Sample records for crop genetic resources

  1. Cotton genetic resources and crop vulnerability

    USDA-ARS?s Scientific Manuscript database

    A report on the genetic vulnerability of cotton was provided to the National Genetic Resources Advisory Council. The report discussed crop vulnerabilities associated with emerging diseases, emerging pests, and a narrowing genetic base. To address these crop vulnerabilities, the report discussed the ...

  2. Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

    PubMed Central

    Dillon, Sally L.; Shapter, Frances M.; Henry, Robert J.; Cordeiro, Giovanni; Izquierdo, Liz; Lee, L. Slade

    2007-01-01

    Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes. PMID:17766842

  3. Valuation of crop genetic resources in Kaski, Nepal: farmers' willingness to pay for rice landraces conservation.

    PubMed

    Poudel, Diwakar; Johnsen, Fred H

    2009-01-01

    Crop genetic resources constitute an important aspect of biodiversity conservation, both because of their direct value to the farmers and due to their indirect global value. This study uses the contingent valuation method to document the economic value of crop genetic resources based on the farmers' willingness to pay for conservation. A total of 107 households in Kaski, Nepal were surveyed in November 2003. Their mean willingness to pay was USD 4.18 for in situ and USD 2.20 for ex situ conservation per annum. Landholding size, household size, education level, socio-economic status, sex of respondent, number of crop landraces grown, and knowledge on biodiversity influenced the willingness to pay for in situ conservation, whereas only landholding size and household size influenced the willingness to pay for ex situ conservation. The respondents were willing to contribute more for in situ than ex situ conservation because of the additional effect of direct use and direct involvement of the farmers in in situ conservation. This study supports the view that economic valuation of crop genetic resources can assist the policy makers in setting conservation priorities.

  4. Harvesting Legume Genomes: Plant Genetic Resources

    USDA-ARS?s Scientific Manuscript database

    Genomics and high through-put phenotyping are ushering in a new era of accessing genetic diversity held in plant genetic resources, the cornerstone of both traditional and genomics-assisted breeding efforts of food legume crops. Acknowledged or not, yield plateaus must be broken given the daunting ...

  5. Cryopreservation of eucalyptus genetic resources

    USDA-ARS?s Scientific Manuscript database

    The long-term preservation of forest genetic resources is a vital part of preserving our forest crops for future generations. Unfortunately there are few genebanks dedicated to forest trees and very few methods aside from field plantings of germplasm collections of elite clonal individuals. The use ...

  6. Genetic diversity in Carthamus tinctorius (Asteraceae; safflower), an underutilized oilseed crop.

    PubMed

    Pearl, Stephanie A; Burke, John M

    2014-10-01

    • Underutilized crops are potentially valuable resources for meeting increasing food demands. Safflower, an oilseed crop, is an example of one such underutilized crop that thrives in moisture-limited areas. Characterization of the genetic diversity maintained within the gene pools of underutilized crops such as safflower is an important step in their further development.• A total of 190 safflower individuals, including 134 USDA accessions, 48 breeding lines from two private North American safflower breeding companies, and eight wild safflower individuals, were genotyped using 133 single nucleotide polymorphism (SNP) markers. We then used the resulting data to assess the amount and distribution of genetic diversity within and among these collections of safflower.• Although just a modest reduction in gene diversity was observed in the commercial breeding lines (relative to the other safflower groupings), safflower domestication was accompanied by a significant decrease in allelic richness. Further, our results suggest that most safflower breeding lines originated from a single pool of diversity within the Old World safflower germplasm.• Taken together, our results suggest that both the safflower germplasm collection and related, wild species harbor previously undocumented genetic diversity that could help fuel future improvement efforts. Paired with analyses of functional diversity, the molecular resources described herein will be thus be useful in the continued development of safflower as an oilseed crop. © 2014 Botanical Society of America, Inc.

  7. Crop Genetics: The Seeds of Revolution.

    ERIC Educational Resources Information Center

    DeYoung, H. Garrett

    1983-01-01

    Current research in plant genetics is described. Benefits of this research (which includes genetic engineering applications) will include reduction/elimination of crop diseases, assurance of genetic stability, and the creation of new crop varieties. (JN)

  8. Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops

    PubMed Central

    Cardi, Teodoro; D’Agostino, Nunzio; Tripodi, Pasquale

    2017-01-01

    In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications. PMID:28275380

  9. Understanding crop genetic diversity under modern plant breeding.

    PubMed

    Fu, Yong-Bi

    2015-11-01

    Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.

  10. Weed seed resources for birds in fields with contrasting conventional and genetically modified herbicide-tolerant crops

    PubMed Central

    Gibbons, David W; Bohan, David A; Rothery, Peter; Stuart, Rick C; Haughton, Alison J; Scott, Rod J; Wilson, Jeremy D; Perry, Joe N; Clark, Suzanne J; Dawson, Robert J.G; Firbank, Les G

    2006-01-01

    The UK Farm Scale Evaluations (FSEs) have shown that the use of broad spectrum herbicides on genetically modified herbicide-tolerant (GMHT) crops can have dramatic effects on weed seed production compared to management of conventional varieties. Here, we use FSE data and information on bird diets to determine how GMHT cropping might change the food resources available to farmland birds. More than 60 fields of each of four crops, spring- and winter-sown oilseed rape, beet and maize, were split, one half being sown with a conventional variety, the other with a GMHT variety. Seed rain from weeds known to be important in the diets of 17 granivorous farmland bird species was measured under the two treatments. In beet and spring oilseed rape, rain of weed seeds important in the diets of 16 bird species was significantly reduced in GMHT compared to conventional halves; for no species did it increase. In winter oilseed rape, rain of weed seeds important in the diets of 10 species was significantly reduced in GMHT halves; for only one species did it increase significantly. By contrast, in maize, rain of weed seeds important in the diets of seven species was significantly greater in GMHT halves; for no species was it reduced. Treatment effects for the total weed seed energy available to each bird species were very similar to those for seed rain alone. Measuring the effects on individual bird species was outside the scope of this study. Despite this, these results suggest that should beet, spring and winter rape crops in the UK be largely replaced by GMHT varieties and managed as in the FSEs, this would markedly reduce important food resources for farmland birds, many of which declined during the last quarter of the twentieth century. By contrast, GMHT maize would be beneficial to farmland birds. PMID:16822753

  11. Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas

    PubMed Central

    Khoury, Colin K.; Heider, Bettina; Castañeda-Álvarez, Nora P.; Achicanoy, Harold A.; Sosa, Chrystian C.; Miller, Richard E.; Scotland, Robert W.; Wood, John R. I.; Rossel, Genoveva; Eserman, Lauren A.; Jarret, Robert L.; Yencho, G. C.; Bernau, Vivian; Juarez, Henry; Sotelo, Steven; de Haan, Stef; Struik, Paul C.

    2015-01-01

    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding. PMID:25954286

  12. Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas].

    PubMed

    Khoury, Colin K; Heider, Bettina; Castañeda-Álvarez, Nora P; Achicanoy, Harold A; Sosa, Chrystian C; Miller, Richard E; Scotland, Robert W; Wood, John R I; Rossel, Genoveva; Eserman, Lauren A; Jarret, Robert L; Yencho, G C; Bernau, Vivian; Juarez, Henry; Sotelo, Steven; de Haan, Stef; Struik, Paul C

    2015-01-01

    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.

  13. 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.

  14. Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement.

    PubMed

    Bohra, Abhishek; Singh, Narendra P

    2015-08-01

    Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

  15. Looking forward to genetically edited fruit crops.

    PubMed

    Nagamangala Kanchiswamy, Chidananda; Sargent, Daniel James; Velasco, Riccardo; Maffei, Massimo E; Malnoy, Mickael

    2015-02-01

    The availability of genome sequences for many fruit crops has redefined the boundaries of genetic engineering and genetically modified (GM) crop plants. However commercialization of GM crops is hindered by numerous regulatory and social hurdles. Here, we focus on recently developed genome-editing tools for fruit crop improvement and their importance from the consumer perspective. Challenges and opportunities for the deployment of new genome-editing tools for fruit plants are also discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution.

    PubMed

    Goron, Travis L; Raizada, Manish N

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

  17. Genetic Engineering and Crop Production.

    ERIC Educational Resources Information Center

    Jones, Helen C.; Frost, S.

    1991-01-01

    With a spotlight upon current agricultural difficulties and environmental dilemmas, this paper considers both the extant and potential applications of genetic engineering with respect to crop production. The nonagricultural factors most likely to sway the impact of this emergent technology upon future crop production are illustrated. (JJK)

  18. Accessing genetic diversity for crop improvement.

    PubMed

    Glaszmann, J C; Kilian, B; Upadhyaya, H D; Varshney, R K

    2010-04-01

    Vast germplasm collections are accessible but their use for crop improvement is limited-efficiently accessing genetic diversity is still a challenge. Molecular markers have clarified the structure of genetic diversity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of 'core reference sets' so as to facilitate material sharing within the scientific community.

  19. Why preserve and evaluate genetic resources in peanut?

    USDA-ARS?s Scientific Manuscript database

    Peanuts are produced in more than 100 countries with a total global total production in 2010 of 37,953,949 metric tons (FAO statistics, 2010). Because peanut is an important crop, it is imperative that its germplasm be preserved in order to conserve the genetic diversity and provide a resource to i...

  20. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

    PubMed Central

    Goron, Travis L.; Raizada, Manish N.

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed “orphan cereals.” Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa. PMID:25852710

  1. International efforts to protect the global cotton genetic resources

    USDA-ARS?s Scientific Manuscript database

    The genetic resources of cotton are classified into five tetraploid species in the primary gene pool, 20 diploid species in the secondary gene pool, and 25 diploid species in the tertiary gene pool. Unlike several globally important grain crops, the Consultative Group on International Agricultural R...

  2. Genetically modified crops and small-scale farmers: main opportunities and challenges.

    PubMed

    Azadi, Hossein; Samiee, Atry; Mahmoudi, Hossein; Jouzi, Zeynab; Khachak, Parisa Rafiaani; De Maeyer, Philippe; Witlox, Frank

    2016-01-01

    Although some important features of genetically modified (GM) crops such as insect resistance, herbicide tolerance, and drought tolerance might seem to be beneficial for small-scale farmers, the adoption of GM technology by smallholders is still slight. Identifying pros and cons of using this technology is important to understand the impacts of GM crops on these farmers. This article reviews the main opportunities and challenges of GM crops for small-scale farmers in developing countries. The most significant advantages of GM crops include being independent to farm size, environment protection, improvement of occupational health issues, and the potential of bio-fortified crops to reduce malnutrition. Challenges faced by small-scale farmers for adoption of GM crops comprise availability and accessibility of GM crop seeds, seed dissemination and price, and the lack of adequate information. In addition, R&D and production costs in using GM crops make it difficult for these farmers to adopt the use of these crops. Moreover, intellectual property right regulations may deprive resource poor farmers from the advantages of GM technology. Finally, concerns on socio-economic and environment safety issues are also addressed in this paper.

  3. Relevance of Crop Biology for Environmental Risk Assessment of Genetically Modified Crops in Africa.

    PubMed

    Akinbo, Olalekan; Hancock, James F; Makinde, Diran

    2015-01-01

    Knowledge about the crop biology of economic crops in Africa is needed for regulators to accurately review dossiers and conduct comprehensive environmental risk assessments (ERAs). This information allows regulators to decide whether biotech crops present a risk to biodiversity, since crossing between domesticated crops and their wild relatives could affect the adaptations of the wild species. The criteria that should be used in the evaluation of African crops for ERA include growth habit, center of origin, center of genetic diversity, proximity of wild relatives, inter-fertility, mode of pollen dispersal, length of pollen viability, mating system, invasiveness, weediness, mode of propagation, mode of seed dispersal, and length of seed dormancy. In this paper, we discuss the crops being genetic engineered in Africa and describe the crop biology of those with native relatives.

  4. SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement

    PubMed Central

    2013-01-01

    Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

  5. Genome resources for climate-resilient cowpea, an essential crop for food security.

    PubMed

    Muñoz-Amatriaín, María; Mirebrahim, Hamid; Xu, Pei; Wanamaker, Steve I; Luo, MingCheng; Alhakami, Hind; Alpert, Matthew; Atokple, Ibrahim; Batieno, Benoit J; Boukar, Ousmane; Bozdag, Serdar; Cisse, Ndiaga; Drabo, Issa; Ehlers, Jeffrey D; Farmer, Andrew; Fatokun, Christian; Gu, Yong Q; Guo, Yi-Ning; Huynh, Bao-Lam; Jackson, Scott A; Kusi, Francis; Lawley, Cynthia T; Lucas, Mitchell R; Ma, Yaqin; Timko, Michael P; Wu, Jiajie; You, Frank; Barkley, Noelle A; Roberts, Philip A; Lonardi, Stefano; Close, Timothy J

    2017-03-01

    Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

  6. The conservation of forest genetic resources: case histories from Canada, Mexico, and the United States

    Treesearch

    F. Thomas Ledig; J. Jesús Vargas-Hernández; Kurt H. Johnsen

    1998-01-01

    The genetic codes of living organisms are natural resources no less than soil, air, and water. Genetic resources-from nucleotide sequences in DNA to selected genotypes, populations, and species-are the raw material in forestry: for breeders, for the forest manager who produces an economic crop, for society that reaps the environmental benefits provided by forests, and...

  7. A Mesoamerican origin of cherimoya (Annona cherimola Mill.): Implications for the conservation of plant genetic resources.

    PubMed

    Larranaga, N; Albertazzi, F J; Fontecha, G; Palmieri, M; Rainer, H; van Zonneveld, M; Hormaza, J I

    2017-08-01

    Knowledge on the structure and distribution of genetic diversity is a key aspect to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1,765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the Neotropics and used as a food source by pre-Columbian cultures, was collected from six different countries across the American continent and amplified with nine highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops. © 2017 John Wiley & Sons Ltd.

  8. MS-based analytical methodologies to characterize genetically modified crops.

    PubMed

    García-Cañas, Virginia; Simó, Carolina; León, Carlos; Ibáñez, Elena; Cifuentes, Alejandro

    2011-01-01

    The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart. Copyright © 2010 Wiley Periodicals, Inc.

  9. Genomic exploitation of genetic variation for crop improvement

    USDA-ARS?s Scientific Manuscript database

    Crop plants produce food, fiber, and fuel that are essential to human civilization and mainstays of economic prosperity. Our society continues to cultivate and improve the crop plants for better quality and productivity with sustainable environments. The process of crop genetic improvement has bee...

  10. First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement

    PubMed Central

    Vicente-Dólera, Nelly; Troadec, Christelle; Moya, Manuel; del Río-Celestino, Mercedes; Pomares-Viciana, Teresa; Bendahmane, Abdelhafid; Picó, Belén; Román, Belén; Gómez, Pedro

    2014-01-01

    Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding. PMID:25386735

  11. Current perspectives on genetically modified crops and detection methods.

    PubMed

    Kamle, Madhu; Kumar, Pradeep; Patra, Jayanta Kumar; Bajpai, Vivek K

    2017-07-01

    Genetically modified (GM) crops are the fastest adopted commodities in the agribiotech industry. This market penetration should provide a sustainable basis for ensuring food supply for growing global populations. The successful completion of two decades of commercial GM crop production (1996-2015) is underscored by the increasing rate of adoption of genetic engineering technology by farmers worldwide. With the advent of introduction of multiple traits stacked together in GM crops for combined herbicide tolerance, insect resistance, drought tolerance or disease resistance, the requirement of reliable and sensitive detection methods for tracing and labeling genetically modified organisms in the food/feed chain has become increasingly important. In addition, several countries have established threshold levels for GM content which trigger legally binding labeling schemes. The labeling of GM crops is mandatory in many countries (such as China, EU, Russia, Australia, New Zealand, Brazil, Israel, Saudi Arabia, Korea, Chile, Philippines, Indonesia, Thailand), whereas in Canada, Hong Kong, USA, South Africa, and Argentina voluntary labeling schemes operate. The rapid adoption of GM crops has increased controversies, and mitigating these issues pertaining to the implementation of effective regulatory measures for the detection of GM crops is essential. DNA-based detection methods have been successfully employed, while the whole genome sequencing using next-generation sequencing (NGS) technologies provides an advanced means for detecting genetically modified organisms and foods/feeds in GM crops. This review article describes the current status of GM crop commercialization and discusses the benefits and shortcomings of common and advanced detection systems for GMs in foods and animal feeds.

  12. Crop resources. [18 papers

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

    Seigler, D.S.

    Eighteen papers originally presented as a symposium on Crop Resources at the 17th annual meeting of the Society for Economic Botany in Urbana, Illinois, June 13 to 17, 1976 comprise this book. The papers are: Potential Wealth in New Crops: Research and Development, L. H. Princen; Plant Introductions--A Source of New Crops, George A. White; Nonfood Uses for Commercial Vegetable Oil Crops, E. H. Pryde; New Industrial Potentials for Carbohydrates, F. H. Otey; The Current Importance of Plants as a Source of Drugs, Norman R. Farnsworth; Potentials for Development of Wild Plants as Row Crops for Use by Man, Arnoldmore » Krochmal and Connie Krochmal; Recent Evidence in Support of the Tropical Origin of New World Crops, C. Earle Smith, Jr.; Requirements for a Green Revolution, G. F. Sprague; How Green Can a Revolution Be, Jack R. Harlan; Increasing Cereal Yields: Evolution under Domestication, J. M. J. de Wet; Hevea Rubber: Past and Future, Ernest P. Imle; Horseradish--Problems and Research in Illinois, A. M. Rhodes; Dioscorea--The Pill Crop, Norman Applezweig; Plant Derivatives for Insect Control, Robert L. Metcalf; Evolutionary Dynamics of Sorghum Domestication, J. M. J. de Wet and Y. Shecter; The Origin and Future of Wheat, E. R. Sears; Current Thoughts on Origins, Present Status, and Future of Soybeans, T. Hymowitz and C. A. Newell; and The Origin of Corn--Studies of the Last Hundred Years, Garrison Wilkes. (MCW)« less

  13. Science and society: protecting crop genetic diversity for food security: political, ethical and technical challenges.

    PubMed

    Esquinas-Alcázar, José

    2005-12-01

    Crop genetic diversity - which is crucial for feeding humanity, for the environment and for sustainable development - is being lost at an alarming rate. Given the enormous interdependence of countries and generations on this genetic diversity, this loss raises critical socio-economic, ethical and political questions. The recent ratification of a binding international treaty, and the development of powerful new technologies to conserve and use resources more effectively, have raised expectations that must now be fulfilled.

  14. Using genetically modified tomato crop plants with purple leaves for absolute weed/crop classification.

    PubMed

    Lati, Ran N; Filin, Sagi; Aly, Radi; Lande, Tal; Levin, Ilan; Eizenberg, Hanan

    2014-07-01

    Weed/crop classification is considered the main problem in developing precise weed-management methodologies, because both crops and weeds share similar hues. Great effort has been invested in the development of classification models, most based on expensive sensors and complicated algorithms. However, satisfactory results are not consistently obtained due to imaging conditions in the field. We report on an innovative approach that combines advances in genetic engineering and robust image-processing methods to detect weeds and distinguish them from crop plants by manipulating the crop's leaf color. We demonstrate this on genetically modified tomato (germplasm AN-113) which expresses a purple leaf color. An autonomous weed/crop classification is performed using an invariant-hue transformation that is applied to images acquired by a standard consumer camera (visible wavelength) and handles variations in illumination intensities. The integration of these methodologies is simple and effective, and classification results were accurate and stable under a wide range of imaging conditions. Using this approach, we simplify the most complicated stage in image-based weed/crop classification models. © 2013 Society of Chemical Industry.

  15. Using the GRIN-Global System to Identify Useful Plant Genetic Resources & Information

    USDA-ARS?s Scientific Manuscript database

    The GRIN-Global (GG) System has been developed to provide the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Service, Bioversity International and the Global C...

  16. Network-assisted crop systems genetics: network inference and integrative analysis.

    PubMed

    Lee, Tak; Kim, Hyojin; Lee, Insuk

    2015-04-01

    Although next-generation sequencing (NGS) technology has enabled the decoding of many crop species genomes, most of the underlying genetic components for economically important crop traits remain to be determined. Network approaches have proven useful for the study of the reference plant, Arabidopsis thaliana, and the success of network-based crop genetics will also require the availability of a genome-scale functional networks for crop species. In this review, we discuss how to construct functional networks and elucidate the holistic view of a crop system. The crop gene network then can be used for gene prioritization and the analysis of resequencing-based genome-wide association study (GWAS) data, the amount of which will rapidly grow in the field of crop science in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. [Assessment of allergenicity of genetically modified food crops].

    PubMed

    Schauzu, M; Pöting, A; Rubin, D; Lampen, A

    2012-03-01

    The placing on the European Union's market of genetically modified crops requires authorization by the European Commission which is based on the proof that the derived foods are as safe as their conventional counterparts. The assessment of potential allergenicity is part of the necessary investigations recommended in the updated Guidance Document of the Scientific Panel on Genetically Modified Organisms (GMO) of the European Food Safety Authority (EFSA), which is based on internationally agreed recommendations. All genetically modified crops which so far have been authorized in the European Union were evaluated by the EFSA GMO Panel which considered it unlikely that their overall allergenicity has been altered.

  18. Freeing Crop Genetics through the Open Source Seed Initiative

    PubMed Central

    Luby, Claire H.; Goldman, Irwin L.

    2016-01-01

    For millennia, seeds have been freely available to use for farming and plant breeding without restriction. Within the past century, however, intellectual property rights (IPRs) have threatened this tradition. In response, a movement has emerged to counter the trend toward increasing consolidation of control and ownership of plant germplasm. One effort, the Open Source Seed Initiative (OSSI, www.osseeds.org), aims to ensure access to crop genetic resources by embracing an open source mechanism that fosters exchange and innovation among farmers, plant breeders, and seed companies. Plant breeders across many sectors have taken the OSSI Pledge to create a protected commons of plant germplasm for future generations. PMID:27093567

  19. Freeing Crop Genetics through the Open Source Seed Initiative.

    PubMed

    Luby, Claire H; Goldman, Irwin L

    2016-04-01

    For millennia, seeds have been freely available to use for farming and plant breeding without restriction. Within the past century, however, intellectual property rights (IPRs) have threatened this tradition. In response, a movement has emerged to counter the trend toward increasing consolidation of control and ownership of plant germplasm. One effort, the Open Source Seed Initiative (OSSI, www.osseeds.org), aims to ensure access to crop genetic resources by embracing an open source mechanism that fosters exchange and innovation among farmers, plant breeders, and seed companies. Plant breeders across many sectors have taken the OSSI Pledge to create a protected commons of plant germplasm for future generations.

  20. Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources

    PubMed Central

    Monteiro, Filipa; Vidigal, Patrícia; Barros, André B.; Monteiro, Ana; Oliveira, Hugo R.; Viegas, Wanda

    2016-01-01

    Rye (Secale cereale L.) is a cereal crop of major importance in many parts of Europe and rye breeders are presently very concerned with the restrict pool of rye genetic resources available. Such narrowing of rye genetic diversity results from the presence of “Petkus” pool in most modern rye varieties as well as “Petkus” × “Carsten” heterotic pool in hybrid rye breeding programs. Previous studies on rye's genetic diversity revealed moreover a common genetic background on landraces (ex situ) and cultivars, regardless of breeding level or geographical origin. Thus evaluation of in situ populations is of utmost importance to unveil “on farm” diversity, which is largely undervalued. Here, we perform the first comprehensive assessment of rye's genetic diversity and population structuring using cultivars, ex situ landraces along a comprehensive sampling of in situ accessions from Portugal, through a molecular-directed analysis using SSRs markers. Rye genetic diversity and population structure analysis does not present any geographical trend but disclosed marked differences between genetic backgrounds of in situ accessions and those of cultivars/ex situ collections. Such genetic distinctiveness of in situ accessions highlights their unexplored potential as new genetic resources, which can be used to boost rye breeding strategies and the production of new varieties. Overall, our study successfully demonstrates the high prospective impact of comparing genetic diversity and structure of cultivars, ex situ, and in situ samples in ascertaining the status of plant genetic resources (PGR). PMID:27630658

  1. Metabolomics of Genetically Modified Crops

    PubMed Central

    Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade. PMID:25334064

  2. Status of market, regulation and research of genetically modified crops in Chile.

    PubMed

    Sánchez, Miguel A; León, Gabriel

    2016-12-25

    Agricultural biotechnology and genetically modified (GM) crops are effective tools to substantially increase productivity, quality, and environmental sustainability in agricultural farming. Furthermore, they may contribute to improving the nutritional content of crops, addressing needs related to public health. Chile has become one of the most important global players for GM seed production for counter-season markets and research purposes. It has a comprehensive regulatory framework to carry out this activity, while at the same time there are numerous regulations from different agencies addressing several aspects related to GM crops. Despite imports of GM food/feed or ingredients for the food industry being allowed without restrictions, Chilean farmers are not using GM seeds for farming purposes because of a lack of clear guidelines. Chile is in a rather contradictory situation about GM crops. The country has invested considerable resources to fund research and development on GM crops, but the lack of clarity in the current regulatory situation precludes the use of such research to develop new products for Chilean farmers. Meanwhile, a larger scientific capacity regarding GM crop research continues to build up in the country. The present study maps and analyses the current regulatory environment for research and production of GM crops in Chile, providing an updated overview of the current status of GM seeds production, research and regulatory issues. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Genetic Modification in Dedicated Bioenergy Crops and Strategies for Gene Confinement

    USDA-ARS?s Scientific Manuscript database

    Genetic modification of dedicated bioenergy crops is in its infancy; however, there are numerous advantages to the use of these tools to improve crops used for biofuels. Potential improved traits through genetic engineering (GE) include herbicide resistance, pest, drought, cold and salt tolerance, l...

  4. Genetically Modified Crops and Food Security

    PubMed Central

    Qaim, Matin; Kouser, Shahzad

    2013-01-01

    The role of genetically modified (GM) crops for food security is the subject of public controversy. GM crops could contribute to food production increases and higher food availability. There may also be impacts on food quality and nutrient composition. Finally, growing GM crops may influence farmers’ income and thus their economic access to food. Smallholder farmers make up a large proportion of the undernourished people worldwide. Our study focuses on this latter aspect and provides the first ex post analysis of food security impacts of GM crops at the micro level. We use comprehensive panel data collected over several years from farm households in India, where insect-resistant GM cotton has been widely adopted. Controlling for other factors, the adoption of GM cotton has significantly improved calorie consumption and dietary quality, resulting from increased family incomes. This technology has reduced food insecurity by 15–20% among cotton-producing households. GM crops alone will not solve the hunger problem, but they can be an important component in a broader food security strategy. PMID:23755155

  5. Genetically modified crops and food security.

    PubMed

    Qaim, Matin; Kouser, Shahzad

    2013-01-01

    The role of genetically modified (GM) crops for food security is the subject of public controversy. GM crops could contribute to food production increases and higher food availability. There may also be impacts on food quality and nutrient composition. Finally, growing GM crops may influence farmers' income and thus their economic access to food. Smallholder farmers make up a large proportion of the undernourished people worldwide. Our study focuses on this latter aspect and provides the first ex post analysis of food security impacts of GM crops at the micro level. We use comprehensive panel data collected over several years from farm households in India, where insect-resistant GM cotton has been widely adopted. Controlling for other factors, the adoption of GM cotton has significantly improved calorie consumption and dietary quality, resulting from increased family incomes. This technology has reduced food insecurity by 15-20% among cotton-producing households. GM crops alone will not solve the hunger problem, but they can be an important component in a broader food security strategy.

  6. From Crop Domestication to Super-domestication

    PubMed Central

    Vaughan, D. A.; Balázs, E.; Heslop-Harrison, J. S.

    2007-01-01

    Research related to crop domestication has been transformed by technologies and discoveries in the genome sciences as well as information-related sciences that are providing new tools for bioinformatics and systems' biology. Rapid progress in archaeobotany and ethnobotany are also contributing new knowledge to understanding crop domestication. This sense of rapid progress is encapsulated in this Special Issue, which contains 18 papers by scientists in botanical, crop sciences and related disciplines on the topic of crop domestication. One paper focuses on current themes in the genetics of crop domestication across crops, whereas other papers have a crop or geographic focus. One feature of progress in the sciences related to crop domestication is the availability of well-characterized germplasm resources in the global network of genetic resources centres (genebanks). Germplasm in genebanks is providing research materials for understanding domestication as well as for plant breeding. In this review, we highlight current genetic themes related to crop domestication. Impressive progress in this field in recent years is transforming plant breeding into crop engineering to meet the human need for increased crop yield with the minimum environmental impact – we consider this to be ‘super-domestication’. While the time scale of domestication of 10 000 years or less is a very short evolutionary time span, the details emerging of what has happened and what is happening provide a window to see where domestication might – and can – advance in the future. PMID:17940074

  7. Molecular, Genetic and Agronomic Approaches to Utilizing Pulses as Cover Crops and Green Manure into Cropping Systems

    PubMed Central

    Tani, Eleni; Abraham, Eleni; Chachalis, Demosthenis; Travlos, Ilias

    2017-01-01

    Cover crops constitute one of the most promising agronomic practices towards a more sustainable agriculture. Their beneficial effects on main crops, soil and environment are many and various, while risks and disadvantages may also appear. Several legumes show a high potential but further research is required in order to suggest the optimal legume cover crops for each case in terms of their productivity and ability to suppress weeds. The additional cost associated with cover crops should also be addressed and in this context the use of grain legumes such as cowpea, faba bean and pea could be of high interest. Some of the aspects of these grain legumes as far as their use as cover crops, their genetic diversity and their breeding using conventional and molecular approaches are discussed in the present review. The specific species seem to have a high potential for use as cover crops, especially if their noticeable genetic diversity is exploited and their breeding focuses on several desirable traits. PMID:28587254

  8. Harnessing quantitative genetics and genomics for understanding and improving complex traits in crops

    USDA-ARS?s Scientific Manuscript database

    Classical quantitative genetics aids crop improvement by providing the means to estimate heritability, genetic correlations, and predicted responses to various selection schemes. Genomics has the potential to aid quantitative genetics and applied crop improvement programs via large-scale, high-thro...

  9. Erosion of Brassica incana Genetic Resources: Causes and Effects

    NASA Astrophysics Data System (ADS)

    Muscolo, A.; Settineri, G.; Mallamaci, C.; Papalia, T.; Sidari, M.

    2017-07-01

    Brassica incana Ten., possessing a number of useful agronomic traits, represents a precious genetic resource to be used in plant breeding programs to broaden the genetic base in most Brassica crop species. B. incana that grows on limestone cliffs is at risk of genetic erosion for environmental constraints and human activities. We studied the pedological conditions of a Calabrian site where the B. incana grows, and we correlated the soil properties to the physiological and biochemical aspects of B. incana to identify the causes and effects of the genetic erosion of this species. Our results evidenced that physical soil conditions did not affect B. incana growth and nutraceutical properties; conversely, biological soil properties modified its properties. We identified leaf pigments and secondary metabolites that can be used routinely as early warning indicators of plant threat, to evaluate in a short term the dynamic behavior of plants leading to species extinction.

  10. Genetically modified crops: detection strategies and biosafety issues.

    PubMed

    Kamle, Suchitra; Ali, Sher

    2013-06-15

    Genetically modified (GM) crops are increasingly gaining acceptance but concurrently consumers' concerns are also increasing. The introduction of Bacillus thuringiensis (Bt) genes into the plants has raised issues related to its risk assessment and biosafety. The International Regulations and the Codex guidelines regulate the biosafety requirements of the GM crops. In addition, these bodies synergize and harmonize the ethical issues related to the release and use of GM products. The labeling of GM crops and their products are mandatory if the genetically modified organism (GMO) content exceeds the levels of a recommended threshold. The new and upcoming GM crops carrying multiple stacked traits likely to be commercialized soon warrant sensitive detection methods both at the DNA and protein levels. Therefore, traceability of the transgene and its protein expression in GM crops is an important issue that needs to be addressed on a priority basis. The advancement in the area of molecular biology has made available several bioanalytical options for the detection of GM crops based on DNA and protein markers. Since the insertion of a gene into the host genome may even cause copy number variation, this may be uncovered using real time PCR. Besides, assessing the exact number of mRNA transcripts of a gene, correlation between the template activity and expressed protein may be established. Here, we present an overview on the production of GM crops, their acceptabilities, detection strategies, biosafety issues and potential impact on society. Further, overall future prospects are also highlighted. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Perspectives on genetically modified crops and food detection.

    PubMed

    Lin, Chih-Hui; Pan, Tzu-Ming

    2016-01-01

    Genetically modified (GM) crops are a major product of the global food industry. From 1996 to 2014, 357 GM crops were approved and the global value of the GM crop market reached 35% of the global commercial seed market in 2014. However, the rapid growth of the GM crop-based industry has also created controversies in many regions, including the European Union, Egypt, and Taiwan. The effective detection and regulation of GM crops/foods are necessary to reduce the impact of these controversies. In this review, the status of GM crops and the technology for their detection are discussed. As the primary gap in GM crop regulation exists in the application of detection technology to field regulation, efforts should be made to develop an integrated, standardized, and high-throughput GM crop detection system. We propose the development of an integrated GM crop detection system, to be used in combination with a standardized international database, a decision support system, high-throughput DNA analysis, and automated sample processing. By integrating these technologies, we hope that the proposed GM crop detection system will provide a method to facilitate comprehensive GM crop regulation. Copyright © 2015. Published by Elsevier B.V.

  12. Enhancing (crop) plant photosynthesis by introducing novel genetic diversity.

    PubMed

    Dann, Marcel; Leister, Dario

    2017-09-26

    Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Author(s).

  13. Cover Crop Chart: An Intuitive Educational Resource for Extension Professionals

    ERIC Educational Resources Information Center

    Liebig, Mark A.; Johnson, Holly; Archer, David; Hendrickson, John; Nichols, Kristine; Schmer, Marty; Tanaka, Don

    2013-01-01

    Interest in cover crops by agricultural producers has increased the need for information regarding the suitability of crops for addressing different production and natural resource goals. To help address this need, staff at the USDA-ARS Northern Great Plains Research Laboratory developed a decision aid called the Cover Crop Chart (CCC). Visually…

  14. Improving crop productivity and resource use efficiency to ensure food security and environmental quality in China.

    PubMed

    Fan, Mingsheng; Shen, Jianbo; Yuan, Lixing; Jiang, Rongfeng; Chen, Xinping; Davies, William J; Zhang, Fusuo

    2012-01-01

    In recent years, agricultural growth in China has accelerated remarkably, but most of this growth has been driven by increased yield per unit area rather than by expansion of the cultivated area. Looking towards 2030, to meet the demand for grain and to feed a growing population on the available arable land, it is suggested that annual crop production should be increased to around 580 Mt and that yield should increase by at least 2% annually. Crop production will become more difficult with climate change, resource scarcity (e.g. land, water, energy, and nutrients) and environmental degradation (e.g. declining soil quality, increased greenhouse gas emissions, and surface water eutrophication). To pursue the fastest and most practical route to improved yield, the near-term strategy is application and extension of existing agricultural technologies. This would lead to substantial improvement in crop and soil management practices, which are currently suboptimal. Two pivotal components are required if we are to follow new trajectories. First, the disciplines of soil management and agronomy need to be given increased emphasis in research and teaching, as part of a grand food security challenge. Second, continued genetic improvement in crop varieties will be vital. However, our view is that the biggest gains from improved technology will come most immediately from combinations of improved crops and improved agronomical practices. The objectives of this paper are to summarize the historical trend of crop production in China and to examine the main constraints to the further increase of crop productivity. The paper provides a perspective on the challenge faced by science and technology in agriculture which must be met both in terms of increased crop productivity but also in increased resource use efficiency and the protection of environmental quality.

  15. Genetic resources offer efficient tools for rice functional genomics research.

    PubMed

    Lo, Shuen-Fang; Fan, Ming-Jen; Hsing, Yue-Ie; Chen, Liang-Jwu; Chen, Shu; Wen, Ien-Chie; Liu, Yi-Lun; Chen, Ku-Ting; Jiang, Mirng-Jier; Lin, Ming-Kuang; Rao, Meng-Yen; Yu, Lin-Chih; Ho, Tuan-Hua David; Yu, Su-May

    2016-05-01

    Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops. © 2015 John Wiley & Sons Ltd.

  16. The Emerging Oilseed Crop Sesamum indicum Enters the "Omics" Era.

    PubMed

    Dossa, Komivi; Diouf, Diaga; Wang, Linhai; Wei, Xin; Zhang, Yanxin; Niang, Mareme; Fonceka, Daniel; Yu, Jingyin; Mmadi, Marie A; Yehouessi, Louis W; Liao, Boshou; Zhang, Xiurong; Cisse, Ndiaga

    2017-01-01

    Sesame ( Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an "orphan crop" to a "genomic resource-rich crop." With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the "Omics" area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.

  17. Current issues connected with usage of genetically modified crops in production of feed and livestock feeding.

    PubMed

    Kwiatek, K; Mazur, M; Sieradzki, Z

    2008-01-01

    Progress, which is brought by new advances in modern molecular biology, allowed interference in the genome of live organisms and gene manipulation. Introducing new genes to the recipient organism enables to give them new features, absent before. Continuous increase in the area of the biotech crops triggers continuous discussion about safety of genetically modified (GM) crops, including food and feed derived from them. Important issue connected with cultivation of genetically modified crops is a horizontal gene transfer and a bacterial antibiotic resistance. Discussion about safety of GM crops concerns also food allergies caused by eating genetically modified food. The problem of genetic modifications of GM crops used for livestock feeding is widely discussed, taking into account Polish feed law.

  18. The state of genetically modified crop regulation in Canada

    PubMed Central

    Smyth, Stuart J

    2014-01-01

    Genetically modified (GM) crops were first commercialized in Canada in 1995 and the 2014 crop represents the 20th year of successful production. Prior to the first commercialization of GM crops, Canada reviewed its existing science-based regulatory framework and adapted the existing framework to allow for risk assessments on the new technology to be undertaken in a timely and efficient manner. The result has been the rapid and widespread adoption of GM varieties of canola, corn and soybeans. The first decade of GM crop production precipitated 2 landmark legal cases relating to patent infringement and economic liability, while the second decade witnessed increased political efforts to have GM crops labeled in Canada as well as significant challenges from the low level comingling of GM crops with non-GM commodities. This article reviews the 20 y of GM crop production in Canada from a social science perspective that includes intellectual property, consumer acceptance and low level presence. PMID:25437238

  19. Cover Crop Chart: An intuitive educational resource for extension professionals

    USDA-ARS?s Scientific Manuscript database

    Interest in cover crops by agricultural producers has increased the need for information regarding the suitability of crops for addressing different production and natural resource goals. To help address this need, staff at the USDA Agricultural Research Service Northern Great Plains Research Labor...

  20. Genetic modification of plant cell walls to enhance biomass yield and biofuel production in bioenergy crops.

    PubMed

    Wang, Yanting; Fan, Chunfen; Hu, Huizhen; Li, Ying; Sun, Dan; Wang, Youmei; Peng, Liangcai

    2016-01-01

    Plant cell walls represent an enormous biomass resource for the generation of biofuels and chemicals. As lignocellulose property principally determines biomass recalcitrance, the genetic modification of plant cell walls has been posed as a powerful solution. Here, we review recent progress in understanding the effects of distinct cell wall polymers (cellulose, hemicelluloses, lignin, pectin, wall proteins) on the enzymatic digestibility of biomass under various physical and chemical pretreatments in herbaceous grasses, major agronomic crops and fast-growing trees. We also compare the main factors of wall polymer features, including cellulose crystallinity (CrI), hemicellulosic Xyl/Ara ratio, monolignol proportion and uronic acid level. Furthermore, the review presents the main gene candidates, such as CesA, GH9, GH10, GT61, GT43 etc., for potential genetic cell wall modification towards enhancing both biomass yield and enzymatic saccharification in genetic mutants and transgenic plants. Regarding cell wall modification, it proposes a novel groove-like cell wall model that highlights to increase amorphous regions (density and depth) of the native cellulose microfibrils, providing a general strategy for bioenergy crop breeding and biofuel processing technology. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. 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.

  2. Spatiotemporal patterns of non-genetically modified crops in the era of expansion of genetically modified food

    PubMed Central

    Sun, Jing; Wu, Wenbin; Tang, Huajun; Liu, Jianguo

    2015-01-01

    Despite heated debates over the safety of genetically modified (GM) food, GM crops have been expanding rapidly. Much research has focused on the expansion of GM crops. However, the spatiotemporal dynamics of non-genetically modified (non-GM) crops are not clear, although they may have significant environmental and agronomic impacts and important policy implications. To understand the dynamics of non-GM crops and to inform the debates among relevant stakeholders, we conducted spatiotemporal analyses of China’s major non-GM soybean production region, the Heilongjiang Province. Even though the total soybean planting area decreased from 2005 to 2010, surprisingly, there were hotspots of increase. The results also showed hotspots of loss as well as a large decline in the number and continuity of soybean plots. Since China is the largest non-GM soybean producer in the world, the decline of its major production region may signal the continual decline of global non-GM soybeans. PMID:26380899

  3. Spatiotemporal patterns of non-genetically modified crops in the era of expansion of genetically modified food.

    PubMed

    Sun, Jing; Wu, Wenbin; Tang, Huajun; Liu, Jianguo

    2015-09-18

    Despite heated debates over the safety of genetically modified (GM) food, GM crops have been expanding rapidly. Much research has focused on the expansion of GM crops. However, the spatiotemporal dynamics of non-genetically modified (non-GM) crops are not clear, although they may have significant environmental and agronomic impacts and important policy implications. To understand the dynamics of non-GM crops and to inform the debates among relevant stakeholders, we conducted spatiotemporal analyses of China's major non-GM soybean production region, the Heilongjiang Province. Even though the total soybean planting area decreased from 2005 to 2010, surprisingly, there were hotspots of increase. The results also showed hotspots of loss as well as a large decline in the number and continuity of soybean plots. Since China is the largest non-GM soybean producer in the world, the decline of its major production region may signal the continual decline of global non-GM soybeans.

  4. The impact of genetically modified crops on soil microbial communities.

    PubMed

    Giovannetti, Manuela; Sbrana, Cristiana; Turrini, Alessandra

    2005-01-01

    Genetically modified (GM) plants represent a potential benefit for environmentally friendly agriculture and human health. Though, poor knowledge is available on potential hazards posed by unintended modifications occurring during genetic manipulation. The increasing amount of reports on ecological risks and benefits of GM plants stresses the need for experimental works aimed at evaluating the impact of GM crops on natural and agro-ecosystems. Major environmental risks associated with GM crops include their potential impact on non-target soil microorganisms playing a fundamental role in crop residues degradation and in biogeochemical cycles. Recent works assessed the effects of GM crops on soil microbial communities on the basis of case-by-case studies, using multimodal experimental approaches involving different target and non-target organisms. Experimental evidences discussed in this review confirm that a precautionary approach should be adopted, by taking into account the risks associated with the unpredictability of transformation events, of their pleiotropic effects and of the fate of transgenes in natural and agro-ecosystems, weighing benefits against costs.

  5. Evolutionary response of landraces to climate change in centers of crop diversity

    PubMed Central

    Mercer, Kristin L; Perales, Hugo R

    2010-01-01

    Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource. PMID:25567941

  6. Evolutionary response of landraces to climate change in centers of crop diversity.

    PubMed

    Mercer, Kristin L; Perales, Hugo R

    2010-09-01

    Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource.

  7. Could Crop Height Impact the Wind Resource at Agriculturally Productive Wind Farm Sites?

    NASA Astrophysics Data System (ADS)

    Vanderwende, B. J.; Lundquist, J. K.

    2013-12-01

    The agriculture-intensive United States Midwest and Great Plains regions feature some of the best wind resources in the nation. Collocation of cropland and wind turbines introduces complex meteorological interactions that could affect both agriculture and wind power production. Crop management practices may modify the wind resource through alterations of land-surface properties. In this study, we used the Weather Research and Forecasting (WRF) model to estimate the impact of crop height variations on the wind resource in the presence of a large turbine array. We parameterized a hypothetical array of 121 1.8 MW turbines at the site of the 2011 Crop/Wind-energy Experiment field campaign using the WRF wind farm parameterization. We estimated the impact of crop choices on power production by altering the aerodynamic roughness length in a region approximately 65 times larger than that occupied by the turbine array. Roughness lengths of 10 cm and 25 cm represent a mature soy crop and a mature corn crop respectively. Results suggest that the presence of the mature corn crop reduces hub-height wind speeds and increases rotor-layer wind shear, even in the presence of a large wind farm which itself modifies the flow. During the night, the influence of the surface was dependent on the boundary layer stability, with strong stability inhibiting the surface drag from modifying the wind resource aloft. Further investigation is required to determine the optimal size, shape, and crop height of the roughness modification to maximize the economic benefit and minimize the cost of such crop management practices.

  8. The Gene Pool Concept Applied to Crop Wild Relatives: An Evolutionary Perspective

    USDA-ARS?s Scientific Manuscript database

    Crop wild relatives (CWR) can provide important resources for the genetic improvement of cultivated species. Because crops are often closely related to many wild species, and because exploration of CWR for useful traits can take many years and substantial resources, the categorization of CWR based o...

  9. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement

    PubMed Central

    Muñoz, Nacira; Liu, Ailin; Kan, Leo; Li, Man-Wah; Lam, Hon-Ming

    2017-01-01

    Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes. PMID:28165413

  10. Bacterial Artificial Chromosome Libraries of Pulse Crops: Characteristics and Applications

    PubMed Central

    Yu, Kangfu

    2012-01-01

    Pulse crops are considered minor on a global scale despite their nutritional value for human consumption. Therefore, they are relatively less extensively studied in comparison with the major crops. The need to improve pulse crop production and quality will increase with the increasing global demand for food security and people's awareness of nutritious food. The improvement of pulse crops will require fully utilizing all their genetic resources. Bacterial artificial chromosome (BAC) libraries of pulse crops are essential genomic resources that have the potential to accelerate gene discovery and enhance molecular breeding in these crops. Here, we review the availability, characteristics, applications, and potential applications of the BAC libraries of pulse crops. PMID:21811383

  11. Shifts and disruptions in resource-use trait syndromes during the evolution of herbaceous crops.

    PubMed

    Milla, Rubén; Morente-López, Javier; Alonso-Rodrigo, J Miguel; Martín-Robles, Nieves; Chapin, F Stuart

    2014-10-22

    Trait-based ecology predicts that evolution in high-resource agricultural environments should select for suites of traits that enable fast resource acquisition and rapid canopy closure. However, crop breeding targets specific agronomic attributes rather than broad trait syndromes. Breeding for specific traits, together with evolution in high-resource environments, might lead to reduced phenotypic integration, according to predictions from the ecological literature. We provide the first comprehensive test of these hypotheses, based on a trait-screening programme of 30 herbaceous crops and their wild progenitors. During crop evolution plants became larger, which enabled them to compete more effectively for light, but they had poorly integrated phenotypes. In a subset of six herbaceous crop species investigated in greater depth, competitiveness for light increased during early plant domestication, whereas diminished phenotypic integration occurred later during crop improvement. Mass-specific leaf and root traits relevant to resource-use strategies (e.g. specific leaf area or tissue density of fine roots) changed during crop evolution, but in diverse and contrasting directions and magnitudes, depending on the crop species. Reductions in phenotypic integration and overinvestment in traits involved in competition for light may affect the chances of upgrading modern herbaceous crops to face current climatic and food security challenges. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  12. Malus sieversii, a valuable genetic resource for disease resistance in apple

    USDA-ARS?s Scientific Manuscript database

    Domesticated crop cultivars inevitably represent a subset of the genetic variation found in their wild ancestors (progenitors) due to genetic bottlenecks that result during the process of crop domestication. Malus sieversii, a wild apple species native to Central Asia, is one of the ancestral proge...

  13. Biosafety management and commercial use of genetically modified crops in China.

    PubMed

    Li, Yunhe; Peng, Yufa; Hallerman, Eric M; Wu, Kongming

    2014-04-01

    As a developing country with relatively limited arable land, China is making great efforts for development and use of genetically modified (GM) crops to boost agricultural productivity. Many GM crop varieties have been developed in China in recent years; in particular, China is playing a leading role in development of insect-resistant GM rice lines. To ensure the safe use of GM crops, biosafety risk assessments are required as an important part of the regulatory oversight of such products. With over 20 years of nationwide promotion of agricultural biotechnology, a relatively well-developed regulatory system for risk assessment and management of GM plants has been developed that establishes a firm basis for safe use of GM crops. So far, a total of seven GM crops involving ten events have been approved for commercial planting, and 5 GM crops with a total of 37 events have been approved for import as processing material in China. However, currently only insect-resistant Bt cotton and disease-resistant papaya have been commercially planted on a large scale. The planting of Bt cotton and disease-resistant papaya have provided efficient protection against cotton bollworms and Papaya ringspot virus (PRSV), respectively. As a consequence, chemical application to these crops has been significantly reduced, enhancing farm income while reducing human and non-target organism exposure to toxic chemicals. This article provides useful information for the colleagues, in particular for them whose mother tongue is not Chinese, to clearly understand the biosafety regulation and commercial use of genetically modified crops in China.

  14. Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp)

    PubMed Central

    Spriggs, Andrew; Henderson, Steven T.; Hand, Melanie L.; Johnson, Susan D.; Taylor, Jennifer M.; Koltunow, Anna

    2018-01-01

    Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads. PMID:29528046

  15. Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

    PubMed

    Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

    2018-02-09

    Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

  16. Pollen resources for pollinators in specialty oilseed crops

    USDA-ARS?s Scientific Manuscript database

    Simplified agroecosystems have depleted habitats for beneficial insects throughout the Midwest and Northern Great Plains of the USA. Beneficial insects include pollinators and natural enemies of crop pests, and both rely heavily on floral resources and habitat diversity to maintain healthy populatio...

  17. Emerging crops in the USDA arid lands germplasm collection

    USDA-ARS?s Scientific Manuscript database

    The USDA National Plant Germplasm System maintains collections of several emerging crops for arid lands at the National Arid Land Plant Genetic Resources Unit in Parlier, CA (NALPGRU). The guayule, jojoba, and prickly pear collections are most active in terms of current research and crop development...

  18. Proteomic evaluation of genetically modified crops: current status and challenges

    PubMed Central

    Gong, Chun Yan; Wang, Tai

    2013-01-01

    Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. “Omics” techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques. PMID:23471542

  19. Proteomic evaluation of genetically modified crops: current status and challenges.

    PubMed

    Gong, Chun Yan; Wang, Tai

    2013-01-01

    Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. "Omics" techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques.

  20. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives.

    PubMed

    Govindaraj, M; Vetriventhan, M; Srinivasan, M

    2015-01-01

    The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable

  1. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

    PubMed Central

    Govindaraj, M.; Vetriventhan, M.; Srinivasan, M.

    2015-01-01

    The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable

  2. Functional Genomics of Drought Tolerance in Bioenergy Crops

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

    Yin, Hengfu; Chen, Rick; Yang, Jun

    2014-01-01

    With the predicted trends in climate change, drought will increasingly impose a grand challenge to biomass production. Most of the bioenergy crops have some degree of drought susceptibility with low water-use efficiency (WUE). It is imperative to improve drought tolerance and WUE in bioenergy crops for sustainable biomass production in arid and semi-arid regions with minimal water input. Genetics and functional genomics can play a critical role in generating knowledge to inform and aid genetic improvement of drought tolerance in bioenergy crops. The molecular aspect of drought response has been extensively investigated in model plants like Arabidopsis, yet our understandingmore » of the molecular mechanisms underlying drought tolerance in bioenergy crops are limited. Crops exhibit various responses to drought stress depending on species and genotype. A rational strategy for studying drought tolerance in bioenergy crops is to translate the knowledge from model plants and pinpoint the unique features associated with individual species and genotypes. In this review, we summarize the general knowledge about drought responsive pathways in plants, with a focus on the identification of commonality and specialty in drought responsive mechanisms among different species and/or genotypes. We describe the genomic resources developed for bioenergy crops and discuss genetic and epigenetic regulation of drought responses. We also examine comparative and evolutionary genomics to leverage the ever-increasing genomics resources and provide new insights beyond what has been known from studies on individual species. Finally, we outline future exploration of drought tolerance using the emerging new technologies.« less

  3. Pleiotropic effects of herbicide-resistance genes on crop yield: a review.

    PubMed

    Darmency, Henri

    2013-08-01

    The rapid adoption of genetically engineered herbicide-resistant crop varieties (HRCVs)-encompassing 83% of all GM crops and nearly 8% of the worldwide arable area-is due to technical efficiency and higher returns. Other herbicide-resistant varieties obtained from genetic resources and mutagenesis have also been successfully released. Although the benefit for weed control is the main criteria for choosing HRCVs, the pleiotropic costs of genes endowing resistance have rarely been investigated in crops. Here the available data of comparisons between isogenic resistant and susceptible varieties are reviewed. Pleiotropic harmful effects on yield are reported in half of the cases, mostly with resistance mechanisms that originate from genetic resources and mutagenesis (atrazine in oilseed rape and millet, trifluralin in millet, imazamox in cotton) rather than genetic engineering (chlorsulfuron and glufosinate in some oilseed rape varieties, glyphosate in soybean). No effect was found for sethoxydim and bromoxynil resistance. Variable minor effects were found for imazamox, chlorsulfuron, glufosinate and glyphosate resistance. The importance of the breeding plan and the genetic background on the emergence of these effects is pointed out. Breeders' efforts to produce better varieties could compensate for the yield loss, which eliminates any possibility of formulating generic conclusions on pleiotropic effects that can be applied to all resistant crops. © 2013 Society of Chemical Industry.

  4. The Emerging Oilseed Crop Sesamum indicum Enters the “Omics” Era

    PubMed Central

    Dossa, Komivi; Diouf, Diaga; Wang, Linhai; Wei, Xin; Zhang, Yanxin; Niang, Mareme; Fonceka, Daniel; Yu, Jingyin; Mmadi, Marie A.; Yehouessi, Louis W.; Liao, Boshou; Zhang, Xiurong; Cisse, Ndiaga

    2017-01-01

    Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an “orphan crop” to a “genomic resource-rich crop.” With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the “Omics” area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop. PMID:28713412

  5. Redesigning the exploitation of wheat genetic resources.

    PubMed

    Longin, C Friedrich H; Reif, Jochen C

    2014-10-01

    More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources. The gathered phenotypic information will enable a targeted choice of accessions with high value for pre-breeding among this plethora of genetic resources. We intend to provoke a paradigm shift in pre-breeding strategies for grain yield, moving away from allele mining toward genome-wide selection to bridge the yield gap between genetic resources and elite breeding pools. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Proposed definition of environmental damage illustrated by the cases of genetically modified crops and invasive species.

    PubMed

    Bartz, Robert; Heink, Ulrich; Kowarik, Ingo

    2010-06-01

    The introduction of non-native plant species and the release of genetically modified (GM) crops can induce environmental changes at gene to ecosystem levels. Regulatory frameworks such as the Convention on Biological Diversity or the EU Deliberate Release Directive aim to prevent environmental damage but do not define the term. Although ecologists and conservationists often refer to environmental effects of GM crops or invasive species as damage, most authors do not disclose their normative assumptions or explain why some environmental impacts are regarded as detrimental and others are not. Thus far, a concise definition of environmental damage is missing and is necessary for a transparent assessment of environmental effects or risks. Therefore, we suggest defining environmental damage as a significant adverse effect on a biotic or abiotic conservation resource (i.e., a biotic or abiotic natural resource that is protected by conservational or environmental legislation) that has an impact on the value of the conservation resource, the conservation resource as an ecosystem component, or the sustainable use of the conservation resource. This definition relies on three normative assumptions: only concrete effects on a conservation resource can be damages; only adverse effects that lead to a decrease in the value of the conservation resource can be damages; and only significant adverse effects constitute damage to a conservation resource. Applying this definition within the framework of environmental risk assessment requires further normative determinations, for example, selection of a threshold to distinguish between adverse and significant adverse effects and approaches for assessing the environmental value of conservation resources. Such determinations, however, are not part of the definition of environmental damage. Rather they are part of the definition's operationalization through assessment procedures, which must be grounded in a comprehensible definition of

  7. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    PubMed

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  8. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops

    PubMed Central

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an “island model” inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of

  9. An integrated model for assessing both crop productivity and agricultural water resources at a large scale

    NASA Astrophysics Data System (ADS)

    Okada, M.; Sakurai, G.; Iizumi, T.; Yokozawa, M.

    2012-12-01

    Agricultural production utilizes regional resources (e.g. river water and ground water) as well as local resources (e.g. temperature, rainfall, solar energy). Future climate changes and increasing demand due to population increases and economic developments would intensively affect the availability of water resources for agricultural production. While many studies assessed the impacts of climate change on agriculture, there are few studies that dynamically account for changes in water resources and crop production. This study proposes an integrated model for assessing both crop productivity and agricultural water resources at a large scale. Also, the irrigation management to subseasonal variability in weather and crop response varies for each region and each crop. To deal with such variations, we used the Markov Chain Monte Carlo technique to quantify regional-specific parameters associated with crop growth and irrigation water estimations. We coupled a large-scale crop model (Sakurai et al. 2012), with a global water resources model, H08 (Hanasaki et al. 2008). The integrated model was consisting of five sub-models for the following processes: land surface, crop growth, river routing, reservoir operation, and anthropogenic water withdrawal. The land surface sub-model was based on a watershed hydrology model, SWAT (Neitsch et al. 2009). Surface and subsurface runoffs simulated by the land surface sub-model were input to the river routing sub-model of the H08 model. A part of regional water resources available for agriculture, simulated by the H08 model, was input as irrigation water to the land surface sub-model. The timing and amount of irrigation water was simulated at a daily step. The integrated model reproduced the observed streamflow in an individual watershed. Additionally, the model accurately reproduced the trends and interannual variations of crop yields. To demonstrate the usefulness of the integrated model, we compared two types of impact assessment of

  10. Conservation priorities for tree crop wild relatives in the United States

    USDA-ARS?s Scientific Manuscript database

    Our native crop wild relatives have proved useful as genetic resources in breeding more productive, nutritious, and resilient crops. Their utilization is expected only to increase with better information on the species and improving breeding tools, but may well be constrained by their limited repres...

  11. Genetic diversity and population structure of an important wild berry crop

    PubMed Central

    Zoratti, Laura; Palmieri, Luisa; Jaakola, Laura; Häggman, Hely

    2015-01-01

    The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north–south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry. PMID:26483325

  12. 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.

  13. Resources for Systems Genetics.

    PubMed

    Williams, Robert W; Williams, Evan G

    2017-01-01

    A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.

  14. Assessment of the safety of foods derived from genetically modified (GM) crops.

    PubMed

    König, A; Cockburn, A; Crevel, R W R; Debruyne, E; Grafstroem, R; Hammerling, U; Kimber, I; Knudsen, I; Kuiper, H A; Peijnenburg, A A C M; Penninks, A H; Poulsen, M; Schauzu, M; Wal, J M

    2004-07-01

    This paper provides guidance on how to assess the safety of foods derived from genetically modified crops (GM crops); it summarises conclusions and recommendations of Working Group 1 of the ENTRANSFOOD project. The paper provides an approach for adapting the test strategy to the characteristics of the modified crop and the introduced trait, and assessing potential unintended effects from the genetic modification. The proposed approach to safety assessment starts with the comparison of the new GM crop with a traditional counterpart that is generally accepted as safe based on a history of human food use (the concept of substantial equivalence). This case-focused approach ensures that foods derived from GM crops that have passed this extensive test-regime are as safe and nutritious as currently consumed plant-derived foods. The approach is suitable for current and future GM crops with more complex modifications. First, the paper reviews test methods developed for the risk assessment of chemicals, including food additives and pesticides, discussing which of these methods are suitable for the assessment of recombinant proteins and whole foods. Second, the paper presents a systematic approach to combine test methods for the safety assessment of foods derived from a specific GM crop. Third, the paper provides an overview on developments in this area that may prove of use in the safety assessment of GM crops, and recommendations for research priorities. It is concluded that the combination of existing test methods provides a sound test-regime to assess the safety of GM crops. Advances in our understanding of molecular biology, biochemistry, and nutrition may in future allow further improvement of test methods that will over time render the safety assessment of foods even more effective and informative. Copryright 2004 Elsevier Ltd.

  15. Genomics of Tropical Fruit Tree Crops

    USDA-ARS?s Scientific Manuscript database

    The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

  16. National Newborn Screening and Genetics Resource Center

    MedlinePlus

    ... GENERAL INFORMATION Conditions Screened by US Programs General Resources Genetics Birth Defects Hearing Screening FOR PROFESSIONALS ACT Sheets(ACMG) General Resources Newborn Screening Genetics Birth Defects FOR FAMILIES FAQs ...

  17. Genome resources for climate-resilient cowpea, an essential crop for food security

    USDA-ARS?s Scientific Manuscript database

    Cowpea is a legume crop that is resilient in hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind those of most other major crop plants. Here we describe foundational g...

  18. Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

    Treesearch

    Aziz Ebrahimi; Abdolkarim Zarei; Shaneka Lawson; Keith E. Woeste; M. J. M. Smulders

    2016-01-01

    Persian walnut (Juglans regia L.) is the world's most widely grown nut crop, but large-scale assessments and comparisons of the genetic diversity of the crop are notably lacking. To guide the conservation and utilization of Persian walnut genetic resources, genotypes (n = 189) from 25 different regions in 14 countries on...

  19. Gene flow in genetically engineered perennial grasses: Lessons for modification of dedicated bioenergy crops

    EPA Science Inventory

    The potential ecological consequences of the commercialization of genetically engineered (GD) crops have been the subject of intense debate, particularly when the GE crops are perennial and capable of outcrossing to wild relatives. The essential ecological impact issues for engi...

  20. Barriers and paths to market for genetically engineered crops.

    PubMed

    Rommens, Caius M

    2010-02-01

    Each year, billions of dollars are invested in efforts to improve crops through genetic engineering (GE). These activities have resulted in a surge of publications and patents on technologies and genes: a momentum in basic research that, unfortunately, is not sustained throughout the subsequent phases of product development. After more than two decades of intensive research, the market for transgenic crops is still dominated by applications of just a handful of methods and genes. This discrepancy between research and development reflects difficulties in understanding and overcoming seven main barriers-to-entry: (1) trait efficacy in the field, (2) critical product concepts, (3) freedom-to-operate, (4) industry support, (5) identity preservation and stewardship, (6) regulatory approval and (7) retail and consumer acceptance. In this review, I describe the various roadblocks to market for transgenic crops and also discuss methods and approaches on how to overcome these, especially in the United States.

  1. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    PubMed Central

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  2. Genetic Resources of Energy Crops: Biological Systems to Combat Climate Change

    USDA-ARS?s Scientific Manuscript database

    Biological systems are expected to contribute to renewable energy production, help stabilize rising levels of green house gases (GHG), and mitigate the risk of global climate change (GCC). Bioenergy crop plants that function as solar energy collectors and thermo-chemical energy storage systems are t...

  3. Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.

    PubMed

    Allnutt, T R; Roper, K; Henry, C

    2008-01-23

    A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed.

  4. Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

    USDA-ARS?s Scientific Manuscript database

    Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

  5. Genetically modified crops: Brazilian law and overview.

    PubMed

    Marinho, C D; Martins, F J O; Amaral Júnior, A T; Gonçalves, L S A; dos Santos, O J A P; Alves, D P; Brasileiro, B P; Peternelli, L A

    2014-07-07

    In Brazil, the first genetically modified (GM) crop was released in 1998, and it is estimated that 84, 78, and 50% of crop areas containing soybean, corn, and cotton, respectively, were transgenic in 2012. This intense and rapid adoption rate confirms that the choice to use technology has been the main factor in developing national agriculture. Thus, this review focuses on understanding these dynamics in the context of farmers, trade relations, and legislation. To accomplish this goal, a survey was conducted using the database of the National Cultivar Registry and the National Service for Plant Variety Protection of the Ministry of Agriculture, Livestock and Supply [Ministério da Agricultura, Pecuária e Abastecimento (MAPA)] between 1998 and October 13, 2013. To date, 36 events have been released: five for soybeans, 18 for corn, 12 for cotton, and one for beans. From these events, 1395 cultivars have been developed and registered: 582 for soybean, 783 for corn and 30 for cotton. Monsanto owns 73.05% of the technologies used to develop these cultivars, while the Dow AgroScience - DuPont partnership and Syngenta have 16.34 and 4.37% ownership, respectively. Thus, the provision of transgenic seeds by these companies is an oligopoly supported by legislation. Moreover, there has been a rapid replacement of conventional crops by GM crops, whose technologies belong almost exclusively to four multinational companies, with the major ownership by Monsanto. These results reflect a warning to the government of the increased dependence on multinational corporations for key agricultural commodities.

  6. Crop Registration: The Pathway to Public Access of Plant Genetic Materials to Build Crops for the Future

    USDA-ARS?s Scientific Manuscript database

    Starting as Crop Science Registrations in the American Journal of the Society of Agronomy in 1926, and continuing 80+ years later in the Journal of Plant Registrations, 11,241 plant cultivars, germplasm, parental lines, genetic stocks and mapping populations have been registered as of December 31, 2...

  7. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation.

    PubMed

    von Wettberg, Eric J B; Chang, Peter L; Başdemir, Fatma; Carrasquila-Garcia, Noelia; Korbu, Lijalem Balcha; Moenga, Susan M; Bedada, Gashaw; Greenlon, Alex; Moriuchi, Ken S; Singh, Vasantika; Cordeiro, Matilde A; Noujdina, Nina V; Dinegde, Kassaye Negash; Shah Sani, Syed Gul Abbas; Getahun, Tsegaye; Vance, Lisa; Bergmann, Emily; Lindsay, Donna; Mamo, Bullo Erena; Warschefsky, Emily J; Dacosta-Calheiros, Emmanuel; Marques, Edward; Yilmaz, Mustafa Abdullah; Cakmak, Ahmet; Rose, Janna; Migneault, Andrew; Krieg, Christopher P; Saylak, Sevgi; Temel, Hamdi; Friesen, Maren L; Siler, Eleanor; Akhmetov, Zhaslan; Ozcelik, Huseyin; Kholova, Jana; Can, Canan; Gaur, Pooran; Yildirim, Mehmet; Sharma, Hari; Vadez, Vincent; Tesfaye, Kassahun; Woldemedhin, Asnake Fikre; Tar'an, Bunyamin; Aydogan, Abdulkadir; Bukun, Bekir; Penmetsa, R Varma; Berger, Jens; Kahraman, Abdullah; Nuzhdin, Sergey V; Cook, Douglas R

    2018-02-13

    Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.

  8. Genetic structure of farmer-managed varieties in clonally-propagated crops.

    PubMed

    Scarcelli, N; Tostain, S; Vigouroux, Y; Luong, V; Baco, M N; Agbangla, C; Daïnou, O; Pham, J L

    2011-08-01

    The relative role of sexual reproduction and mutation in shaping the diversity of clonally propagated crops is largely unknown. We analyzed the genetic diversity of yam-a vegetatively-propagated crop-to gain insight into how these two factors shape its diversity in relation with farmers' classifications. Using 15 microsatellite loci, we analyzed 485 samples of 10 different yam varieties. We identified 33 different genotypes organized in lineages supported by high bootstrap values. We computed the probability that these genotypes appeared by sexual reproduction or mutation within and between each lineage. This allowed us to interpret each lineage as a product of sexual reproduction that has evolved by mutation. Moreover, we clearly noted a similarity between the genetic structure and farmers' classifications. Each variety could thus be interpreted as being the product of sexual reproduction having evolved by mutation. This highly structured diversity of farmer-managed varieties has consequences for the preservation of yam diversity.

  9. The ten years (2004-2014): Progress in peanut genetics and genomics

    USDA-ARS?s Scientific Manuscript database

    Plant breeding, genetics, and genomics play a critical role in sustainable agriculture specifically in improving crop productivity, quality, and resistance to pests and diseases. The germplasm collections have been treasures of crop genetic resources. Utilization of the collections of wild peanut sp...

  10. Gene Flow in Genetically Engineered Perennial Grasses: Lessons for Modification of Dedicated Bioenergy Crops

    USDA-ARS?s Scientific Manuscript database

    Genetic modification of dedicated bioenergy crops, such as switchgrass, will play a major role in crop improvement for a wide range of beneficial traits specific to biofuels. One obstacle that arises regarding transgenic improvement of perennials used for biofuels is the propensity of these plants t...

  11. Connecting Biochemical Photosynthesis Models with Crop Models to Support Crop Improvement

    PubMed Central

    Wu, Alex; Song, Youhong; van Oosterom, Erik J.; Hammer, Graeme L.

    2016-01-01

    The next advance in field crop productivity will likely need to come from improving crop use efficiency of resources (e.g., light, water, and nitrogen), aspects of which are closely linked with overall crop photosynthetic efficiency. Progress in genetic manipulation of photosynthesis is confounded by uncertainties of consequences at crop level because of difficulties connecting across scales. Crop growth and development simulation models that integrate across biological levels of organization and use a gene-to-phenotype modeling approach may present a way forward. There has been a long history of development of crop models capable of simulating dynamics of crop physiological attributes. Many crop models incorporate canopy photosynthesis (source) as a key driver for crop growth, while others derive crop growth from the balance between source- and sink-limitations. Modeling leaf photosynthesis has progressed from empirical modeling via light response curves to a more mechanistic basis, having clearer links to the underlying biochemical processes of photosynthesis. Cross-scale modeling that connects models at the biochemical and crop levels and utilizes developments in upscaling leaf-level models to canopy models has the potential to bridge the gap between photosynthetic manipulation at the biochemical level and its consequences on crop productivity. Here we review approaches to this emerging cross-scale modeling framework and reinforce the need for connections across levels of modeling. Further, we propose strategies for connecting biochemical models of photosynthesis into the cross-scale modeling framework to support crop improvement through photosynthetic manipulation. PMID:27790232

  12. Connecting Biochemical Photosynthesis Models with Crop Models to Support Crop Improvement.

    PubMed

    Wu, Alex; Song, Youhong; van Oosterom, Erik J; Hammer, Graeme L

    2016-01-01

    The next advance in field crop productivity will likely need to come from improving crop use efficiency of resources (e.g., light, water, and nitrogen), aspects of which are closely linked with overall crop photosynthetic efficiency. Progress in genetic manipulation of photosynthesis is confounded by uncertainties of consequences at crop level because of difficulties connecting across scales. Crop growth and development simulation models that integrate across biological levels of organization and use a gene-to-phenotype modeling approach may present a way forward. There has been a long history of development of crop models capable of simulating dynamics of crop physiological attributes. Many crop models incorporate canopy photosynthesis (source) as a key driver for crop growth, while others derive crop growth from the balance between source- and sink-limitations. Modeling leaf photosynthesis has progressed from empirical modeling via light response curves to a more mechanistic basis, having clearer links to the underlying biochemical processes of photosynthesis. Cross-scale modeling that connects models at the biochemical and crop levels and utilizes developments in upscaling leaf-level models to canopy models has the potential to bridge the gap between photosynthetic manipulation at the biochemical level and its consequences on crop productivity. Here we review approaches to this emerging cross-scale modeling framework and reinforce the need for connections across levels of modeling. Further, we propose strategies for connecting biochemical models of photosynthesis into the cross-scale modeling framework to support crop improvement through photosynthetic manipulation.

  13. Priorities for enhancing the ex situ conservation and use of Australian crop wild relatives

    USDA-ARS?s Scientific Manuscript database

    Crop wild relatives - the wild cousins of cultivated plants - are increasingly recognized for their potential to contribute to the productivity, nutritional quality and sustainability of agricultural crops. However, the use of these genetic resources is dependent upon their conservation in genebanks...

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

    PubMed Central

    Shivhare, Radha; Lata, Charu

    2017-01-01

    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

  15. Conservation priorities for tree crop wild relatives in the United States

    Treesearch

    Colin K. Khoury; Stephanie L. Greene; Karen A. Williams; Chrystian C. Sosa; Chris Richards

    2017-01-01

    Crop wild relatives native to the United States have proved useful as genetic resources in breeding more productive, nutritious, and resilient crops. Their utilization is expected to increase with better information about the species and improving breeding tools. But this utilization may be constrained by their limited representation in genebanks and the ongoing loss...

  16. Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

    PubMed

    Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

    2009-01-14

    We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

  17. An overview of genetically modified crop governance, issues and challenges in Malaysia.

    PubMed

    Andrew, Johnny; Ismail, Normaz Wana; Djama, Marcel

    2018-01-01

    The application of agricultural biotechnology attracts the interest of many stakeholders. Genetically modified (GM) crops, for example, have been rapidly increasing in production for the last 20 years. Despite their known benefits, GM crops also pose many concerns not only to human and animal health but also to the environment. Malaysia, in general, allows the use of GM technology applications but it has to come with precautionary and safety measures consistent with the international obligations and domestic legal frameworks. This paper provides an overview of GM crop technology from international and national context and explores the governance and issues surrounding this technology application in Malaysia. Basically, GM research activities in Malaysia are still at an early stage of research and development and most of the GM crops approved for release are limited for food, feed and processing purposes. Even though Malaysia has not planted any GM crops commercially, actions toward such a direction seem promising. Several issues concerning GM crops as discussed in this paper will become more complex as the number of GM crops and varieties commercialised globally increase and Malaysia starts to plant GM crops. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  18. Could Crop Height Affect the Wind Resource at Agriculturally Productive Wind Farm Sites?

    NASA Astrophysics Data System (ADS)

    Vanderwende, Brian; Lundquist, Julie K.

    2016-03-01

    The collocation of cropland and wind turbines in the US Midwest region introduces complex meteorological interactions that could influence both agriculture and wind-power production. Crop management practices may affect the wind resource through alterations of land-surface properties. We use the weather research and forecasting (WRF) model to estimate the impact of crop height variations on the wind resource in the presence of a large turbine array. A hypothetical wind farm consisting of 121 1.8-MW turbines is represented using the WRF model wind-farm parametrization. We represent the impact of selecting soybeans rather than maize by altering the aerodynamic roughness length in a region approximately 65 times larger than that occupied by the turbine array. Roughness lengths of 0.1 and 0.25 m represent the mature soy crop and a mature maize crop, respectively. In all but the most stable atmospheric conditions, statistically significant hub-height wind-speed increases and rotor-layer wind-shear reductions result from switching from maize to soybeans. Based on simulations for the entire month of August 2013, wind-farm energy output increases by 14 %, which would yield a significant monetary gain. Further investigation is required to determine the optimal size, shape, and crop height of the roughness modification to maximize the economic benefit and minimize the cost of such crop-management practices. These considerations must be balanced by other influences on crop choice such as soil requirements and commodity prices.

  19. Could crop height affect the wind resource at agriculturally productive wind farm sites?

    DOE PAGES

    Vanderwende, Brian; Lundquist, Julie K.

    2015-11-07

    The collocation of cropland and wind turbines in the US Midwest region introduces complex meteorological interactions that could influence both agriculture and wind-power production. Crop management practices may affect the wind resource through alterations of land-surface properties. We use the weather research and forecasting (WRF) model to estimate the impact of crop height variations on the wind resource in the presence of a large turbine array. A hypothetical wind farm consisting of 121 1.8-MW turbines is represented using the WRF model wind-farm parametrization. We represent the impact of selecting soybeans rather than maize by altering the aerodynamic roughness length inmore » a region approximately 65 times larger than that occupied by the turbine array. Roughness lengths of 0.1 and 0.25 m represent the mature soy crop and a mature maize crop, respectively. In all but the most stable atmospheric conditions, statistically significant hub-height wind-speed increases and rotor-layer wind-shear reductions result from switching from maize to soybeans. Based on simulations for the entire month of August 2013, wind-farm energy output increases by 14 %, which would yield a significant monetary gain. Further investigation is required to determine the optimal size, shape, and crop height of the roughness modification to maximize the economic benefit and minimize the cost of such crop-management practices. As a result, these considerations must be balanced by other influences on crop choice such as soil requirements and commodity prices.« less

  20. Could crop height affect the wind resource at agriculturally productive wind farm sites?

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

    Vanderwende, Brian; Lundquist, Julie K.

    The collocation of cropland and wind turbines in the US Midwest region introduces complex meteorological interactions that could influence both agriculture and wind-power production. Crop management practices may affect the wind resource through alterations of land-surface properties. We use the weather research and forecasting (WRF) model to estimate the impact of crop height variations on the wind resource in the presence of a large turbine array. A hypothetical wind farm consisting of 121 1.8-MW turbines is represented using the WRF model wind-farm parametrization. We represent the impact of selecting soybeans rather than maize by altering the aerodynamic roughness length inmore » a region approximately 65 times larger than that occupied by the turbine array. Roughness lengths of 0.1 and 0.25 m represent the mature soy crop and a mature maize crop, respectively. In all but the most stable atmospheric conditions, statistically significant hub-height wind-speed increases and rotor-layer wind-shear reductions result from switching from maize to soybeans. Based on simulations for the entire month of August 2013, wind-farm energy output increases by 14 %, which would yield a significant monetary gain. Further investigation is required to determine the optimal size, shape, and crop height of the roughness modification to maximize the economic benefit and minimize the cost of such crop-management practices. As a result, these considerations must be balanced by other influences on crop choice such as soil requirements and commodity prices.« less

  1. Genetically Modified Crops and Nuisance: Exploring the Role of Precaution in Private Law

    ERIC Educational Resources Information Center

    Craik, Neil; Culver, Keith; Siebrasse, Norman

    2007-01-01

    This article critically considers calls for the precautionary principle to inform judicial decision making in a private law context in light of the Hoffman litigation, where it is alleged that the potential for genetic contamination from genetically modified (GM) crops causes an unreasonable interference with the rights of organic farmers to use…

  2. Isozymes and the genetic resources of forest trees

    Treesearch

    A. H. D. Brown; G. F. Moran

    1981-01-01

    Genetic data are an essential prerequisite for analysing the genetic structure of tree populations. The isozyme technique is the best currently available method for obtaining such data. Despite several shortcomings, isozyme data directly evaluate the genetic resources of forest trees, and can thus be used to monitor and manipulate these resources. For example,...

  3. Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?

    PubMed

    Wang, Zeng-Yu; Brummer, E Charles

    2012-11-01

    Genetic engineering offers the opportunity to generate unique genetic variation that is either absent in the sexually compatible gene pool or has very low heritability. The generation of transgenic plants, coupled with breeding, has led to the production of widely used transgenic cultivars in several major cash crops, such as maize, soybean, cotton and canola. The process for regulatory approval of genetically engineered crops is slow and subject to extensive political interference. The situation in forage grasses and legumes is more complicated. Most widely grown forage, turf and bioenergy species (e.g. tall fescue, perennial ryegrass, switchgrass, alfalfa, white clover) are highly self-incompatible and outcrossing. Compared with inbreeding species, they have a high potential to pass their genes to adjacent plants. A major biosafety concern in these species is pollen-mediated transgene flow. Because human consumption is indirect, risk assessment of transgenic forage, turf and bioenergy species has focused on their environmental or ecological impacts. Although significant progress has been made in genetic modification of these species, commercialization of transgenic cultivars is very limited because of the stringent and costly regulatory requirements. To date, the only transgenic forage crop deregulated in the US is 'Roundup Ready' (RR) alfalfa. The approval process for RR alfalfa was complicated, involving several rounds of regulation, deregulation and re-regulation. Nevertheless, commercialization of RR alfalfa is an important step forward in regulatory approval of a perennial outcrossing forage crop. As additional transgenic forage, turf and bioenergy crops are generated and tested, different strategies have been developed to meet regulatory requirements. Recent progress in risk assessment and deregulation of transgenic forage and turf species is summarized and discussed.

  4. Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?

    PubMed Central

    Wang, Zeng-Yu; Brummer, E. Charles

    2012-01-01

    Background Genetic engineering offers the opportunity to generate unique genetic variation that is either absent in the sexually compatible gene pool or has very low heritability. The generation of transgenic plants, coupled with breeding, has led to the production of widely used transgenic cultivars in several major cash crops, such as maize, soybean, cotton and canola. The process for regulatory approval of genetically engineered crops is slow and subject to extensive political interference. The situation in forage grasses and legumes is more complicated. Scope Most widely grown forage, turf and bioenergy species (e.g. tall fescue, perennial ryegrass, switchgrass, alfalfa, white clover) are highly self-incompatible and outcrossing. Compared with inbreeding species, they have a high potential to pass their genes to adjacent plants. A major biosafety concern in these species is pollen-mediated transgene flow. Because human consumption is indirect, risk assessment of transgenic forage, turf and bioenergy species has focused on their environmental or ecological impacts. Although significant progress has been made in genetic modification of these species, commercialization of transgenic cultivars is very limited because of the stringent and costly regulatory requirements. To date, the only transgenic forage crop deregulated in the US is ‘Roundup Ready’ (RR) alfalfa. The approval process for RR alfalfa was complicated, involving several rounds of regulation, deregulation and re-regulation. Nevertheless, commercialization of RR alfalfa is an important step forward in regulatory approval of a perennial outcrossing forage crop. As additional transgenic forage, turf and bioenergy crops are generated and tested, different strategies have been developed to meet regulatory requirements. Recent progress in risk assessment and deregulation of transgenic forage and turf species is summarized and discussed. PMID:22378838

  5. Estimation of crop water requirements using remote sensing for operational water resources management

    NASA Astrophysics Data System (ADS)

    Vasiliades, Lampros; Spiliotopoulos, Marios; Tzabiras, John; Loukas, Athanasios; Mylopoulos, Nikitas

    2015-06-01

    An integrated modeling system, developed in the framework of "Hydromentor" research project, is applied to evaluate crop water requirements for operational water resources management at Lake Karla watershed, Greece. The framework includes coupled components for operation of hydrotechnical projects (reservoir operation and irrigation works) and estimation of agricultural water demands at several spatial scales using remote sensing. The study area was sub-divided into irrigation zones based on land use maps derived from Landsat 5 TM images for the year 2007. Satellite-based energy balance for mapping evapotranspiration with internalized calibration (METRIC) was used to derive actual evapotranspiration (ET) and crop coefficient (ETrF) values from Landsat TM imagery. Agricultural water needs were estimated using the FAO method for each zone and each control node of the system for a number of water resources management strategies. Two operational strategies of hydro-technical project development (present situation without operation of the reservoir and future situation with the operation of the reservoir) are coupled with three water demand strategies. In total, eight (8) water management strategies are evaluated and compared. The results show that, under the existing operational water resources management strategies, the crop water requirements are quite large. However, the operation of the proposed hydro-technical projects in Lake Karla watershed coupled with water demand management measures, like improvement of existing water distribution systems, change of irrigation methods, and changes of crop cultivation could alleviate the problem and lead to sustainable and ecological use of water resources in the study area.

  6. Genetically Modified Herbicide-Tolerant Crops, Weeds, and Herbicides: Overview and Impact.

    PubMed

    Bonny, Sylvie

    2016-01-01

    Genetically modified (GM) crops have been and continue to be a subject of controversy despite their rapid adoption by farmers where approved. For the last two decades, an important matter of debate has been their impact on pesticide use, particularly for herbicide-tolerant (HT) crops. Some claim that these crops bring about a decrease in herbicide use, while others claim the opposite. In fact, since 1996, most cultivated GMOs have been GMHT crops, which involve the use of an associated herbicide, generally glyphosate. In their very first years of adoption, HT crops often led to some decrease in herbicide use. However, the repetition of glyphosate-tolerant crops and of glyphosate only applications in the same fields without sufficient alternation and herbicide diversity has contributed to the appearance of glyphosate-resistant weeds. These weeds have resulted in a rise in the use of glyphosate and other herbicides. This article explores this situation and the impacts of herbicide-resistant weeds, using an interdisciplinary approach and drawing on recent data. The paper analyzes the spread of GMHT crops worldwide and their consequences on herbicide use in the USA in particular. It then addresses the global development of glyphosate-resistant weeds and their impact, particularly focusing on the USA. Finally, the last section explores how industry, farmers, and weed scientists are coping with the spread of resistant weeds. The concluding comments deal more widely with trends in GM crops.

  7. Genetically Modified Herbicide-Tolerant Crops, Weeds, and Herbicides: Overview and Impact

    NASA Astrophysics Data System (ADS)

    Bonny, Sylvie

    2016-01-01

    Genetically modified (GM) crops have been and continue to be a subject of controversy despite their rapid adoption by farmers where approved. For the last two decades, an important matter of debate has been their impact on pesticide use, particularly for herbicide-tolerant (HT) crops. Some claim that these crops bring about a decrease in herbicide use, while others claim the opposite. In fact, since 1996, most cultivated GMOs have been GMHT crops, which involve the use of an associated herbicide, generally glyphosate. In their very first years of adoption, HT crops often led to some decrease in herbicide use. However, the repetition of glyphosate-tolerant crops and of glyphosate only applications in the same fields without sufficient alternation and herbicide diversity has contributed to the appearance of glyphosate-resistant weeds. These weeds have resulted in a rise in the use of glyphosate and other herbicides. This article explores this situation and the impacts of herbicide-resistant weeds, using an interdisciplinary approach and drawing on recent data. The paper analyzes the spread of GMHT crops worldwide and their consequences on herbicide use in the USA in particular. It then addresses the global development of glyphosate-resistant weeds and their impact, particularly focusing on the USA. Finally, the last section explores how industry, farmers, and weed scientists are coping with the spread of resistant weeds. The concluding comments deal more widely with trends in GM crops.

  8. Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

    PubMed Central

    Pazhamala, Lekha; Saxena, Rachit K.; Singh, Vikas K.; Sameerkumar, C. V.; Kumar, Vinay; Sinha, Pallavi; Patel, Kishan; Obala, Jimmy; Kaoneka, Seleman R.; Tongoona, P.; Shimelis, Hussein A.; Gangarao, N. V. P. R.; Odeny, Damaris; Rathore, Abhishek; Dharmaraj, P. S.; Yamini, K. N.; Varshney, Rajeev K.

    2015-01-01

    Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding. PMID:25741349

  9. Safety assessment of foods from genetically modified crops in countries with developing economies.

    PubMed

    Delaney, Bryan

    2015-12-01

    Population growth particularly in countries with developing economies will result in a need to increase food production by 70% by the year 2050. Biotechnology has been utilized to produce genetically modified (GM) crops for insect and weed control with benefits including increased crop yield and will also be used in emerging countries. A multicomponent safety assessment paradigm has been applied to individual GM crops to determine whether they as safe as foods from non-GM crops. This paper reviews methods to assess the safety of foods from GM crops for safe consumption from the first generation of GM crops. The methods can readily be applied to new products developed within country and this paper will emphasize the concept of data portability; that safety data produced in one geographic location is suitable for safety assessment regardless of where it is utilized. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Augmentation of Water Resources Potential and Cropping Intensification Through Watershed Programs.

    PubMed

    Mondal, Biswajit; Singh, Alka; Singh, S D; Kalra, B S; Samal, P; Sinha, M K; Ramajayam, D; Kumar, Suresh

    2018-02-01

      This paper presents the biophysical impact of various interventions made under watershed development programs, in terms of the creation of additional water resources, and resultant changes in land use and cropping patterns in the Bundelkhand region of Madhya Pradesh State, India. Both primary and secondary data gathered from randomly selected watersheds and their corresponding control villages were used in this study. Analysis revealed that emphasis was given primarily to the creation of water resources potential during implementation of the programs, which led to augmentation of surface and groundwater availability for both irrigation and non-agricultural purposes. In addition, other land based interventions for soil and moisture conservation, plantation activities, and so forth, were taken up on both arable and nonarable land, which helped to improve land slope and land use, cropping pattern, agricultural productivity, and vegetation cover.

  11. Effects of adjusting cropping systems on utilization efficiency of climatic resources in Northeast China under future climate scenarios

    NASA Astrophysics Data System (ADS)

    Guo, Jianping; Zhao, Junfang; Xu, Yanhong; Chu, Zheng; Mu, Jia; Zhao, Qian

    Quantitatively evaluating the effects of adjusting cropping systems on the utilization efficiency of climatic resources under climate change is an important task for assessing food security in China. To understand these effects, we used daily climate variables obtained from the regional climate model RegCM3 from 1981 to 2100 under the A1B scenario and crop observations from 53 agro-meteorological experimental stations from 1981 to 2010 in Northeast China. Three one-grade zones of cropping systems were divided by heat, water, topography and crop-type, including the semi-arid areas of the northeast and northwest (III), the one crop area of warm-cool plants in semi-humid plain or hilly regions of the northeast (IV), and the two crop area in irrigated farmland in the Huanghuaihai Plain (VI). An agro-ecological zone model was used to calculate climatic potential productivities. The effects of adjusting cropping systems on climate resource utilization in Northeast China under the A1B scenario were assessed. The results indicated that from 1981 to 2100 in the III, IV and VI areas, the planting boundaries of different cropping systems in Northeast China obviously shifted toward the north and the east based on comprehensively considering the heat and precipitation resources. However, due to high temperature stress, the climatic potential productivity of spring maize was reduced in the future. Therefore, adjusting the cropping system is an effective way to improve the climatic potential productivity and climate resource utilization. Replacing the one crop in one year model (spring maize) by the two crops in one year model (winter wheat and summer maize) significantly increased the total climatic potential productivity and average utilization efficiencies. During the periods of 2011-2040, 2041-2070 and 2071-2100, the average total climatic potential productivities of winter wheat and summer maize increased by 9.36%, 11.88% and 12.13% compared to that of spring maize

  12. Cryopreservation for preservation of potato genetic resources

    PubMed Central

    Niino, Takao; Arizaga, Miriam Valle

    2015-01-01

    Cryopreservation is becoming a very important tool for the long-term storage of plant genetic resources and efficient cryopreservation protocols have been developed for a large number of plant species. Practical procedures, developed using in vitro tissue culture, can be a simple and reliable preservation option of potato genetic resources rather than maintaining by vegetative propagation in genebanks due their allogamous nature. Cryopreserved materials insure a long-term backup of field collections against loss of plant germplasm. Occurrence of genetic variation, in tissue culture cells during prolonged subcultures, can be avoided with suitable cryopreservation protocols that provide high regrowth, leading and facilitating a systematic and strategic cryo-banking of plant genetic resources. Cryopreservation protocols for potato reviewed here, can efficiently complement field and in vitro conservation, providing for preservation of genotypes difficult to preserve by other methods, wild types and other species decided as priority collections. PMID:25931979

  13. The genetic and molecular basis of crop height based on a rice model.

    PubMed

    Liu, Fang; Wang, Pandi; Zhang, Xiaobo; Li, Xiaofei; Yan, Xiaohong; Fu, Donghui; Wu, Gang

    2018-01-01

    This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.

  14. Start with the seed: Native crops, indigenous knowledge, and community seed systems prerequisites for food sovereignty

    USDA-ARS?s Scientific Manuscript database

    The dynamic conservation and sustainable utilization of native crop genetic resources are crucial for food sovereignty of Native American communities. Indigenous knowledge of crop diversity when linked to food traditions, local practices and social norms provide the basis for building sovereign comm...

  15. Energy sorghum--a genetic model for the design of C4 grass bioenergy crops.

    PubMed

    Mullet, John; Morishige, Daryl; McCormick, Ryan; Truong, Sandra; Hilley, Josie; McKinley, Brian; Anderson, Robert; Olson, Sara N; Rooney, William

    2014-07-01

    Sorghum is emerging as an excellent genetic model for the design of C4 grass bioenergy crops. Annual energy Sorghum hybrids also serve as a source of biomass for bioenergy production. Elucidation of Sorghum's flowering time gene regulatory network, and identification of complementary alleles for photoperiod sensitivity, enabled large-scale generation of energy Sorghum hybrids for testing and commercial use. Energy Sorghum hybrids with long vegetative growth phases were found to accumulate more than twice as much biomass as grain Sorghum, owing to extended growing seasons, greater light interception, and higher radiation use efficiency. High biomass yield, efficient nitrogen recycling, and preferential accumulation of stem biomass with low nitrogen content contributed to energy Sorghum's elevated nitrogen use efficiency. Sorghum's integrated genetics-genomics-breeding platform, diverse germplasm, and the opportunity for annual testing of new genetic designs in controlled environments and in multiple field locations is aiding fundamental discovery, and accelerating the improvement of biomass yield and optimization of composition for biofuels production. Recent advances in wide hybridization between Sorghum and other C4 grasses could allow the deployment of improved genetic designs of annual energy Sorghums in the form of wide-hybrid perennial crops. The current trajectory of energy Sorghum genetic improvement indicates that it will be possible to sustainably produce biofuels from C4 grass bioenergy crops that are cost competitive with petroleum-based transportation fuels. © 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.

  16. Use of genetically modified crops and pesticides in Brazil: growing hazards.

    PubMed

    Almeida, Vicente Eduardo Soares de; Friedrich, Karen; Tygel, Alan Freihof; Melgarejo, Leonardo; Carneiro, Fernando Ferreira

    2017-10-01

    Genetically modified (GM) crops were officially authorized in Brazil in 2003. In this documentary study, we aimed to identify possible changes in the patterns of pesticide use after the adoption of this technology over a span of 13 years (2000 to 2012). The following variables were analyzed: Pesticide use (kg), Pesticide use per capita (kg/inhab), Pesticide and herbicide use per area (kg/ha) and productivity (kg/ha). Contrary to the initial expectations of decreasing pesticide use following the adoption of GM crops, overall pesticide use in Brazil increased 1.6-fold between the years 2000 and 2012. During the same period, pesticide use for soybean increased 3-fold. This study shows that the adoption of GM crops in Brazil has led to an increase in pesticide use with possible increases in environmental and human exposure and associated negative impacts.

  17. Drosophila Genetic Resource and Stock Center; The National BioResource Project.

    PubMed

    Yamamoto, Masa-Toshi

    2010-01-01

    The fruit fly, Drosophila melanogaster, is not categorized as a laboratory animal, but it is recognised as one of the most important model organisms for basic biology, life science, and biomedical research. This tiny fly continues to occupy a core place in genetics and genomic approaches to studies of biology and medicine. The basic principles of genetics, including the variations of phenotypes, mutations, genetic linkage, meiotic chromosome segregation, chromosome aberrations, recombination, and precise mapping of genes by genetic as well as cytological means, were all derived from studies of Drosophila. Recombinant DNA technology was developed in the 1970s and Drosophila DNA was the first among multicellular organisms to be cloned. It provided a detailed characterization of genes in combination of classical cytogenetic data. Drosophila thus became the pioneering model organism for various fields of life science research into multicellular organisms. Here, I briefly describe the history of Drosophila research and provide a few examples of the application of the abundant genetic resources of Drosophila to basic biology and medical investigations. A Japanese national project, the National BioResource Project (NBRP) for collection, maintainance, and provision of Drosophila resources, that is well known and admired by researchers in other countries as an important project, is also briefly described.

  18. 76 FR 63278 - Bayer CropScience LP; Determination of Nonregulated Status for Cotton Genetically Engineered for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-12

    ... for Cotton Genetically Engineered for Insect Resistance and Herbicide Tolerance AGENCY: Animal and... determination that a genetically engineered cotton developed by Bayer CropScience LP, designated as TwinLink TM cotton (events T304-40 and GHB119), which has been genetically engineered to be tolerant to the herbicide...

  19. Molecular markers: a potential resource for ginger genetic diversity studies.

    PubMed

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  20. ASSESSING POSSIBLE ECOLOGICAL RISKS OF GENETICALLY MODIFIED CROPS: GENE EXPRESSION ASSAYS AND GENETIC MONITORING OF NON-TARGET ORGANISMS

    EPA Science Inventory

    Widespread planting of genetically modified crops with the Bt transgene pesticide has led to concern over non-target effects of Bt compounds in agroecosystems. While some research suggests that non-target organisms exposed to Bt toxin exhibit reduced fecundity and increased morta...

  1. Influence of precipitation and crop germination on resource selection by mule deer (Odocoileus hemionus) in southwest Colorado

    USGS Publications Warehouse

    Carrollo, Emily M.; Johnson, Heather E.; Fischer, Justin W.; Hammond, Matthew; Dorsey, Patricia D.; Anderson, Charles; Vercauteren, Kurt C.; Walter, W. David

    2017-01-01

    Mule deer (Odocoileus hemionus) populations in the western United States provide many benefits to local economies but can also cause considerable damage to agriculture, particularly damage to lucrative crops. Limited information exists to understand resource selection of mule deer in response to annual variation in crop rotation and climatic conditions. We tested the hypothesis that mule deer select certain crops, and in particular sunflower, based on annual climatic variability. Our objective was to use movements, estimates of home range, and resource selection analysis to identify resources selected by mule deer. We used annually-derived crop-specific datasets along with Global Positioning System collars to monitor 14 mule deer in an agricultural area near public lands in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km2, and for two summer seasons that ranged between 5.51 and 6.24 km2. Mule deer selected areas closer to forest and alfalfa for most periods during 2012, but selected areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection by mule deer because of variability in crop rotation and success of germination of specific crops.

  2. Influence of Precipitation and Crop Germination on Resource Selection by Mule Deer (Odocoileus hemionus) in Southwest Colorado.

    PubMed

    Carrollo, Emily M; Johnson, Heather E; Fischer, Justin W; Hammond, Matthew; Dorsey, Patricia D; Anderson, Charles; Vercauteren, Kurt C; Walter, W David

    2017-11-09

    Mule deer (Odocoileus hemionus) populations in the western United States provide many benefits to local economies but can also cause considerable damage to agriculture, particularly damage to lucrative crops. Limited information exists to understand resource selection of mule deer in response to annual variation in crop rotation and climatic conditions. We tested the hypothesis that mule deer select certain crops, and in particular sunflower, based on annual climatic variability. Our objective was to use movements, estimates of home range, and resource selection analysis to identify resources selected by mule deer. We used annually-derived crop-specific datasets along with Global Positioning System collars to monitor 14 mule deer in an agricultural area near public lands in southwestern Colorado, USA. We estimated home ranges for two winter seasons that ranged between 7.68 and 9.88 km 2 , and for two summer seasons that ranged between 5.51 and 6.24 km 2 . Mule deer selected areas closer to forest and alfalfa for most periods during 2012, but selected areas closer to sunflower in a majority of periods during 2013. Considerable annual variation in climate patterns and precipitation levels appeared to influence selection by mule deer because of variability in crop rotation and success of germination of specific crops.

  3. Do genetically modified crops affect animal reproduction? A review of the ongoing debate.

    PubMed

    Zhang, W; Shi, F

    2011-05-01

    In the past few years, genetically modified (GM) crops aimed at producing food/feed that became part of the regular agriculture in many areas of the world. However, we are uncertain whether GM food and feed can exert potential adverse effects on humans or animals. Of importance, the reproductive toxicology of GM crops has been studied using a number of methods, and by feeding GM crops to a number species of animals to ensure the safety assessment of GM food and feed. It appears that there are no adverse effects of GM crops on many species of animals in acute and short-term feeding studies, but serious debates of effects of long-term and multigenerational feeding studies remain. The aims of this review are to focus on the latest (last 3 to 4 years) findings and debates on reproduction of male and female animals after feeding daily diets containing the GM crops, and to present the possible mechanism(s) to explain their influences.

  4. Agrobacterium-mediated genetic transformation of yam (Dioscorea rotundata): an important tool for functional study of genes and crop improvement

    PubMed Central

    Nyaboga, Evans; Tripathi, Jaindra N.; Manoharan, Rajesh; Tripathi, Leena

    2014-01-01

    Although genetic transformation of clonally propagated crops has been widely studied as a tool for crop improvement and as a vital part of the development of functional genomics resources, there has been no report of any existing Agrobacterium-mediated transformation of yam (Dioscorea spp.) with evidence of stable integration of T-DNA. Yam is an important crop in the tropics and subtropics providing food security and income to over 300 million people. However, yam production remains constrained by increasing levels of field and storage pests and diseases. A major constraint to the development of biotechnological approaches for yam improvement has been the lack of an efficient and robust transformation and regeneration system. In this study, we developed an Agrobacterium-mediated transformation of Dioscorea rotundata using axillary buds as explants. Two cultivars of D. rotundata were transformed using Agrobacterium tumefaciens harboring the binary vectors containing selectable marker and reporter genes. After selection with appropriate concentrations of antibiotic, shoots were developed on shoot induction and elongation medium. The elongated antibiotic-resistant shoots were subsequently rooted on medium supplemented with selection agent. Successful transformation was confirmed by polymerase chain reaction, Southern blot analysis, and reporter genes assay. Expression of gusA gene in transgenic plants was also verified by reverse transcription polymerase chain reaction analysis. Transformation efficiency varied from 9.4 to 18.2% depending on the cultivars, selectable marker genes, and the Agrobacterium strain used for transformation. It took 3–4 months from Agro-infection to regeneration of complete transgenic plant. Here we report an efficient, fast and reproducible protocol for Agrobacterium-mediated transformation of D. rotundata using axillary buds as explants, which provides a useful platform for future genetic engineering studies in this economically important

  5. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

    PubMed Central

    Guignon, V.; Sempere, G.; Sardos, J.; Hueber, Y.; Duvergey, H.; Andrieu, A.; Chase, R.; Jenny, C.; Hazekamp, T.; Irish, B.; Jelali, K.; Adeka, J.; Ayala-Silva, T.; Chao, C.P.; Daniells, J.; Dowiya, B.; Effa effa, B.; Gueco, L.; Herradura, L.; Ibobondji, L.; Kempenaers, E.; Kilangi, J.; Muhangi, S.; Ngo Xuan, P.; Paofa, J.; Pavis, C.; Thiemele, D.; Tossou, C.; Sandoval, J.; Sutanto, A.; Vangu Paka, G.; Yi, G.; Van den houwe, I.; Roux, N.

    2017-01-01

    Abstract Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL: https://www.crop-diversity.org/mgis/ PMID:29220435

  6. Sharing the benefits of genetic resources: from biodiversity to human genetics.

    PubMed

    Schroeder, Doris; Lasén-Díaz, Carolina

    2006-12-01

    Benefit sharing aims to achieve an equitable exchange between the granting of access to a genetic resource and the provision of compensation. The Convention on Biological Diversity (CBD), adopted at the 1992 Earth Summit in Rio de Janeiro, is the only international legal instrument setting out obligations for sharing the benefits derived from the use of biodiversity. The CBD excludes human genetic resources from its scope, however, this article considers whether it should be expanded to include those resources, so as to enable research subjects to claim a share of the benefits to be negotiated on a case-by-case basis. Our conclusion on this question is: 'No, the CBD should not be expanded to include human genetic resources.' There are essential differences between human and non-human genetic resources, and, in the context of research on humans, an essentially fair exchange model is already available between the health care industry and research subjects. Those who contribute to research should receive benefits in the form of accessible new health care products and services, suitable for local health needs and linked to economic prosperity (e.g. jobs). When this exchange model does not apply, as is often the case in developing countries, individually negotiated benefit sharing agreements between researchers and research subjects should not be used as 'window dressing'. Instead, national governments should focus their finances on the best economic investment they could make; the investment in population health and health research as outlined by the World Health Organization's Commission on Macroeconomics and Health; whilst international barriers to such spending need to be removed.

  7. Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

    PubMed Central

    Taranto, Francesca; Pasqualone, Antonella; Mangini, Giacomo; Tripodi, Pasquale; Miazzi, Monica Marilena; Pavan, Stefano; Montemurro, Cinzia

    2017-01-01

    Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs), following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects. PMID:28208645

  8. Bee genera, diversity and abundance in genetically modified canola fields.

    PubMed

    O'Brien, Colton; Arathi, H S

    2018-01-02

    Intensive agricultural practices resulting in large scale habitat loss ranks as the top contributing factors in the global bee decline. Growing Genetically Modified Herbicide Tolerant (GMHT) crops as large monocultures has resulted extensive applications of herbicides leading to the degradation of natural habitats surrounding farmlands. Herbicide tolerance trait is beneficial for crops such as Canola (Brassica napus) that are extremely vulnerable to weed competition. While the trait in itself does not harm pollinators, growing genetically modified herbicide tolerant cultivars indirectly contributes towards pollinator declines through habitat loss. Canola, a mass-flowering crop is highly attractive to bee pollinators and the extensive adoption of the herbicide tolerant trait has led to depletion of non-crop floral resources. Extensive use of herbicide in and near fields with herbicide tolerant cultivars systematically eliminates semi-natural habitats around agricultural fields which consist of non-crop flowering plants. Planting pollinator strips provides floral resources for bees after crop flowering. We document the bee genera in canola and the adjoining pollinator strip. The overlap in bee genera reinforces the importance of pollinator habitats in agricultural landscape.

  9. Potential International Approaches to Ownership/Control of Human Genetic Resources.

    PubMed

    Rhodes, Catherine

    2016-09-01

    In its governance activities for genetic resources, the international community has adopted various approaches to their ownership, including: free access; common heritage of mankind; intellectual property rights; and state sovereign rights. They have also created systems which combine elements of these approaches. While governance of plant and animal genetic resources is well-established internationally, there has not yet been a clear approach selected for human genetic resources. Based on assessment of the goals which international governance of human genetic resources ought to serve, and the implications for how they will be accessed and utilised, it is argued that common heritage of mankind will be the most appropriate approach to adopt to their ownership/control. It does this with the aim of stimulating discussion in this area and providing a starting point for deeper consideration of how a common heritage of mankind, or similar, regime for human genetic resources would function and be implemented.

  10. Molecular genetic characterization of lasquerella new industrial crop using DArTseq markers

    USDA-ARS?s Scientific Manuscript database

    DArTseq, a new SNP-based marker platform, was developed and used to analyze the genetic diversity of the US germplasm collection of lesquerella. Lesquerella is a new oilseed crop in the Brassica family found native in the American Southwest. The potential of the species as a domestic source of indu...

  11. Temporal and spatial control of gene expression in horticultural crops

    PubMed Central

    Dutt, Manjul; Dhekney, Sadanand A; Soriano, Leonardo; Kandel, Raju; Grosser, Jude W

    2014-01-01

    Biotechnology provides plant breeders an additional tool to improve various traits desired by growers and consumers of horticultural crops. It also provides genetic solutions to major problems affecting horticultural crops and can be a means for rapid improvement of a cultivar. With the availability of a number of horticultural genome sequences, it has become relatively easier to utilize these resources to identify DNA sequences for both basic and applied research. Promoters play a key role in plant gene expression and the regulation of gene expression. In recent years, rapid progress has been made on the isolation and evaluation of plant-derived promoters and their use in horticultural crops, as more and more species become amenable to genetic transformation. Our understanding of the tools and techniques of horticultural plant biotechnology has now evolved from a discovery phase to an implementation phase. The availability of a large number of promoters derived from horticultural plants opens up the field for utilization of native sequences and improving crops using precision breeding. In this review, we look at the temporal and spatial control of gene expression in horticultural crops and the usage of a variety of promoters either isolated from horticultural crops or used in horticultural crop improvement. PMID:26504550

  12. Estimation of loss of genetic diversity in modern Japanese cultivars by comparison of diverse genetic resources in Asian pear (Pyrus spp.).

    PubMed

    Nishio, Sogo; Takada, Norio; Saito, Toshihiro; Yamamoto, Toshiya; Iketani, Hiroyuki

    2016-06-14

    Pears (Pyrus spp.) are one of the most important fruit crops in temperate regions. Japanese pear breeding has been carried out for over 100 years, working to release new cultivars that have good fruit quality and other desirable traits. Local cultivar 'Nijisseiki' and its relatives, which have excellent fruit texture, have been repeatedly used as parents in the breeding program. This strategy has led to inbreeding within recent cultivars and selections. To avoid inbreeding depression, we need to clarify the degree of inbreeding among crossbred cultivars and to introgress genetic resources that are genetically different from modern cultivars and selections. The objective of the present study was to clarify the genetic relatedness between modern Japanese pear cultivars and diverse Asian pear genetic resources. We genotyped 207 diverse accessions by using 19 simple sequence repeat (SSR) markers. The heterozygosity and allelic richness of modern cultivars was obviously decreased compared with that of wild individuals, Chinese pear cultivars, and local cultivars. In analyses using Structure software, the 207 accessions were classified into four clusters (K = 4): one consisting primarily of wild individuals, one of Chinese pear cultivars, one of local cultivars from outside the Kanto region, and one containing both local cultivars from the Kanto region and crossbred cultivars. The results of principal coordinate analysis (PCoA) were similar to those from the Structure analysis. Wild individuals and Chinese pears appeared to be distinct from other groups, and crossbred cultivars became closer to 'Nijisseiki' as the year of release became more recent. Both Structure and PCoA results suggest that the modern Japanese pear cultivars are genetically close to local cultivars that originated in the Kanto region, and that the genotypes of the modern cultivars were markedly biased toward 'Nijisseiki'. Introgression of germplasm from Chinese pear and wild individuals that are

  13. Setaria viridis as a Model System to Advance Millet Genetics and Genomics

    DOE PAGES

    Huang, Pu; Shyu, Christine; Coelho, Carla P.; ...

    2016-11-28

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Yet despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools andmore » resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.« less

  14. Setaria viridis as a Model System to Advance Millet Genetics and Genomics

    PubMed Central

    Huang, Pu; Shyu, Christine; Coelho, Carla P.; Cao, Yingying; Brutnell, Thomas P.

    2016-01-01

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops. PMID:27965689

  15. Setaria viridis as a Model System to Advance Millet Genetics and Genomics.

    PubMed

    Huang, Pu; Shyu, Christine; Coelho, Carla P; Cao, Yingying; Brutnell, Thomas P

    2016-01-01

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail ( Setaria viridis ) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica . These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

  16. Setaria viridis as a Model System to Advance Millet Genetics and Genomics

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

    Huang, Pu; Shyu, Christine; Coelho, Carla P.

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Yet despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools andmore » resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.« less

  17. Studies on Monitoring and Tracking Genetic Resources: An Executive Summary

    PubMed Central

    Garrity, George M.; Thompson, Lorraine M.; Ussery, David W.; Paskin, Norman; Baker, Dwight; Desmeth, Philippe; Schindel, D.E.; Ong, P.S.

    2009-01-01

    The principles underlying fair and equitable sharing of benefits derived from the utilization of genetic resources are set out in Article 15 of the UN Convention on Biological Diversity, which stipulate that access to genetic resources is subject to the prior informed consent of the country where such resources are located and to mutually agreed terms regarding the sharing of benefits that could be derived from such access. One issue of particular concern for provider countries is how to monitor and track genetic resources once they have left the provider country and enter into use in a variety of forms. This report was commissioned to provide a detailed review of advances in DNA sequencing technologies, as those methods apply to identification of genetic resources, and the use of globally unique persistent identifiers for persistently linking to data and other forms of digital documentation that is linked to individual genetic resources. While the report was written for an audience with a mixture of technical, legal, and policy backgrounds it is relevant to the genomics community as it is an example of downstream application of genomics information. PMID:21304641

  18. Genomic resources in fruit plants: an assessment of current status.

    PubMed

    Rai, Manoj K; Shekhawat, N S

    2015-01-01

    The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

  19. Allele Mining in Barley Genetic Resources Reveals Genes of Race-Non-Specific Powdery Mildew Resistance

    PubMed Central

    Spies, Annika; Korzun, Viktor; Bayles, Rosemary; Rajaraman, Jeyaraman; Himmelbach, Axel; Hedley, Pete E.; Schweizer, Patrick

    2012-01-01

    Race-non-specific, or quantitative, pathogen resistance is of high importance to plant breeders due to its expected durability. However, it is usually controlled by multiple quantitative trait loci (QTL) and therefore difficult to handle in practice. Knowing the genes that underlie race-non-specific resistance (NR) would allow its exploitation in a more targeted manner. Here, we performed an association-genetic study in a customized worldwide collection of spring barley accessions for candidate genes of race-NR to the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and combined data with results from QTL mapping as well as functional-genomics approaches. This led to the identification of 11 associated genes with converging evidence for an important role in race-NR in the presence of the Mlo gene for basal susceptibility. Outstanding in this respect was the gene encoding the transcription factor WRKY2. The results suggest that unlocking plant genetic resources and integrating functional-genomic with genetic approaches can accelerate the discovery of genes underlying race-NR in barley and other crop plants. PMID:22629270

  20. Genetic resources for maize cell wall biology.

    PubMed

    Penning, Bryan W; Hunter, Charles T; Tayengwa, Reuben; Eveland, Andrea L; Dugard, Christopher K; Olek, Anna T; Vermerris, Wilfred; Koch, Karen E; McCarty, Donald R; Davis, Mark F; Thomas, Steven R; McCann, Maureen C; Carpita, Nicholas C

    2009-12-01

    Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions.

  1. Less waste corn, more land in soybeans, and the switch to genetically modified crops: trends with important implications to wildlife management

    USGS Publications Warehouse

    Krapu, G.L.; Brandt, D.A.; Cox, R.R.

    2004-01-01

    An abundance of waste corn, a key food of many wildlife species, has helped make possible the widespread success of wildlife management in the United States over the past half century. We found waste corn post harvest in Nebraska declined by 47% from 1978 to 1998 due primarily to improvements in combine headers resulting in a marked decline in ear loss. The reduction in waste coincided with major declines in fat storage by sandhill cranes and white-fronted geese during spring migration. Sandhill cranes, northern pintails, white-fronted geese, and lesser snow geese avoided soybeans while staging in spring in the Rainwater Basin Area and Central Platte River Valley. These findings and other literature suggest soybeans are a marginal food for wildlife particularly during periods of high energy requirements. Soybean acreage has increased by 600% in the United States since 1950 and now comprises nearly one-quarter of the nation>'s cropland. With over 80% of the soybean crop now in genetically modified varieties and treated with glyphosate, weed seed is becoming scarce in soybean fields leaving limited food for wildlife on 72 million acres of U.S. cropland. We suggest that the combined effect of increasing efficiency of crop harvesting techniques, expansion of soybeans and other crops poorly suited for wildlife nutrient needs, and more efficient weed control through the shift to genetically modified crops may severely limit seed-eating wildlife populations in the future unless ways are found to replace high energy food sources being lost. We encourage more research to gain greater insight into effects of declining food resources on wildlife populations and propose that the conservation title of the 2002 farm bill be used as a mechanism to replace part of the high-energy food being lost due to changes in production agriculture.

  2. Origins of food crops connect countries worldwide

    PubMed Central

    Achicanoy, Harold A.; Bjorkman, Anne D.; Navarro-Racines, Carlos; Guarino, Luigi; Flores-Palacios, Ximena; Engels, Johannes M. M.; Wiersema, John H.; Dempewolf, Hannes; Sotelo, Steven; Ramírez-Villegas, Julian; Castañeda-Álvarez, Nora P.; Fowler, Cary; Jarvis, Andy; Rieseberg, Loren H.; Struik, Paul C.

    2016-01-01

    Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.

  3. Assessment of exchange of crop in view of change climate and International Treaties.

    PubMed

    Singh, Anil Kumar; Pedapati, Annitaa; Manibhushan

    2015-01-01

    To meet the UN millennium development goal of reducing the number of hungry people to half by 2015, there is utmost need to breed potentially high yielding varieties to match up the requirement along with corrective measures to bridge the gap between the potential yield and yield harvested by farmers. The scenario has changed from free access to limited access of plant genetic resources (PGR) and therefore, it is important to understand the issues in view of national and international agreements, intellectual property rights (IPR'S), climate change conditions and expanded scope of breeders and farmers rights for developed genotypes. For efficient management of PGR, developing countries need to understand the implications of PGR related IPR'S as stronger IPR'S in developed countries could have harmful effects by reduced exchange of genetic resources from developed countries. Keeping in view the existing realities every possible effort should be taken for enrichment of crop gene pool by introducing them from each and every corner of the globe. Keeping these facts in view this paper describes the priorities for introduction and exchange of important crop groups/crops along with some of their potential wild and weedy relatives and thrust has been given to generate awareness among the workers engaged in the breeders/crop improvement works. Information provided in this presentation can be utilized by prospective crop improvement works to plan to meet out the nationalfood security.

  4. Fortifying Horticultural Crops with Essential Amino Acids: A Review.

    PubMed

    Wang, Guoping; Xu, Mengyun; Wang, Wenyi; Galili, Gad

    2017-06-19

    To feed the world's growing population, increasing the yield of crops is not the only important factor, improving crop quality is also important, and it presents a significant challenge. Among the important crops, horticultural crops (particularly fruits and vegetables) provide numerous health compounds, such as vitamins, antioxidants, and amino acids. Essential amino acids are those that cannot be produced by the organism and, therefore, must be obtained from diet, particularly from meat, eggs, and milk, as well as a variety of plants. Extensive efforts have been devoted to increasing the levels of essential amino acids in plants. Yet, these efforts have been met with very little success due to the limited genetic resources for plant breeding and because high essential amino acid content is generally accompanied by limited plant growth. With a deep understanding of the biosynthetic pathways of essential amino acids and their interactions with the regulatory networks in plants, it should be possible to use genetic engineering to improve the essential amino acid content of horticultural plants, rendering these plants more nutritionally favorable crops. In the present report, we describe the recent advances in the enhancement of essential amino acids in horticultural plants and possible future directions towards their bio-fortification.

  5. Tracing back seed and pollen flow within the crop-wild Beta vulgaris complex: genetic distinctiveness vs. hot spots of hybridization over a regional scale.

    PubMed

    Viard, Frédérique; Arnaud, Jean-François; Delescluse, Maxime; Cuguen, Joël

    2004-06-01

    Hybrids between transgenic crops and wild relatives have been documented successfully in a wide range of cultivated species, having implications on conservation and biosafety management. Nonetheless, the magnitude and frequency of hybridization in the wild is still an open question, in particular when considering several populations at the landscape level. The Beta vulgaris complex provides an excellent biological model to tackle this issue. Weed beets contaminating sugar beet fields are expected to act as a relay between wild populations and crops and from crops-to-crops. In one major European sugar beet production area, nine wild populations and 12 weed populations were genetically characterized using cytoplasmic markers specific to the cultivated lines and nuclear microsatellite loci. A tremendous overall genetic differentiation between neighbouring wild and weed populations was depicted. However, genetic admixture analyses at the individual level revealed clear evidence for gene flow between wild and weed populations. In particular, one wild population displayed a high magnitude of nuclear genetic admixture, reinforced by direct seed flow as evidenced by cytoplasmic markers. Altogether, weed beets were shown to act as relay for gene flow between crops to wild populations and crops to crops by pollen and seeds at a landscape level.

  6. Notification: Evaluation of EPA's Management of Resistance Issues Related to Herbicide Tolerant Genetically Engineered Crops

    EPA Pesticide Factsheets

    Project #OPE-FY16-0023, March 25, 2016. The EPA OIG plans to begin preliminary research to assess the EPA's management and oversight of resistance issues related to herbicide tolerant genetically engineered crops.

  7. Accurate measurement of transgene copy number in crop plants using droplet digital PCR

    USDA-ARS?s Scientific Manuscript database

    Technical abstract: Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently ...

  8. The use of whole food animal studies in the safety assessment of genetically modified crops: limitations and recommendations.

    PubMed

    Bartholomaeus, Andrew; Parrott, Wayne; Bondy, Genevieve; Walker, Kate

    2013-11-01

    There is disagreement internationally across major regulatory jurisdictions on the relevance and utility of whole food (WF) toxicity studies on GM crops, with no harmonization of data or regulatory requirements. The scientific value, and therefore animal ethics, of WF studies on GM crops is a matter addressable from the wealth of data available on commercialized GM crops and WF studies on irradiated foods. We reviewed available GM crop WF studies and considered the extent to which they add to the information from agronomic and compositional analyses. No WF toxicity study was identified that convincingly demonstrated toxicological concern or that called into question the adequacy, sufficiency, and reliability of safety assessments based on crop molecular characterization, transgene source, agronomic characteristics, and/or compositional analysis of the GM crop and its near-isogenic line. Predictions of safety based on crop genetics and compositional analyses have provided complete concordance with the results of well-conducted animal testing. However, this concordance is primarily due to the improbability of de novo generation of toxic substances in crop plants using genetic engineering practices and due to the weakness of WF toxicity studies in general. Thus, based on the comparative robustness and reliability of compositional and agronomic considerations and on the absence of any scientific basis for a significant potential for de novo generation of toxicologically significant compositional alterations as a sole result of transgene insertion, the conclusion of this review is that WF animal toxicity studies are unnecessary and scientifically unjustifiable.

  9. The use of whole food animal studies in the safety assessment of genetically modified crops: Limitations and recommendations

    PubMed Central

    Bartholomaeus, Andrew; Parrott, Wayne; Bondy, Genevieve

    2013-01-01

    There is disagreement internationally across major regulatory jurisdictions on the relevance and utility of whole food (WF) toxicity studies on GM crops, with no harmonization of data or regulatory requirements. The scientific value, and therefore animal ethics, of WF studies on GM crops is a matter addressable from the wealth of data available on commercialized GM crops and WF studies on irradiated foods. We reviewed available GM crop WF studies and considered the extent to which they add to the information from agronomic and compositional analyses. No WF toxicity study was identified that convincingly demonstrated toxicological concern or that called into question the adequacy, sufficiency, and reliability of safety assessments based on crop molecular characterization, transgene source, agronomic characteristics, and/or compositional analysis of the GM crop and its near-isogenic line. Predictions of safety based on crop genetics and compositional analyses have provided complete concordance with the results of well-conducted animal testing. However, this concordance is primarily due to the improbability of de novo generation of toxic substances in crop plants using genetic engineering practices and due to the weakness of WF toxicity studies in general. Thus, based on the comparative robustness and reliability of compositional and agronomic considerations and on the absence of any scientific basis for a significant potential for de novo generation of toxicologically significant compositional alterations as a sole result of transgene insertion, the conclusion of this review is that WF animal toxicity studies are unnecessary and scientifically unjustifiable. PMID:24164514

  10. Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

    PubMed Central

    Hill, Camilla B.; Li, Chengdao

    2016-01-01

    Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation

  11. Attitudes of Agricultural Experts Toward Genetically Modified Crops: A Case Study in Southwest Iran.

    PubMed

    Ghanian, Mansour; Ghoochani, Omid M; Kitterlin, Miranda; Jahangiry, Sheida; Zarafshani, Kiumars; Van Passel, Steven; Azadi, Hossein

    2016-04-01

    The production of genetically modified (GM) crops is growing around the world, and with it possible opportunities to combat food insecurity and hunger, as well as solutions to current problems facing conventional agriculture. In this regard the use of GMOs in food and agricultural applications has increased greatly over the past decade. However, the development of GM crops has been a matter of considerable interest and worldwide public controversy. This, in addition to skepticism, has stifled the use of this practice on a large scale in many areas, including Iran. It stands to reason that a greater understanding of this practice could be formed after a review of the existing expert opinions surrounding GM crops. Therefore, the purpose of this study was to analyze the predictors that influence agricultural experts' attitudes toward the development of and policies related to GM crops. Using a descriptive correlational research method, questionnaire data was collected from 65 experts from the Agricultural Organization in the Gotvand district in Southwest Iran. Results indicated that agricultural experts were aware of the environmental benefits and possible risks associated with GM crops. The majority of participants agreed that GM crops could improve food security and accelerate rural development, and were proponents of labeling practices for GM crops. Finally, there was a positive correlation between the perception of benefits and attitudes towards GM crops.

  12. Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations

    USDA-ARS?s Scientific Manuscript database

    Teosinte (Zea mays ssp. parviglumis) has greater genetic diversity than maize inbreds and landraces (Z. mays ssp. mays). There are, however, limited genetic resources to efficiently evaluate and tap this diversity. To broaden resources for genetic diversity studies in maize, we developed and evaluat...

  13. Relay cropping as a sustainable approach: problems and opportunities for sustainable crop production.

    PubMed

    Tanveer, Mohsin; Anjum, Shakeel Ahmad; Hussain, Saddam; Cerdà, Artemi; Ashraf, Umair

    2017-03-01

    Climate change, soil degradation, and depletion of natural resources are becoming the most prominent challenges for crop productivity and environmental sustainability in modern agriculture. In the scenario of conventional farming system, limited chances are available to cope with these issues. Relay cropping is a method of multiple cropping where one crop is seeded into standing second crop well before harvesting of second crop. Relay cropping may solve a number of conflicts such as inefficient use of available resources, controversies in sowing time, fertilizer application, and soil degradation. Relay cropping is a complex suite of different resource-efficient technologies, which possesses the capability to improve soil quality, to increase net return, to increase land equivalent ratio, and to control the weeds and pest infestation. The current review emphasized relay cropping as a tool for crop diversification and environmental sustainability with special focus on soil. Briefly, benefits, constraints, and opportunities of relay cropping keeping the goals of higher crop productivity and sustainability have also been discussed in this review. The research and knowledge gap in relay cropping was also highlighted in order to guide the further studies in future.

  14. Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil.

    PubMed

    Sharpe, Andrew G; Ramsay, Larissa; Sanderson, Lacey-Anne; Fedoruk, Michael J; Clarke, Wayne E; Li, Rong; Kagale, Sateesh; Vijayan, Perumal; Vandenberg, Albert; Bett, Kirstin E

    2013-03-18

    The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model legume (Medicago truncatula). Lentil is a global food crop increasing in importance in the Indian sub-continent and elsewhere due to its nutritional value and quick cooking time. Despite this importance there has been a dearth of genetic and genomic resources for the crop and this has limited the application of marker-assisted selection strategies in breeding. We describe here the development of a deep and diverse transcriptome resource for lentil using next generation sequencing technology. The generation of data in multiple cultivated (L. culinaris) and wild (L. ervoides) genotypes together with the utilization of a bioinformatics workflow enabled the identification of a large collection of SNPs and the subsequent development of a genotyping platform that was used to establish the first comprehensive genetic map of the L. culinaris genome. Extensive collinearity with M. truncatula was evident on the basis of sequence homology between mapped markers and the model genome and large translocations and inversions relative to M. truncatula were identified. An estimate for the time divergence of L. culinaris from L. ervoides and of both from M. truncatula was also calculated. The availability of the genomic and derived molecular marker resources presented here will help change lentil breeding strategies and lead to increased genetic gain in the future.

  15. Integrated Modeling of Crop Growth and Water Resource Management to Project Climate Change Impacts on Crop Production and Irrigation Water Supply and Demand in African Nations

    NASA Astrophysics Data System (ADS)

    Dale, A. L.; Boehlert, B.; Reisenauer, M.; Strzepek, K. M.; Solomon, S.

    2017-12-01

    Climate change poses substantial risks to African agriculture. These risks are exacerbated by concurrent risks to water resources, with water demand for irrigation comprising 80 to 90% of water withdrawals across the continent. Process-based crop growth models are able to estimate both crop demand for irrigation water and crop yields, and are therefore well-suited to analyses of climate change impacts at the food-water nexus. Unfortunately, impact assessments based on these models generally focus on either yields or water demand, rarely both. For this work, we coupled a crop model to a water resource management model in order to predict national trends in the impact of climate change on crop production, irrigation water demand, and the availability of water for irrigation across Africa. The crop model FAO AquaCrop-OS was run at 2ox2o resolution for 17 different climate futures from the CMIP5 archive, nine for Representative Concentration Pathway (RCP) 4.5 and eight for RCP8.5. Percent changes in annual rainfed and irrigated crop production and temporal shifts in monthly irrigation water demand were estimated for the years 2030, 2050, 2070, and 2090 for maize, sorghum, rice, wheat, cotton, sugarcane, fruits & vegetables, roots & tubers, and legumes & soybeans. AquaCrop was then coupled to a water management model (WEAP) in order to project changes in the ability of seven major river basins (the Congo, Niger, Nile, Senegal, Upper Orange, Volta, and Zambezi) to meet irrigation water demand out to 2050 in both average and dry years in the face of both climate change and irrigation expansion. Spatial and temporal trends were identified and interpreted through the lens of potential risk management strategies. Uncertainty in model estimates is reported and discussed.

  16. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics.

    PubMed

    Varshney, Rajeev K; Mohan, S Murali; Gaur, Pooran M; Gangarao, N V P R; Pandey, Manish K; Bohra, Abhishek; Sawargaonkar, Shrikant L; Chitikineni, Annapurna; Kimurto, Paul K; Janila, Pasupuleti; Saxena, K B; Fikre, Asnake; Sharma, Mamta; Rathore, Abhishek; Pratap, Aditya; Tripathi, Shailesh; Datta, Subhojit; Chaturvedi, S K; Mallikarjuna, Nalini; Anuradha, G; Babbar, Anita; Choudhary, Arbind K; Mhase, M B; Bharadwaj, Ch; Mannur, D M; Harer, P N; Guo, Baozhu; Liang, Xuanqiang; Nadarajan, N; Gowda, C L L

    2013-12-01

    Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Accurate measure of transgene copy number in crop plants using droplet digital PCR

    USDA-ARS?s Scientific Manuscript database

    Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy numb...

  18. Breeding for cuticle-associated traits in crop species: traits, targets, and strategies.

    PubMed

    Petit, Johann; Bres, Cécile; Mauxion, Jean-Philippe; Bakan, Bénédicte; Rothan, Christophe

    2017-11-09

    Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Development of an agricultural biotechnology crop product: testing from discovery to commercialization.

    PubMed

    Privalle, Laura S; Chen, Jingwen; Clapper, Gina; Hunst, Penny; Spiegelhalter, Frank; Zhong, Cathy X

    2012-10-17

    "Genetically modified" (GM) or "biotech" crops have been the most rapidly adopted agricultural technology in recent years. The development of a GM crop encompasses trait identification, gene isolation, plant cell transformation, plant regeneration, efficacy evaluation, commercial event identification, safety evaluation, and finally commercial authorization. This is a lengthy, complex, and resource-intensive process. Crops produced through biotechnology are the most highly studied food or food component consumed. Before commercialization, these products are shown to be as safe as conventional crops with respect to feed, food, and the environment. This paper describes this global process and the various analytical tests that must accompany the product during the course of development, throughout its market life, and beyond.

  20. Poultry genetic resource conservation using primordial germ cells

    PubMed Central

    NAKAMURA, Yoshiaki

    2016-01-01

    The majority of poultry genetic resources are maintained in situ in living populations. However, in situ conservation of poultry genetic resources always carries the risk of loss owing to pathogen outbreaks, genetic problems, breeding cessation, or natural disasters. Cryobanking of germplasm in birds has been limited to the use of semen, preventing conservation of the W chromosome and mitochondrial DNA. A further challenge is posed by the structure of avian eggs, which restricts the cryopreservation of ova and fertilized embryos, a technique widely used for mammalian species. By using a unique biological property and accessibility of avian primordial germ cells (PGCs), precursor cells for gametes, which temporally circulate in the vasculature during early development, an avian PGC transplantation technique has been established. To date, several techniques for PGC manipulation including purification, cryopreservation, depletion, and long-term culture have been developed in chickens. PGC transplantation combined with recent advanced PGC manipulation techniques have enabled ex situ conservation of poultry genetic resources in their complete form. Here, the updated technologies for avian PGC manipulation are introduced, and then the concept of a poultry PGC-bank is proposed by considering the biological properties of avian PGCs. PMID:27210834

  1. Connecting Groundwater, Crop Price, and Crop Production Variability in India

    NASA Astrophysics Data System (ADS)

    Pollack, A.; Lobell, D. B.; Jain, M.

    2015-12-01

    Farmers in India rely on groundwater resources for irrigation and production of staple crops that provide over half of the calories consumed domestically each year. While this has been a productive strategy in increasing agricultural production and maintaining high yields, groundwater resources are depleting at a quicker rate than natural resources can replace. This issue gains relevance as climate variability concurrently adds to yearly fluctuations in farmer demand for irrigation each year, which can create high risk for farmers that depend on consistent yields, but do not have access to dwindling water resources. This study investigates variability in groundwater levels from 2005 to 2013 in relation to crop prices and production by analyzing district-level datasets made available through India's government. Through this analysis, we show the impact of groundwater variability on price variability, crop yield, and production during these years. By examining this nine-year timescale, we extend our analysis to forthcoming years to demonstrate the increasing importance of groundwater resources in irrigation, and suggest strategies to reduce the impact of groundwater shortages on crop production and prices.

  2. An overview of the last 10 years of genetically engineered crop safety research.

    PubMed

    Nicolia, Alessandro; Manzo, Alberto; Veronesi, Fabio; Rosellini, Daniele

    2014-03-01

    The technology to produce genetically engineered (GE) plants is celebrating its 30th anniversary and one of the major achievements has been the development of GE crops. The safety of GE crops is crucial for their adoption and has been the object of intense research work often ignored in the public debate. We have reviewed the scientific literature on GE crop safety during the last 10 years, built a classified and manageable list of scientific papers, and analyzed the distribution and composition of the published literature. We selected original research papers, reviews, relevant opinions and reports addressing all the major issues that emerged in the debate on GE crops, trying to catch the scientific consensus that has matured since GE plants became widely cultivated worldwide. The scientific research conducted so far has not detected any significant hazards directly connected with the use of GE crops; however, the debate is still intense. An improvement in the efficacy of scientific communication could have a significant impact on the future of agricultural GE. Our collection of scientific records is available to researchers, communicators and teachers at all levels to help create an informed, balanced public perception on the important issue of GE use in agriculture.

  3. AquaCrop-OS: A tool for resilient management of land and water resources in agriculture

    NASA Astrophysics Data System (ADS)

    Foster, Timothy; Brozovic, Nicholas; Butler, Adrian P.; Neale, Christopher M. U.; Raes, Dirk; Steduto, Pasquale; Fereres, Elias; Hsiao, Theodore C.

    2017-04-01

    Water managers, researchers, and other decision makers worldwide are faced with the challenge of increasing food production under population growth, drought, and rising water scarcity. Crop simulation models are valuable tools in this effort, and, importantly, provide a means of quantifying rapidly crop yield response to water, climate, and field management practices. Here, we introduce a new open-source crop modelling tool called AquaCrop-OS (Foster et al., 2017), which extends the functionality of the globally used FAO AquaCrop model. Through case studies focused on groundwater-fed irrigation in the High Plains and Central Valley of California in the United States, we demonstrate how AquaCrop-OS can be used to understand the local biophysical, behavioural, and institutional drivers of water risks in agricultural production. Furthermore, we also illustrate how AquaCrop-OS can be combined effectively with hydrologic and economic models to support drought risk mitigation and decision-making around water resource management at a range of spatial and temporal scales, and highlight future plans for model development and training. T. Foster, et al. (2017) AquaCrop-OS: An open source version of FAO's crop water productivity model. Agricultural Water Management. 181: 18-22. http://dx.doi.org/10.1016/j.agwat.2016.11.015.

  4. Plant genetics, sustainable agriculture and global food security.

    PubMed

    Ronald, Pamela

    2011-05-01

    The United States and the world face serious societal challenges in the areas of food, environment, energy, and health. Historically, advances in plant genetics have provided new knowledge and technologies needed to address these challenges. Plant genetics remains a key component of global food security, peace, and prosperity for the foreseeable future. Millions of lives depend upon the extent to which crop genetic improvement can keep pace with the growing global population, changing climate, and shrinking environmental resources. While there is still much to be learned about the biology of plant-environment interactions, the fundamental technologies of plant genetic improvement, including crop genetic engineering, are in place, and are expected to play crucial roles in meeting the chronic demands of global food security. However, genetically improved seed is only part of the solution. Such seed must be integrated into ecologically based farming systems and evaluated in light of their environmental, economic, and social impacts-the three pillars of sustainable agriculture. In this review, I describe some lessons learned, over the last decade, of how genetically engineered crops have been integrated into agricultural practices around the world and discuss their current and future contribution to sustainable agricultural systems.

  5. Variables Affecting Secondary School Students' Willingness to Eat Genetically Modified Food Crops

    NASA Astrophysics Data System (ADS)

    Maes, Jasmien; Bourgonjon, Jeroen; Gheysen, Godelieve; Valcke, Martin

    2017-04-01

    A large-scale cross-sectional study (N = 4002) was set up to determine Flemish secondary school students' willingness to eat genetically modified food (WTE) and to link students' WTE to previously identified key variables from research on the acceptance of genetic modification (GM). These variables include subjective and objective knowledge about genetics and biotechnology, perceived risks and benefits of GM food crops, trust in information from different sources about GM, and food neophobia. Differences between WTE-related variables based on students' grade level, educational track, and gender were analyzed. The students displayed a rather indecisive position toward GM food and scored weakly on a genetics and biotechnology knowledge test. WTE correlated most strongly with perceived benefits and subjective and objective knowledge. The results have clear implications for education, as they reiterate the need to strengthen students' scientific knowledge base and to introduce a GM-related debate at a much earlier stage in their school career.

  6. Variables Affecting Secondary School Students' Willingness to Eat Genetically Modified Food Crops

    NASA Astrophysics Data System (ADS)

    Maes, Jasmien; Bourgonjon, Jeroen; Gheysen, Godelieve; Valcke, Martin

    2018-06-01

    A large-scale cross-sectional study ( N = 4002) was set up to determine Flemish secondary school students' willingness to eat genetically modified food (WTE) and to link students' WTE to previously identified key variables from research on the acceptance of genetic modification (GM). These variables include subjective and objective knowledge about genetics and biotechnology, perceived risks and benefits of GM food crops, trust in information from different sources about GM, and food neophobia. Differences between WTE-related variables based on students' grade level, educational track, and gender were analyzed. The students displayed a rather indecisive position toward GM food and scored weakly on a genetics and biotechnology knowledge test. WTE correlated most strongly with perceived benefits and subjective and objective knowledge. The results have clear implications for education, as they reiterate the need to strengthen students' scientific knowledge base and to introduce a GM-related debate at a much earlier stage in their school career.

  7. GM as a route for delivery of sustainable crop protection.

    PubMed

    Bruce, Toby J A

    2012-01-01

    Modern agriculture, with its vast monocultures of lush fertilized crops, provides an ideal environment for adapted pests, weeds, and diseases. This vulnerability has implications for food security: when new pesticide-resistant pest biotypes evolve they can devastate crops. Even with existing crop protection measures, approximately one-third yield losses occur globally. Given the projected increase in demand for food (70% by 2050 according to the UN), sustainable ways of preventing these losses are needed. Development of resistant crop cultivars can make an important contribution. However, traditional crop breeding programmes are limited by the time taken to move resistance traits into elite crop genetic backgrounds and the limited gene pools in which to search for novel resistance. Furthermore, resistance based on single genes does not protect against the full spectrum of pests, weeds, and diseases, and is more likely to break down as pests evolve counter-resistance. Although not necessarily a panacea, GM (genetic modification) techniques greatly facilitate transfer of genes and thus provide a route to overcome these constraints. Effective resistance traits can be precisely and conveniently moved into mainstream crop cultivars. Resistance genes can be stacked to make it harder for pests to evolve counter-resistance and to provide multiple resistances to different attackers. GM-based crop protection could substantially reduce the need for farmers to apply pesticides to their crops and would make agricultural production more efficient in terms of resources used (land, energy, water). These benefits merit consideration by environmentalists willing to keep an open mind on the GM debate.

  8. Orphan legume crops enter the genomics era!

    PubMed

    Varshney, Rajeev K; Close, Timothy J; Singh, Nagendra K; Hoisington, David A; Cook, Douglas R

    2009-04-01

    Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is hampered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation. The driving force is a series of international collaborations that benefit from recent advances in genome sequencing and genotyping technologies. The focus of these activities is the development of genome-scale data sets that can be used in high-throughput approaches to facilitate genomics-assisted breeding in these legumes.

  9. Swedish farmers attitudes, expectations and fears in relation to growing genetically modified crops.

    PubMed

    Lehrman, Anna; Johnson, Katy

    2008-01-01

    This study evaluates a survey about Swedish farmers' attitude towards genetically modified (GM) crops, and their perception concerning potential benefits and drawbacks that cropping of an insect resistant (IR) GM variety would involve. The questions were "tick a box" choices, included in a yearly omnibus survey sent to 1000 Swedish farmers (68% response rate). The results showed that a majority of the farmers were negative, although almost one third claimed to be neutral to GM crops. The farmers recognized several benefits both in terms of agricultural production and for the environment, but they were also highly concerned about the consumers' unwillingness to buy GM products. Farmers perceived an increase in yield, but nearly as many farmers thought that there would be no benefits with growing an IR GM crop. Several differences in hopes and concerns of the farmers surveyed were revealed when they were divided in positive, neutral and negative groups. Farmers negative to GM were more concerned than positive farmers about IR GM crops being dangerous for humans, livestock or other organisms to consume. GM-positive farmers seemed to be most concerned about potential problems with growing a marketable crop and expensive seeds, but saw a reduced health risk to the grower, due to less use of pesticides, as a possible benefit. The results among the GM-neutral farmers were in most cases closely related to the positive farmers' choices, implying that they believe that there are advantages with growing an IR GM crop, but also fear potential drawbacks. This general uncertainty about GM IR crops may prevent them from accepting the new technology.

  10. Ensuring the genetic diversity of potatoes

    USDA-ARS?s Scientific Manuscript database

    Opportunities for advances in the potato crop through genetics are great, since potato has many needs for improvement, and many related species with the traits required are available. Genebanks provide a centralized and specialized resource for providing the services of acquisition, classification, ...

  11. Role of genetic improvement in the Short Rotation Woody Crops Program

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

    Layton, P.A.; Wright, L.L.

    1986-01-01

    A major effort in the Short Rotation Woody Crops Program (SRWCP) is species screening and genetic improvement of selected species. Of the 125 species initially evaluated for SRIC, 20 are being seriously considered with most of emphasis on 16 hardwood species. Range-wide seed collections of 12 species were provenance tested; these include Platanus occidentalis (sycamore), Alnus glutinosa (European black alder), and Robinia pseudoacacia (black locust). Based on the results of these tests, highly productive, site-specific seed sources are being chosen for several geographic regions. Three of these species re currently being bred for increased productivity in SRIC systems. Genetic improvementmore » is viewed as a tool for increasing productivity, having anticipated gains of 40 to 50%. The techniques of somaclonal screening and genetic engineering are being evaluated for their usefulness in the SRIC improvement program. Currently, salt-tolerant Atriplex canescens (four-wing saltbush) and herbicide-resistant Populus spp. are being sought via somaclonal screening. 35 refs., 4 figs., 3 tabs.« less

  12. METHODS FOR DETERMINING EXPOSURE TO AND POTENTIAL ECOLOGICAL EFFECTS OF GENE FLOW FROM GENETICALLY MODIFIED CROPS TO COMPATIBLE RELATIVES

    EPA Science Inventory

    SCIENCE QUESTIONS:

    -Does gene flow occur from genetically modified (GM) crop plants to compatible plants?

    -How can it be measured?

    -Are there ecological consequences of GM crop gene flow to plant communities?



    RESEARCH:

    The objectives ...

  13. COTIP: Cotton TILLING Platform, a Resource for Plant Improvement and Reverse Genetic Studies

    PubMed Central

    Aslam, Usman; Cheema, Hafiza M. N.; Ahmad, Sheraz; Khan, Iqrar A.; Malik, Waqas; Khan, Asif A.

    2016-01-01

    Cotton is cultivated worldwide for its white fiber, of which around 90% is tetraploid upland cotton (Gossypium hirsutum L.) carrying both A and D genome. Since centuries, yield increasing efforts for the cotton crop by conventional breeding approaches have caused an extensive erosion of natural genetic variability. Mutation based improvement strategies provide an effective way of creating new allelic variations. Targeting Induced Local Lesions IN Genomes (TILLING) provides a mutation based reverse genetic strategy to create and evaluate induced genetic variability at DNA level. Here, we report development and testing of TILLING populations of allotetraploid cotton (G. hirsutum) for functional genomic studies and mutation based enrichment of cotton genetic resources. Seed of two cotton cultivars “PB-899 and PB-900” were mutagenized with 0.3 and 0.2% (v/v) ethyl methanesulfonate, respectively. The phenotyping of M1 and M2 populations presented numerous mutants regarding the branching pattern, leaf morphology, disease resistance, photosynthetic lesions and flower sterility. Molecular screening for point mutations was performed by TILLING PCR aided CEL1 mismatch cleavage. To estimate the mutation frequency in the mutant genomes, five gene classes were TILLed in 8000 M2 plants of each var. “PB-899” and “PB-900.” These include actin (GhACT), Pectin Methyl Esterase (GhPME), sucrose synthase (GhSUS), resistance gene analog, and defense response gene (DRGs). The var. PB-899 was harboring 47% higher mutation induction rate than PB-900. The highest rate of mutation frequency was identified for NAC-TF5 (EU706348) of DRGs class, ranging from 1/58 kb in PB-899 to 1/105 kb in PB-900. The mutation screening assay revealed the presence of significant proportion of induced mutations in cotton TILLING populations such as 1/153 kb and 1/326 kb in var. “PB-899” and “PB-900,” respectively. The establishment of a cotton TILLING platform (COTIP) and data obtained from

  14. Molecular genetics research in ADHD: ethical considerations concerning patients' benefit and resource allocation.

    PubMed

    Rothenberger, Lillian Geza

    2012-12-01

    Immense resource allocations have led to great data output in genetic research. Concerning ADHD resources spent on genetic research are less than those spent on clinical research. But there are successful efforts made to increase support for molecular genetics research in ADHD. Concerning genetics no evidence based conclusive results have significant impact on prevention, diagnosis or treatment yet. With regard to ethical aspects like the patients' benefit and limited resources the question arises if it is indicated to think about a new balance of resource allocation between molecular genetics and non-genetics research in ADHD. An ethical reflection was performed focusing on recent genetic studies and reviews based on a selective literature search. There are plausible reasons why genetic research results in ADHD are somehow disappointing for clinical practice so far. Researchers try to overcome these gaps systematically, without knowing what the potential future benefits for the patients might be. Non-genetic diagnostic/therapeutic research may lead to clinically relevant findings within a shorter period of time. On the other hand, non-genetic research in ADHD may be nurtured by genetic approaches. But, with the latter there exist significant risks of harm like stigmatization and concerns regarding data protection. Isolated speeding up resources of genetic research in ADHD seems questionable from an ethical point of view. There is a need to find a new balance of resource allocation between genetic and non-genetic research in ADHD, probably by integrating genetics more systematically into clinical research. A transdisciplinary debate is recommended. Copyright © 2012 Wiley Periodicals, Inc.

  15. Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions

    PubMed Central

    Takahashi, Yu; Somta, Prakit; Muto, Chiaki; Iseki, Kohtaro; Naito, Ken; Pandiyan, Muthaiyan; Natesan, Senthil; Tomooka, Norihiko

    2016-01-01

    The genus Vigna (Fabaceae) consists of five subgenera, and includes more than 100 wild species. In Vigna, 10 crops have been domesticated from three subgenera, Vigna, Plectrotropis, and Ceratotropis. The habitats of wild Vigna species are so diverse that their genomes could harbor various genes responsible for environmental stress adaptation, which could lead to innovations in agriculture. Since some of the gene bank Vigna accessions were unidentified and they seemed to be novel genetic resources, these accessions were identified based on morphological traits. The phylogenetic positions were estimated based on the DNA sequences of nuclear rDNA-ITS and chloroplast atpB-rbcL spacer regions. Based on the results, the potential usefulness of the recently described species V. indica and V. sahyadriana, and some wild Vigna species, i.e., V. aconitifolia, V. dalzelliana, V. khandalensis, V. marina var. oblonga, and V. vexillata, was discussed. PMID:26800459

  16. Creating a cryobank for germplasm of fruit and berry crops: methodological recommendations

    USDA-ARS?s Scientific Manuscript database

    Plant genetic resources are a national treasure in each country. They serve as a basis for developing new and improving existing varieties of plants. In Kazakhstan, a wide selection of cultivated and wild forms grow unique fruit and berry crops, including apple (Malus sieversii (Ledeb.) M. Roem., Ma...

  17. Impacts of Past Land Use Changes on Water Resources: An Analog for Assessing Effects of Proposed Bioenergy Crops

    NASA Astrophysics Data System (ADS)

    Scanlon, B. R.; Schilling, K.; Young, M.; Duncan, I. J.; Gerbens-Leenes, P.

    2011-12-01

    Interest is increasing in renewable energy sources, including bioenergy. However, potential impacts of bioenergy crops on water resources need to be better understood before large scale expansion occurs. This study evaluates the potential for using past land use change impacts on water resources as an analog for assessing future bioenergy crop effects. Impacts were assessed for two cases and methods: (1) changes from perennial to annual crops in the Midwest U.S. using stream hydrograph separation; and (2) changes from perennial grasses and shrubs to annual crops in the Southwest U.S. using unsaturated zone and groundwater data. Results from the Midwest show that expanding the soybean production area by 80,000 km2 increased stream flow by 32%, based on data from Keokuk station in the Upper Mississippi River Basin. Using these relationships, further expansion of annual corn production for biofuels by 10 - 50% would increase streamflow by up to 40%, with related increases in nitrate, phosphate, and sediment pollutant transport to the Gulf of Mexico. The changes in water partitioning are attributed to reducing evapotranspiration, increasing recharge and baseflow discharge to streams. Similar results were found in the southwestern US, where changes from native perennial grasses and shrubs to annual crops increased recharge from ~0.0 to 24 mm/yr, raising water tables by up to 7 m in some regions and flushing accumulated salts into underlying aquifers in the southern High Plains. The changes in water partitioning are related to changes in rooting depth from deep rooted native vegetation to shallow rooted crops and growing season length. Further expansion of annual bioenergy crops, such as changes from Conservation Reserve Program to corn in the Midwest, will continue the trajectory of reducing ET, thereby increasing recharge and baseflow to streams and nutrient export. We hypothesize that changing bioenergy crops from annual crops to perennial grasses, such as switchgrass

  18. 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.

  19. Innovative farmers and regulatory gatekeepers: Genetically modified crops regulation and adoption in developing countries

    PubMed Central

    Sinebo, Woldeyesus; Maredia, Karim

    2016-01-01

    ABSTRACT The regulation of genetically modified (GM) crops is a topical issue in agriculture and environment over the past 2 decades. The objective of this paper is to recount regulatory and adoption practices in some developing countries that have successfully adopted GM crops so that aspiring countries may draw useful lessons and best practices for their biosafatey regulatory regimes. The first 11 mega-GM crops growing countries each with an area of more than one million hectares in 2014 were examined. Only five out of the 11 countries had smooth and orderly adoption of these crops as per the regulatory requirement of each country. In the remaining 6 countries (all developing countries), GM crops were either introduced across borders without official authorization, released prior to regulatory approval or unapproved seeds were sold along with the approved ones in violation to the existing regulations. Rapid expansion of transgenic crops over the past 2 decades in the developing world was a result of an intense desire by farmers to adopt these crops irrespective of regulatory roadblocks. Lack of workable biosafety regulatory system and political will to support GM crops encouraged unauthorized access to GM crop varieties. In certain cases, unregulated access in turn appeared to result in the adoption of substandard or spurious technology which undermined performance and productivity. An optimal interaction among the national agricultural innovation systems, biosafety regulatory bodies, biotech companies and high level policy makers is vital in making a workable regulated progress in the adoption of GM crops. Factoring forgone opportunities to farmers to benefit from GM crops arising from overregulation into biosafety risk analysis and decision making is suggested. Building functional biosafety regulatory systems that balances the needs of farmers to access and utilize the GM technology with the regulatory imperatives to ensure adequate safety to the environment

  20. Genetically modified crops: success, safety assessment, and public concern.

    PubMed

    Singh, Om V; Ghai, Shivani; Paul, Debarati; Jain, Rakesh K

    2006-08-01

    With the emergence of transgenic technologies, new ways to improve the agronomic performance of crops for food, feed, and processing applications have been devised. In addition, ability to express foreign genes using transgenic technologies has opened up options for producing large quantities of commercially important industrial or pharmaceutical products in plants. Despite this high adoption rate and future promises, there is a multitude of concerns about the impact of genetically modified (GM) crops on the environment. Potential contamination of the environment and food chains has prompted detailed consideration of how such crops and the molecules that they produce can be effectively isolated and contained. One of the reasonable steps after creating a transgenic plant is to evaluate its potential benefits and risks to the environment and these should be compared to those generated by traditional agricultural practices. The precautionary approach in risk management of GM plants may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Effective risk assessment and monitoring mechanisms are the basic prerequisites of any legal framework to adequately address the risks and watch out for new risks. Several agencies in different countries monitor the release of GM organisms or frame guidelines for the appropriate application of recombinant organisms in agro-industries so as to assure the safe use of recombinant organisms and to achieve sound overall development. We feel that it is important to establish an internationally harmonized framework for the safe handling of recombinant DNA organisms within a few years.

  1. Seed fates in crop-wild hybrid sunflower: crop allele and maternal effects.

    PubMed

    Pace, Brian A; Alexander, Helen M; Emry, Jason D; Mercer, Kristin L

    2015-02-01

    Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank.

  2. Selective breeding in fish and conservation of genetic resources for aquaculture.

    PubMed

    Lind, C E; Ponzoni, R W; Nguyen, N H; Khaw, H L

    2012-08-01

    To satisfy increasing demands for fish as food, progress must occur towards greater aquaculture productivity whilst retaining the wild and farmed genetic resources that underpin global fish production. We review the main selection methods that have been developed for genetic improvement in aquaculture, and discuss their virtues and shortcomings. Examples of the application of mass, cohort, within family, and combined between-family and within-family selection are given. In addition, we review the manner in which fish genetic resources can be lost at the intra-specific, species and ecosystem levels and discuss options to best prevent this. We illustrate that fundamental principles of genetic management are common in the implementation of both selective breeding and conservation programmes, and should be emphasized in capacity development efforts. We highlight the value of applied genetics approaches for increasing aquaculture productivity and the conservation of fish genetic resources. © 2012 Blackwell Verlag GmbH.

  3. 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

  4. Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae).

    PubMed

    Wang, Maria M H; Gardner, Elliot M; Chung, Richard C K; Chew, Ming Yee; Milan, Abd Rahman; Pereira, Joan T; Zerega, Nyree J C

    2018-06-06

    Underutilized crops and their wild relatives are important resources for crop improvement and food security. Cempedak [Artocarpus integer (Thunb). Merr.] is a significant crop in Malaysia but underutilized elsewhere. Here we performed molecular characterization of cempedak and its putative wild relative bangkong (Artocarpus integer (Thunb). Merr. var. silvestris Corner) to address questions regarding the origin and diversity of cempedak. Using data from 12 microsatellite loci, we assessed the genetic diversity and genetic/geographic structure for 353 cempedak and 175 bangkong accessions from Malaysia and neighboring countries and employed clonal analysis to characterize cempedak cultivars. We conducted haplotype network analyses on the trnH-psbA region in a subset of these samples. We also analyzed key vegetative characters that reportedly differentiate cempedak and bangkong. We show that cempedak and bangkong are sister taxa and distinct genetically and morphologically, but the directionality of domestication origin is unclear. Genetic diversity was generally higher in bangkong than in cempedak. We found a distinct genetic cluster for cempedak from Borneo as compared to cempedak from Peninsular Malaysia. Finally, cempedak cultivars with the same names did not always share the same genetic fingerprint. Cempedak origins are complex, with likely admixture and hybridization with bangkong, warranting further investigation. We provide a baseline of genetic diversity of cempedak and bangkong in Malaysia and found that germplasm collections in Malaysia represent diverse coverage of the four cempedak genetic clusters detected. © 2018 Botanical Society of America.

  5. Lab to farm: applying research on plant genetics and genomics to crop improvement.

    PubMed

    Ronald, Pamela C

    2014-06-01

    Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.

  6. Tempest in a tea pot: How did the public conversation on genetically modified crops drift so far from the facts?

    PubMed

    Goldstein, Daniel A

    2014-06-01

    The debate over genetically modified (GM) crops has raged in Europe since 1996, but had barely risen above a whisper in the USA until recent labeling debates raised public attention. This article will explain GM crops and traits discuss safety assessment provide a view on safety from authoritative organizations discuss selected issues of current debate, and provide the author's perspective as to why the public debate has drifted so far from scientific reality. The economic and environmental benefits of GM crops are beyond scope, but references are provided. GM food and feed undergo comprehensive assessments using recognized approaches to assure they are as safe as the conventional congener. Issues of food safety and nutrition, unrelated to the GM process, may arise when GM foods display novel components or composition. Unanticipated genetic effects in GM crops appear to be limited in contrast to existing variations among conventional varieties resulting from breeding, mutation, and natural mobile genetic elements. Allergenic potential is assessed when selecting genes for introduction into GM crops and remains a theoretical risk to date. Emerging weed and insect resistance is not unique to GM technology and will require the use of integrated pest management/best practices for pest control. Gene flow from GM crops to wild relatives is limited by existing biological barriers but can at time be a relevant consideration in gene selection and planting practices. Insect-resistant GM crops have significantly reduced use of chemical insecticides and appear to have reduced the incidence of pesticide poisoning in areas where small scale farming and hand application are common. Changes in herbicide patterns are more complex and are evolving over time in response to weed resistance management needs. Recent public debate is driven by a combination of unfounded allegations about the technology and purveyors, pseudoscience, and attempts to apply a strict precautionary principle.

  7. Average Amount and Stability of Available Agro-Climate Resources in the Main Maize Cropping Regions in China during 1981-2010

    NASA Astrophysics Data System (ADS)

    Zhao, Jin; Yang, Xiaoguang

    2018-02-01

    The available agro-climate resources that can be absorbed and converted into dry matter could directly affect crop growth and yield under climate change. Knowledge of the average amount and stability of available agro-climate resources for maize in the main cropping regions of China under climate change is essential for farmers and advisors to optimize cropping choices and develop adaptation strategies under limited resources. In this study, the three main maize cropping regions in China—the North China spring maize region (NCS), the Huanghuaihai summer maize region (HS), and the Southwest China mountain maize region (SCM)—were selected as study regions. Based on observed solar radiation, temperature, and precipitation data, we analyzed the spatial distributions and temporal trends in the available agro-climate resources for maize during 1981-2010. During this period, significantly prolonged climatological growing seasons for maize [3.3, 2.0, and 4.7 day (10 yr)-1 in NCS, HS, and SCM] were found in all three regions. However, the spatiotemporal patterns of the available agro-climate resources differed among the three regions. The available heating resources for maize increased significantly in the three regions, and the rates of increase were higher in NCS [95.5°C day (10 yr)-1] and SCM [93.5°C day (10 yr)-1] than that in HS [57.7°C day (10 yr)-1]. Meanwhile, decreasing trends in the available water resources were found in NCS [-5.3 mm (10 yr)-1] and SCM [-5.8 mm (10 yr)-1], whereas an increasing trend was observed in HS [3.0 mm (10 yr)-1]. Increasing trends in the available radiation resources were found in NCS [20.9 MJ m-2 (10 yr)-1] and SCM [25.2 MJ m-2 (10 yr)-1], whereas a decreasing trend was found in HS [11.6 MJ m-2 (10 yr)-1]. Compared with 1981-90, the stability of all three resource types decreased during 1991-2000 and 2001-10 in the three regions. More consideration should be placed on the extreme events caused by more intense climate fluctuations

  8. The Implications of Growing Bioenergy Crops on Water Resources, Carbon and Nitrogen Dynamics

    NASA Astrophysics Data System (ADS)

    Jain, A. K.; Song, Y.; Kheshgi, H. S.

    2016-12-01

    What is the potential for the crops Corn, Miscanthus and switchgrass to meet future energy demands in the U.S.A., and would they mitigate climate change by offsetting fossil fuel greenhouse gas (GHG) emissions? The large-scale cultivation of these bioenergy crops itself could also drive climate change through changes in albedo, evapotranspiration (ET), and GHG emissions. Whether these climate effects will mitigate or exacerbate climate change in the short- and long-term is uncertain. This uncertainty stems from our incomplete understanding of the effects of expanded bioenergy crop production on terrestrial water and energy balance, carbon and nitrogen dynamics, and their interactions. This study aims to understand the implications of growing large-scale bioenergy crops on water resources, carbon and nitrogen dynamics in the United States using a data-modeling framework (ISAM) that we developed. Our study indicates that both Miscanthus and Cave-in-Rock switchgrass can attain high and stable yield over parts of the Midwest, however, this high production is attained at the cost of increased soil water loss as compared to current natural vegetation. Alamo switchgrass can attain high and stable yield in the southern US without significant influence on soil water quantity.

  9. Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production

    PubMed Central

    Fita, Ana; Rodríguez-Burruezo, Adrián; Boscaiu, Monica; Prohens, Jaime; Vicente, Oscar

    2015-01-01

    World population is expected to reach 9.2 × 109 people by 2050. Feeding them will require a boost in crop productivity using innovative approaches. Current agricultural production is very dependent on large amounts of inputs and water availability is a major limiting factor. In addition, the loss of genetic diversity and the threat of climate change make a change of paradigm in plant breeding and agricultural practices necessary. Average yields in all major crops are only a small fraction of record yields, and drought and soil salinity are the main factors responsible for yield reduction. Therefore there is the need to enhance crop productivity by improving crop adaptation. Here we review the present situation and propose the development of crops tolerant to drought and salt stress for addressing the challenge of dramatically increasing food production in the near future. The success in the development of crops adapted to drought and salt depends on the efficient and combined use of genetic engineering and traditional breeding tools. Moreover, we propose the domestication of new halophilic crops to create a ‘saline agriculture’ which will not compete in terms of resources with conventional agriculture. PMID:26617620

  10. Food security: increasing yield and improving resource use efficiency.

    PubMed

    Parry, Martin A J; Hawkesford, Malcolm J

    2010-11-01

    Food production and security will be a major issue for supplying an increasing world population. The problem will almost certainly be exacerbated by climate change. There is a projected need to double food production by 2050. In recent times, the trend has been for incremental modest yield increases for most crops. There is an urgent need to develop integrated and sustainable approaches that will significantly increase both production per unit land area and the resource use efficiency of crops. This review considers some key processes involved in plant growth and development with some examples of ways in which molecular technology, plant breeding and genetics may increase the yield and resource use efficiency of wheat. The successful application of biotechnology to breeding is essential to provide the major increases in production required. However, each crop and each specific agricultural situation presents specific requirements and targets for optimisation. Some increases in production will come about as new varieties are developed which are able to produce satisfactory crops on marginal land presently not considered appropriate for arable crops. Other new varieties will be developed to increase both yield and resource use efficiency on the best land.

  11. Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement

    PubMed Central

    Ronald, Pamela C.

    2014-01-01

    Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability. PMID:24915201

  12. 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.

  13. Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora.

    PubMed

    Sánchez, Miguel A; Cid, Pablo; Navarrete, Humberto; Aguirre, Carlos; Chacón, Gustavo; Salazar, Erika; Prieto, Humberto

    2016-02-01

    The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen-mediated gene flow from GM crops and non-GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national-scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from 'very low' (1) to 'very high' (5)] was developed, showing medium OPs (3) for GM-native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape-Vitis vinifera GM-introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  14. Genetic Resources in the "Calabaza Pipiana" Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models.

    PubMed

    Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E

    2018-01-01

    Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma , known in Mexico as calabaza pipiana , and its wild relative C. argyrosperma ssp. sororia . The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia , and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia , in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies' distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies ( H E = 0.428 in sororia , and H E = 0.410 in argyrosperma ). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation ( F ST ) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low

  15. Improving salinity tolerance of plants through conventional breeding and genetic engineering: An analytical comparison.

    PubMed

    Ashraf, Muhammad; Akram, Nudrat Aisha

    2009-01-01

    The last century has witnessed a substantial improvement in yield potential, quality and disease resistance in crops. This was indeed the outcome of conventional breeding, which was achieved with little or no knowledge of underlying physiological and biochemical phenomena related to a trait. Also the resources utilized on programs involving conventional breeding were not of great magnitude. Plant breeders have also been successful during the last century in producing a few salt-tolerant cultivars/lines of some potential crops through conventional breeding, but this again has utilized modest resources. However, this approach seems now inefficient due to a number of reasons, and alternatively, genetic engineering for improving crop salt tolerance is being actively followed these days by the plant scientists, world-over. A large number of transgenic lines with enhanced salt tolerance of different crops can be deciphered from the literature but up to now only a very few field-tested cultivars/lines are known despite the fact that considerable resources have been expended on the sophisticated protocols employed for generating such transgenics. This review analytically compares the achievements made so far in terms of producing salt-tolerant lines/cultivars through conventional breeding or genetic engineering.

  16. The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions.

    PubMed

    Cheeseman, John M

    2015-04-01

    The effective development of salt tolerant crops requires an understanding that the evolution of halophytes, glycophytes and our major grain crops has involved significantly different processes. Halophytes (and other edaphic endemics) generally arose through colonization of habitats in severe disequilibrium by pre-adapted individuals, rather than by gradual adaptation from populations of 'glycophytes'. Glycophytes, by contrast, occur in low sodium ecosystems, where sodium was and is the major limiting nutrient in herbivore diets, suggesting that their evolution reflects the fact that low sodium individuals experienced lower herbivory and had higher fitness. For domestication/evolution of crop plants, the selective pressure was human imposed and involved humans co-opting functions of defense and reproductive security. Unintended consequences of this included loss of tolerance to various stresses and loss of the genetic variability needed to correct that. Understanding, combining and manipulating all three modes of evolution are now critical to the development of salt tolerant crops, particularly those that will offer food security in countries with few economic resources and limited infrastructure. Such efforts will require exploiting the genetic structures of recently evolved halophytes, the genetic variability of model plants, and endemic halophytes and 'minor' crops that already exist. © 2014 The Author. New Phytologist © 2014 New Phytologist Trust.

  17. Breakthrough in chloroplast genetic engineering of agronomically important crops

    PubMed Central

    Daniell, Henry; Kumar, Shashi; Dufourmantel, Nathalie

    2012-01-01

    Chloroplast genetic engineering offers several unique advantages, including high-level transgene expression, multi-gene engineering in a single transformation event and transgene containment by maternal inheritance, as well as a lack of gene silencing, position and pleiotropic effects and undesirable foreign DNA. More than 40 transgenes have been stably integrated and expressed using the tobacco chloroplast genome to confer desired agronomic traits or express high levels of vaccine antigens and biopharmaceuticals. Despite such significant progress, this technology has not been extended to major crops. However, highly efficient soybean, carrot and cotton plastid transformation has recently been accomplished through somatic embryogenesis using species-specific chloroplast vectors. This review focuses on recent exciting developments in this field and offers directions for further research and development. PMID:15866001

  18. 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

  19. Safety of Pseudomonas chlororaphis as a gene source for genetically modified crops.

    PubMed

    Anderson, Jennifer A; Staley, Jamie; Challender, Mary; Heuton, Jamie

    2018-02-01

    Genetically modified crops undergo extensive evaluation to characterize their food, feed and environmental safety prior to commercial introduction, using a well-established, science-based assessment framework. One component of the safety assessment includes an evaluation of each introduced trait, including its source organism, for potential adverse pathogenic, toxic and allergenic effects. Several Pseudomonas species have a history of safe use in agriculture and certain species represent a source of genes with insecticidal properties. The ipd072Aa gene from P. chlororaphis encodes the IPD072Aa protein, which confers protection against certain coleopteran pests when expressed in maize plants. P. chlororaphis is ubiquitous in the environment, lacks known toxic or allergenic properties, and has a history of safe use in agriculture and in food and feed crops. This information supports, in part, the safety assessment of potential traits, such as IPD072Aa, that are derived from this source organism.

  20. The impact of Genetically Modified (GM) crops in modern agriculture: A review.

    PubMed

    Raman, Ruchir

    2017-10-02

    Genetic modification in plants was first recorded 10,000 years ago in Southwest Asia where humans first bred plants through artificial selection and selective breeding. Since then, advancements in agriculture science and technology have brought about the current GM crop revolution. GM crops are promising to mitigate current and future problems in commercial agriculture, with proven case studies in Indian cotton and Australian canola. However, controversial studies such as the Monarch Butterfly study (1999) and the Séralini affair (2012) along with current problems linked to insect resistance and potential health risks have jeopardised its standing with the public and policymakers, even leading to full and partial bans in certain countries. Nevertheless, the current growth rate of the GM seed market at 9.83-10% CAGR along with promising research avenues in biofortification, precise DNA integration and stress tolerance have forecast it to bring productivity and prosperity to commercial agriculture.

  1. Integration of georeferencing, habitat, sampling, and genetic data for documentation of wild plant genetic resources

    USDA-ARS?s Scientific Manuscript database

    Plant genetic resource collections provide novel materials to the breeding and research communities. Availability of detailed documentation of passport, phenotypic, and genetic data increases the value of the genebank accessions. Inclusion of georeferenced sources, habitats, and sampling data in co...

  2. The Importance of Juvenile Root Traits for Crop Yields

    NASA Astrophysics Data System (ADS)

    White, Philip; Adu, Michael; Broadley, Martin; Brown, Lawrie; Dupuy, Lionel; George, Timothy; Graham, Neil; Hammond, John; Hayden, Rory; Neugebauer, Konrad; Nightingale, Mark; Ramsay, Gavin; Thomas, Catherine; Thompson, Jacqueline; Wishart, Jane; Wright, Gladys

    2014-05-01

    Genetic variation in root system architecture (RSA) is an under-exploited breeding resource. This is partly a consequence of difficulties in the rapid and accurate assessment of subterranean root systems. However, although the characterisation of root systems of large plants in the field are both time-consuming and labour-intensive, high-throughput (HTP) screens of root systems of juvenile plants can be performed in the field, glasshouse or laboratory. It is hypothesised that improving the root systems of juvenile plants can accelerate access to water and essential mineral elements, leading to rapid crop establishment and, consequently, greater yields. This presentation will illustrate how aspects of the juvenile root systems of potato (Solanum tuberosum L.) and oilseed rape (OSR; Brassica napus L.) correlate with crop yields and examine the reasons for such correlations. It will first describe the significant positive relationships between early root system development, phosphorus acquisition, canopy establishment and eventual yield among potato genotypes. It will report the development of a glasshouse assay for root system architecture (RSA) of juvenile potato plants, the correlations between root system architectures measured in the glasshouse and field, and the relationships between aspects of the juvenile root system and crop yields under drought conditions. It will then describe the development of HTP systems for assaying RSA of OSR seedlings, the identification of genetic loci affecting RSA in OSR, the development of mathematical models describing resource acquisition by OSR, and the correlations between root traits recorded in the HTP systems and yields of OSR in the field.

  3. Risk assessment of genetically engineered crops: fitness effects of virus-resistance transgenes in wild Cucurbita pepo.

    PubMed

    Laughlin, Karen D; Power, Alison G; Snow, Allison A; Spencer, Lawrence J

    2009-07-01

    The development of crops genetically engineered for pathogen resistance has raised concerns that crop-to-wild gene flow could release wild or weedy relatives from regulation by the pathogens targeted by the transgenes that confer resistance. Investigation of these risks has also raised questions about the impact of gene flow from conventional crops into wild plant populations. Viruses in natural plant populations can play important roles in plant fecundity and competitive interactions. Here, we show that virus-resistance transgenes and conventional crop genes can increase fecundity of wild plants under virus pressure. We asked how gene flow from a cultivated squash (Cucurbita pepo) engineered for virus resistance would affect the fecundity of wild squash (C. pepo) in the presence and absence of virus pressure. A transgenic squash cultivar was crossed and backcrossed with wild C. pepo from Arkansas. Wild C. pepo, transgenic backcross plants, and non-transgenic backcross plants were compared in field plots in Ithaca, New York, USA. The second and third generations of backcrosses (BC2 and BC3) were used in 2002 and 2003, respectively. One-half of the plants were inoculated with zucchini yellow mosaic virus (ZYMV), and one-half of the plants were maintained as healthy controls. Virus pressure dramatically decreased the fecundity of wild C. pepo plants and non-transgenic backcross plants relative to transgenic backcross plants, which showed continued functioning of the virus-resistance transgene. In 2002, non-transgenic backcross fecundity was slightly higher than wild C. pepo fecundity under virus pressure, indicating a possible benefit of conventional crop alleles, but they did not differ in 2003 when fecundity was lower in both groups. We detected no fitness costs of the transgene in the absence of the virus. If viruses play a role in the population dynamics of wild C. pepo, we predict that gene flow from transgenic, virus-resistant squash and, to a much lesser

  4. Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

    PubMed Central

    Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

    2018-01-01

    Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene

  5. Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators

    PubMed Central

    Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E.; Racine, Ben; Clarke, John; Clarke, Lauren; Gillanders, Elizabeth; Feuer, Eric J.

    2013-01-01

    Summary: Many simulation methods and programs have been developed to simulate genetic data of the human genome. These data have been widely used, for example, to predict properties of populations retrospectively or prospectively according to mathematically intractable genetic models, and to assist the validation, statistical inference and power analysis of a variety of statistical models. However, owing to the differences in type of genetic data of interest, simulation methods, evolutionary features, input and output formats, terminologies and assumptions for different applications, choosing the right tool for a particular study can be a resource-intensive process that usually involves searching, downloading and testing many different simulation programs. Genetic Simulation Resources (GSR) is a website provided by the National Cancer Institute (NCI) that aims to help researchers compare and choose the appropriate simulation tools for their studies. This website allows authors of simulation software to register their applications and describe them with well-defined attributes, thus allowing site users to search and compare simulators according to specified features. Availability: http://popmodels.cancercontrol.cancer.gov/gsr. Contact: gsr@mail.nih.gov PMID:23435068

  6. The myth of natural barriers. Is transgene introgression by genetically modified crops an environmental risk?

    PubMed

    Guarnieri, Vincenzo; Benessia, Alice; Camino, Elena; Barbiero, Giuseppe

    2008-01-01

    Genetically modified (GM) crops under open field conditions are a complex and controversial issue. Ecologists are discussing about the possibility that a transgene belonging to GM plants could spread to native populations through a process known as introgression the stable incorporation of a gene in the host genome able to generate a differentiated population. The ecological consequences of a transgene introgression in plants or bacteria are not yet well understood, but could be significant. In this critical review we consider vertical and horizontal introgression. We analyse the biochemical and genetic constraints, and environmental factors that limit the possibility of transgene spread; meanwhile we show cases in which the natural barriers are overcome. Then we discuss the overall management of GM crops, noting the shortcomings and approximations of risk assessment based on linear thinking typical of the biomolecular approach. Finally we suggest to explicitly weight facts together with values and we encourage the undertaking of an ecological perspective, encompassing the complexity of (non-linear) relations between organisms and the environment.

  7. Genomics of crop wild relatives: expanding the gene pool for crop improvement.

    PubMed

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert J

    2016-04-01

    Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  8. Characteristics and safety assessment of intractable proteins in genetically modified crops.

    PubMed

    Bushey, Dean F; Bannon, Gary A; Delaney, Bryan F; Graser, Gerson; Hefford, Mary; Jiang, Xiaoxu; Lee, Thomas C; Madduri, Krishna M; Pariza, Michael; Privalle, Laura S; Ranjan, Rakesh; Saab-Rincon, Gloria; Schafer, Barry W; Thelen, Jay J; Zhang, John X Q; Harper, Marc S

    2014-07-01

    Genetically modified (GM) crops may contain newly expressed proteins that are described as "intractable". Safety assessment of these proteins may require some adaptations to the current assessment procedures. Intractable proteins are defined here as those proteins with properties that make it extremely difficult or impossible with current methods to express in heterologous systems; isolate, purify, or concentrate; quantify (due to low levels); demonstrate biological activity; or prove equivalency with plant proteins. Five classes of intractable proteins are discussed here: (1) membrane proteins, (2) signaling proteins, (3) transcription factors, (4) N-glycosylated proteins, and (5) resistance proteins (R-proteins, plant pathogen recognition proteins that activate innate immune responses). While the basic tiered weight-of-evidence approach for assessing the safety of GM crops proposed by the International Life Sciences Institute (ILSI) in 2008 is applicable to intractable proteins, new or modified methods may be required. For example, the first two steps in Tier I (hazard identification) analysis, gathering of applicable history of safe use (HOSU) information and bioinformatics analysis, do not require protein isolation. The extremely low level of expression of most intractable proteins should be taken into account while assessing safety of the intractable protein in GM crops. If Tier II (hazard characterization) analyses requiring animal feeding are judged to be necessary, alternatives to feeding high doses of pure protein may be needed. These alternatives are discussed here. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Enhancing the crops to feed the poor.

    PubMed

    Huang, Jikun; Pray, Carl; Rozelle, Scott

    2002-08-08

    Solutions to the problem of how the developing world will meet its future food needs are broader than producing more food, although the successes of the 'Green Revolution' demonstrate the importance of technology in generating the growth in food output in the past. Despite these successes, the world still faces continuing vulnerability to food shortages. Given the necessary funding, it seems likely that conventional crop breeding, as well as emerging technologies based on molecular biology, genetic engineering and natural resource management, will continue to improve productivity in the coming decades.

  10. GeneEd—A Genetics Educational Resource | NIH MedlinePlus the Magazine

    MedlinePlus

    ... of this page please turn Javascript on. Feature: Genetics 101 GeneEd — A Genetics Educational Resource Past Issues / Summer 2013 Table of ... GeneEd website as part of her lessons on genetics. A recently developed educational website about genetics— GeneEd. ...

  11. Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects.

    PubMed

    Bohra, Abhishek; Pandey, Manish K; Jha, Uday C; Singh, Balwant; Singh, Indra P; Datta, Dibendu; Chaturvedi, Sushil K; Nadarajan, N; Varshney, Rajeev K

    2014-06-01

    Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops. The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

  12. 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.

  13. Factors influencing U.S. consumer support for genetic modification to prevent crop disease.

    PubMed

    McComas, Katherine A; Besley, John C; Steinhardt, Joseph

    2014-07-01

    This study examines support for the genetic modification (GM) of crops in the context of preventing "late blight," a devastating potato and tomato disease that caused the Irish Potato Famine in the 1850s and results in substantial crop loss today. We surveyed U.S. adults who do the primary grocery shopping in their household (n = 859). Half of the respondents were randomly assigned to read a vignette describing late blight before responding to questions about GM, whereas the other half read a vignette about generic crop disease before responding to questions. We also examine how the perceived fairness of decision makers relates to GM support and the perceived legitimacy of GM decision making. We found that disease specificity mattered less to support and legitimacy than the perceived fairness of decision makers. The perceived risks of GM to human and environmental health negatively related to GM support and legitimacy, whereas the perceived benefits (e.g. reduced threats to crops and a more secure food supply) positively related to support and legitimacy. Objective knowledge about GM had a small, negative relationship with legitimacy whereas self-assessed familiarity with GM had a positive relationship. Overall, the results offer additional confirmation of past findings from more localized settings that perceived fairness of decision makers matters to support for GM and underscore the importance of considering how risk managers' behaviors and actions are perceived alongside individuals' perceptions about the risks and benefits. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Evaluation and characterization of a genetically diverse Musa germplasm core subset.

    USDA-ARS?s Scientific Manuscript database

    The USDA-ARS, Tropical Agriculture Research Station is responsible for curating germplasm of several regionally and internationally important agricultural crops. Evaluation and characterization of Musa (bananas) genetic resources are an important component of programmed research. In a global coll...

  15. Impacts on Water Management and Crop Production of Regional Cropping System Adaptation to Climate Change

    NASA Astrophysics Data System (ADS)

    Zhong, H.; Sun, L.; Tian, Z.; Liang, Z.; Fischer, G.

    2014-12-01

    China is one of the most populous and fast developing countries, also faces a great pressure on grain production and food security. Multi-cropping system is widely applied in China to fully utilize agro-climatic resources and increase land productivity. As the heat resource keep improving under climate warming, multi-cropping system will also shifting northward, and benefit crop production. But water shortage in North China Plain will constrain the adoption of new multi-cropping system. Effectiveness of multi-cropping system adaptation to climate change will greatly depend on future hydrological change and agriculture water management. So it is necessary to quantitatively express the water demand of different multi-cropping systems under climate change. In this paper, we proposed an integrated climate-cropping system-crops adaptation framework, and specifically focused on: 1) precipitation and hydrological change under future climate change in China; 2) the best multi-cropping system and correspondent crop rotation sequence, and water demand under future agro-climatic resources; 3) attainable crop production with water constraint; and 4) future water management. In order to obtain climate projection and precipitation distribution, global climate change scenario from HADCAM3 is downscaled with regional climate model (PRECIS), historical climate data (1960-1990) was interpolated from more than 700 meteorological observation stations. The regional Agro-ecological Zone (AEZ) model is applied to simulate the best multi-cropping system and crop rotation sequence under projected climate change scenario. Finally, we use the site process-based DSSAT model to estimate attainable crop production and the water deficiency. Our findings indicate that annual land productivity may increase and China can gain benefit from climate change if multi-cropping system would be adopted. This study provides a macro-scale view of agriculture adaptation, and gives suggestions to national

  16. Developing educational resources for population genetics in R: An open and collaborative approach

    USDA-ARS?s Scientific Manuscript database

    The R computing and statistical language community has developed a myriad of resources for conducting populations genetic analyses. However, resources for learning how to carry out population genetic analyses in R are scattered and often incomplete, which can make acquiring this skill unnecessarily ...

  17. Putting the Pieces Together: Clinically Relevant Genetic and Genomic Resources for Hospitalists and Neonatologists.

    PubMed

    Miller, Rebecca; Khromykh, Alina; Babcock, Holly; Jenevein, Callie; Solomon, Benjamin D

    2017-02-01

    Genetic conditions are individually rare but are common in aggregate, and they often present in the neonatal and early pediatric periods. These conditions are often severe, can be difficult to diagnose and manage, and may heavily affect patients, families, health care systems, and society. Because of recent technological advances, the availability and uptake of genetic and genomic testing are increasing rapidly. However, there is a dearth of trained geneticists and genetic counselors to help guide and explain these conditions and relevant tests. To help hospitalists, neonatologists, and related practitioners navigate this complex and evolving field, we have compiled a list of free (mostly Web-based) resources relevant to the diagnosis and management of genetic conditions and related disorders. These resources, which we describe individually, can be useful for nongeneticist clinicians, and some also include material that can be used to explain concepts and conditions to patients or families. The resources presented are divided into the following categories (which overlap): general information, databases of genetic conditions, resources that can help generate differential diagnoses, databases of genetic testing laboratories (to help with logistics of ordering tests), information on newborn screening, and other resources. We also include a separate list of helpful textbooks and manuals. We conclude with 2 examples describing how some of these resources would be used by a pediatric hospitalist or neonatologist during the inpatient management of a child with a suspected genetic condition. Copyright © 2017 by the American Academy of Pediatrics.

  18. Proceedings of the third ISHS international symposium of plant genetic resources volume 1

    USDA-ARS?s Scientific Manuscript database

    The Third International ISHS Symposium on plant genetic resources occurred as Symposium 12 of the International Horticulture Congress in Lisbon, in August 2010. This symposium lasted4 days and emphasized new tools in plant genetic resource management. Six speakers gave invited presentations, and 30 ...

  19. Proceedings of the third ISHS international symposium on plant genetic resources volume 2

    USDA-ARS?s Scientific Manuscript database

    The Third International ISHS Symposium on plant genetic resources occurred as Symposium 12 of the International Horticulture Congress in Lisbon, in August 2010. This symposium lasted4 days and emphasized new tools in plant genetic resource management. Six speakers gave invited presentations, and 30 ...

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. [Genetic variability of the Bemisia tabaci (Gennadius) biotype B (Hemiptera: Aleyrodidae) in vegetable crops in São Luís, state of Maranhão, Brazil].

    PubMed

    Da Silva, Maria C; De Lemos, Raimunda N S; Lima, Luzia H C; Gourlart Filho, Luiz R; Pereira, Silma R F

    2009-01-01

    The RAPD technique is widely used to investigate the distinct genetic characteristics of the complex Bemisia tabaci (Gennadius), which is currently constituted of approximately 41 biotypes. The objective of this research was to characterize populations of whitefly collected in crops of agricultural producing areas in São Luís, MA, like okra, beans and pepper, using RAPD molecular markers. Females from nine whitefly populations were analyzed and compared with B. tabaci biotype B taken from poinsettia culture of Embrapa Genetic Resources and Biotechnology (Brasília, DF). Twelve out of the 20 primers tested produced specific band patterns suitable to confirm that the evaluated specimens belong to the biotype B of B. tabaci, despite the high percentage of detected polymorphism. The analysis of the 96 RAPD molecular markers generated indicated that the populations on okra, beans and pepper were grouped according to the host cultures, sharing 80, 76 and 45% of genetic similarity, respectively, when compared with the control population of B. tabaci biotype B. A lower selective pressure was observed with the population of whitefly collected on pepper and minor genetic variability in the whitefly populations collected on okra and bean, when compared with the control population.

  5. The genetic makeup of a global barnyard millet germplasm collection

    USDA-ARS?s Scientific Manuscript database

    Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this cro...

  6. [The public perception of information about the potential risks of genetically modified crops in the food chain].

    PubMed

    Furnival, Ariadne Chloë; Pinheiro, Sônia Maria

    2008-01-01

    At a time when genetically modified (GM) crops are entering the Brazilian food chain, we present the findings of a study that makes use of a qualitative technique involving focal groups to look into the public's interpretation of the information available about this biotechnological innovation. This methodology produced results that revealed the interconnections drawn by the research subjects between this form of biotechnology, changes to the environment, and food production in general. The mistrust expressed about GM crops was particularly attributed by the participants to the non-availability of comprehensible information in the mass media or on product labels.

  7. The socioeconomics of genetically modified biofortified crops: a systematic review and meta-analysis.

    PubMed

    De Steur, Hans; Wesana, Joshua; Blancquaert, Dieter; Van Der Straeten, Dominique; Gellynck, Xavier

    2017-02-01

    Building upon the growing interest and research on genetically modified (GM) biofortification, its socioeconomic potential has been increasingly examined. We conducted two systematic reviews and meta-analyses to provide comprehensive evidence of consumers' willingness to pay (11 economic valuation studies, 64 estimates) and cost-effectiveness/benefits (five economic evaluation studies, 30 estimates). Worldwide, consumers were willing to pay 23.9% more for GM biofortified food crops. Aside from crop and design-related differences, information provision was deemed crucial. Positive information (nutrition and GM benefits) is associated with the highest consumer willingness to pay, compared with negative, objective, and conflicting GM information, especially when negative information was mentioned last. This health intervention would reduce the aggregated micronutrient deficiency burden in Asia (15.6 million disability-adjusted life years (DALYs)) by 12.5-51.4%, at a low cost of USD 7.9-27.8 per DALY in a pessimistic and optimistic scenario, respectively. Given that GM biofortified crops could tackle hidden hunger in a cost-effective and well-accepted way, its implementation is worth pursuing. A case study on folate biofortification further elaborates on the importance of socioeconomic research and the determinants of their market potential. © 2016 New York Academy of Sciences.

  8. Conserving and managing the trees of the future: genetic resources for Pacific Northwest forests.

    Treesearch

    Sally Duncan

    2003-01-01

    Genetic resource management has historically called for altering the genetic structure of plant populations through selection for traits of interest such as rapid growth. Although this is still a principal component of tree breeding programs in the Pacific Northwest, managing genetic resources now also brings a clear focus on retaining a broad diversity within and...

  9. Land Use, Yield and Quality Changes of Minor Field Crops: Is There Superseded Potential to Be Reinvented in Northern Europe?

    PubMed

    Peltonen-Sainio, Pirjo; Jauhiainen, Lauri; Lehtonen, Heikki

    2016-01-01

    Diversification of agriculture was one of the strengthened aims of the greening payment of European Agricultural Policy (CAP) as diversification provides numerous ecosystems services compared to cereal-intensive crop rotations. This study focuses on current minor crops in Finland that have potential for expanded production and considers changes in their cropping areas, yield trends, breeding gains, roles in crop rotations and potential for improving resilience. Long-term datasets of Natural Resources Institute Finland and farmers' land use data from the Agency of Rural Affairs were used to analyze the above-mentioned trends and changes. The role of minor crops in rotations declined when early and late CAP periods were compared and that of cereal monocultures strengthened. Genetic yield potentials of minor crops have increased as also genetic improvements in quality traits, although some typical trade-offs with improved yields have also appeared. However, the gap between potential and attained yields has expanded, depending on the minor crop, as national yield trends have either stagnated or declined. When comparing genetic improvements of minor crops to those of the emerging major crop, spring wheat, breeding achievements in minor crops were lower. It was evident that the current agricultural policies in the prevailing market and the price environment have not encouraged cultivation of minor crops but further strengthened the role of cereal monocultures. We suggest optimization of agricultural land use, which is a core element of sustainable intensification, as a future means to couple long-term environmental sustainability with better success in economic profitability and social acceptability. This calls for development of effective policy instruments to support farmer's diversification actions.

  10. Land Use, Yield and Quality Changes of Minor Field Crops: Is There Superseded Potential to Be Reinvented in Northern Europe?

    PubMed Central

    Peltonen-Sainio, Pirjo; Jauhiainen, Lauri; Lehtonen, Heikki

    2016-01-01

    Diversification of agriculture was one of the strengthened aims of the greening payment of European Agricultural Policy (CAP) as diversification provides numerous ecosystems services compared to cereal-intensive crop rotations. This study focuses on current minor crops in Finland that have potential for expanded production and considers changes in their cropping areas, yield trends, breeding gains, roles in crop rotations and potential for improving resilience. Long-term datasets of Natural Resources Institute Finland and farmers’ land use data from the Agency of Rural Affairs were used to analyze the above-mentioned trends and changes. The role of minor crops in rotations declined when early and late CAP periods were compared and that of cereal monocultures strengthened. Genetic yield potentials of minor crops have increased as also genetic improvements in quality traits, although some typical trade-offs with improved yields have also appeared. However, the gap between potential and attained yields has expanded, depending on the minor crop, as national yield trends have either stagnated or declined. When comparing genetic improvements of minor crops to those of the emerging major crop, spring wheat, breeding achievements in minor crops were lower. It was evident that the current agricultural policies in the prevailing market and the price environment have not encouraged cultivation of minor crops but further strengthened the role of cereal monocultures. We suggest optimization of agricultural land use, which is a core element of sustainable intensification, as a future means to couple long-term environmental sustainability with better success in economic profitability and social acceptability. This calls for development of effective policy instruments to support farmer’s diversification actions. PMID:27870865

  11. Standards of Practice: Applying Genetics and Genomics Resources to Oncology
.

    PubMed

    Kerber, Alice S; Ledbetter, Nancy J

    2017-04-01

    Knowledge about genetics and genomics and its application to oncology care is rapidly expanding and evolving. As a result, oncology nurses at all levels must develop and maintain their knowledge of genetics and genomics, as well as be aware of resources to guide practice. This article focuses on implementation of the standards described in the updated Genetics/Genomics Nursing: Scope and Standards of Practice by the basic practitioner.
.

  12. Assessing genetic diversity of wild Southeastern American Vaccinium species using microsatellite markers

    USDA-ARS?s Scientific Manuscript database

    The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, preserves genetic resources of fruit crops. This genebank contains more than 1700 Vaccinium accessions from 33 countries. Wild species representat...

  13. The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

    PubMed Central

    Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

    2008-01-01

    The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

  14. Oilseed crops as renewable sources of industrial chemicals

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

    McKeon, T.A.; Lin, Jiann-Tsyh; Goodrich-Tanrikulu, M.

    1995-12-01

    The presence of specific functional groups on a fatty acid confers value for industrial uses. The plant kingdom contains numerous examples of plants that produce seed oils containing fatty acids with epoxy groups, hydroxyl groups, triple bonds or with unusual double bond positions. These fatty acids can be used directly or are readily modified for use in specialty lubricants, plastics and coatings. Many of these plants are not cultivated in the U.S. due to unsuitable climate or growth habit. Such plants provide a source of genes coding for enzymes that will carry out the desired fatty acid modification. Genetic technologymore » allows the transfer of these genes into domestically grown crops such as rapeseed or soybean, with consequent production of the desired fatty acid in the seed oil. One biotechnology company has commercialized a transgenic oilseed crop with an altered fatty acid composition. This talk will review current and projected plans for developing oilseed crops to serve as renewable resources that meet current industrial needs or provide chemical feedstocks for new uses.« less

  15. Genetically Engineered Crops and Certified Organic Agriculture for Improving Nutrition Security in Africa and South Asia.

    PubMed

    Pray, Carl; Ledermann, Samuel

    2016-01-01

    In Africa and South Asia, where nutrition insecurity is severe, two of the most prominent production technologies are genetically modified (GM) crops and certified organic agriculture. We analyze the potential impact pathways from agricultural production to nutrition. Our review of data and the literature reveals increasing farm-level income from cash crop production as the main pathway by which organic agriculture and GM agriculture improve nutrition. Potential secondary pathways include reduced prices of important food crops like maize due to GM maize production and increased food production using organic technology. Potential tertiary pathways are improvements in health due to reduced insecticide use. Challenges to the technologies achieving their impact include the politics of GM agriculture and the certification costs of organic agriculture. Given the importance of agricultural production in addressing nutrition security, accentuated by the post-2015 sustainable development agenda, the chapter concludes by stressing the importance of private and public sector research in improving the productivity and adoption of both GM and organic crops. In addition, the chapter reminds readers that increased farm income and productivity require complementary investments in health, education, food access and women's empowerment to actually improve nutrition security. © 2016 S. Karger AG, Basel.

  16. Transgenic horticultural crops in Asia

    USDA-ARS?s Scientific Manuscript database

    Modern biotechnology applications, including genetic engineering, are a powerful tool to complement the conventional methods of crop improvement. Asia currently has three countries cultivating biotech/transgenic crops – China, India, and the Philippines, but only China commercially grows a transgen...

  17. Sphenostylis stenocarpa (ex. A. Rich.) Harms., a Fading Genetic Resource in a Changing Climate: Prerequisite for Conservation and Sustainability

    PubMed Central

    Nnamani, Catherine Veronica; Ajayi, Sunday Adesola; Oselebe, Happiness Ogba; Atkinson, Christopher John; Igboabuchi, Anastasia Ngozi

    2017-01-01

    The southeastern part of Nigeria is one of the major hotspots of useful plant genetic resources. These endemic species are associated with a rich indigenous knowledge and cultural diversity in relation to their use and conservation. Sphenostylis stenocarpa (ex. A. Rich.) Harms., (African Yam Bean (AYB)), is one such crop within the family of Fabaceae. Its nutritional and eco-friendly characteristics have value in ameliorating malnutrition, hidden hunger and environmental degradation inherent in resource-poor rural and semi-rural communities throughout Africa. However, lack of information from the custodians of this crop is limiting its sustainable development. Therefore, ethnobotanical surveys on the diversity, uses, and constraints limiting the cultivation and use of the crop in southeastern Nigeria were carried out. Five-hundred respondents were randomly selected and data collected through oral interviews and focused group discussion (FGD). Semi-structured questionnaires (SSQ) were also used to elicit information from a spectrum of AYB users comprising community leaders, farmers, market women and consumers in five States. Results showed that the majority of the respondents lacked formal education and were of the age group of 40–50 years, while the female gender dominated with limited access to land and extension officers. Seed coat colour largely determined utilization. Long cooking time, requirement for staking materials, aging of farmers and low market demand were among the major constraints limiting further cultivation and utilization of AYB. In-situ conservation was by hanging dried fruits by the fireside, beside the house, storing in earthenware, calabash gourds, cans and bottles. It is concluded that there is urgent need to scale up conservation through robust linkages between contemporary scientific domains and indigenous peoples in order to harness and incorporate the rich indigenous knowledge in local communities for enhanced scientific knowledge

  18. Sphenostylis stenocarpa (ex. A. Rich.) Harms., a Fading Genetic Resource in a Changing Climate: Prerequisite for Conservation and Sustainability.

    PubMed

    Nnamani, Catherine Veronica; Ajayi, Sunday Adesola; Oselebe, Happiness Ogba; Atkinson, Christopher John; Igboabuchi, Anastasia Ngozi; Ezigbo, Eucharia Chizoba

    2017-07-12

    The southeastern part of Nigeria is one of the major hotspots of useful plant genetic resources. These endemic species are associated with a rich indigenous knowledge and cultural diversity in relation to their use and conservation. Sphenostylis stenocarpa ( e x. A. Rich.) Harms., (African Yam Bean (AYB)), is one such crop within the family of Fabaceae. Its nutritional and eco-friendly characteristics have value in ameliorating malnutrition, hidden hunger and environmental degradation inherent in resource-poor rural and semi-rural communities throughout Africa. However, lack of information from the custodians of this crop is limiting its sustainable development. Therefore, ethnobotanical surveys on the diversity, uses, and constraints limiting the cultivation and use of the crop in southeastern Nigeria were carried out. Five-hundred respondents were randomly selected and data collected through oral interviews and focused group discussion (FGD). Semi-structured questionnaires (SSQ) were also used to elicit information from a spectrum of AYB users comprising community leaders, farmers, market women and consumers in five States. Results showed that the majority of the respondents lacked formal education and were of the age group of 40-50 years, while the female gender dominated with limited access to land and extension officers. Seed coat colour largely determined utilization. Long cooking time, requirement for staking materials, aging of farmers and low market demand were among the major constraints limiting further cultivation and utilization of AYB. In-situ conservation was by hanging dried fruits by the fireside, beside the house, storing in earthenware, calabash gourds, cans and bottles. It is concluded that there is urgent need to scale up conservation through robust linkages between contemporary scientific domains and indigenous peoples in order to harness and incorporate the rich indigenous knowledge in local communities for enhanced scientific knowledge

  19. Golden Rice and 'Golden' crops for human nutrition.

    PubMed

    Beyer, Peter

    2010-11-30

    Micronutrients are essential for a healthy life. Humans do not produce micronutrients, and hence they must obtain them through the foodchain. Staple crops are the predominant food source of mankind, but need to be complemented by other foodstuffs because they are generally deficient in one or the other micronutrient. Breeding for micronutrient-dense crops is not always a viable option because of the absence of genetic variability for the desired trait. Moreover, sterility issues and the complex genetic makeup of some crop plants make them unamenable to conventional breeding. In these cases, genetic modification remains the only viable option. The tools to produce a number of micronutrients in staple crops have recently become available thanks to the identification of the genes involved in the corresponding biochemical pathways at an unprecedented rate. Discarding genetic modification as a viable option is definitely not in the interest of human wellbeing. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. Recent patents on biosafety strategies of selectable marker genes in genetically modified crops.

    PubMed

    Jiang, Yiming; Hu, Xiaoning; Huang, Haiying

    2014-01-01

    Genetically modified crops (GMCs) have been planted world wide since 1990s, but the potential insecurity of selectable marker genes raises the questions about GMC safety. Therefore, several researches have been conducted on marker gene safety issues and recently several patents have been issued on this subject. There are two main approaches to achieve this goal: seeking the biosafety selectable marker and eliminating these insecure marker genes after transformation. Results show that these two systems are quite effective. Recent patents on the two ways are discussed in this review.

  1. The release of genetically modified crops into the environment. Part I. Overview of current status and regulations.

    PubMed

    Nap, Jan-Peter; Metz, Peter L J; Escaler, Marga; Conner, Anthony J

    2003-01-01

    In the past 6 years, the global area of commercially grown, genetically modified (GM) crops has increased more than 30-fold to over 52 million hectares. The number of countries involved has more than doubled. Especially in developing countries, the GM crop area is anticipated to increase rapidly in the coming years. Despite this high adoption rate and future promises, there is a multitude of concerns about the impact of GM crops on the environment. Regulatory approaches in Europe and North America are essentially different. In the EU, it is based on the process of making GM crops; in the US, on the characteristics of the GM product. Many other countries are in the process of establishing regulation based on either system or a mixture. Despite these differences, the information required for risk assessment tends to be similar. Each risk assessment considers the possibility, probability and consequence of harm on a case-by-case basis. For GM crops, the impact of non-use should be added to this evaluation. It is important that the regulation of risk should not turn into the risk of regulation. The best and most appropriate baseline for comparison when performing risk assessment on GM crops is the impact of plants developed by traditional breeding. The latter is an integral and accepted part of agriculture.

  2. A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-Track Cultivar Development

    PubMed Central

    Welling, Matthew T.; Shapter, Tim; Rose, Terry J.; Liu, Lei; Stanger, Rhia; King, Graham J.

    2016-01-01

    Cannabis is a predominantly diecious phenotypically diverse domesticated genus with few if any extant natural populations. International narcotics conventions and associated legislation have constrained the establishment, characterization, and use of Cannabis genetic resource collections. This has resulted in the underutilization of genepool variability in cultivar development and has limited the inclusion of secondary genepools associated with genetic improvement strategies of the Green Revolution. The structured screening of ex situ germplasm and the exploitation of locally-adapted intraspecific traits is expected to facilitate the genetic improvement of Cannabis. However, limited attempts have been made to establish the full extent of genetic resources available for pre-breeding. We present a thorough critical review of Cannabis ex situ genetic resources, and discuss recommendations for conservation, pre-breeding characterization, and genetic analysis that will underpin future cultivar development. We consider East Asian germplasm to be a priority for conservation based on the prolonged historical cultivation of Cannabis in this region over a range of latitudes, along with the apparent high levels of genetic diversity and relatively low representation in published genetic resource collections. Seed cryopreservation could improve conservation by reducing hybridization and genetic drift that may occur during Cannabis germplasm regeneration. Given the unique legal status of Cannabis, we propose the establishment of a global virtual core collection based on the collation of consistent and comprehensive provenance meta-data and the adoption of high-throughput DNA sequencing technologies. This would enable representative core collections to be used for systematic phenotyping, and so underpin breeding strategies for the genetic improvement of Cannabis. PMID:27524992

  3. A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-Track Cultivar Development.

    PubMed

    Welling, Matthew T; Shapter, Tim; Rose, Terry J; Liu, Lei; Stanger, Rhia; King, Graham J

    2016-01-01

    Cannabis is a predominantly diecious phenotypically diverse domesticated genus with few if any extant natural populations. International narcotics conventions and associated legislation have constrained the establishment, characterization, and use of Cannabis genetic resource collections. This has resulted in the underutilization of genepool variability in cultivar development and has limited the inclusion of secondary genepools associated with genetic improvement strategies of the Green Revolution. The structured screening of ex situ germplasm and the exploitation of locally-adapted intraspecific traits is expected to facilitate the genetic improvement of Cannabis. However, limited attempts have been made to establish the full extent of genetic resources available for pre-breeding. We present a thorough critical review of Cannabis ex situ genetic resources, and discuss recommendations for conservation, pre-breeding characterization, and genetic analysis that will underpin future cultivar development. We consider East Asian germplasm to be a priority for conservation based on the prolonged historical cultivation of Cannabis in this region over a range of latitudes, along with the apparent high levels of genetic diversity and relatively low representation in published genetic resource collections. Seed cryopreservation could improve conservation by reducing hybridization and genetic drift that may occur during Cannabis germplasm regeneration. Given the unique legal status of Cannabis, we propose the establishment of a global virtual core collection based on the collation of consistent and comprehensive provenance meta-data and the adoption of high-throughput DNA sequencing technologies. This would enable representative core collections to be used for systematic phenotyping, and so underpin breeding strategies for the genetic improvement of Cannabis.

  4. Climate Change Impacts on Crop Production in Nigeria

    NASA Astrophysics Data System (ADS)

    Mereu, V.; Gallo, A.; Carboni, G.; Spano, D.

    2011-12-01

    The agricultural sector in Nigeria is particularly important for the country's food security, natural resources, and growth agenda. The cultivable areas comprise more than 70% of the total area; however, the cultivated area is about the 35% of the total area. The most important components in the food basket of the nation are cereals and tubers, which include rice, maize, corn, millet, sorghum, yam, and cassava. These crops represent about 80% of the total agricultural product in Nigeria (from NPAFS). The major crops grown in the country can be divided into food crops (produced for consumption) and export products. Despite the importance of the export crops, the primary policy of agriculture is to make Nigeria self-sufficient in its food and fiber requirements. The projected impacts of future climate change on agriculture and water resources are expected to be adverse and extensive in these area. This implies the need for actions and measures to adapt to climate change impacts, and especially as they affect agriculture, the primary sector for Nigerian economy. In the framework of the Project Climate Risk Analysis in Nigeria (founded by World Bank Contract n.7157826), a study was made to assess the potential impact of climate change on the main crops that characterize Nigerian agriculture. The DSSAT-CSM (Decision Support System for Agrotechnology Transfer - Cropping System Model) software, version 4.5 was used for the analysis. Crop simulation models included in DSSAT are tools that simulate physiological processes of crop growth, development and production by combining genetic crop characteristics and environmental (soil and weather) conditions. For each selected crop, the models were calibrated to evaluate climate change impacts on crop production. The climate data used for the analysis are derived by the Regional Circulation Model COSMO-CLM, from 1971 to 2065, at 8 km of spatial resolution. The RCM model output was "perturbed" with 10 Global Climate Models to have

  5. WheatGenome.info: A Resource for Wheat Genomics Resource.

    PubMed

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

  6. Genetic Resources for Maize Cell Wall Biology1[C][W][OA

    PubMed Central

    Penning, Bryan W.; Hunter, Charles T.; Tayengwa, Reuben; Eveland, Andrea L.; Dugard, Christopher K.; Olek, Anna T.; Vermerris, Wilfred; Koch, Karen E.; McCarty, Donald R.; Davis, Mark F.; Thomas, Steven R.; McCann, Maureen C.; Carpita, Nicholas C.

    2009-01-01

    Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions. PMID:19926802

  7. [Comparison of potential yield and resource utilization efficiency of main food crops in three provinces of Northeast China under climate change].

    PubMed

    Wang, Xiao-yu; Yang, Xiao-guang; Sun, Shuang; Xie, Wen-juan

    2015-10-01

    Based on the daily data of 65 meteorological stations from 1961 to 2010 and the crop phenology data in the potential cultivation zones of thermophilic and chimonophilous crops in Northeast China, the crop potential yields were calculated through step-by-step correction method. The spatio-temporal distribution of the crop potential yields at different levels was analyzed. And then we quantified the limitations of temperature and precipitation on the crop potential yields and compared the differences in the climatic resource utilization efficiency. The results showed that the thermal potential yields of six crops (including maize, rice, spring wheat, sorghum, millet and soybean) during the period 1961-2010 deceased from west to east. The climatic potential yields of the five crops (spring wheat not included) were higher in the south than in the north. The potential yield loss rate due to temperature limitations of the six crops presented a spatial distribution pattern and was higher in the east than in the west. Among the six main crops, the yield potential loss rate due to temperature limitation of the soybean was the highest (51%), and those of the other crops fluctuated within the range of 33%-41%. The potential yield loss rate due to water limitation had an obvious regional difference, and was high in Songnen Plain and Changbai Mountains. The potential yield loss rate of spring wheat was the highest (50%), and those of the other four rainfed crops fluctuated within the range of 8%-10%. The solar energy utilization efficiency of the six main crops ranged from 0.9% to 2.7%, in the order of maize> sorghum>rice>millet>spring wheat>soybean. The precipitation utilization efficiency of the maize, sorghum, spring wheat, millet and soybean under rainfed conditions ranged from 8 to 35 kg . hm-2 . mm-1, in the order of maize>sorghum>spring wheat>millet>soybean. In those areas with lower efficiency of solar energy utilization and precipitation utilization, such as Changbai

  8. 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.

  9. Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops.

    PubMed

    Hammer, Graeme L; van Oosterom, Erik; McLean, Greg; Chapman, Scott C; Broad, Ian; Harland, Peter; Muchow, Russell C

    2010-05-01

    Progress in molecular plant breeding is limited by the ability to predict plant phenotype based on its genotype, especially for complex adaptive traits. Suitably constructed crop growth and development models have the potential to bridge this predictability gap. A generic cereal crop growth and development model is outlined here. It is designed to exhibit reliable predictive skill at the crop level while also introducing sufficient physiological rigour for complex phenotypic responses to become emergent properties of the model dynamics. The approach quantifies capture and use of radiation, water, and nitrogen within a framework that predicts the realized growth of major organs based on their potential and whether the supply of carbohydrate and nitrogen can satisfy that potential. The model builds on existing approaches within the APSIM software platform. Experiments on diverse genotypes of sorghum that underpin the development and testing of the adapted crop model are detailed. Genotypes differing in height were found to differ in biomass partitioning among organs and a tall hybrid had significantly increased radiation use efficiency: a novel finding in sorghum. Introducing these genetic effects associated with plant height into the model generated emergent simulated phenotypic differences in green leaf area retention during grain filling via effects associated with nitrogen dynamics. The relevance to plant breeding of this capability in complex trait dissection and simulation is discussed.

  10. Genetic control of inflorescence architecture in legumes

    PubMed Central

    Benlloch, Reyes; Berbel, Ana; Ali, Latifeh; Gohari, Gholamreza; Millán, Teresa; Madueño, Francisco

    2015-01-01

    The architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. Inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. Elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to being able to breed key architectural traits in crop species. Inflorescence architecture depends on the identity and activity of the meristems in the inflorescence apex, which determines when flowers are formed, how many are produced and their relative position in the inflorescence axis. Arabidopsis thaliana, where the genetic control of inflorescence development is best known, has a simple inflorescence, where the primary inflorescence meristem directly produces the flowers, which are thus borne in the main inflorescence axis. In contrast, legumes represent a more complex inflorescence type, the compound inflorescence, where flowers are not directly borne in the main inflorescence axis but, instead, they are formed by secondary or higher order inflorescence meristems. Studies in model legumes such as pea (Pisum sativum) or Medicago truncatula have led to a rather good knowledge of the genetic control of the development of the legume compound inflorescence. In addition, the increasing availability of genetic and genomic tools for legumes is allowing to rapidly extending this knowledge to other grain legume crops. This review aims to describe the current knowledge of the genetic network controlling inflorescence development in legumes. It also discusses how the combination of this knowledge with the use of emerging genomic tools and resources may allow rapid advances in the breeding of grain legume crops. PMID:26257753

  11. Putting mechanisms into crop production models.

    PubMed

    Boote, Kenneth J; Jones, James W; White, Jeffrey W; Asseng, Senthold; Lizaso, Jon I

    2013-09-01

    Crop growth models dynamically simulate processes of C, N and water balance on daily or hourly time-steps to predict crop growth and development and at season-end, final yield. Their ability to integrate effects of genetics, environment and crop management have led to applications ranging from understanding gene function to predicting potential impacts of climate change. The history of crop models is reviewed briefly, and their level of mechanistic detail for assimilation and respiration, ranging from hourly leaf-to-canopy assimilation to daily radiation-use efficiency is discussed. Crop models have improved steadily over the past 30-40 years, but much work remains. Improvements are needed for the prediction of transpiration response to elevated CO₂ and high temperature effects on phenology and reproductive fertility, and simulation of root growth and nutrient uptake under stressful edaphic conditions. Mechanistic improvements are needed to better connect crop growth to genetics and to soil fertility, soil waterlogging and pest damage. Because crop models integrate multiple processes and consider impacts of environment and management, they have excellent potential for linking research from genomics and allied disciplines to crop responses at the field scale, thus providing a valuable tool for deciphering genotype by environment by management effects. © 2013 John Wiley & Sons Ltd.

  12. Limited and time-delayed internal resource allocation generates oscillations and chaos in the dynamics of citrus crops

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

    Ye, Xujun, E-mail: yexujun@cc.hirosaki-u.ac.jp; Faculty of Agriculture and Life Sciences, Hirosaki University, Aomori 036-8561; Sakai, Kenshi, E-mail: ken@cc.tuat.ac.jp

    Alternate bearing or masting is a yield variability phenomenon in perennial crops. The complex dynamics in this phenomenon have stimulated much ecological research. Motivated by data from an eight-year experiment with forty-eight individual trees, we explored the mechanism inherent to these dynamics in Satsuma mandarin (Citrus unshiu Marc.). By integrating high-resolution imaging technology, we found that the canopy structure and reproduction output of individual citrus crops are mutually dependent on each other. Furthermore, it was revealed that the mature leaves in early season contribute their energy to the fruiting of the current growing season, whereas the younger leaves show amore » delayed contribution to the next growing season. We thus hypothesized that the annual yield variability might be caused by the limited and time-delayed resource allocation in individual plants. A novel lattice model based on this hypothesis demonstrates that this pattern of resource allocation will generate oscillations and chaos in citrus yield.« less

  13. Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops?

    PubMed Central

    Patterson, Sara E.; Bolivar-Medina, Jenny L.; Falbel, Tanya G.; Hedtcke, Janet L.; Nevarez-McBride, Danielle; Maule, Andrew F.; Zalapa, Juan E.

    2016-01-01

    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 abscission process. Understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality and greater sustainability. As plant scientists, we have learned significant amounts about this process through the study of model plants such as Arabidopsis, tomato, rice, and maize. While these model systems have provided significant valuable information, we are sometimes challenged to use this knowledge effectively as variables including the economic value of the crop, the uniformity of the crop, ploidy levels, flowering and crossing mechanisms, ethylene responses, cultural requirements, responses to changes in environment, and cellular and tissue specific morphological differences can significantly influence outcomes. The value of genomic resources for lesser-studied crops such as cranberries and grapes and the orphan crop fonio will also be considered. PMID:26858730

  14. Are We on the Right Track: Can Our Understanding of Abscission in Model Systems Promote or Derail Making Improvements in Less Studied Crops?

    PubMed

    Patterson, Sara E; Bolivar-Medina, Jenny L; Falbel, Tanya G; Hedtcke, Janet L; Nevarez-McBride, Danielle; Maule, Andrew F; Zalapa, Juan E

    2015-01-01

    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 abscission process. Understanding this process can not only lead to genetic improvement, but also changes in cultural practices and management that will contribute to higher yields, improved quality and greater sustainability. As plant scientists, we have learned significant amounts about this process through the study of model plants such as Arabidopsis, tomato, rice, and maize. While these model systems have provided significant valuable information, we are sometimes challenged to use this knowledge effectively as variables including the economic value of the crop, the uniformity of the crop, ploidy levels, flowering and crossing mechanisms, ethylene responses, cultural requirements, responses to changes in environment, and cellular and tissue specific morphological differences can significantly influence outcomes. The value of genomic resources for lesser-studied crops such as cranberries and grapes and the orphan crop fonio will also be considered.

  15. AN APPROACH TO TRANSGENIC CROP MONITORING

    EPA Science Inventory

    Remote sensing by aerial or satellite images may provide a method of identifying transgenic pesticidal crop distribution in the landscape. Genetically engineered crops containing bacterial gene(s) that express an insecticidal protein from Bacillus thuringiensis (Bt) are regulated...

  16. Genetic structure and isolation by distance in a landrace of Thai rice

    PubMed Central

    Pusadee, Tonapha; Jamjod, Sansanee; Chiang, Yu-Chung; Rerkasem, Benjavan; Schaal, Barbara A.

    2009-01-01

    Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans. PMID:19651617

  17. Genetically modified crops and aquatic ecosystems: considerations for environmental risk assessment and non-target organism testing.

    PubMed

    Carstens, Keri; Anderson, Jennifer; Bachman, Pamela; De Schrijver, Adinda; Dively, Galen; Federici, Brian; Hamer, Mick; Gielkens, Marco; Jensen, Peter; Lamp, William; Rauschen, Stefan; Ridley, Geoff; Romeis, Jörg; Waggoner, Annabel

    2012-08-01

    Environmental risk assessments (ERA) support regulatory decisions for the commercial cultivation of genetically modified (GM) crops. The ERA for terrestrial agroecosystems is well-developed, whereas guidance for ERA of GM crops in aquatic ecosystems is not as well-defined. The purpose of this document is to demonstrate how comprehensive problem formulation can be used to develop a conceptual model and to identify potential exposure pathways, using Bacillus thuringiensis (Bt) maize as a case study. Within problem formulation, the insecticidal trait, the crop, the receiving environment, and protection goals were characterized, and a conceptual model was developed to identify routes through which aquatic organisms may be exposed to insecticidal proteins in maize tissue. Following a tiered approach for exposure assessment, worst-case exposures were estimated using standardized models, and factors mitigating exposure were described. Based on exposure estimates, shredders were identified as the functional group most likely to be exposed to insecticidal proteins. However, even using worst-case assumptions, the exposure of shredders to Bt maize was low and studies supporting the current risk assessments were deemed adequate. Determining if early tier toxicity studies are necessary to inform the risk assessment for a specific GM crop should be done on a case by case basis, and should be guided by thorough problem formulation and exposure assessment. The processes used to develop the Bt maize case study are intended to serve as a model for performing risk assessments on future traits and crops.

  18. Strategies for conserving forest genetic resources in the face of climate change

    Treesearch

    John Bradley St. Clair; Glenn Thomas Howe

    2011-01-01

    Conservation of genetic diversity is important for continued evolution of populations to new environments, as well as continued availability of traits of interest in genetic improvement programs. Rapidly changing climates present new threats to the conservation of forest genetic resources. We can no longer assume that in situ reserves will continue to preserve existing...

  19. ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs).

    PubMed

    Mishra, Smriti; Shah, Mohammad I; Sarkar, Malay; Asati, Nimisha; Rout, Chittaranjan

    2018-01-01

    Interstitial lung diseases (ILDs) are a diverse group of ∼200 acute and chronic pulmonary disorders that are characterized by variable amounts of inflammation, fibrosis and architectural distortion with substantial morbidity and mortality. Inaccurate and delayed diagnoses increase the risk, especially in developing countries. Studies have indicated the significant roles of genetic elements in ILDs pathogenesis. Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis and identification of diagnostics-based biomarkers. This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches, literature-mining and DCGs-microRNA (miRNAs)-single nucleotide polymorphisms (SNPs) association analyses. To provide statistical significance to disease-gene association, ILD-specificity index and hypergeomatric test scores were also incorporated. Association analyses of miRNAs, SNPs and pathways responsible for the pathogenesis of different sub-classes of ILDs were also incorporated. Manually verified 299 DCGs and their significant associations with 1932 SNPs, 2966 miRNAs and 9170 miR-polymorphisms were also provided. Furthermore, 216 literature-mined and proposed biomarkers were identified. The ILDgenDB resource provides user-friendly browsing and extensive query-based information retrieval systems. Additionally, this resource also facilitates graphical view of predicted DCGs-SNPs/miRNAs and literature associated DCGs-ILDs interactions for each ILD to facilitate efficient data interpretation. Outcomes of analyses suggested the significant involvement of immune system and defense mechanisms in ILDs pathogenesis. This resource may potentially facilitate genetic-based disease monitoring and

  20. Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

    PubMed Central

    Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  1. Genetically modified foods and social concerns.

    PubMed

    Maghari, Behrokh Mohajer; Ardekani, Ali M

    2011-07-01

    Biotechnology is providing us with a wide range of options for how we can use agricultural and commercial forestry lands. The cultivation of genetically modified (GM) crops on millions of hectares of lands and their injection into our food chain is a huge global genetic experiment involving all living beings. Considering the fast pace of new advances in production of genetically modified crops, consumers, farmers and policymakers worldwide are challenged to reach a consensus on a clear vision for the future of world food supply. The current food biotechnology debate illustrates the serious conflict between two groups: 1) Agri-biotech investors and their affiliated scientists who consider agricultural biotechnology as a solution to food shortage, the scarcity of environmental resources and weeds and pests infestations; and 2) independent scientists, environmentalists, farmers and consumers who warn that genetically modified food introduces new risks to food security, the environment and human health such as loss of biodiversity; the emergence of superweeds and superpests; the increase of antibiotic resistance, food allergies and other unintended effects. This article reviews major viewpoints which are currently debated in the food biotechnology sector in the world. It also lays the ground-work for deep debate on benefits and risks of Biotech-crops for human health, ecosystems and biodiversity. In this context, although some regulations exist, there is a need for continuous vigilance for all countries involved in producing genetically engineered food to follow the international scientific bio-safety testing guidelines containing reliable pre-release experiments and post-release track of transgenic plants to protect public health and avoid future environmental harm.

  2. A portable expression resource for engineering cross-species genetic circuits and pathways

    PubMed Central

    Kushwaha, Manish; Salis, Howard M.

    2015-01-01

    Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. PMID:26184393

  3. Ethical reflections on herbicide-resistant crops.

    PubMed

    Madsen, Kathrine Hauge; Sandøe, Peter

    2005-03-01

    The introduction of genetically modified (GM) crops has caused a fierce public debate in Europe. Much of the controversy centres on possible risks to the environment. A specific problem here is that risk perception of the scientific experts differs from that of the public. In this paper, risks associated with herbicide-resistant crops are presented from the point of view of experts and lay people. In the public perception, herbicide-resistant (HR) crops are troublesome because of their association with two technologies: genetic engineering of crops and the use of herbicides. These technologies are perceived as risky because they seem to share certain features: in particular, their long-term effects are unknown and they are dreaded. Other value questions also come into play. The public seems to be concerned that risks are not outweighed by usefulness, that using HR crops is the wrong path to sustainable agriculture, that the individual's right to choose GM-free products may be violated, and that these crops are unnatural. In contrast, on the issue of the uncertainty inherent in risk assessment, experts and the public seem to share a good deal of ground. Copyright 2005 Society of Chemical Industry

  4. 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.

  5. Modelling adaptation to climate change of Ecuadorian agriculture and associated water resources: uncertainties in coastal and highland cropping systems

    NASA Astrophysics Data System (ADS)

    Ruiz-Ramos, Margarita; Bastidas, Wellington; Cóndor, Amparo; Villacís, Marcos; Calderón, Marco; Herrera, Mario; Zambrano, José Luis; Lizaso, Jon; Hernández, Carlos; Rodríguez, Alfredo; Capa-Morocho, Mirian

    2016-04-01

    Climate change threatens sustainability of farms and associated water resources in Ecuador. Although the last IPCC report (AR5) provides a general framework for adaptation, , impact assessment and especially adaptation analysis should be site-specific, taking into account both biophysical and social aspects. The objective of this study is to analyse the climate change impacts and to sustainable adaptations to optimize the crop yield. Furthermore is also aimed to weave agronomical and hydrometeorological aspects, to improve the modelling of the coastal ("costa") and highland ("sierra") cropping systems in Ecuador, from the agricultural production and water resources points of view. The final aim is to support decision makers, at national and local institutions, for technological implementation of structural adaptation strategies, and to support farmers for their autonomous adaptation actions to cope with the climate change impacts and that allow equal access to resources and appropriate technologies. . A diagnosis of the current situation in terms of data availability and reliability was previously done, and the main sources of uncertainty for agricultural projections have been identified: weather data, especially precipitation projections, soil data below the upper 30 cm, and equivalent experimental protocol for ecophysiological crop field measurements. For reducing these uncertainties, several methodologies are being discussed. This study was funded by PROMETEO program from Ecuador through SENESCYT (M. Ruiz-Ramos contract), and by the project COOP-XV-25 funded by Universidad Politécnica de Madrid.

  6. Bioinformatics in the orphan crops.

    PubMed

    Armstead, Ian; Huang, Lin; Ravagnani, Adriana; Robson, Paul; Ougham, Helen

    2009-11-01

    Orphan crops are those which are grown as food, animal feed or other crops of some importance in agriculture, but which have not yet received the investment of research effort or funding required to develop significant public bioinformatics resources. Where an orphan crop is related to a well-characterised model plant species, comparative genomics and bioinformatics can often, though not always, be exploited to assist research and crop improvement. This review addresses some challenges and opportunities presented by bioinformatics in the orphan crops, using three examples: forage grasses from the genera Lolium and Festuca, forage legumes and the second generation energy crop Miscanthus.

  7. The potential of climate change adjustment in crops: A synthesis

    USDA-ARS?s Scientific Manuscript database

    This chapter covers a study on various field crops like cereals, legumes, oil seeds, vegetables, cash crops, underutilized crops, and energy crops and their genetic adjustment to changing climates. More than 30 major field crops have been covered in different chapters of this book, which highlight h...

  8. PatGen--a consolidated resource for searching genetic patent sequences.

    PubMed

    Rouse, Richard J D; Castagnetto, Jesus; Niedner, Roland H

    2005-04-15

    Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. PatGen can be searched at http://www.patgendb.com rjdrouse@patentinformatics.com.

  9. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

    NASA Astrophysics Data System (ADS)

    Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

    2014-10-01

    This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

  10. Gene co-ops and the biotrade: translating genetic resource rights into sustainable development.

    PubMed

    Reid, W V

    1996-04-01

    The 1992 Convention on Biological Diversity marks a basic change in the international status of genetic resources. Prior to the Convention, these resources were considered to be the "heritage of mankind.' Although the intent of this open access regime was to ensure the widespread availability of genetic resources for agriculture and industry, commercial use of the resources provided no additional economic incentive for conservation by source countries. The Biodiversity Convention corrects this policy failure by establishing that states have sovereign rights over their genetic resources, thereby enabling market incentives to complement various multilateral mechanisms that might directly fund biodiversity conservation. A number of obstacles face countries that are translating this broad right to regulate access into specific policies, laws, and regulations designed to meet conservation and development objectives. A review of these obstacles and of trends in technological development suggest that nations and developing country institutions should take a set of actions to develop access legislation and Material Transfer Agreements, establish biodiversity "cooperatives' and intermediary institutions to facilitate information exchange, develop minimum standards for access legislation, and require that prior informed consent of local communities be obtained by all biodiversity collectors.

  11. Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

    PubMed Central

    Chen, Ruikun; Hara, Takashi; Ohsawa, Ryo; Yoshioka, Yosuke

    2017-01-01

    Diversity analysis of rapeseed accessions preserved in the Japanese Genebank can provide valuable information for breeding programs. In this study, 582 accessions were genotyped with 30 SSR markers covering all 19 rapeseed chromosomes. These markers amplified 311 alleles (10.37 alleles per marker; range, 3–39). The genetic diversity of Japanese accessions was lower than that of overseas accessions. Analysis of molecular variance indicated significant genetic differentiation between Japanese and overseas accessions. Small but significant differences were found among geographical groups in Japan, and genetic differentiation tended to increase with geographical distance. STRUCTURE analysis indicated the presence of two main genetic clusters in the NARO rapeseed collection. With the membership probabilities threshold, 227 accessions mostly originating from overseas were assigned to one subgroup, and 276 accessions mostly originating from Japan were assigned to the other subgroup. The remaining 79 accessions are assigned to admixed group. The core collection constructed comprises 96 accessions of diverse origin. It represents the whole collection well and thus it may be useful for rapeseed genetic research and breeding programs. The core collection improves the efficiency of management, evaluation, and utilization of genetic resources. PMID:28744177

  12. Assessment of future crop yield and agricultural sustainable water use in north china plain using multiple crop models

    NASA Astrophysics Data System (ADS)

    Huang, G.

    2016-12-01

    Currently, studying crop-water response mechanism has become an important part in the development of new irrigation technology and optimal water allocation in water-scarce regions, which is of great significance to crop growth guidance, sustainable utilization of agricultural water, as well as the sustainable development of regional agriculture. Using multiple crop models(AquaCrop,SWAP,DNDC), this paper presents the results of simulating crop growth and agricultural water consumption of the winter-wheat and maize cropping system in north china plain. These areas are short of water resources, but generates about 23% of grain production for China. By analyzing the crop yields and the water consumption of the traditional flooding irrigation, the paper demonstrates quantitative evaluation of the potential amount of water use that can be reduced by using high-efficient irrigation approaches, such as drip irrigation. To maintain food supply and conserve water resources, the research concludes sustainable irrigation methods for the three provinces for sustainable utilization of agricultural water.

  13. Response to issues on GM agriculture in Africa: Are transgenic crops safe?

    PubMed

    Adenle, Ademola A

    2011-10-08

    The controversies surrounding transgenic crops, often called Genetically Modified Organisms (GMOs), call for a need to raise the level of public awareness of Genetic Modification (GM) technology in Africa. This should be accomplished by educating the public about the potential benefits and risks that may be associated with this new technology. In the last 15 years, GM crop producing countries have benefited from adoption of this new technology in the form of improved crop productivity, food security, and quality of life. The increased income to resource-poor farmers is a key benefit at the individual level especially as most countries using this technology are in the developing world, including three African countries (South Africa, Burkina Faso and Egypt). Despite clear benefits to countries and farmers who grow GMOs, many people are concerned about suspected potential risks associated with GMOs. This sparks debate as to whether GM technology should be adopted or not. Given the concerns regarding the safety of GMO products, thorough scientific investigation of safe application of GMOs is required. The objective of this paper is to respond to the issues of GM agriculture in Africa and some of the issues surrounding the adoption of GM crops between developed and developing countries. In this article, I analyse relevant papers relating to the adoption of GM technology particularly in developing countries including the few African countries that have adopted GM crops. The issues discussed span a wide range including: safety; potential benefits and risks; disputes between the United States of America (USA) and the European Union (EU) over adoption of GM crops with a focus on Africa continent. This article is concluded by summarising the issues raised and how GM technology can be adopted for agricultural development in Africa.

  14. Response to issues on GM agriculture in Africa: Are transgenic crops safe?

    PubMed Central

    2011-01-01

    The controversies surrounding transgenic crops, often called Genetically Modified Organisms (GMOs), call for a need to raise the level of public awareness of Genetic Modification (GM) technology in Africa. This should be accomplished by educating the public about the potential benefits and risks that may be associated with this new technology. In the last 15 years, GM crop producing countries have benefited from adoption of this new technology in the form of improved crop productivity, food security, and quality of life. The increased income to resource-poor farmers is a key benefit at the individual level especially as most countries using this technology are in the developing world, including three African countries (South Africa, Burkina Faso and Egypt). Despite clear benefits to countries and farmers who grow GMOs, many people are concerned about suspected potential risks associated with GMOs. This sparks debate as to whether GM technology should be adopted or not. Given the concerns regarding the safety of GMO products, thorough scientific investigation of safe application of GMOs is required. The objective of this paper is to respond to the issues of GM agriculture in Africa and some of the issues surrounding the adoption of GM crops between developed and developing countries. In this article, I analyse relevant papers relating to the adoption of GM technology particularly in developing countries including the few African countries that have adopted GM crops. The issues discussed span a wide range including: safety; potential benefits and risks; disputes between the United States of America (USA) and the European Union (EU) over adoption of GM crops with a focus on Africa continent. This article is concluded by summarising the issues raised and how GM technology can be adopted for agricultural development in Africa. PMID:21981823

  15. Safety assessment, detection and traceability, and societal aspects of genetically modified foods. European Network on Safety Assessment of Genetically Modified Food Crops (ENTRANSFOOD). Concluding remarks.

    PubMed

    Kuiper, H A; König, A; Kleter, G A; Hammes, W P; Knudsen, I

    2004-07-01

    The most important results from the EU-sponsored ENTRANSFOOD Thematic Network project are reviewed, including the design of a detailed step-wise procedure for the risk assessment of foods derived from genetically modified crops based on the latest scientific developments, evaluation of topical risk assessment issues, and the formulation of proposals for improved risk management and public involvement in the risk analysis process. Copyright 2004 Elsevier Ltd.

  16. The Contribution of Buckwheat Genetic Resources to Health and Dietary Diversity

    PubMed Central

    Sytar, Oksana; Brestic, Marian; Zivcak, Marek; Tran, Lam-Son Phan

    2016-01-01

    Despite several reports on the beneficial effects of buckwheat in prevention of human diseases, little attention has been devoted to the variability of biochemical and physiological traits in different buckwheat genetic resources. This review describes the biochemical evaluation of buckwheat genetic resources and the identification of elite genotypes for plant breeding and exploitation. The various types of bioactive compounds present in different varieties provide basic background information needed for the efficient production of buckwheat foods with added value. In this review, we will provide an integrated view of the biochemistry of bioactive compounds of buckwheat plants of different origin, especially of fagopyrin, proteins and amino acids, as well as of other phenolic compounds including rutin and chlorogenic acid. In addition to the genetic background, the effect of different growth conditions is discussed. The health effects of fagopyrin, phenolic acids, specific proteins and rutin are also presented. PMID:27252586

  17. The first crop plant genetically engineered to release an insect pheromone for defence

    PubMed Central

    Bruce, Toby J.A.; Aradottir, Gudbjorg I.; Smart, Lesley E.; Martin, Janet L.; Caulfield, John C.; Doherty, Angela; Sparks, Caroline A.; Woodcock, Christine M.; Birkett, Michael A.; Napier, Johnathan A.; Jones, Huw D.; Pickett, John A.

    2015-01-01

    Insect pheromones offer potential for managing pests of crop plants. Volatility and instability are problems for deployment in agriculture but could be solved by expressing genes for the biosynthesis of pheromones in the crop plants. This has now been achieved by genetically engineering a hexaploid variety of wheat to release (E)-β-farnesene (Eβf), the alarm pheromone for many pest aphids, using a synthetic gene based on a sequence from peppermint with a plastid targeting amino acid sequence, with or without a gene for biosynthesis of the precursor farnesyl diphosphate. Pure Eβf was produced in stably transformed wheat lines with no other detectable phenotype but requiring targeting of the gene produced to the plastid. In laboratory behavioural assays, three species of cereal aphids were repelled and foraging was increased for a parasitic natural enemy. Although these studies show considerable potential for aphid control, field trials employing the single and double constructs showed no reduction in aphids or increase in parasitism. Insect numbers were low and climatic conditions erratic suggesting the need for further trials or a closer imitation, in the plant, of alarm pheromone release. PMID:26108150

  18. Maize Genetic Resources Collections – Utilizing a Treasure Trove

    USDA-ARS?s Scientific Manuscript database

    The maize genetic resource collection managed by the USDA-ARS's National Plant Germplasm System is heavily utilized by researchers and educators. A collection of landraces, inbred lines from public and private sector sources, synthetics and key populations, it serves both as a living snapshot of th...

  19. Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China.

    PubMed

    Wang, Yanjie; Wang, Yanli; Sun, Xiaodong; Caiji, Zhuoma; Yang, Jingbiao; Cui, Di; Cao, Guilan; Ma, Xiaoding; Han, Bing; Xue, Dayuan; Han, Longzhi

    2016-10-27

    Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation. The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China. The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3-30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In

  20. Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus

    PubMed Central

    Slavov, Gancho; Allison, Gordon; Bosch, Maurice

    2013-01-01

    Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field. PMID:23847628

  1. RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

    PubMed Central

    2010-01-01

    Background Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community. Description The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns. Conclusions RoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables. PMID:20691054

  2. Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

    PubMed Central

    Rodriguez-Bonilla, Lorraine; Cuevas, Hugo E.; Montero-Rojas, Milly; Bird-Pico, Fernando; Luciano-Rosario, Dianiris; Siritunga, Dimuth

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388

  3. Gramene 2013: comparative plant genomics resources.

    PubMed

    Monaco, Marcela K; Stein, Joshua; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; Jiao, Yinping; Lu, Zhenyuan; Bolser, Dan; Kerhornou, Arnaud; Staines, Dan; Walts, Brandon; Wu, Guanming; D'Eustachio, Peter; Haw, Robin; Croft, David; Kersey, Paul J; Stein, Lincoln; Jaiswal, Pankaj; Ware, Doreen

    2014-01-01

    Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

  4. Elevating crop disease resistance with cloned genes

    PubMed Central

    Jones, Jonathan D. G.; Witek, Kamil; Verweij, Walter; Jupe, Florian; Cooke, David; Dorling, Stephen; Tomlinson, Laurence; Smoker, Matthew; Perkins, Sara; Foster, Simon

    2014-01-01

    Essentially all plant species exhibit heritable genetic variation for resistance to a variety of plant diseases caused by fungi, bacteria, oomycetes or viruses. Disease losses in crop monocultures are already significant, and would be greater but for applications of disease-controlling agrichemicals. For sustainable intensification of crop production, we argue that disease control should as far as possible be achieved using genetics rather than using costly recurrent chemical sprays. The latter imply CO2 emissions from diesel fuel and potential soil compaction from tractor journeys. Great progress has been made in the past 25 years in our understanding of the molecular basis of plant disease resistance mechanisms, and of how pathogens circumvent them. These insights can inform more sophisticated approaches to elevating disease resistance in crops that help us tip the evolutionary balance in favour of the crop and away from the pathogen. We illustrate this theme with an account of a genetically modified (GM) blight-resistant potato trial in Norwich, using the Rpi-vnt1.1 gene isolated from a wild relative of potato, Solanum venturii, and introduced by GM methods into the potato variety Desiree. PMID:24535396

  5. Soil Fungal Resources in Annual Cropping Systems and Their Potential for Management

    PubMed Central

    Esmaeili Taheri, Ahmad; Bainard, Luke D.; Yang, Chao; Navarro-Borrell, Adriana; Hamel, Chantal

    2014-01-01

    Soil fungi are a critical component of agroecosystems and provide ecological services that impact the production of food and bioproducts. Effective management of fungal resources is essential to optimize the productivity and sustainability of agricultural ecosystems. In this review, we (i) highlight the functional groups of fungi that play key roles in agricultural ecosystems, (ii) examine the influence of agronomic practices on these fungi, and (iii) propose ways to improve the management and contribution of soil fungi to annual cropping systems. Many of these key soil fungal organisms (i.e., arbuscular mycorrhizal fungi and fungal root endophytes) interact directly with plants and are determinants of the efficiency of agroecosystems. In turn, plants largely control rhizosphere fungi through the production of carbon and energy rich compounds and of bioactive phytochemicals, making them a powerful tool for the management of soil fungal diversity in agriculture. The use of crop rotations and selection of optimal plant genotypes can be used to improve soil biodiversity and promote beneficial soil fungi. In addition, other agronomic practices (e.g., no-till, microbial inoculants, and biochemical amendments) can be used to enhance the effect of beneficial fungi and increase the health and productivity of cultivated soils. PMID:25247177

  6. Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes

    PubMed Central

    Sharma, Shivali; Upadhyaya, H. D.; Varshney, R. K.; Gowda, C. L. L.

    2013-01-01

    The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs. PMID:23970889

  7. 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.

  8. Water savings of redistributing global crop production

    NASA Astrophysics Data System (ADS)

    Davis, Kyle; Seveso, Antonio; Rulli, Maria Cristina; D'Odorico, Paolo

    2016-04-01

    Human demand for crop production is expected to increase substantially in the coming decades as a result of population growth, richer diets and biofuel use. For food production to keep pace, unprecedented amounts of resources - water, fertilizers, energy - will be required. This has led to calls for 'sustainable intensification' in which yields are increased on existing croplands while seeking to minimize impacts on water and other agricultural resources. Recent studies have quantified aspects of this, showing that there is a large potential to improve crop yields and increase harvest frequencies to better meet human demand. Though promising, both solutions would necessitate large additional inputs of water and fertilizer in order to be achieved under current technologies. However, the question of whether the current distribution of crops is, in fact, the best for realizing maximized production has not been considered to date. To this end, we ask: Is it possible to minimize water demand by simply growing crops where soil and climate conditions are best suited? Here we use maps of agro-ecological suitability - a measure of physical and chemical soil fertility - for 15 major food crops to identify differences between current crop distributions and where they can most suitably be planted. By redistributing crops across currently cultivated lands, we determine what distribution of crops would maintain current calorie production and agricultural value while minimizing the water demand of crop production. In doing this, our study provides a novel tool for policy makers and managers to integrate food security, environmental sustainability, and rural livelihoods by improving the use of freshwater resources without compromising crop calorie production or rural livelihoods.

  9. Origins of food crops connect countries worldwide.

    USDA-ARS?s Scientific Manuscript database

    Crop genetic diversity is concentrated within specific geographic regions worldwide. While access to this diversity is critical to continued increases in agricultural productivity, the geopolitical significance of the geography of crop diversity has not been quantified. We assess the degree to which...

  10. Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

    PubMed

    Qian, Lunwen; Hickey, Lee T; Stahl, Andreas; Werner, Christian R; Hayes, Ben; Snowdon, Rod J; Voss-Fels, Kai P

    2017-01-01

    In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool

  11. Options and legal requirements for national and regional animal genetic resources collections

    USDA-ARS?s Scientific Manuscript database

    The contraction of animal genetic resources on a global scale has motivated countries to establish gene banks as a mechanism to conserve national resources. Gene banks should establish a set of policies that insure they are complying with national laws. The two primary areas of consideration are ho...

  12. Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

    PubMed Central

    Migicovsky, Zoë; Myles, Sean

    2017-01-01

    Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain. Thus, MAS holds particular promise in perennials since they are often costly and time-consuming to grow to maturity and evaluate. Well-characterized germplasm that breeders can tap into for improving perennials is often limited in genetic diversity. Wild relatives are a largely untapped source of desirable traits including disease resistance, fruit quality, and rootstock characteristics. This review focuses on the use of genomics-assisted breeding in perennials, especially as it relates to the introgression of useful traits from wild relatives. The identification of genetic markers predictive of beneficial phenotypes derived from wild relatives is hampered by genomic tools designed for domesticated species that are often ill-suited for use in wild relatives. There is therefore an urgent need for better genomic resources from wild relatives. A further barrier to exploiting wild diversity through genomics is the phenotyping bottleneck: well-powered genetic mapping requires accurate and cost-effective characterization of large collections of diverse wild germplasm. While genomics will always be used in combination with traditional breeding methods, it is a powerful tool for accelerating the speed and reducing the costs of breeding while harvesting the potential of wild relatives for improving perennial crops. PMID:28421095

  13. Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops.

    PubMed

    Migicovsky, Zoë; Myles, Sean

    2017-01-01

    Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain. Thus, MAS holds particular promise in perennials since they are often costly and time-consuming to grow to maturity and evaluate. Well-characterized germplasm that breeders can tap into for improving perennials is often limited in genetic diversity. Wild relatives are a largely untapped source of desirable traits including disease resistance, fruit quality, and rootstock characteristics. This review focuses on the use of genomics-assisted breeding in perennials, especially as it relates to the introgression of useful traits from wild relatives. The identification of genetic markers predictive of beneficial phenotypes derived from wild relatives is hampered by genomic tools designed for domesticated species that are often ill-suited for use in wild relatives. There is therefore an urgent need for better genomic resources from wild relatives. A further barrier to exploiting wild diversity through genomics is the phenotyping bottleneck: well-powered genetic mapping requires accurate and cost-effective characterization of large collections of diverse wild germplasm. While genomics will always be used in combination with traditional breeding methods, it is a powerful tool for accelerating the speed and reducing the costs of breeding while harvesting the potential of wild relatives for improving perennial crops.

  14. REMOTE SENSING TECHNIQUES FOR MONITORING GENETICALLY ENGINEERED CROP CULTIVATION

    EPA Science Inventory

    Crops bioengineered to contain toxins derived from Bacillus thuringensis (Bt) are under regulatory scrutiny by USEPA under the FIFRA legislation. The agency has declared these crops to be "in the public good" based on the reduced use of pesticides required for management of these...

  15. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Treesearch

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

  16. Corporate control and global governance of marine genetic resources

    PubMed Central

    Österblom, Henrik

    2018-01-01

    Who owns ocean biodiversity? This is an increasingly relevant question, given the legal uncertainties associated with the use of genetic resources from areas beyond national jurisdiction, which cover half of the Earth’s surface. We accessed 38 million records of genetic sequences associated with patents and created a database of 12,998 sequences extracted from 862 marine species. We identified >1600 sequences from 91 species associated with deep-sea and hydrothermal vent systems, reflecting commercial interest in organisms from remote ocean areas, as well as a capacity to collect and use the genes of such species. A single corporation registered 47% of all marine sequences included in gene patents, exceeding the combined share of 220 other companies (37%). Universities and their commercialization partners registered 12%. Actors located or headquartered in 10 countries registered 98% of all patent sequences, and 165 countries were unrepresented. Our findings highlight the importance of inclusive participation by all states in international negotiations and the urgency of clarifying the legal regime around access and benefit sharing of marine genetic resources. We identify a need for greater transparency regarding species provenance, transfer of patent ownership, and activities of corporations with a disproportionate influence over the patenting of marine biodiversity. We suggest that identifying these key actors is a critical step toward encouraging innovation, fostering greater equity, and promoting better ocean stewardship. PMID:29881777

  17. Crop improvement and conservation through tissue culture techniques

    USDA-ARS?s Scientific Manuscript database

    Crop improvement through classic breeding and/or genetic engineering methods is possible in the majority of cultivated crops. However, gene manipulations, chromosome duplication, protoplast fusion, bioassays, interspecific cross recovery involve tissue culture techniques. For vegetatively propagated...

  18. Coupled Crop/Hydrology Model to Estimate Expanded Irrigation Impact on Water Resources

    NASA Astrophysics Data System (ADS)

    Handyside, C. T.; Cruise, J.

    2017-12-01

    A coupled agricultural and hydrologic systems model is used to examine the environmental impact of irrigation in the Southeast. A gridded crop model for the Southeast is used to determine regional irrigation demand. This irrigation demand is used in a regional hydrologic model to determine the hydrologic impact of irrigation. For the Southeast to maintain/expand irrigated agricultural production and provide adaptation to climate change and climate variability it will require integrated agricultural and hydrologic system models that can calculate irrigation demand and the impact of the this demand on the river hydrology. These integrated models can be used as (1) historical tools to examine vulnerability of expanded irrigation to past climate extremes (2) future tools to examine the sustainability of expanded irrigation under future climate scenarios and (3) a real-time tool to allow dynamic water resource management. Such tools are necessary to assure stakeholders and the public that irrigation can be carried out in a sustainable manner. The system tools to be discussed include a gridded version of the crop modeling system (DSSAT). The gridded model is referred to as GriDSSAT. The irrigation demand from GriDSSAT is coupled to a regional hydrologic model developed by the Eastern Forest Environmental Threat Assessment Center of the USDA Forest Service) (WaSSI). The crop model provides the dynamic irrigation demand which is a function of the weather. The hydrologic model includes all other competing uses of water. Examples of use the crop model coupled with the hydrologic model include historical analyses which show the change in hydrology as additional acres of irrigated land are added to water sheds. The first order change in hydrology is computed in terms of changes in the Water Availability Stress Index (WASSI) which is the ratio of water demand (irrigation, public water supply, industrial use, etc.) and water availability from the hydrologic model. Also

  19. Recombinase Polymerase Amplification (RPA) of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

    PubMed Central

    Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

    2014-01-01

    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops. PMID:25310647

  20. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops.

    PubMed

    Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

    2014-10-10

    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37-42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15-25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  1. 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

  2. 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

  3. Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives.

    PubMed

    Warschefsky, Emily; Penmetsa, R Varma; Cook, Douglas R; von Wettberg, Eric J B

    2014-10-01

    The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings. © 2014 Botanical Society of America, Inc.

  4. Regulatory challenges for GM crops in developing economies: the African experience.

    PubMed

    Nang'ayo, Francis; Simiyu-Wafukho, Stella; Oikeh, Sylvester O

    2014-12-01

    Globally, transgenic or genetically modified (GM) crops are considered regulated products that are subject to regulatory oversight during trans-boundary movement, testing and environmental release. In Africa, regulations for transgenic crops are based on the outcomes of the historic Earth Summit Conference held in Rio, Brazil two decades ago, namely, the adoption of the Convention on Biological Diversity (CBD) and the subsequent adoption of the Cartagena Protocol on Biosafety. To exploit the potential benefits of transgenic crops while safeguarding the potential risks on human health and environment, most African countries have signed and ratified the CBD and the Cartagena Protocol on Biosafety. Consequently, these countries are required to take appropriate legal, administrative and other measures to ensure that the handling and utilization of living modified organisms are undertaken in a manner that reduces the risks to humans and the environment. These countries are also expected to provide regulatory oversight on transgenic crops through functional national biosafety frameworks (NBFs). While in principle this approach is ideal, NBFs in most African countries are steeped in a host of policy, legal and operational challenges that appear to be at cross-purposes with the noble efforts of seeking to access, test and deliver promising GM crops for use by resource-limited farmers in Africa. In this paper we discuss the regulatory challenges faced during the development and commercialization of GM crops based on experiences from countries in Sub-Saharan Africa.

  5. Genetic Diversity of Cowpea (Vigna unguiculata (L.) Walp.) Accession in Kenya Gene Bank Based on Simple Sequence Repeat Markers.

    PubMed

    Wamalwa, Emily N; Muoma, John; Wekesa, Clabe

    2016-01-01

    Increased agricultural production is an urgent issue. Projected global population is 9 million people by mid of this century. Estimation projects death of 1 million people for lack of food quality (micronutrient deficit) and quantity (protein deficit). Majority of these people will be living in developing countries. Other global challenges include shrinking cultivable lands, salinity, and flooding due to climate changes, new emerging pathogens, and pests. These affect crop production. Furthermore, they are major threats to crop genetic resources and food security. Genetic diversity in cultivated crops indicates gene pool richness. It is the greatest resource for plant breeders to select lines that enhance food security. This study was conducted by Masinde Muliro University to evaluate genetic diversity in 19 cowpea accessions from Kenya national gene bank. Accessions clustered into two major groups. High divergence was observed between accessions from Ethiopia and Australia and those from Western Kenya. Upper Volta accessions were closely related to those from Western Kenya. Low variation was observed between accessions from Eastern and Rift Valley than those from Western and Coastal regions of Kenya. Diversity obtained in this study can further be exploited for the improvement of cowpea in Kenya as a measure of food security.

  6. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.

    PubMed

    Varshney, Rajeev K; Chen, Wenbin; Li, Yupeng; Bharti, Arvind K; Saxena, Rachit K; Schlueter, Jessica A; Donoghue, Mark T A; Azam, Sarwar; Fan, Guangyi; Whaley, Adam M; Farmer, Andrew D; Sheridan, Jaime; Iwata, Aiko; Tuteja, Reetu; Penmetsa, R Varma; Wu, Wei; Upadhyaya, Hari D; Yang, Shiaw-Pyng; Shah, Trushar; Saxena, K B; Michael, Todd; McCombie, W Richard; Yang, Bicheng; Zhang, Gengyun; Yang, Huanming; Wang, Jun; Spillane, Charles; Cook, Douglas R; May, Gregory D; Xu, Xun; Jackson, Scott A

    2011-11-06

    Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.

  7. Adaptation of the ToxRTool to Assess the Reliability of Toxicology Studies Conducted with Genetically Modified Crops and Implications for Future Safety Testing.

    PubMed

    Koch, Michael S; DeSesso, John M; Williams, Amy Lavin; Michalek, Suzanne; Hammond, Bruce

    2016-01-01

    To determine the reliability of food safety studies carried out in rodents with genetically modified (GM) crops, a Food Safety Study Reliability Tool (FSSRTool) was adapted from the European Centre for the Validation of Alternative Methods' (ECVAM) ToxRTool. Reliability was defined as the inherent quality of the study with regard to use of standardized testing methodology, full documentation of experimental procedures and results, and the plausibility of the findings. Codex guidelines for GM crop safety evaluations indicate toxicology studies are not needed when comparability of the GM crop to its conventional counterpart has been demonstrated. This guidance notwithstanding, animal feeding studies have routinely been conducted with GM crops, but their conclusions on safety are not always consistent. To accurately evaluate potential risks from GM crops, risk assessors need clearly interpretable results from reliable studies. The development of the FSSRTool, which provides the user with a means of assessing the reliability of a toxicology study to inform risk assessment, is discussed. Its application to the body of literature on GM crop food safety studies demonstrates that reliable studies report no toxicologically relevant differences between rodents fed GM crops or their non-GM comparators.

  8. 76 FR 35396 - Notice of Intent To Reestablish the National Genetic Resources Advisory Council, and Request for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-17

    ... DEPARTMENT OF AGRICULTURE Agricultural Research Service Notice of Intent To Reestablish the National Genetic Resources Advisory Council, and Request for Nominations AGENCY: Agricultural Research... intent to reestablish the National Genetic Resources Advisory Council. The notice was published in the...

  9. Benefits of genetically modified crops for the poor: household income, nutrition, and health.

    PubMed

    Qaim, Matin

    2010-11-30

    The potential impacts of genetically modified (GM) crops on income, poverty and nutrition in developing countries continue to be the subject of public controversy. Here, a review of the evidence is given. As an example of a first-generation GM technology, the effects of insect-resistant Bt cotton are analysed. Bt cotton has already been adopted by millions of small-scale farmers, in India, China, and South Africa among others. On average, farmers benefit from insecticide savings, higher effective yields and sizeable income gains. Insights from India suggest that Bt cotton is employment generating and poverty reducing. As an example of a second-generation technology, the likely impacts of beta-carotene-rich Golden Rice are analysed from an ex ante perspective. Vitamin A deficiency is a serious nutritional problem, causing multiple adverse health outcomes. Simulations for India show that Golden Rice could reduce related health problems significantly, preventing up to 40,000 child deaths every year. These examples clearly demonstrate that GM crops can contribute to poverty reduction and food security in developing countries. To realise such social benefits on a larger scale requires more public support for research targeted to the poor, as well as more efficient regulatory and technology delivery systems. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. A future scenario of the global regulatory landscape regarding genome-edited crops

    PubMed Central

    Araki, Motoko

    2017-01-01

    ABSTRACT The global agricultural landscape regarding the commercial cultivation of genetically modified (GM) crops is mosaic. Meanwhile, a new plant breeding technique, genome editing is expected to make genetic engineering-mediated crop breeding more socially acceptable because it can be used to develop crop varieties without introducing transgenes, which have hampered the regulatory review and public acceptance of GM crops. The present study revealed that product- and process-based concepts have been implemented to regulate GM crops in 30 countries. Moreover, this study analyzed the regulatory responses to genome-edited crops in the USA, Argentina, Sweden and New Zealand. The findings suggested that countries will likely be divided in their policies on genome-edited crops: Some will deregulate transgene-free crops, while others will regulate all types of crops that have been modified by genome editing. These implications are discussed from the viewpoint of public acceptance. PMID:27960622

  11. Role of genomics in promoting the utilization of plant genetic resources in genebanks

    PubMed Central

    Wambugu, Peterson W; Ndjiondjop, Marie-Noelle

    2018-01-01

    Abstract Global efforts have seen the world’s plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended PMID:29688255

  12. 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.

  13. Rapid simulated gastric fluid digestion of in-seed/grain proteins expressed in genetically engineered crops.

    PubMed

    Schafer, Barry W; Embrey, Shawna K; Herman, Rod A

    2016-11-01

    The speed of simulated gastric digestion of proteins expressed in genetically engineered (GE) crops is commonly used to inform the allergenicity risk assessment. However, persistence of purified proteins in simulated gastric fluid (SGF) is poorly correlated with the allergenic status of proteins. It has been proposed that the plant or food matrix may affect the digestion of proteins and should be considered in interpreting digestion results. Here the SGF digestion of several GE proteins both as purified preparations and in soybean, corn, and cotton seed/grain extracts (in-matrix) are compared. Cry1F, Cry1Ac, phosphinothricin acetyltransferase (PAT), aryloxyalkanoate dioxygenase-1 (AAD-1), aryloxyalkanoate dioxygenase-12 (AAD-12), and double mutant 5-enol pyruvylshikimate-3-phosphate synthase (2mEPSPS) were all found to rapidly digest both as purified protein preparations and in seed/grain extracts from GE crops expressing these proteins. Based on these results, purified protein from microbial sources is a suitable surrogate for proteins in-matrix when conducting SGF digestion studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. On the rationale and interpretation of the Farm Scale Evaluations of genetically modified herbicide-tolerant crops.

    PubMed Central

    Squire, G R; Brooks, D R; Bohan, D A; Champion, G T; Daniels, R E; Haughton, A J; Hawes, C; Heard, M S; Hill, M O; May, M J; Osborne, J L; Perry, J N; Roy, D B; Woiwod, I P; Firbank, L G

    2003-01-01

    Farmland biodiversity and food webs were compared in conventional and genetically modified herbicide-tolerant (GMHT) crops of beet (Beta vulgaris L.), maize (Zea mays L.) and both spring and winter oilseed rape (Brassica napus L.). GMHT and conventional varieties were sown in a split-field experimental design, at 60-70 sites for each crop, spread over three starting years beginning in 2000. This paper provides a background to the study and the rationale for its design and interpretation. It shows how data on environment, field management and the biota are used to assess the current state of the ecosystem, to define the typical arable field and to devise criteria for selecting, sampling and auditing experimental sites in the Farm Scale Evaluations. The main functional and taxonomic groups in the habitat are ranked according to their likely sensitivity to GMHT cropping, and the most responsive target organisms are defined. The value of the seedbank as a baseline and as an indicator of historical trends is proposed. Evidence from experiments during the twentieth century is analysed to show that large changes in field management have affected sensitive groups in the biota by ca. 50% during a year or short run of years--a figure against which to assess any positive or negative effects of GMHT cropping. The analysis leads to a summary of factors that were, and were not, examined in the first 3 years of the study and points to where modelling can be used to extrapolate the effects to the landscape and the agricultural region. PMID:14561314

  15. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies

    PubMed Central

    Cerqueira-Silva, Carlos Bernard M.; Jesus, Onildo N.; Santos, Elisa S. L.; Corrêa, Ronan X.; Souza, Anete P.

    2014-01-01

    Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit. PMID:25196515

  16. Market organization and animal genetic resource management: a revealed preference analysis of sheep pricing.

    PubMed

    Tindano, K; Moula, N; Leroy, P; Traoré, A; Antoine-Moussiaux, N

    2017-10-01

    Farm animal genetic resources are threatened worldwide. Participation in markets, while representing a crucial way out of poverty for many smallholders, affects genetic management choices with associated sustainability concerns. This paper proposes a contextualized study of the interactions between markets and animal genetic resources management, in the case of sheep markets in Ouagadougou, Burkina Faso. It focusses on the organization of marketing chains and the valuation of genetic characteristics by value chain actors. Marketing chain characterization was tackled through semi-structured interviews with 25 exporters and 15 butchers, both specialized in sheep. Moreover, revealed preference methods were applied to analyse the impact of animals' attributes on market pricing. Data were collected from 338 transactions during three different periods: Eid al-Adha, Christmas and New Year period, and a neutral period. The neutral period is understood as a period not close to any event likely to influence the demand for sheep. The results show that physical characteristics such as live weight, height at withers and coat colour have a strong influence on the animals' prices. Live weight has also had an increasing marginal impact on price. The different markets (local butcher, feasts, export market, sacrifices) represent distinct demands for genetic characteristics, entailing interesting consequences for animal genetic resource management. Any breeding programme should therefore take this diversity into account to allow this sector to contribute better to a sustainable development of the country.

  17. Genetic algorithm parameters tuning for resource-constrained project scheduling problem

    NASA Astrophysics Data System (ADS)

    Tian, Xingke; Yuan, Shengrui

    2018-04-01

    Project Scheduling Problem (RCPSP) is a kind of important scheduling problem. To achieve a certain optimal goal such as the shortest duration, the smallest cost, the resource balance and so on, it is required to arrange the start and finish of all tasks under the condition of satisfying project timing constraints and resource constraints. In theory, the problem belongs to the NP-hard problem, and the model is abundant. Many combinatorial optimization problems are special cases of RCPSP, such as job shop scheduling, flow shop scheduling and so on. At present, the genetic algorithm (GA) has been used to deal with the classical RCPSP problem and achieved remarkable results. Vast scholars have also studied the improved genetic algorithm for the RCPSP problem, which makes it to solve the RCPSP problem more efficiently and accurately. However, for the selection of the main parameters of the genetic algorithm, there is no parameter optimization in these studies. Generally, we used the empirical method, but it cannot ensure to meet the optimal parameters. In this paper, the problem was carried out, which is the blind selection of parameters in the process of solving the RCPSP problem. We made sampling analysis, the establishment of proxy model and ultimately solved the optimal parameters.

  18. A community resource for exploring and utilizing genetic diversity in the USDA Pea Single Plant Plus Collection

    USDA-ARS?s Scientific Manuscript database

    Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed, and fodder, and many breeding programs exist to develop cultivars adapted to these end uses. In order to conserve genetic diversity useful to researchers, large pea collections have been constructed by numerous na...

  19. Halophytes As Bioenergy Crops

    PubMed Central

    Sharma, Rita; Wungrampha, Silas; Singh, Vinay; Pareek, Ashwani; Sharma, Manoj K.

    2016-01-01

    Shrinking arable land due to soil salinization and, depleting fresh water resources pose serious worldwide constraints to crop productivity. A vision of using plant feedstock for biofuel production can only be realized if we can identify alternate species that can be grown on saline soils and therefore, would not compete for the resources required for conventional agriculture. Halophytes have remarkable ability to grow under high salinity conditions. They can be irrigated with seawater without compromising their biomass and seed yields making them good alternate candidates as bioenergy crops. Both oil produced from the seeds and the lignocellulosic biomass of halophytes can be utilized for biofuel production. Several researchers across the globe have recognized this potential and assessed several halophytes for their tolerance to salt, seed oil contents and composition of their lignocellulosic biomass. Here, we review current advances and highlight the key species of halophytes analyzed for this purpose. We have critically assessed the challenges and opportunities associated with using halophytes as bioenergy crops. PMID:27679645

  20. Endemic insular and coastal Tunisian date palm genetic diversity.

    PubMed

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.

  1. Embracing Complexity of Crop Phytobiomes with a Multidisciplinary Roadmap for Phytobiomes Research and an Industry-Academic Research Alliance

    NASA Astrophysics Data System (ADS)

    Eversole, K.

    2016-12-01

    To meet the demands of a global human population expected to exceed 9.6 billion by 2055, crop productivity in sustainable agricultural systems must improve considerably in the face of a steadily changing climate and increased biotic and abiotic stressors. Traditional agricultural sciences have relied mostly on research within individual disciplines and linear, reductionist approaches for crop improvement. While significant advancements have been made in developing and characterizing genetic and genomic resources for crops, we still have a very limited understanding of genotype by environment x management (GxExM) interactions that determine productivity, sustainability, quality, and the ability to withstand biotic and abiotic stressors. Embracing complexity and the non-linear organization and regulation of biological systems would enable a paradigm shift in breeding and crop production by allowing us to move towards a holistic, systems level approach that integrates a wide range of disciplines (e.g., geophysics, biology, agronomy, physiology, genomics, genetics, breeding, physics, pattern recognition, feedback loops, modeling, and engineering) and knowledge about crop phytobiomes (i.e., plants, their associated macro- and micro-organisms, and the geophysical environment of distinct geographical sites). By focusing on the phytobiome, we will be able to elucidate, quantify, model, predict, act, manipulate, and prevent and ultimately prescribe the cropping systems, methods, and management practices most suited for a particular farm, grassland, or forest. The recently released, multidisciplinary roadmap entitled Phytobiomes: A Roadmap for Research and Translation and the new International Alliance for Phytobiomes Research, an industry-academic consortium, will be presented.

  2. Weed control changes and genetically modified herbicide tolerant crops in the USA 1996-2012.

    PubMed

    Brookes, Graham

    2014-01-01

    Crops that have been genetically modified (GM) to be tolerant to herbicides have been widely grown in the USA since 1996. The rapid and widespread adoption of this technology reflects the important economic and environmental benefits that farmers have derived from its use (equal to $21.7 billion additional farm income and a 225 million kg reduction in herbicide active ingredient use 1996-2012). During this time, weed control practices in these crops relative to the 'conventional alternative' have evolved to reflect experience of using the technology, the challenges that have arisen and the increasing focus in recent years on developing sustainable production systems. This paper examines the evidence on the changing nature of herbicides used with these crops and in particular how farmers addressed the challenge of weed resistance. The evidence shows that use of the technology has resulted in a net reduction in both the amount of herbicide used and the associated environmental impact, as measured by the EIQ indicator when compared to what can reasonably be expected if the area planted to GM HT crops reverted to conventional production methods. It also facilitated many farmers being able to derive the economic and environmental benefits associated with switching from a plough-based to a no tillage or conservation tillage production system. In terms of herbicide use, the technology has also contributed to a change the profile of herbicides used. A broad range of, mostly selective herbicides has been replaced by one or 2 broad-spectrum herbicides (mostly glyphosate) used in conjunction with one or 2 other (complementary) herbicides. Since the mid-2000s, the average amount of herbicide applied and the associated environmental load, as measured by the EIQ indicator, have increased on both GM HT and conventional crops. A primary reason for these changes has been increasing incidence of weed species developing populations resistant to herbicides and increased awareness of

  3. DNA barcoding simplifies environmental risk assessment of genetically modified crops in biodiverse regions.

    PubMed

    Nzeduru, Chinyere V; Ronca, Sandra; Wilkinson, Mike J

    2012-01-01

    Transgenes encoding for insecticidal crystal (Cry) proteins from the soil-dwelling bacterium Bacillus Thuringiensis have been widely introduced into Genetically Modified (GM) crops to confer protection against insect pests. Concern that these transgenes may also harm beneficial or otherwise valued insects (so-called Non Target Organisms, NTOs) represents a major element of the Environmental Risk Assessments (ERAs) used by all countries prior to commercial release. Compiling a comprehensive list of potentially susceptible NTOs is therefore a necessary part of an ERA for any Cry toxin-containing GM crop. In partly-characterised and biodiverse countries, NTO identification is slowed by the need for taxonomic expertise and time to enable morphological identifications. This limitation represents a potentially serious barrier to timely adoption of GM technology in some developing countries. We consider Bt Cry1A cowpea (Vigna unguiculata) in Nigeria as an exemplar to demonstrate how COI barcoding can provide a simple and cost-effective means of addressing this problem. Over a period of eight weeks, we collected 163 insects from cowpea flowers across the agroecological and geographic range of the crop in Nigeria. These individuals included 32 Operational Taxonomic Units (OTUs) spanning four Orders and that could mostly be assigned to genus or species level. They included 12 Lepidopterans and two Coleopterans (both potentially sensitive to different groups of Cry proteins). Thus, barcode-assisted diagnoses were highly harmonised across groups (typically to genus or species level) and so were insensitive to expertise or knowledge gaps. Decisively, the entire study was completed within four months at a cost of less than 10,000 US$. The broader implications of the findings for food security and the capacity for safe adoption of GM technology are briefly explored.

  4. Genetic control of ascorbic acid biosynthesis and recycling in horticultural crops

    NASA Astrophysics Data System (ADS)

    Mellidou, Ifigeneia; Kanellis, Angelos K.

    2017-07-01

    Ascorbic acid (AsA) is an essential compound present in almost all living organisms that has important functions in several aspects of plant growth and development, hormone signalling, as well as stress defense networks. In recent years, the genetic regulation of AsA metabolic pathways has received much attention due to its beneficial role in human diet. Despite the great variability within species, genotypes, tissues and developmental stages, AsA accumulation is considered to be controlled by the fine orchestration of net biosynthesis, recycling, degradation/oxidation, and/or intercellular and intracellular transport. To date, several structural genes from the AsA metabolic pathways and transcription factors are considered to significantly affect AsA in plant tissues, either at the level of activity, transcription or translation via feedback inhibition. Yet, all the emerging studies support the notion that the steps proceeding through GDP-L-galactose phosphorylase and to a lesser extent through GDP-D-mannose-3,5-epimerase are control points in governing AsA pool size in several species. In this mini review, we discuss the current consensus of the genetic regulation of AsA biosynthesis and recycling, with a focus on horticultural crops. The aspects of AsA degradation and transport are not discussed herein. Novel insights of how this multifaceted trait is regulated are critical to prioritize candidate genes for follow-up studies towards improving the nutritional value of fruits and vegetables.

  5. DNA-informed breeding of rosaceous crops: promises, progress and prospects

    PubMed Central

    Peace, Cameron P

    2017-01-01

    Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the ‘chasm’ between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists. PMID:28326185

  6. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered.

  7. 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

  8. 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.

  9. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice

    PubMed Central

    Shrestha, Rosemary; Matteis, Luca; Skofic, Milko; Portugal, Arllet; McLaren, Graham; Hyman, Glenn; Arnaud, Elizabeth

    2012-01-01

    The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP. PMID:22934074

  10. The California Biomass Crop Adoption Model estimates biofuel feedstock crop production across diverse agro-ecological zones within the state, under different future climates

    NASA Astrophysics Data System (ADS)

    Kaffka, S.; Jenner, M.; Bucaram, S.; George, N.

    2012-12-01

    Both regulators and businesses need realistic estimates for the potential production of biomass feedstocks for biofuels and bioproducts. This includes the need to understand how climate change will affect mid-tem and longer-term crop performance and relative advantage. The California Biomass Crop Adoption Model is a partial mathematical programming optimization model that estimates the profit level needed for new crop adoption, and the crop(s) displaced when a biomass feedstock crop is added to the state's diverse set of cropping systems, in diverse regions of the state. Both yield and crop price, as elements of profit, can be varied. Crop adoption is tested against current farmer preferences derived from analysis of 10 years crop production data for all crops produced in California, collected by the California Department of Pesticide Regulation. Analysis of this extensive data set resulted in 45 distinctive, representative farming systems distributed across the state's diverse agro-ecological regions. Estimated yields and water use are derived from field trials combined with crop simulation, reported elsewhere. Crop simulation is carried out under different weather and climate assumptions. Besides crop adoption and displacement, crop resource use is also accounted, derived from partial budgets used for each crop's cost of production. Systematically increasing biofuel crop price identified areas of the state where different types of crops were most likely to be adopted. Oilseed crops like canola that can be used for biodiesel production had the greatest potential to be grown in the Sacramento Valley and other northern regions, while sugar beets (for ethanol) had the greatest potential in the northern San Joaquin Valley region, and sweet sorghum in the southern San Joaquin Valley. Up to approximately 10% of existing annual cropland in California was available for new crop adoption. New crops are adopted if the entire cropping system becomes more profitable. In

  11. Catchment Area Treatment (CAT) Plan and Crop Area Optimization for Integrated Management in a Water Resource Project

    NASA Astrophysics Data System (ADS)

    Jaiswal, R. K.; Thomas, T.; Galkate, R. V.; Ghosh, N. C.; Singh, S.

    2013-09-01

    A scientifically developed catchment area treatment (CAT) plan and optimized pattern of crop areas may be the key for sustainable development of water resource, profitability in agriculture and improvement of overall economy in drought affected Bundelkhand region of Madhya Pradesh (India). In this study, an attempt has been made to develop a CAT plan using spatial variation of geology, geomorphology, soil, drainage, land use in geographical information system for selection of soil and water conservation measures and crop area optimization using linear programming for maximization of return considering water availability, area affinity, fertilizers, social and market constraints in Benisagar reservoir project of Chhatarpur district (M.P.). The scientifically developed CAT plan based on overlaying of spatial information consists of 58 mechanical measure (49 boulder bunds, 1 check dam, 7 cully plug and 1 percolation tank), 2.60 km2 land for agro forestry, 2.08 km2 land for afforestation in Benisagar dam and 67 mechanical measures (45 boulder bunds and 22 gully plugs), 7.79 km2 land for agro forestry, 5.24 km2 land for afforestation in Beniganj weir catchment with various agronomic measures for agriculture areas. The linear programming has been used for optimization of crop areas in Benisagar command for sustainable development considering various scenarios of water availability, efficiencies, affinity and fertilizers availability in the command. Considering present supply condition of water, fertilizers, area affinity and making command self sufficient in most of crops, the net benefit can be increase to Rs. 1.93 crores from 41.70 km2 irrigable area in Benisagar command by optimizing cropping pattern and reducing losses during conveyance and application of water.

  12. The GCP molecular marker toolkit, an instrument for use in breeding food security crops.

    PubMed

    Van Damme, Veerle; Gómez-Paniagua, Humberto; de Vicente, M Carmen

    2011-12-01

    Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities.

  13. Use of Carabids for the Post-Market Environmental Monitoring of Genetically Modified Crops

    PubMed Central

    Skoková Habuštová, Oxana; Svobodová, Zdeňka; Cagáň, Ľudovít; Sehnal, František

    2017-01-01

    Post-market environmental monitoring (PMEM) of genetically modified (GM) crops is required by EU legislation and has been a subject of debate for many years; however, no consensus on the methodology to be used has been reached. We explored the suitability of carabid beetles as surrogates for the detection of unintended effects of GM crops in general PMEM surveillance. Our study combines data on carabid communities from five maize field trials in Central Europe. Altogether, 86 species and 58,304 individuals were collected. Modeling based on the gradual elimination of the least abundant species, or of the fewest categories of functional traits, showed that a trait-based analysis of the most common species may be suitable for PMEM. Species represented by fewer than 230 individuals (all localities combined) should be excluded and species with an abundance higher than 600 should be preserved for statistical analyses. Sixteen species, representing 15 categories of functional traits fulfill these criteria, are typical dominant inhabitants of agroecocoenoses in Central Europe, are easy to determine, and their functional classification is well known. The effect of sampling year is negligible when at least four samples are collected during maize development beginning from 1 April. The recommended methodology fulfills PMEM requirements, including applicability to large-scale use. However, suggested thresholds of carabid comparability should be verified before definitive conclusions are drawn. PMID:28353663

  14. Water footprint of crop production for different crop structures in the Hebei southern plain, North China

    NASA Astrophysics Data System (ADS)

    Chu, Yingmin; Shen, Yanjun; Yuan, Zaijian

    2017-06-01

    The North China Plain (NCP) has a serious shortage of freshwater resources, and crop production consumes approximately 75 % of the region's water. To estimate water consumption of different crops and crop structures in the NCP, the Hebei southern plain (HSP) was selected as a study area, as it is a typical region of groundwater overdraft in the NCP. In this study, the water footprint (WF) of crop production, comprised of green, blue and grey water footprints, and its annual variation were analyzed. The results demonstrated the following: (1) the WF from the production of main crops was 41.8 km3 in 2012. Winter wheat, summer maize and vegetables were the top water-consuming crops in the HSP. The water footprint intensity (WFI) of cotton was the largest, and for vegetables, it was the smallest; (2) the total WF, WFblue, WFgreen and WFgrey for 13 years (2000-2012) of crop production were 604.8, 288.5, 141.3 and 175.0 km3, respectively, with an annual downtrend from 2000 to 2012; (3) winter wheat, summer maize and vegetables consumed the most groundwater, and their blue water footprint (WFblue) accounted for 74.2 % of the total WFblue in the HSP; (4) the crop structure scenarios analysis indicated that, with approximately 20 % of arable land cultivated with winter wheat-summer maize in rotation, 38.99 % spring maize, 10 % vegetables and 10 % fruiters, a sustainable utilization of groundwater resources can be promoted, and a sufficient supply of food, including vegetables and fruits, can be ensured in the HSP.

  15. Transgenic Crops: Implications for Biodiversity and Sustainable Agriculture

    ERIC Educational Resources Information Center

    Garcia, Maria Alice; Altieri, Miguel A.

    2005-01-01

    The potential for genetically modified (GM) crops to threaten biodiversity conservation and sustainable agriculture is substantial. Megadiverse countries and centers of origin and/or diversity of crop species are particularly vulnerable regions. The future of sustainable agriculture may be irreversibly jeopardized by contamination of in situ…

  16. Can genomics deliver climate-change ready crops?

    PubMed

    Varshney, Rajeev K; Singh, Vikas K; Kumar, Arvind; Powell, Wayne; Sorrells, Mark E

    2018-04-20

    Development of climate resilient crops with accelerating genetic gains in crops will require integration of different disciplines/technologies, to see the impact in the farmer's field. In this review, we summarize how we are utilizing our germplasm collections to identify superior alleles/haplotypes through NGS based sequencing approaches and how genomics-enabled technologies together with precise phenotyping are being used in crop breeding. Pre-breeding and genomics-assisted breeding approaches are contributing to the more efficient development of climate-resilient crops. It is anticipated that the integration of several disciplines/technologies will result in the delivery of climate change ready crops in less time. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. [Review of transgenic crop breeding in China].

    PubMed

    Huang, Dafang

    2015-06-01

    The development history and fundamental experience of transgenic crops (Genetically modified crops) breeding in China for near 30 years were reviewed. It was illustrated that a scientific research, development and industrialization system of transgenic crops including gene discovery, transformation, variety breeding, commercialization, application and biosafety assessment has been initially established which was few in number in the world. The research innovative capacity of transgenic cotton, rice and corn has been lifted. The research features as well as relative advantages have been initially formed. The problems and challenges of transgenic crop development were discussed. In addition, three suggestions of promoting commercialization, speeding up implementation of the Major National Project of GM Crops, and enhancing science communication were made.

  18. Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

    USDA-ARS?s Scientific Manuscript database

    Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

  19. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

    PubMed

    Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

    2016-01-01

    Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat

  20. Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis

    PubMed Central

    Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

    2016-01-01

    A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement. PMID:26799483

  1. Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis.

    PubMed

    Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

    2016-01-01

    A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement.

  2. Developmental Pathways Are Blueprints for Designing Successful Crops

    PubMed Central

    Trevaskis, Ben

    2018-01-01

    Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene–gene or gene–environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted. PMID:29922318

  3. Developmental Pathways Are Blueprints for Designing Successful Crops.

    PubMed

    Trevaskis, Ben

    2018-01-01

    Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.

  4. Assessment of the nutritional values of genetically modified wheat, corn, and tomato crops.

    PubMed

    Venneria, Eugenia; Fanasca, Simone; Monastra, Giovanni; Finotti, Enrico; Ambra, Roberto; Azzini, Elena; Durazzo, Alessandra; Foddai, Maria Stella; Maiani, Giuseppe

    2008-10-08

    The genetic modification in fruit and vegetables could lead to changes in metabolic pathways and, therefore, to the variation of the molecular pattern, with particular attention to antioxidant compounds not well-described in the literature. The aim of the present study was to compare the quality composition of transgenic wheat ( Triticum durum L.), corn ( Zea mays L.), and tomato ( Lycopersicum esculentum Mill.) to the nontransgenic control with a similar genetic background. In the first experiment, Ofanto wheat cultivar containing the tobacco rab1 gene and nontransgenic Ofanto were used. The second experiment compared two transgenic lines of corn containing Bacillus thuringiensis "Cry toxin" gene (PR33P67 and Pegaso Bt) to their nontransgenic forms. The third experiment was conducted on transgenic tomato ( Lycopersicum esculentum Mill.) containing the Agrobacterium rhizogenes rolD gene and its nontransgenic control (cv. Tondino). Conventional and genetically modified crops were compared in terms of fatty acids content, unsaponifiable fraction of antioxidants, total phenols, polyphenols, carotenoids, vitamin C, total antioxidant activity, and mineral composition. No significant differences were observed for qualitative traits analyzed in wheat and corn samples. In tomato samples, the total antioxidant activity (TAA), measured by FRAP assay, and the naringenin content showed a lower value in genetically modified organism (GMO) samples (0.35 mmol of Fe (2+) 100 g (-1) and 2.82 mg 100 g (-1), respectively), in comparison to its nontransgenic control (0.41 mmol of Fe (2+) 100 g (-1) and 4.17 mg 100 g (-1), respectively). On the basis of the principle of substantial equivalence, as articulated by the World Health Organization, the Organization for Economic Cooperation and Development, and the United Nations Food and Agriculture Organization, these data support the conclusion that GM events are nutritionally similar to conventional varieties of wheat, corn, and tomato on

  5. Crop Species Diversity Changes in the United States: 1978–2012

    PubMed Central

    Aguilar, Jonathan; Gramig, Greta G.; Hendrickson, John R.; Archer, David W.; Forcella, Frank; Liebig, Mark A.

    2015-01-01

    Anecdotal accounts regarding reduced US cropping system diversity have raised concerns about negative impacts of increasingly homogeneous cropping systems. However, formal analyses to document such changes are lacking. Using US Agriculture Census data, which are collected every five years, we quantified crop species diversity from 1978 to 2012, for the contiguous US on a county level basis. We used Shannon diversity indices expressed as effective number of crop species (ENCS) to quantify crop diversity. We then evaluated changes in county-level crop diversity both nationally and for each of the eight Farm Resource Regions developed by the National Agriculture Statistics Service. During the 34 years we considered in our analyses, both national and regional ENCS changed. Nationally, crop diversity was lower in 2012 than in 1978. However, our analyses also revealed interesting trends between and within different Resource Regions. Overall, the Heartland Resource Region had the lowest crop diversity whereas the Fruitful Rim and Northern Crescent had the highest. In contrast to the other Resource Regions, the Mississippi Portal had significantly higher crop diversity in 2012 than in 1978. Also, within regions there were differences between counties in crop diversity. Spatial autocorrelation revealed clustering of low and high ENCS and this trend became stronger over time. These results show that, nationally counties have been clustering into areas of either low diversity or high diversity. Moreover, a significant trend of more counties shifting to lower rather than to higher crop diversity was detected. The clustering and shifting demonstrates a trend toward crop diversity loss and attendant homogenization of agricultural production systems, which could have far-reaching consequences for provision of ecosystem system services associated with agricultural systems as well as food system sustainability. PMID:26308552

  6. Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

    PubMed Central

    Ramage, Elizabeth; Weiss, Eli J.; Radey, Matthew; Hayden, Hillary S.; Held, Kiara G.; Huse, Holly K.; Zurawski, Daniel V.; Brittnacher, Mitchell J.; Manoil, Colin

    2015-01-01

    ABSTRACT Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains. PMID:25845845

  7. 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.

  8. Advances in Genetical Genomics of Plants

    PubMed Central

    Joosen, R.V.L.; Ligterink, W.; Hilhorst, H.W.M.; Keurentjes, J.J.B.

    2009-01-01

    Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research. PMID:20514216

  9. 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.

  10. Resources for human genetics on the World Wide Web.

    PubMed

    Osborne, L R; Lee, J R; Scherer, S W

    1997-09-01

    A little over a century ago, the HMS Beagle sailed the Pacific Ocean bringing Charles Darwin to the perfect environment in which to piece together his observations forming the theory of evolution. Now, geneticists and laypeople alike surf the equally formidable waters of the internet in search of enlightenment. Here, we attempt to help you navigate towards resources for human genetics by providing maps to three destinations: The Human Genome Project (Box 1), education (Box 2), and human genetic diseases (Box 3). For each, we highlight a few sites that we consider are the most informative and original. A more extensive list containing other useful sites has been compiled and posted on a 'jump site' at: http:/(/)www.cgdn.generes.ca/.

  11. Diversifying mechanisms in the on-farm evolution of crop mixtures.

    PubMed

    Thomas, Mathieu; Thépot, Stéphanie; Galic, Nathalie; Jouanne-Pin, Sophie; Remoué, Carine; Goldringer, Isabelle

    2015-06-01

    While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio-genetic model is an original experimental evolution design referred to as on-farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environments. We studied a French farmer-led initiative where a mixture of four wheat landraces called 'Mélange de Touselles' (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty-one space-time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a 'common-garden' experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within-variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes. © 2015 John Wiley & Sons Ltd.

  12. Legume crops phylogeny and genetic diversity for science and breeding

    USDA-ARS?s Scientific Manuscript database

    Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal ...

  13. Camelina as a sustainable oilseed crop: contributions of plant breeding and genetic engineering.

    PubMed

    Vollmann, Johann; Eynck, Christina

    2015-04-01

    Camelina is an underutilized Brassicaceae oilseed plant with a considerable agronomic potential for biofuel and vegetable oil production in temperate regions. In contrast to most Brassicaceae, camelina is resistant to alternaria black spot and other diseases and pests. Sequencing of the camelina genome revealed an undifferentiated allohexaploid genome with a comparatively large number of genes and low percentage of repetitive DNA. As there is a close relationship between camelina and the genetic model plant Arabidopsis, this review aims at exploring the potential of translating basic Arabidopsis results into a camelina oilseed crop for food and non-food applications. Recently, Arabidopsis genes for drought resistance or increased photosynthesis and overall productivity have successfully been expressed in camelina. In addition, gene constructs affecting lipid metabolism pathways have been engineered into camelina for synthesizing either long-chain polyunsaturated fatty acids, hydroxy fatty acids or high-oleic oils in particular camelina strains, which is of great interest in human food, industrial or biofuel applications, respectively. These results confirm the potential of camelina to serve as a biotechnology platform in biorefinery applications thus justifying further investment in breeding and genetic research for combining agronomic potential, unique oil quality features and biosafety into an agricultural production system. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Soil Health Educational Resources

    ERIC Educational Resources Information Center

    Hoorman, James J.

    2015-01-01

    Soil health and cover crops are topics of interest to farmers, gardeners, and students. Three soil health and cover crop demonstrations provide educational resources. Demonstrations one outlines two educational cover crop seed displays, including the advantages and disadvantages. Demonstration two shows how to construct and grow a cover crop root…

  15. Conflicts of interest among committee members in the National Academies’ genetically engineered crop study

    PubMed Central

    2017-01-01

    The National Academies of Sciences, Engineering and Medicine (NASEM) publishes numerous reports each year that are received with high esteem by the scientific community and public policy makers. The NASEM has internal standards for selecting committee members that author its reports, mostly from academia, and vetting conflicts of interest. This study examines whether there were any financial conflicts of interest (COIs) among the twenty invited committee members who wrote the 2016 report on genetically engineered (GE) crops. Our results showed that six panel members had one or more reportable financial COIs, none of which were disclosed in the report. We also report on institutional COIs held by the NASEM related to the report. The difference between our findings and the NASEM reporting standards are discussed. PMID:28245228

  16. MOLECULAR GENETIC TOOLS FOR ASSESSING THE STATUS AND VULNERABILITY OF AQUATIC RESOURCES

    EPA Science Inventory

    Development of ecological indicators that efficiently capture the present condition and project future vulnerabilities of biological resources is critical to sound environmental management. For this reason, the ORD's Ecological Research Program is developing genetic methodologies...

  17. Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics--current achievements and perspectives.

    PubMed

    Barkla, Bronwyn J; Castellanos-Cervantes, Thelma; de León, José L Diaz; Matros, Andrea; Mock, Hans-Peter; Perez-Alfocea, Francisco; Salekdeh, Ghasem H; Witzel, Katja; Zörb, Christian

    2013-06-01

    Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Biomass resources in California

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

    Tiangco, V.M.; Sethi, P.S.

    1993-12-31

    The biomass resources in California which have potential for energy conversion were assessed and characterized through the project funded by the California Energy Commission and the US Department of Energy`s Western Regional Biomass Energy Program (WRBEP). The results indicate that there is an abundance of biomass resources as yet untouched by the industry due to technical, economic, and environmental problems, and other barriers. These biomass resources include residues from field and seed crops, fruit and nut crops, vegetable crops, and nursery crops; food processing wastes; forest slash; energy crops; lumber mill waste; urban wood waste; urban yard waste; livestock manure;more » and chaparral. The estimated total potential of these biomass resource is approximately 47 million bone dry tons (BDT), which is equivalent to 780 billion MJ (740 trillion Btu). About 7 million BDT (132 billion MJ or 124 trillion Btu) of biomass residue was used for generating electricity by 66 direct combustion facilities with gross capacity of about 800 MW. This tonnage accounts for only about 15% of the total biomass resource potential identified in this study. The barriers interfering with the biomass utilization both in the on-site harvesting, collection, storage, handling, transportation, and conversion to energy are identified. The question whether these barriers present significant impact to biomass {open_quotes}availability{close_quotes} and {open_quotes}sustainability{close_quotes} remains to be answered.« less

  19. Tradeoffs between water requirements and yield stability in annual vs. perennial crops

    NASA Astrophysics Data System (ADS)

    Vico, Giulia; Brunsell, Nathaniel A.

    2018-02-01

    Population growth and changes in climate and diets will likely further increase the pressure on agriculture and water resources globally. Currently, staple crops are obtained from annuals plants. A shift towards perennial crops may enhance many ecosystem services, but at the cost of higher water requirements and lower yields. It is still unclear when the advantages of perennial crops overcome their disadvantages and perennial crops are thus a sustainable solution. Here we combine a probabilistic description of the soil water balance and crop development with an extensive dataset of traits of congeneric annuals and perennials to identify the conditions for which perennial crops are more viable than annual ones with reference to yield, yield stability, and effective use of water. We show that the larger and more developed roots of perennial crops allow a better exploitation of soil water resources and a reduction of yield variability with respect to annual species, but their yields remain lower when considering grain crops. Furthermore, perennial crops have higher and more variable irrigation requirements and lower water productivity. These results are important to understand the potential consequences for yield, its stability, and water resource use of a shift from annual to perennial crops and, more generally, if perennial crops may be more resilient than annual crops in the face of climatic fluctuations.

  20. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries.

    PubMed

    Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

    2015-01-01

    Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production's effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.

  1. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

    PubMed Central

    Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

    2015-01-01

    Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species. PMID:25767477

  2. 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

  3. Defining a genetic ideotype for crop improvement.

    PubMed

    Trethowan, Richard M

    2014-01-01

    While plant breeders traditionally base selection on phenotype, the development of genetic ideotypes can help focus the selection process. This chapter provides a road map for the establishment of a refined genetic ideotype. The first step is an accurate definition of the target environment including the underlying constraints, their probability of occurrence, and impact on phenotype. Once the environmental constraints are established, the wealth of information on plant physiological responses to stresses, known gene information, and knowledge of genotype ×environment and gene × environment interaction help refine the target ideotype and form a basis for cross prediction.Once a genetic ideotype is defined the challenge remains to build the ideotype in a plant breeding program. A number of strategies including marker-assisted recurrent selection and genomic selection can be used that also provide valuable information for the optimization of genetic ideotype. However, the informatics required to underpin the realization of the genetic ideotype then becomes crucial. The reduced cost of genotyping and the need to combine pedigree, phenotypic, and genetic data in a structured way for analysis and interpretation often become the rate-limiting steps, thus reducing genetic gain. Systems for managing these data and an example of ideotype construction for a defined environment type are discussed.

  4. Weed control changes and genetically modified herbicide tolerant crops in the USA 1996–2012

    PubMed Central

    Brookes, Graham

    2014-01-01

    Crops that have been genetically modified (GM) to be tolerant to herbicides have been widely grown in the USA since 1996. The rapid and widespread adoption of this technology reflects the important economic and environmental benefits that farmers have derived from its use (equal to $21.7 billion additional farm income and a 225 million kg reduction in herbicide active ingredient use 1996–2012). During this time, weed control practices in these crops relative to the ‘conventional alternative’ have evolved to reflect experience of using the technology, the challenges that have arisen and the increasing focus in recent years on developing sustainable production systems. This paper examines the evidence on the changing nature of herbicides used with these crops and in particular how farmers addressed the challenge of weed resistance. The evidence shows that use of the technology has resulted in a net reduction in both the amount of herbicide used and the associated environmental impact, as measured by the EIQ indicator when compared to what can reasonably be expected if the area planted to GM HT crops reverted to conventional production methods. It also facilitated many farmers being able to derive the economic and environmental benefits associated with switching from a plough-based to a no tillage or conservation tillage production system. In terms of herbicide use, the technology has also contributed to a change the profile of herbicides used. A broad range of, mostly selective herbicides has been replaced by one or 2 broad-spectrum herbicides (mostly glyphosate) used in conjunction with one or 2 other (complementary) herbicides. Since the mid-2000s, the average amount of herbicide applied and the associated environmental load, as measured by the EIQ indicator, have increased on both GM HT and conventional crops. A primary reason for these changes has been increasing incidence of weed species developing populations resistant to herbicides and increased

  5. Procedure to select test organisms for environmental risk assessment of genetically modified crops in aquatic systems.

    PubMed

    Hilbeck, Angelika; Bundschuh, Rebecca; Bundschuh, Mirco; Hofmann, Frieder; Oehen, Bernadette; Otto, Mathias; Schulz, Ralf; Trtikova, Miluse

    2017-11-01

    For a long time, the environmental risk assessment (ERA) of genetically modified (GM) crops focused mainly on terrestrial ecosystems. This changed when it was scientifically established that aquatic ecosystems are exposed to GM crop residues that may negatively affect aquatic species. To assist the risk assessment process, we present a tool to identify ecologically relevant species usable in tiered testing prior to authorization or for biological monitoring in the field. The tool is derived from a selection procedure for terrestrial ecosystems with substantial but necessary changes to adequately consider the differences in the type of ecosystems. By using available information from the Water Framework Directive (2000/60/EC), the procedure can draw upon existing biological data on aquatic systems. The proposed procedure for aquatic ecosystems was tested for the first time during an expert workshop in 2013, using the cultivation of Bacillus thuringiensis (Bt) maize as the GM crop and 1 stream type as the receiving environment in the model system. During this workshop, species executing important ecological functions in aquatic environments were identified in a stepwise procedure according to predefined ecological criteria. By doing so, we demonstrated that the procedure is practicable with regard to its goal: From the initial long list of 141 potentially exposed aquatic species, 7 species and 1 genus were identified as the most suitable candidates for nontarget testing programs. Integr Environ Assess Manag 2017;13:974-979. © 2017 SETAC. © 2017 SETAC.

  6. Environmental biosafety and transgenic potato in a centre of diversity for this crop.

    PubMed

    Celis, Carolina; Scurrah, Maria; Cowgill, Sue; Chumbiauca, Susana; Green, Jayne; Franco, Javier; Main, Gladys; Kiezebrink, Daan; Visser, Richard G F; Atkinson, Howard J

    2004-11-11

    The Nuffield Council on Bioethics suggests that introgression of genetic material into related species in centres of crop biodiversity is an insufficient justification to bar the use of genetically modified crops in the developing world. They consider that a precautionary approach to forgo the possible benefits invokes the fallacy of thinking that doing nothing is itself without risk to the poor. Here we report findings relevant to this and other aspects of environmental biosafety for genetically modified potato in its main centre of biodiversity, the central Andes. We studied genetically modified potato clones that provide resistance to nematodes, principal pests of Andean potato crops. We show that there is no harm to many non-target organisms, but gene flow occurs to wild relatives growing near potato crops. If stable introgression were to result, the fitness of these wild species could be altered. We therefore transformed the male sterile cultivar Revolucion to provide a genetically modified nematode-resistant potato to evaluate the benefits that this provides until the possibility of stable introgression to wild relatives is determined. Thus, scientific progress is possible without compromise to the precautionary principle.

  7. Accounting for soil biotic effects on soil health and crop productivity in the design of crop rotations.

    PubMed

    Dias, Teresa; Dukes, Angela; Antunes, Pedro M

    2015-02-01

    There is an urgent need for novel agronomic improvements capable of boosting crop yields while alleviating environmental impacts. One such approach is the use of optimized crop rotations. However, a set of measurements that can serve as guiding principles for the design of crop rotations is lacking. Crop rotations take advantage of niche complementarity, enabling the optimization of nutrient use and the reduction of pests and specialist pathogen loads. However, despite the recognized importance of plant-soil microbial interactions and feedbacks for crop yield and soil health, this is ignored in the selection and management of crops for rotation systems. We review the literature and propose criteria for the design of crop rotations focusing on the roles of soil biota and feedback on crop productivity and soil health. We consider that identifying specific key organisms or consortia capable of influencing plant productivity is more important as a predictor of soil health and crop productivity than assessing the overall soil microbial diversity per se. As such, we propose that setting up soil feedback studies and applying genetic sequencing tools towards the development of soil biotic community databases has a strong potential to enable the establishment of improved soil health indicators for optimized crop rotations. © 2014 Society of Chemical Industry.

  8. Space Data for Crop Management

    NASA Technical Reports Server (NTRS)

    1990-01-01

    CROPIX, Inc., formed in 1984 by Frank Lamb, president of the Eastern Oregon Farming Company, monitors primarily potato crops in a 20,000 square mile area of northern Oregon and central Washington. Potatoes are a high value specialty crop that can be more profitable to the farmer if he has advance knowledge of market conditions, knows when to harvest, and when to take it to market. By processing and collecting data collected by the NASA-developed Landsat Earth Resources survey satellites, Lamb is able to provide accurate information on crop acreage and conditions on a more timely basis than the routine estimates by the USDA. CROPIX uses Landsat data to make acreage estimates of crops, and to calculate a field-by-field vegetative index number. CROPIX then distributes to its customers a booklet containing color-coded maps, an inventory of crops, plus data and graphs on crop conditions and other valuable information.

  9. Maize-grain legume intercropping for enhanced resource use efficiency and crop productivity in the Guinea savanna of northern Ghana.

    PubMed

    Kermah, Michael; Franke, Angelinus C; Adjei-Nsiah, Samuel; Ahiabor, Benjamin D K; Abaidoo, Robert C; Giller, Ken E

    2017-11-01

    Smallholder farmers in the Guinea savanna practise cereal-legume intercropping to mitigate risks of crop failure in mono-cropping. The productivity of cereal-legume intercrops could be influenced by the spatial arrangement of the intercrops and the soil fertility status. Knowledge on the effect of soil fertility status on intercrop productivity is generally lacking in the Guinea savanna despite the wide variability in soil fertility status in farmers' fields, and the productivity of within-row spatial arrangement of intercrops relative to the distinct-row systems under on-farm conditions has not been studied in the region. We studied effects of maize-legume spatial intercropping patterns and soil fertility status on resource use efficiency, crop productivity and economic profitability under on-farm conditions in the Guinea savanna. Treatments consisted of maize-legume intercropped within-row, 1 row of maize alternated with one row of legume, 2 rows of maize alternated with 2 rows of legume, a sole maize crop and a sole legume crop. These were assessed in the southern Guinea savanna (SGS) and the northern Guinea savanna (NGS) of northern Ghana for two seasons using three fields differing in soil fertility in each agro-ecological zone. Each treatment received 25 kg P and 30 kg K ha -1 at sowing, while maize received 25 kg (intercrop) or 50 kg (sole) N ha -1 at 3 and 6 weeks after sowing. The experiment was conducted in a randomised complete block design with each block of treatments replicated four times per fertility level at each site. Better soil conditions and rainfall in the SGS resulted in 48, 38 and 9% more maize, soybean and groundnut grain yield, respectively produced than in the NGS, while 11% more cowpea grain yield was produced in the NGS. Sole crops of maize and legumes produced significantly more grain yield per unit area than the respective intercrops of maize and legumes. Land equivalent ratios (LERs) of all intercrop patterns were greater than

  10. Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

    PubMed

    Collier, Ray; Dasgupta, Kasturi; Xing, Yan-Ping; Hernandez, Bryan Tarape; Shao, Min; Rohozinski, Dominica; Kovak, Emma; Lin, Jeanie; de Oliveira, Maria Luiza P; Stover, Ed; McCue, Kent F; Harmon, Frank G; Blechl, Ann; Thomson, James G; Thilmony, Roger

    2017-06-01

    Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  11. Assessing genetically modified crops to minimize the risk of increased food allergy: a review.

    PubMed

    Goodman, Richard E; Hefle, Susan L; Taylor, Steven L; van Ree, Ronald

    2005-06-01

    The first genetically modified (GM) crops approved for food use (tomato and soybean) were evaluated for safety by the United States Food and Drug Administration prior to commercial production. Among other factors, those products and all additional GM crops that have been grown commercially have been evaluated for potential increases in allergenic properties using methods that are consistent with the current understanding of food allergens and knowledge regarding the prediction of allergenic activity. Although there have been refinements, the key aspects of the evaluation have not changed. The allergenic properties of the gene donor and the host (recipient) organisms are considered in determining the appropriate testing strategy. The amino acid sequence of the encoded protein is compared to all known allergens to determine whether the protein is a known allergen or is sufficiently similar to any known allergen to indicate an increased probability of allergic cross-reactivity. Stability of the protein in the presence of acid with the stomach protease pepsin is tested as a risk factor for food allergenicity. In vitro or in vivo human IgE binding are tested when appropriate, if the gene donor is an allergen or the sequence of the protein is similar to an allergen. Serum donors and skin test subjects are selected based on their proven allergic responses to the gene donor or to material containing the allergen that was matched in sequence. While some scientists and regulators have suggested using animal models, performing broadly targeted serum IgE testing or extensive pre- or post-market clinical tests, current evidence does not support these tests as being predictive or practical. Based on the evidence to date, the current assessment process has worked well to prevent the unintended introduction of allergens in commercial GM crops.

  12. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics

    PubMed Central

    Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

    2016-01-01

    Background Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. Results We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Conclusions Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been

  13. Complementary crops and landscape features sustain wild bee communities.

    PubMed

    Martins, Kyle T; Albert, Cécile H; Lechowicz, Martin J; Gonzalez, Andrew

    2018-06-01

    Wild bees, which are important for commercial pollination, depend on floral and nesting resources both at farms and in the surrounding landscape. Mass-flowering crops are only in bloom for a few weeks and unable to support bee populations that persist throughout the year. Farm fields and orchards that flower in succession potentially can extend the availability of floral resources for pollinators. However, it is unclear whether the same bee species or genera will forage from one crop to the next, which bees specialize on particular crops, and to what degree inter-crop visitation patterns will be mediated by landscape context. We therefore studied local- and landscape-level drivers of bee diversity and species turnover in apple orchards, blueberry fields, and raspberry fields that bloom sequentially in southern Quebec, Canada. Despite the presence of high bee species turnover, orchards and small fruit fields complemented each other phenologically by supporting two bee genera essential to their pollination: mining bees (Andrena spp.) and bumble bees (Bombus spp.). A number of bee species specialized on apple, blueberry, or raspberry blossoms, suggesting that all three crops could be used to promote regional bee diversity. Bee diversity (rarefied richness, wild bee abundance) was highest across crops in landscapes containing hedgerows, meadows, and suburban areas that provide ancillary nesting and floral resources throughout the spring and summer. Promoting phenological complementarity in floral resources at the farmstead and landscape scales is essential to sustaining diverse wild bee populations. © 2018 by the Ecological Society of America.

  14. Fiber resources

    Treesearch

    P. J. Ince

    2004-01-01

    In economics, primary inputs or factors of production define the term ‘resources.’ Resources include land resources (plants, animals, and minerals), labor, capital, and entrepreneurship. Almost all pulp and paper fiber resources are plant materials obtained from trees or agricultural crops. These resources encompass plant materials harvested directly from the land (...

  15. An ultrasensitive label-free electrochemiluminescent immunosensor for measuring Cry1Ab level and genetically modified crops content.

    PubMed

    Gao, Hongfei; Wen, Luke; Wu, Yuhua; Fu, Zhifeng; Wu, Gang

    2017-11-15

    The development of genetically modified (GM) insect-resistant crops has aroused great public concern about the risks on the eco-environment resulting from a release of toxic Cry proteins (such as Cry1Ab) to the soil. Therefore, it is of crucial importance to measure the Cry proteins level and the GM crops content. Here, we have tested for the first time a method that uses novel carbon nanospheres (CNPs) label-free electrochemiluminescent (ECL) immunosensor for the ultrasensitive quantification of Cry1Ab and GM crops. In this work, novel CNPs were prepared from printer toner with a very facile approach, and linked with anti-Cry1Ab antibodies to modify a golden working electrode. The immunoreaction between Cry1Ab and its antibody formed an immunocomplex on the bioreceptor region of the sensor, which inhibited electron transfer between the electrode surface and the ECL substance, leading to a decrease of ECL response. Under the optimal conditions, the fabricated label-free ECL immunosensor determined Cry1Ab down to 3.0pgmL -1 within a linear range of 0.010-1.0ngmL -1 , showing significant improvement of sensitivity than that of most previous reports. Meanwhile, the proposed method was successfully applied for GM rice BT63 and GM maize MON810 detections down to 0.010% and 0.020%, respectively. Due to its outstanding advantages such as high sensitivity, ideal selectivity, simple fabrication, rapid detection, and low cost, the developed method can be considered as a powerful and pioneering tool for GM crops detection. Its use can also be extended to other toxin protein sensing in foods. Copyright © 2017. Published by Elsevier B.V.

  16. 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

  17. 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

  18. Flexible Job-Shop Scheduling with Dual-Resource Constraints to Minimize Tardiness Using Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Paksi, A. B. N.; Ma'ruf, A.

    2016-02-01

    In general, both machines and human resources are needed for processing a job on production floor. However, most classical scheduling problems have ignored the possible constraint caused by availability of workers and have considered only machines as a limited resource. In addition, along with production technology development, routing flexibility appears as a consequence of high product variety and medium demand for each product. Routing flexibility is caused by capability of machines that offers more than one machining process. This paper presents a method to address scheduling problem constrained by both machines and workers, considering routing flexibility. Scheduling in a Dual-Resource Constrained shop is categorized as NP-hard problem that needs long computational time. Meta-heuristic approach, based on Genetic Algorithm, is used due to its practical implementation in industry. Developed Genetic Algorithm uses indirect chromosome representative and procedure to transform chromosome into Gantt chart. Genetic operators, namely selection, elitism, crossover, and mutation are developed to search the best fitness value until steady state condition is achieved. A case study in a manufacturing SME is used to minimize tardiness as objective function. The algorithm has shown 25.6% reduction of tardiness, equal to 43.5 hours.

  19. Crop-associated virus reduces the rooting depth of non-crop perennial native grass more than non-crop-associated virus with known viral suppressor of RNA silencing (VSR).

    PubMed

    Malmstrom, Carolyn M; Bigelow, Patrick; Trębicki, Piotr; Busch, Anna K; Friel, Colleen; Cole, Ellen; Abdel-Azim, Heba; Phillippo, Colin; Alexander, Helen M

    2017-09-15

    As agricultural acreage expanded and came to dominate landscapes across the world, viruses gained opportunities to move between crop and wild native plants. In the Midwestern USA, virus exchange currently occurs between widespread annual Poaceae crops and remnant native perennial prairie grasses now under consideration as bioenergy feedstocks. In this region, the common aphid species Rhopalosiphum padi L. (the bird cherry-oat aphid) transmits several virus species in the family Luteoviridae, including Barley yellow dwarf virus (BYDV-PAV, genus Luteovirus) and Cereal yellow dwarf virus (CYDV-RPV and -RPS, genus Polerovirus). The yellow dwarf virus (YDV) species in these two genera share genetic similarities in their 3'-ends, but diverge in the 5'-regions. Most notably, CYDVs encode a P0 viral suppressor of RNA silencing (VSR) absent in BYDV-PAV. Because BYDV-PAV has been reported more frequently in annual cereals and CYDVs in perennial non-crop grasses, we examine the hypothesis that the viruses' genetic differences reflect different affinities for crop and non-crop hosts. Specifically, we ask (i) whether CYDVs might persist within and affect a native non-crop grass more strongly than BYDV-PAV, on the grounds that the polerovirus VSR could better moderate the defenses of a well-defended perennial, and (ii) whether the opposite pattern of effects might occur in a less defended annual crop. Because previous work found that the VSR of CYDV-RPS possessed greater silencing suppressor efficiency than that of CYDV-RPV, we further explored (iii) whether a novel grass-associated CYDV-RPS isolate would influence a native non-crop grass more strongly than a comparable CYDV-RPV isolate. In growth chamber studies, we found support for this hypothesis: only grass-associated CYDV-RPS stunted the shoots and crowns of Panicum virgatum L. (switchgrass), a perennial native North American prairie grass, whereas crop-associated BYDV-PAV (and coinfection with BYDV-PAV and CYDV-RPS) most

  20. 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

  1. Development of resources and tools for mapping genetic sources of phenotypic variation

    USDA-ARS?s Scientific Manuscript database

    Commercial and experimental genetic resources were established and investigated for a range of reproductive and disease susceptibility phenotypes. The phenotyping efforts were accompanied with RNA and whole genome sequencing and novel assemblies of the swine genome. The efforts were complemented wit...

  2. Impacts of crop insurance on water withdrawals for irrigation

    NASA Astrophysics Data System (ADS)

    Deryugina, Tatyana; Konar, Megan

    2017-12-01

    Agricultural production remains particularly vulnerable to weather fluctuations and extreme events, such as droughts, floods, and heat waves. Crop insurance is a risk management tool developed to mitigate some of this weather risk and protect farmer income in times of poor production. However, crop insurance may have unintended consequences for water resources sustainability, as the vast majority of freshwater withdrawals go to agriculture. The causal impact of crop insurance on water use in agriculture remains poorly understood. Here, we determine the empirical relationship between crop insurance and irrigation water withdrawals in the United States. Importantly, we use an instrumental variables approach to establish causality. Our methodology exploits a major policy change in the crop insurance system - the 1994 Federal Crop Insurance Reform Act - which imposed crop insurance requirements on farmers. We find that a 1% increase in insured crop acreage leads to a 0.223% increase in irrigation withdrawals, with most coming from groundwater aquifers. We identify farmers growing more groundwater-fed cotton as an important mechanism contributing to increased withdrawals. A 1% increase in insured crop acreage leads to a 0.624% increase in cotton acreage, or 95,602 acres. These results demonstrate that crop insurance causally leads to more irrigation withdrawals. More broadly, this work underscores the importance of determining causality in the water-food nexus as we endeavor to achieve global food security and water resources sustainability.

  3. Calorie increase and water savings of redistributing global crop production

    NASA Astrophysics Data System (ADS)

    Davis, K. F.; Seveso, A.; Rulli, M. C.; D'Odorico, P.

    2015-12-01

    Human demand for crop production is expected to increase substantially in the coming decades as a result of population growth, richer diets and biofuel use. In order for food production to keep pace, unprecedented amounts of resources - water, fertilizers, energy - will be required. This has led to calls for 'sustainable intensification' in which yields are increased on existing croplands while seeking to minimize impacts on water and other agricultural resources. Recent studies have quantified aspects of this, showing that there is a large potential to improve crop yields and increase harvest frequencies to better meet human demand. Though promising, both solutions would necessitate large additional inputs of water and fertilizer in order to be achieved under current technologies. However, the question of whether the current distribution of crops is, in fact, the best for realizing maximized production has not been considered to date. To this end, we ask: Is it possible to increase calorie production and minimize water demand by simply growing crops where soil and climate conditions are best suited? Here we use maps of agro-ecological suitability - a measure of physical and chemical soil fertility - for 15 major food crops to identify differences between current crop distributions and where they can most suitably be planted. By redistributing crops across currently cultivated lands, we determine the potential improvement in calorie production as well as the associated change in water demand. We also consider what distribution of crops would maintain current calorie production while minimizing crop water demand. In doing all of this, our study provides a novel tool for improving crop calorie production without necessarily increasing resource demands.

  4. Impacts of changing cropping pattern on virtual water flows related to crops transfer: a case study for the Hetao irrigation district, China.

    PubMed

    Liu, Jing; Wu, Pute; Wang, Yubao; Zhao, Xining; Sun, Shikun; Cao, Xinchun

    2014-11-01

    Analysis of cropping patterns is a prerequisite for their optimisation, and evaluation of virtual water flows could shed new light on water resources management. This study is intended to explore the effects of cropping pattern changes between 1960 and 2008 on virtual water flows related to crops transfer in the Hetao irrigation district, China. (1) The sown area of crops increased at an average rate of 3.57 × 10(3) ha year(-1) while the proportion of sown grain crops decreased from 92.83% in the 1960s to 50.22% in the 2000s. (2) Virtual water content decreased during the study period while net virtual water exports increased since the 1980s. (3) Assuming that the cropping pattern was constant and was equal to the average 1960s value, accumulated net virtual water export in 1980-2008 would have been 4.76 × 10(9) m(3) greater than that in the actual cropping pattern scenario. Cropping pattern changes in the Hetao irrigation district could not only be seen as resulting from the pursuit for higher economic returns, but also as a feedback response to limited water resources. A systematic framework is still needed for future cropping pattern planning by taking food security, continued agricultural expansion and other constraints into consideration. © 2014 Society of Chemical Industry.

  5. Challenges in testing genetically modified crops for potential increases in endogenous allergen expression for safety.

    PubMed

    Panda, R; Ariyarathna, H; Amnuaycheewa, P; Tetteh, A; Pramod, S N; Taylor, S L; Ballmer-Weber, B K; Goodman, R E

    2013-02-01

    Premarket, genetically modified (GM) plants are assessed for potential risks of food allergy. The major risk would be transfer of a gene encoding an allergen or protein nearly identical to an allergen into a different food source, which can be assessed by specific serum testing. The potential that a newly expressed protein might become an allergen is evaluated based on resistance to digestion in pepsin and abundance in food fractions. If the modified plant is a common allergenic source (e.g. soybean), regulatory guidelines suggest testing for increases in the expression of endogenous allergens. Some regulators request evaluating endogenous allergens for rarely allergenic plants (e.g. maize and rice). Since allergic individuals must avoid foods containing their allergen (e.g. peanut, soybean, maize, or rice), the relevance of the tests is unclear. Furthermore, no acceptance criteria are established and little is known about the natural variation in allergen concentrations in these crops. Our results demonstrate a 15-fold difference in the major maize allergen, lipid transfer protein between nine varieties, and complex variation in IgE binding to various soybean varieties. We question the value of evaluating endogenous allergens in GM plants unless the intent of the modification was production of a hypoallergenic crop. © 2012 John Wiley & Sons A/S.

  6. Messages promoting genetic modification of crops in the context of climate change: Evidence for psychological reactance.

    PubMed

    Lu, Hang; McComas, Katherine A; Besley, John C

    2017-01-01

    Genetic modification (GM) of crops and climate change are arguably two of today's most challenging science communication issues. Increasingly, these two issues are connected in messages proposing GM as a viable option for ensuring global food security threatened by climate change. This study examines the effects of messages promoting the benefits of GM in the context of climate change. Further, it examines whether explicit reference to "climate change," or "global warming" in a GM message results in different effects than each other, or an implicit climate reference. An online sample of U.S. participants (N = 1050) were randomly assigned to one of four conditions: "climate change" cue, "global warming" cue, implicit cue, or control (no message). Generally speaking, framing GM crops as a way to help ensure global food security proved to be an effective messaging strategy in increasing positive attitudes toward GM. In addition, the implicit cue condition led to liberals having more positive attitudes and behavioral intentions toward GM than the "climate change" cue condition, an effect mediated by message evaluations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Identifying traits for genotypic adaptation using crop models.

    PubMed

    Ramirez-Villegas, Julian; Watson, James; Challinor, Andrew J

    2015-06-01

    Genotypic adaptation involves the incorporation of novel traits in crop varieties so as to enhance food productivity and stability and is expected to be one of the most important adaptation strategies to future climate change. Simulation modelling can provide the basis for evaluating the biophysical potential of crop traits for genotypic adaptation. This review focuses on the use of models for assessing the potential benefits of genotypic adaptation as a response strategy to projected climate change impacts. Some key crop responses to the environment, as well as the role of models and model ensembles for assessing impacts and adaptation, are first reviewed. Next, the review describes crop-climate models can help focus the development of future-adapted crop germplasm in breeding programmes. While recently published modelling studies have demonstrated the potential of genotypic adaptation strategies and ideotype design, it is argued that, for model-based studies of genotypic adaptation to be used in crop breeding, it is critical that modelled traits are better grounded in genetic and physiological knowledge. To this aim, two main goals need to be pursued in future studies: (i) a better understanding of plant processes that limit productivity under future climate change; and (ii) a coupling between genetic and crop growth models-perhaps at the expense of the number of traits analysed. Importantly, the latter may imply additional complexity (and likely uncertainty) in crop modelling studies. Hence, appropriately constraining processes and parameters in models and a shift from simply quantifying uncertainty to actually quantifying robustness towards modelling choices are two key aspects that need to be included into future crop model-based analyses of genotypic adaptation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species.

    PubMed

    Mason, A S; Snowdon, R J

    2016-11-01

    Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

  9. Advancing Crop Transformation in the Era of Genome Editing.

    PubMed

    Altpeter, Fredy; Springer, Nathan M; Bartley, Laura E; Blechl, Ann E; Brutnell, Thomas P; Citovsky, Vitaly; Conrad, Liza J; Gelvin, Stanton B; Jackson, David P; Kausch, Albert P; Lemaux, Peggy G; Medford, June I; Orozco-Cárdenas, Martha L; Tricoli, David M; Van Eck, Joyce; Voytas, Daniel F; Walbot, Virginia; Wang, Kan; Zhang, Zhanyuan J; Stewart, C Neal

    2016-07-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. © 2016 American Society of Plant Biologists. All rights reserved.

  10. CROP type analysis using Landsat digital data

    NASA Technical Reports Server (NTRS)

    Brown, C. E.; Thomas, R. W.; Wall, S. L.

    1981-01-01

    Classification and statistical sampling techniques for crop type discrimination using Landsat digital data have been developed by the University of California in cooperation with NASA and the California Department of Water Resources. Ratioed bands (MSS 7/5 and 5/4) and a sun-angle corrected Euclidean albedo band were prepared from data for the Sacramento Valley for five different dates. The test area was stratified into general crop groupings based on the particular patterns of irrigation timing for each crop. Data classified within each stratum were used to produce a crop type map. Comparison with ground data indicates that certain crops and crop groups are discernable. Small grains and rice are easily identifiable, as are deciduous fruit varieties as a group. However, it is not feasible to separate various fruit and nut varieties, or separate vegetable crops with these techniques at present.

  11. Trends in pesticide use on soybean, corn and cotton since the introduction of major genetically modified crops in the United States.

    PubMed

    Coupe, Richard H; Capel, Paul D

    2016-05-01

    Genetically modified (GM) varieties of soybean, corn and cotton have largely replaced conventional varieties in the United States. The most widely used applications of GM technology have been the development of crops that are resistant to a specific broad-spectrum herbicide (primarily glyphosate) or that produce insecticidal compounds within the plant itself. With the widespread adoption of GM crops, a decline in the use of conventional pesticides was expected. There has been a reduction in the annual herbicide application rate to corn since the advent of GM crops, but the herbicide application rate is mostly unchanged for cotton. Herbicide use on soybean has increased. There has been a substantial reduction in the amount of insecticides used on both corn and cotton since the introduction of GM crops. The observed changes in pesticide use are likely to be the result of many factors, including the introduction of GM crops, regulatory restrictions on some conventional pesticides, introduction of new pesticide technologies and changes in farming practices. In order to help protect human and environmental health and to help agriculture plan for the future, more detailed and complete documentation on pesticide use is needed on a frequent and ongoing basis. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  12. Establishing sugarcane (Saccharum spp.) genetic resources for in vitro storage and cryopreservation

    USDA-ARS?s Scientific Manuscript database

    Sugarcane (Saccharum spp.) is used to produce sugar, a variety of alcoholic beverages, bagasse and industrial ethanol utilized in making fuel. In production fields, sugarcane is propagated vegetatively and currently, the crop’s genetic resources are also preserved as field plantings. The National Pl...

  13. [Genetically modified crops: promises and good intentions are not enough (refutation to Espinoza et aL 2004, Rev. Biol. Trop. 52 (3): 727-732)].

    PubMed

    García, Jaime E G

    2007-06-01

    The arguments presented by Espinoza et al. in their paper "Relationship of genetically modified crops with the environment and health of the Costa Rican human population" published in this journal (Rev. Biol. Trop. 52: 727-732, 2004) are questioned and refuted. The arguments are confronted with evidence offered by scientists and national and international independent organizations around the world (e.g. World Health Organization, Consumers International, Physicians and Scientists for Responsible Application of Science and Technology, International Union for Conservation of Nature and Natural Resources, the Council of the University of Costa Rica, and the Independent Science Panel) showing the current uncertainty and limitations of science in this area, as well as those of proposed and applied biosafety approaches. Environment, biodiversity and food security are so important and basic matters, that there is need of serious testing, particularly when promises seem to be based on environmentally dangerous ideas promoted half a century ago by the so called "green revolution". Debate should continue, based on a holistic analysis of facts and with ethical reasoning, avoiding emotional positions that can confuse virtual reality with reality.

  14. Molecular approaches to improvement of Jatropha curcas Linn. as a sustainable energy crop.

    PubMed

    Sudhakar Johnson, T; Eswaran, Nalini; Sujatha, M

    2011-09-01

    With the increase in crude oil prices, climate change concerns and limited reserves of fossil fuel, attention has been diverted to alternate renewable energy sources such as biofuel and biomass. Among the potential biofuel crops, Jatropha curcas L, a non-domesticated shrub, has been gaining importance as the most promising oilseed, as it does not compete with the edible oil supplies. Economic relevance of J. curcas for biodiesel production has promoted world-wide prospecting of its germplasm for crop improvement and breeding. However, lack of adequate genetic variation and non-availability of improved varieties limited its prospects of being a successful energy crop. In this review, we present the progress made in molecular breeding approaches with particular reference to tissue culture and genetic transformation, genetic diversity assessment using molecular markers, large-scale transcriptome and proteome studies, identification of candidate genes for trait improvement, whole genome sequencing and the current interest by various public and private sector companies in commercial-scale cultivation, which highlights the revival of Jatropha as a sustainable energy crop. The information generated from molecular markers, transcriptome profiling and whole genome sequencing could accelerate the genetic upgradation of J. curcas through molecular breeding.

  15. Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development

    PubMed Central

    Hooftman, Danny A P; Flavell, Andrew J; Jansen, Hans; den Nijs, Hans C M; Syed, Naeem H; Sørensen, Anker P; Orozco-ter Wengel, Pablo; van de Wiel, Clemens C M

    2011-01-01

    Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter's ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent's habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence. PMID:25568012

  16. Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development.

    PubMed

    Hooftman, Danny A P; Flavell, Andrew J; Jansen, Hans; den Nijs, Hans C M; Syed, Naeem H; Sørensen, Anker P; Orozco-Ter Wengel, Pablo; van de Wiel, Clemens C M

    2011-09-01

    Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter's ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent's habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.

  17. Genetic and environmental limitations on crop responses to elevated [CO2

    USDA-ARS?s Scientific Manuscript database

    While the future crop growing environment is likely to be warmer and with more variable water availability, the stimulation of C3 photosynthesis by elevated CO2 concentration provides a potential benefit of global climate change. However, experimental field studies suggest that C3 crops fall short o...

  18. General considerations in testing and evaluating crop varieties for agroforestry systems

    Treesearch

    Lolita N. Ragus

    1993-01-01

    Introduction of new crops in agroforestry is often suggested as a way to improve productivity. This paper provides general guidelines in selecting companion plant combinations and general considerations in evaluating, testing, naming, maintaining genetic purity and distributing crop varieties to farmers.

  19. The Use of Cover Crops as Climate-Smart Management in Midwest Cropping Systems

    NASA Astrophysics Data System (ADS)

    Basche, A.; Miguez, F.; Archontoulis, S.; Kaspar, T.

    2014-12-01

    The observed trends in the Midwestern United States of increasing rainfall variability will likely continue into the future. Events such as individual days of heavy rain as well as seasons of floods and droughts have large impacts on agricultural productivity and the natural resource base that underpins it. Such events lead to increased soil erosion, decreased water quality and reduced corn and soybean yields. Winter cover crops offer the potential to buffer many of these impacts because they essentially double the time for a living plant to protect and improve the soil. However, at present, cover crops are infrequently utilized in the Midwest (representing 1-2% of row cropped land cover) in particular due to producer concerns over higher costs and management, limited time and winter growing conditions as well as the potential harm to corn yields. In order to expand their use, there is a need to quantify how cover crops impact Midwest cropping systems in the long term and namely to understand how to optimize the benefits of cover crops while minimizing their impacts on cash crops. We are working with APSIM, a cropping systems platform, to specifically quantify the long term future impacts of cover crop incorporation in corn-based cropping systems. In general, our regional analysis showed only minor changes to corn and soybean yields (<1% differences) when a cover crop was or was not included in the simulation. Further, a "bad spring" scenario (where every third year had an abnormally wet/cold spring and cover crop termination and planting cash crop were within one day) did not result in any major changes to cash crop yields. Through simulations we estimate an average increase of 4-9% organic matter improvement in the topsoil and an average decrease in soil erosion of 14-32% depending on cover crop planting date and growth. Our work is part of the Climate and Corn-based Cropping Systems Coordinated Agriculture Project (CSCAP), a collaboration of eleven Midwestern

  20. U.S. Sorghum genetic resources collection: 15 years of progress (2001-2016)

    USDA-ARS?s Scientific Manuscript database

    The U.S. sorghum genetic resources collection at Griffin, GA, is one of the largest collections in the National Plant Germplasm System. In 2001, improved maintenance was greatly needed as accessions weren’t regenerated routinely, viability tests weren’t conducted, and most seed was stored in 4C inst...

  1. The food and environmental safety of Bt crops.

    PubMed

    Koch, Michael S; Ward, Jason M; Levine, Steven L; Baum, James A; Vicini, John L; Hammond, Bruce G

    2015-01-01

    Bacillus thuringiensis (Bt) microbial pesticides have a 50-year history of safety in agriculture. Cry proteins are among the active insecticidal ingredients in these pesticides, and genes coding for Cry proteins have been introduced into agricultural crops using modern biotechnology. The Cry gene sequences are often modified to enable effective expression in planta and several Cry proteins have been modified to increase biological activity against the target pest(s). Additionally, the domains of different but structurally conserved Cry proteins can be combined to produce chimeric proteins with enhanced insecticidal properties. Environmental studies are performed and include invertebrates, mammals, and avian species. Mammalian studies used to support the food and feed safety assessment are also used to support the wild mammal assessment. In addition to the NTO assessment, the environmental assessment includes a comparative assessment between the Bt crop and the appropriate conventional control that is genetically similar but lacks the introduced trait to address unintended effects. Specific phenotypic, agronomic, and ecological characteristics are measured in the Bt crop and the conventional control to evaluate whether the introduction of the insect resistance has resulted in any changes that might cause ecological harm in terms of altered weed characteristics, susceptibility to pests, or adverse environmental impact. Additionally, environmental interaction data are collected in field experiments for Bt crop to evaluate potential adverse effects. Further to the agronomic and phenotypic evaluation, potential movement of transgenes from a genetically modified crop plants into wild relatives is assessed for a new pest resistance gene in a new crop. This review summarizes the evidence for safety of crops containing Cry proteins for humans, livestock, and other non-target organisms.

  2. The food and environmental safety of Bt crops

    PubMed Central

    Koch, Michael S.; Ward, Jason M.; Levine, Steven L.; Baum, James A.; Vicini, John L.; Hammond, Bruce G.

    2015-01-01

    Bacillus thuringiensis (Bt) microbial pesticides have a 50-year history of safety in agriculture. Cry proteins are among the active insecticidal ingredients in these pesticides, and genes coding for Cry proteins have been introduced into agricultural crops using modern biotechnology. The Cry gene sequences are often modified to enable effective expression in planta and several Cry proteins have been modified to increase biological activity against the target pest(s). Additionally, the domains of different but structurally conserved Cry proteins can be combined to produce chimeric proteins with enhanced insecticidal properties. Environmental studies are performed and include invertebrates, mammals, and avian species. Mammalian studies used to support the food and feed safety assessment are also used to support the wild mammal assessment. In addition to the NTO assessment, the environmental assessment includes a comparative assessment between the Bt crop and the appropriate conventional control that is genetically similar but lacks the introduced trait to address unintended effects. Specific phenotypic, agronomic, and ecological characteristics are measured in the Bt crop and the conventional control to evaluate whether the introduction of the insect resistance has resulted in any changes that might cause ecological harm in terms of altered weed characteristics, susceptibility to pests, or adverse environmental impact. Additionally, environmental interaction data are collected in field experiments for Bt crop to evaluate potential adverse effects. Further to the agronomic and phenotypic evaluation, potential movement of transgenes from a genetically modified crop plants into wild relatives is assessed for a new pest resistance gene in a new crop. This review summarizes the evidence for safety of crops containing Cry proteins for humans, livestock, and other non-target organisms. PMID:25972882

  3. Targeting carbon for crop yield and drought resilience

    PubMed Central

    Griffiths, Cara A

    2017-01-01

    Abstract Current methods of crop improvement are not keeping pace with projected increases in population growth. Breeding, focused around key traits of stem height and disease resistance, delivered the step‐change yield improvements of the green revolution of the 1960s. However, subsequently, yield increases through conventional breeding have been below the projected requirement of 2.4% per year required by 2050. Genetic modification (GM) mainly for herbicide tolerance and insect resistance has been transformational, akin to a second green revolution, although GM has yet to make major inroads into intrinsic yield processes themselves. Drought imposes the major restriction on crop yields globally but, as yet, has not benefited substantially from genetic improvement and still presents a major challenge to agriculture. Much still has to be learnt about the complex process of how drought limits yield and what should be targeted. Mechanisms of drought adaptation from the natural environment cannot be taken into crops without significant modification for the agricultural environment because mechanisms of drought tolerance are often in contrast with mechanisms of high productivity required in agriculture. However, through convergence of fundamental and translational science, it would appear that a mechanism of sucrose allocation in crops can be modified for both productivity and resilience to drought and other stresses. Recent publications show how this mechanism can be targeted by GM, natural variation and a new chemical approach. Here, with an emphasis on drought, we highlight how understanding fundamental science about how crops grow, develop and what limits their growth and yield can be combined with targeted genetic selection and pioneering chemical intervention technology for transformational yield improvements. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID

  4. Incorporating Primary Literature in Undergraduate Crop Science Courses

    ERIC Educational Resources Information Center

    Scott, Lori K.; Simmons, Steve R.

    2006-01-01

    Primary literature is an underutilized learning resource for undergraduate courses in crop science. Reading assignments from scientific journals were utilized in an undergraduate University of Minnesota crop physiology course at Southwest Minnesota State University from 2002 to 2004. The subjects of the articles corresponded to the lecture topics.…

  5. Policy-Led Comparative Environmental Risk Assessment of Genetically Modified Crops: Testing for Increased Risk Rather Than Profiling Phenotypes Leads to Predictable and Transparent Decision-Making

    PubMed Central

    Raybould, Alan; Macdonald, Phil

    2018-01-01

    We describe two contrasting methods of comparative environmental risk assessment for genetically modified (GM) crops. Both are science-based, in the sense that they use science to help make decisions, but they differ in the relationship between science and policy. Policy-led comparative risk assessment begins by defining what would be regarded as unacceptable changes when the use a particular GM crop replaces an accepted use of another crop. Hypotheses that these changes will not occur are tested using existing or new data, and corroboration or falsification of the hypotheses is used to inform decision-making. Science-led comparative risk assessment, on the other hand, tends to test null hypotheses of no difference between a GM crop and a comparator. The variables that are compared may have little or no relevance to any previously stated policy objective and hence decision-making tends to be ad hoc in response to possibly spurious statistical significance. We argue that policy-led comparative risk assessment is the far more effective method. With this in mind, we caution that phenotypic profiling of GM crops, particularly with omics methods, is potentially detrimental to risk assessment. PMID:29755975

  6. Development and Application of Loop-Mediated Isothermal Amplification Assays for Rapid Visual Detection of cry2Ab and cry3A Genes in Genetically-Modified Crops

    PubMed Central

    Li, Feiwu; Yan, Wei; Long, Likun; Qi, Xing; Li, Congcong; Zhang, Shihong

    2014-01-01

    The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field. PMID:25167136

  7. Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops.

    PubMed

    Li, Feiwu; Yan, Wei; Long, Likun; Qi, Xing; Li, Congcong; Zhang, Shihong

    2014-08-27

    The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

  8. Lentil genetic and genomic resources

    USDA-ARS?s Scientific Manuscript database

    Lentil (Lens culinaris spp. culinaris) has a long history associated with the early civilizations 11,000 BP in southwestern Asia. The progenitor taxon is Lens culinaris spp. orientalis. The primary source of germplasm for lentil crop improvement is from the International Center for Agricultural Rese...

  9. The benefits of herbicide-resistant crops.

    PubMed

    Green, Jerry M

    2012-10-01

    Since 1996, genetically modified herbicide-resistant crops, primarily glyphosate-resistant soybean, corn, cotton and canola, have helped to revolutionize weed management and have become an important tool in crop production practices. Glyphosate-resistant crops have enabled the implementation of weed management practices that have improved yield and profitability while better protecting the environment. Growers have recognized their benefits and have made glyphosate-resistant crops the most rapidly adopted technology in the history of agriculture. Weed management systems with glyphosate-resistant crops have often relied on glyphosate alone, have been easy to use and have been effective, economical and more environmentally friendly than the systems they have replaced. Glyphosate has worked extremely well in controlling weeds in glyphosate-resistant crops for more than a decade, but some key weeds have evolved resistance, and using glyphosate alone has proved unsustainable. Now, growers need to renew their weed management practices and use glyphosate with other cultural, mechanical and herbicide options in integrated systems. New multiple-herbicide-resistant crops with resistance to glyphosate and other herbicides will expand the utility of existing herbicide technologies and will be an important component of future weed management systems that help to sustain the current benefits of high-efficiency and high-production agriculture. Copyright © 2012 Society of Chemical Industry.

  10. Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons

    PubMed Central

    Laloi, G.; Montarry, J.; Guibert, M.; Andrivon, D.; Michot, D.

    2016-01-01

    ABSTRACT Ascochyta blight, caused by the necrotrophic ascomycete Didymella pinodes, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520 D. pinodes strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses. IMPORTANCE Ascochyta blight, caused by Didymella pinodes, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. PMID:27208102

  11. Advancing Crop Transformation in the Era of Genome Editing[OPEN

    PubMed Central

    Blechl, Ann E.; Brutnell, Thomas P.; Conrad, Liza J.; Gelvin, Stanton B.; Jackson, David P.; Kausch, Albert P.; Lemaux, Peggy G.; Medford, June I.; Orozco-Cárdenas, Martha L.; Tricoli, David M.; Van Eck, Joyce; Voytas, Daniel F.

    2016-01-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

  12. Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia.

    PubMed

    Thomas, Evert; Tovar, Eduardo; Villafañe, Carolina; Bocanegra, José Leonardo; Moreno, Rodrigo

    2017-12-01

    Crop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs. Our findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future. Given (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian

  13. Australia’s food system is highly dependent on foreign crop diversity

    USDA-ARS?s Scientific Manuscript database

    The food crops that are now produced or consumed in Australia were initially domesticated and evolved over time in specific geographic regions across the planet. Genetic diversity within these crops and their wild relatives is considered to be historically particularly rich within these regions. Los...

  14. Environmental impacts of genetically modified plants: A review.

    PubMed

    Tsatsakis, Aristidis M; Nawaz, Muhammad Amjad; Kouretas, Demetrios; Balias, Georgios; Savolainen, Kai; Tutelyan, Victor A; Golokhvast, Kirill S; Lee, Jeong Dong; Yang, Seung Hwan; Chung, Gyuhwa

    2017-07-01

    Powerful scientific techniques have caused dramatic expansion of genetically modified crops leading to altered agricultural practices posing direct and indirect environmental implications. Despite the enhanced yield potential, risks and biosafety concerns associated with such GM crops are the fundamental issues to be addressed. An increasing interest can be noted among the researchers and policy makers in exploring unintended effects of transgenes associated with gene flow, flow of naked DNA, weediness and chemical toxicity. The current state of knowledge reveals that GM crops impart damaging impacts on the environment such as modification in crop pervasiveness or invasiveness, the emergence of herbicide and insecticide tolerance, transgene stacking and disturbed biodiversity, but these impacts require a more in-depth view and critical research so as to unveil further facts. Most of the reviewed scientific resources provide similar conclusions and currently there is an insufficient amount of data available and up until today, the consumption of GM plant products are safe for consumption to a greater extent with few exceptions. This paper updates the undesirable impacts of GM crops and their products on target and non-target species and attempts to shed light on the emerging challenges and threats associated with it. Underpinning research also realizes the influence of GM crops on a disturbance in biodiversity, development of resistance and evolution slightly resembles with the effects of non-GM cultivation. Future prospects are also discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Not all GMOs are crop plants: non-plant GMO applications in agriculture

    USDA-ARS?s Scientific Manuscript database

    In the time since the tools of modern biotechnology have become available, the most commonly applied and often discussed genetically modified organisms are genetically modified crop plants, although genetic engineering is also being used successfully in organisms other than plants, including bacteri...

  16. Development of agribiotechnology and biosafety regulations used to assess safety of genetically modified crops in Bangladesh.

    PubMed

    Nasiruddin, Khondoker M; Nasim, Anwar

    2007-01-01

    Bangladesh is on the verge of adopting genetically modified (GM) crops for commercial cultivation and consumption as feed and food. Most of the laboratories are engaged in tissue culture and molecular characterization on plants, whereas some have started living modified organism research with shortages of trained manpower, infrastructure, and funding. Nutritionally improved Golden Rice, biotech brinjal, and late blight-resistant potato are in contained trials in a greenhouse, and potato ring spot virus-resistant papaya is in the process of approval for a field trial. The government has taken some initiative in support of GM organism research, which include the formation of a Biotechnology Department in all institutes and the formation of the apex body, the National Task Force Committee on Biotechnology of Bangladesh under the chairpersonship of the Prime Minister. Biosafety policy guidelines and related aspects of biotechnology issues have been approved, and the laws are in the process of being promulgated. Being a party to the Cartagena Protocol, proper biosafety measures are regulated by the appropriate authority as stated. Although there are no laws made yet directly for biosafety of GM crops/foods, the relevant laws on agriculture, medicine, food, import, trade, environment, etc. may suffice and explain the situation.

  17. Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat.

    PubMed

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-03-28

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.

  18. Advances in Agrobacterium tumefaciens-mediated genetic transformation of graminaceous crops.

    PubMed

    Singh, Roshan Kumar; Prasad, Manoj

    2016-05-01

    Steady increase in global population poses several challenges to plant science research, including demand for increased crop productivity, grain yield, nutritional quality and improved tolerance to different environmental factors. Transgene-based approaches are promising to address these challenges by transferring potential candidate genes to host organisms through different strategies. Agrobacterium-mediated gene transfer is one such strategy which is well known for enabling efficient gene transfer in both monocot and dicots. Due to its versatility, this technique underwent several advancements including development of improved in vitro plant regeneration system, co-cultivation and selection methods, and use of hyper-virulent strains of Agrobacterium tumefaciens harbouring super-binary vectors. The efficiency of this method has also been enhanced by the use of acetosyringone to induce the activity of vir genes, silver nitrate to reduce the Agrobacterium-induced necrosis and cysteine to avoid callus browning during co-cultivation. In the last two decades, extensive efforts have been invested towards achieving efficient Agrobacterium-mediated transformation in cereals. Though high-efficiency transformation systems have been developed for rice and maize, comparatively lesser progress has been reported in other graminaceous crops. In this context, the present review discusses the progress made in Agrobacterium-mediated transformation system in rice, maize, wheat, barley, sorghum, sugarcane, Brachypodium, millets, bioenergy and forage and turf grasses. In addition, it also provides an overview of the genes that have been recently transferred to these graminaceous crops using Agrobacterium, bottlenecks in this technique and future possibilities for crop improvement.

  19. Cover Crop Chart: An Outreach Tool for Agricultural Producers

    USDA-ARS?s Scientific Manuscript database

    Interest in cover crops by farmers and ranchers throughout the Northern Great Plains has increased the need for information on the suitability of a diverse portfolio of crops for different production and management resource goals. To help address this need, Northern Great Plains Research Laboratory...

  20. 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.

  1. Engineering Mycorrhizal Symbioses to Alter Plant Metabolism and Improve Crop Health

    PubMed Central

    French, Katherine E.

    2017-01-01

    Creating sustainable bioeconomies for the 21st century relies on optimizing the use of biological resources to improve agricultural productivity and create new products. Arbuscular mycorrhizae (phylum Glomeromycota) form symbiotic relationships with over 80% of vascular plants. In return for carbon, these fungi improve plant health and tolerance to environmental stress. This symbiosis is over 400 million years old and there are currently over 200 known arbuscular mycorrhizae, with dozens of new species described annually. Metagenomic sequencing of native soil communities, from species-rich meadows to mangroves, suggests biologically diverse habitats support a variety of mycorrhizal species with potential agricultural, medical, and biotechnological applications. This review looks at the effect of mycorrhizae on plant metabolism and how we can harness this symbiosis to improve crop health. I will first describe the mechanisms that underlie this symbiosis and what physiological, metabolic, and environmental factors trigger these plant-fungal relationships. These include mycorrhizal manipulation of host genetic expression, host mitochondrial and plastid proliferation, and increased production of terpenoids and jasmonic acid by the host plant. I will then discuss the effects of mycorrhizae on plant root and foliar secondary metabolism. I subsequently outline how mycorrhizae induce three key benefits in crops: defense against pathogen and herbivore attack, drought resistance, and heavy metal tolerance. I conclude with an overview of current efforts to harness mycorrhizal diversity to improve crop health through customized inoculum. I argue future research should embrace synthetic biology to create mycorrhizal chasses with improved symbiotic abilities and potentially novel functions to improve plant health. As the effects of climate change and anthropogenic disturbance increase, the global diversity of arbuscular mycorrhizal fungi should be monitored and protected to

  2. Engineering Mycorrhizal Symbioses to Alter Plant Metabolism and Improve Crop Health.

    PubMed

    French, Katherine E

    2017-01-01

    Creating sustainable bioeconomies for the 21st century relies on optimizing the use of biological resources to improve agricultural productivity and create new products. Arbuscular mycorrhizae (phylum Glomeromycota) form symbiotic relationships with over 80% of vascular plants. In return for carbon, these fungi improve plant health and tolerance to environmental stress. This symbiosis is over 400 million years old and there are currently over 200 known arbuscular mycorrhizae, with dozens of new species described annually. Metagenomic sequencing of native soil communities, from species-rich meadows to mangroves, suggests biologically diverse habitats support a variety of mycorrhizal species with potential agricultural, medical, and biotechnological applications. This review looks at the effect of mycorrhizae on plant metabolism and how we can harness this symbiosis to improve crop health. I will first describe the mechanisms that underlie this symbiosis and what physiological, metabolic, and environmental factors trigger these plant-fungal relationships. These include mycorrhizal manipulation of host genetic expression, host mitochondrial and plastid proliferation, and increased production of terpenoids and jasmonic acid by the host plant. I will then discuss the effects of mycorrhizae on plant root and foliar secondary metabolism. I subsequently outline how mycorrhizae induce three key benefits in crops: defense against pathogen and herbivore attack, drought resistance, and heavy metal tolerance. I conclude with an overview of current efforts to harness mycorrhizal diversity to improve crop health through customized inoculum. I argue future research should embrace synthetic biology to create mycorrhizal chasses with improved symbiotic abilities and potentially novel functions to improve plant health. As the effects of climate change and anthropogenic disturbance increase, the global diversity of arbuscular mycorrhizal fungi should be monitored and protected to

  3. Computational allergenicity prediction of transgenic proteins expressed in genetically modified crops.

    PubMed

    Verma, Alok Kumar; Misra, Amita; Subash, Swarna; Das, Mukul; Dwivedi, Premendra D

    2011-09-01

    Development of genetically modified (GM) crops is on increase to improve food quality, increase harvest yields, and reduce the dependency on chemical pesticides. Before their release in marketplace, they should be scrutinized for their safety. Several guidelines of different regulatory agencies like ILSI, WHO Codex, OECD, and so on for allergenicity evaluation of transgenics are available and sequence homology analysis is the first test to determine the allergenic potential of inserted proteins. Therefore, to test and validate, 312 allergenic, 100 non-allergenic, and 48 inserted proteins were assessed for sequence similarity using 8-mer, 80-mer, and full FASTA search. On performing sequence homology studies, ~94% the allergenic proteins gave exact matches for 8-mer and 80-mer homology. However, 20 allergenic proteins showed non-allergenic behavior. Out of 100 non-allergenic proteins, seven qualified as allergens. None of the inserted proteins demonstrated allergenic behavior. In order to improve the predictability, proteins showing anomalous behavior were tested by Algpred and ADFS separately. Use of Algpred and ADFS softwares reduced the tendency of false prediction to a great extent (74-78%). In conclusion, routine sequence homology needs to be coupled with some other bioinformatic method like ADFS/Algpred to reduce false allergenicity prediction of novel proteins.

  4. Blue and green water use of cultivating selected crops in Malaysia

    NASA Astrophysics Data System (ADS)

    Harun, Siti Norliyana; Hanafiah, Marlia M.

    2018-04-01

    Sustainability of water resources should be a concern parallel to the fast pace of economic development. This study was conducted to estimate the total water consumption of growing 9 crops in Peninsular Malaysia which divided into two category of crops; fruits and vegetables, i.e. mandarin, banana, mango, pineapple, watermelon, cucumber, eggplant, green bean and lettuce. The water footprint of these crops was estimated based on 9 years data of climate and crop (2005-2013). The crop water use was determined using CROPWAT 8.0 model and Penman-Monteith equation. It was found that the green water footprint for cultivating 9 crops was higher compared to blue water footprint. The blue water footprint ranged from 20.97m3/ton to 197.84m3/ton, whereas the green water footprint ranged from 129.8m3/ton to 1586.2m3/ton. Banana has the highest total water footprint (1717.10m3/ton) and the lowest total water footprint was obtained for cucumber (175.07m3/ton). In conclusion, water consumption for cultivating agricultural crops will accelerate the competition on the consumption of clean water with the other sectors. However, the availability of water resource in Peninsular Malaysia is still sufficient to fulfill the demands for water at the present time. Further study should include grey water as well as an indicator for water quality to help in assessing the sustainable, efficient and equitable use of water resources.

  5. Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

    USDA-ARS?s Scientific Manuscript database

    The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access t...

  6. Environmental health impacts of feeding crops to farmed fish.

    PubMed

    Fry, Jillian P; Love, David C; MacDonald, Graham K; West, Paul C; Engstrom, Peder M; Nachman, Keeve E; Lawrence, Robert S

    2016-05-01

    Half of the seafood consumed globally now comes from aquaculture, or farmed seafood. Aquaculture therefore plays an increasingly important role in the global food system, the environment, and human health. Traditionally, aquaculture feed has contained high levels of wild fish, which is unsustainable for ocean ecosystems as demand grows. The aquaculture industry is shifting to crop-based feed ingredients, such as soy, to replace wild fish as a feed source and allow for continued industry growth. This shift fundamentally links seafood production to terrestrial agriculture, and multidisciplinary research is needed to understand the ecological and environmental health implications. We provide basic estimates of the agricultural resource use associated with producing the top five crops used in commercial aquaculture feed. Aquaculture's environmental footprint may now include nutrient and pesticide runoff from industrial crop production, and depending on where and how feed crops are produced, could be indirectly linked to associated negative health outcomes. We summarize key environmental health research on health effects associated with exposure to air, water, and soil contaminated by industrial crop production. Our review also finds that changes in the nutritional content of farmed seafood products due to altered feed composition could impact human nutrition. Based on our literature reviews and estimates of resource use, we present a conceptual framework describing the potential links between increasing use of crop-based ingredients in aquaculture and human health. Additional data and geographic sourcing information for crop-based ingredients are needed to fully assess the environmental health implications of this trend. This is especially critical in the context of a food system that is using both aquatic and terrestrial resources at unsustainable rates. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons.

    PubMed

    Laloi, G; Montarry, J; Guibert, M; Andrivon, D; Michot, D; Le May, C

    2016-07-15

    Ascochyta blight, caused by the necrotrophic ascomycete Didymella pinodes, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520 D. pinodes strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses. Ascochyta blight, caused by Didymella pinodes, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  8. A Meta-Analysis of Effects of Bt Crops on Honey Bees (Hymenoptera: Apidae)

    PubMed Central

    Duan, Jian J.; Marvier, Michelle; Huesing, Joseph; Dively, Galen; Huang, Zachary Y.

    2008-01-01

    Background Honey bees (Apis mellifera L.) are the most important pollinators of many agricultural crops worldwide and are a key test species used in the tiered safety assessment of genetically engineered insect-resistant crops. There is concern that widespread planting of these transgenic crops could harm honey bee populations. Methodology/Principal Findings We conducted a meta-analysis of 25 studies that independently assessed potential effects of Bt Cry proteins on honey bee survival (or mortality). Our results show that Bt Cry proteins used in genetically modified crops commercialized for control of lepidopteran and coleopteran pests do not negatively affect the survival of either honey bee larvae or adults in laboratory settings. Conclusions/Significance Although the additional stresses that honey bees face in the field could, in principle, modify their susceptibility to Cry proteins or lead to indirect effects, our findings support safety assessments that have not detected any direct negative effects of Bt crops for this vital insect pollinator. PMID:18183296

  9. Hands-On Crops! How Long-Term Activities Improve Students' Knowledge of Crop Species. A Pretest-Posttest Study of the Greenhouse Project

    ERIC Educational Resources Information Center

    Fritsch, Eva-Maria; Lechner-Walz, Cornelia; Dreesmann, Daniel C.

    2015-01-01

    In terms of sustainability, renewable resources, nourishment and healthy diet, crops are important to the public. Thus, knowledge of crops is needed in order to enable people to participate in public discussions and take responsibility. This is in contrast to former surveys showing that students' knowledge of and interest in plants in general,…

  10. MATERNAL EFFECTS IN ADVANCED HYBRIDS OF GENETICALLY MODIFIED AND NON-GENETICALLY MODIFIED BRASSICA SPECIES

    EPA Science Inventory

    Identification of fitness traits potentially impacted by gene flow from genetically modified (GM) crops to compatible relatives is of interest in risk assessments for GM crops. Reciprocal crosses were made between GM canola, Brassica napus cv. RaideRR that expresses CP4 EPSPS fo...

  11. Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses.

    PubMed

    Muthamilarasan, Mehanathan; Prasad, Manoj

    2015-01-01

    Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.

  12. Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

    PubMed Central

    Remington, David L.; Leinonen, Päivi H.; Leppälä, Johanna; Savolainen, Outi

    2013-01-01

    Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs. PMID:23979581

  13. Molecular fingerprinting of cacao (Theobroma cacao L.) genetic resources in the Dominican Republic

    USDA-ARS?s Scientific Manuscript database

    Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic ranking 11th in the world and number one in organic cacao exports. Dominican cacao genetic resources are maintained, propagated and distributed nationally out of the IDIAF’s Mata Larga research stations. T...

  14. Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops

    PubMed Central

    Farrar, Kerrie; Bryant, David; Cope-Selby, Naomi

    2014-01-01

    Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant–microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant–microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant–microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications. PMID:25431199

  15. The Myth of Coexistence: Why Transgenic Crops Are Not Compatible With Agroecologically Based Systems of Production

    ERIC Educational Resources Information Center

    Altieri, Miguel

    2005-01-01

    The coexistence of genetically modified (GM) crops and non-GM crops is a myth because the movement of transgenes beyond their intended destinations is a certainty, and this leads to genetic contamination of organic farms and other systems. It is unlikely that transgenes can be retracted once they have escaped, thus the damage to the purity of…

  16. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    PubMed

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  17. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    PubMed Central

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  18. Biotech/GM crops in horticulture: plum cv. HoneySweet resistant to plum pox virus

    USDA-ARS?s Scientific Manuscript database

    Commercialization of Biotech crops started in 1995. By 2011, genetically modified (GM) crops were grown world-wide on 160 million ha. Only 114.507 ha of GM crops were grown in Europe, of that, 114.490 ha were Bt maize and 17 ha were potato for industrial starch production. Currently, developing c...

  19. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    PubMed

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  20. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications

    PubMed Central

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide. PMID:28107530

  1. Not all GMOs are crop plants: non-plant GMO applications in agriculture.

    PubMed

    Hokanson, K E; Dawson, W O; Handler, A M; Schetelig, M F; St Leger, R J

    2014-12-01

    Since tools of modern biotechnology have become available, the most commonly applied and often discussed genetically modified organisms are genetically modified crop plants, although genetic engineering is also being used successfully in organisms other than plants, including bacteria, fungi, insects, and viruses. Many of these organisms, as with crop plants, are being engineered for applications in agriculture, to control plant insect pests or diseases. This paper reviews the genetically modified non-plant organisms that have been the subject of permit approvals for environmental release by the United States Department of Agriculture/Animal and Plant Health Inspection Service since the US began regulating genetically modified organisms. This is an indication of the breadth and progress of research in the area of non-plant genetically modified organisms. This review includes three examples of promising research on non-plant genetically modified organisms for application in agriculture: (1) insects for insect pest control using improved vector systems; (2) fungal pathogens of insects to control insect pests; and (3) virus for use as transient-expression vectors for disease control in plants.

  2. What limits the use of crop wild relatives for crop improvement? Contrasting case studies (Zea mays and Helianthus annuus L.) provide clues to identify and overcome limiting factors

    USDA-ARS?s Scientific Manuscript database

    The vast genetic potential present in crop wild relatives (CWR) is often difficult to tap, as identification and transfer of superior alleles into breeding pools to create new crop cultivars is challenging. Conservation of CWR has always been predicated on the promise of new and useful traits, and t...

  3. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.

    PubMed

    Eppig, Janan T

    2017-07-01

    The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. © The Author 2017. Published by Oxford University Press.

  4. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse

    PubMed Central

    Eppig, Janan T.

    2017-01-01

    Abstract The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. PMID:28838066

  5. THE POTENTIAL ROLE OF REMOTE SENSING IN TRANSGENIC CROP MONITORING PROGRAMS

    EPA Science Inventory

    Sustainable agriculture combines efficient production with wise stewardship of the earth's resources. Development of environmentally benign production techniques is one focus of sustainable agriculture. The new transgenic crops producing toxic proteins that target specific crop p...

  6. Targeting carbon for crop yield and drought resilience.

    PubMed

    Griffiths, Cara A; Paul, Matthew J

    2017-11-01

    Current methods of crop improvement are not keeping pace with projected increases in population growth. Breeding, focused around key traits of stem height and disease resistance, delivered the step-change yield improvements of the green revolution of the 1960s. However, subsequently, yield increases through conventional breeding have been below the projected requirement of 2.4% per year required by 2050. Genetic modification (GM) mainly for herbicide tolerance and insect resistance has been transformational, akin to a second green revolution, although GM has yet to make major inroads into intrinsic yield processes themselves. Drought imposes the major restriction on crop yields globally but, as yet, has not benefited substantially from genetic improvement and still presents a major challenge to agriculture. Much still has to be learnt about the complex process of how drought limits yield and what should be targeted. Mechanisms of drought adaptation from the natural environment cannot be taken into crops without significant modification for the agricultural environment because mechanisms of drought tolerance are often in contrast with mechanisms of high productivity required in agriculture. However, through convergence of fundamental and translational science, it would appear that a mechanism of sucrose allocation in crops can be modified for both productivity and resilience to drought and other stresses. Recent publications show how this mechanism can be targeted by GM, natural variation and a new chemical approach. Here, with an emphasis on drought, we highlight how understanding fundamental science about how crops grow, develop and what limits their growth and yield can be combined with targeted genetic selection and pioneering chemical intervention technology for transformational yield improvements. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2017 The Authors

  7. Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions.

    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; van de Wiel, Clemens C M; Visser, Richard G F

    2012-10-01

    With the development of transgenic crop varieties, crop-wild hybridization has received considerable consideration with regard to the potential of transgenes to be transferred to wild species. Although many studies have shown that crops can hybridize with their wild relatives and that the resulting hybrids may show improved fitness over the wild parents, little is still known on the genetic contribution of the crop parent to the performance of the hybrids. In this study, we investigated the vigour of lettuce hybrids using 98 F(2:3) families from a cross between cultivated lettuce and its wild relative Lactuca serriola under non-stress conditions and under drought, salinity and nutrient deficiency. Using single nucleotide polymorphism markers, we mapped quantitative trait loci associated with plant vigour in the F(2:3) families and determined the allelic contribution of the two parents. Seventeen QTLs (quantitative trait loci) associated with vigour and six QTLs associated with the accumulation of ions (Na(+), Cl(-) and K(+)) were mapped on the nine linkage groups of lettuce. Seven of the vigour QTLs had a positive effect from the crop allele and six had a positive effect from the wild allele across treatments, and four QTLs had a positive effect from the crop allele in one treatment and from the wild allele in another treatment. Based on the allelic effect of the QTLs and their location on the genetic map, we could suggest genomic locations where transgene integration should be avoided when aiming at the mitigation of its persistence once crop-wild hybridization takes place.

  8. Beyond botany to genetic resource preservation: the S. P. Vander Kloet Vaccinium L. collections

    USDA-ARS?s Scientific Manuscript database

    Dr. S. P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a...

  9. Chapter VIII. Contributions of propagation techniques and genetic modification to breeding - genetic engineering for disease resistance

    USDA-ARS?s Scientific Manuscript database

    Genetic engineering offers an opportunity to develop flower bulb crops with resistance to fungal, viral, and bacterial pathogens. Several of the flower bulb crops, Lilium spp., Gladiolus, Zantedeschia, Muscari, Hyacinthus, Narcissus, Ornithogalum, Iris, and Alstroemeria, have been transformed with t...

  10. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics

    PubMed Central

    Mustafiz, Ananda; Kumari, Sumita; Karan, Ratna

    2016-01-01

    Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population. PMID:27252584

  11. Economic impact of GM crops

    PubMed Central

    Brookes, Graham; Barfoot, Peter

    2014-01-01

    A key part of any assessment of the global value of crop biotechnology in agriculture is an examination of its economic impact at the farm level. This paper follows earlier annual studies which examined economic impacts on yields, key costs of production, direct farm income and effects, and impacts on the production base of the four main crops of soybeans, corn, cotton and canola. The commercialization of genetically modified (GM) crops has continued to occur at a rapid rate, with important changes in both the overall level of adoption and impact occurring in 2012. This annual updated analysis shows that there have been very significant net economic benefits at the farm level amounting to $18.8 billion in 2012 and $116.6 billion for the 17-year period (in nominal terms). These economic gains have been divided roughly 50% each to farmers in developed and developing countries. GM technology have also made important contributions to increasing global production levels of the four main crops, having added 122 million tonnes and 230 million tonnes respectively, to the global production of soybeans and maize since the introduction of the technology in the mid-1990s. PMID:24637520

  12. Crop physiology calibration in the CLM

    DOE PAGES

    Bilionis, I.; Drewniak, B. A.; Constantinescu, E. M.

    2015-04-15

    Farming is using more of the land surface, as population increases and agriculture is increasingly applied for non-nutritional purposes such as biofuel production. This agricultural expansion exerts an increasing impact on the terrestrial carbon cycle. In order to understand the impact of such processes, the Community Land Model (CLM) has been augmented with a CLM-Crop extension that simulates the development of three crop types: maize, soybean, and spring wheat. The CLM-Crop model is a complex system that relies on a suite of parametric inputs that govern plant growth under a given atmospheric forcing and available resources. CLM-Crop development used measurementsmore » of gross primary productivity (GPP) and net ecosystem exchange (NEE) from AmeriFlux sites to choose parameter values that optimize crop productivity in the model. In this paper, we calibrate these parameters for one crop type, soybean, in order to provide a faithful projection in terms of both plant development and net carbon exchange. Calibration is performed in a Bayesian framework by developing a scalable and adaptive scheme based on sequential Monte Carlo (SMC). The model showed significant improvement of crop productivity with the new calibrated parameters. We demonstrate that the calibrated parameters are applicable across alternative years and different sites.« less

  13. Crop physiology calibration in the CLM

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

    Bilionis, I.; Drewniak, B. A.; Constantinescu, E. M.

    Farming is using more of the land surface, as population increases and agriculture is increasingly applied for non-nutritional purposes such as biofuel production. This agricultural expansion exerts an increasing impact on the terrestrial carbon cycle. In order to understand the impact of such processes, the Community Land Model (CLM) has been augmented with a CLM-Crop extension that simulates the development of three crop types: maize, soybean, and spring wheat. The CLM-Crop model is a complex system that relies on a suite of parametric inputs that govern plant growth under a given atmospheric forcing and available resources. CLM-Crop development used measurementsmore » of gross primary productivity (GPP) and net ecosystem exchange (NEE) from AmeriFlux sites to choose parameter values that optimize crop productivity in the model. In this paper, we calibrate these parameters for one crop type, soybean, in order to provide a faithful projection in terms of both plant development and net carbon exchange. Calibration is performed in a Bayesian framework by developing a scalable and adaptive scheme based on sequential Monte Carlo (SMC). The model showed significant improvement of crop productivity with the new calibrated parameters. We demonstrate that the calibrated parameters are applicable across alternative years and different sites.« less

  14. Open access resources for genome-wide association mapping in rice

    PubMed Central

    McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  15. Genetic variations in the digestibility in sheep of selected whole-crop cereals used as silages.

    PubMed

    Emile, J C; Jobim, C C; Surault, F; Barrière, Y

    2007-09-01

    Whole-plant winter cereals could be of great interest if used as silages for ruminant feeding as opposed to summer crops in that they would spare water resources or valorize low-input management. This study aimed to compare the feeding value of rye, barley, wheat (two genotypes) and triticale (six genotypes). The cereals were sown in October and harvested as silage in June. Forages were offered to Texel castrated sheep in order to evaluate the organic matter digestibility (OMd). The OMd of the wheat cultivars was higher (61.6%, P<0.05) than those of barley (57.2%) and rye (54.7%) but no different from that of triticale (60.6%). Within the triticale genotypes, OMd ranged from 54.7 to 62.3%. The presence of rough barbs should explain the relatively low intake of the cereals with the exception of wheat. Winter cereals provide good-quality forage for feeding ruminants. Wheat has a higher nutritional value than barley and rye and a wide variability for digestibility seems to exist within the triticale cultivars. Such variability in a species known for its ability to be cropped under limiting conditions should be explored in much greater depth as it could result in providing farmers with genotypes of good quality with an acceptable yield at a lower cost.

  16. HYBRIDIZATION STUDY BETWEEN GENETICALLY MODIFIED BRASSICA NAPUS AND NON-GENETICALLY MODIFIED B. NAPUS AND B. RAPA

    EPA Science Inventory

    Gene exchange between cultivated crops and wild species has gained significance in recent years because of concerns regarding the potential for gene flow between genetically modified (GM) crops and their domesticated and wild relatives. As part of our ecological effects of gene ...

  17. A preliminary assessment of genetic relationships among agronomically important cultivars of black pepper

    PubMed Central

    Joy, Nisha; Abraham, Z; Soniya, EV

    2007-01-01

    Background The impact of diseases such as Phytophthora foot rot and the replacement of unproductive cultivars by high yielding ones has brought about the disappearance of varieties in Piper species, like any other crop. Black pepper (King of spices), is a major spice crop consumed throughout the world. It is widely cultivated across various parts of the world apart from India. The different cultivars may be genetically related and could be a source of valuable genes for disease resistance and an increase in quantity and quality. Even though Western Ghats in India is believed to be the site of origin of this crop, numerous accessions from the NBPGR have not yet been evaluated. Our study aims to investigate the genetic relatedness in major cultivars of black pepper using Amplified Fragment Length Polymorphism. Results Amplified Fragment Length Polymorphic (AFLP) DNA analysis was performed in thirty popular cultivars of black pepper from National Bureau of Plant Genetic Resources (NBPGR), India. Fingerprint profiles were generated initially with, five different primer combinations, from which three primer pair combinations (EAGC/MCAA, EAGG/MCTA and EAGC/MCTG) gave consistent and scorable banding patterns. From 173 scorable markers, 158(> 90%) were polymorphic which shows there is considerable variation in the available germplasm. The dendrogram derived by unweighted pair group method analysis (UPGMA) grouped the accessions into three major clusters and four diverse cultivars with only 30% similarity. Karimunda, a widely grown and popular cultivar was unique in the fingerprint profiles obtained. Conclusion There are currently few fingerprinting studies using the valuable spice crop black pepper. We found considerable genetic variability among cultivars of black pepper. Fingerprinting analysis with AFLP proved to be an ideal tool for cultivar identification and phylogenetic studies. It shows the high level of polymorphism and the unique characterization of the major

  18. Performance of the CELSS Antarctic Analog Project (CAAP) Crop Production System

    NASA Technical Reports Server (NTRS)

    Bubenheim, David L.; Flynn, Michael T.; Bates, Maynard; Schlick, Greg; Kliss, Mark (Technical Monitor)

    1998-01-01

    Regenerative life support systems potentially offer a level of self-sufficiency and a concomitant decrease in logistics and associated costs in support of space exploration and habitation missions. Current state-of-the-art in plant based, regenerative life support requires resources in excess of resource allocations proposed for candidate mission scenarios. Feasibility thresholds have been identified for candidate exploration missions. The goal of this paper is to review recent advances in performance achieved in the CELSS Antarctic Analog Project (CAAP) in light of likely resource constraints. A prototype CAAP crop production chamber has been constructed and operated at the Ames Research Center. The chamber includes a number of unique hardware and software components focused on attempts to increase production efficiency, increase energy efficiency, and control the flow of energy and mass through the system to achieve enhanced performance efficiency. Both single crop, batch production, and continuous cultivation of mixed crops Product ion scenarios have been completed. The crop productivity as well as engineering performance of the chamber will be described. For each scenario, energy required and partitioned for lighting, cooling, pumps, fans, etc. is quantified. Crop production and the resulting lighting efficiency and energy conversion efficiencies are presented. In the mixed-crop scenario, with up to 25 different crops under cultivation, 17 sq m of crop area provided a mean of 515 g edible biomass per day (83% of the approximately 620 g required for one person). Lighting efficiency (moles on photons kWh-1) approached 4 and the conversion efficiency of light energy to biomass was greatly enhanced compared with conventional growing systems. Engineering and biological performance achieved place plant-based life support systems at the threshold of feasibility.

  19. Biotechnologies for the management of genetic resources for food and agriculture.

    PubMed

    Lidder, Preetmoninder; Sonnino, Andrea

    2012-01-01

    In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can

  20. LARGE AREA MONITORING FOR PESTICIDAL TRANSGENIC CROPS: HOW SPECTRAL IMAGING MAY PLAY A ROLE

    EPA Science Inventory

    Crops genetically engineered to contain a bacterial gene that expresses an insecticidal protein from Bacillus thuringiensis are regulated by EPA under the Federal Insecticide Fungicide and Rodenticide Act (FIFRA). EPA has declared crops containing transgenic pesticidal traits to...

  1. Crop stubble needs and opportunities

    USDA-ARS?s Scientific Manuscript database

    Farmers in Australia and elsewhere around the world are being offered opportunities to market their crop residues as a bioenergy feedstock, but many are not aware of how that could affect their soil resources. This report shares information from the USDA-ARS Renewable Energy Assessment Project (REAP...

  2. Navigating complexity to breed disease-resistant crops

    USDA-ARS?s Scientific Manuscript database

    Crop losses due to disease constitute a burden to global food security and agricultural sustainability. The use of genetic resistance is an environmentally-friendly way to reduce these losses. This paper considers the insights derived from various lines of research on disease resistance and manageme...

  3. Research in remote sensing of agriculture, earth resources, and man's environment

    NASA Technical Reports Server (NTRS)

    Landgrebe, D. A.

    1975-01-01

    Progress is reported for several projects involving the utilization of LANDSAT remote sensing capabilities. Areas under study include crop inventory, crop identification, crop yield prediction, forest resources evaluation, land resources evaluation and soil classification. Numerical methods for image processing are discussed, particularly those for image enhancement and analysis.

  4. Genetics and genomics of the Cucurbitaceae: genetic resources of cucumber

    USDA-ARS?s Scientific Manuscript database

    The Cucurbitaceae or vine crop family includes many important vegetables collectively referred to as cucurbits. Within Cucurbitacae, the genus Cucumis includes cultivated species C. sativus (cucumber) and C. melo (melon), as well as wild species including C. hystrix, C. callosus, and C. sativus var....

  5. New carrot and garlic germplasm to advance breeding and understand crop origins

    USDA-ARS?s Scientific Manuscript database

    The genetic variation provided by diverse plant germplasm is the basic building material used for crop improvement that shapes the crops we grow today. Wild carrot from the U.S. provided the cytoplasm used to develop a reliable system to produce hybrid carrots that account for most of the commercial...

  6. Plant Adaptation to Acid Soils: The Molecular Basis for Crop Aluminum Resistance.

    PubMed

    Kochian, Leon V; Piñeros, Miguel A; Liu, Jiping; Magalhaes, Jurandir V

    2015-01-01

    Aluminum (Al) toxicity in acid soils is a significant limitation to crop production worldwide, as approximately 50% of the world's potentially arable soil is acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring resistance to Al toxicity has been a focus of intense research interest in the decade since the last article on crop acid soil tolerance was published in this journal. An impressive amount of progress has been made during that time that has greatly increased our understanding of the diversity of Al resistance genes and mechanisms, how resistance gene expression is regulated and triggered by Al and Al-induced signals, and how the proteins encoded by these genes function and are regulated. This review examines the state of our understanding of the physiological, genetic, and molecular bases for crop Al tolerance, looking at the novel Al resistance genes and mechanisms that have been identified over the past ten years. Additionally, it examines how the integration of molecular and genetic analyses of crop Al resistance is starting to be exploited for the improvement of crop plants grown on acid soils via both molecular-assisted breeding and biotechnology approaches.

  7. Juridical and sociocultural problems on the definition of a law concerning property, usage and access to genetic resources in Colombia.

    PubMed

    Calle, R

    1996-04-01

    The property, usage, and access to genetic resources, is today one of the primary topics in international business, as a result of the strategic importance of the resources for the biotechnology industry. Internationally, the sovereignty that each country has over its natural patrimony is recognized. However, the new laws of international marketing have obligated countries in the process of development, such as Colombia, to adopt and copy a concept of intellectual property on living resources that does not have anything to do with the country's sociocultural identity, and sometimes even does not take into account its material enjoyment. The new juridical movement that treats genetic resources as private property produces a cultural conflict between indigenous populations, Afro-Americans and peasants, because for them the genetic resources are an element of community life. In these communities, knowledge is freely transmitted; it is an understanding that they have to conserve their agricultural customs and the relationship that they have with the environment. They do not recognize the term "property' according to patenting laws. These elements have to be considered, respected, and guaranteed in the laws that recognize the genetic resources in the country. On the other hand, not even countries that are pioneers in biotechnological development can adopt a concept about patents that is in agreement with the particularities that the living materials possess. This is obviously the reason for the numerous discussions on the legal interpretation, as well as complicated debates in court. Confronting that situation, there are countries rich in biodiversity, such as Colombia, but which do not have a proper concept and are not economically strong in the international context. These countries have to copy inadequate protection policies that do not take into account all their rights. This paper describes some of the technical, juridical, and sociocultural difficulties which

  8. NASA crop calendars: Wheat, barley, oats, rye, sorghum, soybeans, corn

    NASA Technical Reports Server (NTRS)

    Stuckey, M. R.; Anderson, E. N.

    1975-01-01

    Crop calenders used to determine when Earth Resources Technology Satellite ERTS data would provide the most accurate wheat acreage information and to minimize the amount of ground verified information needed are presented. Since barley, oats, and rye are considered 'confusion crops, i.e., hard to differentiate from wheat in ERTS imagery, specific dates are estimated for these crops in the following stages of development: (1) seed-bed operation, (2) planting or seeding, (3) intermediate growth, (4) dormancy, (5) development of crop to full ground cover, (6) heading or tasseling, and flowering, (7) harvesting, and (8) posting-harvest operations. Dormancy dates are included for fall-snow crops. A synopsis is given of each states' growing conditions, special cropping practices, and other characteristics which are helpful in identifying crops from ERTS imagery.

  9. Crop improvement using life cycle datasets acquired under field conditions.

    PubMed

    Mochida, Keiichi; Saisho, Daisuke; Hirayama, Takashi

    2015-01-01

    Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer "designed crops" to prevent yield shortfalls because of environmental fluctuations due to future climate change.

  10. Genome-editing technologies and their potential application in horticultural crop breeding

    PubMed Central

    Xiong, Jin-Song; Ding, Jing; Li, Yi

    2015-01-01

    Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

  11. Development of agricultural biotechnology and biosafety regulations used to assess the safety of genetically modified crops in Iran.

    PubMed

    Mousavi, Amir; Malboobi, Mohammad A; Esmailzadeh, Nasrin S

    2007-01-01

    Rapid progress in the application of biotechnological methodologies and development of genetically modified crops in Iran necessitated intensive efforts to establish proper organizations and prepare required rules and regulations at the national level to ensure safe application of biotechnology in all pertinent aspects. Practically, preparation of a national biotechnology strategic plan in the country coincided with development of a national biosafety framework that was the basis for the drafted biosafety law. Although biosafety measures were observed by researchers voluntarily, the establishment of national biosafety organizations since the year 2000 built a great capacity to deal with biosafety issues in the present and future time, particularly with respect to food and agricultural biotechnology.

  12. One crop breeding cycle from starvation? How engineering crop photosynthesis for rising CO2 and temperature could be one important route to alleviation.

    PubMed

    Kromdijk, Johannes; Long, Stephen P

    2016-03-16

    crop genetic engineering should be employed. This will require vastly increased public and private investment to support translation of first discovery in laboratories to replicated field trials, and an urgent re-evaluation of regulation of crop genetic engineering. © 2016 The Authors.

  13. Genetically engineered crops and pesticide use in U.S. maize and soybeans

    PubMed Central

    Perry, Edward D.; Ciliberto, Federico; Hennessy, David A.; Moschini, GianCarlo

    2016-01-01

    The widespread adoption of genetically engineered (GE) crops has clearly led to changes in pesticide use, but the nature and extent of these impacts remain open questions. We study this issue with a unique, large, and representative sample of plot-level choices made by U.S. maize and soybean farmers from 1998 to 2011. On average, adopters of GE glyphosate-tolerant (GT) soybeans used 28% (0.30 kg/ha) more herbicide than nonadopters, adopters of GT maize used 1.2% (0.03 kg/ha) less herbicide than nonadopters, and adopters of GE insect-resistant (IR) maize used 11.2% (0.013 kg/ha) less insecticide than nonadopters. When pesticides are weighted by the environmental impact quotient, however, we find that (relative to nonadopters) GE adopters used about the same amount of soybean herbicides, 9.8% less of maize herbicides, and 10.4% less of maize insecticides. In addition, the results indicate that the difference in pesticide use between GE and non-GE adopters has changed significantly over time. For both soybean and maize, GT adopters used increasingly more herbicides relative to nonadopters, whereas adopters of IR maize used increasingly less insecticides. The estimated pattern of change in herbicide use over time is consistent with the emergence of glyphosate weed resistance. PMID:27652335

  14. African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

    PubMed Central

    Mwai, Okeyo; Hanotte, Olivier; Kwon, Young-Jun; Cho, Seoae

    2015-01-01

    At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers. PMID:26104394

  15. A global overview of biotech (GM) crops: adoption, impact and future prospects.

    PubMed

    James, Clive

    2010-01-01

    In the early 1990s, some were skeptical that genetically modified (GM) crops, now referred to as biotech crops, could deliver improved products and make an impact at the farm level. There was even more skepticism that developing countries would adopt biotech crops. The adoption of and commercialization of biotech crops in 2008 is reviewed. The impact of biotech crops are summarized including their contribution to: global food, feed and fiber security; a safer environment; a more sustainable agriculture; and the alleviation of poverty, and hunger in the developing countries of the world. Future prospects are discussed. Notably, Egypt planted Bt maize for the first time in 2008 thereby becoming the first country in the Arab world to commercialize biotech crops.

  16. Towards a globally optimized crop distribution: Integrating water use, nutrition, and economic value

    NASA Astrophysics Data System (ADS)

    Davis, K. F.; Seveso, A.; Rulli, M. C.; D'Odorico, P.

    2016-12-01

    Human demand for crop production is expected to increase substantially in the coming decades as a result of population growth, richer diets and biofuel use. In order for food production to keep pace, unprecedented amounts of resources - water, fertilizers, energy - will be required. This has led to calls for `sustainable intensification' in which yields are increased on existing croplands while seeking to minimize impacts on water and other agricultural resources. Recent studies have quantified aspects of this, showing that there is a large potential to improve crop yields and increase harvest frequencies to better meet human demand. Though promising, both solutions would necessitate large additional inputs of water and fertilizer in order to be achieved under current technologies. However, the question of whether the current distribution of crops is, in fact, the best for realizing sustainable production has not been considered to date. To this end, we ask: Is it possible to increase crop production and economic value while minimizing water demand by simply growing crops where soil and climate conditions are best suited? Here we use maps of yields and evapotranspiration for 14 major food crops to identify differences between current crop distributions and where they can most suitably be planted. By redistributing crops across currently cultivated lands, we determine the potential improvements in calorie (+12%) and protein (+51%) production, economic output (+41%) and water demand (-5%). This approach can also incorporate the impact of future climate on cropland suitability, and as such, be used to provide optimized cropping patterns under climate change. Thus, our study provides a novel tool towards achieving sustainable intensification that can be used to recommend optimal crop distributions in the face of a changing climate while simultaneously accounting for food security, freshwater resources, and livelihoods.

  17. Cisgenics - A Sustainable Approach for Crop Improvement

    PubMed Central

    Telem, R.S.; Wani, Shabir. H.; Singh, N.B.; Nandini, R.; Sadhukhan, R.; Bhattacharya, S.; Mandal, N.

    2013-01-01

    The implication of molecular biology in crop improvement is now more than three decades old. Not surprisingly, technology has moved on, and there are a number of new techniques that may or may not come under the genetically modified (GM) banner and, therefore, GM regulations. In cisgenic technology, cisgenes from crossable plants are used and it is a single procedure of gene introduction whereby the problem of linkage drag of other genes is overcome. The gene used in cisgenic approach is similar compared with classical breeding and cisgenic plant should be treated equally as classically bred plant and differently from transgenic plants. Therefore, it offers a sturdy reference to treat cisgenic plants similarly as classically bred plants, by exemption of cisgenesis from the current GMO legislations. This review covers the implications of cisgenesis towards the sustainable development in the genetic improvement of crops and considers the prospects for the technology. PMID:24396278

  18. Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae).

    PubMed

    Birnbaum, Kenneth; Desalle, Rob; Peters, Charles M; Benfey, Philip N

    2003-11-01

    Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.

  19. Could Crop Roughness Impact the Wind Resource at Agriculturally Productive Wind Farm Sites?

    NASA Astrophysics Data System (ADS)

    Vanderwende, B. J.; Lundquist, J. K.

    2014-12-01

    The high concentration of both large-scale agriculture and wind power production in the United States Midwest region raises new questions concerning the interaction of the two activities. For instance, it is known from internal boundary layer theory that changes in the roughness of the land-surface resulting from crop choices could modify the momentum field aloft. Upward propagation of such an effect might impact the properties of the winds encountered by modern turbines, which typically span a layer from about 40 to 120 meters above the surface. As direct observation of such interaction would require impractical interference in the planting schedules of farmers, we use numerical modeling to quantify the magnitude of crop-roughness effects. To simulate a collocated farm and turbine array, we use version 3.4.1 of the Weather Research and Forecasting model (WRF). The hypothetical farm is inserted near the real location of the 2013 Crop Wind Energy Experiment (CWEX). Reanalyses provide representative initial and boundary conditions. A month-long period spanning August 2013 is used to evaluate the differences in flows above corn (maize) and soybean crops at the mature, reproductive stage. Simulations are performed comparing the flow above each surface regime, both in the absence and presence of a wind farm, which consists of a parameterized 11x11 array of 1.8 MW Vestas V90 turbines. Appreciable differences in rotor-layer wind speeds emerge. The use of soybeans results in an increase in wind speeds and a corresponding reduction in rotor-layer shear when compared to corn. Despite the turbulent nature of flow within a wind farm, high stability reduces the impact of crop roughness on the flow aloft, particularly in the upper portion of the rotor disk. We use these results to estimate the economic impact of crop selection on wind power producers.

  20. Estimating yield gaps at the cropping system level.

    PubMed

    Guilpart, Nicolas; Grassini, Patricio; Sadras, Victor O; Timsina, Jagadish; Cassman, Kenneth G

    2017-05-01

    Yield gap analyses of individual crops have been used to estimate opportunities for increasing crop production at local to global scales, thus providing information crucial to food security. However, increases in crop production can also be achieved by improving cropping system yield through modification of spatial and temporal arrangement of individual crops. In this paper we define the cropping system yield potential as the output from the combination of crops that gives the highest energy yield per unit of land and time, and the cropping system yield gap as the difference between actual energy yield of an existing cropping system and the cropping system yield potential. Then, we provide a framework to identify alternative cropping systems which can be evaluated against the current ones. A proof-of-concept is provided with irrigated rice-maize systems at four locations in Bangladesh that represent a range of climatic conditions in that country. The proposed framework identified (i) realistic alternative cropping systems at each location, and (ii) two locations where expected improvements in crop production from changes in cropping intensity (number of crops per year) were 43% to 64% higher than from improving the management of individual crops within the current cropping systems. The proposed framework provides a tool to help assess food production capacity of new systems ( e.g. with increased cropping intensity) arising from climate change, and assess resource requirements (water and N) and associated environmental footprint per unit of land and production of these new systems. By expanding yield gap analysis from individual crops to the cropping system level and applying it to new systems, this framework could also be helpful to bridge the gap between yield gap analysis and cropping/farming system design.