorological weeks (MW), respectively. However, effective monsoon rainfall started at 24th MW (rainfall 92.7 mm, p > 56.7 % for 50 mm rainfall) and was terminated by the end of 40th MW (rainfall 90.7 mm, p < 59.6 % for 50 mm rainfall). During crop growth periods (seed to seed, 21st to 45th MW), the island received an average weekly rainfall of 65.1 ± 25.9 mm, while the corresponding weekly CWR was 47.8 ± 5.4 mm. Despite net water surplus of 353.9 mm during crop growth periods, there was a deficit of 159.5 mm water during MW of 18-23 (seedling raising) and MW of 41-45 (flowering to maturity stages). Water stress was observed in early lag vegetative stage of crop growth (32nd MW). The total dry spell frequency during panicle initiation and heading stage was computed as 40 of which 6 dry spells were >7 days in duration and reflected a significant (p < 0.05) increasing trend (at 0.22 days year(-1)) over the years (1982-2010). The present study highlights the adaptive capacity of crop planning including abiotic stress-tolerant cultivars to monsoon rainfall variability for sustaining rainfed rice production vis-à-vis food and livelihood security in vulnerable islands of coastal ecosystem.

Global crop yield response to extreme heat stress under multiple climate change futures

NASA Astrophysics Data System (ADS)

Deryng, D.; Conway, D.; Ramankutty, N.; Price, J.; Warren, R.

2014-12-01

Extreme heat stress during the crop reproductive period can be critical for crop productivity. Projected changes in the frequency and severity of extreme climatic events are expected to negatively impact crop yields and global food production. This study applies the global crop model PEGASUS to quantify, for the first time at the global scale, impacts of extreme heat stress on maize, spring wheat and soybean yields resulting from 72 climate change scenarios for the 21st century. Our results project maize to face progressively worse impacts under a range of RCPs but spring wheat and soybean to improve globally through to the 2080s due to CO2 fertilization effects, even though parts of the tropic and sub-tropic regions could face substantial yield declines. We find extreme heat stress at anthesis (HSA) by the 2080s (relative to the 1980s) under RCP 8.5, taking into account CO2 fertilization effects, could double global losses of maize yield (dY = -12.8 ± 6.7% versus -7.0 ± 5.3% without HSA), reduce projected gains in spring wheat yield by half (dY = 34.3 ± 13.5% versus 72.0 ± 10.9% without HSA) and in soybean yield by a quarter (dY = 15.3 ± 26.5% versus 20.4 ± 22.1% without HSA). The range reflects uncertainty due to differences between climate model scenarios; soybean exhibits both positive and negative impacts, maize is generally negative and spring wheat generally positive. Furthermore, when assuming CO2 fertilization effects to be negligible, we observe drastic climate mitigation policy as in RCP 2.6 could avoid more than 80% of the global average yield losses otherwise expected by the 2080s under RCP 8.5. We show large disparities in climate impacts across regions and find extreme heat stress adversely affects major producing regions and lower income countries.

Global crop yield response to extreme heat stress under multiple climate change futures

NASA Astrophysics Data System (ADS)

Deryng, Delphine; Conway, Declan; Ramankutty, Navin; Price, Jeff; Warren, Rachel

2014-03-01

Extreme heat stress during the crop reproductive period can be critical for crop productivity. Projected changes in the frequency and severity of extreme climatic events are expected to negatively impact crop yields and global food production. This study applies the global crop model PEGASUS to quantify, for the first time at the global scale, impacts of extreme heat stress on maize, spring wheat and soybean yields resulting from 72 climate change scenarios for the 21st century. Our results project maize to face progressively worse impacts under a range of RCPs but spring wheat and soybean to improve globally through to the 2080s due to CO2 fertilization effects, even though parts of the tropic and sub-tropic regions could face substantial yield declines. We find extreme heat stress at anthesis (HSA) by the 2080s (relative to the 1980s) under RCP 8.5, taking into account CO2 fertilization effects, could double global losses of maize yield (ΔY = -12.8 ± 6.7% versus - 7.0 ± 5.3% without HSA), reduce projected gains in spring wheat yield by half (ΔY = 34.3 ± 13.5% versus 72.0 ± 10.9% without HSA) and in soybean yield by a quarter (ΔY = 15.3 ± 26.5% versus 20.4 ± 22.1% without HSA). The range reflects uncertainty due to differences between climate model scenarios; soybean exhibits both positive and negative impacts, maize is generally negative and spring wheat generally positive. Furthermore, when assuming CO2 fertilization effects to be negligible, we observe drastic climate mitigation policy as in RCP 2.6 could avoid more than 80% of the global average yield losses otherwise expected by the 2080s under RCP 8.5. We show large disparities in climate impacts across regions and find extreme heat stress adversely affects major producing regions and lower income countries.

Anticipating on amplifying water stress: Optimal crop production supported by anticipatory water management

NASA Astrophysics Data System (ADS)

Bartholomeus, Ruud; van den Eertwegh, Gé; Simons, Gijs

2015-04-01

Agricultural crop yields depend largely on the soil moisture conditions in the root zone. Drought but especially an excess of water in the root zone and herewith limited availability of soil oxygen reduces crop yield. With ongoing climate change, more prolonged dry periods alternate with more intensive rainfall events, which changes soil moisture dynamics. With unaltered water management practices, reduced crop yield due to both drought stress and waterlogging will increase. Therefore, both farmers and water management authorities need to be provided with opportunities to reduce risks of decreasing crop yields. In The Netherlands, agricultural production of crops represents a market exceeding 2 billion euros annually. Given the increased variability in meteorological conditions and the resulting larger variations in soil moisture contents, it is of large economic importance to provide farmers and water management authorities with tools to mitigate risks of reduced crop yield by anticipatory water management, both at field and at regional scale. We provide the development and the field application of a decision support system (DSS), which allows to optimize crop yield by timely anticipation on drought and waterlogging situations. By using this DSS, we will minimize plant water stress through automated drainage and irrigation management. In order to optimize soil moisture conditions for crop growth, the interacting processes in the soil-plant-atmosphere system need to be considered explicitly. Our study comprises both the set-up and application of the DSS on a pilot plot in The Netherlands, in order to evaluate its implementation into daily agricultural practice. The DSS focusses on anticipatory water management at the field scale, i.e. the unit scale of interest to a farmer. We combine parallel field measurements ('observe'), process-based model simulations ('predict'), and the novel Climate Adaptive Drainage (CAD) system ('adjust') to optimize soil moisture conditions. CAD is used both for controlled drainage practices and for sub-irrigation. The DSS has a core of the plot-scale SWAP model (soil-water-atmosphere-plant), extended with a process-based module for the simulation of oxygen stress for plant roots. This module involves macro-scale and micro-scale gas diffusion, as well as the plant physiological demand of oxygen, to simulate transpiration reduction due to limited oxygen availability. Continuous measurements of soil moisture content, groundwater level, and drainage level are used to calibrate the SWAP model each day. This leads to an optimal reproduction of the actual soil moisture conditions by data assimilation in the first step in the DSS process. During the next step, near-future (+10 days) soil moisture conditions and drought and oxygen stress are predicted using weather forecasts. Finally, optimal drainage levels to minimize stress are simulated, which can be established by CAD. Linkage to a grid-based hydrological simulation model (SPHY) facilitates studying the spatial dynamics of soil moisture and associated implications for management at the regional scale. Thus, by using local-scale measurements, process-based models and weather forecasts to anticipate on near-future conditions, not only field-scale water management but also regional surface water management can be optimized both in space and time.

Opportunistic Market-Driven Regional Shifts of Cropping Practices Reduce Food Production Capacity of China

NASA Astrophysics Data System (ADS)

Yuan, Wenping; Liu, Shuguang; Liu, Wei; Zhao, Shuqing; Dong, Wenjie; Tao, Fulu; Chen, Min; Lin, Hui

2018-04-01

China is facing the challenge of feeding a growing population with the declining cropland and increasing shortage of water resources under the changing climate. This study identified that the opportunistic profit-driven shifts of planting areas and crop species composition have strongly reduced the food production capacity of China. First, the regional cultivation patterns of major crops in China have substantially shifted during the past five decades. Southeast and South China, the regions with abundant water resources and fewer natural disasters, have lost large planting areas of cropland in order to pursue industry and commerce. Meanwhile, Northeast and Northwest China, the regions with low water resources and frequent natural disasters, have witnessed increases in planting areas. These macroshifts have reduced the national food production by 1.02% per year. The lost grain production would have been enough to feed 13 million people. Second, the spatial shifts have been accompanied by major changes in crop species composition, with substantial increases in planting area and production of maize, due to its low water consumption and high economic returns. Consequently, the stockpile of maize in China has accounted for more than half of global stockpile, and the stock to use ratio of maize in China has exceeded the reliable level. Market-driven regional shifts of cropping practices have resulted in larger irrigation requirements and aggravated environmental stresses. Our results highlighted the need for Chinese food policies to consider the spatial shifts in cultivation, and the planting crop compositions limited by regional water resources and climate change.

Differentially delayed root proteome responses to salt stress in sugar cane varieties.

PubMed

Pacheco, Cinthya Mirella; Pestana-Calsa, Maria Clara; Gozzo, Fabio Cesar; Mansur Custodio Nogueira, Rejane Jurema; Menossi, Marcelo; Calsa, Tercilio

2013-12-06

Soil salinity is a limiting factor to sugar cane crop development, although in general plants present variable mechanisms of tolerance to salinity stress. The molecular basis underlying these mechanisms can be inferred by using proteomic analysis. Thus, the objective of this work was to identify differentially expressed proteins in sugar cane plants submitted to salinity stress. For that, a greenhouse experiment was established with four sugar cane varieties and two salt conditions, 0 mM (control) and 200 mM NaCl. Physiological and proteomics analyses were performed after 2 and 72 h of stress induction by salt. Distinct physiological responses to salinity stress were observed in the varieties and linked to tolerance mechanisms. In proteomic analysis, the roots soluble protein fraction was extracted, quantified, and analyzed through bidimensional electrophoresis. Gel images analyses were done computationally, where in each contrast only one variable was considered (salinity condition or variety). Differential spots were excised, digested by trypsin, and identified via mass spectrometry. The tolerant variety RB867515 showed the highest accumulation of proteins involved in growth, development, carbohydrate and energy metabolism, reactive oxygen species metabolization, protein protection, and membrane stabilization after 2 h of stress. On the other hand, the presence of these proteins in the sensitive variety was verified only in stress treatment after 72 h. These data indicate that these stress responses pathways play a role in the tolerance to salinity in sugar cane, and their effectiveness for phenotypical tolerance depends on early stress detection and activation of the coding genes expression.

A vacuolar H(+)-pyrophosphatase differential activation and energy coupling integrate the responses of weeds and crops to drought stress.

PubMed

Venancio, Josimara Barcelos; Catunda, Michelle Guedes; Ogliari, Juarez; Rima, Janaína Aparecida Hottz; Okorokova-Facanha, Anna Lvovna; Okorokov, Lev Alexandrovitich; Facanha, Arnoldo Rocha

2014-06-01

Cyperus rotundus L. is a C4 weed of large vegetative and reproductive vigor endowed with competitive advantages over most crop species mainly under adverse environmental conditions. Vacuole functions are critical for the mechanisms of drought resistance, and here the modulation of the primary system of vacuolar ion transport is investigated during a transient water stress imposed to this weed and to C4 crop species (Zea mays L.). The vacuolar H(+) pumps, the H(+)-ATPase and H(+)-PPiase, expression, activities and the energy coupling were spectrophotometrically investigated as key elements in the differential drought-resistance mechanisms developed by weeds and crops. In C. rotundus tonoplasts, ATP hydrolysis was more sensitive to drought than its coupled H(+) transport, which was in turn at least 3-folds faster than that mediated by the H(+)-PPiase. Its PPi hydrolysis was only slightly affected by severe water deficit, contrasting with the disruption induced in the PPi-dependent H(+)-gradient. This effect was antagonized by plant rehydration as the H(+)-PPiase activity was highly stimulated, reassuming a coupled PPi-driven H(+) pumping. Maize tonoplasts exhibited 2-4 times lower hydrolytic activities than that of C. rotundus, but were able to overactivate specifically PPi-dependent H(+) pumping in response to stress relief, resulting in an enhanced H(+)-pumps coupling efficiency. These results together with immunoanalysis revealed profiles consistent with pre- and post-translational changes occurring on the tonoplast H(+)-pumps, which differ between weeds and crops upon water deficit. The evidences highlight an unusual modulation of the H(+)-PPiase energy coupling as a key biochemical change related to environmental stresses adaptive capacity of plants. Copyright © 2014 Elsevier B.V. All rights reserved.

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During times of Water Stress

DOE PAGES

Gunda, Thushara; Turner, B. L.; Tidwell, Vincent C.

2018-03-14

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responsesmore » to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. In conclusion, continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.« less

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During times of Water Stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunda, Thushara; Turner, B. L.; Tidwell, Vincent C.

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responsesmore » to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. In conclusion, continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.« less

The Influential Role of Sociocultural Feedbacks on Community-Managed Irrigation System Behaviors During Times of Water Stress

NASA Astrophysics Data System (ADS)

Gunda, T.; Turner, B. L.; Tidwell, V. C.

2018-04-01

Sociohydrological studies use interdisciplinary approaches to explore the complex interactions between physical and social water systems and increase our understanding of emergent and paradoxical system behaviors. The dynamics of community values and social cohesion, however, have received little attention in modeling studies due to quantification challenges. Social structures associated with community-managed irrigation systems around the world, in particular, reflect these communities' experiences with a multitude of natural and social shocks. Using the Valdez acequia (a communally-managed irrigation community in northern New Mexico) as a simulation case study, we evaluate the impact of that community's social structure in governing its responses to water availability stresses posed by climate change. Specifically, a system dynamics model (developed using insights from community stakeholders and multiple disciplines that captures biophysical, socioeconomic, and sociocultural dynamics of acequia systems) was used to generate counterfactual trajectories to explore how the community would behave with streamflow conditions expected under climate change. We found that earlier peak flows, combined with adaptive measures of shifting crop selection, allowed for greater production of higher value crops and fewer people leaving the acequia. The economic benefits were lost, however, if downstream water pressures increased. Even with significant reductions in agricultural profitability, feedbacks associated with community cohesion buffered the community's population and land parcel sizes from more detrimental impacts, indicating the community's resilience under natural and social stresses. Continued exploration of social structures is warranted to better understand these systems' responses to stress and identify possible leverage points for strengthening community resilience.

A project to evaluate moisture stress and phenological factors in corn and soybean areas of southwestern and south-central Minnesota

NASA Technical Reports Server (NTRS)

Rust, R. H.; Robert, P. (Principal Investigator)

1981-01-01

The capability of aerial color infrared photography for identifying and locating soilscapes most susceptible to drought development or those having different soil drainages was evaluated. Although west central and southwestern Minnesota had a significant precipitation deficit during the 1980 crop season, indications of plant stress were not observed either from ground observation or through interpretation of imagery at the selected sampling sites. Well-drained soil was more depleted during the "maximium green peak" period than the poorly drained soil. The recharge was more evident on the poorly drained site in the fall. Measurements of leaf water potential and leaf temperature for corn and soybean leaves were made by multispectral band scanner and recorded for analysis.

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

PubMed Central

Carter, Kelsey R.; Carrell, Alyssa A.; Jun, Se-Ran; Jawdy, Sara S.; Vélez, Jessica M.; Gunter, Lee E.; Yang, Zamin; Nookaew, Intawat; Engle, Nancy L.; Lu, Tse-Yuan S.; Schadt, Christopher W.; Tschaplinski, Timothy J.; Tuskan, Gerald A.; Pelletier, Dale A.; Weston, David J.

2018-01-01

ABSTRACT Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress. IMPORTANCE The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth. PMID:29404422

Abiotic Stresses Shift Belowground Populus -Associated Bacteria Toward a Core Stress Microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timm, Collin M.; Carter, Kelsey R.; Carrell, Alyssa A.

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome ofPopulus deltoideschanges in response to diverse environmental conditions, including water limitation, light limitation (shading),more » and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.« less

Abiotic Stresses Shift Belowground Populus -Associated Bacteria Toward a Core Stress Microbiome

DOE PAGES

Timm, Collin M.; Carter, Kelsey R.; Carrell, Alyssa A.; ...

2018-01-23

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome ofPopulus deltoideschanges in response to diverse environmental conditions, including water limitation, light limitation (shading),more » and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.« less

Conventional and simplified canopy temperature indices predict water stress in sunflower

USDA-ARS?s Scientific Manuscript database

Two indicators based on remotely-sensed canopy temperature were used in northern Colorado to monitor water stress in sunflower under six levels of regulated deficit irrigation. The two indicators included the widely-used Crop Water Stress Index (CWSI) and the new Degrees Above Non-stressed Canopy at...

Increasing Crop Diversity Mitigates Weather Variations and Improves Yield Stability

PubMed Central

Gaudin, Amélie C. M.; Tolhurst, Tor N.; Ker, Alan P.; Janovicek, Ken; Tortora, Cristina; Martin, Ralph C.; Deen, William

2015-01-01

Cropping sequence diversification provides a systems approach to reduce yield variations and improve resilience to multiple environmental stresses. Yield advantages of more diverse crop rotations and their synergistic effects with reduced tillage are well documented, but few studies have quantified the impact of these management practices on yields and their stability when soil moisture is limiting or in excess. Using yield and weather data obtained from a 31-year long term rotation and tillage trial in Ontario, we tested whether crop rotation diversity is associated with greater yield stability when abnormal weather conditions occur. We used parametric and non-parametric approaches to quantify the impact of rotation diversity (monocrop, 2-crops, 3-crops without or with one or two legume cover crops) and tillage (conventional or reduced tillage) on yield probabilities and the benefits of crop diversity under different soil moisture and temperature scenarios. Although the magnitude of rotation benefits varied with crops, weather patterns and tillage, yield stability significantly increased when corn and soybean were integrated into more diverse rotations. Introducing small grains into short corn-soybean rotation was enough to provide substantial benefits on long-term soybean yields and their stability while the effects on corn were mostly associated with the temporal niche provided by small grains for underseeded red clover or alfalfa. Crop diversification strategies increased the probability of harnessing favorable growing conditions while decreasing the risk of crop failure. In hot and dry years, diversification of corn-soybean rotations and reduced tillage increased yield by 7% and 22% for corn and soybean respectively. Given the additional advantages associated with cropping system diversification, such a strategy provides a more comprehensive approach to lowering yield variability and improving the resilience of cropping systems to multiple environmental stresses. This could help to sustain future yield levels in challenging production environments. PMID:25658914

Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean

PubMed Central

Neupane, Achal; Nepal, Madhav P.; Piya, Sarbottam; Subramanian, Senthil; Rohila, Jai S.; Reese, R. Neil; Benson, Benjamin V.

2013-01-01

Mitogen-activated protein kinase (MAPK) genes in eukaryotes regulate various developmental and physiological processes including those associated with biotic and abiotic stresses. Although MAPKs in some plant species including Arabidopsis have been identified, they are yet to be identified in soybean. Major objectives of this study were to identify GmMAPKs, assess their evolutionary relationships, and analyze their functional divergence. We identified a total of 38 MAPKs, eleven MAPKKs, and 150 MAPKKKs in soybean. Within the GmMAPK family, we also identified a new clade of six genes: four genes with TEY and two genes with TQY motifs requiring further investigation into possible legume-specific functions. The results indicated the expansion of the GmMAPK families attributable to the ancestral polyploidy events followed by chromosomal rearrangements. The GmMAPK and GmMAPKKK families were substantially larger than those in other plant species. The duplicated GmMAPK members presented complex evolutionary relationships and functional divergence when compared to their counterparts in Arabidopsis. We also highlighted existing nomenclatural issues, stressing the need for nomenclatural consistency. GmMAPK identification is vital to soybean crop improvement, and novel insights into the evolutionary relationships will enhance our understanding about plant genome evolution. PMID:24137047

OsSUV3 functions in cadmium and zinc stress tolerance in rice (Oryza sativa L. cv IR64).

PubMed

Sahoo, Ranjan Kumar; Tuteja, Narendra

2014-01-01

Protein of nuclear encoded SUV3 (suppressor of Var 3) gene is a DNA and RNA helicase, localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. To overcome the abiotic stress-induced loss of crop yield, a multi-stress tolerant trait is required. Beside salinity stress the heavy metals including cadmium and zinc also affect the yield and quality of food crops. Since rice is a one of the staple food therefore it is important to develop a multi-stress including salinity and metal tolerant variety. Recently we have reported the role of OsSUV3 in salinity stress tolerance in rice; however, its role in metal stress has not been studied so far. Here we report that in response to cadmium and zinc stress the OsSUV3 transcript level is induced in rice and its overexpression in transgenic IR64 rice plants confers the metal stress tolerance. In addition to its previously reported role in salinity stress tolerance, this study further shows the role of OsSUV3 helicase in cadmium and zinc stress tolerance suggesting its involvement in multi-stress tolerance.

Drought tolerance and proteomics studies of transgenic wheat containing the maize C4 phosphoenolpyruvate carboxylase (PEPC) gene.

PubMed

Qin, Na; Xu, Weigang; Hu, Lin; Li, Yan; Wang, Huiwei; Qi, Xueli; Fang, Yuhui; Hua, Xia

2016-11-01

Enhancing drought tolerance of crops has been a great challenge in crop improvement. Here, we report the maize phosphoenolpyruvate carboxylase (PEPC) gene was able to confer drought tolerance and increase grain yield in transgenic wheat (Triticum aestivum L.) plants. The improved of drought tolerance was associated with higher levels of proline, soluble sugar, soluble protein, and higher water use efficiency. The transgenic wheat plants had also a more extensive root system as well as increased photosynthetic capacity during stress treatments. The increased grain yield of the transgenic wheat was contributed by improved biomass, larger spike and grain numbers, and heavier 1000-grain weight under drought-stress conditions. Under non-stressed conditions, there were no significant increases in these of the measured traits except for photosynthetic rate when compared with parental wheat. Proteomic research showed that the expression levels of some proteins, including chlorophyll A-B binding protein and pyruvate, phosphate dikinase, which are related to photosynthesis, PAP fibrillin, which is involved in cytoskeleton synthesis, S-adenosylmethionine synthetase, which catalyzes methionine synthesis, were induced in the transgenic wheat under drought stress. Additionally, the expression of glutamine synthetase, which is involved in ammonia assimilation, was induced by drought stress in the wheat. Our study shows that PEPC can improve both stress tolerance and grain yield in wheat, demonstrating the efficacy of PEPC in crop improvement.

Optical fluorescence biosensor for plant water stress detection

NASA Astrophysics Data System (ADS)

Chong, Jenny P. C.; Liew, O. W.; Li, B. Q.; Asundi, A. K.

2007-05-01

Precision farming in arable agriculture and horticulture allows conservative use of resources that are applied according to plant needs. The growing concern for sustainability in crop production has accentuated the significance of our work to develop a rapid, sensitive and non-destructive spectroscopic method for real-time monitoring of plant water stress. Elucidation of crop water status before the onset of irreversible cellular damage is critical for effective water management to ensure maximum crop yield and profit margin. A two-component bio-sensing system comprising transgenic 'Indicator Plants' and a spectrometer-linked stereoscopic microscope was developed to detect early signs of water stress before the permanent wilting point is reached. The 'Indicator Plants' are transgenic Petunia hybrida genetically engineered with a drought-responsive promoter-linked enhanced green fluorescent protein marker gene (EGFP). No EGFP fluorescence was detected prior to induction of dehydration stress. Fluorescence emission intensity increased with dehydration period and was found mainly in the stems, leaf veins and leaf tips. While fluorescence emission above endogenous background was detectable after 2 hours of water stress treatment, the plants reached permanent wilting point after 6 hours, showing that our system was able to detect water stress prior to plant entry into the stage of irreversible damage. Future work will be geared towards overcoming biological and instrument-related difficulties encountered in our initial detection system.

Evaluation of a Community Reintegration Outpatient Program Service for Community-Dwelling Persons with Spinal Cord Injury

PubMed Central

Bain, Patricia; Hébert, Debbie; Hitzig, Sander L.

2014-01-01

Objective. To evaluate the effectiveness of a community reintegration outpatient (CROP) service for promoting well-being and community participation following spinal cord injury (SCI). Participants. Community-dwelling adults (N = 14) with traumatic and nontraumatic SCI. Interventions. The CROP service is a 12-week (1 × week; 120 minutes) interprofessional closed therapeutic education service. Main Outcome Measure(s). Moorong Self-Efficacy Scale (MSES); Impact on Participation and Autonomy (IPA); Positive Affect and Negative Affect Scale (PANAS); Coping Inventory of Stressful Situations (CISS); World Health Organization Quality of Life (WHOQOL-BREF); semistructured qualitative interviews. Methods. Twenty-one participants were recruited from two subsequent CROP services, with only 14 persons completing all data assessments. Data were collected at baseline (week 0), at exit (week 12), and at a three-month follow-up. Semistructured interviews were conducted at exit. Results. Self-efficacy (MSES) and positive affect (PANAS) improved from baseline to exit (P < .05), but the changes were not maintained at follow-up. Qualitative analysis identified four major themes related to therapeutic benefits: (1) role of self; (2) knowledge acquisition; (3) skill application; and (4) group processes. Conclusions. Participation in a therapeutic education service has the potential to improve well-being in persons with SCI, but there is a need to identify strategies to maintain long-term gains. PMID:25574397

Drought will not leave your glass empty: Low risk of hydraulic failure revealed by long-term drought observations in world's top wine regions.

PubMed

Charrier, Guillaume; Delzon, Sylvain; Domec, Jean-Christophe; Zhang, Li; Delmas, Chloe E L; Merlin, Isabelle; Corso, Deborah; King, Andrew; Ojeda, Hernan; Ollat, Nathalie; Prieto, Jorge A; Scholach, Thibaut; Skinner, Paul; van Leeuwen, Cornelis; Gambetta, Gregory A

2018-01-01

Grapevines are crops of global economic importance that will face increasing drought stress because many varieties are described as highly sensitive to hydraulic failure as frequency and intensity of summer drought increase. We developed and used novel approaches to define water stress thresholds for preventing hydraulic failure, which were compared to the drought stress experienced over a decade in two of the world's top wine regions, Napa and Bordeaux. We identified the physiological thresholds for drought-induced mortality in stems and leaves and found small intervarietal differences. Long-term observations in Napa and Bordeaux revealed that grapevines never reach their lethal water-potential thresholds under seasonal droughts, owing to a vulnerability segmentation promoting petiole embolism and leaf mortality. Our findings will aid farmers in reducing water use without risking grapevine hydraulic integrity.

Drought will not leave your glass empty: Low risk of hydraulic failure revealed by long-term drought observations in world’s top wine regions

PubMed Central

Charrier, Guillaume; Delzon, Sylvain; Domec, Jean-Christophe; Zhang, Li; Delmas, Chloe E. L.; Merlin, Isabelle; Corso, Deborah; King, Andrew; Ojeda, Hernan; Ollat, Nathalie; Prieto, Jorge A.; Scholach, Thibaut; Skinner, Paul; van Leeuwen, Cornelis; Gambetta, Gregory A.

2018-01-01

Grapevines are crops of global economic importance that will face increasing drought stress because many varieties are described as highly sensitive to hydraulic failure as frequency and intensity of summer drought increase. We developed and used novel approaches to define water stress thresholds for preventing hydraulic failure, which were compared to the drought stress experienced over a decade in two of the world’s top wine regions, Napa and Bordeaux. We identified the physiological thresholds for drought-induced mortality in stems and leaves and found small intervarietal differences. Long-term observations in Napa and Bordeaux revealed that grapevines never reach their lethal water-potential thresholds under seasonal droughts, owing to a vulnerability segmentation promoting petiole embolism and leaf mortality. Our findings will aid farmers in reducing water use without risking grapevine hydraulic integrity. PMID:29404405

Osmotic adjustment and the growth response of seven vegetable crops following water-deficit stress. [Phaseolus vulgaris L. ; Beta vulgaris L. ; Abelmoschus esculentus; Pisum sativum L. ; Capsicum annuum L. ; Spinacia oleracea L. ; Lycopersicon esculentum Mill

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wullschleger, S.D.; Oosterhuis, D.M.

Growth-chamber studies were conducted to examine the ability of seven vegetable crops- Blue Lake beam (Phaseolus vulgaris L.) Detroit Dark Red beet (Beta vulgaris L.) Burgundy okra (Abelmoschus esculentus) (Moench), Little Marvel pea (Pisum sativum L), California Wonder bell pepper (Capsicum annuum L), New Zealand spinach (Spinacia oleracea L), and Beefsteak tomato (Lycopersicon esculentum Mill.) - to adjust osmotically in response to water-deficit stress. Water stress was imposed by withholding water for 3 days, and the adjustment of leaf and root osmotic potentials upon relief of the stress and rehydration were monitored with thermocouple psychrometers. Despite similar reductions in leafmore » water potential and stomatal conductance among the species studied reductions in lead water potential an stomatal conductance among the species, crop-specific differences were observed in leak and root osmotic adjustment. Leaf osmotic adjustment was observed for bean, pepper, and tomato following water-deficit stress. Root osmotic adjustment was significant in bean, okra, pea and tomato. Furthermore, differences in leaf and root osmotic adjustment were also observed among five tomato cultivars. Leaf osmotic adjustment was not associated with the maintenance of leaf growth following water-deficit stress, since leaf expansion of water-stressed bean and pepper, two species capable of osmotic adjustment, was similar to that of spinach, which exhibited no leaf osmotic adjustment.« less

Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) confers tolerance to both nitrogen starvation and drought stress in Arabidopsis.

PubMed

Li, Wei-wei; Chen, Ming; Zhong, Li; Liu, Jia-ming; Xu, Zhao-shi; Li, Lian-cheng; Zhou, Yong-Bin; Guo, Chang-Hong; Ma, You-Zhi

2015-12-25

Autophagy is an evolutionarily conserved biological process in all eukaryotes for the degradation of intracellular components for nutrient recycling. Autophagy is known to be involved in responses to low nitrogen stress in Arabidopsis. Foxtail millet has strong abiotic stress resistance to both low nutrient and drought stress. However, to date, there have only been a few genes reported to be related with abiotic stress resistance in foxtail millet. In this study, we identified an autophagy-related gene, SiATG8a, from foxtail millet. SiATG8a is mainly expressed in stems and its expression was dramatically induced by drought stress and nitrogen starvation treatments. SiATG8a was localized in the membrane and cytoplasm of foxtail millet. Overexpression of SiATG8a in Arabidopsis conferred tolerance to both nitrogen starvation and to drought stress. Under nitrogen starvation conditions, the SiATG8a transgenic plants had larger root and leaf areas and accumulated more total nitrogen than wild-type plants. The transgenic plants had lower total protein concentrations than did the WT plants. Under drought stress, the SiATG8a transgenic plants had higher survival rates, chlorophyll content, and proline content, but had lower MDA content than wild type plants. Taken together, our results represent the first identified case where overexpression of autophagy related gene can simultaneously improve plant resistance to low nitrogen and drought stresses. These findings implicate plant autophagy in plant stress responses to low nitrogen and drought and should be helpful in efforts to improve stresses resistance to nitrogen starvation and drought of crops by genetic transformation. Copyright © 2015 Elsevier Inc. All rights reserved.

Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress

DOE PAGES

Dash, Madhumita; Yordanov, Yordan S.; Georgieva, Tatyana; ...

2017-02-10

Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here in this study, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) genemore » with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.« less

Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dash, Madhumita; Yordanov, Yordan S.; Georgieva, Tatyana

Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here in this study, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) genemore » with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.« less

Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan.

PubMed

Nithin, Chandran; Thomas, Amal; Basak, Jolly; Bahadur, Ranjit Prasad

2017-11-15

Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Hence, genome-wide identification of miRNAs and lncRNAs in C. cajan is extremely important to understand their role in PTGR with a possible implication to generate improve variety of crops. We have identified 616 mature miRNAs in C. cajan belonging to 118 families, of which 578 are novel and not reported in MirBase21. A total of 1373 target sequences were identified for 180 miRNAs. Of these, 298 targets were characterized at the protein level. Besides, we have also predicted 3919 lncRNAs. Additionally, we have identified 87 of the predicted lncRNAs to be targeted by 66 miRNAs. miRNA and lncRNAs in plants are known to control a variety of traits including yield, quality and stress tolerance. Owing to its agricultural importance and medicinal value, the identified miRNA, lncRNA and their targets in C. cajan may be useful for genome editing to improve better quality crop. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of C. cajan agricultural traits.

Constitutive and stress-inducible overexpression of a native aquaporin gene (MusaPIP2;6) in transgenic banana plants signals its pivotal role in salt tolerance.

PubMed

Sreedharan, Shareena; Shekhawat, Upendra K Singh; Ganapathi, Thumballi R

2015-05-01

High soil salinity constitutes a major abiotic stress and an important limiting factor in cultivation of crop plants worldwide. Here, we report the identification and characterization of a aquaporin gene, MusaPIP2;6 which is involved in salt stress signaling in banana. MusaPIP2;6 was firstly identified based on comparative analysis of stressed and non-stressed banana tissue derived EST data sets and later overexpression in transgenic banana plants was performed to study its tangible functions in banana plants. The overexpression of MusaPIP2;6 in transgenic banana plants using constitutive or inducible promoter led to higher salt tolerance as compared to equivalent untransformed control plants. Cellular localization assay performed using transiently transformed onion peel cells indicated that MusaPIP2;6 protein tagged with green fluorescent protein was translocated to the plasma membrane. MusaPIP2;6-overexpressing banana plants displayed better photosynthetic efficiency and lower membrane damage under salt stress conditions. Our results suggest that MusaPIP2;6 is involved in salt stress signaling and tolerance in banana.

Drinking From the Same Straw: Crop Growth and Evidence of Water Transfer from Native Shrubs to Millet in a Sahelian Agro-Ecosystem

NASA Astrophysics Data System (ADS)

Bogie, N. A.; Bayala, R.; Fogel, M. L.; Diedhiou, I.; Dick, R.; Ghezzehei, T. A.

2015-12-01

A changing climate along with human and animal population pressure can have a devastating effect on crop yields and food security in the Sudano-Sahel. Agricultural solutions to address soil degradation and crop water stress are needed to combat this increasingly difficult situation. Significant differences in crop success have been observed in peanut and millet grown in association with two native evergreen shrubs Piliostigma reticulatum, and Guiera senegalensis at the sites of Nioro du Rip and Keur Matar, respectively. We investigate how farmers can increase crop productivity by capitalizing on the evolutionary adaptation of native shrubs to the harsh Sudano-Sahelian environment as well as the physical mechanisms at work in the system that can lead to more robust yields. Soil moisture, transpiration rate, crop growth and soil and leaf water potential data were collected during a dry season millet irrigation experiment where stress was imposed in the intercropped system. Despite lower soil moisture content, crops grown in association with shrubs have increased biomass production and a faster development cycle. An isotopic tracer study investigating hydraulic redistribution was carried out by injecting deuterated water into the roots of three shrubs at one meter depth and sampling shrubs and nearby crops for isotopic analysis of plant water. Deuterium Enriched water was found in the shrubs of two out of three plots. Deuterium enriched water was found in the crops and shrubs in all three plots. These findings build on work that was completed in 2004 at the site, but point to larger differences in crop growth and strong evidence for the sharing of hydraulically redistributed water. Using even the limited resources that farmers possess, this agroforestry technique can be expanded over wide swaths of the Sahel.

Plant Water Stress Affects Interactions Between an Invasive and a Naturalized Aphid Species on Cereal Crops.

PubMed

Foote, N E; Davis, T S; Crowder, D W; Bosque-Pérez, N A; Eigenbrode, S D

2017-06-01

In cereal cropping systems of the Pacific Northwestern United States (PNW), climate change is projected to increase the frequency of drought during summer months, which could increase water stress for crop plants. Yet, it remains uncertain how interactions between herbivore species are affected by drought stress. Here, interactions between two cereal aphids present in PNW cereal systems, Metopolophium festucae (Theobald) subsp. cerealium (a newly invasive species) and Rhopalosiphum padi L. (a naturalized species), were tested relative to wheat water stress. When aphids were confined in leaf cages on wheat, asymmetrical facilitation occurred; per capita fecundity of R. padi was increased by 46% when M. festucae cerealium was also present, compared to when only R. padi was present. Imposed water stress did not influence this interaction. When aphids were confined on whole wheat plants, asymmetrical competition occurred; cocolonization inhibited M. festucae cerealium population growth but did not affect R. padi population growth. Under conditions of plant water stress, however, the inhibitory effect of R. padi on M. festucae cerealium was not observed. We conclude that beneficial effects of cocolonization on R. padi are due to a localized plant response to M. festucae cerealium feeding, and that cocolonization of plants is likely to suppress M. festucae cerealium populations under ample water conditions, but not when plants are water stressed. This suggests that plant responses to water stress alter the outcome of competition between herbivore species, with implications for the structure of pest communities on wheat during periods of drought. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Climatically driven yield variability of major crops in Khakassia (South Siberia)

NASA Astrophysics Data System (ADS)

Babushkina, Elena A.; Belokopytova, Liliana V.; Zhirnova, Dina F.; Shah, Santosh K.; Kostyakova, Tatiana V.

2018-06-01

We investigated the variability of yield of the three main crop cultures in the Khakassia Republic: spring wheat, spring barley, and oats. In terms of yield values, variability characteristics, and climatic response, the agricultural territory of Khakassia can be divided into three zones: (1) the Northern Zone, where crops yield has a high positive response to the amount of precipitation, May-July, and a moderately negative one to the temperatures of the same period; (2) the Central Zone, where crops yield depends mainly on temperatures; and (3) the Southern Zone, where climate has the least expressed impact on yield. The dominant pattern in the crops yield is caused by water stress during periods of high temperatures and low moisture supply with heat stress as additional reason. Differences between zones are due to combinations of temperature latitudinal gradient, precipitation altitudinal gradient, and the presence of a well-developed hydrological network and the irrigational system as moisture sources in the Central Zone. More detailed analysis shows differences in the climatic sensitivity of crops during phases of their vegetative growth and grain development and, to a lesser extent, during harvesting period. Multifactor linear regression models were constructed to estimate climate- and autocorrelation-induced variability of the crops yield. These models allowed prediction of the possibility of yield decreasing by at least 2-11% in the next decade due to increasing of the regional summer temperatures.

Climatically driven yield variability of major crops in Khakassia (South Siberia)

NASA Astrophysics Data System (ADS)

Babushkina, Elena A.; Belokopytova, Liliana V.; Zhirnova, Dina F.; Shah, Santosh K.; Kostyakova, Tatiana V.

2017-12-01

We investigated the variability of yield of the three main crop cultures in the Khakassia Republic: spring wheat, spring barley, and oats. In terms of yield values, variability characteristics, and climatic response, the agricultural territory of Khakassia can be divided into three zones: (1) the Northern Zone, where crops yield has a high positive response to the amount of precipitation, May-July, and a moderately negative one to the temperatures of the same period; (2) the Central Zone, where crops yield depends mainly on temperatures; and (3) the Southern Zone, where climate has the least expressed impact on yield. The dominant pattern in the crops yield is caused by water stress during periods of high temperatures and low moisture supply with heat stress as additional reason. Differences between zones are due to combinations of temperature latitudinal gradient, precipitation altitudinal gradient, and the presence of a well-developed hydrological network and the irrigational system as moisture sources in the Central Zone. More detailed analysis shows differences in the climatic sensitivity of crops during phases of their vegetative growth and grain development and, to a lesser extent, during harvesting period. Multifactor linear regression models were constructed to estimate climate- and autocorrelation-induced variability of the crops yield. These models allowed prediction of the possibility of yield decreasing by at least 2-11% in the next decade due to increasing of the regional summer temperatures.

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

PubMed Central

Ferreira, Thais H. S.; Tsunada, Max S.; Bassi, Denis; Araújo, Pedro; Mattiello, Lucia; Guidelli, Giovanna V.; Righetto, Germanna L.; Gonçalves, Vanessa R.; Lakshmanan, Prakash; Menossi, Marcelo

2017-01-01

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments. PMID:28690620

Cowpea: a legume crop for a challenging environment.

PubMed

Carvalho, Márcia; Lino-Neto, Teresa; Rosa, Eduardo; Carnide, Valdemar

2017-10-01

Cowpea is a grain legume native from Africa and is a primary source of protein for millions of people in sub-Saharan Africa and other parts of the developing world. The main important characteristics of this crop include a good protein quality with a high nutritional value, its nitrogen-fixing ability, and an ability to be more drought- and heat-tolerant than most of its legume relatives. In a research perspective, studies of cowpea are relatively scarce, despite its relevance to agriculture in the developing world and its resilience to stress. The present review provides an overview of different aspects of cowpea, with a special emphasis on the molecular markers for assessing genetic diversity, as well as on biochemical and transcriptomic data with respect to evaluating cowpea drought stress tolerance. The integration of both datasets will be useful for the improvement of cowpea because research on drought stress tolerance is of major interest for this crop in a challenging environment. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.).

PubMed

Liang, Wanwan; Yang, Bo; Yu, Bao-Jun; Zhou, Zili; Li, Cui; Jia, Ming; Sun, Yun; Zhang, Yue; Wu, Feifei; Zhang, Hanfeng; Wang, Boya; Deyholos, Michael K; Jiang, Yuan-Qing

2013-06-11

Eukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. Canola (oilseed rape, Brassica napus) is a major crop in temperate regions. Identification and characterization of MAPK and MAPK kinases (MAPKK/MKK) of canola will help to elucidate their role in responses to abiotic and biotic stresses. We describe the identification and analysis of seven MKK (BnaMKK) and 12 MPK (BnaMPK) members from canola. Sequence alignments and phylogenetic analyses of the predicted amino acid sequences of BnaMKKs and BnaMPKs classified them into four different groups. We also examined the subcellular localization of four and two members of BnaMKK and BnaMPK gene families, respectively, using green fluorescent protein (GFP) and, found GFP signals in both nuclei and cytoplasm. Furthermore, we identified several interesting interaction pairs through yeast two-hybrid (Y2H) analysis of interactions between BnaMKKs and BnaMPKs, as well as BnaMPK and BnaWRKYs. We defined contiguous signaling modules including BnaMKK9-BnaMPK1/2-BnaWRKY53, BnaMKK2/4/5-BnaMPK3/6-BnaWRKY20/26 and BnaMKK9-BnaMPK5/9/19/20. Of these, several interactions had not been previously described in any species. Selected interactions were validated in vivo by a bimolecular fluorescence complementation (BiFC) assay. Transcriptional responses of a subset of canola MKK and MPK genes to stimuli including fungal pathogens, hormones and abiotic stress treatments were analyzed through real-time RT-PCR and we identified a few of BnaMKKs and BnaMPKs responding to salicylic acid (SA), oxalic acid (OA), Sclerotinia sclerotiorum or other stress conditions. Comparisons of expression patterns of putative orthologs in canola and Arabidopsis showed that transcript expression patterns were generally conserved, with some differences suggestive of sub-functionalization. We identified seven MKK and 12 MPK genes from canola and examined their phylogenetic relationships, transcript expression patterns, subcellular localization, and protein-protein interactions. Not all expression patterns and interactions were conserved between canola and Arabidopsis, highlighting the limitations of drawing inferences about crops from model species. The data presented here provide the first systematic description of MKK-MPK-WRKY signaling modules in canola and will further improve our understanding of defense responses in general and provide a basis for future crop improvement.

Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants

PubMed Central

Almeida, Diego M.; Oliveira, M. Margarida; Saibo, Nelson J. M.

2017-01-01

Abstract Soil salinity is a major abiotic stress that results in considerable crop yield losses worldwide. However, some plant genotypes show a high tolerance to soil salinity, as they manage to maintain a high K+/Na+ ratio in the cytosol, in contrast to salt stress susceptible genotypes. Although, different plant genotypes show different salt tolerance mechanisms, they all rely on the regulation and function of K+ and Na+ transporters and H+ pumps, which generate the driving force for K+ and Na+ transport. In this review we will introduce salt stress responses in plants and summarize the current knowledge about the most important ion transporters that facilitate intra- and intercellular K+ and Na+ homeostasis in these organisms. We will describe and discuss the regulation and function of the H+-ATPases, H+-PPases, SOS1, HKTs, and NHXs, including the specific tissues where they work and their response to salt stress. PMID:28350038

Challenges facing European agriculture and possible biotechnological solutions.

PubMed

Ricroch, Agnès; Harwood, Wendy; Svobodová, Zdeňka; Sági, László; Hundleby, Penelope; Badea, Elena Marcela; Rosca, Ioan; Cruz, Gabriela; Salema Fevereiro, Manuel Pedro; Marfà Riera, Victoria; Jansson, Stefan; Morandini, Piero; Bojinov, Bojin; Cetiner, Selim; Custers, René; Schrader, Uwe; Jacobsen, Hans-Joerg; Martin-Laffon, Jacqueline; Boisron, Audrey; Kuntz, Marcel

2016-10-01

Agriculture faces many challenges to maximize yields while it is required to operate in an environmentally sustainable manner. In the present study, we analyze the major agricultural challenges identified by European farmers (primarily related to biotic stresses) in 13 countries, namely Belgium, Bulgaria, the Czech Republic, France, Germany, Hungary, Italy, Portugal, Romania, Spain, Sweden, UK and Turkey, for nine major crops (barley, beet, grapevine, maize, oilseed rape, olive, potato, sunflower and wheat). Most biotic stresses (BSs) are related to fungi or insects, but viral diseases, bacterial diseases and even parasitic plants have an important impact on yield and harvest quality. We examine how these challenges have been addressed by public and private research sectors, using either conventional breeding, marker-assisted selection, transgenesis, cisgenesis, RNAi technology or mutagenesis. Both national surveys and scientific literature analysis followed by text mining were employed to evaluate genetic engineering (GE) and non-GE approaches. This is the first report of text mining of the scientific literature on plant breeding and agricultural biotechnology research. For the nine major crops in Europe, 128 BS challenges were identified with 40% of these addressed neither in the scientific literature nor in recent European public research programs. We found evidence that the private sector was addressing only a few of these "neglected" challenges. Consequently, there are considerable gaps between farmer's needs and current breeding and biotechnology research. We also provide evidence that the current political situation in certain European countries is an impediment to GE research in order to address these agricultural challenges in the future. This study should also contribute to the decision-making process on future pertinent international consortia to fill the identified research gaps.

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress.

PubMed

Leisner, Courtney P; Yendrek, Craig R; Ainsworth, Elizabeth A

2017-12-12

Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms underpinning crop responses to abiotic stress. Soybean (Glycine max L. Merr. cv. Pioneer 93B15) was grown in natural production environments with projected changes to environmental conditions predicted for the end of the century, including decreased precipitation, increased tropospheric ozone concentrations ([O 3 ]), or increased temperature. All three environmental stresses significantly decreased leaf-level photosynthesis and stomatal conductance, leading to significant losses in seed yield. This was driven by a significant decrease in the number of pods per node for all abiotic stress treatments. To understand the underlying transcriptomic response involved in the yield response to environmental stress, RNA-Sequencing analysis was performed on the soybean seed coat, a tissue that plays an essential role in regulating carbon and nitrogen transport to developing seeds. Gene expression analysis revealed 49, 148 and 1,576 differentially expressed genes in the soybean seed coat in response to drought, elevated [O 3 ] and elevated temperature, respectively. Elevated [O 3 ] and drought did not elicit substantive transcriptional changes in the soybean seed coat. However, this may be due to the timing of sampling and does not preclude impacts of those stresses on different tissues or different stages in seed coat development. Expression of genes involved in DNA replication and metabolic processes were enriched in the seed coat under high temperate stress, suggesting that the timing of events that are important for cell division and proper seed development were altered in a stressful growth environment.

Seed priming and transgenerational drought memory improves tolerance against salt stress in bread wheat.

PubMed

Tabassum, Tahira; Farooq, Muhammad; Ahmad, Riaz; Zohaib, Ali; Wahid, Abdul

2017-09-01

This study was conducted to evaluate the potential of seed priming following terminal drought on tolerance against salt stress in bread wheat. Drought was imposed in field sown wheat at reproductive stage (BBCH growth stage 49) and was maintained till physiological maturity (BBCH growth stage 83). Seeds of bread wheat, collected from crop raised under terminal drought and/or well-watered conditions, were subjected to hydropriming and osmopriming (with 1.5% CaCl 2 ) and were sown in soil-filled pots. After stand establishment, salt stress treatments viz. 10 mM NaCl (control) and 100 mM NaCl were imposed. Seed from terminal drought stressed source had less fat (5%), and more fibers (11%), proteins (22%) and total soluble phenolics (514%) than well-watered seed source. Salt stress reduced the plant growth, perturbed water relations and decreased yield. However, an increase in osmolytes accumulation (4-18%), malondialdehyde (MDA) (27-35%) and tissue Na + contents (149-332%) was observed under salt stress. The seeds collected from drought stressed crop had better tolerance against salt stress as indicated by better yield (28%), improved water relations (3-18%), osmolytes accumulation (21-33%), and less MDA (8%) and Na contents (35%) than progeny of well-watered crop. Seed priming, osmopriming in particular, further improved the tolerance against salt stress through improvement in leaf area, water relations, leaf proline, glycine betaine and grain yield while lowering MDA and Na + contents. In conclusion, changed seed composition during terminal drought and seed priming improved the salt tolerance in wheat by modulating the water relations, osmolytes accumulation and lipid peroxidation. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Detecting Crop Functional Response to a Heat Wave using Airborne Reflectance and Sun-induced Chlorophyll Fluorescence Measurements

NASA Astrophysics Data System (ADS)

Yang, P.; Van der Tol, C.; Rascher, U.; Damm, A.; Schickling, A.; Verhoef, W.

2016-12-01

This study presents an analysis of airborne measured reflectance (R) and solar-induced chlorophyll fluorescence (SIF) as indicators of high temperature stress in agricultural crops. We used atmospherically corrected R and retrievals of SIF in the O2-A band as obtained from HyPlant data over C3 crops (rapeseed, wheat and barley) and a C4 crop (corn) in Germany before (30th June) and during (2nd July) a heat wave in 2015. The availability of airborne data during this heat wave allowed us to detect fluorescence emission efficiency changes as an indicator of crop photosynthetic performance in response to temperature fluctuations. We found that SIF is affected relatively stronger by heat stress than R. This is according to expectation, because the R spectrum is determined by leaf properties and canopy structure, whereas top-of-canopy (TOC) SIF is also affected by the temperature dependent efficiencies of photochemical and non-photochemical quenching of fluorescence. With the model 'Soil Canopy Observation of Photosynthesis and Energy fluxes (SCOPE), we differentiated leaf optical parameters and canopy structure from the fluorescence quantum emission efficiency (FQE), i.e. the ratio of fluorescence production to light absorption of photosystems. The leaf optical and canopy structure parameters were retrieved from R by inversion of the radiative transfer module 'RTMo' of SCOPE. The retrieved parameters were further used to estimate the FQE from SIF measurements. It appeared that both the leaf water content CW and the FQE responded to the heat wave, but the responses were different for C3 and C4 crops. A slight reduction of CW occurred in C3 crops between the two days, but not in the C4 crop. The reduction of FQE was only significant in C3 crops, and ranged from 18% to 31% for various C3 species. These findings agree with the general knowledge that C4 plants are better adapted to high temperature than C3 plants, and comply with simulations from a biochemical model for C3 and C4 crops in SCOPE. It is concluded that the combination of hyperspectral R and SIF enables the differentiation of long-term and short term responses to heat stress.

Abscisic Acid and abiotic stress signaling.

PubMed

Tuteja, Narendra

2007-05-01

Abiotic stress is severe environmental stress, which impairs crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in responce to changing physiological and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to stress include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression through interacting with their corrosponding cis-acting elements such as DRE/CRT, ABRE and MYCRS/MYBRS, respectively. Understanding these mechanisms is important to improve stress tolerance in crops plants. This article first describes the general pathway for plant stress response followed by roles of ABA and transcription factors in stress tolerance including the regulation of ABA biosynthesis.

Abscisic Acid and Abiotic Stress Signaling

PubMed Central

2007-01-01

Abiotic stress is severe environmental stress, which impairs crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in responce to changing physiological and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to stress include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression through interacting with their corrosponding cis-acting elements such as DRE/CRT, ABRE and MYCRS/MYBRS, respectively. Understanding these mechanisms is important to improve stress tolerance in crops plants. This article first describes the general pathway for plant stress response followed by roles of ABA and transcription factors in stress tolerance including the regulation of ABA biosynthesis. PMID:19516981

Global Expression Profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi

PubMed Central

Chawade, Aakash; Lindlöf, Angelica; Olsson, Björn; Olsson, Olof

2013-01-01

Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated. PMID:24349120

Plant responses to environmental stresses—from gene to biotechnology

PubMed Central

Ahanger, Mohammad Abass; Akram, Nudrat Aisha; Ashraf, Muhammad; Alyemeni, Mohammed Nasser; Wijaya, Leonard

2017-01-01

Abstract Increasing global population, urbanization and industrialization are increasing the rate of conversion of arable land into wasteland. Supplying food to an ever-increasing population is one of the biggest challenges that agriculturalists and plant scientists are currently confronting. Environmental stresses make this situation even graver. Despite the induction of several tolerance mechanisms, sensitive plants often fail to survive under environmental extremes. New technological approaches are imperative. Conventional breeding methods have a limited potential to improve plant genomes against environmental stress. Recently, genetic engineering has contributed enormously to the development of genetically modified varieties of different crops such as cotton, maize, rice, canola and soybean. The identification of stress-responsive genes and their subsequent introgression or overexpression within sensitive crop species are now being widely carried out by plant scientists. Engineering of important tolerance pathways, like antioxidant enzymes, osmolyte accumulation, membrane-localized transporters for efficient compartmentation of deleterious ions and accumulation of essential elements and resistance against pests or pathogens is also an area that has been intensively researched. In this review, the role of biotechnology and its successes, prospects and challenges in developing stress-tolerant crop cultivars are discussed. PMID:28775828

A Dehydration-Induced Eukaryotic Translation Initiation Factor iso4G Identified in a Slow Wilting Soybean Cultivar Enhances Abiotic Stress Tolerance in Arabidopsis

PubMed Central

Gallino, Juan P.; Ruibal, Cecilia; Casaretto, Esteban; Fleitas, Andrea L.; Bonnecarrère, Victoria; Borsani, Omar; Vidal, Sabina

2018-01-01

Water is usually the main limiting factor for soybean productivity worldwide and yet advances in genetic improvement for drought resistance in this crop are still limited. In the present study, we investigated the physiological and molecular responses to drought in two soybean contrasting genotypes, a slow wilting N7001 and a drought sensitive TJS2049 cultivars. Measurements of stomatal conductance, carbon isotope ratios and accumulated dry matter showed that N7001 responds to drought by employing mechanisms resulting in a more efficient water use than TJS2049. To provide an insight into the molecular mechanisms that these cultivars employ to deal with water stress, their early and late transcriptional responses to drought were analyzed by suppression subtractive hybridization. A number of differentially regulated genes from N7001 were identified and their expression pattern was compared between in this genotype and TJS2049. Overall, the data set indicated that N7001 responds to drought earlier than TJ2049 by up-regulating a larger number of genes, most of them encoding proteins with regulatory and signaling functions. The data supports the idea that at least some of the phenotypic differences between slow wilting and drought sensitive plants may rely on the regulation of the level and timing of expression of specific genes. One of the genes that exhibited a marked N7001-specific drought induction profile encoded a eukaryotic translation initiation factor iso4G (GmeIFiso4G-1a). GmeIFiso4G-1a is one of four members of this protein family in soybean, all of them sharing high sequence identity with each other. In silico analysis of GmeIFiso4G-1 promoter sequences suggested a possible functional specialization between distinct family members, which can attain differences at the transcriptional level. Conditional overexpression of GmeIFiso4G-1a in Arabidopsis conferred the transgenic plants increased tolerance to osmotic, salt, drought and low temperature stress, providing a strong experimental evidence for a direct association between a protein of this class and general abiotic stress tolerance mechanisms. Moreover, the results of this work reinforce the importance of the control of protein synthesis as a central mechanism of stress adaptation and opens up for new strategies for improving crop performance under stress. PMID:29552022

A Dehydration-Induced Eukaryotic Translation Initiation Factor iso4G Identified in a Slow Wilting Soybean Cultivar Enhances Abiotic Stress Tolerance in Arabidopsis.

PubMed

Gallino, Juan P; Ruibal, Cecilia; Casaretto, Esteban; Fleitas, Andrea L; Bonnecarrère, Victoria; Borsani, Omar; Vidal, Sabina

2018-01-01

Water is usually the main limiting factor for soybean productivity worldwide and yet advances in genetic improvement for drought resistance in this crop are still limited. In the present study, we investigated the physiological and molecular responses to drought in two soybean contrasting genotypes, a slow wilting N7001 and a drought sensitive TJS2049 cultivars. Measurements of stomatal conductance, carbon isotope ratios and accumulated dry matter showed that N7001 responds to drought by employing mechanisms resulting in a more efficient water use than TJS2049. To provide an insight into the molecular mechanisms that these cultivars employ to deal with water stress, their early and late transcriptional responses to drought were analyzed by suppression subtractive hybridization. A number of differentially regulated genes from N7001 were identified and their expression pattern was compared between in this genotype and TJS2049. Overall, the data set indicated that N7001 responds to drought earlier than TJ2049 by up-regulating a larger number of genes, most of them encoding proteins with regulatory and signaling functions. The data supports the idea that at least some of the phenotypic differences between slow wilting and drought sensitive plants may rely on the regulation of the level and timing of expression of specific genes. One of the genes that exhibited a marked N7001-specific drought induction profile encoded a eukaryotic translation initiation factor iso4G ( GmeIFiso4G-1a ). GmeIFiso4G-1a is one of four members of this protein family in soybean, all of them sharing high sequence identity with each other. In silico analysis of GmeIFiso4G-1 promoter sequences suggested a possible functional specialization between distinct family members, which can attain differences at the transcriptional level. Conditional overexpression of GmeIFiso4G-1a in Arabidopsis conferred the transgenic plants increased tolerance to osmotic, salt, drought and low temperature stress, providing a strong experimental evidence for a direct association between a protein of this class and general abiotic stress tolerance mechanisms. Moreover, the results of this work reinforce the importance of the control of protein synthesis as a central mechanism of stress adaptation and opens up for new strategies for improving crop performance under stress.

Development of dynamic wheat crop model in ISAM and estimation of impacts of environmental factors on wheat production in India

NASA Astrophysics Data System (ADS)

Gahlot, S.; Lin, T. S.; Jain, A. K.; Baidya Roy, S.; Sehgal, V. K.; Dhakar, R.

2017-12-01

With changing environmental conditions, such as climate and elevated atmospheric CO2 concentrations, questions about food security can be answered by modeling crops based on our understanding of the dynamic crop growth processes and interactions between the crops and their environment in the form of carbon, water and energy fluxes. These interactions and their effect on cropland ecosystems are non-linear because of the feedback mechanisms. Hence, process-based modelling approach can be used to conduct numerical experiments to derive insights into these processes and interactive feedbacks. In this study we have implemented dynamic crop growth processes for wheat into a data-modeling framework, Integrated Science Assessment Model (ISAM), to estimate the impacts of different factors like CO2 fertilization, irrigation, nitrogen limitation and climate change on wheat in India. In specific, we have implemented wheat-specific phenology, C3 photosynthesis mechanism and phenology-specific carbon allocation schemes for assimilated carbon to leaf, stem, root and grain pools. Crop growth limiting stress factors like nutrients, temperature and light have been included. The impact of high temperatures on leaf senescence, anthesis and grain filling has been modeled and found to be causing significant reduction in yield in the recent years. Field data from an experimental wheat site located at the Indian Agricultural Research Institute (IARI), New Delhi, India has been collected for aboveground biomass and leaf area index (LAI) for two growing seasons 2014-15 and 2015-16. This data has been used to study the phenology, growing season length, thermal requirements and growth stages of wheat. Using the field data, the dynamic model for wheat has been evaluated for the site level seasonal variability in leaf area index (LAI) and aboveground biomass. The variations in carbon, water and energy fluxes, plant height and rooting depth have been analyzed on the site level. Model experiments have been performed to calculate the yield for wheat for India for the historical years. In order to identify wheat production regions in India that are prone to one or multiple stresses in years to come, model experiments have been performed based on future climate scenarios RCP 4.5 and 8.5.

Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis.

PubMed

Ordóñez-Baquera, Perla Lucía; González-Rodríguez, Everardo; Aguado-Santacruz, Gerardo Armando; Rascón-Cruz, Quintín; Conesa, Ana; Moreno-Brito, Verónica; Echavarria, Raquel; Dominguez-Viveros, Joel

2017-02-01

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate signal transduction, development, metabolism, and stress responses in plants through post-transcriptional degradation and/or translational repression of target mRNAs. Several studies have addressed the role of miRNAs in model plant species, but miRNA expression and function in economically important forage crops, such as Bouteloua gracilis (Poaceae), a high-quality and drought-resistant grass distributed in semiarid regions of the United States and northern Mexico remain unknown. We applied high-throughput sequencing technology and bioinformatics analysis and identified 31 conserved miRNA families and 53 novel putative miRNAs with different abundance of reads in chlorophyllic cell cultures derived from B. gracilis. Some conserved miRNA families were highly abundant and possessed predicted targets involved in metabolism, plant growth and development, and stress responses. We also predicted additional identified novel miRNAs with specific targets, including B. gracilis ESTs, which were detected under drought stress conditions. Here we report 31 conserved miRNA families and 53 putative novel miRNAs in B. gracilis. Our results suggested the presence of regulatory miRNAs involved in modulating physiological and stress responses in this grass species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transcriptome Analysis of Two Species of Jute in Response to Polyethylene Glycol (PEG)- induced Drought Stress.

PubMed

Yang, Zemao; Dai, Zhigang; Lu, Ruike; Wu, Bibo; Tang, Qing; Xu, Ying; Cheng, Chaohua; Su, Jianguang

2017-11-29

Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.

Aluminum stress signaling in plants

PubMed Central

Baluska, Frantisek; Matsumoto, Hideaki

2009-01-01

Aluminum (Al) toxicity is a major constraint for crop production in acidic soil worldwide. When the soil pH is lower than 5, Al3+ is released to the soil and enters into root tip cell ceases root development of plant. In acid soil with high mineral content, Al is the major cause of phytotoxicity. The target of Al toxicity is the root tip, in which Al exposure causes inhibition of cell elongation and cell division, leading to root stunting accompanied by reduced water and nutrient uptake. A variety of genes have been identified that are induced or repressed upon Al exposure. At tissue level, the distal part of the transition zone is the most sensitive to Al. At cellular and molecular level, many cell components are implicated in the Al toxicity including DNA in nucleus, numerous cytoplastic compounds, mitochondria, the plasma membrane and the cell wall. Although it is difficult to distinguish the primary targets from the secondary effects so far, understanding of the target sites of the Al toxicity is helpful for elucidating the mechanisms by which Al exerts its deleterious effects on root growth. To develop high tolerance against Al stress is the major goal of plant sciences. This review examines our current understanding of the Al signaling with the physiological, genetic and molecular approaches to improve the crop performance under the Al toxicity. New discoveries will open up new avenues of molecular/physiological inquiry that should greatly advance our understanding of Al tolerance mechanisms. Additionally, these breakthroughs will provide new molecular resources for improving the crop Al tolerance via molecular-assisted breeding and biotechnology. PMID:19820334

Proteomic Techniques and Management of Flooding Tolerance in Soybean.

PubMed

Komatsu, Setsuko; Tougou, Makoto; Nanjo, Yohei

2015-09-04

Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant, and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and grain yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean. There were limitations in soybean materials, such as mutants and varieties, while they were abundant in rice and Arabidopsis. In this review, plant proteomic technologies are introduced and flooding tolerance mechanisms of soybeans are summarized to assist in the improvement of flooding tolerance in soybeans. This work will expedite transgenic or marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Role of Ethylene and Its Cross Talk with Other Signaling Molecules in Plant Responses to Heavy Metal Stress1

PubMed Central

Thao, Nguyen Phuong; Khan, M. Iqbal R.; Thu, Nguyen Binh Anh; Hoang, Xuan Lan Thi; Asgher, Mohd; Khan, Nafees A.; Tran, Lam-Son Phan

2015-01-01

Excessive heavy metals (HMs) in agricultural lands cause toxicities to plants, resulting in declines in crop productivity. Recent advances in ethylene biology research have established that ethylene is not only responsible for many important physiological activities in plants but also plays a pivotal role in HM stress tolerance. The manipulation of ethylene in plants to cope with HM stress through various approaches targeting either ethylene biosynthesis or the ethylene signaling pathway has brought promising outcomes. This review covers ethylene production and signal transduction in plant responses to HM stress, cross talk between ethylene and other signaling molecules under adverse HM stress conditions, and approaches to modify ethylene action to improve HM tolerance. From our current understanding about ethylene and its regulatory activities, it is believed that the optimization of endogenous ethylene levels in plants under HM stress would pave the way for developing transgenic crops with improved HM tolerance. PMID:26246451

The Art of Being Flexible: How to Escape from Shade, Salt, and Drought1

PubMed Central

Pierik, Ronald; Testerink, Christa

2014-01-01

Environmental stresses, such as shading of the shoot, drought, and soil salinity, threaten plant growth, yield, and survival. Plants can alleviate the impact of these stresses through various modes of phenotypic plasticity, such as shade avoidance and halotropism. Here, we review the current state of knowledge regarding the mechanisms that control plant developmental responses to shade, salt, and drought stress. We discuss plant hormones and cellular signaling pathways that control shoot branching and elongation responses to shade and root architecture modulation in response to drought and salinity. Because belowground stresses also result in aboveground changes and vice versa, we then outline how a wider palette of plant phenotypic traits is affected by the individual stresses. Consequently, we argue for a research agenda that integrates multiple plant organs, responses, and stresses. This will generate the scientific understanding needed for future crop improvement programs aiming at crops that can maintain yields under variable and suboptimal conditions. PMID:24972713

Parsing multiple processes of high temperature impacts on corn/soybean yield using a newly developed CLM-APSIM modeling framework

NASA Astrophysics Data System (ADS)

Peng, B.; Guan, K.; Chen, M.

2016-12-01

Future agricultural production faces a grand challenge of higher temperature under climate change. There are multiple physiological or metabolic processes of how high temperature affects crop yield. Specifically, we consider the following major processes: (1) direct temperature effects on photosynthesis and respiration; (2) speed-up growth rate and the shortening of growing season; (3) heat stress during reproductive stage (flowering and grain-filling); (4) high-temperature induced increase of atmospheric water demands. In this work, we use a newly developed modeling framework (CLM-APSIM) to simulate the corn and soybean growth and explicitly parse the above four processes. By combining the strength of CLM in modeling surface biophysical (e.g., hydrology and energy balance) and biogeochemical (e.g., photosynthesis and carbon-nitrogen interactions), as well as that of APSIM in modeling crop phenology and reproductive stress, the newly developed CLM-APSIM modeling framework enables us to diagnose the impacts of high temperature stress through different processes at various crop phenology stages. Ground measurements from the advanced SoyFACE facility at University of Illinois is used here to calibrate, validate, and improve the CLM-APSIM modeling framework at the site level. We finally use the CLM-APSIM modeling framework to project crop yield for the whole US Corn Belt under different climate scenarios.

Unlocking the potential of orphan legumes.

PubMed

Cullis, Christopher; Kunert, Karl J

2017-04-01

Orphan, or underutilized, legumes are domesticated legumes with useful properties, but with less importance than major world crops due to use and supply constraints. However, they play a significant role in many developing countries, providing food security and nutrition to consumers, as well as income to resource-poor farmers. They have been largely neglected by both researchers and industry due to their limited economic importance in the global market. Orphan legumes are better adapted than the major legume crops to extreme soil and climatic conditions, with high tolerance to abiotic environmental stresses such as drought. As a stress response they can also produce compounds with pharmaceutical value. Orphan legumes are therefore a likely source of important traits for introduction into major crops to aid in combating the stresses associated with global climate change. Modern large-scale genomics techniques are now being applied to many of these previously understudied crops, with the first successes reported in the genomics area. However, greater investment of resources and manpower are necessary if the potential of orphan legumes is to be unlocked and applied in the future. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A critical review on fungi mediated plant responses with special emphasis to Piriformospora indica on improved production and protection of crops.

PubMed

Ansari, Mohammad Wahid; Trivedi, Dipesh Kumar; Sahoo, Ranjan Kumar; Gill, Sarvajeet Singh; Tuteja, Narendra

2013-09-01

The beneficial fungi are potentially useful in agriculture sector to avail several services to crop plants such as water status, nutrient enrichment, stress tolerance, protection, weed control and bio-control. Natural agro-ecosystem relies on fungi because of it takes part in soil organic matter decomposition, nutrient acquisition, organic matter recycling, nutrient recycling, antagonism against plant pests, and crop management. The crucial role of fungi in normalizing the toxic effects of phenols, HCN and ROS by β-CAS, ACC demainase and antioxidant enzymes in plants is well documented. Fungi also play a part in various physiological processes such as water uptake, stomatal movement, mineral uptake, photosynthesis and biosynthesis of lignan, auxins and ethylene to improve growth and enhance plant fitness to cope heat, cold, salinity, drought and heavy metal stress. Here, we highlighted the ethylene- and cyclophilin A (CypA)-mediated response of Piriformospora indica for sustainable crop production under adverse environmental conditions. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Marker-assisted selection in plant breeding for salinity tolerance.

PubMed

Ashraf, M; Akram, N A; Mehboob-Ur-Rahman; Foolad, M R

2012-01-01

Marker-assisted selection (MAS) is the process of using morphological, biochemical, or DNA markers as indirect selection criteria for selecting agriculturally important traits in crop breeding. This process is used to improve the effectiveness or efficiency of selection for the traits of interest in breeding programs. The significance of MAS as a tool for crop improvement has been extensively investigated in different crop -species and for different traits. The use of MAS for manipulating simple/qualitative traits is straightforward and has been well reported. However, MAS for the improvement of complex/polygenic traits, including plant tolerance/resistance to abiotic stresses, is more complicated, although its usefulness has been recognized. With the recent advances in marker technology, including high-throughput genotyping of plants, together with the development of nested association mapping populations, it is expected that the utility of MAS for breeding for stress tolerance traits will increase. In this chapter, we describe the basic procedure for using MAS in crop breeding for salt tolerance.

When and What Meteorological Stresses Will Maize Crops Meet in the future in France?

NASA Astrophysics Data System (ADS)

Caubel, J.

2015-12-01

Climate change is expected to modify overall climatic conditions and therefore, suitability for cropping. Assessment of when and what meteorological stresses will crops meet in the future is highly useful for planners and land managers who can apply adaptation strategies to improve agricultural potentialities. We propose to evaluate the impacts of climate change on suitability for maize cropping in terms of ecophysiology (e.g., heat stress during grain filling), yield quality (e.g., thermal conditions on protein content) and cultural practices performance (e.g., days available for harvest according to risk of waterlogged soil compaction) in two French areas. The Midi-Pyrénées (southern) and Ile-de-France (northern) regions were chosen as representing the two distinct climates when dividing France into southern and northern parts. The Midi-Pyrénées region is a major irrigated maize producer but could become penalizing in the future because of heat and water stress. By contrast, northern France could become a more suitable area thanks to the expected increasing temperature. To confirm our assumptions, we used the method assessment for crop-climate suitability developed in Caubel et al. (2015) and based on the sub-annual analysis of agroclimatic indicators calculated over phenological periods. Indicators have been calculated using climatic data from 1950 to 2100 simulated by the global climate ARPEGE at the meso-scale SAFRAN (8 km resolution) for the two areas and forced by a greenhouse effect corresponding to the SRES A1B scenario (similar to RCP 6.0). The evaluation was done for two distinct varieties in terms of precocity. Agroclimatic indicators characterizing water deficit and water excess impacts on crop were calculated for three soils with contrasting soil water reserves and depths. Finally, the evaluation was performed with a unique sowing date (the current one), and with an optimized sowing date according to water and thermal requirements for emergence. Consequences on phenology and therefore meteorological stresses enabled to decide where and when adapting the sowing date will be useful for improving maize potentiality. This work is carried out under the research program ORACLE (Opportunities and Risks of Agrosystems & forests in response to CLimate, socio-economic and policy changEs in France).

Environmental study of ERTS-1 imagery: Lake Champlain and Vermont

NASA Technical Reports Server (NTRS)

Lind, A. O.; Henson, E. B.; Pelton, J. O.

1973-01-01

Environmental concerns of the State of Vermont currently being stressed include water quality in Lake Champlain and a state-wide land use and capability plan. Significant results obtained from ERTS-1 relate directly to the above concerns. Industrial water pollution and turbidity in Lake Champlain have been identified and mapped and the ERTS pollution data will be used in the developing court suit which Vermont has initiated against the polluters. ERTS imagery has also provided a foundation for updating and revising land use inventories. Major classes of land use have been identified and mapped, and substantial progress has been made toward the mapping of such land use divisions as crop and forest type, and wetlands.

Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.).

PubMed

Muthamilarasan, Mehanathan; Khandelwal, Rohit; Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.

Plants under stress by parasitic plants.

PubMed

Hegenauer, Volker; Körner, Max; Albert, Markus

2017-08-01

In addition to other biotic stresses, parasitic plants pose an additional threat to plants and cause crop losses, worldwide. Plant parasites directly connect to the vasculature of host plants thereby stealing water, nutrients, and carbohydrates consequently leading to tremendously reduced biomass and losses in seed yields of the infected host plants. Initial steps to understand the molecular resistance mechanisms and the successes in ancient and recent breeding efforts will provide fundamental knowledge to further generate crop plants that will resist attacks by plant parasites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetically modified (GM) crops: milestones and new advances in crop improvement.

PubMed

Kamthan, Ayushi; Chaudhuri, Abira; Kamthan, Mohan; Datta, Asis

2016-09-01

New advances in crop genetic engineering can significantly pace up the development of genetically improved varieties with enhanced yield, nutrition and tolerance to biotic and abiotic stresses. Genetically modified (GM) crops can act as powerful complement to the crops produced by laborious and time consuming conventional breeding methods to meet the worldwide demand for quality foods. GM crops can help fight malnutrition due to enhanced yield, nutritional quality and increased resistance to various biotic and abiotic stresses. However, several biosafety issues and public concerns are associated with cultivation of GM crops developed by transgenesis, i.e., introduction of genes from distantly related organism. To meet these concerns, researchers have developed alternative concepts of cisgenesis and intragenesis which involve transformation of plants with genetic material derived from the species itself or from closely related species capable of sexual hybridization, respectively. Recombinase technology aimed at site-specific integration of transgene can help to overcome limitations of traditional genetic engineering methods based on random integration of multiple copy of transgene into plant genome leading to gene silencing and unpredictable expression pattern. Besides, recently developed technology of genome editing using engineered nucleases, permit the modification or mutation of genes of interest without involving foreign DNA, and as a result, plants developed with this technology might be considered as non-transgenic genetically altered plants. This would open the doors for the development and commercialization of transgenic plants with superior phenotypes even in countries where GM crops are poorly accepted. This review is an attempt to summarize various past achievements of GM technology in crop improvement, recent progress and new advances in the field to develop improved varieties aimed for better consumer acceptance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolff, D.

In agricultural crop improvement, yield under various stress conditions and limiting factors is assessed experimentally. Of the stresses on plants which affect yield are those due to insects. Ostrinia nubilalis, the European corn borer (corn borer) is a major pest in sweet and field corn in the U.S. There are many ways to fight crop pests such as the corn borer, including (1) application of chemical insecticides, (2) application of natural predators and, (3) improving crop resistance through plant genetics programs. Randomized field trials are used to determine the effectiveness of pest management programs. These trials frequently consist of randomlymore » selected crop plots to which well-defined input regimes are instituted. For example, corn borers might be released onto crop plots in several densities at various stages of crop development, then sprayed with different levels of pesticide. These experiments are duplicated across regions and, in some cases across the country, to determine, in this instance for example, the best pesticide application rate for a given pest density and crop development stage. In order to release these pests onto crop plots, one must have an adequate supply of the insect pest. In winter months studies are carried out in the laboratory to examine chemical and natural pesticide effectiveness, as well as such things as the role of pheromones in moth behavior. The advantage in field trials is that yield data can be garnered directly. In this country, insects are raised for crop research primarily through the US Department of Agriculture, in cooperation with public Land Grant Universities and, by the private sector agricultural concerns - seed companies and others. This study quantifies the airborne allergen exposure of persons working in a Land Grant University entomology lab were allergy to European corn borer was suspected.« less

Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress.

PubMed

Wang, Haibo; Zhao, Shuang; Mao, Ke; Dong, Qinglong; Liang, Bowen; Li, Chao; Wei, Zhiwei; Li, Mingjun; Ma, Fengwang

2018-06-26

Improvement of water-use efficiency (WUE) can effectively reduce production losses caused by drought stress. A better understanding of the genetic determination of WUE in crops under drought stress has great potential value for developing cultivars adapted to arid regions. To identify the genetic loci associated with WUE and reveal genes responsible for the trait in apple, we aim to map the quantitative trait loci (QTLs) for carbon isotope composition, the proxy for WUE, applying two contrasting irrigating regimes over the two-year experiment and search for the candidate genes encompassed in the mapped QTLs. We constructed a high-density genetic linkage map with 10,172 markers of apple, using single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RADseq) and a final segregating population of 350 seedlings from the cross of Honeycrisp and Qinguan. In total, 33 QTLs were identified for carbon isotope composition in apple under both well-watered and drought-stressed conditions. Three QTLs were stable over 2 years under drought stress on linkage groups LG8, LG15 and LG16, as validated by Kompetitive Allele-Specific PCR (KASP) assays. In those validated QTLs, 258 genes were screened according to their Gene Ontology functional annotations. Among them, 28 genes were identified, which exhibited significant responses to drought stress in 'Honeycrisp' and/or 'Qinguan'. These genes are involved in signaling, photosynthesis, response to stresses, carbohydrate metabolism, protein metabolism and modification, hormone metabolism and transport, transport, respiration, transcriptional regulation, and development regulation. They, especially those for photoprotection and relevant signal transduction, are potential candidate genes connected with WUE regulation in drought-stressed apple. We detected three stable QTLs for carbon isotope composition in apple under drought stress over 2 years, and validated them by KASP assay. Twenty-eight candidate genes encompassed in these QTLs were identified. These stable genetic loci and series of genes provided here serve as a foundation for further studies on marker-assisted selection of high WUE and regulatory mechanism of WUE in apple exposed to drought conditions, respectively.

The effects of climate change associated abiotic stresses on maize phytochemical defenses

USDA-ARS?s Scientific Manuscript database

Reliable large-scale maize production is an essential component of global food security; however, sustained efforts are needed to ensure optimized resilience under diverse crop stress conditions. Climate changes are expected to increase the frequency and intensity of both abiotic and biotic stress. ...

Ascophyllum nodosum Seaweed Extract Alleviates Drought Stress in Arabidopsis by Affecting Photosynthetic Performance and Related Gene Expression.

PubMed

Santaniello, Antonietta; Scartazza, Andrea; Gresta, Francesco; Loreti, Elena; Biasone, Alessandro; Di Tommaso, Donatella; Piaggesi, Alberto; Perata, Pierdomenico

2017-01-01

Drought represents one of the most relevant abiotic stress affecting growth and yield of crop plants. In order to improve the agricultural productivity within the limited water and land resources, it is mandatory to increase crop yields in presence of unfavorable environmental stresses. The use of biostimulants, often containing seaweed extracts, represents one of the options for farmers willing to alleviate abiotic stress consequences on crops. In this work, we investigated the responses of Arabidopsis plants treated with an extract from the brown alga Ascophyllum nodosum (ANE), under drought stress conditions, demonstrating that ANE positively influences Arabidopsis survival. Pre-treatment with ANE induced a partial stomatal closure, associated with changes in the expression levels of genes involved in ABA-responsive and antioxidant system pathways. The pre-activation of these pathways results in a stronger ability of ANE-treated plants to maintain a better photosynthetic performance compared to untreated plants throughout the dehydration period, combined with a higher capacity to dissipate the excess of energy as heat in the reaction centers of photosystem II. Our results suggest that drought stressed plants treated with ANE are able to maintain a strong stomatal control and relatively higher values of both water use efficiency (WUE) and mesophyll conductance during the last phase of dehydration. Simultaneously, the activation of a pre-induced antioxidant defense system, in combination with a more efficient energy dissipation mechanism, prevents irreversible damages to the photosynthetic apparatus. In conclusion, pre-treatment with ANE is effective to acclimate plants to the incoming stress, promoting an increased WUE and dehydration tolerance.

Ascophyllum nodosum Seaweed Extract Alleviates Drought Stress in Arabidopsis by Affecting Photosynthetic Performance and Related Gene Expression

PubMed Central

Santaniello, Antonietta; Scartazza, Andrea; Gresta, Francesco; Loreti, Elena; Biasone, Alessandro; Di Tommaso, Donatella; Piaggesi, Alberto; Perata, Pierdomenico

2017-01-01

Drought represents one of the most relevant abiotic stress affecting growth and yield of crop plants. In order to improve the agricultural productivity within the limited water and land resources, it is mandatory to increase crop yields in presence of unfavorable environmental stresses. The use of biostimulants, often containing seaweed extracts, represents one of the options for farmers willing to alleviate abiotic stress consequences on crops. In this work, we investigated the responses of Arabidopsis plants treated with an extract from the brown alga Ascophyllum nodosum (ANE), under drought stress conditions, demonstrating that ANE positively influences Arabidopsis survival. Pre-treatment with ANE induced a partial stomatal closure, associated with changes in the expression levels of genes involved in ABA-responsive and antioxidant system pathways. The pre-activation of these pathways results in a stronger ability of ANE-treated plants to maintain a better photosynthetic performance compared to untreated plants throughout the dehydration period, combined with a higher capacity to dissipate the excess of energy as heat in the reaction centers of photosystem II. Our results suggest that drought stressed plants treated with ANE are able to maintain a strong stomatal control and relatively higher values of both water use efficiency (WUE) and mesophyll conductance during the last phase of dehydration. Simultaneously, the activation of a pre-induced antioxidant defense system, in combination with a more efficient energy dissipation mechanism, prevents irreversible damages to the photosynthetic apparatus. In conclusion, pre-treatment with ANE is effective to acclimate plants to the incoming stress, promoting an increased WUE and dehydration tolerance. PMID:28824691

Comparison of Leaf Sheath Transcriptome Profiles with Physiological Traits of Bread Wheat Cultivars under Salinity Stress

PubMed Central

Trittermann, Christine; Berger, Bettina; Roy, Stuart J.; Seki, Motoaki; Shinozaki, Kazuo; Tester, Mark

2015-01-01

Salinity stress has significant negative effects on plant biomass production and crop yield. Salinity tolerance is controlled by complex systems of gene expression and ion transport. The relationship between specific features of mild salinity stress adaptation and gene expression was analyzed using four commercial varieties of bread wheat (Triticum aestivum) that have different levels of salinity tolerance. The high-throughput phenotyping system in The Plant Accelerator at the Australian Plant Phenomics Facility revealed variation in shoot relative growth rate and salinity tolerance among the four cultivars. Comparative analysis of gene expression in the leaf sheaths identified genes whose functions are potentially linked to shoot biomass development and salinity tolerance. Early responses to mild salinity stress through changes in gene expression have an influence on the acquisition of stress tolerance and improvement in biomass accumulation during the early “osmotic” phase of salinity stress. In addition, results revealed transcript profiles for the wheat cultivars that were different from those of usual stress-inducible genes, but were related to those of plant growth. These findings suggest that, in the process of breeding, selection of specific traits with various salinity stress-inducible genes in commercial bread wheat has led to adaptation to mild salinity conditions. PMID:26244554

Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression[W][OA

PubMed Central

Reddy, Anireddy S.N.; Ali, Gul S.; Celesnik, Helena; Day, Irene S.

2011-01-01

Abiotic and biotic stresses are major limiting factors of crop yields and cause billions of dollars of losses annually around the world. It is hoped that understanding at the molecular level how plants respond to adverse conditions and adapt to a changing environment will help in developing plants that can better cope with stresses. Acquisition of stress tolerance requires orchestration of a multitude of biochemical and physiological changes, and most of these depend on changes in gene expression. Research during the last two decades has established that different stresses cause signal-specific changes in cellular Ca2+ level, which functions as a messenger in modulating diverse physiological processes that are important for stress adaptation. In recent years, many Ca2+ and Ca2+/calmodulin (CaM) binding transcription factors (TFs) have been identified in plants. Functional analyses of some of these TFs indicate that they play key roles in stress signaling pathways. Here, we review recent progress in this area with emphasis on the roles of Ca2+- and Ca2+/CaM-regulated transcription in stress responses. We will discuss emerging paradigms in the field, highlight the areas that need further investigation, and present some promising novel high-throughput tools to address Ca2+-regulated transcriptional networks. PMID:21642548

Assessing the Impact of Climatic Variability and Change on Maize Production in the Midwestern USA

NASA Astrophysics Data System (ADS)

Andresen, J.; Jain, A. K.; Niyogi, D. S.; Alagarswamy, G.; Biehl, L.; Delamater, P.; Doering, O.; Elias, A.; Elmore, R.; Gramig, B.; Hart, C.; Kellner, O.; Liu, X.; Mohankumar, E.; Prokopy, L. S.; Song, C.; Todey, D.; Widhalm, M.

2013-12-01

Weather and climate remain among the most important uncontrollable factors in agricultural production systems. In this study, three process-based crop simulation models were used to identify the impacts of climate on the production of maize in the Midwestern U.S.A. during the past century. The 12-state region is a key global production area, responsible for more than 80% of U.S. domestic and 25% of total global production. The study is a part of the Useful to Useable (U2U) Project, a USDA NIFA-sponsored project seeking to improve the resilience and profitability of farming operations in the region amid climate variability and change. Three process-based crop simulation models were used in the study: CERES-Maize (DSSAT, Hoogenboom et al., 2012), the Hybrid-Maize model (Yang et al., 2004), and the Integrated Science Assessment Model (ISAM, Song et al., 2013). Model validation was carried out with individual plot and county observations. The models were run with 4 to 50 km spatial resolution gridded weather data for representative soils and cultivars, 1981-2012, to examine spatial and temporal yield variability within the region. We also examined the influence of different crop models and spatial scales on regional scale yield estimation, as well as a yield gap analysis between observed and attainable yields. An additional study was carried out with the CERES-Maize model at 18 individual site locations 1901-2012 to examine longer term historical trends. For all simulations, all input variables were held constant in order to isolate the impacts of climate. In general, the model estimates were in good agreement with observed yields, especially in central sections of the region. Regionally, low precipitation and soil moisture stress were chief limitations to simulated crop yields. The study suggests that at least part of the observed yield increases in the region during recent decades have occurred as the result of wetter, less stressful growing season weather conditions.

Satellite-based mapping of field-scale stress indicators for crop yield forecasting: an application over Mead, NE

NASA Astrophysics Data System (ADS)

Yang, Y.; Anderson, M. C.; Gao, F.; Wardlow, B.; Hain, C.; Otkin, J.; Sun, L.; Dulaney, W.

2017-12-01

In agricultural regions, water is one of the most widely limiting factors of crop performance and production. Evapotranspiration (ET) describes crop water use through transpiration and water lost through direct soil evaporation, which makes it a good indicator of soil moisture availability and vegetation health and thus has been an integral part of many yield estimation efforts. The Evaporative Stress Index (ESI) describes temporal anomalies in a normalized evapotranspiration metric (fRET) as derived from satellite remote sensing and has demonstrated capacity to explain regional yield variability in water limited crop growing regions. However, its performance in some regions where the vegetation cycle is intensively managed appears to be degraded. In this study we generated maps of ET, fRET, and ESI at high spatiotemporal resolution (30-m pixels, daily timesteps) using a multi-sensor data fusion method, integrating information from satellite platforms with good temporal coverage and other platforms that provide field-scale spatial detail. The study was conducted over the period 2010-2014, covering a region around Mead, Nebraska that includes both rainfed and irrigated crops. Correlations between ESI and measurements of corn yield are investigated at both the field and county level to assess the value of ESI as a yield forecasting tool. To examine the role of phenology in ESI-yield correlations, annual input fRET timeseries were aligned by both calendar day and by biophysically relevant dates (e.g. days since planting or emergence). Results demonstrate that mapping of fRET and ESI at 30-m has the advantage of being able to resolve different crop types with varying phenology. The study also suggests that incorporating phenological information significantly improves yield-correlations by accounting for effects of phenology such as variable planting date and emergence date. The yield-ESI relationship in this study well captures the inter-annual variability of yields and thus has potential to be used for yield prediction, or for ingestion into a crop simulation model as a crop-specific moisture stress function.

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics-An Important Nutri-Cereal of Future.

PubMed

Sood, Salej; Kumar, Anil; Babu, B Kalyana; Gaur, Vikram S; Pandey, Dinesh; Kant, Lakshmi; Pattnayak, Arunava

2016-01-01

The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [ Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2-4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet.

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

PubMed Central

Sood, Salej; Kumar, Anil; Babu, B. Kalyana; Gaur, Vikram S.; Pandey, Dinesh; Kant, Lakshmi; Pattnayak, Arunava

2016-01-01

The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2–4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet. PMID:27881984

Current, Short Term, Future and Star Wars Research Projects for Ornamental Crops

USDA-ARS?s Scientific Manuscript database

The USDA-ARS Greenhouse Production Research Group is involved in fundamental and developmental plant research aimed at developing tools for early stress detection and efficient agrochemical utilization for protected horticulture crops. The group conducts basic plant biology research with the goal o...

Can genomics boost productivity of orphan crops?

USDA-ARS?s Scientific Manuscript database

Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

Mitigation technologies to control high-temperature stress in crop plants

USDA-ARS?s Scientific Manuscript database

The book entitled “Crop Responses to Global Warming” describes the traditional historical shifts within the earth’s atmospheric temperature and weighs the evidence regarding anthropogenetic elicited changes within the level of temperature. There is not an abundant study to elucidate the shift in te...

Water Stress & Biomass Monitoring and SWAP Modeling of Irrigated Crops in Saratov Region of Russia

NASA Astrophysics Data System (ADS)

Zeyliger, Anatoly; Ermolaeva, Olga

2016-04-01

Development of modern irrigation technologies are balanced between the need to maximize production and the need to minimize water use which provides harmonious interaction of irrigated systems with closely-spaced environment. Thus requires an understanding of complex interrelationships between landscape and underground of irrigated and adjacent areas in present and future conditions aiming to minimize development of negative scenarios. In this way in each irrigated areas a combination of specific factors and drivers must be recognized and evaluated. Much can be obtained by improving the efficiency use of water applied for irrigation. Modern RS monitoring technologies offers the opportunity to develop and implement an effective irrigation control program permitting today to increase efficiency of irrigation water use. These technologies provide parameters with both high temporal and adequate spatial needed to monitor agrohydrological parameters of irrigated agricultural crops. Combination of these parameters with meteorological and biophysical parameters can be used to estimate crop water stress defined as ratio between actual (ETa) and potential (ETc) evapotranspiration. Aggregation of actual values of crop water stress with biomass (yield) data predicted by agrohydrological model based on weather forecasting and scenarios of irrigation water application may be used for indication of both rational timing and amount of irrigation water allocation. This type of analysis facilitating an efficient water management can be easily extended to irrigated areas by developing maps of water efficiency application serving as an irrigation advice system for farmers at his fields and as a decision support tool for the authorities on the large perimeter irrigation management. This contribution aims to communicate an illustrative explanation about the practical application of a data combination of agrohydrological modeling and ground & space based monitoring. For this aim some results of analyzing water stress during growing season of 2012 and yielded biomass of crops three types of crops alfalfa, corn and soya irrigated by sprinkling machines at left bank of Volga River at Saratov Region of Russia are presented and analyzed. For that a combination of data received from satellite, local meteorological station and farmers as well as SWAP model was used. Analyze of data sets of monitored water deficit of each crop averaged for irrigation period was done by linear regression with yielded biomass values. Following analyze of effectiveness of irrigation water application was done by SWAP agrohydrological model.

Biotechnological applications in in vitro plant regeneration studies of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, Dinesh Kumar

2016-04-01

Biotechnology holds promise for genetic improvement of important vegetable crops. Broccoli (Brassica oleracea L. var. italica) is an important vegetable crop of the family Brassicaceae. However, various biotic and abiotic stresses cause enormous crop yield losses during commercial cultivation of broccoli. Establishment of a reliable, reproducible and efficient in vitro plant regeneration system with cell and tissue culture is a vital prerequisite for biotechnological application of crop improvement programme. An in vitro plant regeneration technique refers to culturing, cell division, cell multiplication, de-differentiation and differentiation of cells, protoplasts, tissues and organs on defined liquid/solid medium under aseptic and controlled environment. Recent progress in the field of plant tissue culture has made this area one of the most dynamic and promising in experimental biology. There are many published reports on in vitro plant regeneration studies in broccoli including direct organogenesis, indirect organogenesis and somatic embryogenesis. This review summarizes those plant regeneration studies in broccoli that could be helpful in drawing the attention of the researchers and scientists to work on it to produce healthy, biotic and abiotic stress resistant plant material and to carry out genetic transformation studies for the production of transgenic plants.

Metabolomic Profiling of Soybeans (Glycine Max L.) Reveals Importance of Sugar and Nitogen Metabolisms under Drought and Heat Stress

USDA-ARS?s Scientific Manuscript database

Soybean, an important legume crop, is continually threatened by abiotic stresses, especially drought and heat stress. At molecular levels, reduced yields due to drought and heat stress can be seen in the alterations of metabolic homeostasis of vegetative tissues. A global metabolomics approach can b...

Does crop rotational diversity increase soil microbial resistance and resilience to drought and flooding?

NASA Astrophysics Data System (ADS)

Schnecker, Jörg; Calderon, Francisco; Cavigelli, Michel; Lehman, Michael; Tiemann, Lisa; Grandy, Stuart

2017-04-01

Future climate scenarios indicate more frequent and stronger extreme weather events. This includes more severe droughts but also an increase in heavy rain events and flooding. Agricultural systems are of special interest in this context because of their role in food security but also because of their potentially changing role in global carbon and nutrient cycling under these extreme conditions. Plant diversification strategies like more complex crop rotations which support more diverse soil microbial communities with higher functional redundancy might be more resistant to drought and flooding and could help to reduce impacts on microbial carbon and nutrient cycling. To test how crop diversification affects the response of soil microbial processes to drought and flooding and reoccurring drought and flooding, we manipulated water regimes in lab incubation experiments using soils from four long term rotation experiments across the USA, including a low (one or two crops) vs. high (>3 crops) diversity rotations at each site. The sites range from low precipitation (Colorado), over intermediate precipitation (Michigan and South Dakota) to high precipitation in Maryland. Replicate sets of samples were either allowed to dry out, were gradually flooded or kept at a constant water content (control). We monitored CO2 production during five stress cycles. Additionally, we determined microbial biomass, enzyme activities and N pools during the first and last stress cycle in soils from the precipitation extremes. After a total incubation length of 165 days and five stress cycles only the soils from short rotations in Maryland and South Dakota that had been subjected to reoccurring drought showed significantly less cumulative CO2 loss compared to their respective controls. All the other sites and rotation length did not significantly differ from control when subjected to reoccurring drought or flooding. A Principal component analysis using all measured parameters of Colorado and Maryland soils showed a clear clustering of samples by site and in case of Maryland also by rotation length before the first stress. During the stress, samples were significantly separated by the treatment (drought and flooding). Immediately after the stress, samples again clustered by site and rotation length. After four stress cycles, soils from the long rotation in Colorado were the only samples that did not show a significant response to the laboratory treatments anymore. Our results indicate that agricultural soils, irrespective of the climatic region they are from and the rotation regime, are highly susceptible to changes in water content, especially drought. We did however also found that all tested soils were quickly recovering from the applied stress treatment and that plant diversification might help to increase the microbial resistance to water stress in certain soil systems.

Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants

PubMed Central

Khan, M. Iqbal R.; Fatma, Mehar; Per, Tasir S.; Anjum, Naser A.; Khan, Nafees A.

2015-01-01

Abiotic stresses (such as metals/metalloids, salinity, ozone, UV-B radiation, extreme temperatures, and drought) are among the most challenging threats to agricultural system and economic yield of crop plants. These stresses (in isolation and/or combination) induce numerous adverse effects in plants, impair biochemical/physiological and molecular processes, and eventually cause severe reductions in plant growth, development and overall productivity. Phytohormones have been recognized as a strong tool for sustainably alleviating adverse effects of abiotic stresses in crop plants. In particular, the significance of salicylic acid (SA) has been increasingly recognized in improved plant abiotic stress-tolerance via SA-mediated control of major plant-metabolic processes. However, the basic biochemical/physiological and molecular mechanisms that potentially underpin SA-induced plant-tolerance to major abiotic stresses remain least discussed. Based on recent reports, this paper: (a) overviews historical background and biosynthesis of SA under both optimal and stressful environments in plants; (b) critically appraises the role of SA in plants exposed to major abiotic stresses; (c) cross-talks potential mechanisms potentially governing SA-induced plant abiotic stress-tolerance; and finally (d) briefly highlights major aspects so far unexplored in the current context. PMID:26175738

[Effects of soil water status on gas exchange of peanut and early rice leaves].

PubMed

Chen, Jiazhou; Lü, Guoan; He, Yuanqiu

2005-01-01

The gas exchange characteristics of peanut and early rice leaves were investigated in experimental plots under different soil water conditions over a long growth period. The results showed that at the branching stage of peanut, the stomatal conductance (Gs) and transpiration rate (Tr) decreased slightly under mild and moderate soil water stress, while the net photosynthetic rate (Pn) and leaf water use efficiency (WUE) increased. The Gs/Tr ratio also increased under mild water stress, but decreased under moderate water stress. At podding stage, the Gs, Tr, Gs/Tr ratio and Pn decreased, while WUE increased significantly under mild and moderate water stress. The peanut was suffered from water stress at its pod setting stage. At the grain filling stage of early rice, the Gs, Tr and Gs/Tr ratio fluctuated insignificantly under mild and moderate water stress, while Pn and WUE increased significantly, with an increase in grain yield under mild water stress. It's suggested that the combination of Gs and Gs/Tr ratio could be a reference index for crop water stress, namely, crops could be hazarded by water stress when Gs and Gs/Tr decreased synchronously.

Growth, physiology and yield of durum wheat (Triticum durum) treated with sewage sludge under water stress conditions

PubMed Central

Boudjabi, Sonia; Kribaa, Mohammed; Chenchouni, Haroun

2015-01-01

In arid and semi-arid areas, low soil fertility and water deficit considerably limit crop production. The use of sewage sludge as an organic amendment could contribute to the improvement of soil fertility and hence the agronomic production. The study aims to highlight the behaviour of durum wheat to the application of sewage sludge associated with water stress. The assessment focused on morphophysiological parameters of the wheat plant and yield. Under greenhouse conditions, the variety Mohamed Ben Bachir was treated by four water stress levels (100 %, 80 %, 50 % and 30 %). Each stress level comprised five fertilizer treatments: 20, 50 and 100 t/ha of dry sludge, 35 kg/ha of urea, and a control with no fertilization. Results revealed a significant loss in water content and chlorophyll a in leaves. Water stress negatively affected the development of wheat plants by reducing significantly seed yield, leaf area and biomass produced. Plant’s responses to water stress manifested by an accumulation of proline and a decrease in total phosphorus. However, the increasing doses of sewage sludge limited the effect of water stress. Our findings showed an increase in the amount of chlorophyll pigments, leaf area, total phosphorus, biomass and yield. In addition, excessive accumulation of proline (1.11 ± 1.03 µg/g DM) was recorded as a result of the high concentration of sludge (100 t/ha DM). The application of sewage sludge is beneficial for the wheat crop, but the high accumulation of proline in plants treated with high dose of sludge suggests to properly consider this fact. The application of sludge should be used with caution in soils where water is limited. Because the combined effect of these two factors could result in a fatal osmotic stress to crop development. PMID:26417365

Effect of drought and heat stresses on plant growth and yield: a review

NASA Astrophysics Data System (ADS)

Lipiec, J.; Doussan, C.; Nosalewicz, A.; Kondracka, K.

2013-12-01

Drought and heat stresses are important threat limitations to plant growth and sustainable agriculture worldwide. Our objective is to provide a review of plant responses and adaptations to drought and elevated temperature including roots, shoots, and final yield and management approaches for alleviating adverse effects of the stresses based mostly on recent literature. The sections of the paper deal with plant responses including root growth, transpiration, photosynthesis, water use efficiency, phenotypic flexibility, accumulation of compounds of low molecular mass (eg proline and gibberellins), and expression of some genes and proteins for increasing the tolerance to the abiotic stresses. Soil and crop management practices to alleviate negative effects of drought and heat stresses are also discussed. Investigations involving determination of plant assimilate partitioning, phenotypic plasticity, and identification of most stress-tolerant plant genotypes are essential for understanding the complexity of the responses and for future plant breeding. The adverse effects of drought and heat stress can be mitigated by soil management practices, crop establishment, and foliar application of growth regulators by maintaining an appropriate level of water in the leaves due to osmotic adjustment and stomatal performance.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

PubMed

Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

2014-01-01

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves

PubMed Central

Chen, Wei Wei; Xu, Jia Meng; Jin, Jian Feng; Lou, He Qiang; Fan, Wei

2017-01-01

Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE, ALS1, STAR1, ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity. PMID:28846612

Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves.

PubMed

Chen, Wei Wei; Xu, Jia Meng; Jin, Jian Feng; Lou, He Qiang; Fan, Wei; Yang, Jian Li

2017-08-27

Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE , ALS1 , STAR1 , ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity.

Biochar-manure compost in conjunction with pyroligneous solution alleviated salt stress and improved leaf bioactivity of maize in a saline soil from central China: a 2-year field experiment.

PubMed

Lashari, Muhammad Siddique; Ye, Yingxin; Ji, Haishi; Li, Lianqing; Kibue, Grace Wanjiru; Lu, Haifei; Zheng, Jufeng; Pan, Genxing

2015-04-01

Salinity is a major stress threatening crop production in dry lands. A 2-year field experiment was conducted to assess the potential of a biochar product to alleviate salt-stress to a maize crop in a saline soil. The soil was amended with a compost at 12 t ha(-1) of wheat straw biochar and poultry manure compost (BPC), and a diluted pyroligneous solution (PS) at 0.15 t ha(-1) (BPC-PS). Changes in soil salinity and plant performance, leaf bioactivity were examined in the first (BPC-PS1) and second (BPC-PS2) year following a single amendment. While soil salinity significantly decreased, there were large increases in leaf area index, plant performance, and maize grain yield, with a considerable decrease in leaf electrolyte leakage when grown in amendments. Maize leaf sap nitrogen, phosphorus and potassium increased while sodium and chloride decreased, leaf bioactivity related to osmotic stress was significantly improved following the treatments. These effects were generally greater in the second than in the first year. A combined amendment of crop straw biochar with manure compost plus pyroligneous solution could help combat salinity stress to maize and improve productivity in saline croplands in arid/semi-arid regions threatened increasingly by global climate change. © 2014 Society of Chemical Industry.