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Sample records for agronomically important trait

  1. Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.)

    PubMed Central

    Jaiswal, Vandana; Gahlaut, Vijay; Meher, Prabina Kumar; Mir, Reyazul Rouf; Jaiswal, Jai Prakash; Rao, Atmakuri Ramakrishna; Balyan, Harindra Singh; Gupta, Pushpendra Kumar

    2016-01-01

    Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910–2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method. PMID:27441835

  2. Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.).

    PubMed

    Jaiswal, Vandana; Gahlaut, Vijay; Meher, Prabina Kumar; Mir, Reyazul Rouf; Jaiswal, Jai Prakash; Rao, Atmakuri Ramakrishna; Balyan, Harindra Singh; Gupta, Pushpendra Kumar

    2016-01-01

    Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910-2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method. PMID:27441835

  3. Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.).

    PubMed

    Jaiswal, Vandana; Gahlaut, Vijay; Meher, Prabina Kumar; Mir, Reyazul Rouf; Jaiswal, Jai Prakash; Rao, Atmakuri Ramakrishna; Balyan, Harindra Singh; Gupta, Pushpendra Kumar

    2016-01-01

    Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910-2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method.

  4. Association Mapping for Important Agronomic Traits in Core Collection of Rice (Oryza sativa L.) with SSR Markers

    PubMed Central

    Zhang, Peng; Liu, Xiangdong; Tong, Hanhua; Lu, Yonggen; Li, Jinquan

    2014-01-01

    Mining elite genes within rice landraces is of importance for the improvement of cultivated rice. An association mapping for 12 agronomic traits was carried out using a core collection of rice consisting of 150 landraces (Panel 1) with 274 simple sequence repeat (SSR) markers, and the mapping results were further verified using a Chinese national rice micro-core collection (Panel 2) and a collection from a global molecular breeding program (Panel 3). Our results showed that (1) 76 significant (P<0.05) trait-marker associations were detected using mixed linear model (MLM) within Panel 1 in two years, among which 32% were identical with previously mapped QTLs, and 11 significant associations had >10% explained ratio of genetic variation; (2) A total of seven aforementioned trait-marker associations were verified within Panel 2 and 3 when using a general linear model (GLM) and 55 SSR markers of the 76 significant trait-marker associations. However, no significant trait-marker association was found to be identical within three panels when using the MLM model; (3) several desirable alleles of the loci which showed significant trait-marker associations were identified. The research provided important information for further mining these elite genes within rice landraces and using them for rice breeding. PMID:25360796

  5. Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics.

    PubMed

    Farfan, Ivan D Barrero; De La Fuente, Gerald N; Murray, Seth C; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L; Kolomiets, Mike

    2015-01-01

    The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.

  6. Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics

    PubMed Central

    Farfan, Ivan D. Barrero; De La Fuente, Gerald N.; Murray, Seth C.; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L.; Kolomiets, Mike

    2015-01-01

    The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines. PMID:25714370

  7. Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics.

    PubMed

    Farfan, Ivan D Barrero; De La Fuente, Gerald N; Murray, Seth C; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L; Kolomiets, Mike

    2015-01-01

    The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines. PMID:25714370

  8. Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping.

    PubMed

    Reif, Jochen C; Liu, Wenxin; Gowda, Manje; Maurer, Hans Peter; Möhring, Jens; Fischer, Sandra; Schechert, Axel; Würschum, Tobias

    2010-11-01

    Epistatic interactions may contribute substantially to the hybrid performance of sugar beet. The main goal of our study was to dissect the genetic basis of eight important physiological and agronomic traits using two different biometrical models for joint linkage association mapping. A total of 197 genotypes of an elite breeding population were evaluated in multi-location trials and fingerprinted with 194 SNP markers. Two different statistical models were used for the genome-wide scan for marker-trait associations: Model A, which corrects for the genetic background with markers as cofactors and Model B, which additionally models a population effect. Based on the extent of linkage disequilibrium in the parental population, we estimated that for a genome-wide scan at least 100 equally spaced markers are necessary. We mapped across the eight traits 39 QTL for Model A and 22 for Model B. Only 11% of the total number of QTL were identified based on Models A and B, which indicates that both models are complementary. Epistasis was detected only for two out of the eight traits, and contributed only to a minor extent to the genotypic variance. This low relevance of epistasis implies that in sugar beet breeding the prediction of performance of three-way hybrids is feasible with high accuracy based on the means of their single crosses.

  9. QTL of three agronomically important traits and their interactions with environment in a European x Chinese rapeseed population.

    PubMed

    Zhao, Jian-Yi; Becker, Heiko C; Ding, Hou-Dong; Zhang, Yao-Feng; Zhang, Dong-Qing; Ecke, Wolfgang

    2005-09-01

    A rapeseed population consisted of 282 doubled haploid (DH) lines derived from a cross between a European vality "Sallux" and a Chinese inbred line "Gaoyou" was planted in 4 locations, 2 in Xi'an and Hangzhou, China, and 2 in Goettingen, Germany. Field experiments were carried out to obtain agronomically phenotypic data from above four environments. A linkage map including 125 SSR-markers was constructed and QTL analyses was performed using mixed model approach to detect QTLs showing additive (a), epistasis (aa) as well as their interactions with environments (QE) for three important agronomic traits: plant height, flowering time and maturity. The results demonstrated that each trait was controlled by several QTLs with additive effect and a number of QTLs with epistatic and QE interaction effects. Plant height was controlled by many QTLs (12 loci with a or combined ae, 5 loci with ae). Additive effects were predominant,totally explained 75% of the phenotypic variation and often combined with digenic epistasis. Of 12 main QTLs, 9 showed Gaoyou alleles decreasing plant height. Most of QTLs with QE effects showed ecologically favourable alleles in diverse regions. Five of 7 ae loci showed Gaoyou alleles in Hangzhou and all the ae loci but one had Sollux alleles in two locations of Germany increasing plant height. The digenic epistatic main effect accounted for one third of total additive main effects. In this study,we discovered 7 and 8 loci having significant additive main effects upon flowering time and maturity, respectively. Of them, early flowering and maturity alleles were respectively 6 and 5 derived from Chinese parent Gaoyou. All these QTLs together accounted for around 60% of the phenotypic variation for each trait. Significant ae interactions were detected for flowering time and maturity and parental alleles showed almost evenly dispersal at all environments. Three of 8 main QTLs for maturity were located at similar or identical positions as QTLs for

  10. QTL of three agronomically important traits and their interactions with environment in a European x Chinese rapeseed population.

    PubMed

    Zhao, Jian-Yi; Becker, Heiko C; Ding, Hou-Dong; Zhang, Yao-Feng; Zhang, Dong-Qing; Ecke, Wolfgang

    2005-09-01

    A rapeseed population consisted of 282 doubled haploid (DH) lines derived from a cross between a European vality "Sallux" and a Chinese inbred line "Gaoyou" was planted in 4 locations, 2 in Xi'an and Hangzhou, China, and 2 in Goettingen, Germany. Field experiments were carried out to obtain agronomically phenotypic data from above four environments. A linkage map including 125 SSR-markers was constructed and QTL analyses was performed using mixed model approach to detect QTLs showing additive (a), epistasis (aa) as well as their interactions with environments (QE) for three important agronomic traits: plant height, flowering time and maturity. The results demonstrated that each trait was controlled by several QTLs with additive effect and a number of QTLs with epistatic and QE interaction effects. Plant height was controlled by many QTLs (12 loci with a or combined ae, 5 loci with ae). Additive effects were predominant,totally explained 75% of the phenotypic variation and often combined with digenic epistasis. Of 12 main QTLs, 9 showed Gaoyou alleles decreasing plant height. Most of QTLs with QE effects showed ecologically favourable alleles in diverse regions. Five of 7 ae loci showed Gaoyou alleles in Hangzhou and all the ae loci but one had Sollux alleles in two locations of Germany increasing plant height. The digenic epistatic main effect accounted for one third of total additive main effects. In this study,we discovered 7 and 8 loci having significant additive main effects upon flowering time and maturity, respectively. Of them, early flowering and maturity alleles were respectively 6 and 5 derived from Chinese parent Gaoyou. All these QTLs together accounted for around 60% of the phenotypic variation for each trait. Significant ae interactions were detected for flowering time and maturity and parental alleles showed almost evenly dispersal at all environments. Three of 8 main QTLs for maturity were located at similar or identical positions as QTLs for

  11. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis.

    PubMed

    D'hoop, Björn B; Keizer, Paul L C; Paulo, M João; Visser, Richard G F; van Eeuwijk, Fred A; van Eck, Herman J

    2014-03-01

    Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Two association mapping panels were analysed for marker-trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL. PMID:24408376

  12. Metabolic prediction of important agronomic traits in hybrid rice (Oryza sativa L.).

    PubMed

    Dan, Zhiwu; Hu, Jun; Zhou, Wei; Yao, Guoxin; Zhu, Renshan; Zhu, Yingguo; Huang, Wenchao

    2016-01-01

    Hybrid crops have contributed greatly to improvements in global food and fodder production over the past several decades. Nevertheless, the growing population and changing climate have produced food crises and energy shortages. Breeding new elite hybrid varieties is currently an urgent task, but present breeding procedures are time-consuming and labour-intensive. In this study, parental metabolic information was utilized to predict three polygenic traits in hybrid rice. A complete diallel cross population consisting of eighteen rice inbred lines was constructed, and the hybrids' plant height, heading date and grain yield per plant were predicted using 525 metabolites. Metabolic prediction models were built using the partial least square regression method, with predictive abilities ranging from 0.858 to 0.977 for the hybrid phenotypes, relative heterosis, and specific combining ability. Only slight changes in predictive ability were observed between hybrid populations, and nearly no changes were detected between reciprocal hybrids. The outcomes of prediction of the three highly polygenic traits demonstrated that metabolic prediction was an accurate (high predictive abilities) and efficient (unaffected by population genetic structures) strategy for screening promising superior hybrid rice. Exploitation of this pre-hybridization strategy may contribute to rice production improvement and accelerate breeding programs. PMID:26907211

  13. Metabolic prediction of important agronomic traits in hybrid rice (Oryza sativa L.)

    PubMed Central

    Dan, Zhiwu; Hu, Jun; Zhou, Wei; Yao, Guoxin; Zhu, Renshan; Zhu, Yingguo; Huang, Wenchao

    2016-01-01

    Hybrid crops have contributed greatly to improvements in global food and fodder production over the past several decades. Nevertheless, the growing population and changing climate have produced food crises and energy shortages. Breeding new elite hybrid varieties is currently an urgent task, but present breeding procedures are time-consuming and labour-intensive. In this study, parental metabolic information was utilized to predict three polygenic traits in hybrid rice. A complete diallel cross population consisting of eighteen rice inbred lines was constructed, and the hybrids’ plant height, heading date and grain yield per plant were predicted using 525 metabolites. Metabolic prediction models were built using the partial least square regression method, with predictive abilities ranging from 0.858 to 0.977 for the hybrid phenotypes, relative heterosis, and specific combining ability. Only slight changes in predictive ability were observed between hybrid populations, and nearly no changes were detected between reciprocal hybrids. The outcomes of prediction of the three highly polygenic traits demonstrated that metabolic prediction was an accurate (high predictive abilities) and efficient (unaffected by population genetic structures) strategy for screening promising superior hybrid rice. Exploitation of this pre-hybridization strategy may contribute to rice production improvement and accelerate breeding programs. PMID:26907211

  14. Genetic mapping of quantitative trait loci associated with important agronomic traits in the spring wheat (Triticum aestivum L.) cross ‘Louise’ by ‘Penawawa’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic factors underlying agronomic traits in common wheat (Triticum aestivum L.) is essential to making gains from selection during the breeding process. A set of 188 recombinant inbred lines from a ‘Louise’ by ‘Penawawa’ mapping population was grown in two crop years at two loc...

  15. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.

    PubMed

    Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San

    2016-07-01

    Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes. PMID:27166667

  16. Roles of UV-damaged DNA binding protein 1 (DDB1) in epigenetically modifying multiple traits of agronomic importance in tomato.

    PubMed

    Tang, Xiaofeng; Liu, Jikai; Huang, Shengxiong; Shi, Wei; Miao, Min; Tang, Dan Feng; Niu, Xiangli; Xiao, Fangming; Liu, Yongsheng

    2012-12-01

    Epigenetic regulation participates broadly in many fundamentally cellular and physiological processes. In this study, we found that DDB1, a protein originally identified as a factor involved in DNA repairing, plays important roles in regulating organ size, growth habit and photosynthesis in tomato via an epigenetic manner. We generated transgenic tomato plants overexpressing an alternatively spliced DDB1 transcript (DDB1(F) , prevalently present in tomato tissues) and found the primary transformants displayed small-fruited "cherry tomato" in companion with strikingly enhanced shoot branching and biomass, dark-green leaves with elevated chlorophyll accumulation, and increased soluble solids in fruits. Significantly, these phenotypic alterations did not segregate with the DDB1(F) transgene in subsequent generations, suggesting that the effect of DDB1(F) on multiple agronomic traits is implemented via an epigenetic manner and is inheritable over generations. We speculate that DDB1, as a core subunit in the recently identified CUL4-based E3 ligase complex, mediates the 26S proteasome-dependent degradation of a large number of proteins, some of which might be required for perpetuating epigenetic marks on chromatins. PMID:23073016

  17. Whole genome association study for drought, aflatoxin resistance, and important agronomic traits in maize in a sub-tropical environment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary maize (Zea mays L.) production areas are in temperate regions throughout the world, where most maize breeding is focused. Important but lower yielding maize growing regions, such as the sub-tropics, experience unique challenges the greatest of which are drought stress and aflatoxin conta...

  18. Quantitative trait locus analysis of multiple agronomic traits in the model legume Lotus japonicus.

    PubMed

    Gondo, Takahiro; Sato, Shusei; Okumura, Kenji; Tabata, Satoshi; Akashi, Ryo; Isobe, Sachiko

    2007-07-01

    The first quantitative trait locus (QTL) analysis of multiple agronomic traits in the model legume Lotus japonicus was performed with a population of recombinant inbred lines derived from Miyakojima MG-20 x Gifu B-129. Thirteen agronomic traits were evaluated in 2004 and 2005: traits of vegetative parts (plant height, stem thickness, leaf length, leaf width, plant regrowth, plant shape, and stem color), flowering traits (flowering time and degree), and pod and seed traits (pod length, pod width, seeds per pod, and seed mass). A total of 40 QTLs were detected that explained 5%-69% of total variation. The QTL that explained the most variation was that for stem color, which was detected in the same region of chromosome 2 in both years. Some QTLs were colocated, especially those for pod and seed traits. Seed mass QTLs were located at 5 locations that mapped to the corresponding genomic positions of equivalent QTLs in soybean, pea, chickpea, and mung bean. This study provides fundamental information for breeding of agronomically important legume crops.

  19. Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea.

    PubMed

    Kujur, Alice; Upadhyaya, Hari D; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-05-05

    We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20-0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9-39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.

  20. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus

    PubMed Central

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A. P.; Wittkop, Benjamin; Snowdon, Rod J.; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  1. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus.

    PubMed

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A P; Wittkop, Benjamin; Snowdon, Rod J; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.

  2. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus.

    PubMed

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A P; Wittkop, Benjamin; Snowdon, Rod J; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  3. Quantitative genetic analysis of agronomic and morphological traits in sorghum, Sorghum bicolor

    PubMed Central

    Mohammed, Riyazaddin; Are, Ashok K.; Bhavanasi, Ramaiah; Munghate, Rajendra S.; Kavi Kishor, Polavarapu B.; Sharma, Hari C.

    2015-01-01

    The productivity in sorghum is low, owing to various biotic and abiotic constraints. Combining insect resistance with desirable agronomic and morphological traits is important to increase sorghum productivity. Therefore, it is important to understand the variability for various agronomic traits, their heritabilities and nature of gene action to develop appropriate strategies for crop improvement. Therefore, a full diallel set of 10 parents and their 90 crosses including reciprocals were evaluated in replicated trials during the 2013–14 rainy and postrainy seasons. The crosses between the parents with early- and late-flowering flowered early, indicating dominance of earliness for anthesis in the test material used. Association between the shoot fly resistance, morphological, and agronomic traits suggested complex interactions between shoot fly resistance and morphological traits. Significance of the mean sum of squares for GCA (general combining ability) and SCA (specific combining ability) of all the studied traits suggested the importance of both additive and non-additive components in inheritance of these traits. The GCA/SCA, and the predictability ratios indicated predominance of additive gene effects for majority of the traits studied. High broad-sense and narrow-sense heritability estimates were observed for most of the morphological and agronomic traits. The significance of reciprocal combining ability effects for days to 50% flowering, plant height and 100 seed weight, suggested maternal effects for inheritance of these traits. Plant height and grain yield across seasons, days to 50% flowering, inflorescence exsertion, and panicle shape in the postrainy season showed greater specific combining ability variance, indicating the predominance of non-additive type of gene action/epistatic interactions in controlling the expression of these traits. Additive gene action in the rainy season, and dominance in the postrainy season for days to 50% flowering and plant

  4. Quantitative genetic analysis of agronomic and morphological traits in sorghum, Sorghum bicolor.

    PubMed

    Mohammed, Riyazaddin; Are, Ashok K; Bhavanasi, Ramaiah; Munghate, Rajendra S; Kavi Kishor, Polavarapu B; Sharma, Hari C

    2015-01-01

    The productivity in sorghum is low, owing to various biotic and abiotic constraints. Combining insect resistance with desirable agronomic and morphological traits is important to increase sorghum productivity. Therefore, it is important to understand the variability for various agronomic traits, their heritabilities and nature of gene action to develop appropriate strategies for crop improvement. Therefore, a full diallel set of 10 parents and their 90 crosses including reciprocals were evaluated in replicated trials during the 2013-14 rainy and postrainy seasons. The crosses between the parents with early- and late-flowering flowered early, indicating dominance of earliness for anthesis in the test material used. Association between the shoot fly resistance, morphological, and agronomic traits suggested complex interactions between shoot fly resistance and morphological traits. Significance of the mean sum of squares for GCA (general combining ability) and SCA (specific combining ability) of all the studied traits suggested the importance of both additive and non-additive components in inheritance of these traits. The GCA/SCA, and the predictability ratios indicated predominance of additive gene effects for majority of the traits studied. High broad-sense and narrow-sense heritability estimates were observed for most of the morphological and agronomic traits. The significance of reciprocal combining ability effects for days to 50% flowering, plant height and 100 seed weight, suggested maternal effects for inheritance of these traits. Plant height and grain yield across seasons, days to 50% flowering, inflorescence exsertion, and panicle shape in the postrainy season showed greater specific combining ability variance, indicating the predominance of non-additive type of gene action/epistatic interactions in controlling the expression of these traits. Additive gene action in the rainy season, and dominance in the postrainy season for days to 50% flowering and plant

  5. Sugarcane Functional Genomics: Gene Discovery for Agronomic Trait Development

    PubMed Central

    Menossi, M.; Silva-Filho, M. C.; Vincentz, M.; Van-Sluys, M.-A.; Souza, G. M.

    2008-01-01

    Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs. PMID:18273390

  6. Genetic dissection of agronomic traits in Capsicum baccatum var. pendulum.

    PubMed

    Moulin, M M; Rodrigues, R; Bento, C S; Gonçalves, L S A; Santos, J O; Sudré, C P; Viana, A P

    2015-03-20

    Genetic mapping is very useful for dissecting complex agronomic traits. Genetic mapping allows for identification of quantitative trait loci (QTL), provide knowledge on a gene position and its adjacent region, and enable prediction of evolutionary mechanisms, in addition to contributing to synteny studies. The aim of this study was to predict genetic values associated with different agronomic traits evaluated in an F2 population of Capsicum baccatum var. pendulum. Previously, a reference genetic map for C. baccatum was constructed, which included 183 markers (42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplification of polymorphic DNA) arranged in 16 linkage groups. The map was used to identify QTL associated with 11 agronomic traits, including plant height, crown diameter, number of days to flowering, days to fruiting, number of fruits per plant, average fruit weight, fruit length, fruit diameter, fruit pulp thickness, soluble solids, and fruit dry weight. QTL mapping was performed by standard interval mapping. The number of small QTL effects ranged from 3-11, with a total of 61 QTL detected in 9 linkage groups. This is the first report involving QTL analysis for C. baccatum species.

  7. Descriptive statistics and correlation analysis of agronomic traits in a maize recombinant inbred line population.

    PubMed

    Zhang, H M; Hui, G Q; Luo, Q; Sun, Y; Liu, X H

    2014-01-01

    Maize (Zea mays L.) is one of the most important crops in the world. In this study, 13 agronomic traits of a recombinant inbred line population that was derived from the cross between Mo17 and Huangzao4 were investigated in maize: ear diameter, ear length, ear axis diameter, ear weight, plant height, ear height, days to pollen shed (DPS), days to silking (DS), the interval between DPS and DS, 100-kernel weight, kernel test weight, ear kernel weight, and kernel rate. Furthermore, the descriptive statistics and correlation analysis of the 13 traits were performed using the SPSS 11.5 software. The results providing the phenotypic data here are needed for the quantitative trait locus mapping of these agronomic traits. PMID:24535873

  8. Population structure and association mapping of yield contributing agronomic traits in foxtail millet.

    PubMed

    Gupta, Sarika; Kumari, Kajal; Muthamilarasan, Mehanathan; Parida, Swarup Kumar; Prasad, Manoj

    2014-06-01

    Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of

  9. Heritability of Oleic Acid Seed Content in Soybean Oil and its Genetic Correlation with Fatty Acid and Agronomic Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oleic acid seed content is an important determinant of the nutritional value and the oxidative stability of soybean oil. Breeding for higher oleate content mandates the estimation of the heritability and the genetic correlations between oleate and fatty acid traits and between oleate and agronomic t...

  10. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.)

    PubMed Central

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0–55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R2 = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R2 = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R2 = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481–scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64–scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782–Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353–Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  11. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    PubMed

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.

  12. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    PubMed

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  13. Has selection for improved agronomic traits made reed canarygrass invasive?

    PubMed

    Jakubowski, Andrew R; Casler, Michael D; Jackson, Randall D

    2011-01-01

    Plant breeders have played an essential role in improving agricultural crops, and their efforts will be critical to meet the increasing demand for cellulosic bioenergy feedstocks. However, a major concern is the potential development of novel invasive species that result from breeders' efforts to improve agronomic traits in a crop. We use reed canarygrass as a case study to evaluate the potential of plant breeding to give rise to invasive species. Reed canarygrass has been improved by breeders for use as a forage crop, but it is unclear whether breeding efforts have given rise to more vigorous populations of the species. We evaluated cultivars, European wild, and North American invader populations in upland and wetland environments to identify differences in vigor between the groups of populations. While cultivars were among the most vigorous populations in an agricultural environment (upland soils with nitrogen addition), there were no differences in above- or below-ground production between any populations in wetland environments. These results suggest that breeding has only marginally increased vigor in upland environments and that these gains are not maintained in wetland environments. Breeding focuses on selection for improvements of a specific target population of environments, and stability across a wide range of environments has proved elusive for even the most intensively bred crops. We conclude that breeding efforts are not responsible for wetland invasion by reed canarygrass and offer guidelines that will help reduce the possibility of breeding programs releasing cultivars that will become invasive. PMID:21991347

  14. Heritability of drought resistance traits and correlation of drought resistance and agronomic traits in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inheritance of traits is important for developing effective breeding schemes for improving desired traits. The aims of this study were to estimate the heritabilities (h2) of drought resistance traits and the genotypic (rG) and phenotypic (rP) correlations between drought resistance traits under str...

  15. Genes associated with agronomic traits in non-heading Chinese cabbage identified by expression profiling

    PubMed Central

    2014-01-01

    Background The genomes of non-heading Chinese cabbage (Brassica rapa ssp. chinensis), heading Chinese cabbage (Brassica rapa ssp. pekinensis) and their close relative Arabidopsis thaliana have provided important resources for studying the evolution and genetic improvement of cruciferous plants. Natural growing conditions present these plants with a variety of physiological challenges for which they have a repertoire of genes that ensure adaptability and normal growth. We investigated the differential expressions of genes that control adaptability and development in plants growing in the natural environment to study underlying mechanisms of their expression. Results Using digital gene expression tag profiling, we constructed an expression profile to identify genes related to important agronomic traits under natural growing conditions. Among three non-heading Chinese cabbage cultivars, we found thousands of genes that exhibited significant differences in expression levels at five developmental stages. Through comparative analysis and previous reports, we identified several candidate genes associated with late flowering, cold tolerance, self-incompatibility, and leaf color. Two genes related to cold tolerance were verified using quantitative real-time PCR. Conclusions We identified a large number of genes associated with important agronomic traits of non-heading Chinese cabbage. This analysis will provide a wealth of resources for molecular-assisted breeding of cabbage. The raw data and detailed results of this analysis are available at the website http://nhccdata.njau.edu.cn. PMID:24655567

  16. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter

    PubMed Central

    Yu, Ju-Kyung; Graznak, Elizabeth; Breseghello, Flavio; Tefera, Hailu; Sorrells, Mark E

    2007-01-01

    Background Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Results Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. Conclusion The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia. PMID:17565675

  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. Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms).

    PubMed

    Gao, Wei; Baars, Johan J P; Maliepaard, Chris; Visser, Richard G F; Zhang, Jinxia; Sonnenberg, Anton S M

    2016-12-01

    The demand for button mushrooms of high quality is increasing. Superior button mushroom varieties require the combination of multiple traits to maximize productivity and quality. Very often these traits are correlated and should, therefore, be evaluated together rather than as single traits. In order to unravel the genetic architecture of multiple traits of Agaricus bisporus and the genetic correlations among traits, we have investigated a total of six agronomic and quality traits through multi-trait QTL analyses in a mixed-model. Traits were evaluated in three heterokaryon sets. Significant phenotypic correlations were observed among traits. For instance, earliness (ER) correlated to firmness (FM), cap color, and compost colonization, and FM correlated to scales (SC). QTLs of different traits located on the same chromosomes genetically explains the phenotypic correlations. QTL detected on chromosome 10 mainly affects three traits, i.e., ER, FM and SC. It explained 31.4 % phenotypic variation of SC on mushroom cap (heterokaryon Set 1), 14.9 % that of the FM (heterokaryon Set 3), and 14.2 % that of ER (heterokaryon Set 3). High value alleles from the wild parental line showed beneficial effects for several traits, suggesting that the wild germplasm is a valuable donor in terms of those traits. Due to the limitations of recombination pattern, we only made a start at understanding the genetic base for several agronomic and quality traits in button mushrooms. PMID:27620731

  19. Association Analysis of Simple Sequence Repeat (SSR) Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

    PubMed Central

    Chen, Liang; Sun, Xiaoyan; Yang, Yong; Liu, Hongmei; Xu, Qingguo

    2015-01-01

    associated with SW; five single-associated markers were associated with SC; seven single-associated markers were associated with SCP; three single-associated markers were associated with SL. Especially, we observed that the genetic variation of SW was explained 11.6 % by M37 marker. It is interesting to observe that nine markers (M1, M2, M35, M54 marker was associated with both BCS and SC; M3, M4 markers were associated with BCS, SW, and SC; M19 marker was associated with both pH and PD, M40 marker was associated with both SCP and SW; and M193 marker was associated with both PH and SL) were associated with more than two agronomic traits. Notably, Branch count per spike (BCS) was explained by four markers (M1, M2, M3, and M4) exceeding 10 %. These identified marker alleles associated with agronomic traits could provide important information and markers for molecular-assisted breeding that facilitate the breeding process in tall fescue. PMID:26186338

  20. Genome-wide association study of agronomic traits in common bean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genome-wide association study (GWAS) using a global Andean diversity panel (ADP) of 237 genotypes of common bean, Phaseolus vulgaris was conducted to gain insight into the genetic architecture of several agronomic traits controlling phenology, biomass, yield components and seed yield. The panel wa...

  1. Disease evaluations and agronomic traits of advanced peanut breeding lines in 2015

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 20 commercially available peanut cultivars and high-oleic advanced breeding lines were evaluated in small field plots in 2015 for agronomic traits (crop value, yield, seed grade, and characteristics). Environmental conditions in 2015 were not favorable for Sclerotinia blight, southern bl...

  2. Disease evaluations and agronomic traits of advanced peanut breeding lines in 2014

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 23 commercially available peanut cultivars and high-oleic advanced breeding lines were evaluated in small field plots in 2014 for agronomic traits (crop value, yield, seed grade, and characteristics) and resistance to soilborne diseases. Among the 16 runner entries evaluated, Tamrun OL11...

  3. Association mapping of agronomic and quality traits in USDA pea single-plant collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping is an efficient approach for the identification of the molecular basis of agronomic traits in crop plants. For this purpose in pea (Pisum sativum L.), we genotyped and phenotyped individual lines of the single-plant derived core collection of the USDA pea single-plant (PSP) colle...

  4. Genetic and association mapping study of wheat agronomic traits under contrasting water regimes.

    PubMed

    Dodig, Dejan; Zoric, Miroslav; Kobiljski, Borislav; Savic, Jasna; Kandic, Vesna; Quarrie, Steve; Barnes, Jeremy

    2012-01-01

    Genetic analyses and association mapping were performed on a winter wheat core collection of 96 accessions sampled from a variety of geographic origins. Twenty-four agronomic traits were evaluated over 3 years under fully irrigated, rainfed and drought treatments. Grain yield was the most sensitive trait to water deficit and was highly correlated with above-ground biomass per plant and number of kernels per m(2). The germplasm was structured into four subpopulations. The association of 46 SSR loci distributed throughout the wheat genome with yield and agronomic traits was analyzed using a general linear model, where subpopulation information was used to control false-positive or spurious marker-trait associations (MTAs). A total of 26, 21 and 29 significant (P < 0.001) MTAs were identified in irrigated, rainfed and drought treatments, respectively. The marker effects ranged from 14.0 to 50.8%. Combined across all treatments, 34 significant (P < 0.001) MTAs were identified with nine markers, and R(2) ranged from 14.5 to 50.2%. Marker psp3200 (6DS) and particularly gwm484 (2DS) were associated with many significant MTAs in each treatment and explained the greatest proportion of phenotypic variation. Although we were not able to recognize any marker related to grain yield under drought stress, a number of MTAs associated with developmental and agronomic traits highly correlated with grain yield under drought were identified.

  5. Genetic mapping and QTL analysis of agronomic traits in Indian Mucuna pruriens using an intraspecific F₂population.

    PubMed

    Mahesh, S; Leelambika, M; Jaheer, Md; Anithakumari, A M; Sathyanarayana, N

    2016-03-01

    Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M. pruriens has been developed based on amplified fragment length polymorphism (AFLP) markers using 200 F₂ progenies derived from a cross between wild and cultivated genotypes. The resulting linkage map comprised 129 AFLP markers dispersed over 13 linkage groups spanning a total distance of 618.88 cM with an average marker interval of 4.79 cM. For the first time, three QTLs explaining about 6.05-14.77% of the corresponding total phenotypic variation for three quantitative (seed) traits and, eight QTLs explaining about 25.96% of the corresponding total phenotypic variation for three qualitative traits have been detected on four linkage groups. The map presented here will pave a way for mapping of genes/QTLs for the important agronomic and horticultural traits contrasting between the parents used in this study. PMID:27019430

  6. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    PubMed

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-05-13

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

  7. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    PubMed

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-01-01

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content. PMID:27323023

  8. Identification of Quantitative Trait Loci for the Phenolic Acid Contents and Their Association with Agronomic Traits in Tibetan Wild Barley.

    PubMed

    Cai, Shengguan; Han, Zhigang; Huang, Yuqing; Hu, Hongliang; Dai, Fei; Zhang, Guoping

    2016-02-01

    Phenolic acids have been of considerable interest in human nutrition because of their strong antioxidative properties. However, even in a widely grown crop, such as barley, their genetic architecture is still unclear. In this study, genetic control of two main phenolic acids, ferulic acid (FA) and p-coumaric acid (p-CA), and their associations with agronomic traits were investigated among 134 Tibetan wild barley accessions. A genome-wide association study (GWAS) identified three DArT markers (bpb-2723, bpb-7199, and bpb-7273) associated with p-CA content and one marker (bpb-3653) associated with FA content in 2 consecutive years. The contents of the two phenolic acids were positively correlated with some agronomic traits, such as the first internode length, plant height, and some grain color parameters, and negatively correlated with the thousand-grain weight (TGW). This study provides DNA markers for barley breeding programs to improve the contents of phenolic acids.

  9. [Numerical taxonomy of agronomic trait in cultivated Lonicera japonica].

    PubMed

    Zhang, Shan-Shan; Huang, Lu-Qi; Yuan, Yuan; Chen, Ping

    2014-04-01

    Sixty-three morphological traits from 743 specimens of the 41 taxa within the cultivated Lonicera japonica were observed and measured, such as the height of plants, the length of leaf, the width of leaf, the length of anther, the alabastrum's number of one branch, the color of alabastrum and so on. A numerical taxonomy is presented by using the cluster analysis, principal components analysis (PCA) and factor analysis. Sixteen of 63 characters were screened by means of PCA and used for cluster analysis of 41 taxa with the method of Ward linkage and average euclidean distance. The cluster analysis showed that the 41 taxa could be divided into 5 groups when the Euclidean distance coefficient was 11.84. The factor analysis indicated that the shape of leaf, color of alabastrum, the pilosity and color of twiggery were of significance for the cultivated L. japonica classification. The results of this study will be a base for the core collection and breeding of L. japonica.

  10. Retention of agronomically important variation in germplasm core collections: implications for allele mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to d...

  11. Genetic diversity, population structure, and association mapping of agronomic traits in waxy and normal maize inbred lines.

    PubMed

    Sa, K J; Park, J Y; Choi, S H; Kim, B W; Park, K J; Lee, J K

    2015-01-01

    Understanding genetic diversity, population structure, and linkage disequilibrium is a prerequisite for the association mapping of complex traits in a target population. In this study, the genetic diversity and population structure of 40 waxy and 40 normal inbred maize lines were investigated using 10 morphological traits and 200 simple sequence repeat (SSR) markers. Based on a population structure analysis, the 80 maize inbred lines were divided into three groups: I, II, and admixed. Significant marker-trait associations were identified between the markers and the 10 morphological traits, which were studied according to the model used to confirm the association. Using a general linear model, the lowest R(2) value (9.03) was detected in umc1139, which was associated with ear number, and the highest (43.97) was in umc1858, which was associated with plant height. Using a mixed linear model, the lowest R(2) value (18.74) was in umc1279, which was associated with ear weight; the highest (27.66) was in umc1858, which was associated with 100-kernel weight. The SSR markers identified in the present study may serve as useful molecular markers for selecting important yield and agronomic traits. These results will be useful for marker-assisted selection in maize breeding programs, to help breeders choose parental lines and markers for crosses.

  12. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.))

    PubMed Central

    Hu, Xin; Ren, Jing; Ren, Xifeng; Huang, Sisi; Sabiel, Salih A. I.; Luo, Mingcheng; Nevo, Eviatar; Fu, Chunjie; Peng, Junhua; Sun, Dongfa

    2015-01-01

    Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection. PMID:26110423

  13. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa).

    PubMed

    Zorrilla-Fontanesi, Yasmín; Cabeza, Amalia; Domínguez, Pedro; Medina, Juan Jesús; Valpuesta, Victoriano; Denoyes-Rothan, Beatrice; Sánchez-Sevilla, José F; Amaya, Iraida

    2011-09-01

    Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.

  14. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica).

    PubMed

    Jia, Guanqing; Huang, Xuehui; Zhi, Hui; Zhao, Yan; Zhao, Qiang; Li, Wenjun; Chai, Yang; Yang, Lifang; Liu, Kunyan; Lu, Hengyun; Zhu, Chuanrang; Lu, Yiqi; Zhou, Congcong; Fan, Danlin; Weng, Qijun; Guo, Yunli; Huang, Tao; Zhang, Lei; Lu, Tingting; Feng, Qi; Hao, Hangfei; Liu, Hongkuan; Lu, Ping; Zhang, Ning; Li, Yuhui; Guo, Erhu; Wang, Shujun; Wang, Suying; Liu, Jinrong; Zhang, Wenfei; Chen, Guoqiu; Zhang, Baojin; Li, Wei; Wang, Yongfang; Li, Haiquan; Zhao, Baohua; Li, Jiayang; Diao, Xianmin; Han, Bin

    2013-08-01

    Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.

  15. Genetic analyses of agronomic traits in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.)

    PubMed Central

    Li, Chunhua; Kobayashi, Kiwa; Yoshida, Yasuko; Ohsawa, Ryo

    2012-01-01

    The consumption of products made from Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) has increased in recent years in Japan. Increased consumer demand has led to recognition of the need for early varieties of this crop with high and stable yields. In order to accomplish this, more information is needed on the genetic mechanisms affecting earliness and yield. We conducted genetic analysis of 3 agronomic traits (days to flowering, plant height and total seed weight per plant) to segregate F2 and F3 populations derived from a cross between Tartary buckwheat cultivars ‘Hokuriku No. 4’ and ‘Ishisoba’. Broad-sense heritability estimates for days to flowering, plant height and total seed weight were 0.70, 0.62 and 0.75, respectively, in F3 population. Narrow-sense heritability for total seed weight (0.51) was highest, followed by heritability for days to flowering (0.37), with heritability for plant height (0.26) lowest. Later flowering was associated with increased plant height and higher yields. From the F4 generation, we identified twelve candidate plants with earlier maturity and reduced plant height compared to ‘Hokuriku No. 4’, but almost the same total seed weight. These results suggest that hybridization breeding using the single seed descent (SSD) method is an effective approach for improving agronomic characteristics of Tartary buckwheat. PMID:23341743

  16. Genetic analyses of agronomic traits in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.).

    PubMed

    Li, Chunhua; Kobayashi, Kiwa; Yoshida, Yasuko; Ohsawa, Ryo

    2012-12-01

    The consumption of products made from Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) has increased in recent years in Japan. Increased consumer demand has led to recognition of the need for early varieties of this crop with high and stable yields. In order to accomplish this, more information is needed on the genetic mechanisms affecting earliness and yield. We conducted genetic analysis of 3 agronomic traits (days to flowering, plant height and total seed weight per plant) to segregate F(2) and F(3) populations derived from a cross between Tartary buckwheat cultivars 'Hokuriku No. 4' and 'Ishisoba'. Broad-sense heritability estimates for days to flowering, plant height and total seed weight were 0.70, 0.62 and 0.75, respectively, in F(3) population. Narrow-sense heritability for total seed weight (0.51) was highest, followed by heritability for days to flowering (0.37), with heritability for plant height (0.26) lowest. Later flowering was associated with increased plant height and higher yields. From the F(4) generation, we identified twelve candidate plants with earlier maturity and reduced plant height compared to 'Hokuriku No. 4', but almost the same total seed weight. These results suggest that hybridization breeding using the single seed descent (SSD) method is an effective approach for improving agronomic characteristics of Tartary buckwheat.

  17. Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaea L.) mini-core collection.

    PubMed

    Jiang, Huifang; Huang, Li; Ren, Xiaoping; Chen, Yuning; Zhou, Xiaojing; Xia, Youlin; Huang, Jiaquan; Lei, Yong; Yan, Liying; Wan, Liyun; Liao, Boshou

    2014-02-01

    Association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut (Arachis hypogaea L.) mini-core collection in China comprising 298 accessions was genotyped using 109 simple sequence repeat (SSR) markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than 0.05, indicating that there were no or weak relationships between accessions of the mini-core collection. For 15 agronomic traits in the peanut panel, generally the Q + K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q + K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection.

  18. Correlations and path analysis among agronomic and technological traits of upland cotton.

    PubMed

    Farias, F J C; Carvalho, L P; Silva Filho, J L; Teodoro, P E

    2016-01-01

    To date, path analysis has been used with the aim of breeding different cultures. However, for cotton, there have been few studies using this analysis, and all of these have used fiber productivity as the primary dependent variable. Therefore, the aim of the present study was to identify agronomic and technological properties that can be used as criteria for direct and indirect phenotypes in selecting cotton genotypes with better fibers. We evaluated 16 upland cotton genotypes in eight trials conducted during the harvest 2008/2009 in the State of Mato Grosso, using a randomized block design with four replicates. The evaluated traits were: plant height, average boll weight, percentage of fiber, cotton seed yield, fiber length, uniformity of fiber, short fiber index, fiber strength, elongation, maturity of the fibers, micronaire, reflectance, and the degree of yellowing. Phenotypic correlations between the traits and cotton fiber yield (main dependent variable) were unfolded in direct and indirect effects through path analysis. Fiber strength, uniformity of fiber, and reflectance were found to influence fiber length, and therefore, these traits are recommended for both direct and indirect selection of cotton genotypes. PMID:27525939

  19. Genetic divergence among accessions of Axonopus jesuiticus x A. scoparius based on morphological and agronomical traits.

    PubMed

    Scheffer-Basso, Simone M; Favaretto, Adriana; Felini, Vanderleia; Gomes, Claudinei C; Carneiro, Luis E; Cecchin, Kalinca

    2014-03-01

    This study had the objective of assessing the genetic divergence in giant missionary grass (Axonopus jesuiticus x A. scoparius) germplasm based on morphological and agronomic traits. Five accessions were evaluated in the field: V14337, V14403, V14404, V14405 and V14406. Three contrasting groups were formed using the UPGMA clustering method: V14337 and V14404 formed one group, V14403 and V14405 formed another, and V14406 was isolated from the other accessions. The most striking traits for the identification of the accessions were the height of the plant and the change color of the leaf. Only V14406 accession had purplish green leaves. The other four accessions differed with regards to plant height and dry matter production, with superiority of V14337 and V14404 accessions. The high similarity, as assessed by the mean Euclidean distance, suggests that V14337 and V14404 share the same genotype. The genotypic variability among accessions indicates their potential use in breeding programs.

  20. Use of morpho-agronomic traits and DNA profiling for classification of genetic diversity in papaya.

    PubMed

    de Jesus, O N; de Freitas, J P X; Dantas, J L L; de Oliveira, E J

    2013-03-11

    We examined the genetic diversity of papaya (Carica papaya) based on morpho-agronomic and molecular data. Twenty-seven genotypes grown in Brazil were analyzed with 11 AFLP primer combinations, 23 ISSR markers, 22 qualitative, and 30 quantitative descriptors. For the joint analyses, we used the Gower algorithm (Joint Gower) and the average value of the individual dissimilarity matrix for each type of data (Average-Joint Gower); 359 AFLP and 52 ISSR polymorphic bands were found. Approximately 29.2 and 7.7% of the AFLP and ISSR bands, respectively, were genotype-specific and may therefore be used for papaya variety protection. Although there was a significant correlation between the qualitative and quantitative descriptor dissimilarity matrices (r = 0.43), the morpho-agronomic data were not highly correlated with the molecular data. Moreover, correlation between AFLP and ISSR dissimilarity matrices was nearly null (r = -0.01). Joint Gower analysis of all data showed high correlations, especially for AFLP markers, most likely due to the larger number of bands, generating a strong bias in the diversity estimates. The Average-Joint Gower analysis allowed a better balance between the correlations for the continuous and the discrete variables. The results generated by clustering analysis distinguished 5 genetically distinct groups. While we found that papaya genotypes are significantly variable for many traits, we observed that Average-Joint Gower analysis allowed for genotype clustering based on the most widely used criterion for classifying papaya genotypes, which is fruit type ('Formosa' or 'Solo'). This information helps provide an accurate estimate of the genetic diversity and structure of papaya germplasm, which will be used for further breeding strategies.

  1. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean.

    PubMed

    Sonah, Humira; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

    2015-02-01

    Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.

  2. Agronomic Competencies: A Comparison of Their Use and Perceived Importance.

    ERIC Educational Resources Information Center

    Scanlon, D. C.; Pennock, R., Jr.

    1987-01-01

    Reported is a survey designed to assess the relationship between essential competencies as perceived by faculty, and job needs as perceived by graduates of the agronomy department at Pennyslvania State University. Results indicated that while various competencies were valued differently, raters did not disagree on what were important competencies.…

  3. Agronomic Weeds.

    ERIC Educational Resources Information Center

    Hartwig, Nathan L.

    This agriculture extension service publication from Pennsylvania State University examines agronomic weed problems and control. Contents include a listing of the characteristics of weeds, a section on herbicides, and a section on the important weeds of agronomic crops in Pennsylvania. The herbicide section discusses systemic herbicides, contact…

  4. Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals

    PubMed Central

    Chen, Wei; Wang, Wensheng; Peng, Meng; Gong, Liang; Gao, Yanqiang; Wan, Jian; Wang, Shouchuang; Shi, Lei; Zhou, Bin; Li, Zongmei; Peng, Xiaoxi; Yang, Chenkun; Qu, Lianghuan; Liu, Xianqing; Luo, Jie

    2016-01-01

    The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits. PMID:27698483

  5. Glucose, stem dry weight variation, principal component and cluster analysis for some agronomic traits among 16 regenerated Crotalaria juncea accessions for potential cellulosic ethanol.

    PubMed

    Morris, J Bradley; Antonious, George F

    2013-01-01

    The objectives of this research were to identify candidate sunn hemp accessions having high concentrations of cellulose for use as parents in breeding for cellulose and to determine variability for glucose content and some important agronomic traits among sunn hemp accessions. Since sunn hemp is an under-utilized species, glucose content and agronomic trait variation is essential for the identification of superior sunn hemp accessions for use as potential ethanol for biofuel. Sixteen sunn hemp accessions including the following plant introductions (expressed as glucose concentration) and stem dry weights were studied. "Sixteen sunn hemp accessions including the following plant introductions (expressed as glucose concentration) and stem dry weights were studied." In addition, to verify variability, these traits plus morphological, phenological, and seed reproductive traits were analyzed using multivariate and cluster analysis. The accessions, PI 250487, PI 337080, and PI 219717 produced the highest glucose concentrations (859, 809, and 770 mg g(-1) stem dry weight, respectively), however PI 468956 produced the highest stem dry weight (258 g). Branching significantly correlated with foliage (r(2) = 0.67**) and relative maturity (r(2) = 0.60*), while maturity had a significantly negative correlation with seed number (r(2) = -0.67**) and plant width (r(2) = -0.53*) as well. Seed number significantly correlated with plant width (r(2) = 0.57*). Average linkage cluster analysis grouped the 16 sunn hemp accessions into well-defined phenotypes with four distinct seed-producing groups and one outlier. Based on multivariate and cluster analysis, sufficient variation among these16 sunn hemp accessions exists to support the development of cellulosic ethanol producing cultivars with improved architecture, early maturity, seed yield, glucose concentrations, and stem dry weights. PMID:23356343

  6. Cultivar x binary mixture interaction effect on agronomic traits in orchardgrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted to evaluate and characterize the agronomic value, including dry matter yield and forage quality of 25 orchardgrass cultivars grown in monoculture and binary mixtures with alfalfa under supplemental irrigation from 2009 to 2012 at a Millville, UT, field site. Orchardgrass monoc...

  7. Photo-biotechnology as a tool to improve agronomic traits in crops.

    PubMed

    Gururani, Mayank Anand; Ganesan, Markkandan; Song, Pill-Soon

    2015-01-01

    Phytochromes are photosensory phosphoproteins with crucial roles in plant developmental responses to light. Functional studies of individual phytochromes have revealed their distinct roles in the plant's life cycle. Given the importance of phytochromes in key plant developmental processes, genetically manipulating phytochrome expression offers a promising approach to crop improvement. Photo-biotechnology refers to the transgenic expression of phytochrome transgenes or variants of such transgenes. Several studies have indicated that crop cultivars can be improved by modulating the expression of phytochrome genes. The improved traits include enhanced yield, improved grass quality, shade-tolerance, and stress resistance. In this review, we discuss the transgenic expression of phytochrome A and its hyperactive mutant (Ser599Ala-PhyA) in selected crops, such as Zoysia japonica (Japanese lawn grass), Agrostis stolonifera (creeping bentgrass), Oryza sativa (rice), Solanum tuberosum (potato), and Ipomea batatas (sweet potato). The transgenic expression of PhyA and its mutant in various plant species imparts biotechnologically useful traits. Here, we highlight recent advances in the field of photo-biotechnology and review the results of studies in which phytochromes or variants of phytochromes were transgenically expressed in various plant species. We conclude that photo-biotechnology offers an excellent platform for developing crops with improved properties. PMID:25532679

  8. Photo-biotechnology as a tool to improve agronomic traits in crops.

    PubMed

    Gururani, Mayank Anand; Ganesan, Markkandan; Song, Pill-Soon

    2015-01-01

    Phytochromes are photosensory phosphoproteins with crucial roles in plant developmental responses to light. Functional studies of individual phytochromes have revealed their distinct roles in the plant's life cycle. Given the importance of phytochromes in key plant developmental processes, genetically manipulating phytochrome expression offers a promising approach to crop improvement. Photo-biotechnology refers to the transgenic expression of phytochrome transgenes or variants of such transgenes. Several studies have indicated that crop cultivars can be improved by modulating the expression of phytochrome genes. The improved traits include enhanced yield, improved grass quality, shade-tolerance, and stress resistance. In this review, we discuss the transgenic expression of phytochrome A and its hyperactive mutant (Ser599Ala-PhyA) in selected crops, such as Zoysia japonica (Japanese lawn grass), Agrostis stolonifera (creeping bentgrass), Oryza sativa (rice), Solanum tuberosum (potato), and Ipomea batatas (sweet potato). The transgenic expression of PhyA and its mutant in various plant species imparts biotechnologically useful traits. Here, we highlight recent advances in the field of photo-biotechnology and review the results of studies in which phytochromes or variants of phytochromes were transgenically expressed in various plant species. We conclude that photo-biotechnology offers an excellent platform for developing crops with improved properties.

  9. Genomewide association studies for 50 agronomic traits in peanut using the 'reference set' comprising 300 genotypes from 48 countries of the semi-arid tropics of the world.

    PubMed

    Pandey, Manish K; Upadhyaya, Hari D; Rathore, Abhishek; Vadez, Vincent; Sheshshayee, M S; Sriswathi, Manda; Govil, Mansee; Kumar, Ashish; Gowda, M V C; Sharma, Shivali; Hamidou, Falalou; Kumar, V Anil; Khera, Pawan; Bhat, Ramesh S; Khan, Aamir W; Singh, Sube; Li, Hongjie; Monyo, Emmanuel; Nadaf, H L; Mukri, Ganapati; Jackson, Scott A; Guo, Baozhu; Liang, Xuanqiang; Varshney, Rajeev K

    2014-01-01

    Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (p value > 2.1 × 10-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components. PMID:25140620

  10. Inheritance of the physiological traits for drought reistance under terminal drought conditions and genotypic correlations with agronomic traits in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breeding for terminal drought resistance in peanut can increase their productivity in drought-prone environments and reduce aflatoxin contamination. To improve selection efficiency for superior drought-resistant genotypes, a study of inheritance of traits is worthy, and provides useful information ...

  11. Agronomic and kernel compositional traits of blue maize landraces from the southwestern United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiple races of maize have been cultivated for centuries in the southwestern USA and northern Mexico. These landraces, used primarily for human food consumption, display considerable genetic variation for traits such as kernel color and texture. Traditional cultivation of these landraces has decli...

  12. Genetic diversity of Capsicum chinensis (Solanaceae) accessions based on molecular markers and morphological and agronomic traits.

    PubMed

    Finger, F L; Lannes, S D; Schuelter, A R; Doege, J; Comerlato, A P; Gonçalves, L S A; Ferreira, F R A; Clovis, L R; Scapim, C A

    2010-01-01

    We estimated the genetic diversity of 49 accessions of the hot pepper species Capsicum chinensis through analyses of 12 physicochemical traits of the fruit, eight multi-categorical variables, and with 32 RAPD primers. Data from the physicochemical traits were submitted to analysis of variance to estimate the genetic parameters, and their means were clustered by the Scott-Knott test. The matrices from the individual and combined distance were estimated by multivariate analyses before applying Tocher's optimization method. All physicochemical traits were examined for genetic variability by analysis of variance. The responses of these traits showed more contribution from genetic than from environmental factors, except the percentage of dry biomass, content of soluble solids and vitamin C level. Total capsaicin had the greatest genetic divergence. Nine clusters were formed from the quantitative data based on the generalized distance of Mahalanobis, using Tocher's method; four were formed from the multi-categorical data using the Cole-Rodgers coefficient, and eight were formed from the molecular data using the Nei and Li coefficient. The accessions were distributed into 14 groups using Tocher's method, and no significant correlation between pungency and origin was detected. Uni- and multivariate analyses permitted the identification of marked genetic diversity and fruit attributes capable of being improved through breeding programs. PMID:20882481

  13. Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower ( Helianthus annuus L.).

    PubMed

    Mokrani, L; Gentzbittel, L; Azanza, F; Fitamant, L; Al-Chaarani, G; Sarrafi, A

    2002-12-01

    Crosses were made between two inbred lines of sunflower. Parents and 118 F(3) families were planted in the field in a randomized complete block design in two replications. Genetic control for some agronomical traits: grain weight by plant (GWP), 1,000-grain weight (TGW), percentage of oil in grain (POG) and sowing to flowering date (STF) was investigated in F(3) families and their parents. Genetic variability was observed among the 118 F(3) families for all the traits studied. Genetic gain was obtained when the best F(3) family, or the mean of 10% of the selected families was compared with the best parent for GWP, TWG and POG. Heritability was 0.23 for GWP, 0.55 for TGW, 0.57 for POG and 0.32 for STF. A set of 244 F(3) families from the same cross, including the above 118 mentioned families and their two parents, were screened with 276 AFLP and microsatellite markers and a linkage map was constructed based on 170 markers. Two putative QTLs for the GWP trait ( gmp), one QTL for TGW ( tgw), six QTLs for POG ( pog) and two for STF ( stf) were detected. The percentage of phenotypic variance explained by each QTL ranged from 2.6% to 70.9%. The percentage of total phenotypic variance explained was 50.7% for GWP, 5.4% for TGW, 90.4% for POG and 89.3% for STF. Although these regions need to be more-precisely mapped, the information obtained should help in marker-assisted selection.

  14. Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L

    NASA Astrophysics Data System (ADS)

    Abdurakhmonov, Ibrokhim Y.; Buriev, Zabardast T.; Saha, Sukumar; Jenkins, Johnie N.; Abdukarimov, Abdusattor; Pepper, Alan E.

    2014-01-01

    Simultaneous improvement of fibre quality, early-flowering, early-maturity and productivity in Upland cotton (G. hirsutum) is a challenging task for conventional breeding. The influence of red/far-red light ratio on the fibre length prompted us to examine the phenotypic effects of RNA interference (RNAi) of the cotton PHYA1 gene. Here we show a suppression of up to ~70% for the PHYA1 transcript, and compensatory overexpression of up to ~20-fold in the remaining phytochromes in somatically regenerated PHYA1 RNAi cotton plants. Two independent transformants of three generations exhibited vigorous root and vegetative growth, early-flowering, significantly improved upper half mean fibre length and an improvement in other major fibre characteristics. Small decreases in lint traits were observed but seed cotton yield was increased an average 10-17% compared with controls. RNAi-associated phenotypes were heritable and transferable via sexual hybridization. These results should aid in the development of early-maturing and productive Upland cultivars with superior fibre quality.

  15. Single nucleotide polymorphisms in HSP17.8 and their association with agronomic traits in barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Small heat shock protein 17.8 (HSP17.8) is produced abundantly in plant cells under heat and other stress conditions and may play an important role in plant tolerance to stress environments. However, HSP17.8 may be differentially expressed in different accessions of a crop species exposed to identic...

  16. Field experimental design comparisons to detect field effects associated with agronomic traits in Upland cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Field variation is one of the important factors that can have a significant impact on genetic data analysis. Ineffective control of field variation may result in an inflated residual variance and/or biased estimation of genetic variations and/or effects. In this study, we addressed this problem by m...

  17. An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials.

    PubMed

    Tanhuanpää, Pirjo; Manninen, Outi; Beattie, Aaron; Eckstein, Peter; Scoles, Graham; Rossnagel, Brian; Kiviharju, Elina

    2012-04-01

    The first doubled haploid oat linkage map constructed at MTT Agrifood Research Finland was supplemented with additional microsatellites and Diversity Array Technology (DArT) markers to produce a map containing 1058 DNA markers and 34 linkage groups. The map was used to locate quantitative trait loci (QTLs) for 11 important breeding traits analyzed from Finnish and Canadian field trials. The new markers enabled most of the linkage groups to be anchored to the 'Kanota' × 'Ogle' oat ( Avena sativa L.) reference map and allowed comparison of the QTLs located in this study with those found previously. Two to 12 QTLs for each trait were discovered, of which several were expressed consistently across several environments.

  18. Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

    PubMed Central

    Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R.

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models. PMID:25785447

  19. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    PubMed

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  20. QTLs for agronomic and cell wall traits in a maize RIL progeny derived from a cross between an old Minnesota13 line and a modern Iodent line.

    PubMed

    Barrière, Yves; Méchin, Valérie; Lefevre, Bruno; Maltese, Stéphane

    2012-08-01

    In order to contribute to the inventory of genomic areas involved in maize cell wall lignification and degradability, QTL analyses were investigated in a RIL progeny between an old Minnesota13 dent line (WM13) and a modern Iodent line (RIo). Significant variation for agronomic- and cell wall-related traits was observed for the RIL per se (plants without ears) and topcross (whole plants) experiments after crossing with both old (Ia153) and modern tester (RFl) lines. Three QTLs for stover (plant without ear) yield were observed in per se experiments, with alleles increasing yield originating from RIo in two genomic locations with the highest effects. However, no QTL for whole plant yield was detected in topcross experiments, despite the fact that two QTLs for starch content were shown with increasing alleles originating from the modern RIo line. Fifteen lignin QTLs were shown, including a QTL for Klason lignins in per se experiments, located in bin 2.04, which explained 43 % of the observed genetic variation. Thirteen QTLs for p-hydroxycinnamic acid contents and nine QTLs related to the monomeric composition of lignin were shown in per se experiments, with syringaldehyde and diferulate QTLs explaining nearly 25 % of trait variations. Nine and seven QTLs for cell wall digestibility were mapped in per se and topcross experiments, respectively. Five of the per se QTLs explained more than 15 % of the variation, up to nearly 25 %. QTL positions in bins 2.06, 5.04, 5.08 and 8.02 for ADL/NDF, IVNDFD, lignin structure and/or p-hydroxycinnamic acid contents have not been previously shown and were thus first identified in the RIo × WM13 progeny. Based on QTL colocalizations, differences in cell wall degradability between RIo and WM13 were less often related to acid detergent lignin (ADL) content than in previous RIL investigations. QTL colocalizations then highlighted the probable importance of ferulate cross linkages in variation for cell wall digestibility. No

  1. Characterization of agronomic and quality traits and HSW-G5 compositions from the progenies of common wheat (Triticum aestivum L.) with different protein content.

    PubMed

    Bian, M; Sun, D K; Sun, D F; Sun, G L

    2015-01-01

    High molecular weight glutenin subunits (HMW-GS) play an essential role in wheat processing quality. In this study, we evaluated the genetic pattern with HMW-GS composition between generations and examined whether agronomic and quality traits were correlated with each other. A wheat (Triticum aestivum L.) cultivar with high protein content and 2 cultivars with low protein content were subjected to a reciprocal cross. Sixteen agronomic and 4 quality characteristics were investigated. A total of 216 seeds from each F2 generation were chosen randomly and analyzed for HMW-GS composition using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Agronomic and quality characteristics were not significantly different between reciprocal crosses, indicating no cytoplasmic effect on the characteristics studied. The separation ratio of 2 HMW-GS loci was 9:3:3:1, indicating no linkage between any 2 loci. The novel HMW-GS N was detected in cultivar R145, which did not follow the Mendelian segregation ratio. A Glu-A1a(1) band was not detected in 1 individual from Tian8901xR145. Average grain weight per spike was significantly correlated with quality characteristics and may be a suitable criterion for selecting high protein content in wheat breeding programs. PMID:25867343

  2. Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

    PubMed

    Bert, P-F; Jouan, I; Tourvieille de Labrouhe, D; Serre, F; Philippon, J; Nicolas, P; Vear, F

    2003-06-01

    Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

  3. Association of SSR markers with important fiber traits in Upland cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this research are to: 1) report on the diversity in agronomic and fiber traits of the selected cotton germplasm released by the public breeders and private industries, 2) detect the genetic diversity among these lines using SSR markers, and 3) identify the SSR markers association w...

  4. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel.

    PubMed

    Yang, Ning; Lu, Yanli; Yang, Xiaohong; Huang, Juan; Zhou, Yang; Ali, Farhan; Wen, Weiwei; Liu, Jie; Li, Jiansheng; Yan, Jianbing

    2014-09-01

    Association mapping is a powerful approach for dissecting the genetic architecture of complex quantitative traits using high-density SNP markers in maize. Here, we expanded our association panel size from 368 to 513 inbred lines with 0.5 million high quality SNPs using a two-step data-imputation method which combines identity by descent (IBD) based projection and k-nearest neighbor (KNN) algorithm. Genome-wide association studies (GWAS) were carried out for 17 agronomic traits with a panel of 513 inbred lines applying both mixed linear model (MLM) and a new method, the Anderson-Darling (A-D) test. Ten loci for five traits were identified using the MLM method at the Bonferroni-corrected threshold -log10 (P) >5.74 (α=1). Many loci ranging from one to 34 loci (107 loci for plant height) were identified for 17 traits using the A-D test at the Bonferroni-corrected threshold -log10 (P) >7.05 (α=0.05) using 556809 SNPs. Many known loci and new candidate loci were only observed by the A-D test, a few of which were also detected in independent linkage analysis. This study indicates that combining IBD based projection and KNN algorithm is an efficient imputation method for inferring large missing genotype segments. In addition, we showed that the A-D test is a useful complement for GWAS analysis of complex quantitative traits. Especially for traits with abnormal phenotype distribution, controlled by moderate effect loci or rare variations, the A-D test balances false positives and statistical power. The candidate SNPs and associated genes also provide a rich resource for maize genetics and breeding.

  5. The Genetic Basis of Heterosis: Multiparental Quantitative Trait Loci Mapping Reveals Contrasted Levels of Apparent Overdominance Among Traits of Agronomical Interest in Maize (Zea mays L.)

    PubMed Central

    Larièpe, A.; Mangin, B.; Jasson, S.; Combes, V.; Dumas, F.; Jamin, P.; Lariagon, C.; Jolivot, D.; Madur, D.; Fiévet, J.; Gallais, A.; Dubreuil, P.; Charcosset, A.; Moreau, L.

    2012-01-01

    Understanding the genetic bases underlying heterosis is a major issue in maize (Zea mays L.). We extended the North Carolina design III (NCIII) by using three populations of recombinant inbred lines derived from three parental lines belonging to different heterotic pools, crossed with each parental line to obtain nine families of hybrids. A total of 1253 hybrids were evaluated for grain moisture, silking date, plant height, and grain yield. Quantitative trait loci (QTL) mapping was carried out on the six families obtained from crosses to parental lines following the “classical” NCIII method and with a multiparental connected model on the global design, adding the three families obtained from crosses to the nonparental line. Results of the QTL detection highlighted that most of the QTL detected for grain yield displayed apparent overdominance effects and limited differences between heterozygous genotypes, whereas for grain moisture predominance of additive effects was observed. For plant height and silking date results were intermediate. Except for grain yield, most of the QTL identified showed significant additive-by-additive epistatic interactions. High correlation observed between heterosis and the heterozygosity of hybrids at markers confirms the complex genetic basis and the role of dominance in heterosis. An important proportion of QTL detected were located close to the centromeres. We hypothesized that the lower recombination in these regions favors the detection of (i) linked QTL in repulsion phase, leading to apparent overdominance for heterotic traits and (ii) linked QTL in coupling phase, reinforcing apparent additive effects of linked QTL for the other traits. PMID:22135356

  6. Perceived importance of employees' traits in the service industry.

    PubMed

    Lange, Rense; Houran, James

    2009-04-01

    Selection assessments are common practice to help reduce employee turnover in the service industry, but as too little is known about employees' characteristics, which are valued most highly by human resources professionals, a sample of 108 managers and human resources professionals rated the perceived importance of 31 performance traits for Line, Middle, and Senior employees. Rasch scaling analyses indicated strong consensus among the respondents. Nonsocial skills, abilities, and traits such as Ethical Awareness, Self-motivation, Writing Skills, Verbal Ability, Creativity, and Problem Solving were rated as more important for higher level employees. By contrast, traits which directly affect the interaction with customers and coworkers (Service Orientation, Communication Style, Agreeableness, Sense of Humor, Sensitivity to Diversity, Group Process, and Team Building) were rated as more important for lower level employees. Respondents' age and sex did not substantially alter these findings. Results are discussed in terms of improving industry professionals' perceived ecological and external validities of generic and customized assessments of employee. PMID:19610487

  7. Identification of an emergent and atypical Pseudomonas viridiflava lineage causing bacteriosis in plants of agronomic importance in a Spanish region.

    PubMed

    González, Ana J; Rodicio, M Rosario; Mendoza, M Carmen

    2003-05-01

    Pseudomonas strains with an atypical LOPAT profile (where LOPAT is a series of determinative tests: L, levan production; O, oxidase production; P, pectinolitic activity; A, arginine dihydrolase production; and T, tobacco hypersensibility) can be regarded as emergent pathogens in the Principality of Asturias (Spain), where they have been causing, since 1999, severe damage in at least three taxonomically unrelated orchard plants of agronomic importance: common bean (Phaseolus vulgaris), kiwifruit (Actinidia deliciosa), and lettuce (Lactuca sativa). These strains are mainly differentiated by production of yellowish mucoid material in hypersucrose medium, used for the levan test, and by a variable pectinolytic activity on different potato varieties. The atypical organisms were identified as Pseudomonas viridiflava based on their 16S rRNA sequences. Among them a certain intraspecies genetic heterogeneity was detected by randomly amplified polymorphic DNA (RAPD) typing. To differentiate between isolates of P. viridiflava and Pseudomonas syringae pathovars, a 16S ribosomal DNA restriction fragment length polymorphism method employing the restriction endonucleases SacI and HinfI was developed. This could be used as a means of reliable species determination after the usual phenotypical characterization, which includes the LOPAT tests. PMID:12732569

  8. Heritability and correlations among agronomic traits associated with reduced stink-bug damage in an F2:3 soybean population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In Brazil, the most important insect pest causing economic damage to soybean are stink bugs. The objective of the current research was to evaluate genetic parameters and correlations among different traits associated with plant development and yield traits, in an F2:3 soybean population. A populatio...

  9. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.).

    PubMed

    Fowler, D B; N'Diaye, A; Laudencia-Chingcuanco, D; Pozniak, C J

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar 'Norstar' as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability's reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic islands

  10. Selection of parents for crossing based on genotyping and phenotyping for stripe rust (Puccinia striiformis) resistance and agronomic traits in bread wheat breeding.

    PubMed

    Khan, Muhammad Irfaq; Khan, Mir Ajab; Khan, Abdul Jabbar; Khattak, Gul Sanat Shah; Mohammad, Tila; Ahmad, Mushtaq

    2011-01-01

    Bread wheat (Triticum aestivum L.) germplasm consisting of 45 genotypes were clustered phenotypically using ten morphological traits and Area Under Disease Progress Curve (AUDPC) as measure of stripe rust resistance. The clustering was ratified by using twenty three molecular markers (SSR, EST and STS) linked to stripe rust (Puccinia striiformis f. sp. tritici) resistant QTLs. The aim was to asses the extent of genetic variability among the genotypes in order to select the parents for crossing between the resistant and susceptible genotypes with respect to stripe rust. The Euclidian dissimilarity values resulted from phenotypic data regarding morphological traits and AUDPC were used to construct a dendrogram for clustering the accessions. Using un-weighted pair group method with arithmetic means, another dendrogram resulted from the similarity coefficient values was used to distinguish the genotypes with respect to stripe rust. Clustering based on phenotypic data produced two major groups and five clusters (with Euclidian dissimilarity ranging from 244 to 16.16) whereas genotypic data yielded two major groups and four clusters (with percent similarity coefficient values ranging from 0.1 to 46.0) to separate the gene pool into highly resistant, resistant, moderately resistant, moderately susceptible and susceptible genotypes. With few exceptions, the outcome of both type of clustering was almost similar and resistant as well as susceptible genotypes came in the same clusters of molecular genotyping as yielded by phenotypic clustering. As a result seven genotypes (Bakhtawar-92, Frontana, Saleem 2000, Tatara, Inqilab-91, Fakhre Sarhad and Karwan) of diverse genetic background were selected for pyramiding stripe rust resistant genes as well as some other agronomic traits after hybridization.

  11. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.)

    PubMed Central

    Fowler, D. B.; N'Diaye, A.; Laudencia-Chingcuanco, D.; Pozniak, C. J.

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar ‘Norstar’ as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability’s reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic

  12. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.).

    PubMed

    Fowler, D B; N'Diaye, A; Laudencia-Chingcuanco, D; Pozniak, C J

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar 'Norstar' as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability's reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic islands

  13. Evaluation of agronomic traits and spectral reflectance in Pacific Northwest winter wheat under rain-fed and irrigated conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The US Pacific Northwest (PNW) is a major winter wheat mega-environment characterized by a high latitude and a Mediterranean-like climate. Wheat production is predominantly rain-fed and often subject to low soil moisture. As result, discovery and introgression of drought-adaptive traits in modern cu...

  14. Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods.

    PubMed

    Satish, Lakkakula; Shilpha, Jayabalan; Pandian, Subramani; Rency, Arockiam Sagina; Rathinapriya, Periyasamy; Ceasar, Stanislaus Antony; Largia, Muthiah Joe Virgin; Kumar, Are Ashok; Ramesh, Manikandan

    2016-01-15

    Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and directed amplification of minisatellite-region DNA (DAMD). Totally 15 ISSR, 8 RAPD and 7 DAMD primers generated 263 amplification products, accounting for 84.6% polymorphism across all the genotypes. The Mantel's test of correlation revealed the best correlation between ISSR and cumulative data with a correlation coefficient (r) of 0.84. Assessment of population diversity indicated that the maximum intra population genetic diversity was recorded among high FeZn lines (HFL) having maximum values of Nei's genetic diversity (h) (0.244), Shannon information index (I) (0.368) and the percentage of polymorphic loci (Pp) (72.65%) while the corresponding lowest values of 0.074, 0.109 and 17.95% respectively were observed among the members of MDT subpopulation. The mean coefficient of gene differentiation (GST) and the gene flow (Nm) between populations were observed to be 0.396 and 0.7680 respectively. The analysis of molecular variance (AMOVA) suggested that maximum genetic variation exists within populations (95%) than among populations (5%). Thus the information obtained from this study could be utilized in sorghum breeding programmes for the development of varieties with improved nutrition and agronomic values in future.

  15. Assessing molecular and morpho-agronomical diversity and identification of ISSR markers associated with fruit traits in quince (Cydonia oblonga).

    PubMed

    Ganopoulos, I; Merkouropoulos, G; Pantazis, S; Tsipouridis, C; Tsaftaris, A

    2011-01-01

    Quince is a deciduous tree known to the countries around the Mediterranean since antiquity. Nowadays, quince is used as an ornamental plant, and as a rootstock for pear trees, with its fruit being appreciated mainly for production of jam and sweets rather than for raw consumption. Quince leaves contain compounds with antioxidant, antimicrobial and anticancerous properties that have been the focus of recent research on pharmaceutical and medical uses as well as for food preservatives. An orchard has been established in Greece, composed of quince varieties (Cydonia oblonga, N = 49) collected from different sites of the country (mainly from home gardens), constituting a unique quince gene bank collection for southeast Europe. We made a phenotypic analysis using 26 morphological plus seven agronomical descriptors coupled with molecular techniques in order to examine the genetic diversity within the collection. Principal component analysis using the 33 descriptors identified 10 components explaining the existence of more than 70% of the total variation. Subsequent cluster analysis classified most of the previously identified productive varieties of the quince orchard in the same clade of a dendrogram. Molecular analysis generated by 13 inter-simple sequence repeat primers amplified 139 bands, including 109 polymorphic bands, indicating a level of polymorphism of 79%; mean gene diversity was calculated to be 0.309. Using stepwise multiple regression analysis, a number of markers significantly associated with fire blight susceptibility, yield, mean fruit weight, citric acid content, soluble solid content, and fruit drop were identified. Hence, data extracted by multiple regression analysis could be useful in marker-assisted breeding programs, especially when no previous genetic information is available. PMID:22095599

  16. Importance of species traits for species distribution in fragmented landscapes.

    PubMed

    Tremlová, Katerina; Münzbergová, Zuzana

    2007-04-01

    Knowledge of the relationship between species traits and species distribution in fragmented landscapes is important for understanding current distribution patterns and as background information for predictive models of the effect of future landscape changes. The existing studies on the topic suffer from several drawbacks. First, they usually consider only traits related to dispersal ability and not growth. Furthermore, they do not apply phylogenetic corrections, and we thus do not know how considerations of phylogenetic relationships can alter the conclusions. Finally, they usually apply only one technique to calculate habitat isolation, and we do not know how other isolation measures would change the results. We studied the issues using 30 species forming congeneric pairs occurring in fragmented dry grasslands. We measured traits related to dispersal, survival, and growth in the species and recorded distribution of the species in 215 grassland fragments. We show many strong relationships between species traits related to both dispersal and growth and species distribution in the landscape, such as the positive relationship between habitat occupancy and anemochory and negative relationships between habitat occupancy and seed dormancy. The directions of these relationships, however, often change after application of phylogenetic correction. For example, more isolated habitats host species with smaller seeds. After phylogenetic correction, however, they turn out to host species with larger seeds. The conclusions also partly change depending on how we calculate habitat isolation. Specifically, habitat isolation calculated from occupied habitats only has the highest predictive power. This indicates slow dynamics of the species. All the results support the expectation that species traits have a high potential to explain patterns of species distribution in the landscape and that they can be used to build predictive models of species distribution. The specific conclusions

  17. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea

    PubMed Central

    Bajaj, Deepak; Srivastava, Rishi; Nath, Manoj; Tripathi, Shailesh; Bharadwaj, Chellapilla; Upadhyaya, Hari D.; Tyagi, Akhilesh K.; Parida, Swarup K.

    2016-01-01

    The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10–15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea. PMID:27148286

  18. EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea.

    PubMed

    Bajaj, Deepak; Srivastava, Rishi; Nath, Manoj; Tripathi, Shailesh; Bharadwaj, Chellapilla; Upadhyaya, Hari D; Tyagi, Akhilesh K; Parida, Swarup K

    2016-01-01

    The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea. PMID:27148286

  19. Phenotypic variation in the agronomic and morphological traits of Pisum sativum L. germplasm obtained from different parts of the world.

    PubMed

    Nisar, M; Ghafoor, A; Khan, M R

    2011-01-01

    A total of 286 genotypes were collected from 39 countries of the world and were evaluated to determine the phenotypic diversity for 17 quantitative traits. Higher degree of coefficient of variation were recorded for grain yield(-5) (52.46%), biomass(-5) (45.73%), fresh pod width(-10) (47.24%), dry pod weight(-1) (40.33%), plant height(-1) (35.25%), harvest index (32.70%) and number of branches(-5). Cluster-II clearly reflected that late genotypes were having lightest pods weight, shortest pod width, and pod length; low grain yield, biomass and harvest index. While genotypes in Cluster-III were in contrast to Cluster-II having heaviest pods weight, longest pods width and length, highest grain yield, biomass and harvest index. Higher PC(-1) values have been determined for days to flower initiation which consequently were contributing weighed positive to days to pods picking, days to flower completion, days to dry pod appearance, days to plant harvesting while negatively contributed to yield producing traits, indicating that late flowering pea germplasm emphasizes more on the vegetative growth and was low yielding. However, higher PC(-2) values have been obtained for number of branches(-5), grain yield and biomass while lower values for days to flowering, days to pods picking, days to flower completion, days to dry pod appearance and days to plant harvesting confirming the fact that early genotypes were high yielding.

  20. Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

    PubMed Central

    Srivastava, Rishi; Bajaj, Deepak; Malik, Ayushi; Singh, Mohar; Parida, Swarup K.

    2016-01-01

    The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement. PMID:27680662

  1. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers

    PubMed Central

    Perez-Lara, Enid; Semagn, Kassa; Chen, Hua; Iqbal, Muhammad; N’Diaye, Amidou; Kamran, Atif; Navabi, Alireza; Pozniak, Curtis; Spaner, Dean

    2016-01-01

    We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars ‘Cutler’ and ‘AC Barrie’ using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study

  2. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers.

    PubMed

    Perez-Lara, Enid; Semagn, Kassa; Chen, Hua; Iqbal, Muhammad; N'Diaye, Amidou; Kamran, Atif; Navabi, Alireza; Pozniak, Curtis; Spaner, Dean

    2016-01-01

    We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using

  3. Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley.

    PubMed

    Li, J Z; Huang, X Q; Heinrichs, F; Ganal, M W; Röder, M S

    2006-05-01

    Hordeum vulgare subsp. spontaneum, the wild progenitor of barley, is a potential source of useful genetic variation for barley breeding programs. The objective of this study was to map quantitative trait loci (QTLs) in an advanced backcross population of barley. A total of 207 BC3 lines were developed using the 2-rowed German spring cultivar Hordeum vulgare subsp. vulgare 'Brenda' as a recurrent parent and the H. vulgare subsp. spontaneum accession HS584 as a donor parent. The lines were genotyped by 108 simple-sequence repeat (SSR) markers and evaluated in field tests for the measurement of grain yield and its components, such as ear length, spikelet number per spike, grain number per spike, spike number, and 1000-grain mass, as well as heading date and plant height. A total of 100 QTLs were detected. Ten QTLs with increasing effects were found for ear length, spikelet number, and grain number per spike. Three QTLs contributed by HS584 were found to significantly decrease days to heading across all years at 2 locations. In addition, 2 QTLs from HS584 on chromosomes 2H and 3H were associated with resistance to leaf rust. Based on genotypic data obtained from this population, 55 introgression lines carrying 1 or 2 donor segments were selected to develop a set of doubled-haploid lines, which will be used to reconfirm and investigate the effects of 100 QTLs for future genetic studies.

  4. [Chromosome composition of wheat-rye lines and the influence of rye chromosomes on disease resistance and agronomic traits].

    PubMed

    Chumanova, E V; Efremova, T T; Trubacheeva, N V; Arbuzova, V S; Rosseeva, L P

    2014-11-01

    Identification of the chromosomal composition of common wheat lines with rye chromosomes was carried out using genomic in situ hybridization and 1RS- and 5P-specific PCR markers. It was demonstrated that wheat chromosomes 5A or 5D were substituted by rye chromosome 5R in the wheat-rye lines. It was established that one of the lines with complex disease resistance contained rye chromosome 5R and T1RS.1BL, while another line was found to contain, in addition to T1RS.1BL, a new Robertsonian translocation, T5AS.5RL. Substitution of the wheat chromosome 5A with the dominant Vrn-A1 gene for the Onokhoiskaya rye chromosome 5R led to lengthening of the germination-heading period or to a change in the type of development. A negative influence of T1RS.1BL on SDS sedimentation volume and grain hardness was demonstrated, along with a positive effect of the combination of T1RS. BL and 5R(5D) substitution on grain protein content. Quantitative traits of the 5R(5A) and 5R(5D) substitution lines were at the level of recipient cultivars. A line with two translocations, T1RS.1BL + T5AS.5R1, appeared to be more productive as compared to the line carrying T1RS.1BL in combination with the 5R(5D) substitution.

  5. The legume NOOT-BOP-COCH-LIKE genes are conserved regulators of abscission, a major agronomical trait in cultivated crops.

    PubMed

    Couzigou, Jean-Malo; Magne, Kevin; Mondy, Samuel; Cosson, Viviane; Clements, Jonathan; Ratet, Pascal

    2016-01-01

    Plants are able to lose organs selectively through a process called abscission. This process relies on the differentiation of specialized territories at the junction between organs and the plant body that are called abscission zones (AZ). Several genes control the formation or functioning of these AZ. We have characterized BLADE-ON-PETIOLE (BOP) orthologues from several legume plants and studied their roles in the abscission process using a mutant approach. Here, we show that the Medicago truncatula NODULE ROOT (NOOT), the Pisum sativum COCHLEATA (COCH) and their orthologue in Lotus japonicus are strictly necessary for the abscission of not only petals, but also leaflets, leaves and fruits. We also showed that the expression pattern of the M. truncatula pNOOT::GUS fusion is associated with functional and vestigial AZs when expressed in Arabidopsis. In addition, we show that the stip mutant from Lupinus angustifolius, defective in stipule formation and leaf abscission, is mutated in a BOP orthologue. In conclusion, this study shows that this clade of proteins plays an important conserved role in promoting abscission of all aerial organs studied so far.

  6. The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

    PubMed Central

    2011-01-01

    Background Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research. PMID:21208403

  7. Use of Genomics in Economically Important Traits in Ovine Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this review is to summarize relevant results from the use of genomics in sheep. Genomics has been used to identify genes associated with production, reproduction, carcass traits, and disease-related traits in sheep. A brief discussion on the concept of genomics is included. Genome-w...

  8. Genome-wide association studies of agronomic and quality traits in a set of German winter barley (Hordeum vulgare L.) cultivars using Diversity Arrays Technology (DArT).

    PubMed

    Lex, Jeannette; Ahlemeyer, Jutta; Friedt, Wolfgang; Ordon, Frank

    2014-08-01

    A set of about 100 winter barley (Hordeum vulgare L.) cultivars, comprising diverse and economically important German barley elite germplasm released during the last six decades, was previously genotypically characterized by single nucleotide polymorphism (SNP) markers using the Illumina GoldenGate BeadArray Technology to detect associations with phenotypic data estimated in three-year field trials at 12 locations. In order to identify further associations and to obtain information on whether the marker type influences the outcome of association genetics studies, the set of winter barley cultivars was re-analyzed using Diversity Arrays Technology (DArT) markers. As with the analysis of the SNPs, only polymorphic markers present at an allele frequency >5% were included to detect associations in a mixed linear model (MLM) approach using the TASSEL software (P ≤ 0.001). The population structure and kinship matrix were estimated on 72 simple sequence repeats (SSRs) covering the whole barley genome. The respective average linkage disequilibrium (LD) analyzed with DArT markers was estimated at 5.73 cM. A total of 52 markers gave significant associations with at least one of the traits estimated which, therefore, may be suitable for marker-assisted breeding. In addition, by comparing the results to those generated using the Illumina GoldenGate BeadArray Technology, it turned out that a different number of associations for respective traits is detected, depending on the marker system. However, as only a few of the respective DArT and Illumina markers are present in a common map, no comprehensive comparison of the detected associations was feasible, but some were probably detected in the same chromosomal regions. Because of the identification of additional marker-trait associations, it may be recommended to use both marker techniques in genome-wide association studies.

  9. Sorghum Dw1, an agronomically important gene for lodging resistance, encodes a novel protein involved in cell proliferation.

    PubMed

    Yamaguchi, Miki; Fujimoto, Haruka; Hirano, Ko; Araki-Nakamura, Satoko; Ohmae-Shinohara, Kozue; Fujii, Akihiro; Tsunashima, Masako; Song, Xian Jun; Ito, Yusuke; Nagae, Rie; Wu, Jianzhong; Mizuno, Hiroshi; Yonemaru, Jun-Ichi; Matsumoto, Takashi; Kitano, Hidemi; Matsuoka, Makoto; Kasuga, Shigemitsu; Sazuka, Takashi

    2016-01-01

    Semi-dwarfing genes have contributed to enhanced lodging resistance, resulting in increased crop productivity. In the history of grain sorghum breeding, the spontaneous mutation, dw1 found in Memphis in 1905, was the first widely used semi-dwarfing gene. Here, we report the identification and characterization of Dw1. We performed quantitative trait locus (QTL) analysis and cloning, and revealed that Dw1 encodes a novel uncharacterized protein. Knockdown or T-DNA insertion lines of orthologous genes in rice and Arabidopsis also showed semi-dwarfism similar to that of a nearly isogenic line (NIL) carrying dw1 (NIL-dw1) of sorghum. A histological analysis of the NIL-dw1 revealed that the longitudinal parenchymal cell lengths of the internode were almost the same between NIL-dw1 and wildtype, while the number of cells per internode was significantly reduced in NIL-dw1. NIL-dw1dw3, carrying both dw1 and dw3 (involved in auxin transport), showed a synergistic phenotype. These observations demonstrate that the dw1 reduced the cell proliferation activity in the internodes, and the synergistic effect of dw1 and dw3 contributes to improved lodging resistance and mechanical harvesting. PMID:27329702

  10. Sorghum Dw1, an agronomically important gene for lodging resistance, encodes a novel protein involved in cell proliferation

    PubMed Central

    Yamaguchi, Miki; Fujimoto, Haruka; Hirano, Ko; Araki-Nakamura, Satoko; Ohmae-Shinohara, Kozue; Fujii, Akihiro; Tsunashima, Masako; Song, Xian Jun; Ito, Yusuke; Nagae, Rie; Wu, Jianzhong; Mizuno, Hiroshi; Yonemaru, Jun-ichi; Matsumoto, Takashi; Kitano, Hidemi; Matsuoka, Makoto; Kasuga, Shigemitsu; Sazuka, Takashi

    2016-01-01

    Semi-dwarfing genes have contributed to enhanced lodging resistance, resulting in increased crop productivity. In the history of grain sorghum breeding, the spontaneous mutation, dw1 found in Memphis in 1905, was the first widely used semi-dwarfing gene. Here, we report the identification and characterization of Dw1. We performed quantitative trait locus (QTL) analysis and cloning, and revealed that Dw1 encodes a novel uncharacterized protein. Knockdown or T-DNA insertion lines of orthologous genes in rice and Arabidopsis also showed semi-dwarfism similar to that of a nearly isogenic line (NIL) carrying dw1 (NIL-dw1) of sorghum. A histological analysis of the NIL-dw1 revealed that the longitudinal parenchymal cell lengths of the internode were almost the same between NIL-dw1 and wildtype, while the number of cells per internode was significantly reduced in NIL-dw1. NIL-dw1dw3, carrying both dw1 and dw3 (involved in auxin transport), showed a synergistic phenotype. These observations demonstrate that the dw1 reduced the cell proliferation activity in the internodes, and the synergistic effect of dw1 and dw3 contributes to improved lodging resistance and mechanical harvesting. PMID:27329702

  11. Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species.

    PubMed

    Hughes, L M; Bao, J; Hu, Z-L; Honavar, V; Reecy, J M

    2008-06-01

    Ontologies help to identify and formally define the entities and relationships in specific domains of interest. Bio-ontologies, in particular, play a central role in the annotation, integration, analysis, and interpretation of biological data. Missing from the number of bio-ontologies is one that includes phenotypic trait information found in livestock species. As a result, the Animal Trait Ontology (ATO) project being carried out under the auspices of the USDA-National Animal Genome Research Program is aimed at the development of a standardized trait ontology for farm animals and software tools to assist the research community in collaborative creation, editing, maintenance, and use of such an ontology. The ATO is currently inclusive of cattle, pig, and chicken species, and will include other livestock species in the future. The ATO will eventually be linked to other species (e.g., human, rat, mouse) so that comparative analysis can be efficiently performed between species. PMID:18272850

  12. Development of introgression lines and advanced backcross QTL analysis for disease resistance, oil quality and yield component traits in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, several synthetics have been developed at ICRISAT. Furthermore, two synthetic amphidiploids viz., ISATGR 1212 (A. duranensis...

  13. Highly interactive nature of flower-specific enhancers and promoters, and its potential impact on tissue-specific expression and engineering of multiple genes or agronomic traits.

    PubMed

    Wen, Zhifeng; Yang, Yazhou; Zhang, Jinjin; Wang, Xiping; Singer, Stacy; Liu, Zhongchi; Yang, Yingjun; Yan, Guohua; Liu, Zongrang

    2014-09-01

    Molecular stacking enables multiple traits to be effectively engineered in crops using a single vector. However, the co-existence of distinct plant promoters in the same transgenic unit might, like their mammalian counterparts, interfere with one another. In this study, we devised a novel approach to investigate enhancer-promoter and promoter-promoter interactions in transgenic plants and demonstrated that three of four flower-specific enhancer/promoters were capable of distantly activating a pollen- and stigma-specific Pps promoter (fused to the cytotoxic DT-A gene) in other tissues, as revealed by novel tissue ablation phenotypes in transgenic plants. The NtAGI1 enhancer exclusively activated stamen- and carpel-specific DT-A expression, thus resulting in tissue ablation in an orientation-independent manner; this activation was completely abolished by the insertion of an enhancer-blocking insulator (EXOB) between the NtAGI1 enhancer and Pps promoter. Similarly, AGL8 and AP1Lb1, but not AP1La, promoters also activated distinct tissue-specific DT-A expression and ablation, with the former causing global growth retardation and the latter ablating apical inflorescences. While the tissue specificity of the enhancer/promoters generally defined their activation specificities, the strength of their activity in particular tissues or developmental stages appeared to determine whether activation actually occurred. Our findings provide the first evidence that plant-derived enhancer/promoters can distantly interact/interfere with one another, which could pose potential problems for the tissue-specific engineering of multiple traits using a single-vector stacking approach. Therefore, our work highlights the importance of adopting enhancer-blocking insulators in transformation vectors to minimize promoter-promoter interactions. The practical and fundamental significance of these findings will be discussed.

  14. Genetic parameters and correlations of collar rot resistance with important biochemical and yield traits in opium poppy (Papaver somniferum L.).

    PubMed

    Trivedi, Mala; Tiwari, Rajesh K; Dhawan, Om P

    2006-01-01

    Collar rot, caused by Rhizoctonia solani Kühn, is one of the most severe fungal diseases of opium poppy. In this study, heritability, genetic advance and correlation for 10 agronomic, 1 physiological, 3 biochemical and 1 chemical traits with disease severity index (DSI) for collar rot were assessed in 35 accessions of opium poppy. Most of the economically important characters, like seed and capsule straw yield per plant, oil and protein content of seeds, peroxidase activity in leaves, morphine content of capsule straw and DSI for collar rot showed high heritability as well as genetic advance. Highly significant negative correlation between DSI and seed yield clearly shows that as the disease progresses in plants, seed yield declines, chiefly due to premature death of infected plants as well as low seed and capsule setting in the survived population of susceptible plants. Similarly, a highly significant negative correlation between peroxidase activity and DSI indicated that marker-assisted selection of disease-resistant plants based on high peroxidase activity would be effective and survived susceptible plants could be removed from the population to stop further spread.

  15. Whole Genome Mapping in a Wheat Doubled Haploid Population Using SSRs and TRAPS and the Identification of QTL for Agronomic Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) analysis allows the identification of genomic regions associated with quantitative traits, which provides an estimation of the number and chromosomal location of genes involved and leads to the identification of molecular markers suitable for marker-assisted selection (...

  16. Inbreeding depression for economically important traits of Mazandaran native fowls.

    PubMed

    Rahmanian, A; Hafezian, H; Rahimi, G H; Farhadi, A; Baneh, H

    2015-01-01

    1. The objective was to investigate inbreeding depression for some economic traits of Mazandaran native fowls using data collected from 1992 to 2012 (21 generations) using a REML 2. The mean inbreeding coefficient (F) for the whole population and dams was 4.67% and 4.12%, respectively, and most of the inbred birds (75.79%) and inbred dams (72.58%) had F < 12.5%. 3. Individual and dam inbreeding trends were 0.55% and 0.53% per year. 4. Inbreeding depression for body weight at hatch, at 8 weeks and 12 weeks of age, age at sexual maturity, weight at sexual maturity, egg weight at 1st d of laying and average egg weight at 28, 30 and 32 weeks of laying due to a 1% increase in individual inbreeding were -0.11 g, -3.1 g, -1.3 g, 0.15 d, 0.59 g, -0.05 g and -0.03 g, respectively. 5. A 1% increase in maternal inbreeding resulted in a reduction of 0.06, 0.6 and 3.6 g in body weight at hatch, 8 weeks and 12 weeks of age.

  17. Agronomic importance of first development of chickpea (Cicer arietinum L.) under semi-arid conditions: II. Seed imbibition.

    PubMed

    Ulukan, H; Bayraktar, N; Oksel, A; Gursoy, M; Kocak, N

    2012-02-15

    Due to the slowness growth and weakness of the first developments of chickpea (Cicer arietinum L.), it could not combated with weeds and easily caught up by Ascochyta blight (Ascochyta rabiei (Pass) Labr.) disease. Additionally, due to biotic and abiotic stress factors, esp. at the late sowing, important seed yield losses could be happened. To be able to avoid from them is only possible to accelerate of its first development as possible as. So, one of the best solutions to is to use chemical compounds such as Humic Acid (HA) known soil regulator under the semi-arid conditions. With this aim this research was performed in a Randomized Complete Block Design (RCBD) with four replications under semi-arid field conditions during (2008/2009) and (2009/2010) in Turkiye. Two cultivars (V1 = Gokce and V2 = Ispanyol) and four seed imbibition methods (A0 = 0, A1 = Tap Water, A2 = 1/2 Tap Water + 1/2 Humic acid (HA), A3 = Full HA, as w/w) and seven yield components Plant Height (PH), Number of Branches per Plant (NBP), Number of Pods per Plant (NPP), First Pod Height (NFP), Number of Seeds per Pod (NSP), Seed Weight per Plant (SWP) and 100-Seed weight (HSW) were investigated. The PH and FPH were affected the A0, the NBP, NPP and NSP were affected the A2 and the SWP and HSW were given the varied but not clear responses according to varieties for all the parameters in A1. The A0 and A1 were encouraged the germination and top soil of the plant but, the A2 to A3 were encouraged root system's development. It was concluded that the A2 is a promising method which makes the maximum and positive effect to the first development of the chickpea agronomy under the semi-arid conditions.

  18. 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.

  19. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

    PubMed Central

    Thoquet, Philippe; Ghérardi, Michele; Journet, Etienne-Pascal; Kereszt, Attila; Ané, Jean-Michel; Prosperi, Jean-Marie; Huguet, Thierry

    2002-01-01

    Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM) and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16). Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa), implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant. PMID:11825338

  20. Genome-wide mapping of spike-related and agronomic traits in a common wheat population derived from a supernumerary parent and an elite parent

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In wheat (Triticum aestivum L), exotic genotypes express a broad range of spike-related traits and could be used as a source of new genes to enrich the germplasm for wheat breeding programs. In the present study, a population of 163 recombinant inbred lines derived from a cross between an elite line...

  1. The importance of retaining a phylogenetic perspective in traits-based community analyses

    SciTech Connect

    Poteat, Monica D.; Buchwalter, David B.; Jacobus, Luke M.

    2015-04-08

    1) Many environmental stressors manifest their effects via physiological processes (traits) that can differ significantly among species and species groups. We compiled available data for three traits related to the bioconcentration of the toxic metal cadmium (Cd) from 42 aquatic insect species representing orders Ephemeroptera (mayfly), Plecoptera (stonefly), and Trichoptera (caddisfly). These traits included the propensity to take up Cd from water (uptake rate constant, ku), the ability to excrete Cd (efflux rate constant, ke), and the net result of these two processes (bioconcentration factor, BCF). 2) Ranges in these Cd bioaccumulation traits varied in magnitude across lineages (some lineages had a greater tendency to bioaccumulate Cd than others). Overlap in the ranges of trait values among different lineages was common and highlights situations where species from different lineages can share a similar trait state, but represent the high end of possible physiological values for one lineage and the low end for another. 3) Variance around the mean trait state differed widely across clades, suggesting that some groups (e.g., Ephemerellidae) are inherently more variable than others (e.g., Perlidae). Thus, trait variability/lability is at least partially a function of lineage. 4) Akaike information criterion (AIC) comparisons of statistical models were more often driven by clade than by other potential biological or ecological explanation tested. Clade-driven models generally improved with increasing taxonomic resolution. 5) Altogether, these findings suggest that lineage provides context for the analysis of species traits, and that failure to consider lineage in community-based analysis of traits may obscure important patterns of species responses to environmental change.

  2. The importance of retaining a phylogenetic perspective in traits-based community analyses

    DOE PAGES

    Poteat, Monica D.; Buchwalter, David B.; Jacobus, Luke M.

    2015-04-08

    1) Many environmental stressors manifest their effects via physiological processes (traits) that can differ significantly among species and species groups. We compiled available data for three traits related to the bioconcentration of the toxic metal cadmium (Cd) from 42 aquatic insect species representing orders Ephemeroptera (mayfly), Plecoptera (stonefly), and Trichoptera (caddisfly). These traits included the propensity to take up Cd from water (uptake rate constant, ku), the ability to excrete Cd (efflux rate constant, ke), and the net result of these two processes (bioconcentration factor, BCF). 2) Ranges in these Cd bioaccumulation traits varied in magnitude across lineages (some lineagesmore » had a greater tendency to bioaccumulate Cd than others). Overlap in the ranges of trait values among different lineages was common and highlights situations where species from different lineages can share a similar trait state, but represent the high end of possible physiological values for one lineage and the low end for another. 3) Variance around the mean trait state differed widely across clades, suggesting that some groups (e.g., Ephemerellidae) are inherently more variable than others (e.g., Perlidae). Thus, trait variability/lability is at least partially a function of lineage. 4) Akaike information criterion (AIC) comparisons of statistical models were more often driven by clade than by other potential biological or ecological explanation tested. Clade-driven models generally improved with increasing taxonomic resolution. 5) Altogether, these findings suggest that lineage provides context for the analysis of species traits, and that failure to consider lineage in community-based analysis of traits may obscure important patterns of species responses to environmental change.« less

  3. Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests

    PubMed Central

    Wright, Ian J.; Ackerly, David D.; Bongers, Frans; Harms, Kyle E.; Ibarra-Manriquez, Guillermo; Martinez-Ramos, Miguel; Mazer, Susan J.; Muller-Landau, Helene C.; Paz, Horacio; Pitman, Nigel C. A.; Poorter, Lourens; Silman, Miles R.; Vriesendorp, Corine F.; Webb, Cam O.; Westoby, Mark; Wright, S. Joseph

    2007-01-01

    Background and Aims When ecologically important plant traits are correlated they may be said to constitute an ecological ‘strategy’ dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests. Methods Six traits were studied: specific leaf area (SLA), the average size of leaves, seed and fruit, typical maximum plant height, and wood density (WD). Trait relationships were quantified across species at each individual forest as well as across the dataset as a whole. ‘Phylogenetic’ analyses were used to test for correlations among evolutionary trait-divergences and to ascertain whether interspecific relationships were biased by strong taxonomic patterning in the traits. Key Results The interspecific and phylogenetic analyses yielded congruent results. Seed and fruit size were expected, and confirmed, to be tightly related. As expected, plant height was correlated with each of seed and fruit size, albeit weakly. Weak support was found for an expected positive relationship between leaf and fruit size. The prediction that SLA and WD would be negatively correlated was not supported. Otherwise the traits were predicted to be largely unrelated, being representatives of putatively independent strategy dimensions. This was indeed the case, although WD was consistently, negatively related to leaf size. Conclusions The dimensions represented by SLA, seed/fruit size and leaf size were essentially independent and thus conveyed largely independent information about plant strategies. To a lesser extent the same was true for plant height and WD. Our tentative explanation for negative WD–leaf size relationships, now also known from other

  4. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  5. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data. PMID:26881747

  6. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  7. The soil microbial community predicts the importance of plant traits in plant-soil feedback.

    PubMed

    Ke, Po-Ju; Miki, Takeshi; Ding, Tzung-Su

    2015-04-01

    Reciprocal interaction between plant and soil (plant-soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant-microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms. We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi). Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions. We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology.

  8. Autochthonous arbuscular mycorrhizal fungi and Bacillus thuringiensis from a degraded Mediterranean area can be used to improve physiological traits and performance of a plant of agronomic interest under drought conditions.

    PubMed

    Armada, Elisabeth; Azcón, Rosario; López-Castillo, Olga M; Calvo-Polanco, Mónica; Ruiz-Lozano, Juan Manuel

    2015-05-01

    Studies have shown that some microorganisms autochthonous from stressful environments are beneficial when used with autochthonous plants, but these microorganisms rarely have been tested with allochthonous plants of agronomic interest. This study investigates the effectiveness of drought-adapted autochthonous microorganisms [Bacillus thuringiensis (Bt) and a consortium of arbuscular mycorrhizal (AM) fungi] from a degraded Mediterranean area to improve plant growth and physiology in Zea mays under drought stress. Maize plants were inoculated or not with B. thuringiensis, a consortium of AM fungi or a combination of both microorganisms. Plants were cultivated under well-watered conditions or subjected to drought stress. Several physiological parameters were measured, including among others, plant growth, photosynthetic efficiency, nutrients content, oxidative damage to lipids, accumulation of proline and antioxidant compounds, root hydraulic conductivity and the expression of plant aquaporin genes. Under drought conditions, the inoculation of Bt increased significantly the accumulation of nutrients. The combined inoculation of both microorganisms decreased the oxidative damage to lipids and accumulation of proline induced by drought. Several maize aquaporins able to transport water, CO2 and other compounds were regulated by the microbial inoculants. The impact of these microorganisms on plant drought tolerance was complementary, since Bt increased mainly plant nutrition and AM fungi were more active improving stress tolerance/homeostatic mechanisms, including regulation of plant aquaporins with several putative physiological functions. Thus, the use of autochthonous beneficial microorganisms from a degraded Mediterranean area is useful to protect not only native plants against drought, but also an agronomically important plant such as maize.

  9. RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping

    PubMed Central

    2013-01-01

    Background Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Using this knowledge, it is important to develop genomic resources for the oleiferous types of B. rapa. This will allow more involved molecular mapping, in-depth study of molecular mechanisms underlying important agronomic traits and introgression of traits from B. rapa to major oilseed crops - B. juncea (AABB) and B. napus (AACC). The study explores the availability of SNPs in RNA-seq generated contigs of three oleiferous lines of B. rapa - Candle (ssp. oleifera, turnip rape), YSPB-24 and Tetra (ssp. trilocularis, Yellow sarson) and their use in genome-wide linkage mapping and specific-region fine mapping using a RIL population between Chiifu and Tetra. Results RNA-seq was carried out on the RNA isolated from young inflorescences containing unopened floral buds, floral axis and small leaves, using Illumina paired-end sequencing technology. Sequence assembly was carried out using the Velvet de-novo programme and the assembled contigs were organised against Chiifu gene models, available in the BRAD-CDS database. RNA-seq confirmed the presence of more than 17,000 single-copy gene models described in the BRAD database. The assembled contigs and the BRAD gene models were analyzed for the presence of SSRs and SNPs. While the number of SSRs was limited, more than 0.2 million SNPs were observed between Chiifu and the three oleiferous lines. Assays for SNPs were designed using KASPar technology and tested on a F7-RIL population derived from a Chiifu x Tetra cross. The design of the SNP assays were based on three considerations - the 50 bp flanking region of the SNPs should be strictly similar, the SNP should have a read-depth of ≥7 and no exon/intron junction should be present within the 101 bp target region. Using these criteria, a total of 640 markers

  10. Seed traits and genes important for translational biology – highlights from recent discoveries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seeds provide foods, feeds, and fuels. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural species. In this review, seed traits important for agriculture are discussed with an emphasis...

  11. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

    PubMed Central

    2013-01-01

    Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different

  12. Few crop traits accurately predict variables important to productivity of processing sweet corn

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recovery, case production, and gross profit margin, hereafter called ‘processor variables’, are as important metrics to processing sweet corn as grain yield is to field corn production. However, crop traits such as ear number or ear mass alone are reported in sweet corn production research rather t...

  13. Importation route of the sickle cell trait into Portugal: contribution of molecular epidemiology.

    PubMed

    Lavinha, J; Gonçalves, J; Faustino, P; Romão, L; Osório-Almeida, L; Peres, M J; Picanço, I; Martins, M C; Ducrocq, R; Labie, D

    1992-12-01

    To elucidate the origin and spread of the sickle cell trait into the Portuguese population, we examined nine polymorphic DNA markers within the beta globin gene cluster defining the haplotype. The population sample included 64 sickle-cell-gene-bearing individuals from defined Portuguese-speaking white, black, and Asian Indian populations. The nature and geographic distribution of the different beta S haplotypes in Portugal suggest that the sickle cell trait has been imported twice: between the eighth and the thirteenth centuries from the Mediterranean basin (in association with the Benin haplotype) and after the fifteenth century from black Africa over an Atlantic route (Senegal and Bantu haplotypes).

  14. Autochthonous arbuscular mycorrhizal fungi and Bacillus thuringiensis from a degraded Mediterranean area can be used to improve physiological traits and performance of a plant of agronomic interest under drought conditions.

    PubMed

    Armada, Elisabeth; Azcón, Rosario; López-Castillo, Olga M; Calvo-Polanco, Mónica; Ruiz-Lozano, Juan Manuel

    2015-05-01

    Studies have shown that some microorganisms autochthonous from stressful environments are beneficial when used with autochthonous plants, but these microorganisms rarely have been tested with allochthonous plants of agronomic interest. This study investigates the effectiveness of drought-adapted autochthonous microorganisms [Bacillus thuringiensis (Bt) and a consortium of arbuscular mycorrhizal (AM) fungi] from a degraded Mediterranean area to improve plant growth and physiology in Zea mays under drought stress. Maize plants were inoculated or not with B. thuringiensis, a consortium of AM fungi or a combination of both microorganisms. Plants were cultivated under well-watered conditions or subjected to drought stress. Several physiological parameters were measured, including among others, plant growth, photosynthetic efficiency, nutrients content, oxidative damage to lipids, accumulation of proline and antioxidant compounds, root hydraulic conductivity and the expression of plant aquaporin genes. Under drought conditions, the inoculation of Bt increased significantly the accumulation of nutrients. The combined inoculation of both microorganisms decreased the oxidative damage to lipids and accumulation of proline induced by drought. Several maize aquaporins able to transport water, CO2 and other compounds were regulated by the microbial inoculants. The impact of these microorganisms on plant drought tolerance was complementary, since Bt increased mainly plant nutrition and AM fungi were more active improving stress tolerance/homeostatic mechanisms, including regulation of plant aquaporins with several putative physiological functions. Thus, the use of autochthonous beneficial microorganisms from a degraded Mediterranean area is useful to protect not only native plants against drought, but also an agronomically important plant such as maize. PMID:25813343

  15. Seed traits and genes important for translational biology--highlights from recent discoveries.

    PubMed

    Martínez-Andújar, Cristina; Martin, Ruth C; Nonogaki, Hiroyuki

    2012-01-01

    Seeds provide food, feed, fiber and fuel. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural crops. In this review, seed traits and genes that are potentially important for agricultural applications are discussed. Over the long period of crop domestication, seed traits have been modified through intentional or unintentional selections. While most selections have led to seed traits favorable for agricultural consumption, such as larger seeds with higher nutritional value than the wild type, other manipulations in modern breeding sometimes led to negative traits, such as vivipary, precocious germination on the maternal plant or reduced seed vigor, as a side effect during the improvement of other characteristics. Greater effort is needed to overcome these problems that have emerged as a consequence of crop improvement. Seed biology researchers have characterized the function of many genes in the last decade, including those associated with seed domestication, which may be useful in addressing critical issues in modern agriculture, such as the prevention of vivipary and seed shattering or the enhancement of yields. Recent discoveries in seed biology research are highlighted in this review, with an emphasis on their potential for translational biology.

  16. Detection of QTL for forage yield, lodging resistance and spring vigor traits in alfalfa (Medicago sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alfalfa (Medicago sativa L.) is an internationally significant forage crop. Forage yield, lodging resistance and spring vigor are important agronomic traits conditioned by quantitative genetic and environmental effects. The objective of this study was to identify quantitative trait loci (QTL) and mo...

  17. Comprehensive association analysis for 50 agronomic traits in peanut using the "reference set" comprising 300 genotypes from 48 countries of the semi-arid tropics of the world

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut is an important source of nutrition and supports livelihood for millions of small-holder farmers in the semi-arid tropics (SAT) of world. Newly developed peanut cultivars could not yield to its original potential due to several biotic and abiotic stress factors. Under such circumstances, the ...

  18. Assortative mating in poison-dart frogs based on an ecologically important trait.

    PubMed

    Reynolds, R Graham; Fitzpatrick, Benjamin M

    2007-09-01

    The origin of new species can be influenced by both deterministic and stochastic factors. Mate choice and natural selection may be important deterministic causes of speciation (as opposed to the essentially stochastic factors of geographic isolation and genetic drift). Theoretical models predict that speciation is more likely when mate choice depends on an ecologically important trait that is subject to divergent natural selection, although many authors have considered such mating/ecology pleiotropy, or "magic-traits" to be unlikely. However, phenotypic signals are important in both mate choice and ecological processes such as avoiding predation. In chemically defended species, it may be that the phenotypic characteristics influencing mate choice are the same signals being used to transmit a warning to potential predators, although few studies have demonstrated this in wild populations. We tested for assortative mating between two color morphs of the Strawberry Poison-Dart Frog, Dendrobates pumilio, a group with striking geographic variation in aposematic color patterns. We found that females significantly prefer individuals of their own morph under two different light treatments, indicating strong assortative mating based on multiple coloration cues that are also important ecological signals. This study provides a rare example of one phenotypic trait affecting both ecological viability and nonrandom mating, indicating that mating/ecology pleiotropy is plausible in wild populations, particularly for organisms that are aposematically colored and visually orienting. PMID:17767594

  19. Integrated translational genomics for analysis of complex traits in sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We will report on the integration of sequencing and genotype data from natural variation (by whole genome resequencing [wgs] or genotype by sequencing [gbs]), transcriptome (RNA-seq) and mutant analysis (also by wgs) with the goal of identifying genes controlling important agronomic traits and tran...

  20. Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS).

    PubMed

    Pootakham, Wirulda; Jomchai, Nukoon; Ruang-Areerate, Panthita; Shearman, Jeremy R; Sonthirod, Chutima; Sangsrakru, Duangjai; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-05-01

    Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.

  1. Associated effects of copy number variants on economically important traits in Spanish Holstein dairy cattle.

    PubMed

    Ben Sassi, Neila; González-Recio, Óscar; de Paz-Del Río, Raquel; Rodríguez-Ramilo, Silvia T; Fernández, Ana I

    2016-08-01

    Copy number variants (CNV) are structural variants consisting of duplications or deletions of genomic fragments longer than 1 kb that present variability in the population and are heritable. The objective of this study was to identify CNV regions (CNVR) associated with 7 economically important traits (production, functional, and type traits) in Holstein cattle: fat yield, protein yield, somatic cell count, days open, stature, foot angle, and udder depth. Copy number variants were detected by using deep-sequencing data from 10 sequenced bulls and the Bovine SNP chip array hybridization signals. To reduce the number of false-positive calls, only CNV identified by both sequencing and Bovine SNP chip assays were kept in the final data set. This resulted in 823 CNVR. After filtering by minor allele frequency >0.01, a total of 90 CNVR appeared segregating in the bulls that had phenotypic data. Linear and quadratic CNVR effects were estimated using Bayesian approaches. A total of 15 CNVR were associated with the traits included in the analysis. One CNVR was associated with fat and protein yield, another 1 with fat yield, 3 with stature, 1 with foot angle, 7 with udder depth, and only 1 with days open. Among the genes located within these regions, highlighted were the MTHFSD gene that belongs to the folate metabolism genes, which play critical roles in regulating milk protein synthesis; the SNRPE gene that is related to several morphological pathologies; and the NF1 gene, which is associated with potential effects on fertility traits. The results obtained in the current study revealed that these CNVR segregate in the Holstein population, and therefore some potential exists to increase the frequencies of the favorable alleles in the population after independent validation of results in this study. However, genetic variance explained by the variants reported in this study was small. PMID:27209136

  2. Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.).

    PubMed

    Massa, Alicia N; Manrique-Carpintero, Norma C; Coombs, Joseph J; Zarka, Daniel G; Boone, Anne E; Kirk, William W; Hackett, Christine A; Bryan, Glenn J; Douches, David S

    2015-09-14

    The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between "Jacqueline Lee" and "MSG227-2" were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in "Jacqueline Lee." The best SNP marker mapped ~0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ~0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications.

  3. Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.)

    PubMed Central

    Massa, Alicia N.; Manrique-Carpintero, Norma C.; Coombs, Joseph J.; Zarka, Daniel G.; Boone, Anne E.; Kirk, William W.; Hackett, Christine A.; Bryan, Glenn J.; Douches, David S.

    2015-01-01

    The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between “Jacqueline Lee” and “MSG227-2” were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in “Jacqueline Lee.” The best SNP marker mapped ∼0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ∼0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications. PMID:26374597

  4. Genetic and genomic analyses for economically important traits and their applications in molecular breeding of cultured fish.

    PubMed

    Tong, JinGou; Sun, XiaoWen

    2015-02-01

    The traits of cultured fish must continually be genetically improved to supply high-quality animal protein for human consumption. Economically important fish traits are controlled by multiple gene quantitative trait loci (QTL), most of which have minor effects, but a few genes may have major effects useful for molecular breeding. In this review, we chose relevant studies on some of the most intensively cultured fish and concisely summarize progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades. The potential applications of these major-effect genes and their associated markers in marker-assisted selection and molecular breeding, as well as future research directions are also discussed. These genetic and genomic analyses will be valuable for elucidating the mechanisms modulating economically important traits and to establish more effective molecular breeding techniques in fish.

  5. Habitat effects on the relative importance of trait- and density-mediated indirect interactions.

    PubMed

    Trussell, Geoffrey C; Ewanchuk, Patrick J; Matassa, Catherine M

    2006-11-01

    Classical views of trophic cascades emphasize the primacy of consumptive predator effects on prey populations to the transmission of indirect effects [density-mediated indirect interactions (DMIIs)]. However, trophic cascades can also emerge without changes in the density of interacting species because of non-consumptive predator effects on prey traits such as foraging behaviour [trait-mediated indirect interactions (TMIIs)]. Although ecologists appreciate this point, measurements of the relative importance of each indirect predator effect are rare. Experiments with a three-level, rocky shore food chain containing an invasive predatory crab (Carcinus maenas), an intermediate consumer (the snail, Nucella lapillus) and a basal resource (the barnacle, Semibalanus balanoides) revealed that the strength of TMIIs is comparable with, or exceeds, that of DMIIs. Moreover, the sign and strength of each indirect predator effect depends on whether it is measured in risky or refuge habitats. Because habitat shifts are often responsible for the emergence of TMIIs, attention to the sign and strength of these interactions in both habitats will improve our understanding of the link between individual behaviour and community dynamics.

  6. Habitat effects on the relative importance of trait- and density-mediated indirect interactions.

    PubMed

    Trussell, Geoffrey C; Ewanchuk, Patrick J; Matassa, Catherine M

    2006-11-01

    Classical views of trophic cascades emphasize the primacy of consumptive predator effects on prey populations to the transmission of indirect effects [density-mediated indirect interactions (DMIIs)]. However, trophic cascades can also emerge without changes in the density of interacting species because of non-consumptive predator effects on prey traits such as foraging behaviour [trait-mediated indirect interactions (TMIIs)]. Although ecologists appreciate this point, measurements of the relative importance of each indirect predator effect are rare. Experiments with a three-level, rocky shore food chain containing an invasive predatory crab (Carcinus maenas), an intermediate consumer (the snail, Nucella lapillus) and a basal resource (the barnacle, Semibalanus balanoides) revealed that the strength of TMIIs is comparable with, or exceeds, that of DMIIs. Moreover, the sign and strength of each indirect predator effect depends on whether it is measured in risky or refuge habitats. Because habitat shifts are often responsible for the emergence of TMIIs, attention to the sign and strength of these interactions in both habitats will improve our understanding of the link between individual behaviour and community dynamics. PMID:17040327

  7. Are Photosynthetic Characteristics and Energetic Cost Important Invasive Traits for Alien Sonneratia Species in South China?

    PubMed

    Li, Feng-Lan; Zan, Qi-Jie; Hu, Zheng-Yu; Shin, Paul-K S; Cheung, Siu-Gin; Wong, Yuk-Shan; Tam, Nora Fung-Yee; Lei, An-Ping

    2016-01-01

    A higher photosynthesis and lower energetic cost are recognized as important characteristics for invasive species, but whether these traits are also important for the ability of alien mangrove species to become invasive has seldom been reported. A microcosm study was conducted to compare the photosynthetic characteristics, energetic cost indices and other growth traits between two alien species (Sonneratia apetala and S. caseolaris) and four native mangrove species over four seasons in a subtropical mangrove nature reserve in Shenzhen, South China. The aim of the study was to evaluate the invasive potential of Sonneratia based on these physiological responses. The annual average net photosynthetic rate (Pn), stomatal conductance (Gs) and total carbon assimilation per unit leaf area (Atotal) of the two alien Sonneratia species were significantly higher than the values of the native mangroves. In contrast, the opposite results were obtained for the leaf construction cost (CC) per unit dry mass (CCM) and CC per unit area (CCA) values. The higher Atotal and lower CC values resulted in a 72% higher photosynthetic energy-use efficiency (PEUE) for Sonneratia compared to native mangroves, leading to a higher relative growth rate (RGR) of the biomass and height of Sonneratia with the respective values being 51% and 119% higher than those of the native species. Higher photosynthetic indices for Sonneratia compared to native species were found in all seasons except winter, whereas lower CC values were found in all four seasons. The present findings reveal that alien Sonneratia species may adapt well and become invasive in subtropical mangrove wetlands in Shenzhen due to their higher photosynthetic characteristics coupled with lower costs in energy use, leading to a higher PEUE. The comparison of these physiological responses between S. apetala and S. caseolaris reveal that the former species is more invasive than the latter one, thus requiring more attention in future.

  8. Are Photosynthetic Characteristics and Energetic Cost Important Invasive Traits for Alien Sonneratia Species in South China?

    PubMed Central

    Li, Feng-Lan; Zan, Qi-Jie; Hu, Zheng-Yu; Shin, Paul-K. S.; Cheung, Siu-Gin; Wong, Yuk-Shan; Tam, Nora Fung-Yee; Lei, An-Ping

    2016-01-01

    A higher photosynthesis and lower energetic cost are recognized as important characteristics for invasive species, but whether these traits are also important for the ability of alien mangrove species to become invasive has seldom been reported. A microcosm study was conducted to compare the photosynthetic characteristics, energetic cost indices and other growth traits between two alien species (Sonneratia apetala and S. caseolaris) and four native mangrove species over four seasons in a subtropical mangrove nature reserve in Shenzhen, South China. The aim of the study was to evaluate the invasive potential of Sonneratia based on these physiological responses. The annual average net photosynthetic rate (Pn), stomatal conductance (Gs) and total carbon assimilation per unit leaf area (Atotal) of the two alien Sonneratia species were significantly higher than the values of the native mangroves. In contrast, the opposite results were obtained for the leaf construction cost (CC) per unit dry mass (CCM) and CC per unit area (CCA) values. The higher Atotal and lower CC values resulted in a 72% higher photosynthetic energy-use efficiency (PEUE) for Sonneratia compared to native mangroves, leading to a higher relative growth rate (RGR) of the biomass and height of Sonneratia with the respective values being 51% and 119% higher than those of the native species. Higher photosynthetic indices for Sonneratia compared to native species were found in all seasons except winter, whereas lower CC values were found in all four seasons. The present findings reveal that alien Sonneratia species may adapt well and become invasive in subtropical mangrove wetlands in Shenzhen due to their higher photosynthetic characteristics coupled with lower costs in energy use, leading to a higher PEUE. The comparison of these physiological responses between S. apetala and S. caseolaris reveal that the former species is more invasive than the latter one, thus requiring more attention in future. PMID

  9. Neonatal piglet traits of importance for survival in crates and indoor pens.

    PubMed

    Pedersen, L J; Berg, P; Jørgensen, G; Andersen, I L

    2011-04-01

    ,1050) = 18, P < 0.0001). In both CT and PN, the birth weight, body temperature 2 h after birth, and birth process were important traits related to crushing, starvation, and disease. Neither housing nor breeding value influenced mortality or traits of importance for the inborn viability of piglets. The results emphasize that the microclimate in the PN for newborn piglets and its heat-preserving properties are more important for survival than whether the sow is crated or penned.

  10. The angiosperm phloem sieve tube system: a role in mediating traits important to modern agriculture.

    PubMed

    Ham, Byung-Kook; Lucas, William J

    2014-04-01

    The plant vascular system serves a vital function by distributing water, nutrients and hormones essential for growth and development to the various organs of the plant. In this review, attention is focused on the role played by the phloem as the conduit for delivery of both photosynthate and information macromolecules, especially from the context of its mediation in traits that are important to modern agriculture. Resource allocation of sugars and amino acids, by the phloem, to specific sink tissues is of importance to crop yield and global food security. Current findings are discussed in the context of a hierarchical control network that operates to integrate resource allocation to competing sinks. The role of plasmodesmata that connect companion cells to neighbouring sieve elements and phloem parenchyma cells is evaluated in terms of their function as valves, connecting the sieve tube pressure manifold system to the various plant tissues. Recent studies have also revealed that plasmodesmata and the phloem sieve tube system function cooperatively to mediate the long-distance delivery of proteins and a diverse array of RNA species. Delivery of these information macromolecules is discussed in terms of their roles in control over the vegetative-to-floral transition, tuberization in potato, stress-related signalling involving miRNAs, and genetic reprogramming through the delivery of 24-nucleotide small RNAs that function in transcriptional gene silencing in recipient sink organs. Finally, we discuss important future research areas that could contribute to developing agricultural crops with engineered performance characteristics for enhance yield potential.

  11. Selection index based on the relative importance of traits and possibilities in breeding popcorn.

    PubMed

    Vieira, R A; Rocha, R; Scapim, C A; Amaral Júnior, A T; Vivas, M

    2016-01-01

    One of the major difficulties faced by popcorn breeders is the negative correlation between popping expansion (PE) and grain yield (GY). It is necessary to overcome this difficulty to obtain promising genotypes. One helpful tool in this process is a selection index because it allows multiple features of interest to be selected. Thus, the present study proposes a new and comprehensive selection index applied in 169 half-sib families in UEM-Co1 and UEM-Co2 composites during two cycles of recurrent selection. An experiment was conducted in a 13 x 13 lattice square in the 2004/2005 and 2006/2007 crop years in Maringá, Paraná State, and PE and GY were evaluated. To calculate Fi statistics, the following relative importance (RI) assignments were used: 0.5 for both PE and GY, and 0.70 and 0.30 for PE and GY, respectively. Families were classified according to Fi values such that Fi = 0 indicated that genotypes met the average of those selected by direct selection, Fi < 0 indicated that genotypes fell below the average of those selected, and Fi > 0 indicated that genotypes exceeded the average of those selected. Thus, desirable values of Fi were positive, indicating that the selected families were higher than those families that would be selected by direct selection for both traits. Therefore, we concluded that the novel Fi statistic was satisfactory for family selection because simultaneous and higher gains for both traits in both composites were obtained. PMID:27173260

  12. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle

    PubMed Central

    Jiang, Zhihua; Michal, Jennifer J.; Chen, Jie; Daniels, Tyler F.; Kunej, Tanja; Garcia, Matthew D.; Gaskins, Charles T.; Busboom, Jan R.; Alexander, Leeson J.; Wright Jr., Raymond W.; MacNeil, Michael D.

    2009-01-01

    Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F2 animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (≤ 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another. PMID:19727437

  13. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle.

    PubMed

    Jiang, Zhihua; Michal, Jennifer J; Chen, Jie; Daniels, Tyler F; Kunej, Tanja; Garcia, Matthew D; Gaskins, Charles T; Busboom, Jan R; Alexander, Leeson J; Wright, Raymond W; Macneil, Michael D

    2009-07-29

    Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F(2) animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (< or = 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.

  14. Assessing the Importance of Intraspecific Variability in Dung Beetle Functional Traits.

    PubMed

    Griffiths, Hannah M; Louzada, Julio; Bardgett, Richard D; Barlow, Jos

    2016-01-01

    Functional diversity indices are used to facilitate a mechanistic understanding of many theoretical and applied questions in current ecological research. The use of mean trait values in functional indices assumes that traits are robust, in that greater variability exists between than within species. While the assertion of robust traits has been explored in plants, there exists little information on the source and extent of variability in the functional traits of higher trophic level organisms. Here we investigated variability in two functionally relevant dung beetle traits, measured from individuals collected from three primary forest sites containing distinct beetle communities: body mass and back leg length. In doing so we too addressed the following questions: (i) what is the contribution of intra vs. interspecific differences in trait values; (ii) what sample size is needed to provide representative species mean trait values; and (iii) what impact does omission of intraspecific trait information have on the calculation of functional diversity (FD) indices from naturally assembled communities? At the population level, interspecific differences explained the majority of variability in measured traits (between 94% and 96%). In accordance with this, the error associated with calculating FD without inclusion of intraspecific variability was low, less than 20% in all cases. This suggests that complete sampling to capture intraspecific variance in traits is not necessary even when investigating the FD of small and/or naturally formed communities. To gain an accurate estimation of species mean trait values we encourage the measurement of 30-60 individuals and, where possible, these should be taken from specimens collected from the site of study.

  15. Assessing the Importance of Intraspecific Variability in Dung Beetle Functional Traits

    PubMed Central

    Griffiths, Hannah M.; Louzada, Julio; Bardgett, Richard D.; Barlow, Jos

    2016-01-01

    Functional diversity indices are used to facilitate a mechanistic understanding of many theoretical and applied questions in current ecological research. The use of mean trait values in functional indices assumes that traits are robust, in that greater variability exists between than within species. While the assertion of robust traits has been explored in plants, there exists little information on the source and extent of variability in the functional traits of higher trophic level organisms. Here we investigated variability in two functionally relevant dung beetle traits, measured from individuals collected from three primary forest sites containing distinct beetle communities: body mass and back leg length. In doing so we too addressed the following questions: (i) what is the contribution of intra vs. interspecific differences in trait values; (ii) what sample size is needed to provide representative species mean trait values; and (iii) what impact does omission of intraspecific trait information have on the calculation of functional diversity (FD) indices from naturally assembled communities? At the population level, interspecific differences explained the majority of variability in measured traits (between 94% and 96%). In accordance with this, the error associated with calculating FD without inclusion of intraspecific variability was low, less than 20% in all cases. This suggests that complete sampling to capture intraspecific variance in traits is not necessary even when investigating the FD of small and/or naturally formed communities. To gain an accurate estimation of species mean trait values we encourage the measurement of 30–60 individuals and, where possible, these should be taken from specimens collected from the site of study. PMID:26939121

  16. The relative importance of trait vs. genetic differentiation for the outcome of interactions among plant genotypes.

    PubMed

    Abbott, Jessica M; Stachowicz, John J

    2016-01-01

    Functional trait differences and genetic distance are increasingly used as metrics to predict the. outcome of species interactions and the maintenance of diversity. We apply these ideas to intraspecific diversity for the seagrass Zostera marina (eelgrass), by explicitly testing the influence of trait distance and genetic relatedness on the outcome of pairwise interactions among eelgrass genotypes. Increasing trait distance (but not relatedness) between eelgrass genotypes decreased the likelihood that both would persist over a year-long field experiment, contrary to our expectations based on niche partitioning. In plots in which one genotype excluded another, the biomass and growth of the remaining genotype increased with the trait distance and genetic relatedness of the initial pair, presumably due to a legacy of past interactions. Together these results suggest that sustained competition among functionally similar genotypes did not produce a clear winner, but rapid exclusion occurred among genotypes with distinct trait combinations. Borrowing from coexistence theory, we argue that fitness differences between genotypes with distinct traits overwhelmed any stabilizing effects of niche differentiation. Previously observed effects of eelgrass genetic diversity on performance may rely on nonadditive interactions among multiple genotypes or sufficient environmental heterogeneity to increase stabilizing forces and/or interactions. PMID:27008778

  17. The relative importance of trait vs. genetic differentiation for the outcome of interactions among plant genotypes.

    PubMed

    Abbott, Jessica M; Stachowicz, John J

    2016-01-01

    Functional trait differences and genetic distance are increasingly used as metrics to predict the. outcome of species interactions and the maintenance of diversity. We apply these ideas to intraspecific diversity for the seagrass Zostera marina (eelgrass), by explicitly testing the influence of trait distance and genetic relatedness on the outcome of pairwise interactions among eelgrass genotypes. Increasing trait distance (but not relatedness) between eelgrass genotypes decreased the likelihood that both would persist over a year-long field experiment, contrary to our expectations based on niche partitioning. In plots in which one genotype excluded another, the biomass and growth of the remaining genotype increased with the trait distance and genetic relatedness of the initial pair, presumably due to a legacy of past interactions. Together these results suggest that sustained competition among functionally similar genotypes did not produce a clear winner, but rapid exclusion occurred among genotypes with distinct trait combinations. Borrowing from coexistence theory, we argue that fitness differences between genotypes with distinct traits overwhelmed any stabilizing effects of niche differentiation. Previously observed effects of eelgrass genetic diversity on performance may rely on nonadditive interactions among multiple genotypes or sufficient environmental heterogeneity to increase stabilizing forces and/or interactions.

  18. Research Review: The Importance of Callous-Unemotional Traits for Developmental Models of Aggressive and Antisocial Behavior

    ERIC Educational Resources Information Center

    Frick, Paul J.; White, Stuart F.

    2008-01-01

    The current paper reviews research suggesting that the presence of a callous and unemotional interpersonal style designates an important subgroup of antisocial and aggressive youth. Specifically, callous-unemotional (CU) traits (e.g., lack of guilt, absence of empathy, callous use of others) seem to be relatively stable across childhood and…

  19. An Exploratory Study of the Effect of Professional Internships on Students' Perception of the Importance of Employment Traits

    ERIC Educational Resources Information Center

    Green, Brian Patrick; Graybeal, Patricia; Madison, Roland L.

    2011-01-01

    The authors measured the effects of a formal internship on students' perceptions of the importance of traits employees consider during the hiring process. Prior studies have reported that accounting firms perceive students with internship experience as better entry-level accountants. This perception may be related to changes in student beliefs…

  20. Salt effects on functional traits in model and in economically important Lotus species.

    PubMed

    Uchiya, P; Escaray, F J; Bilenca, D; Pieckenstain, F; Ruiz, O A; Menéndez, A B

    2016-07-01

    A common stress on plants is NaCl-derived soil salinity. Genus Lotus comprises model and economically important species, which have been studied regarding physiological responses to salinity. Leaf area ratio (LAR), root length ratio (RLR) and their components, specific leaf area (SLA) and leaf mass fraction (LMF) and specific root length (SRL) and root mass fraction (RMF) might be affected by high soil salinity. We characterised L. tenuis, L. corniculatus, L. filicaulis, L. creticus, L. burtii and L. japonicus grown under different salt concentrations (0, 50, 100 and 150 mm NaCl) on the basis of SLA, LMF, SRL and RMF using PCA. We also assessed effects of different salt concentrations on LAR and RLR in each species, and explored whether changes in these traits provide fitness benefit. Salinity (150 mm NaCl) increased LAR in L. burtii and L. corniculatus, but not in the remaining species. The highest salt concentration caused a decrease of RLR in L. japonicus Gifu, but not in the remaining species. Changes in LAR and RLR would not be adaptive, according to adaptiveness analysis, with the exception of SLA changes in L. corniculatus. PCA revealed that under favourable conditions plants optimise surfaces for light and nutrient acquisition (SLA and SRL), whereas at higher salt concentrations they favour carbon allocation to leaves and roots (LMF and RMF) in detriment to their surfaces. PCA also showed that L. creticus subjected to saline treatment was distinguished from the remaining Lotus species. We suggest that augmented carbon partitioning to leaves and roots could constitute a salt-alleviating mechanism through toxic ion dilution. PMID:27007305

  1. The importance of aboveground–belowground interactions on the evolution and maintenance of variation in plant defense traits

    PubMed Central

    van Geem, Moniek; Gols, Rieta; van Dam, Nicole M.; van der Putten, Wim H.; Fortuna, Taiadjana; Harvey, Jeffrey A.

    2013-01-01

    Over the past two decades a growing body of empirical research has shown that many ecological processes are mediated by a complex array of indirect interactions occurring between rhizosphere-inhabiting organisms and those found on aboveground plant parts. Aboveground–belowground studies have thus far focused on elucidating processes and underlying mechanisms that mediate the behavior and performance of invertebrates in opposite ecosystem compartments. Less is known about genetic variation in plant traits such as defense as that may be driven by above- and belowground trophic interactions. For instance, although our understanding of genetic variation in aboveground plant traits and its effects on community-level interactions is well developed, little is known about the importance of aboveground–belowground interactions in driving this variation. Plant traits may have evolved in response to selection pressures from above- and below-ground interactions from antagonists and mutualists. Here, we discuss gaps in our understanding of genetic variation in plant-related traits as they relate to aboveground and belowground multitrophic interactions. When metabolic resources are limiting, multiple attacks by antagonists in both domains may lead to trade-offs. In nature, these trade-offs may critically depend upon their effects on plant fitness. Natural enemies of herbivores may also influence selection for different traits via top–down control. At larger scales these interactions may generate evolutionary “hotspots” where the expression of various plant traits is the result of strong reciprocal selection via direct and indirect interactions. The role of abiotic factors in driving genetic variation in plant traits is also discussed. PMID:24348484

  2. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

    PubMed Central

    2014-01-01

    Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

  3. Evolution in response to social selection: the importance of interactive effects of traits on fitness.

    PubMed

    Westneat, David F

    2012-03-01

    Social interactions have a powerful effect on the evolutionary process. Recent attempts to synthesize models of social selection with equations for indirect genetic effects (McGlothlin et al. 2010) provide a broad theoretical base from which to study selection and evolutionary response in the context of social interactions. However, this framework concludes that social selection will lead to evolution only if the traits carried by social partners are nonrandomly associated. I suggest this conclusion is incomplete, and that traits that do not covary between social partners can nevertheless lead to evolution via interactive effects on fitness. Such effects occur when there are functional interactions between traits, and as an example I use the interplay in water striders (Gerridae) between grasping appendages carried by males and spines by females. Functional interactive effects between traits can be incorporated into both the equations for social selection and the general model of social evolution proposed by McGlothlin et al. These expanded equations would accommodate adaptive coevolution in social interactions, integrate the quantitative genetic approach to social evolution with game theoretical approaches, and stimulate some new questions about the process of social evolution.

  4. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    PubMed Central

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

  5. Molecular and Morpho-Agronomical Characterization of Root Architecture at Seedling and Reproductive Stages for Drought Tolerance in Wheat.

    PubMed

    Tomar, Ram Sewak Singh; Tiwari, Sushma; Vinod; Naik, Bhojaraja K; Chand, Suresh; Deshmukh, Rupesh; Mallick, Niharika; Singh, Sanjay; Singh, Nagendra Kumar; Tomar, S M S

    2016-01-01

    Water availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root architecture is important for water and nutrition acquisition for all crops, including wheat. A set of 158 diverse wheat genotypes of Australian (72) and Indian (86) origin were studied for morpho-agronomical traits in field under irrigated and drought stress conditions during 2010-11 and 2011-12.Out of these 31 Indian wheat genotypes comprising 28 hexaploid (Triticum aestivum L.) and 3 tetraploid (T. durum) were characterized for root traits at reproductive stage in polyvinyl chloride (PVC) pipes. Roots of drought tolerant genotypes grew upto137cm (C306) as compared to sensitive one of 63cm with a mean value of 94.8cm. Root architecture traits of four drought tolerant (C306, HW2004, HD2888 and NI5439) and drought sensitive (HD2877, HD2012, HD2851 and MACS2496) genotypes were also observed at 6 and 9 days old seedling stage. The genotypes did not show any significant variation for root traits except for longer coleoptiles and shoot and higher absorptive surface area in drought tolerant genotypes. The visible evaluation of root images using WinRhizo Tron root scanner of drought tolerant genotype HW2004 indicated compact root system with longer depth while drought sensitive genotype HD2877 exhibited higher horizontal root spread and less depth at reproductive stage. Thirty SSR markers were used to study genetic variation which ranged from 0.12 to 0.77 with an average value of 0.57. The genotypes were categorized into three subgroups as highly tolerant, sensitive, moderately sensitive and tolerant as intermediate group based on UPGMA cluster, STRUCTURE and principal coordinate analyses. The genotypic clustering was positively correlated to grouping based on root and morpho-agronomical traits. The genetic variability identified in current study demonstrated these traits can be used to improve drought tolerance and association

  6. Molecular and Morpho-Agronomical Characterization of Root Architecture at Seedling and Reproductive Stages for Drought Tolerance in Wheat

    PubMed Central

    Vinod; Naik, Bhojaraja K.; Chand, Suresh; Deshmukh, Rupesh; Mallick, Niharika; Singh, Sanjay; Singh, Nagendra Kumar; Tomar, S. M. S.

    2016-01-01

    Water availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root architecture is important for water and nutrition acquisition for all crops, including wheat. A set of 158 diverse wheat genotypes of Australian (72) and Indian (86) origin were studied for morpho-agronomical traits in field under irrigated and drought stress conditions during 2010–11 and 2011-12.Out of these 31 Indian wheat genotypes comprising 28 hexaploid (Triticum aestivum L.) and 3 tetraploid (T. durum) were characterized for root traits at reproductive stage in polyvinyl chloride (PVC) pipes. Roots of drought tolerant genotypes grew upto137cm (C306) as compared to sensitive one of 63cm with a mean value of 94.8cm. Root architecture traits of four drought tolerant (C306, HW2004, HD2888 and NI5439) and drought sensitive (HD2877, HD2012, HD2851 and MACS2496) genotypes were also observed at 6 and 9 days old seedling stage. The genotypes did not show any significant variation for root traits except for longer coleoptiles and shoot and higher absorptive surface area in drought tolerant genotypes. The visible evaluation of root images using WinRhizo Tron root scanner of drought tolerant genotype HW2004 indicated compact root system with longer depth while drought sensitive genotype HD2877 exhibited higher horizontal root spread and less depth at reproductive stage. Thirty SSR markers were used to study genetic variation which ranged from 0.12 to 0.77 with an average value of 0.57. The genotypes were categorized into three subgroups as highly tolerant, sensitive, moderately sensitive and tolerant as intermediate group based on UPGMA cluster, STRUCTURE and principal coordinate analyses. The genotypic clustering was positively correlated to grouping based on root and morpho-agronomical traits. The genetic variability identified in current study demonstrated these traits can be used to improve drought tolerance and association

  7. Big Five personality traits: are they really important for the subjective well-being of Indians?

    PubMed

    Tanksale, Deepa

    2015-02-01

    This study empirically examined the relationship between the Big Five personality traits and subjective well-being (SWB) in India. SWB variables used were life satisfaction, positive affect and negative affect. A total of 183 participants in the age range 30-40 years from Pune, India, completed the personality and SWB measures. Backward stepwise regression analysis showed that the Big Five traits accounted for 17% of the variance in life satisfaction, 35% variance in positive affect and 28% variance in negative affect. Conscientiousness emerged as the strongest predictor of life satisfaction. In line with the earlier research findings, neuroticism and extraversion were found to predict negative affect and positive affect, respectively. Neither openness to experience nor agreeableness contributed to SWB. The research emphasises the need to revisit the association between personality and SWB across different cultures, especially non-western cultures.

  8. Brain vasopressin is an important regulator of maternal behavior independent of dams' trait anxiety

    PubMed Central

    Bosch, Oliver J.; Neumann, Inga D.

    2008-01-01

    The neuropeptide arginine vasopressin (AVP) is arguably among the most potent regulators of social behaviors in mammals identified to date. However, only the related neuropeptide oxytocin (OXT) has been shown to promote maternal behavior. Here, we assess the role of AVP in maternal care, in particular in arched back nursing, pup retrieval, and pup contact by using complementary pharmacological and genetic approaches. Also, experiments were performed in rat dams with differences in trait anxiety, i.e., rats bred for either high (HAB) or low (LAB) anxiety-related behavior as well as nonselected (NAB) dams. Viral vector-mediated up-regulation of AVP V1a receptors (AVP-Rs) within the medial preoptic area of lactating NAB rats and chronic central AVP treatment of NAB and LAB dams improved, whereas local blockade of AVP-R expression by means of antisense oligodeoxynucleotides or central AVP-R antagonism impaired, maternal care in NAB dams. Also, in HAB rats with a genetically determined elevated brain AVP activity, intrinsically high levels of maternal care were reversed by blockade of AVP-R actions. Treatment-induced impairment of AVP-mediated maternal behavior increased adult emotionality and impaired social interactions in male offspring of NAB dams. These findings provide direct evidence for an essential and highly potent role of brain AVP in promoting maternal behavior, which seems to be independent of the dam's trait anxiety. PMID:18955705

  9. Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)

    PubMed Central

    Guan, Dailu; Luo, Nanjian; Tan, Xiaoshan; Zhao, Zhongquan; Huang, Yongfu; Na, Risu; Zhang, Jiahua; Zhao, Yongju

    2016-01-01

    Goats (Capra hircus) are one of the oldest livestock domesticated species, and have been used for their milk, meat, hair and skins over much of the world. Detection of selection footprints in genomic regions can provide potential insights for understanding the genetic mechanism of specific phenotypic traits and better guide in animal breeding. The study presented here has generated 192.747G raw data and identified more than 5.03 million single-nucleotide polymorphisms (SNPs) and 334,151 Indels (insertions and deletions). In addition, we identified 155 and 294 candidate regions harboring 86 and 97 genes based on allele frequency differences in Dazu black goats (DBG) and Inner Mongolia cashmere goats (IMCG), respectively. Populations differentiation reflected by Fst values detected 368 putative selective sweep regions including 164 genes. The top 1% regions of both low heterozygosity and high genetic differentiation contained 239 (135 genes) and 176 (106 genes) candidate regions in DBG and IMCG, respectively. These genes were related to reproductive and productive traits, such as “neurohypophyseal hormone activity” and “adipocytokine signaling pathway”. These findings may be conducive to molecular breeding and the long-term preservation of the valuable genetic resources for this species. PMID:27796358

  10. Agronomical parameters, sugar profile and antioxidant compounds of "Catherine" peach cultivar influenced by different plum rootstocks.

    PubMed

    Font i Forcada, Carolina; Gogorcena, Yolanda; Moreno, María Ángeles

    2014-02-03

    The influence of seven plum rootstocks (Adesoto, Monpol, Montizo, Puebla de Soto 67 AD, PM 105 AD, St. Julien GF 655/2 and Constantí 1) on individual and total sugars, as well as on antioxidant content in fruit flesh of "Catherine" peaches, was evaluated for three years. Agronomical and basic fruit quality parameters were also determined. At twelve years after budding, significant differences were found between rootstocks for the different agronomic and fruit quality traits evaluated. The Pollizo plum rootstocks Adesoto and PM 105 AD seem to induce higher sweetness to peach fruits, based on soluble solids content, individual (sucrose, fructose and sorbitol) and total sugars. A clear tendency was also observed with the rootstock Adesoto, inducing the highest content of phenolics, flavonoids, vitamin C and relative antioxidant capacity (RAC). Thus, the results of this study demonstrate the significant effect of rootstock on the sugar profile and phytochemical characteristics of peach fruits. In addition, this work shows the importance of the sugar profile, because specific sugars play an important role in peach flavour quality, as well as the studied phytochemical compounds when looking for high quality peaches with enhanced health properties.

  11. Compositional and Agronomic Evaluation of Sorghum Biomass as a Potential Feedstock for Renewable Fuels

    SciTech Connect

    Dahlberg, J.; Wolfrum, E.; Bean, B.; Rooney, W. L.

    2011-12-01

    One goal of the Biomass Research and Development Technical Advisory Committee was to replace 30% of current U.S. petroleum consumption with biofuels by 2030. This will take mixtures of various feedstocks; an annual biomass feedstock such as sorghum will play an important role in meeting this goal. Commercial forage sorghum samples collected from field trials grown in Bushland, TX in 2007 were evaluated for both agronomic and compositional traits. Biomass compositional analysis of the samples was performed at the National Renewable Energy Lab in Golden, CO following NREL Laboratory Analytical Procedures. Depending on the specific cultivar, several additional years of yield data for this location were considered in establishing agronomic potential. Results confirm that sorghum forages can produce high biomass yields over multiple years and varied growing conditions. In addition, the composition of sorghum shows significant variation, as would be expected for most crops. Using theoretical estimates for ethanol production, the sorghum commercial forages examined in this study could produce an average of 6147 L ha{sup -1} of renewable fuels. Given its genetic variability, a known genomic sequence, a robust seed industry, and biomass composition, sorghum will be an important annual feedstock to meet the alternative fuel production goals legislated by the US Energy Security Act of 2007.

  12. Fine-tuning tomato agronomic properties by computational genome redesign.

    PubMed

    Carrera, Javier; Fernández Del Carmen, Asun; Fernández-Muñoz, Rafael; Rambla, Jose Luis; Pons, Clara; Jaramillo, Alfonso; Elena, Santiago F; Granell, Antonio

    2012-01-01

    Considering cells as biofactories, we aimed to optimize its internal processes by using the same engineering principles that large industries are implementing nowadays: lean manufacturing. We have applied reverse engineering computational methods to transcriptomic, metabolomic and phenomic data obtained from a collection of tomato recombinant inbreed lines to formulate a kinetic and constraint-based model that efficiently describes the cellular metabolism from expression of a minimal core of genes. Based on predicted metabolic profiles, a close association with agronomic and organoleptic properties of the ripe fruit was revealed with high statistical confidence. Inspired in a synthetic biology approach, the model was used for exploring the landscape of all possible local transcriptional changes with the aim of engineering tomato fruits with fine-tuned biotechnological properties. The method was validated by the ability of the proposed genomes, engineered for modified desired agronomic traits, to recapitulate experimental correlations between associated metabolites. PMID:22685389

  13. Genomic signatures reveal new evidences for selection of important traits in domestic cattle.

    PubMed

    Xu, Lingyang; Bickhart, Derek M; Cole, John B; Schroeder, Steven G; Song, Jiuzhou; Tassell, Curtis P Van; Sonstegard, Tad S; Liu, George E

    2015-03-01

    We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health. PMID:25431480

  14. Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

    PubMed Central

    Xu, Lingyang; Bickhart, Derek M.; Cole, John B.; Schroeder, Steven G.; Song, Jiuzhou; Tassell, Curtis P. Van; Sonstegard, Tad S.; Liu, George E.

    2015-01-01

    We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, and ABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5, and NUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health. PMID:25431480

  15. An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits.

    PubMed

    Vilanova, S; Romero, C; Abbott, A G; Llácer, G; Badenes, M L

    2003-07-01

    A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.

  16. Quantitative genetic parameters for yield, plant growth and cone chemical traits in hop (Humulus lupulus L.)

    PubMed Central

    2014-01-01

    Background Most traits targeted in the genetic improvement of hop are quantitative in nature. Improvement based on selection of these traits requires a comprehensive understanding of their inheritance. This study estimated quantitative genetic parameters for 20 traits related to three key objectives for the genetic improvement of hop: cone chemistry, cone yield and agronomic characteristics. Results Significant heritable genetic variation was identified for α-acid and β-acid, as well as their components and relative proportions. Estimates of narrow-sense heritability for these traits (h 2  = 0.15 to 0.29) were lower than those reported in previous hop studies, but were based on a broader suite of families (108 from European, North American and hybrid origins). Narrow-sense heritabilities are reported for hop growth traits for the first time (h 2  = 0.04 to 0.20), relating to important agronomic characteristics such as emergence, height and lateral morphology. Cone chemistry and growth traits were significantly genetically correlated, such that families with more vigorous vegetative growth were associated with lower α-acid and β-acid levels. This trend may reflect the underlying population structure of founder genotypes (European and North American origins) as well as past selection in the Australian environment. Although male and female hop plants are thought to be indistinguishable until flowering, sex was found to influence variation in many growth traits, with male and female plants displaying differences in vegetative morphology from emergence to cone maturity. Conclusions This study reveals important insights into the genetic control of quantitative hop traits. The information gained will provide hop breeders with a greater understanding of the additive genetic factors which affect selection of cone chemistry, yield and agronomic characteristics in hop, aiding in the future development of improved cultivars. PMID:24524684

  17. Identification of quantitative trait loci(QTL) controlling important fatty acids in peanut (Arachis hypogaea L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acids play important role in controlling oil quality of peanut. In addition to the major fatty acids, oleic acid (C18:1) and linoleic acid (C18:2) accounting for about 80%, there are several minor fatty acids accounting for about 20% in peanut oil, such as palmitic acid (PA, C16:0), stearic (S...

  18. Quantitative trait loci for yield and related traits in the wheat population Ning7840 x Clark.

    PubMed

    Marza, F; Bai, G-H; Carver, B F; Zhou, W-C

    2006-02-01

    Grain yield and associated agronomic traits are important factors in wheat (Triticum aestivum L.) improvement. Knowledge regarding the number, genomic location, and effect of quantitative trait loci (QTL) would facilitate marker-assisted selection and the development of cultivars with desirable characteristics. Our objectives were to identify QTLs directly and indirectly affecting grain yield expression. A population of 132 F12 recombinant inbred lines (RILs) was derived by single-seed descent from a cross between the Chinese facultative wheat Ning7840 and the US soft red winter wheat Clark. Phenotypic data were collected for 15 yield and other agronomic traits in the RILs and parental lines from three locations in Oklahoma from 2001 to 2003. Twenty-nine linkage groups, consisting of 363 AFLP and 47 SSR markers, were identified. Using composite interval mapping (CIM) analysis, 10, 16, 30, and 14 QTLs were detected for yield, yield components, plant adaptation (shattering and lodging resistance, heading date, and plant height), and spike morphology traits, respectively. The QTL effects ranged from 7 to 23%. Marker alleles from Clark were associated with a positive effect for the majority of QTLs for yield and yield components, but gene dispersion was the rule rather than the exception for this RIL population. Often, QTLs were detected in proximal positions for different traits. Consistent, co-localized QTLs were identified in linkage groups 1AL, 1B, 4B, 5A, 6A, and 7A, and less consistent but unique QTLs were identified on 2BL, 2BS, 2DL, and 6B. Results of this study provide a benchmark for future efforts on QTL identification for yield traits. PMID:16369760

  19. Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

    PubMed Central

    Petersen, Jessica L.; Mickelson, James R.; Rendahl, Aaron K.; Valberg, Stephanie J.; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Capomaccio, Stefano; Cappelli, Katia; Cothran, E. Gus; Distl, Ottmar; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T.; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; Wade, Claire M.; McCue, Molly E.

    2013-01-01

    Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. PMID:23349635

  20. Genome-wide analysis reveals selection for important traits in domestic horse breeds.

    PubMed

    Petersen, Jessica L; Mickelson, James R; Rendahl, Aaron K; Valberg, Stephanie J; Andersson, Lisa S; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M; Borges, Alexandre S; Brama, Pieter; da Câmara Machado, Artur; Capomaccio, Stefano; Cappelli, Katia; Cothran, E Gus; Distl, Ottmar; Fox-Clipsham, Laura; Graves, Kathryn T; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A; Mikko, Sofia; Orr, Nicholas; Penedo, M Cecilia T; Piercy, Richard J; Raekallio, Marja; Rieder, Stefan; Røed, Knut H; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; Wade, Claire M; McCue, Molly E

    2013-01-01

    Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

  1. Relative importance of phenotypic trait matching and species' abundances in determining plant-avian seed dispersal interactions in a small insular community.

    PubMed

    González-Castro, Aarón; Yang, Suann; Nogales, Manuel; Carlo, Tomás A

    2015-03-05

    Network theory has provided a general way to understand mutualistic plant-animal interactions at the community level. However, the mechanisms responsible for interaction patterns remain controversial. In this study we use a combination of statistical models and probability matrices to evaluate the relative importance of species morphological and nutritional (phenotypic) traits and species abundance in determining interactions between fleshy-fruited plants and birds that disperse their seeds. The models included variables associated with species abundance, a suite of variables associated with phenotypic traits (fruit diameter, bird bill width, fruit nutrient compounds), and the species identity of the avian disperser. Results show that both phenotypic traits and species abundance are important determinants of pairwise interactions. However, when considered separately, fruit diameter and bill width were more important in determining seed dispersal interactions. The effect of fruit compounds was less substantial and only important when considered together with abundance-related variables and/or the factor 'animal species'.

  2. Construct validity of adolescents' self-reported big five personality traits: importance of conceptual breadth and initial validation of a short measure.

    PubMed

    Morizot, Julien

    2014-10-01

    While there are a number of short personality trait measures that have been validated for use with adults, few are specifically validated for use with adolescents. To trust such measures, it must be demonstrated that they have adequate construct validity. According to the view of construct validity as a unifying form of validity requiring the integration of different complementary sources of information, this article reports the evaluation of content, factor, convergent, and criterion validities as well as reliability of adolescents' self-reported personality traits. Moreover, this study sought to address an inherent potential limitation of short personality trait measures, namely their limited conceptual breadth. In this study, starting with items from a known measure, after the language-level was adjusted for use with adolescents, items tapping fundamental primary traits were added to determine the impact of added conceptual breadth on the psychometric properties of the scales. The resulting new measure was named the Big Five Personality Trait Short Questionnaire (BFPTSQ). A group of expert judges considered the items to have adequate content validity. Using data from a community sample of early adolescents, the results confirmed the factor validity of the Big Five structure in adolescence as well as its measurement invariance across genders. More important, the added items did improve the convergent and criterion validities of the scales, but did not negatively affect their reliability. This study supports the construct validity of adolescents' self-reported personality traits and points to the importance of conceptual breadth in short personality measures.

  3. Agronomical Parameters, Sugar Profile and Antioxidant Compounds of “Catherine” Peach Cultivar Influenced by Different Plum Rootstocks

    PubMed Central

    Font i Forcada, Carolina; Gogorcena, Yolanda; Moreno, María Ángeles

    2014-01-01

    The influence of seven plum rootstocks (Adesoto, Monpol, Montizo, Puebla de Soto 67 AD, PM 105 AD, St. Julien GF 655/2 and Constantí 1) on individual and total sugars, as well as on antioxidant content in fruit flesh of “Catherine” peaches, was evaluated for three years. Agronomical and basic fruit quality parameters were also determined. At twelve years after budding, significant differences were found between rootstocks for the different agronomic and fruit quality traits evaluated. The Pollizo plum rootstocks Adesoto and PM 105 AD seem to induce higher sweetness to peach fruits, based on soluble solids content, individual (sucrose, fructose and sorbitol) and total sugars. A clear tendency was also observed with the rootstock Adesoto, inducing the highest content of phenolics, flavonoids, vitamin C and relative antioxidant capacity (RAC). Thus, the results of this study demonstrate the significant effect of rootstock on the sugar profile and phytochemical characteristics of peach fruits. In addition, this work shows the importance of the sugar profile, because specific sugars play an important role in peach flavour quality, as well as the studied phytochemical compounds when looking for high quality peaches with enhanced health properties. PMID:24496242

  4. Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.

    PubMed

    Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F

    2013-01-01

    'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236

  5. Survival in macaroni penguins and the relative importance of different drivers: individual traits, predation pressure and environmental variability.

    PubMed

    Horswill, Catharine; Matthiopoulos, Jason; Green, Jonathan A; Meredith, Michael P; Forcada, Jaume; Peat, Helen; Preston, Mark; Trathan, Phil N; Ratcliffe, Norman

    2014-09-01

    Understanding the demographic response of free-living animal populations to different drivers is the first step towards reliable prediction of population trends. Penguins have exhibited dramatic declines in population size, and many studies have linked this to bottom-up processes altering the abundance of prey species. The effects of individual traits have been considered to a lesser extent, and top-down regulation through predation has been largely overlooked due to the difficulties in empirically measuring this at sea where it usually occurs. For 10 years (2003-2012), macaroni penguins (Eudyptes chrysolophus) were marked with subcutaneous electronic transponder tags and re-encountered using an automated gateway system fitted at the entrance to the colony. We used multistate mark-recapture modelling to identify the different drivers influencing survival rates and a sensitivity analysis to assess their relative importance across different life stages. Survival rates were low and variable during the fledging year (mean = 0·33), increasing to much higher levels from age 1 onwards (mean = 0·89). We show that survival of macaroni penguins is driven by a combination of individual quality, top-down predation pressure and bottom-up environmental forces. The relative importance of these covariates was age specific. During the fledging year, survival rates were most sensitive to top-down predation pressure, followed by individual fledging mass, and finally bottom-up environmental effects. In contrast, birds older than 1 year showed a similar response to bottom-up environmental effects and top-down predation pressure. We infer from our results that macaroni penguins will most likely be negatively impacted by an increase in the local population size of giant petrels. Furthermore, this population is, at least in the short term, likely to be positively influenced by local warming. More broadly, our results highlight the importance of considering multiple causal effects across

  6. Survival in macaroni penguins and the relative importance of different drivers: individual traits, predation pressure and environmental variability.

    PubMed

    Horswill, Catharine; Matthiopoulos, Jason; Green, Jonathan A; Meredith, Michael P; Forcada, Jaume; Peat, Helen; Preston, Mark; Trathan, Phil N; Ratcliffe, Norman

    2014-09-01

    Understanding the demographic response of free-living animal populations to different drivers is the first step towards reliable prediction of population trends. Penguins have exhibited dramatic declines in population size, and many studies have linked this to bottom-up processes altering the abundance of prey species. The effects of individual traits have been considered to a lesser extent, and top-down regulation through predation has been largely overlooked due to the difficulties in empirically measuring this at sea where it usually occurs. For 10 years (2003-2012), macaroni penguins (Eudyptes chrysolophus) were marked with subcutaneous electronic transponder tags and re-encountered using an automated gateway system fitted at the entrance to the colony. We used multistate mark-recapture modelling to identify the different drivers influencing survival rates and a sensitivity analysis to assess their relative importance across different life stages. Survival rates were low and variable during the fledging year (mean = 0·33), increasing to much higher levels from age 1 onwards (mean = 0·89). We show that survival of macaroni penguins is driven by a combination of individual quality, top-down predation pressure and bottom-up environmental forces. The relative importance of these covariates was age specific. During the fledging year, survival rates were most sensitive to top-down predation pressure, followed by individual fledging mass, and finally bottom-up environmental effects. In contrast, birds older than 1 year showed a similar response to bottom-up environmental effects and top-down predation pressure. We infer from our results that macaroni penguins will most likely be negatively impacted by an increase in the local population size of giant petrels. Furthermore, this population is, at least in the short term, likely to be positively influenced by local warming. More broadly, our results highlight the importance of considering multiple causal effects across

  7. Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality.

    PubMed

    Waples, R S

    2016-10-01

    The relationship between life-history traits and the key eco-evolutionary parameters effective population size (Ne) and Ne/N is revisited for iteroparous species with overlapping generations, with a focus on the annual rate of adult mortality (d). Analytical methods based on populations with arbitrarily long adult lifespans are used to evaluate the influence of d on Ne, Ne/N and the factors that determine these parameters: adult abundance (N), generation length (T), age at maturity (α), the ratio of variance to mean reproductive success in one season by individuals of the same age (φ) and lifetime variance in reproductive success of individuals in a cohort (Vk•). Although the resulting estimators of N, T and Vk• are upwardly biased for species with short adult lifespans, the estimate of Ne/N is largely unbiased because biases in T are compensated for by biases in Vk• and N. For the first time, the contrasting effects of T and Vk• on Ne and Ne/N are jointly considered with respect to d and φ. A simple function of d and α based on the assumption of constant vital rates is shown to be a robust predictor (R(2)=0.78) of Ne/N in an empirical data set of life tables for 63 animal and plant species with diverse life histories. Results presented here should provide important context for interpreting the surge of genetically based estimates of Ne that has been fueled by the genomics revolution. PMID:27273324

  8. Association of green stem disorder with agronomic traits in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Green stem disorder of soybean (GSD) is the occurrence of non-senescent, fleshy green stems of plants with normal, fully mature pods and seeds. Data on GSD incidence based on a percentage of plants in plots showing symptoms were collected for soybean cultivars in 86 trials from 2009 to 2012 at seven...

  9. A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli.

    PubMed

    Phan, Katherine; Ferenci, Thomas

    2013-10-01

    Bacterial species are internally diverse in genomic and multi-locus gene comparisons. The ecological causes of phenotypic and genotypic diversity within species are far less well understood. Here, we focus on the competitive fitness for growth on nutrients within Escherichia coli, an internally rich species. Competition experiments in nutrient-limited chemostats revealed that members of the ECOR collection exhibited a wide continuum of competitive abilities, with some fitter and some less fit than the lab strain MG1655. We observed an inverse relationship between competitiveness and the resistance of strains to detergent and antibiotic, consistent with the notion that membrane permeability and competitive fitness are linked by a trade-off between self-preservation and nutritional competence (SPANC); high permeability has a postulated cost in antibacterial sensitivity whereas a low permeability has a cost in nutrient affinity. Isolates moved along the markedly nonlinear trade-off curve by mutational adaptation; an ECOR strain sensitive to antibacterials and a good competitor was easily converted by mutation into a mutant with higher resistance but poorer competition in the presence of low antibiotic concentrations. Conversely, a resistant ECOR strain changed into a better competitor after a short period of selection under nutrient limitation. In both directions, mutations can affect porin proteins and outer membrane permeability, as indicated by protein analysis, gene sequencing and an independent assay of outer membrane permeability. The extensive, species-wide diversity of E. coli in ecologically important traits can thus be explained as an evolutionary consequence of a SPANC trade-off driven by antagonistic pleiotropy.

  10. Survival in macaroni penguins and the relative importance of different drivers: individual traits, predation pressure and environmental variability

    PubMed Central

    Horswill, Catharine; Matthiopoulos, Jason; Green, Jonathan A; Meredith, Michael P; Forcada, Jaume; Peat, Helen; Preston, Mark; Trathan, Phil N; Ratcliffe, Norman

    2014-01-01

    Understanding the demographic response of free-living animal populations to different drivers is the first step towards reliable prediction of population trends. Penguins have exhibited dramatic declines in population size, and many studies have linked this to bottom-up processes altering the abundance of prey species. The effects of individual traits have been considered to a lesser extent, and top-down regulation through predation has been largely overlooked due to the difficulties in empirically measuring this at sea where it usually occurs. For 10 years (2003–2012), macaroni penguins (Eudyptes chrysolophus) were marked with subcutaneous electronic transponder tags and re-encountered using an automated gateway system fitted at the entrance to the colony. We used multistate mark–recapture modelling to identify the different drivers influencing survival rates and a sensitivity analysis to assess their relative importance across different life stages. Survival rates were low and variable during the fledging year (mean = 0·33), increasing to much higher levels from age 1 onwards (mean = 0·89). We show that survival of macaroni penguins is driven by a combination of individual quality, top-down predation pressure and bottom-up environmental forces. The relative importance of these covariates was age specific. During the fledging year, survival rates were most sensitive to top-down predation pressure, followed by individual fledging mass, and finally bottom-up environmental effects. In contrast, birds older than 1 year showed a similar response to bottom-up environmental effects and top-down predation pressure. We infer from our results that macaroni penguins will most likely be negatively impacted by an increase in the local population size of giant petrels. Furthermore, this population is, at least in the short term, likely to be positively influenced by local warming. More broadly, our results highlight the importance of considering multiple causal

  11. Evolutionary outcomes should inform plant breeding and transgenic approaches to drought tolerance in crop species: the importance of xylem traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic-assisted breeding and transgenic approaches to crop improvement are presently targeting phenotypic traits that allegedly confer drought tolerance. A news feature published in Nature Biotechnology last year suggests that these efforts may not be proceeding with sufficient haste, considering t...

  12. Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production.

    PubMed

    Basarab, J A; Beauchemin, K A; Baron, V S; Ominski, K H; Guan, L L; Miller, S P; Crowley, J J

    2013-06-01

    Genetic selection for residual feed intake (RFI) is an indirect approach for reducing enteric methane (CH4) emissions in beef and dairy cattle. RFI is moderately heritable (0.26 to 0.43), moderately repeatable across diets (0.33 to 0.67) and independent of body size and production, and when adjusted for off-test ultrasound backfat thickness (RFI fat) is also independent of body fatness in growing animals. It is highly dependent on accurate measurement of individual animal feed intake. Within-animal repeatability of feed intake is moderate (0.29 to 0.49) with distinctive diurnal patterns associated with cattle type, diet and genotype, necessitating the recording of feed intake for at least 35 days. In addition, direct measurement of enteric CH4 production will likely be more variable and expensive than measuring feed intake and if conducted should be expressed as CH4 production (g/animal per day) adjusted for body size, growth, body composition and dry matter intake (DMI) or as residual CH4 production. A further disadvantage of a direct CH4 phenotype is that the relationships of enteric CH4 production on other economically important traits are largely unknown. Selection for low RFI fat (efficient, -RFI fat) will result in cattle that consume less dry matter (DMI) and have an improved feed conversion ratio (FCR) compared with high RFI fat cattle (inefficient; +RFI fat). Few antagonistic effects have been reported for the relationships of RFI fat on carcass and meat quality, fertility, cow lifetime productivity and adaptability to stress or extensive grazing conditions. Low RFI fat cattle also produce 15% to 25% less enteric CH4 than +RFI fat cattle, since DMI is positively related to enteric methane (CH4) production. In addition, lower DMI and feeding duration and frequency, and a different rumen bacterial profile that improves rumen fermentation in -RFI fat cattle may favor a 1% to 2% improvement in dry matter and CP digestibility compared with +RFI fat cattle. Rate

  13. QTLs for important breeding characteristics in the doubled haploid oat progeny.

    PubMed

    Tanhuanpää, Pirjo; Manninen, Outi; Kiviharju, Elina

    2010-06-01

    A homozygous mapping population, consisting of doubled haploid (DH) oat (Avena sativa L.) plants generated through anther culture of F1 plants from the cross between the Finnish cultivar 'Aslak' and the Swedish cultivar 'Matilda', was used to construct an oat linkage map. Ten agronomic and quality traits were analyzed in the DH plants from field trials in 2005 and 2006. Leaf blotch (caused by Pyrenophora avenae) resistance was also evaluated in a greenhouse test with 2 different isolates. One to 8 quantitative trait loci (QTLs) were found to be associated with each trait studied. Some chromosomal regions affected more than 1 trait; for example, 4 regions affected both protein and oil content. This study gives valuable information to oat breeders concerning the inheritance of important traits, and it provides potential tools to assist breeding.

  14. A new broccoli × broccoli immortal mapping population and framework genetic map: tools for breeders and complex trait analysis.

    PubMed

    Walley, Peter Glen; Carder, John; Skipper, Emma; Mathas, Evy; Lynn, James; Pink, David; Buchanan-Wollaston, Vicky

    2012-02-01

    A unique broccoli × broccoli doubled haploid (DH) population has been created from the F(1) of a cross between two DH broccoli lines derived from cultivars Green Duke and Marathon. We genotyped 154 individuals from this population with simple sequence repeat and amplified fragment length polymorphism markers to create a B. oleracea L. var. italica 'intra-crop' specific framework linkage map. The map is composed of nine linkage groups with a total length of 946.7 cM. Previous published B. oleracea maps have been constructed using diverse crosses between morphotypes of B. oleracea; this map therefore represents a useful breeding resource for the dissection of broccoli specific traits. Phenotype data have been collected from the population over five growing seasons; the framework linkage map has been used to locate quantitative trait loci for agronomically important broccoli traits including head weight (saleable yield), head diameter, stalk diameter, weight loss and relative weight loss during storage, as well as traits for broccoli leaf architecture. This population and associated linkage map will aid breeders to directly map agronomically important traits for the improvement of elite broccoli cultivars. PMID:22038485

  15. Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population. I: a soil-filled box screen.

    PubMed

    MacMillan, K; Emrich, K; Piepho, H-P; Mullins, C E; Price, A H

    2006-10-01

    Altering root system architecture is considered a method of improving crop water and soil nutrient capture. The analysis of quantitative trait loci (QTLs) for root traits has revealed inconsistency in the same population evaluated in different environments. It must be clarified if this is due to genotype x environment interaction or considerations of statistics if the value of QTLs for marker-assisted breeding is to be estimated. A modified split-plot design was used where a main plot corresponded to a separate experiment. The main plot factor had four treatments (environments), which were completely randomized among eight trials, so that each treatment was replicated twice. The sub-plot factor consisted of 168 recombinant inbreed lines of the Bala x Azucena rice mapping population, randomly allocated to the seven soil-filled boxes. The aim of the trial was to quantify QTL x environment interaction. The treatments were chosen to alter partitioning to roots; consisting of a control treatment (high-soil nitrogen, high light and high-water content) and further treatments where light, soil nitrogen or soil water was reduced singly. After 4 weeks growth, maximum root length (MRL), maximum root thickness, root mass below 50 cm, total plant dry mass (%), root mass and shoot length were measured. The treatments affected plant growth as predicted; low nitrogen and drought increased relative root partitioning, low-light decreased it. The parental varieties Bala and Azucena differed significantly for all traits. Broad-sense heritability of most traits was high (57-86%). Variation due to treatment was the most important influence on the variance, while genotype was next. Genotype x environment interaction was detected for all traits except MRL, although the proportion of variation due to this interaction was generally small. It is concluded that genotype x environment interaction is present but less important than genotypic variation. A companion paper presents QTL x

  16. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  17. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-12-28

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources.

  18. Identification of nutrient and physical seed trait QTL in the model legume Lotus japonicus.

    PubMed

    Klein, Melinda A; Grusak, Michael A

    2009-08-01

    Legume seeds have the potential to provide a significant portion of essential micronutrients to the human diet. To identify the genetic basis for seed nutrient density, quantitative trait locus (QTL) analysis was conducted with the Miyakojima MG-20 x Gifu B-129 recombinant inbred population from the model legume Lotus japonicus. This population was grown to seed under greenhouse conditions in 2006 and 2007. Phenotypic data were collected for seed calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and zinc (Zn) concentrations and content. Data for physical seed traits (average seed mass and seed-pod allocation values) were also collected. Based on these phenotypic data, QTL analyses identified 103 QTL linked to 55 different molecular markers. Transgressive segregation, identified within this recombinant inbred population for both seed nutrient and physical traits, suggests new allelic combinations are available for agronomic trait improvement. QTL co-localization was also seen, suggesting that common transport processes might contribute to seed nutrient loading. Identification of loci involved in seed mineral density can be an important first step in identifying the genetic factors and, consequently, the physiological processes involved in mineral distribution to developing seeds. Longer term research efforts will focus on facilitating agronomic breeding efforts through ortholog identification in related crop legumes.

  19. The Influence of Organized Physical Activity (including Gymnastics) on Young Adult Skeletal Traits: Is Maturity Phase Important?

    PubMed Central

    Bernardoni, Brittney; Scerpella, Tamara A.; Rosenbaum, Paula F.; Kanaley, Jill A.; Raab, Lindsay N.; Li, Quefeng; Wang, Sijian; Dowthwaite, Jodi N.

    2015-01-01

    We prospectively evaluated adolescent organized physical activity (PA) as a factor in adult female bone traits. Annual DXA scans accompanied semi-annual records of anthropometry, maturity and PA for 42 participants in this preliminary analysis (criteria: appropriately timed DXA scans at ~1 year pre-menarche [predictor] and ~5 years post-menarche [dependent variable]). Regression analysis evaluated total adolescent inter-scan PA and PA over 3 maturity sub-phases as predictors of young adult bone outcomes: 1) bone mineral content (BMC), geometry and strength indices at non-dominant distal radius and femoral neck; 2) sub-head BMC; 3) lumbar spine BMC. Analyses accounted for baseline gynecological age (years pre- or post-menarche), baseline bone status, adult body size and inter-scan body size change. Gymnastics training was evaluated as a potentially independent predictor, but did not improve models for any outcomes (p<0.07). Pre-menarcheal bone traits were strong predictors of most adult outcomes (semi-partial r2 = 0.21-0.59, p≤0.001). Adult 1/3 radius and sub-head BMC were predicted by both total PA and PA 1-3 years post-menarche (p<0.03). PA 3-5 years post-menarche predicted femoral narrow neck width, endosteal diameter and buckling ratio (p<0.05). Thus, participation in organized physical activity programs throughout middle and high school may reduce lifetime fracture risk in females. PMID:25386845

  20. The Influence of Organized Physical Activity (Including Gymnastics) on Young Adult Skeletal Traits: Is Maturity Phase Important?

    PubMed

    Bernardoni, Brittney; Scerpella, Tamara A; Rosenbaum, Paula F; Kanaley, Jill A; Raab, Lindsay N; Li, Quefeng; Wang, Sijian; Dowthwaite, Jodi N

    2015-05-01

    We prospectively evaluated adolescent organized physical activity (PA) as a factor in adult female bone traits. Annual DXA scans accompanied semiannual records of anthropometry, maturity, and PA for 42 participants in this preliminary analysis (criteria: appropriately timed DXA scans at ~1 year premenarche [predictor] and ~5 years postmenarche [dependent variable]). Regression analysis evaluated total adolescent interscan PA and PA over 3 maturity subphases as predictors of young adult bone outcomes: 1) bone mineral content (BMC), geometry, and strength indices at nondominant distal radius and femoral neck; 2) subhead BMC; 3) lumbar spine BMC. Analyses accounted for baseline gynecological age (years pre- or postmenarche), baseline bone status, adult body size and interscan body size change. Gymnastics training was evaluated as a potentially independent predictor, but did not improve models for any outcomes (p > .07). Premenarcheal bone traits were strong predictors of most adult outcomes (semipartial r2 = .21-0.59, p ≤ .001). Adult 1/3 radius and subhead BMC were predicted by both total PA and PA 1-3 years postmenarche (p < .03). PA 3-5 years postmenarche predicted femoral narrow neck width, endosteal diameter, and buckling ratio (p < .05). Thus, participation in organized physical activity programs throughout middle and high school may reduce lifetime fracture risk in females. PMID:25386845

  1. Shaping melons: agronomic and genetic characterization of QTLs that modify melon fruit morphology.

    PubMed

    Fernandez-Silva, Iria; Moreno, Eduard; Essafi, Ali; Fergany, Mohamed; Garcia-Mas, Jordi; Martín-Hernandez, Ana Montserrat; Alvarez, Jose María; Monforte, Antonio J

    2010-09-01

    The consistency of quantitative trait locus (QTL) effects among genetic backgrounds is a key factor for introgressing QTLs from initial mapping experiments into applied breeding programs. We have selected four QTLs (fs6.4, fw4.3, fw4.4 and fw8.1) involved in melon fruit morphology that had previously been detected in a collection of introgression lines derived from the cross between a Spanish cultivar, "Piel de Sapo," and the Korean accession PI161375 (Songwan Charmi). Introgression lines harboring these QTLs were crossed with an array of melon inbred lines representative of the most important cultivar types. Hybrids of the introgression and inbred lines, with the appropriate controls, were evaluated in replicated agronomic trials. The effects of the QTLs were consistent among the different genetic backgrounds, demonstrating the utility of these QTLs for applied breeding programs in modifying melon fruit morphology. Three QTLs, fw4.4, fs6.4 and fs12.1 were subjected to further study in order to map them more accurately by substitution mapping using a new set of introgression lines with recombination events within the QTL chromosome region. The position of the QTLs was narrowed down to 36-5 cM, depending on the QTL. The results presented in the current study set the basis for the use of these QTLs in applied breeding programs and for the molecular characterization of the genes underlying them.

  2. Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

    PubMed Central

    Yasui, Yasuo; Hirakawa, Hideki; Ueno, Mariko; Matsui, Katsuhiro; Katsube-Tanaka, Tomoyuki; Yang, Soo Jung; Aii, Jotaro; Sato, Shingo; Mori, Masashi

    2016-01-01

    Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits. PMID:27037832

  3. Advances in Phenotyping of Functional Traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In plants, functional traits are morphological, biochemical, physiological, structural, phenological, or behavioral characteristics that are expressed in phenotypes of individual plants,that are relevant to the plant’s role in the ecosystem or its agronomic performance. By themselves, functional tra...

  4. Genetic Variability and Selection Criteria in Rice Mutant Lines as Revealed by Quantitative Traits

    PubMed Central

    Oladosu, Yusuff; Rafii, M. Y.; Abdullah, Norhani; Abdul Malek, Mohammad; Rahim, H. A.; Hussin, Ghazali; Abdul Latif, Mohammad; Kareem, Isiaka

    2014-01-01

    Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice. PMID:25431777

  5. Predicting the impacts of climate change on animal distributions: the importance of local adaptation and species' traits

    SciTech Connect

    HELLMANN, J. J.; LOBO, N. F.

    2011-12-20

    response of species to climate change, but our experiments suggest that other processes may act in some species that reduce the likelihood of geographic range change. In the first part of our DOE grant (ending 2008) we argued that the process of local adaptation of populations within a species range, followed by climatic changes that occur too quickly for adaptive evolution, is an underappreciated mechanism by which climate change could affect biodiversity. When this process acts, species ranges may not shift readily toward the poles, slowing the rate of species and biome change. To test this claim, we performed an experiment comparing core and peripheral populations in a series of field observations, translocation experiments, and genetic analyses. The papers in Appendix A were generated from 2005-2008 funding. In the second part of the DOE grant (ending 2011) we studied which traits promote population differentiation and local adaptation by building genomic resources for our study species and using these resources to reveal differences in gene expression in peripheral and core populations. The papers in Appendix B were generated from 2008-2011 funding. This work was pursued with two butterfly species that have contrasting life history traits (body size and resource specialization) and occupy a common ecosystem and a latitudinal range. These species enabled us to test the following hypotheses using a single phylogenetic group.

  6. Contrasting responses of root morphology and root-exuded organic acids to low phosphorus availability in three important food crops with divergent root traits

    PubMed Central

    Wang, Yan-Liang; Almvik, Marit; Clarke, Nicholas; Eich-Greatorex, Susanne; Øgaard, Anne Falk; Krogstad, Tore; Lambers, Hans; Clarke, Jihong Liu

    2015-01-01

    Phosphorus (P) is an important element for crop productivity and is widely applied in fertilizers. Most P fertilizers applied to land are sorbed onto soil particles, so research on improving plant uptake of less easily available P is important. In the current study, we investigated the responses in root morphology and root-exuded organic acids (OAs) to low available P (1 μM P) and sufficient P (50 μM P) in barley, canola and micropropagated seedlings of potato—three important food crops with divergent root traits, using a hydroponic plant growth system. We hypothesized that the dicots canola and tuber-producing potato and the monocot barley would respond differently under various P availabilities. WinRHIZO and liquid chromatography triple quadrupole mass spectrometry results suggested that under low P availability, canola developed longer roots and exhibited the fastest root exudation rate for citric acid. Barley showed a reduction in root length and root surface area and an increase in root-exuded malic acid under low-P conditions. Potato exuded relatively small amounts of OAs under low P, while there was a marked increase in root tips. Based on the results, we conclude that different crops show divergent morphological and physiological responses to low P availability, having evolved specific traits of root morphology and root exudation that enhance their P-uptake capacity under low-P conditions. These results could underpin future efforts to improve P uptake of the three crops that are of importance for future sustainable crop production. PMID:26286222

  7. Contrasting responses of root morphology and root-exuded organic acids to low phosphorus availability in three important food crops with divergent root traits.

    PubMed

    Wang, Yan-Liang; Almvik, Marit; Clarke, Nicholas; Eich-Greatorex, Susanne; Øgaard, Anne Falk; Krogstad, Tore; Lambers, Hans; Clarke, Jihong Liu

    2015-08-17

    Phosphorus (P) is an important element for crop productivity and is widely applied in fertilizers. Most P fertilizers applied to land are sorbed onto soil particles, so research on improving plant uptake of less easily available P is important. In the current study, we investigated the responses in root morphology and root-exuded organic acids (OAs) to low available P (1 μM P) and sufficient P (50 μM P) in barley, canola and micropropagated seedlings of potato-three important food crops with divergent root traits, using a hydroponic plant growth system. We hypothesized that the dicots canola and tuber-producing potato and the monocot barley would respond differently under various P availabilities. WinRHIZO and liquid chromatography triple quadrupole mass spectrometry results suggested that under low P availability, canola developed longer roots and exhibited the fastest root exudation rate for citric acid. Barley showed a reduction in root length and root surface area and an increase in root-exuded malic acid under low-P conditions. Potato exuded relatively small amounts of OAs under low P, while there was a marked increase in root tips. Based on the results, we conclude that different crops show divergent morphological and physiological responses to low P availability, having evolved specific traits of root morphology and root exudation that enhance their P-uptake capacity under low-P conditions. These results could underpin future efforts to improve P uptake of the three crops that are of importance for future sustainable crop production.

  8. Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research.

    PubMed

    Shi, Yeyin; Thomasson, J Alex; Murray, Seth C; Pugh, N Ace; Rooney, William L; Shafian, Sanaz; Rajan, Nithya; Rouze, Gregory; Morgan, Cristine L S; Neely, Haly L; Rana, Aman; Bagavathiannan, Muthu V; Henrickson, James; Bowden, Ezekiel; Valasek, John; Olsenholler, Jeff; Bishop, Michael P; Sheridan, Ryan; Putman, Eric B; Popescu, Sorin; Burks, Travis; Cope, Dale; Ibrahim, Amir; McCutchen, Billy F; Baltensperger, David D; Avant, Robert V; Vidrine, Misty; Yang, Chenghai

    2016-01-01

    Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1-the summer 2015 and winter 2016 growing seasons-of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and

  9. Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research.

    PubMed

    Shi, Yeyin; Thomasson, J Alex; Murray, Seth C; Pugh, N Ace; Rooney, William L; Shafian, Sanaz; Rajan, Nithya; Rouze, Gregory; Morgan, Cristine L S; Neely, Haly L; Rana, Aman; Bagavathiannan, Muthu V; Henrickson, James; Bowden, Ezekiel; Valasek, John; Olsenholler, Jeff; Bishop, Michael P; Sheridan, Ryan; Putman, Eric B; Popescu, Sorin; Burks, Travis; Cope, Dale; Ibrahim, Amir; McCutchen, Billy F; Baltensperger, David D; Avant, Robert V; Vidrine, Misty; Yang, Chenghai

    2016-01-01

    Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1-the summer 2015 and winter 2016 growing seasons-of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and

  10. Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

    PubMed Central

    Shi, Yeyin; Thomasson, J. Alex; Murray, Seth C.; Pugh, N. Ace; Rooney, William L.; Shafian, Sanaz; Rajan, Nithya; Rouze, Gregory; Morgan, Cristine L. S.; Neely, Haly L.; Rana, Aman; Bagavathiannan, Muthu V.; Henrickson, James; Bowden, Ezekiel; Valasek, John; Olsenholler, Jeff; Bishop, Michael P.; Sheridan, Ryan; Putman, Eric B.; Popescu, Sorin; Burks, Travis; Cope, Dale; Ibrahim, Amir; McCutchen, Billy F.; Baltensperger, David D.; Avant, Robert V.; Vidrine, Misty; Yang, Chenghai

    2016-01-01

    Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1—the summer 2015 and winter 2016 growing seasons–of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project’s goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first

  11. Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

    PubMed Central

    Deluc, Laurent G; Quilici, David R; Decendit, Alain; Grimplet, Jérôme; Wheatley, Matthew D; Schlauch, Karen A; Mérillon, Jean-Michel; Cushman, John C; Cramer, Grant R

    2009-01-01

    significant anthocyanin content, exhibited increased photoprotection mechanisms under water deficit conditions. Water deficit increased ABA, proline, sugar and anthocyanin concentrations in Cabernet Sauvignon, but not Chardonnay berries, consistent with the hypothesis that ABA enhanced accumulation of these compounds. Water deficit increased the transcript abundance of lipoxygenase and hydroperoxide lyase in fatty metabolism, a pathway known to affect berry and wine aromas. These changes in metabolism have important impacts on berry flavor and quality characteristics. Several of these metabolites are known to contribute to increased human-health benefits. PMID:19426499

  12. A sequential quantitative trait locus fine-mapping strategy using recombinant-derived progeny.

    PubMed

    Yang, Qin; Zhang, Dongfeng; Xu, Mingliang

    2012-04-01

    A thorough understanding of the quantitative trait loci (QTLs) that underlie agronomically important traits in crops would greatly increase agricultural productivity. Although advances have been made in QTL cloning, the majority of QTLs remain unknown because of their low heritability and minor contributions to phenotypic performance. Here we summarize the key advantages and disadvantages of current QTL fine-mapping methodologies, and then introduce a sequential QTL fine-mapping strategy based on both genotypes and phenotypes of progeny derived from recombinants. With this mapping strategy, experimental errors could be dramatically diminished so as to reveal the authentic genetic effect of target QTLs. The number of progeny required to detect QTLs at various R2 values was calculated, and the backcross generation suitable to start QTL fine-mapping was also estimated. This mapping strategy has proved to be very powerful in narrowing down QTL regions, particularly minor-effect QTLs, as revealed by fine-mapping of various resistance QTLs in maize. Application of this sequential QTL mapping strategy should accelerate cloning of agronomically important QTLs, which is currently a substantial challenge in crops. PMID:22348858

  13. Know your community - Biochar: agronomic and environmental uses community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The “Biochar: Agronomic and Environmental Uses” Community was formed in November 2010 (https://www.agronomy.org/membership/communities/biochar-agronomic-and-environmental-uses). The community’s initial function has been providing a forum at the tri-society’s national meetings to fill the need for a ...

  14. Delaying colostrum intake by one day has important effects on metabolic traits and on gastrointestinal and metabolic hormones in neonatal calves.

    PubMed

    Hadorn, U; Hammon, H; Bruckmaier, R M; Blum, J W

    1997-10-01

    Effects on metabolic and endocrine traits of feeding colostrum on d 1 and 2, then mature milk up to d 7, or glucose or water on d 1, colostrum on d 2 and 3 and then mature milk up to d 7 were studied in calves. Calves fed colostrum within the first 24 h after birth had significantly higher rectal temperatures, heart rates and respiratory frequencies than calves provided only water or glucose. Significantly elevated plasma nonesterified fatty acid and bilirubin concentrations on d 1 and 2 of life in calves fed only water on d 1 compared with calves of the other groups mirrored reduced energy intake. Fecal consistency was significantly higher during wk 1 of life, and gastrin and glucose-dependent insulinotropic polypeptide increased only on d 1 and/or 2 of life in calves already fed colostrum on d 1, expressing improved functioning of the gastrointestinal tract. Significantly higher plasma globulin levels up to d 7 in calves fed colostrum on d 1 than in those starting colostrum intake only on d 2 demonstrated significantly enhanced efficiency of gamma-globulin absorption. Furthermore, significantly higher circulating glucose, albumin, insulin, insulin-like growth factor-I concentrations and significantly lower urea levels in calves fed colostrum on d 1 compared with those fed colostrum starting on d 2 of life indicated stimulation of anabolic processes. In conclusion, colostrum intake by calves within the first 24 h of life is needed not only for an adequate immune status, but also to produce the additional important and favorable effects on metabolic and endocrine traits and on vitality.

  15. Haplotype hitchhiking promotes trait coselection in Brassica napus.

    PubMed

    Qian, Lunwen; Qian, Wei; Snowdon, Rod J

    2016-07-01

    Local haplotype patterns surrounding densely spaced DNA markers with significant trait associations can reveal information on selective sweeps and genome diversity associated with important crop traits. Relationships between haplotype and phenotype diversity, coupled with analysis of gene content in conserved haplotype blocks, can provide insight into coselection for nonrelated traits. We performed genome-wide analysis of haplotypes associated with the important physiological and agronomic traits leaf chlorophyll and seed glucosinolate content, respectively, in the major oilseed crop species Brassica napus. A locus on chromosome A01 showed opposite effects on leaf chlorophyll content and seed glucosinolate content, attributed to strong linkage disequilibrium (LD) between orthologues of the chlorophyll biosynthesis genes EARLY LIGHT-INDUCED PROTEIN and CHLOROPHYLL SYNTHASE, and the glucosinolate synthesis gene ATP SULFURYLASE 1. Another conserved haplotype block, on chromosome A02, contained a number of chlorophyll-related genes in LD with orthologues of the key glucosinolate biosynthesis genes METHYLTHIOALKYMALATE SYNTHASE-LIKE 1 and 3. Multigene haplogroups were found to have a significantly greater contribution to variation for chlorophyll content than haplotypes for any single gene, suggesting positive effects of additive locus accumulation. Detailed reanalysis of population substructure revealed a clade of ten related accessions exhibiting high leaf chlorophyll and low seed glucosinolate content. These accessions each carried one of the above-mentioned haplotypes from A01 or A02, generally in combination with further chlorophyll-associated haplotypes from chromosomes A05 and/or C05. The phenotypic rather than pleiotropic correlations between leaf chlorophyll content index and seed GSL suggest that LD may have led to inadvertent coselection for these two traits. PMID:26800855

  16. Do Callous-Unemotional Traits Moderate the Relative Importance of Parental Coercion versus Warmth in Child Conduct Problems? An Observational Study

    ERIC Educational Resources Information Center

    Pasalich, Dave S.; Dadds, Mark R.; Hawes, David J.; Brennan, John

    2011-01-01

    Background: Research suggests that parenting has little influence on the development of antisocial behavior in children with callous-unemotional (CU) traits. We aimed to extend and improve on prior studies examining the moderating role of CU traits on associations between parenting and conduct problems, by using independent observations of two key…

  17. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies

    PubMed Central

    Jain, Meha; Flynn, Dan FB; Prager, Case M; Hart, Georgia M; DeVan, Caroline M; Ahrestani, Farshid S; Palmer, Matthew I; Bunker, Daniel E; Knops, Johannes MH; Jouseau, Claire F; Naeem, Shahid

    2014-01-01

    The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait-based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance-weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning. PMID:24455165

  18. The importance of the regional species pool, ecological species traits and local habitat conditions for the colonization of restored river reaches by fish.

    PubMed

    Stoll, Stefan; Kail, Jochem; Lorenz, Armin W; Sundermann, Andrea; Haase, Peter

    2014-01-01

    It is commonly assumed that the colonization of restored river reaches by fish depends on the regional species pools; however, quantifications of the relationship between the composition of the regional species pool and restoration outcome are lacking. We analyzed data from 18 German river restoration projects and adjacent river reaches constituting the regional species pools of the restored reaches. We found that the ability of statistical models to describe the fish assemblages established in the restored reaches was greater when these models were based on 'biotic' variables relating to the regional species pool and the ecological traits of species rather than on 'abiotic' variables relating to the hydromorphological habitat structure of the restored habitats and descriptors of the restoration projects. For species presence in restored reaches, 'biotic' variables explained 34% of variability, with the occurrence rate of a species in the regional species pool being the most important variable, while 'abiotic' variables explained only the negligible amount of 2% of variability. For fish density in restored reaches, about twice the amount of variability was explained by 'biotic' (38%) compared to 'abiotic' (21%) variables, with species density in the regional species pool being most important. These results indicate that the colonization of restored river reaches by fish is largely determined by the assemblages in the surrounding species pool. Knowledge of species presence and abundance in the regional species pool can be used to estimate the likelihood of fish species becoming established in restored reaches.

  19. Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.)

    PubMed Central

    2012-01-01

    Background Pigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea. Results A population of 186 F2:3 lines derived from an intra-specific cross between inbred lines ‘Pusa Dwarf’ and ‘HDM04-1’ was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant. Conclusions A large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant

  20. [Effects of stereoscopic cultivation on soil microorganism, enzyme activity and the agronomic characters of Panax notoginseng].

    PubMed

    Liao, Pei-ran; Cui, Xiu-ming; Lan, Lei; Chen, Wei-dong; Wang, Cheng-xiao; Yang, Xiao-yan; Liu, Da-hui; Yang, Ye

    2015-08-01

    Compartments of soil microorganism and enzymes between stereoscopic cultivation (three storeys) and field cultivation (CK) of Panax notoginseng were carried out, and the effects on P. notoginseng agronomic characters were also studied. Results show that concentration of soil microorganism of stereoscopic cultivation was lower than field cultivation; the activity of soil urea enzyme, saccharase and neutral phosphatase increased from lower storey to upper storey; the activity of soil urea enzyme and saccharase of lower and upper storeys were significantly lower than CK; agronomic characters of stereoscopic cultivated P. notoginsengin were inferior to field cultivation, the middle storey with the best agronomic characters among the three storeys. The correlation analysis showed that fungi, actinomycetes and neutral phosphatase were significantly correlated with P. notoginseng agronomic characters; concentration of soil fungi and bacteria were significantly correlated with the soil relative water content; actinomycete and neutral phosphatase were significantly correlated with soil pH and relative water content, respectively; the activities of soil urea enzyme and saccharase were significantly correlated with the soil daily maximum temperature difference. Inconclusion, The current research shows that the imbalance of soil microorganism and the acutely changing of soil enzyme activity were the main reasons that caused the agronomic characters of stereoscopic cultivated P. notoginseng were worse than field cultivation. Thus improves the concentration of soil microorganism and enzyme activity near to field soil by improving the structure of stereoscopic cultivation is very important. And it was the direction which we are endeavoring that built better soil ecological environment for P. notoginseng of stereoscopic cultivation.

  1. [Effects of stereoscopic cultivation on soil microorganism, enzyme activity and the agronomic characters of Panax notoginseng].

    PubMed

    Liao, Pei-ran; Cui, Xiu-ming; Lan, Lei; Chen, Wei-dong; Wang, Cheng-xiao; Yang, Xiao-yan; Liu, Da-hui; Yang, Ye

    2015-08-01

    Compartments of soil microorganism and enzymes between stereoscopic cultivation (three storeys) and field cultivation (CK) of Panax notoginseng were carried out, and the effects on P. notoginseng agronomic characters were also studied. Results show that concentration of soil microorganism of stereoscopic cultivation was lower than field cultivation; the activity of soil urea enzyme, saccharase and neutral phosphatase increased from lower storey to upper storey; the activity of soil urea enzyme and saccharase of lower and upper storeys were significantly lower than CK; agronomic characters of stereoscopic cultivated P. notoginsengin were inferior to field cultivation, the middle storey with the best agronomic characters among the three storeys. The correlation analysis showed that fungi, actinomycetes and neutral phosphatase were significantly correlated with P. notoginseng agronomic characters; concentration of soil fungi and bacteria were significantly correlated with the soil relative water content; actinomycete and neutral phosphatase were significantly correlated with soil pH and relative water content, respectively; the activities of soil urea enzyme and saccharase were significantly correlated with the soil daily maximum temperature difference. Inconclusion, The current research shows that the imbalance of soil microorganism and the acutely changing of soil enzyme activity were the main reasons that caused the agronomic characters of stereoscopic cultivated P. notoginseng were worse than field cultivation. Thus improves the concentration of soil microorganism and enzyme activity near to field soil by improving the structure of stereoscopic cultivation is very important. And it was the direction which we are endeavoring that built better soil ecological environment for P. notoginseng of stereoscopic cultivation. PMID:26677687

  2. Engineering Value-Added Traits in Cereal Crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cereal crops – chiefly wheat, rice, maize, sorghum, and pearl millet – are the main food source for more than two-thirds of the world population. Conventional breeding is mainly responsible for the genetic improvement of cereal crops and has resulted in cultivars with superior agronomic traits. Ho...

  3. Effect of agronomical practices on carpology, fruit and oil composition, and oil sensory properties, in olive (Olea europaea L.).

    PubMed

    Rosati, Adolfo; Cafiero, Caterina; Paoletti, Andrea; Alfei, Barbara; Caporali, Silvia; Casciani, Lorena; Valentini, Massimiliano

    2014-09-15

    We examined whether some agronomical practices (i.e. organic vs. conventional) affect olive fruit and oil composition, and oil sensory properties. Fruit characteristics (i.e. fresh and dry weight of pulp and pit, oil content on a fresh and dry weight basis) did not differ. Oil chemical traits did not differ except for increased content of polyphenols in the organic treatments, and some changes in the acidic composition. Sensory analysis revealed increased bitterness (both cultivars) and pungency (Frantoio) and decreased sweetness (Frantoio) in the organic treatment. Fruit metabolomic analysis with HRMAS-NMR indicated significant changes in some compounds including glycocholate, fatty acids, NADPH, NADP+, some amino acids, thymidine, trigonelline, nicotinic acid, 5,6-dihydrouracil, hesanal, cis-olefin, β-D-glucose, propanal and some unassigned species. The results suggest that agronomical practices may have effects on fruit composition that may be difficult to detect unless a broad-spectrum analysis is used.

  4. 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

  5. A Survey of Fertilizer Dealers: I. Sources of Agronomic Training.

    ERIC Educational Resources Information Center

    Schmitt, M. A.

    1988-01-01

    Reports on a survey of fertilizer dealers which was conducted to: assess where and from whom local fertilizer dealers obtain agronomic training; evaluate the effectiveness of various dealer training; and determine the needs and objectives of future training programs. (TW)

  6. A Survey of Fertilizer Dealers: II. Sources of Agronomic Information.

    ERIC Educational Resources Information Center

    Schmitt, M. A.

    1988-01-01

    Reports on a survey of fertilizer dealers that was conducted to assess how the dealers were obtaining their agronomic information, aside from formal training sessions, and determine if these sources of information were satisfactory in fulfilling the dealers' needs. (TW)

  7. Integrating Agronomic Principles with Management Experience in Introductory Agronomy.

    ERIC Educational Resources Information Center

    Vorst, J. J.

    1989-01-01

    Explains the use of a cropping systems project to teach agronomic principles and crop management techniques, and to enhance communication skills. Provides a sample progress report instructions sheet which was used for the project. (Author/RT)

  8. Quantitative Trait Locus Mapping of Yield-Related Components and Oligogenic Control of the Cap Color of the Button Mushroom, Agaricus bisporus

    PubMed Central

    Rodier, Anne; Rousseau, Thierry; Savoie, Jean-Michel

    2012-01-01

    As in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits in Agaricus bisporus through the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m2, earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. The PPC1 locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom. PMID:22267676

  9. Quantitative trait locus mapping of yield-related components and oligogenic control of the cap color of the button mushroom, Agaricus bisporus.

    PubMed

    Foulongne-Oriol, Marie; Rodier, Anne; Rousseau, Thierry; Savoie, Jean-Michel

    2012-04-01

    As in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits in Agaricus bisporus through the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m(2), earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. The PPC1 locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom. PMID:22267676

  10. Agronomic use of biotechnologically processed grape wastes.

    PubMed

    Ferrer, J; Páez, G; Mármol, Z; Ramones, E; Chandler, C; Marín, M; Ferrer, A

    2001-01-01

    Grape waste was composted by biodegradation and subsequently used as an organic fertilizer for 20 day-corn. Combinations of recently compressed grape waste and hen droppings (10% w/w) were prepared to study the activating effect of hen droppings and the effect of aeration on the composting process. The final hydrogen potential (pH), %C, %N and C/N ratio, indicated an adequate development of the bioprocess. Satisfactory results were observed when the products were applied at several doses (1,000-4,000 kg/ ha) as a soil conditioner for corn seed germination in greenhouses. Only the addition of hen droppings had a significant effect (P < 0.05) on corn dry matter (14% increase). A dose of 3000 kg/ha was considered as optimal and was used supplemented with triple superphosphate (TSP) in agronomic trials. All the treatments produced greater corn dry matter (P < 0.05) than the chemical industrial fertilizer used as a control (0.52-0.71 g/pot for the organic fertilizers vs 0.45 g/pot for the control). Anaerobic conditions and hen droppings addition significantly produced (P < 0.05) higher corn dry matter. PMID:11315808

  11. The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J × SM/J murine model.

    PubMed

    Lawson, Heather A; Lee, Arthur; Fawcett, Gloria L; Wang, Bing; Pletscher, L Susan; Maxwell, Taylor J; Ehrich, Thomas H; Kenney-Hunt, Jane P; Wolf, Jason B; Semenkovich, Clay F; Cheverud, James M

    2011-04-01

    Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci that affect serum glucose and insulin levels and response to glucose stress in an F(16) Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG,SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We found that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context-dependent and that the same genomic sequence can affect traits differently depending on an individual's sex and/or dietary environment. Our results have important implications for studies of complex traits in humans.

  12. Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench.

    PubMed

    Shiringani, Amukelani Lacrecia; Frisch, Matthias; Friedt, Wolfgang

    2010-07-01

    The productivity of sorghum is mainly determined by quantitative traits such as grain yield and stem sugar-related characteristics. Substantial crop improvement has been achieved by breeding in the last decades. Today, genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement. We have investigated QTL associated with the sugar components (Brix, glucose, sucrose, and total sugar content) and sugar-related agronomic traits (flowering date, plant height, stem diameter, tiller number per plant, fresh panicle weight, and estimated juice weight) in four different environments (two locations) using a population of 188 recombinant inbred lines (RILs) from a cross between grain (M71) and sweet sorghum (SS79). A genetic map with 157 AFLP, SSR, and EST-SSR markers was constructed, and several QTLs were detected using composite interval mapping (CIM). Further, additive x additive interaction and QTL x environmental interaction were estimated. CIM identified more than five additive QTLs in most traits explaining a range of 6.0-26.1% of the phenotypic variation. A total of 24 digenic epistatic locus pairs were identified in seven traits, supporting the hypothesis that QTL analysis without considering epistasis can result in biased estimates. QTLs showing multiple effects were identified, where the major QTL on SBI-06 was significantly associated with most of the traits, i.e., flowering date, plant height, Brix, sucrose, and sugar content. Four out of ten traits studied showed a significant QTL x environmental interaction. Our results are an important step toward marker-assisted selection for sugar-related traits and biofuel yield in sorghum. PMID:20229249

  13. Potentials of engineered nanoparticles as fertilizers for increasing agronomic productions.

    PubMed

    Liu, Ruiqiang; Lal, Rattan

    2015-05-01

    Development and application of new types of fertilizers using innovative nanotechnology are one of the potentially effective options of significantly enhancing the global agricultural productions needed to meet the future demands of the growing population. Indeed, the review of available literature indicates that some engineered nanomaterials can enhance plant-growth in certain concentration ranges and could be used as nanofertilizers in agriculture to increase agronomic yields of crops and/or minimize environmental pollution. This article summarizes this type of nanomaterials under four categories: macronutrient nanofertilizers, micronutrient nanofertilizers, nutrient-loaded nanofertilizers, and plant-growth-enhancing nanomaterials. Each category is discussed respectively with reference to nanomaterials' chemical composition, particle size, concentrations applied, benefited plant species, plant incubation methods, and plant-growth enhancement aspects and the rates. The importance, research directions, and research requirements of each nanofertilizer category for achieving sustainable agriculture are also specifically examined. Finally, this review suggests that development of N and P macronutrient nanofertilizers is a high research and development priority both for food production and environmental protection.

  14. Agronomic characteristics of five different urban waste digestates.

    PubMed

    Tampio, Elina; Salo, Tapio; Rintala, Jukka

    2016-03-15

    The use of digestate in agriculture is an efficient way to recycle materials and to decrease the use of mineral fertilizers. The agronomic characteristics of the digestates can promote plant growth and soil properties after digestate fertilization but also harmful effects can arise due to digestate quality, e.g. pH, organic matter and heavy metal content. The objective of this study was to evaluate the differences and similarities in agronomic characteristics and the value of five urban waste digestates from different biogas plants treating either food waste, organic fraction of organic solid waste or a mixture of waste-activated sludge and vegetable waste. The digestate agronomic characteristics were studied with chemical analyses and the availability of nutrients was also assessed with growth experiments and soil mineralization tests. All studied urban digestates produced 5-30% higher ryegrass yields compared to a control mineral fertilizer with a similar inorganic nitrogen concentration, while the feedstock source affected the agronomic value. Food waste and organic fraction of municipal solid waste digestates were characterized by high agronomic value due to the availability of nutrients and low heavy metal load. Waste-activated sludge as part of the feedstock mixture, however, increased the heavy metal content and reduced nitrogen availability to the plant, thus reducing the fertilizer value of the digestate. PMID:26773433

  15. Agronomic characteristics of five different urban waste digestates.

    PubMed

    Tampio, Elina; Salo, Tapio; Rintala, Jukka

    2016-03-15

    The use of digestate in agriculture is an efficient way to recycle materials and to decrease the use of mineral fertilizers. The agronomic characteristics of the digestates can promote plant growth and soil properties after digestate fertilization but also harmful effects can arise due to digestate quality, e.g. pH, organic matter and heavy metal content. The objective of this study was to evaluate the differences and similarities in agronomic characteristics and the value of five urban waste digestates from different biogas plants treating either food waste, organic fraction of organic solid waste or a mixture of waste-activated sludge and vegetable waste. The digestate agronomic characteristics were studied with chemical analyses and the availability of nutrients was also assessed with growth experiments and soil mineralization tests. All studied urban digestates produced 5-30% higher ryegrass yields compared to a control mineral fertilizer with a similar inorganic nitrogen concentration, while the feedstock source affected the agronomic value. Food waste and organic fraction of municipal solid waste digestates were characterized by high agronomic value due to the availability of nutrients and low heavy metal load. Waste-activated sludge as part of the feedstock mixture, however, increased the heavy metal content and reduced nitrogen availability to the plant, thus reducing the fertilizer value of the digestate.

  16. Transgenic strawberry: state of the art for improved traits.

    PubMed

    Qin, Yonghua; Teixeira da Silva, Jaime A; Zhang, Lingxiao; Zhang, Shanglong

    2008-01-01

    Strawberry (Fragaria x ananassa Duch.), a member of the Rosaceae family, is one of the most important fruit crops cultivated worldwide. Strawberry is unique within the Rosaceae because it is a rapidly growing herbaceous perennial with a small genome, short reproductive cycle, and facile vegetative and generative propagation for genetic transformation. For these reasons, strawberry has been recognized as excellent germplasm for genetic and molecular studies for the Rosaceae family. Although traditional breeding methods have achieved steady improvement in agronomic traits, the lack of useful economic characters still remains a major challenge. Genetic transformation has opened a new era for greater creativity in strawberry breeding and germplasm by offering an effective method for creating new varieties that selectively targets a specific interested gene or a few heterologous traits. Enormous advances have been made in strawberry genetic transformation since the first transgenic strawberry plant was obtained in 1990. This paper reviews recent progress in genetic transformation of strawberry on increasing resistance to viruses, fungi, insects, herbicides, stress, and achieving better quality. Problems and prospects for future applications of genetic transformation in strawberry are also discussed.

  17. Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses

    PubMed Central

    Ramakrishnan, M.; Antony Ceasar, S.; Duraipandiyan, V.; Vinod, K. K.; Kalpana, Krishnan; Al-Dhabi, N. A.; Ignacimuthu, S.

    2016-01-01

    Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal

  18. Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses.

    PubMed

    Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Vinod, K K; Kalpana, Krishnan; Al-Dhabi, N A; Ignacimuthu, S

    2016-01-01

    Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal

  19. Power and Autistic Traits.

    PubMed

    Overskeid, Geir

    2016-01-01

    Autistic traits can help people gain and sustain power, and has probably done so throughout history, says the present paper. A number of testable claims follow from this assumption. First, the powerful should have more autistic traits than others - which they do appear to have. Among other things, powerful people, and those with many autistic traits, tend to prefer solitary activities and are often aloof. Moreover, they are often rigid and socially insensitive, low on empathy and with low scores on the trait of agreeableness - and as a rule they do not have many friends. Both groups are also more self-centered than others, more honest, less submissive, more sensitive to slights, and with a stronger tendency to engage in abstract thinking. They tend to behave in bossy or dominant ways, and their moral judgment is more based on rules than on feelings. In addition to experimental evidence, I cite biographies showing that a surprising number of presidents, prime ministers and other powerful people seem to have had traits like those in question - and interestingly, in animals, leaders are often rigid and insensitive to group members' needs and feelings, mostly acting the way they are themselves inclined to, not responding much to others. Problem solving is important in leadership, and people with many autistic traits appear often to be better thinkers than typical subjects with similar IQs. However, these and other congruities could be coincidences. Hence the question of whether traits the two groups have in common also have a common cause constitutes a strong test of the paper's thesis - and a common cause does appear to exist, in the form of testosterone's effects on the central nervous system. Finally, there is evidence that, other things equal, powerful men have more reproductive success than others. If men wielding power do indeed have more autistic traits than those less powerful, this will lead to, other things equal, such traits becoming more common - which can

  20. Power and Autistic Traits.

    PubMed

    Overskeid, Geir

    2016-01-01

    Autistic traits can help people gain and sustain power, and has probably done so throughout history, says the present paper. A number of testable claims follow from this assumption. First, the powerful should have more autistic traits than others - which they do appear to have. Among other things, powerful people, and those with many autistic traits, tend to prefer solitary activities and are often aloof. Moreover, they are often rigid and socially insensitive, low on empathy and with low scores on the trait of agreeableness - and as a rule they do not have many friends. Both groups are also more self-centered than others, more honest, less submissive, more sensitive to slights, and with a stronger tendency to engage in abstract thinking. They tend to behave in bossy or dominant ways, and their moral judgment is more based on rules than on feelings. In addition to experimental evidence, I cite biographies showing that a surprising number of presidents, prime ministers and other powerful people seem to have had traits like those in question - and interestingly, in animals, leaders are often rigid and insensitive to group members' needs and feelings, mostly acting the way they are themselves inclined to, not responding much to others. Problem solving is important in leadership, and people with many autistic traits appear often to be better thinkers than typical subjects with similar IQs. However, these and other congruities could be coincidences. Hence the question of whether traits the two groups have in common also have a common cause constitutes a strong test of the paper's thesis - and a common cause does appear to exist, in the form of testosterone's effects on the central nervous system. Finally, there is evidence that, other things equal, powerful men have more reproductive success than others. If men wielding power do indeed have more autistic traits than those less powerful, this will lead to, other things equal, such traits becoming more common - which can

  1. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Desirable agronomic traits are similar for common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (Triticum turgidum durum, 2n = 4x = 28, genome, AABB). However, they are genetically isolated from each other due to an unequal number of ge...

  2. Seeds' physicochemical traits and mucilage protection against aluminum effect during germination and root elongation as important factors in a biofuel seed crop (Ricinus communis).

    PubMed

    Silva, Giovanni Eustáquio Alves; Ramos, Flávia Toledo; de Faria, Ana Paula; França, Marcel Giovanni Costa

    2014-10-01

    We determined the length, volume, dry biomass, and density in seeds of five castor bean cultivars and verified notable physicochemical trait differences. Seeds were then subjected to different toxic aluminum (Al) concentrations to evaluate germination, relative root elongation, and the role of root apices' rhizosphere mucilage layer. Seeds' physicochemical traits were associated with Al toxicity responses, and the absence of Al in cotyledons near to the embryo was revealed by Al-hematoxylin staining, indicating that Al did not induce significant germination reduction rates between cultivars. However, in the more sensitive cultivar, Al was found around the embryo, contributing to subsequent growth inhibition. After this, to investigate the role of mucilage in Al tolerance, an assay was conducted using NH4Cl to remove root mucilage before or after exposure to different Al concentrations. Sequentially, the roots were stained with hematoxylin and a quantitative analysis of staining intensity was obtained. These results revealed the significant contribution of the mucilage layer to Al toxicity responses in castor bean seedlings. Root growth elongation under Al toxicity confirmed the role of the mucilage layer, which jointly indicated the differential Al tolerance between cultivars and an efficient Al-exclusion mechanism in the tolerant cultivar.

  3. Biochar: A synthesis of its agronomic impact beyond carbon sequestration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar has been recently heralded as an amendment to revitalize degraded soils, improve soil carbon sequestration, increase agronomic productivity and enter into future carbon trading markets. However, scientific and economic technicalities may limit the ability of biochar to consistently deliver o...

  4. Agronomic performance of five banana cultivars under protected cultivation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Banana has been grown both in open-field and protected cultivation in Turkey. So far protected cultivation is very popular due to the high yield and quality. The objective of the study was to evaluate agronomic performance of five new banana cultivars under plastic greenhouse. ‘MA 13’, ‘Williams’, ‘...

  5. Data access and interchange in agronomic and natural resources management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Challenges related to agriculture and natural resource management have never been greater. Comprehensive agronomic and natural resources data relevant to climate change, food security, bioenergy, and sustainable water supply are rare and in demand. Data used for policy development must be rigorous...

  6. Pattern of Variation of Fruit Traits and Phenol Content in Olive Fruits from Six Different Cultivars.

    PubMed

    Talhaoui, Nassima; Gómez-Caravaca, Ana María; León, Lorenzo; De la Rosa, Raúl; Fernández-Gutiérrez, Alberto; Segura-Carretero, Antonio

    2015-12-01

    In the present study, olive fruits from six cultivars grown under similar agronomical and environmental conditions were collected at four different times during fruit ripening. Some agronomical traits were determined, and general increases in the size of the fruit and oil contents were recorded for all cultivars. The phenolic fraction in fruits was also identified and quantified during the same period using high-performance liquid chromatography-diode array detection-time-of-flight-mass spectrometry. Thus, a total of 57 phenolic compounds were determined, and qualitative and quantitative differences among cultivars and also among sampling times were observed. In contrast to the agronomical traits, a general decrease of total phenolic compounds was observed, characterized by a domination of secoiridoids at the beginning of ripening and by a domination of simple phenols and flavonoids in the end. This is the first time that four of the six cultivars have been studied regarding phenolic compounds evolution during ripening.

  7. Exploring Potential of Pearl Millet Germplasm Association Panel for Association Mapping of Drought Tolerance Traits

    PubMed Central

    Sehgal, Deepmala; Skot, Leif; Singh, Richa; Srivastava, Rakesh Kumar; Das, Sankar Prasad; Taunk, Jyoti; Sharma, Parbodh C.; Pal, Ram; Raj, Bhasker; Hash, Charles T.; Yadav, Rattan S.

    2015-01-01

    A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with ‘stay green’ phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet

  8. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.

    PubMed

    Sehgal, Deepmala; Skot, Leif; Singh, Richa; Srivastava, Rakesh Kumar; Das, Sankar Prasad; Taunk, Jyoti; Sharma, Parbodh C; Pal, Ram; Raj, Bhasker; Hash, Charles T; Yadav, Rattan S

    2015-01-01

    A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet

  9. Biochar: a synthesis of its agronomic impact beyond carbon sequestration.

    PubMed

    Spokas, Kurt A; Cantrell, Keri B; Novak, Jeffrey M; Archer, David W; Ippolito, James A; Collins, Harold P; Boateng, Akwasi A; Lima, Isabel M; Lamb, Marshall C; McAloon, Andrew J; Lentz, Rodrick D; Nichols, Kristine A

    2012-01-01

    Biochar has been heralded as an amendment to revitalize degraded soils, improve soil carbon sequestration, increase agronomic productivity, and enter into future carbon trading markets. However, scientific and economic technicalties may limit the ability of biochar to consistently deliver on these expectations. Past research has demonstrated that biochar is part of the black carbon continuum with variable properties due to the net result of production (e.g., feedstock and pyrolysis conditions) and postproduction factors (storage or activation). Therefore, biochar is not a single entity but rather spans a wide range of black carbon forms. Biochar is black carbon, but not all black carbon is biochar. Agronomic benefits arising from biochar additions to degraded soils have been emphasized, but negligible and negative agronomic effects have also been reported. Fifty percent of the reviewed studies reported yield increases after black carbon or biochar additions, with the remainder of the studies reporting alarming decreases to no significant differences. Hardwood biochar (black carbon) produced by traditional methods (kilns or soil pits) possessed the most consistent yield increases when added to soils. The universality of this conclusion requires further evaluation due to the highly skewed feedstock preferences within existing studies. With global population expanding while the amount of arable land remains limited, restoring soil quality to nonproductive soils could be key to meeting future global food production, food security, and energy supplies; biochar may play a role in this endeavor. Biochar economics are often marginally viable and are tightly tied to the assumed duration of agronomic benefits. Further research is needed to determine the conditions under which biochar can provide economic and agronomic benefits and to elucidate the fundamental mechanisms responsible for these benefits. PMID:22751040

  10. Agronomic Suitability of Bioenergy Crops in Mississippi

    SciTech Connect

    Lemus, Rocky; Baldwin, Brian; Lang, David

    2011-10-01

    ‚€Ã‚¢ How will these crops affect fertilizer use and water quality? • What kind of water management is needed to maintain a productive crop? The answers to these questions will help supporting institutions across the state to improve land assessment and agronomic management practices for biomass production. In the last decade, energy supply has become a worldwide problem. Bioenergy crops could supply energy in the future. Bioenergy crops are plants, usually perennial grasses and trees, that produce a lot of biomass that can be converted into energy. Bioenergy crops can be grown for two energy markets: power generation, such as heat and electricity, or liquid fuel, such as cellulosic ethanol. These resources could reduce petroleum dependency and greenhouse gas production. Woody plants and herbaceous warm-season grasses, such as switchgrass, giant miscanthus,energy cane, and high yielding sorghums, could be major sources of biomass in Mississippi.

  11. The impact of the SSIIa null mutations on grain traits and composition in durum wheat

    PubMed Central

    Botticella, Ermelinda; Sestili, Francesco; Ferrazzano, Gianluca; Mantovani, Paola; Cammerata, Alessandro; D’Egidio, Maria Grazia; Lafiandra, Domenico

    2016-01-01

    Starch represents a major nutrient in the human diet providing essentially a source of energy. More recently the modification of its composition has been associated with new functionalities both at the nutritional and technological level. Targeting the major starch biosynthetic enzymes has been shown to be a valuable strategy to manipulate the amylose-amylopectin ratio in reserve starch. In the present work a breeding strategy aiming to produce a set of SSIIa (starch synthases IIa) null durum wheat is described. We have characterized major traits such as seed weight, total starch, amylose, protein and β-glucan content in a set of mutant families derived from the introgression of the SSIIa null trait into Svevo, an elite Italian durum wheat cultivar. A large degree of variability was detected and used to select wheat lines with either improved quality traits or agronomic performances. Semolina of a set of two SSIIa null lines showed new rheological behavior and an increased content of all major dietary fiber components, namely arabinoxylans, β-glucans and resistant starch. Furthermore the investigation of gene expression highlighted important differences in some genes involved in starch and β-glucans biosynthesis. PMID:27795682

  12. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

    PubMed Central

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  13. Variations with modest effects have an important role in the genetic background of type 2 diabetes and diabetes-related traits.

    PubMed

    Fujita, Hayato; Hara, Kazuo; Shojima, Nobuhiro; Horikoshi, Momoko; Iwata, Minoru; Hirota, Yushi; Tobe, Kazuyuki; Seino, Susumu; Kadowaki, Takashi

    2012-12-01

    The aim of the present study was to explore the role of variations with modest effects (previously identified by a large-scale meta-analysis in European populations) in the genetic background of type 2 diabetes (T2D) and diabetes-related traits in a Japanese population. We enrolled 2632 Japanese subjects with T2D and 2050 non-diabetic subjects. We analyzed nine single-nucleotide polymorphisms (SNPs), including rs340874 (PROX1), rs4607517 (GCK), rs2191349 (DGKB-TMEM195), rs7034200 (GLIS3), rs10885122 (ADRA2A), rs174550 (FADS1), rs11605924 (CRY2), rs10830963 (MTNR1B) and rs35767 (IGF1). rs340874 (PROX1) and rs174550 (FADS1) were significantly associated with T2D (P=0.0078, OR: 1.12; and P=0.0071, OR: 1.12, respectively). Subjects with more risk alleles related to nine SNPs had an increased risk of T2D (P=0.0017), as well as a higher fasting plasma glucose level (P=0.018), higher HbA(1c) level (P=0.013) and lower HOMA-β (P=0.033) compared with subjects who had fewer risk alleles. We identified a significant association of a SNP of FADS1 and a SNP near PROX1 with T2D in a Japanese population. The present findings suggest that inclusion of SNPs with a tendency to increase the disease risk captured more of the genetic background of T2D than that revealed by only assessing significant SNPs.

  14. Agronomic Performance of Low Phytic Acid Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low phytic acid (LPA) genotypes of wheat are one approach to improving the nutritional quality of wheat by reducing the concentration of phytic acid in the aleurone layer, thus reducing the chelation of nutritionally important minerals and improving the bioavailability of phosphorus. Field studies ...

  15. AGRONOMIC PERFORMANCE OF DALLISGRASS TISSUE CULTURE REGENERANTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Common dallisgrass, Paspalum dilatatum, is a pentaploid obligate apomict and efforts to improve this important forage grass have not been successful because of its asexual reproduction and irregular meiosis. An apomictic hexaploid biotype, known as Uruguayan dallisgrass, is a new source of genetic v...

  16. Assessment of anthocyanin and agronomic trait variation in some commonly used medicinal legumes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several legumes including Canavalia ensiformis, Desmodium adscendens, Indigofera suffruticosa, Senna covesii, and S. occidentalis are currently used as medicinal plants. These species contain anthocyanins as well with potential to be used in the pharmaceutical markets. The USDA, ARS, Plant Genetic R...

  17. Efect of tri-species chromosome shuffling on agronomic and fiber traits in Upland cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gossypium barbadense (L.), G. tomentosum (Seem.), G. mustelinum (Watt.) and G. darwinii (Watt.) are in the primary gene pool of Upland cotton (G. hirsutum). They share a common chromosome number (2n=52), similar AD-genome architecture, and form reasonably fertile F1 hybrids. However, reduced transm...

  18. Genomics Tools Available For Unravelling Mechanisms Underlying Agronomical Traits in Strawberry With More To Come

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequen...

  19. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequen...

  20. Disease evaluations and agronomic traits of advanced peanut breeding lines in 2012

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 38 peanut cultivars and high-oleic advanced breeding lines were evaluated in small field plots in 2012 for yield, seed grade and size, and resistance to Sclerotinia minor and Sclerotium rolfsii. Among the 14 Spanish entries, the cultivar Tamnut 06 (3258 lbs/acre) and breeding line 140-1O...

  1. Genetic and agronomic assessment of cob traits in corn under low and normal nitrogen management conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With rising energy demands and costs for fossil fuels, alternative energy from renewable sources such as maize cobs will become competitive. Maize cobs have beneficial characteristics for utilization as feedstock including compact tissue, high cellulose content, and low ash and nitrogen content. Nit...

  2. Genome-wide association studies of morphological and agronomical traits in cultivated tepary beans (Phaseolus acutifolius)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tepary bean (Phaseolus acutifolius A. Gray) is adapted to high temperature arid agroecological zones. In light of the ongoing and rapid changes in the world climate, the evaluation and development of alternate grain legume species that have similar nutritional and culinary characteristics as common ...

  3. Screening of lettuce germplasm for agronomic traits under low water conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    After a preliminary screening of over 3,500 varieties, we selected 200 cultivars of butterhead, cos, crisphead, leaf, and stem lettuce (Lactuca sativa L.) and wild prickly lettuce (Lactuca serriola L.) to test under high water (150% ET) and low water (50% ET) conditions in the field, and tracked com...

  4. Power and Autistic Traits

    PubMed Central

    Overskeid, Geir

    2016-01-01

    Autistic traits can help people gain and sustain power, and has probably done so throughout history, says the present paper. A number of testable claims follow from this assumption. First, the powerful should have more autistic traits than others – which they do appear to have. Among other things, powerful people, and those with many autistic traits, tend to prefer solitary activities and are often aloof. Moreover, they are often rigid and socially insensitive, low on empathy and with low scores on the trait of agreeableness – and as a rule they do not have many friends. Both groups are also more self-centered than others, more honest, less submissive, more sensitive to slights, and with a stronger tendency to engage in abstract thinking. They tend to behave in bossy or dominant ways, and their moral judgment is more based on rules than on feelings. In addition to experimental evidence, I cite biographies showing that a surprising number of presidents, prime ministers and other powerful people seem to have had traits like those in question – and interestingly, in animals, leaders are often rigid and insensitive to group members’ needs and feelings, mostly acting the way they are themselves inclined to, not responding much to others. Problem solving is important in leadership, and people with many autistic traits appear often to be better thinkers than typical subjects with similar IQs. However, these and other congruities could be coincidences. Hence the question of whether traits the two groups have in common also have a common cause constitutes a strong test of the paper’s thesis – and a common cause does appear to exist, in the form of testosterone’s effects on the central nervous system. Finally, there is evidence that, other things equal, powerful men have more reproductive success than others. If men wielding power do indeed have more autistic traits than those less powerful, this will lead to, other things equal, such traits becoming more

  5. Power and Autistic Traits

    PubMed Central

    Overskeid, Geir

    2016-01-01

    Autistic traits can help people gain and sustain power, and has probably done so throughout history, says the present paper. A number of testable claims follow from this assumption. First, the powerful should have more autistic traits than others – which they do appear to have. Among other things, powerful people, and those with many autistic traits, tend to prefer solitary activities and are often aloof. Moreover, they are often rigid and socially insensitive, low on empathy and with low scores on the trait of agreeableness – and as a rule they do not have many friends. Both groups are also more self-centered than others, more honest, less submissive, more sensitive to slights, and with a stronger tendency to engage in abstract thinking. They tend to behave in bossy or dominant ways, and their moral judgment is more based on rules than on feelings. In addition to experimental evidence, I cite biographies showing that a surprising number of presidents, prime ministers and other powerful people seem to have had traits like those in question – and interestingly, in animals, leaders are often rigid and insensitive to group members’ needs and feelings, mostly acting the way they are themselves inclined to, not responding much to others. Problem solving is important in leadership, and people with many autistic traits appear often to be better thinkers than typical subjects with similar IQs. However, these and other congruities could be coincidences. Hence the question of whether traits the two groups have in common also have a common cause constitutes a strong test of the paper’s thesis – and a common cause does appear to exist, in the form of testosterone’s effects on the central nervous system. Finally, there is evidence that, other things equal, powerful men have more reproductive success than others. If men wielding power do indeed have more autistic traits than those less powerful, this will lead to, other things equal, such traits becoming more

  6. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon.

    PubMed

    Argyris, Jason M; Pujol, Marta; Martín-Hernández, Ana Montserrat; Garcia-Mas, Jordi

    2015-09-01

    The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.

  7. Refuges, flower strips, biodiversity and agronomic interest.

    PubMed

    Roy, Grégory; Wateau, Karine; Legrand, Mickaël; Oste, Sandrine

    2008-01-01

    . Results showed that in France it was mainly syrphids that control aphid populations. The choice of flowers Families to include in flower strip is important. You have to avoid choosing the same plant family as the one of the crop you want to protect because you would risk to attract pests and diseases in the field. In fact, it's important to choose the optimal diversity of plant Family and not the greatest diversity.

  8. Interval Mapping of Quantitative Trait Loci Employing Correlated Trait Complexes

    PubMed Central

    Korol, A. B.; Ronin, Y. I.; Kirzhner, V. M.

    1995-01-01

    An approach to increase the resolution power of interval mapping of quantitative trait (QT) loci is proposed, based on analysis of correlated trait complexes. For a given set of QTs, the broad sense heritability attributed to a QT locus (QTL) (say, A/ a) is an increasing function of the number of traits. Thus, for some traits x and y, H(xy)(2) (A/ a) >/= H(x)(2) (A/ a). The last inequality holds even if y does not depend on A/ a at all, but x and y are correlated within the groups AA, Aa and aa due to nongenetic factors and segregation of genes from other chromosomes. A simple relationship connects H(2) (both in single trait and two-trait analysis) with the expected LOD value, ELOD = -1/2N log(1 - H(2)). Thus, situations could exist that from the inequality H(xy)(2) (A/ a) >/= H(x)(2) (A/ a) a higher resolution is provided by the two-trait analysis as compared to the single-trait analysis, in spite of the increased number of parameters. Employing LOD-score procedure to simulated backcross data, we showed that the resolution power of the QTL mapping model can be elevated if correlation between QTs is taken into account. The method allows us to test numerous biologically important hypotheses concerning manifold effects of genomic segments on the defined trait complex (means, variances and correlations). PMID:7672584

  9. Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

    PubMed Central

    Bernardo, Amy; Wang, Shan; St. Amand, Paul; Bai, Guihua

    2015-01-01

    With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat. PMID:26625271

  10. Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid.

    PubMed

    Bhattacharyya, Paromik; Kumaria, Suman; Tandon, Pramod

    2015-09-01

    Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.

  11. Copper accumulation in vineyard soils: Rhizosphere processes and agronomic practices to limit its toxicity.

    PubMed

    Brunetto, Gustavo; Bastos de Melo, George Wellington; Terzano, Roberto; Del Buono, Daniele; Astolfi, Stefania; Tomasi, Nicola; Pii, Youry; Mimmo, Tanja; Cesco, Stefano

    2016-11-01

    Viticulture represents an important agricultural practice in many countries worldwide. Yet, the continuous use of fungicides has caused copper (Cu) accumulation in soils, which represent a major environmental and toxicological concern. Despite being an important micronutrient, Cu can be a potential toxicant at high concentrations since it may cause morphological, anatomical and physiological changes in plants, decreasing both food productivity and quality. Rhizosphere processes can, however, actively control the uptake and translocation of Cu in plants. In particular, root exudates affecting the chemical, physical and biological characteristics of the rhizosphere, might reduce the availability of Cu in the soil and hence its absorption. In addition, this review will aim at discussing the advantages and disadvantages of agronomic practices, such as liming, the use of pesticides, the application of organic matter, biochar and coal fly ashes, the inoculation with bacteria and/or mycorrhizal fungi and the intercropping, in alleviating Cu toxicity symptoms. PMID:27513550

  12. Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

    PubMed

    Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

    2013-04-02

    Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

  13. Path analysis of agro-industrial traits in sweet sorghum.

    PubMed

    Lombardi, G M R; Nunes, J A R; Parrella, R A C; Teixeira, D H L; Bruzi, A T; Durães, N N L; Fagundes, T G

    2015-12-09

    Sweet sorghum has considerable potential for ethanol production due to its succulent stalks that contain directly fermentable sugars. Since many traits need to be considered in the selection process to breed superior cultivars for ethanol production, then correlations between the traits might be of use to help the breeder define optimal improvement strategies. The aim of this study was to investigate the association between the principal agro-industrial traits in sweet sorghum, and to evaluate the direct and indirect effects of primary and secondary traits on ethanol production per hectare. In total, 45 sweet sorghum genotypes (lineage/hybrids) were evaluated in an experiment designed in an alpha lattice 5 x 9. The data were analyzed using a mixed model approach. A detailed study of simple correlations was accomplished using path analysis. The experimental precision was high, with an accuracy above 76%. The various genotypes showed genetic variation for all agronomic and industrial traits, except stalk diameter. Some agro-industrial traits showed significant simple correlations with ethanol production, but according to the path analysis, some of these traits did not show a significant direct or indirect effect on ethanol production. The results highlighted the primary and secondary traits with practical relevance to sweet sorghum breeding, since they showed director indirect effects on ethanol production.

  14. Association of environmental traits with the geographic ranges of ticks (Acari: Ixodidae) of medical and veterinary importance in the western Palearctic. A digital data set.

    PubMed

    Estrada-Peña, A; Farkas, Robert; Jaenson, Thomas G T; Koenen, Frank; Madder, Maxime; Pascucci, Ilaria; Salman, Mo; Tarrés-Call, Jordi; Jongejan, Frans

    2013-03-01

    We compiled information on the distribution of ticks in the western Palearctic (11°W, 45°E; 29°N, 71°N), published during 1970-2010. The literature search was filtered by the tick's species name and an unambiguous reference to the point of capture. Records from some curated collections were included. We focused on tick species of importance to human and animal health, in particular: Ixodes ricinus, Dermacentor marginatus, D. reticulatus, Haemaphysalis punctata, H. sulcata, Hyalomma marginatum, Hy. lusitanicum, Rhipicephalus annulatus, R. bursa, and the R. sanguineus group. A few records of other species (I. canisuga, I. hexagonus, Hy. impeltatum, Hy. anatolicum, Hy. excavatum, Hy. scupense) were also included. A total of 10,280 records was included in the data set. Almost 42 % of published references are not adequately referenced (and not included in the data set), host is reported for only 61 % of records and a reference to time of collection is missed for 84 % of published records. Ixodes ricinus accounted for 44.3 % of total records, with H. marginatum and D. marginatus accounting for 7.1 and 8.1 % of records, respectively. The lack of homogeneity of the references and potential pitfalls in the compilation were addressed to create a digital data set of the records of the ticks. We attached to every record a coherent set of quantitative descriptors for the site of reporting, namely gridded interpolated monthly climate and remotely sensed data on vegetation (NDVI). We also attached categorical descriptors of the habitat: a standard classification of land biomes and an ad hoc classification of the target territory from remotely sensed temperature and NDVI data. A descriptive analysis of the data revealed that a principal components reduction of the environmental (temperature and NDVI) variables described the distribution of the species in the target territory. However, categorical descriptors of the habitat were less effective. We stressed the importance of

  15. Geographic Variation in the Acoustic Traits of Greater Horseshoe Bats: Testing the Importance of Drift and Ecological Selection in Evolutionary Processes

    PubMed Central

    Sun, Keping; Luo, Li; Kimball, Rebecca T.; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Li, Guohong; Feng, Jiang

    2013-01-01

    Patterns of intraspecific geographic variation of signaling systems provide insight into the microevolutionary processes driving phenotypic divergence. The acoustic calls of bats are sensitive to diverse evolutionary forces, but processes that shape call variation are largely unexplored. In China, Rhinolophus ferrumequinum displays a diverse call frequency and inhabits a heterogeneous landscape, presenting an excellent opportunity for this kind of research. We quantified geographic variation in resting frequency (RF) of echolocation calls, estimated genetic structure and phylogeny of R. ferrumequinum populations, and combined this with climatic factors to test three hypotheses to explain acoustic variation: genetic drift, cultural drift, and local adaptation. Our results demonstrated significant regional divergence in frequency and phylogeny among the bat populations in China's northeast (NE), central-east (CE) and southwest (SW) regions. The CE region had higher frequencies than the NE and SW regions. Drivers of RF divergence were estimated in the entire range and just the CE/NE region (since these two regions form a clade). In both cases, RF divergence was not correlated with mtDNA or nDNA genetic distance, but was significantly correlated with geographic distance and mean annual temperature, indicating cultural drift and ecological selection pressures are likely important in shaping RF divergence among different regions in China. PMID:23950926

  16. Fate of atrazine in a soil under different agronomic management practices.

    PubMed

    Prado, B; Fuentes, M; Verhulst, N; Govaerts, B; De León, F; Zamora, O

    2014-01-01

    Agricultural management affects the movement of atrazine in soil and leaching to groundwater. The objective of this study was to determine atrazine adsorption in a soil after 20 years of atrazine application under agronomic management practices differing in tillage practice (conventional and zero tillage), residue management (with and without residue retention) and crop rotation (wheat-maize rotation and maize monoculture). Atrazine sorption was determined using batch and column experiments. In the batch experiment, the highest distribution coefficient Kd (1.1 L kg(-1)) at 0-10 cm soil depth was observed under zero tillage, crop rotation and residue retention (conservation agriculture). The key factor in adsorption was soil organic matter content and type. This was confirmed in the column experiment, in which the highest Kd values were observed in treatments with residue retention, under either zero or conventional tillage (0.81 and 0.68 L kg(-1), respectively). Under zero tillage, the fact that there was no soil movement helped to increase the Kd. The increased soil organic matter content with conservation agriculture may be more important than preferential flow due to higher pore connectivity in the same system. The soil's capacity to adsorb 2-hydroxyatrazine (HA), an important atrazine metabolite, was more important than its capacity to adsorb atrazine, and was similar under all four management practices (Kd ranged from 30 to 40 L kg(-1)). The HA adsorption was attributed to the type and amount of clay in the soil, which is unaffected by agronomic management. Soils under conservation agriculture had higher atrazine retention potential than soils under conventional tillage, the system that predominates in the study area. PMID:25190559

  17. Increased intracellular calcium level and impaired nutrient absorption are important pathogenicity traits in the chicken intestinal epithelium during Campylobacter jejuni colonization.

    PubMed

    Awad, Wageha A; Smorodchenko, Alina; Hess, Claudia; Aschenbach, Jörg R; Molnár, Andor; Dublecz, Károly; Khayal, Basel; Pohl, Elena E; Hess, Michael

    2015-08-01

    intestinal function, performance, and Campylobacter colonization. Altogether, these findings indicate that Campylobacter is not entirely a commensal and can be recognized as an important factor contributing to an impaired chicken gut health.

  18. Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics

    PubMed Central

    Studholme, David J.; Harris, Beverley; Le Cocq, Kate; Winsbury, Rebecca; Perera, Venura; Ryder, Lauren; Ward, Jane L.; Beale, Michael H.; Thornton, Chris R.; Grant, Murray

    2013-01-01

    Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits. PMID:23908658

  19. Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.).

    PubMed

    Mandel, Jennifer R; McAssey, Edward V; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M

    2014-01-01

    Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations. PMID:24914686

  20. Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

    PubMed

    Studholme, David J; Harris, Beverley; Le Cocq, Kate; Winsbury, Rebecca; Perera, Venura; Ryder, Lauren; Ward, Jane L; Beale, Michael H; Thornton, Chris R; Grant, Murray

    2013-01-01

    Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.

  1. Molecular Evolution of Candidate Genes for Crop-Related Traits in Sunflower (Helianthus annuus L.)

    PubMed Central

    Mandel, Jennifer R.; McAssey, Edward V.; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M.

    2014-01-01

    Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations. PMID:24914686

  2. The agronomic science of spatial and temporal water management:How much, when and where

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The agronomic sciences are those that are applied to soil and water management and crop production, including soil, water and plant sciences and related disciplines. The science of spatial and temporal water management includes many agronomic science factors, including soil physics, biophysics, plan...

  3. Influence of Agronomic and Climatic Factors on Fusarium Infestation and Mycotoxin Contamination of Cereals in Norway

    PubMed Central

    Bernhoft, A.; Torp, M.; Clasen, P.-E.; Løes, A.-K.; Kristoffersen, A.B.

    2012-01-01

    A total of 602 samples of organically and conventionally grown barley, oats and wheat was collected at grain harvest during 2002–2004 in Norway. Organic and conventional samples were comparable pairs regarding cereal species, growing site and harvest time, and were analysed for Fusarium mould and mycotoxins. Agronomic and climatic factors explained 10–30% of the variation in Fusarium species and mycotoxins. Significantly lower Fusarium infestation and concentrations of important mycotoxins were found in the organic cereals. The mycotoxins deoxynivalenol (DON) and HT-2 toxin (HT-2) constitute the main risk for human and animal health in Norwegian cereals. The impacts of various agronomic and climatic factors on DON and HT-2 as well as on their main producers F. graminearum and F. langsethiae and on total Fusarium were tested by multivariate statistics. Crop rotation with non-cereals was found to reduce all investigated characteristics significantly – mycotoxin concentrations as well as various Fusarium infestations. No use of mineral fertilisers and herbicides was also found to decrease F. graminearum, whereas lodged fields increased the occurrence of this species. No use of herbicides was also found to decrease F. langsethiae, but for this species the occurrence was lower in lodged fields. Total Fusarium infestation was decreased with no use of fungicides or mineral fertilisers, and with crop rotation, as well as by using herbicides and increased by lodged fields. Clay and to some extent silty soils seemed to reduce F. graminearum in comparison with sandy soils. Concerning climate factors, low temperature before grain harvest was found to increase DON; and high air humidity before harvest to increase HT-2. F. graminearum was negatively correlated with precipitation in July but correlated with air humidity before harvest. F. langsethiae was correlated with temperature in July. Total Fusarium increased with increasing precipitation in July. Organic cereal

  4. Influence of agronomic and climatic factors on Fusarium infestation and mycotoxin contamination of cereals in Norway.

    PubMed

    Bernhoft, A; Torp, M; Clasen, P-E; Løes, A-K; Kristoffersen, A B

    2012-01-01

    A total of 602 samples of organically and conventionally grown barley, oats and wheat was collected at grain harvest during 2002-2004 in Norway. Organic and conventional samples were comparable pairs regarding cereal species, growing site and harvest time, and were analysed for Fusarium mould and mycotoxins. Agronomic and climatic factors explained 10-30% of the variation in Fusarium species and mycotoxins. Significantly lower Fusarium infestation and concentrations of important mycotoxins were found in the organic cereals. The mycotoxins deoxynivalenol (DON) and HT-2 toxin (HT-2) constitute the main risk for human and animal health in Norwegian cereals. The impacts of various agronomic and climatic factors on DON and HT-2 as well as on their main producers F. graminearum and F. langsethiae and on total Fusarium were tested by multivariate statistics. Crop rotation with non-cereals was found to reduce all investigated characteristics significantly--mycotoxin concentrations as well as various Fusarium infestations. No use of mineral fertilisers and herbicides was also found to decrease F. graminearum, whereas lodged fields increased the occurrence of this species. No use of herbicides was also found to decrease F. langsethiae, but for this species the occurrence was lower in lodged fields. Total Fusarium infestation was decreased with no use of fungicides or mineral fertilisers, and with crop rotation, as well as by using herbicides and increased by lodged fields. Clay and to some extent silty soils seemed to reduce F. graminearum in comparison with sandy soils. Concerning climate factors, low temperature before grain harvest was found to increase DON; and high air humidity before harvest to increase HT-2. F. graminearum was negatively correlated with precipitation in July but correlated with air humidity before harvest. F. langsethiae was correlated with temperature in July. Total Fusarium increased with increasing precipitation in July. Organic cereal farmers have

  5. Phylogenetic conservatism of functional traits in microorganisms.

    PubMed

    Martiny, Adam C; Treseder, Kathleen; Pusch, Gordon

    2013-04-01

    A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

  6. Automatic detection and agronomic characterization of olive groves using high-resolution imagery and LIDAR data

    NASA Astrophysics Data System (ADS)

    Caruso, T.; Rühl, J.; Sciortino, R.; Marra, F. P.; La Scalia, G.

    2014-10-01

    The Common Agricultural Policy of the European Union grants subsidies for olive production. Areas of intensified olive farming will be of major importance for the increasing demand for oil production of the next decades, and countries with a high ratio of intensively and super-intensively managed olive groves will be more competitive than others, since they are able to reduce production costs. It can be estimated that about 25-40% of the Sicilian oliviculture must be defined as "marginal". Modern olive cultivation systems, which permit the mechanization of pruning and harvest operations, are limited. Agronomists, landscape planners, policy decision-makers and other professionals have a growing need for accurate and cost-effective information on land use in general and agronomic parameters in the particular. The availability of high spatial resolution imagery has enabled researchers to propose analysis tools on agricultural parcel and tree level. In our study, we test the performance of WorldView-2 imagery relative to the detection of olive groves and the delineation of olive tree crowns, using an object-oriented approach of image classification in combined use with LIDAR data. We selected two sites, which differ in their environmental conditions and in their agronomic parameters of olive grove cultivation. The main advantage of the proposed methodology is the low necessary quantity of data input and its automatibility. However, it should be applied in other study areas to test if the good results of accuracy assessment can be confirmed. Data extracted by the proposed methodology can be used as input data for decision-making support systems for olive grove management.

  7. Agronomic conditions and crop evolution in ancient Near East agriculture

    PubMed Central

    Aguilera, Mònica; Buxó, Ramón

    2014-01-01

    The appearance of agriculture in the Fertile Crescent has propelled the development of Western civilization. Here we investigate the evolution of agronomic conditions in this region by reconstructing cereal kernel weight and using stable carbon and nitrogen isotope signatures of kernels and charcoal from a set of 11 Upper Mesopotamia archaeological sites, with chronologies spanning from the onset of agriculture to the turn of the era. We show that water availability for crops, inferred from carbon isotope discrimination (Δ13C), was two- to fourfold higher in the past than at present, with a maximum between 10,000 and 8,000 cal BP. Nitrogen isotope composition (δ15N) decreased over time, which suggests cultivation occurring under gradually less fertile soil conditions. Domesticated cereals showed a progressive increase in kernel weight over several millennia following domestication. Our results provide a first comprehensive view of agricultural evolution in the Near East inferred directly from archaeobotanical remains. PMID:24853475

  8. Agronomic conditions and crop evolution in ancient Near East agriculture.

    PubMed

    Araus, José L; Ferrio, Juan P; Voltas, Jordi; Aguilera, Mònica; Buxó, Ramón

    2014-05-23

    The appearance of agriculture in the Fertile Crescent propelled the development of Western civilization. Here we investigate the evolution of agronomic conditions in this region by reconstructing cereal kernel weight and using stable carbon and nitrogen isotope signatures of kernels and charcoal from a set of 11 Upper Mesopotamia archaeological sites, with chronologies spanning from the onset of agriculture to the turn of the era. We show that water availability for crops, inferred from carbon isotope discrimination (Δ(13)C), was two- to fourfold higher in the past than at present, with a maximum between 10,000 and 8,000 cal BP. Nitrogen isotope composition (δ(15)N) decreased over time, which suggests cultivation occurring under gradually less-fertile soil conditions. Domesticated cereals showed a progressive increase in kernel weight over several millennia following domestication. Our results provide a first comprehensive view of agricultural evolution in the Near East inferred directly from archaeobotanical remains.

  9. Agronomic conditions and crop evolution in ancient Near East agriculture.

    PubMed

    Araus, José L; Ferrio, Juan P; Voltas, Jordi; Aguilera, Mònica; Buxó, Ramón

    2014-01-01

    The appearance of agriculture in the Fertile Crescent propelled the development of Western civilization. Here we investigate the evolution of agronomic conditions in this region by reconstructing cereal kernel weight and using stable carbon and nitrogen isotope signatures of kernels and charcoal from a set of 11 Upper Mesopotamia archaeological sites, with chronologies spanning from the onset of agriculture to the turn of the era. We show that water availability for crops, inferred from carbon isotope discrimination (Δ(13)C), was two- to fourfold higher in the past than at present, with a maximum between 10,000 and 8,000 cal BP. Nitrogen isotope composition (δ(15)N) decreased over time, which suggests cultivation occurring under gradually less-fertile soil conditions. Domesticated cereals showed a progressive increase in kernel weight over several millennia following domestication. Our results provide a first comprehensive view of agricultural evolution in the Near East inferred directly from archaeobotanical remains. PMID:24853475

  10. Spectral-agronomic relationships of corn, soybean and wheat canopies

    NASA Technical Reports Server (NTRS)

    Bauer, M. E. (Principal Investigator); Daughtry, C. S. T.; Vanderbilt, V. C.

    1981-01-01

    During the past six years several thousand reflectance spectra of corn, soybean, and wheat canopies were acquired and analyzed. The relationships of biophysical variables, including leaf area index, percent soil cover, chlorophyll and water content, to the visible and infrared reflectance of canopies are described. The effects on reflectance of cultural, environmental, and stress factors such as planting data, seeding rate, row spacing, cultivar, soil type and nitrogen fertilization are also examined. The conclusions are that several key agronomic variables including leaf area index, development stage and degree of stress are strongly related to spectral reflectance and that it should be possible to estimate these descriptions of crop condition from satellite acquired multispectral data.

  11. Characterization of selenium-enriched wheat by agronomic biofortification.

    PubMed

    Galinha, Catarina; Sánchez-Martínez, María; Pacheco, Adriano M G; Freitas, Maria do Carmo; Coutinho, José; Maçãs, Benvindo; Almeida, Ana Sofia; Pérez-Corona, María Teresa; Madrid, Yolanda; Wolterbeek, Hubert T

    2015-07-01

    Agronomic biofortification of staple crops is an effective way to enhance their contents in essential nutrients up the food chain, with a view to correcting for their deficiencies in animal or human status. Selenium (Se) is one such case, for its uneven distribution in the continental crust and, therefore, in agricultural lands easily translates into substantial variation in nutritional intakes. Cereals are far from being the main sources of Se on a content basis, but they are likely the major contributors to intake on a dietary basis. To assess their potential to assimilate and biotransform Se, bread and durum wheat were enriched with Se through foliar and soil addition at an equivalent field rate of 100 g of Se per hectare (ha), using sodium selenate and sodium selenite as Se-supplementation matrices, in actual field conditions throughout. Biotransformation of inorganic Se was evaluated by using HPLC-ICP-MS after enzymatic hydrolysis for Se-species extraction in the resulting mature wheat grains. Selenomethionine and Se(VI) were identified and quantified: the former was the predominant species, representing 70-100 % of the total Se in samples; the maximum amount of inorganic Se was below 5 %. These results were similar for both supplementation methods and for both wheat varieties. Judging from the present results, one can conclude that agronomic biofortification of wheat may improve the nutritional quality of wheat grains with significant amounts of selenomethionine, which is an attractive option for increasing the Se status in human diets through Se-enriched, wheat-based foodstuff.

  12. Propagation Techniques and Agronomic Requirements for the Cultivation of Barbados Aloe (Aloe vera (L.) Burm. F.)—A Review

    PubMed Central

    Cristiano, Giuseppe; Murillo-Amador, Bernardo; De Lucia, Barbara

    2016-01-01

    Barbados aloe (Aloe vera (L.) Burm. F.) has traditionally been used for healing in natural medicine. However, aloe is now attracting great interest in the global market due to its bioactive chemicals which are extracted from the leaves and used in industrial preparations for pharmaceutical, cosmetic, and food products. Aloe originated from tropical and sub-tropical Africa, but it is also now cultivated in warm climatic areas of Asia, Europe, and America. In this review, the most important factors affecting aloe production are described. We focus on propagation techniques, sustainable agronomic practices and efficient post harvesting and processing systems. PMID:27721816

  13. Sickle Cell Trait

    MedlinePlus

    ... About Us Information For... Media Policy Makers Sickle Cell Trait Language: English Español (Spanish) Recommend on Facebook ... the trait on to their children. How Sickle Cell Trait is Inherited If both parents have SCT, ...

  14. The Trait in Latent Trait Theory.

    ERIC Educational Resources Information Center

    Levine, Michael V.

    Significant to a latent trait or item response theory analysis of a mental test is the determination of exactly what is being quantified. The following are practical problems to be considered in the formulation of a good theory: (1) deciding whether two tests measure the same trait or traits; (2) analyzing the relative contributions of a pair of…

  15. Importance of Macrophyte Quality in Determining Life-History Traits of the Apple Snails Pomacea canaliculata: Implications for Bottom-Up Management of an Invasive Herbivorous Pest in Constructed Wetlands

    PubMed Central

    Yam, Rita S. W.; Fan, Yen-Tzu; Wang, Tzu-Ting

    2016-01-01

    Pomacea canaliculata (Ampullariidae) has extensively invaded most Asian constructed wetlands and its massive herbivory of macrophytes has become a major cause of ecosystem dysfunctioning of these restored habitats. We conducted non-choice laboratory feeding experiments of P. canaliculata using five common macrophyte species in constructed wetlands including Ipomoea aquatica, Commelina communis, Nymphoides coreana, Acorus calamus and Phragmites australis. Effects of macrophytes on snail feeding, growth and fecundity responses were evaluated. Results indicated that P. canaliculata reared on Ipomoea had the highest feeding and growth rates with highest reproductive output, but all individuals fed with Phragmites showed lowest feeding rates and little growth with poorest reproductive output. Plant N and P contents were important for enhancing palatability, supporting growth and offspring quantity of P. canaliculata, whilst toughness, cellulose and phenolics had critically deterrent effects on various life-history traits. Although snail offspring quality was generally consistent regardless of maternal feeding conditions, the reduced growth and offspring quantity of the poorly-fed snails in constructed wetlands dominated by the less-palatable macrophytes could limit the invasive success of P. canaliculata. Effective bottom-up control of P. canaliculata in constructed wetlands should involve selective planting strategy using macrophytes with low nutrient and high toughness, cellulose and phenolic contents. PMID:26927135

  16. Importance of Macrophyte Quality in Determining Life-History Traits of the Apple Snails Pomacea canaliculata: Implications for Bottom-Up Management of an Invasive Herbivorous Pest in Constructed Wetlands.

    PubMed

    Yam, Rita S W; Fan, Yen-Tzu; Wang, Tzu-Ting

    2016-02-24

    Pomacea canaliculata (Ampullariidae) has extensively invaded most Asian constructed wetlands and its massive herbivory of macrophytes has become a major cause of ecosystem dysfunctioning of these restored habitats. We conducted non-choice laboratory feeding experiments of P. canaliculata using five common macrophyte species in constructed wetlands including Ipomoea aquatica, Commelina communis, Nymphoides coreana, Acorus calamus and Phragmites australis. Effects of macrophytes on snail feeding, growth and fecundity responses were evaluated. Results indicated that P. canaliculata reared on Ipomoea had the highest feeding and growth rates with highest reproductive output, but all individuals fed with Phragmites showed lowest feeding rates and little growth with poorest reproductive output. Plant N and P contents were important for enhancing palatability, supporting growth and offspring quantity of P. canaliculata, whilst toughness, cellulose and phenolics had critically deterrent effects on various life-history traits. Although snail offspring quality was generally consistent regardless of maternal feeding conditions, the reduced growth and offspring quantity of the poorly-fed snails in constructed wetlands dominated by the less-palatable macrophytes could limit the invasive success of P. canaliculata. Effective bottom-up control of P. canaliculata in constructed wetlands should involve selective planting strategy using macrophytes with low nutrient and high toughness, cellulose and phenolic contents.

  17. Correlations between traits in soybean (Glycine max L.) naturally infected with Asian rust (Phakopsora pachyrhizi).

    PubMed

    Rodrigues, B; Serafim, F; Nogueira, A P O; Hamawaki, O T; de Sousa, L B; Hamawaki, R L

    2015-12-22

    Soybean (Glycine max L.)-breeding programs aim to develop cultivars with high grain yields and high tolerance to Asian soybean rust (Phakopsora pachyrhizi). Considering that the traits targeted for breeding are mainly quantitative in nature, knowledge of associations between traits allows the breeder to formulate indirect selection strategies. In this study, we investigated phenotypic, genotypic, and environmental correlations between the agronomic traits of soybean plants naturally infected with P. pachyrhizi, and identified agronomic traits that would be useful in indirectly selecting soybean genotypes for high yields. The study was conducted on the Capim Branco Farm, Uberlândia, Brazil, with 15 soybean genotypes, which were cultivated in a completely randomized block design with four replications. Fourteen phenotypic traits were evaluated using the GENES software. The phenotypic and genotypic correlations were positive and of a high magnitude between the total number of pods and the number of pods with two or three grains, indicating that the total number of pods is a useful trait for the indirect selection of soybean genotypes for high grain yields. Strong environmental correlations were found between plant height at blooming and maturity and grain yield and yield components.

  18. Biological Implications in Cassava for the Production of Amylose-Free Starch: Impact on Root Yield and Related Traits

    PubMed Central

    Karlström, Amanda; Calle, Fernando; Salazar, Sandra; Morante, Nelson; Dufour, Dominique; Ceballos, Hernán

    2016-01-01

    Cassava (Manihot esculenta, Crantz) is an important food security crop, but it is becoming an important raw material for different industrial applications. Cassava is the second most important source of starch worldwide. Novel starch properties are of interest to the starch industry, and one them is the recently identified amylose-free (waxy) cassava starch. Waxy mutants have been found in different crops and have been often associated with a yield penalty. There are ongoing efforts to develop commercial cassava varieties with amylose-free starch. However, little information is available regarding the biological and agronomic implications of starch mutations in cassava, nor in other root and tuber crops. In this study, siblings from eight full-sib families, segregating for the waxy trait, were used to determine if the mutation has implications for yield, dry matter content (DMC) and harvest index in cassava. A total of 87 waxy and 87 wild-type starch genotypes from the eight families were used in the study. The only significant effect of starch type was on DMC (p < 0.01), with waxy clones having a 0.8% lower content than their wild type counterparts. There was no effect of starch type on fresh root yield (FRY), adjusted FRY and harvest index. It is not clear if lower DMC is a pleiotropic effect of the waxy starch mutation or else the result of linked genes introgressed along with the mutation. It is expected that commercial waxy cassava varieties will have competitive FRYs but special efforts will be required to attain adequate DMCs. This study contributes to the limited knowledge available of the impact of starch mutations on the agronomic performance of root and tuber crops. PMID:27242813

  19. Biological Implications in Cassava for the Production of Amylose-Free Starch: Impact on Root Yield and Related Traits.

    PubMed

    Karlström, Amanda; Calle, Fernando; Salazar, Sandra; Morante, Nelson; Dufour, Dominique; Ceballos, Hernán

    2016-01-01

    Cassava (Manihot esculenta, Crantz) is an important food security crop, but it is becoming an important raw material for different industrial applications. Cassava is the second most important source of starch worldwide. Novel starch properties are of interest to the starch industry, and one them is the recently identified amylose-free (waxy) cassava starch. Waxy mutants have been found in different crops and have been often associated with a yield penalty. There are ongoing efforts to develop commercial cassava varieties with amylose-free starch. However, little information is available regarding the biological and agronomic implications of starch mutations in cassava, nor in other root and tuber crops. In this study, siblings from eight full-sib families, segregating for the waxy trait, were used to determine if the mutation has implications for yield, dry matter content (DMC) and harvest index in cassava. A total of 87 waxy and 87 wild-type starch genotypes from the eight families were used in the study. The only significant effect of starch type was on DMC (p < 0.01), with waxy clones having a 0.8% lower content than their wild type counterparts. There was no effect of starch type on fresh root yield (FRY), adjusted FRY and harvest index. It is not clear if lower DMC is a pleiotropic effect of the waxy starch mutation or else the result of linked genes introgressed along with the mutation. It is expected that commercial waxy cassava varieties will have competitive FRYs but special efforts will be required to attain adequate DMCs. This study contributes to the limited knowledge available of the impact of starch mutations on the agronomic performance of root and tuber crops. PMID:27242813

  20. Biological Implications in Cassava for the Production of Amylose-Free Starch: Impact on Root Yield and Related Traits.

    PubMed

    Karlström, Amanda; Calle, Fernando; Salazar, Sandra; Morante, Nelson; Dufour, Dominique; Ceballos, Hernán

    2016-01-01

    Cassava (Manihot esculenta, Crantz) is an important food security crop, but it is becoming an important raw material for different industrial applications. Cassava is the second most important source of starch worldwide. Novel starch properties are of interest to the starch industry, and one them is the recently identified amylose-free (waxy) cassava starch. Waxy mutants have been found in different crops and have been often associated with a yield penalty. There are ongoing efforts to develop commercial cassava varieties with amylose-free starch. However, little information is available regarding the biological and agronomic implications of starch mutations in cassava, nor in other root and tuber crops. In this study, siblings from eight full-sib families, segregating for the waxy trait, were used to determine if the mutation has implications for yield, dry matter content (DMC) and harvest index in cassava. A total of 87 waxy and 87 wild-type starch genotypes from the eight families were used in the study. The only significant effect of starch type was on DMC (p < 0.01), with waxy clones having a 0.8% lower content than their wild type counterparts. There was no effect of starch type on fresh root yield (FRY), adjusted FRY and harvest index. It is not clear if lower DMC is a pleiotropic effect of the waxy starch mutation or else the result of linked genes introgressed along with the mutation. It is expected that commercial waxy cassava varieties will have competitive FRYs but special efforts will be required to attain adequate DMCs. This study contributes to the limited knowledge available of the impact of starch mutations on the agronomic performance of root and tuber crops.

  1. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm.

    PubMed

    Abdurakhmonov, Ibrokhim Y; Saha, Sukumar; Jenkins, Jonnie N; Buriev, Zabardast T; Shermatov, Shukhrat E; Scheffler, Brain E; Pepper, Alan E; Yu, John Z; Kohel, Russell J; Abdukarimov, Abdusattor

    2009-07-01

    Cotton is the world's leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r (2) >or= 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r (2) >or= 0.2 was reduced to approximately 5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at 'moderate to strong' and 'strong to very strong' evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources. PMID:19067183

  2. Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects.

    PubMed Central

    Melchinger, A E; Utz, H F; Schön, C C

    1998-01-01

    The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples N = 344 and 107 of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL x environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS. PMID:9584111

  3. Multi-trait mimicry and the relative salience of individual traits.

    PubMed

    Kazemi, Baharan; Gamberale-Stille, Gabriella; Leimar, Olof

    2015-11-01

    Mimicry occurs when one species gains protection from predators by resembling an unprofitable model species. The degree of mimic-model similarity is variable in nature and is closely related to the number of traits that the mimic shares with its model. Here, we experimentally test the hypothesis that the relative salience of traits, as perceived by a predator, is an important determinant of the degree of mimic-model similarity required for successful mimicry. We manipulated the relative salience of the traits of a two-trait artificial model prey, and subsequently tested the survival of mimics of the different traits. The unrewarded model prey had two colour traits, black and blue, and the rewarded prey had two combinations of green, brown and grey shades. Blue tits were used as predators. We found that the birds perceived the black and blue traits to be similarly salient in one treatment, and mimic-model similarity in both traits was then required for high mimic success. In a second treatment, the blue trait was the most salient trait, and mimic-model similarity in this trait alone achieved high success. Our results thus support the idea that similar salience of model traits can explain the occurrence of multi-trait mimicry.

  4. Genetic variation for dry matter yield, forage quality, and seed traits among the half-sib progency of nine orchardgrass germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A potential strategy to address the lack of success of North American orchardgrass (Dactylis glomerata L.) breeding programs to increase forage yield and other agronomic traits is the incorporation of novel sources of germplasm. In an attempt to identify novel orchardgrass germplasm sources with ag...

  5. Linkages Among Agronomic, Environmental and Weed Management Characteristics in North American Sweet Corn

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Performance of weed management systems varies greatly across the landscape in both growers’ fields and in experimental trials conducted by agricultural scientists. Using agronomic, environmental, and weed management information from growers’ fields and experimental trials, we identified dominant ch...

  6. I.4 Screening Experimental Designs for Quantitative Trait Loci, Association Mapping, Genotype-by Environment Interaction, and Other Investigations

    PubMed Central

    Federer, Walter T.; Crossa, José

    2012-01-01

    Crop breeding programs using conventional approaches, as well as new biotechnological tools, rely heavily on data resulting from the evaluation of genotypes in different environmental conditions (agronomic practices, locations, and years). Statistical methods used for designing field and laboratory trials and for analyzing the data originating from those trials need to be accurate and efficient. The statistical analysis of multi-environment trails (MET) is useful for assessing genotype × environment interaction (GEI), mapping quantitative trait loci (QTLs), and studying QTL × environment interaction (QEI). Large populations are required for scientific study of QEI, and for determining the association between molecular markers and quantitative trait variability. Therefore, appropriate control of local variability through efficient experimental design is of key importance. In this chapter we present and explain several classes of augmented designs useful for achieving control of variability and assessing genotype effects in a practical and efficient manner. A popular procedure for unreplicated designs is the one known as “systematically spaced checks.” Augmented designs contain “c” check or standard treatments replicated “r” times, and “n” new treatments or genotypes included once (usually) in the experiment. PMID:22675304

  7. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

    PubMed Central

    Pauli, Duke; Andrade-Sanchez, Pedro; Carmo-Silva, A. Elizabete; Gazave, Elodie; French, Andrew N.; Heun, John; Hunsaker, Douglas J.; Lipka, Alexander E.; Setter, Tim L.; Strand, Robert J.; Thorp, Kelly R.; Wang, Sam; White, Jeffrey W.; Gore, Michael A.

    2016-01-01

    The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010–2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars. PMID:26818078

  8. Agronomic and environmental implications of enhanced s-triazine degradation

    USGS Publications Warehouse

    Krutz, L. J.; Dale L. Shaner,; Mark A. Weaver,; Webb, Richard M.; Zablotowicz, Robert M.; Reddy, Krishna N.; Huang, Y.; Thompson, S. J.

    2010-01-01

    Novel catabolic pathways enabling rapid detoxification of s-triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s-triazine mineralization, i.e. atzABCDEF and trzNDF, occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s-triazine herbicides for weed control, and, with the exception of acidic soil conditions and s-triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s-triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s-triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s-triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted. 

  9. Organic complexed superphosphates (CSP): physicochemical characterization and agronomical properties.

    PubMed

    Erro, Javier; Urrutia, Oscar; Baigorri, Roberto; Aparicio-Tejo, Pedro; Irigoyen, Ignacio; Storino, Francesco; Torino, Francesco; Mandado, Marcos; Yvin, Jean Claude; Garcia-Mina, Jose M

    2012-02-29

    A new type of superphosphate (organic complexed superphosphate (CSP)) has been developed by the introduction of organic chelating agents, preferably a humic acid (HA), into the chemical reaction of single superphosphate (SSP) production. This modification yielded a product containing monocalcium phosphate complexed by the chelating organic agent through Ca bridges. Theoretically, the presence of these monocalcium-phosphate-humic complexes (MPHC) inhibits phosphate fixation in soil, thus increasing P fertilizer efficiency. This study investigateed the structural and functional features of CSP fertilizers produced employing diverse HA with different structural features. To this end were used complementary analytical techniques: solid-phase ³¹P NMR, ¹³C NMR, laser-confocal microscopy, X-ray diffraction, and molecular modeling. Finally, the agronomical efficiency of four CSP have been compared with that of SSP as P sources for wheat plants grown in both alkaline and acidic soils in greenhouse pot trials under controlled conditions. The results obtained from the diverse analytical studies showed the formation of MPHC in CSP. Plant-soil studies showed that CSP products were more efficient than SSP in providing available phosphate for wheat plants cultivated in various soils with different physicochemical features. This fact is probably associated with the ability of CSP complexes to inhibit phosphate fixation in soil. PMID:22300509

  10. TaER Expression Is Associated with Transpiration Efficiency Traits and Yield in Bread Wheat.

    PubMed

    Zheng, Jiacheng; Yang, Zhiyuan; Madgwick, Pippa J; Carmo-Silva, Elizabete; Parry, Martin A J; Hu, Yin-Gang

    2015-01-01

    that TaER could be exploitable for manipulating important agronomical traits in wheat improvement.

  11. Uncertainty quantified trait predictions

    NASA Astrophysics Data System (ADS)

    Fazayeli, Farideh; Kattge, Jens; Banerjee, Arindam; Schrodt, Franziska; Reich, Peter

    2015-04-01

    Functional traits of organisms are key to understanding and predicting biodiversity and ecological change, which motivates continuous collection of traits and their integration into global databases. Such composite trait matrices are inherently sparse, severely limiting their usefulness for further analyses. On the other hand, traits are characterized by the phylogenetic trait signal, trait-trait correlations and environmental constraints, all of which provide information that could be used to statistically fill gaps. We propose the application of probabilistic models which, for the first time, utilize all three characteristics to fill gaps in trait databases and predict trait values at larger spatial scales. For this purpose we introduce BHPMF, a hierarchical Bayesian extension of Probabilistic Matrix Factorization (PMF). PMF is a machine learning technique which exploits the correlation structure of sparse matrices to impute missing entries. BHPMF additionally utilizes the taxonomic hierarchy for trait prediction. Implemented in the context of a Gibbs Sampler MCMC approach BHPMF provides uncertainty estimates for each trait prediction. We present comprehensive experimental results on the problem of plant trait prediction using the largest database of plant traits, where BHPMF shows strong empirical performance in uncertainty quantified trait prediction, outperforming the state-of-the-art based on point estimates. Further, we show that BHPMF is more accurate when it is confident, whereas the error is high when the uncertainty is high.

  12. QTLs for Biomass and Developmental Traits in Switchgrass (Panicum virgatum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and genomic resources have recently been developed for the bioenergy crop switchgrass (Panicum virgatum). Despite these advances, little research has been focused on identifying genetic loci involved in natural variation of important bioenergy traits, including biomass. Quantitative trait l...

  13. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus

    PubMed Central

    Zhao, Weiguo; Wang, Xiaodong; Wang, Hao; Tian, Jianhua; Li, Baojun; Chen, Li; Chao, Hongbo; Long, Yan; Xiang, Jun; Gan, Jianping; Liang, Wusheng; Li, Maoteng

    2016-01-01

    Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments. PMID:26858737

  14. Applied Mathematics for agronomical engineers in Spain at UPM

    NASA Astrophysics Data System (ADS)

    Anton, J. M.; Grau, J. B.; Tarquis, A. M.; Fabregat, J.; Sanchez, M. E.

    2009-04-01

    Mathematics, created or discovered, are a global human conceptual endowment, containing large systems of knowledge, and varied skills to use definite parts of them, in creation or discovery, or for applications, e.g. in Physics, or notably in engineering behaviour. When getting upper intellectual levels in the 19th century, the agronomical science and praxis was noticeably or mainly organised in Spain in agronomical engineering schools and also in institutes, together with technician schools, also with different lower lever centres, and they have evolved with progress and they are much changing at present to a EEES schema (Bolonia process). They work in different lines that need some basis or skills from mathematics. The vocation to start such careers, that have varied curriculums, contains only some mathematics, and the number of credits for mathematics is restrained because time is necessary for other initial sciences such as applied chemistry, biology, ecology and soil sciences, but some basis and skill of maths are needed, also with Physics, at least for electricity, machines, construction, economics at initial ground levels, and also for Statistics that are here considered part of Applied Mathematics. The ways of teaching mathematical basis and skills are especial, and are different from the practical ways needed e. g. for Soil Sciences, and they involve especial efforts from students, and especial controls or exams that guide much learning. The mathematics have a very large accepted content that uses mostly a standard logic, and that is remarkably stable and international, rather similar notation and expressions being used with different main languages. For engineering the logical basis is really often not taught, but the use of it is transferred, especially for calculus that requires both adapted somehow simplified schemas and the learning of a specific skill to use it, and also for linear algebra. The basic forms of differential calculus in several

  15. Motivational Traits of Elite Young Soccer Players

    ERIC Educational Resources Information Center

    Stewart, Craig; Meyers, Michael C.

    2004-01-01

    Among the most overlooked aspects in the development of elite young soccer players is that of specific psychological traits. Of those traits, motivation has important implications for programs whose objectives are identification and cultivation of young, skilled performers. The growth in popularity of soccer by youth and the successes experienced…

  16. Valence Effects in Reasoning About Evaluative Traits

    ERIC Educational Resources Information Center

    Heyman, Gail D.; Giles, Jessica W.

    2004-01-01

    Trait conceptions, such as smart, antisocial, and shy, can serve as tools for interpreting and making predictions about the social world. An understanding of children?s trait conceptions can lead to important insights into the way children acquire an understanding of human mental life. The present study was designed to examine positivity biases…

  17. Multiple Trait Analysis of Genetic Mapping for Quantitative Trait Loci

    PubMed Central

    Jiang, C.; Zeng, Z. B.

    1995-01-01

    We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses. PMID:7672582

  18. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae)

    PubMed Central

    Larranaga, Nerea; Hormaza, José I.

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management. PMID:26284104

  19. Relation of agronomic and multispectral reflectance characteristics of spring wheat canopies

    NASA Technical Reports Server (NTRS)

    Bauer, M. E. (Principal Investigator); Ahlrichs, J. S.

    1982-01-01

    The relationships between crop canopy variables such as leaf area index (LAI) and their multispectral reflectance properties were investigated along with the potential for estimating canopy variables from remotely sensed reflectance measurements. Reflectance spectra over the 0.4 to 2.5 micron wavelength range were acquired during each of the major development stages of spring wheat canopies at Williston, North Dakota, during three seasons. Treatments included planting date, N fertilization, cultivar, and soil moisture. Agronomic measurements included development stage, biomass, LAI, and percent soil cover. High correlations were found between reflectance and percent cover, LAI, and biomass. A near infrared wavelength band, 0.76 to 0.90 microns, was most important in explaining variation in LAI and percent cover, while a middle infrared band, 2.08 to 2.35 microns, explained the most variation in biomass and plant water content. Transformations, including the near infrared/red reflectance ratio and greenness index, were also highly correlated to canopy variables. The relationship of canopy variables to reflectance decreased as the crop began to ripen. the canopy variables could be accurately predicted using measurements from three to five wavelength bands. The wavelength bands proposed for the thematic mapper sensor were more strongly related to the canopy variables than the LANDSAT MSS bands.

  20. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae).

    PubMed

    Larranaga, Nerea; Hormaza, José I

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.

  1. Carbon and water cycling in flooded and rainfed rice (Oryza Sativa) ecosystem: Disentangling agronomical and ecological aspects of water use efficiency

    NASA Astrophysics Data System (ADS)

    Nay-Htoon, Bhone; Xue, Wei; Dubbert, Maren; Lindner, Steve; Cuntz, Matthias; Ko, Jonghan; Tenhunen, John; Werner, Christiane

    2015-04-01

    Agricultural crops play an important role in the global carbon and water cycling process and there is intense research to understand and predict carbon and water fluxes, productivity and water use of cultivated crops under climate change. Mechanistic understanding of the trade of between ecosystem water use efficiency and agronomic water use efficiency to maintain higher crop yield and productive water loss is necessary for the ecosystem sustainability. . We compared water and carbon fluxes of paddy and rainfed rice by canopy scale gas exchange measurements, crop growth, and daily evapotranspiration, transpiration and carbon flux modeling. According to our findings, evaporation contributed strongly (maximum 100% to minimum 45%) to paddy rice evapotranspiration while transpiration of rainfed is almost 50 % of daily evapotranspiration. Water use efficiency (WUE) was higher in rainfed rice both from an agronomic (WUEagro, i.e. grain yield per evapotranspiration) and ecosystem (WUEeco, i.e. gross primary production per evapotranspiration) perspective. However, rainfed rice showed also high ecosystem respiration losses and a slightly lower crop yield, demonstrating that higher WUE in rainfed rice comes at the expense of higher respiration losses of assimilated carbon and lower plant production, compared to paddy rice. Our results highlighted the need to partition water and carbon fluxes to improve our mechanistic understanding of water use efficiency and environmental impact of different agricultural practices. Keywords: Rainfed rice, Paddy rice, water use efficiency, Transpiration/Evapotranspiration, ecosystem WUE, agronomic WUE, Evapotranspiration

  2. Soybean genetic transformation: A valuable tool for the functional study of genes and the production of agronomically improved plants

    PubMed Central

    Homrich, Milena Schenkel; Wiebke-Strohm, Beatriz; Weber, Ricardo Luís Mayer; Bodanese-Zanettini, Maria Helena

    2012-01-01

    Transgenic plants represent an invaluable tool for molecular, genetic, biochemical and physiological studies by gene overexpression or silencing, transposon-based mutagenesis, protein sub-cellular localization and/or promoter characterization as well as a breakthrough for breeding programs, allowing the production of novel and genetically diverse genotypes. However, the stable transformation of soybean cannot yet be considered to be routine because it depends on the ability to combine efficient transformation and regeneration techniques. Two methods have been used with relative success to produce completely and stably transformed plants: particle bombardment and the Agrobacterium tumefaciens system. In addition, transformation by Agrobacterium rhizogenes has been used as a powerful tool for functional studies. Most available information on gene function is based on heterologous expression systems. However, as the activity of many promoters or proteins frequently depends on specific interactions that only occur in homologous backgrounds, a final confirmation based on a homologous expression system is desirable. With respect to soybean biotech improvement, transgenic lines with agronomical, nutritional and pharmaceutical traits have been obtained, including herbicide-tolerant soybeans, which represented the principal biotech crop in 2011, occupying 47% of the global biotech area. PMID:23412849

  3. Bio-effectors from waste materials as growth promoters for tomato plants, an agronomic and metabolomic study

    NASA Astrophysics Data System (ADS)

    Abou Chehade, Lara; Chami, Ziad Al; De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

    2015-04-01

    In organic farming, where nutrient management is constrained and sustainability is claimed, bio-effectors pave their way. Considering selected bio-effectors, this study integrates metabolomics to agronomy in depicting induced relevant phenomena. Extracts of three agro-industrial wastes (Lemon processing residues, Fennel processing residues and Brewer's spent grain) are being investigated as sources of bio-effectors for the third trial consequently. Corresponding individual and mixture aqueous extracts are assessed for their synergistic and/or single agronomic and qualitative performances on soil-grown tomato, compared to both a control and humic acid treatments. A metabolomic profiling of tomato fruits via the Proton Nuclear Magnetic Resonance (NMR) spectroscopy, as holistic indicator of fruit quality and extract-induced responses, complements crop productivity and organoleptic/nutritional qualitative analyses. Results are expected to show mainly an enhancement of the fruit qualitative traits, and to confirm partly the previous results of better crop productivity and metabolism enhancement. Waste-derived bio-effectors could be, accordingly, demonstrated as potential candidates of plant-enhancing substances. Keywords: bio-effectors, organic farming, agro-industrial wastes, nuclear magnetic resonance (NMR), tomato.

  4. Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato.

    PubMed

    Li, Li; Paulo, Maria-João; van Eeuwijk, Fred; Gebhardt, Christiane

    2010-11-01

    Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed.

  5. Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer.

    PubMed

    Covarrubias-Pazaran, Giovanny

    2016-01-01

    Most traits of agronomic importance are quantitative in nature, and genetic markers have been used for decades to dissect such traits. Recently, genomic selection has earned attention as next generation sequencing technologies became feasible for major and minor crops. Mixed models have become a key tool for fitting genomic selection models, but most current genomic selection software can only include a single variance component other than the error, making hybrid prediction using additive, dominance and epistatic effects unfeasible for species displaying heterotic effects. Moreover, Likelihood-based software for fitting mixed models with multiple random effects that allows the user to specify the variance-covariance structure of random effects has not been fully exploited. A new open-source R package called sommer is presented to facilitate the use of mixed models for genomic selection and hybrid prediction purposes using more than one variance component and allowing specification of covariance structures. The use of sommer for genomic prediction is demonstrated through several examples using maize and wheat genotypic and phenotypic data. At its core, the program contains three algorithms for estimating variance components: Average information (AI), Expectation-Maximization (EM) and Efficient Mixed Model Association (EMMA). Kernels for calculating the additive, dominance and epistatic relationship matrices are included, along with other useful functions for genomic analysis. Results from sommer were comparable to other software, but the analysis was faster than Bayesian counterparts in the magnitude of hours to days. In addition, ability to deal with missing data, combined with greater flexibility and speed than other REML-based software was achieved by putting together some of the most efficient algorithms to fit models in a gentle environment such as R. PMID:27271781

  6. Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer

    PubMed Central

    2016-01-01

    Most traits of agronomic importance are quantitative in nature, and genetic markers have been used for decades to dissect such traits. Recently, genomic selection has earned attention as next generation sequencing technologies became feasible for major and minor crops. Mixed models have become a key tool for fitting genomic selection models, but most current genomic selection software can only include a single variance component other than the error, making hybrid prediction using additive, dominance and epistatic effects unfeasible for species displaying heterotic effects. Moreover, Likelihood-based software for fitting mixed models with multiple random effects that allows the user to specify the variance-covariance structure of random effects has not been fully exploited. A new open-source R package called sommer is presented to facilitate the use of mixed models for genomic selection and hybrid prediction purposes using more than one variance component and allowing specification of covariance structures. The use of sommer for genomic prediction is demonstrated through several examples using maize and wheat genotypic and phenotypic data. At its core, the program contains three algorithms for estimating variance components: Average information (AI), Expectation-Maximization (EM) and Efficient Mixed Model Association (EMMA). Kernels for calculating the additive, dominance and epistatic relationship matrices are included, along with other useful functions for genomic analysis. Results from sommer were comparable to other software, but the analysis was faster than Bayesian counterparts in the magnitude of hours to days. In addition, ability to deal with missing data, combined with greater flexibility and speed than other REML-based software was achieved by putting together some of the most efficient algorithms to fit models in a gentle environment such as R. PMID:27271781

  7. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

    PubMed

    Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

    2008-12-01

    The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and

  8. Contrasting agronomic response of biochar amendment to a Mediterranean Cambisol: Incubation vs. field experiment

    NASA Astrophysics Data System (ADS)

    De la Rosa, José M.; Paneque, Marina; De Celis, Reyes; Miller, Ana Z.; Knicker, Heike

    2015-04-01

    The application of biochar to soil is being proposed as a novel approach to establish a significant long-term sink for atmospheric carbon dioxide in terrestrial ecosystems. In addition, biochars offer a simple, sustainable tool for managing organic wastes and to produce added value products. Numerous research studies pointed out that biochar can act as a soil conditioner enhancing plant growth by supplying and, more importantly, retaining nutrients and by providing other services such as improving soil physical and biological properties [1]. However, the effectiveness of biochar in enhancing plant fertility is a function of soil type, climate, and type of crop [2] but also of the biochar properties. The inherent variability of biochars due to different feedstock and production conditions implies a high variability of their effect on soil properties and productivity. Furthermore, due to the irreversibility of biochar application, it is necessary to perform detailed studies to achieve a high level of certainty that adding biochar to agricultural soils, for whatever reason, will not negatively affect soil health and productivity. The major goals of this research were: i) understanding how the properties of 5 different biochars produced by using different feedstock and pyrolysis conditions are related to their agronomic response, and ii) assessing the agronomic effect of biochar amendment under field conditions of a typical Mediterranean non-irrigated plantation. Four of the used biochars were produced by pyrolysis from wood (2), paper sludge (1) and sewage sludge (1), at temperatures up to 620 °C. The fifth biochar was produced from old grapevine wood by applying the traditional kiln method. Biochars were analysed for elemental composition (C, H, N), pH, WHC and ash contents. The H/C and O/C atomic ratios suggested high aromaticity of all biochars, which was confirmed by 13C solid-state NMR spectroscopy. The FT-IR spectra indicated the presence of lignin residues in

  9. Landscape of genomic diversity and trait discovery in soybean

    PubMed Central

    Valliyodan, Babu; Dan Qiu; Patil, Gunvant; Zeng, Peng; Huang, Jiaying; Dai, Lu; Chen, Chengxuan; Li, Yanjun; Joshi, Trupti; Song, Li; Vuong, Tri D.; Musket, Theresa A.; Xu, Dong; Shannon, J. Grover; Shifeng, Cheng; Liu, Xin; Nguyen, Henry T.

    2016-01-01

    Cultivated soybean [Glycine max (L.) Merr.] is a primary source of vegetable oil and protein. We report a landscape analysis of genome-wide genetic variation and an association study of major domestication and agronomic traits in soybean. A total of 106 soybean genomes representing wild, landraces, and elite lines were re-sequenced at an average of 17x depth with a 97.5% coverage. Over 10 million high-quality SNPs were discovered, and 35.34% of these have not been previously reported. Additionally, 159 putative domestication sweeps were identified, which includes 54.34 Mbp (4.9%) and 4,414 genes; 146 regions were involved in artificial selection during domestication. A genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding. PMID:27029319

  10. Relationship between Agronomic Parameters, Phenolic Composition of Grape Skin, and Texture Properties of Vitis vinifera L. cv. Tempranillo.

    PubMed

    García-Estévez, Ignacio; Andrés-García, Paula; Alcalde-Eon, Cristina; Giacosa, Simone; Rolle, Luca; Rivas-Gonzalo, Julián C; Quijada-Morín, Natalia; Escribano-Bailón, M Teresa

    2015-09-01

    The relationship between the agronomic parameters of grapevine and the phenolic composition of skin of Vitis vinifera L. cv. Tempranillo grapes was assessed. The physical and mechanical properties of berries and their skins were also determined and correlated to the chemical composition. Results showed a significant negative correlation between grapevine vigor-related parameters (such as leaf area and bunch weight) and anthocyanin composition, whereas the percentage (w/w) of seeds was negatively correlated with the amount of flavanols of grape skins. Texture properties of grape skins also showed an important relationship with chemical composition. Berry hardness showed a negative correlation with the coumaroyl-anthocyanin derivatives, but it was positively correlated to skin flavanic composition. Moreover, significant regressions with high coefficients of determination were found between phenolic composition and grapevine vigor-related and texture variables, thus pointing out that these parameters might be useful for estimating the phenolic composition of grape skins.

  11. A farm-level analysis of economic and agronomic impacts of gradual climate warming

    SciTech Connect

    Kaiser, H.M.; Sampath, R.; Riha, S.J.; Wilks, D.S.; Rossiter, D.G.

    1993-05-01

    The potential economic and agronomic impacts of gradual climate warming are examined at the farm level. Three models of the relevant climatic, agronomic, and economic processes are developed and linked to address climate change impacts and agricultural adaptability. Several climate warming severity. The results indicate that grain farmers in southern Minnesota can effectively adapt to a gradually changing climate (warmer and either wetter or drier) by adopting later maturing cultivars, changing crop mix, and altering the timing of field operations to take advantage of a longer growing season resulting from climate warming.

  12. FishTraits Database

    USGS Publications Warehouse

    Angermeier, Paul L.; Frimpong, Emmanuel A.

    2009-01-01

    The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

  13. Improving agronomic water use efficiency in tomato by rootstock-mediated hormonal regulation of leaf biomass.

    PubMed

    Cantero-Navarro, Elena; Romero-Aranda, Remedios; Fernández-Muñoz, Rafael; Martínez-Andújar, Cristina; Pérez-Alfocea, Francisco; Albacete, Alfonso

    2016-10-01

    Water availability is the most important factor limiting food production, thus developing new scientific strategies to allow crops to more efficiently use water could be crucial in a world with a growing population. Tomato is a highly water consuming crop and improving its water use efficiency (WUE) implies positive economic and environmental effects. This work aimed to study and exploit root-derived hormonal traits to improve WUE in tomato by grafting on selected rootstocks. Firstly, root-related hormonal parameters associated to WUE were identified in a population of recombinant inbred lines (RILs) derived from the wild tomato species Solanum pimpinellifolium. A principal component analysis (PCA) revealed that some hormonal traits were associated with productivity (plant biomass and photosynthesis) and WUE in the RIL population. Leaf ABA concentration was associated to the first component (PC1) of the PCA, which explained a 60% of the variance in WUE, while the ethylene precursor ACC and the ratio ACC/ABA were also associated to PC1 but in the opposite direction. Secondly, we selected RILs according to their extreme biomass (high, B, low, b) and water use (high, W, low, w), and studied the differential effect of shoot and root on WUE by reciprocal grafting. In absence of any imposed stress, there were no rootstock effects on vegetative shoot growth and water relations. Finally, we exploited the previously identified root-related hormonal traits by grafting a commercial tomato variety onto the selected RILs to improve WUE. Interestingly, rootstocks that induced low biomass and water use, 'bw', improved fruit yield and WUE (defined as fruit yield/water use) by up to 40% compared to self-grafted plants. Although other hormonal factors appear implicated in this response, xylem ACC concentration seems an important root-derived trait that inhibits leaf growth but does not limit fruit yield. Thus tomato WUE can be improved exploiting rootstock-derived hormonal signals

  14. Improving agronomic water use efficiency in tomato by rootstock-mediated hormonal regulation of leaf biomass.

    PubMed

    Cantero-Navarro, Elena; Romero-Aranda, Remedios; Fernández-Muñoz, Rafael; Martínez-Andújar, Cristina; Pérez-Alfocea, Francisco; Albacete, Alfonso

    2016-10-01

    Water availability is the most important factor limiting food production, thus developing new scientific strategies to allow crops to more efficiently use water could be crucial in a world with a growing population. Tomato is a highly water consuming crop and improving its water use efficiency (WUE) implies positive economic and environmental effects. This work aimed to study and exploit root-derived hormonal traits to improve WUE in tomato by grafting on selected rootstocks. Firstly, root-related hormonal parameters associated to WUE were identified in a population of recombinant inbred lines (RILs) derived from the wild tomato species Solanum pimpinellifolium. A principal component analysis (PCA) revealed that some hormonal traits were associated with productivity (plant biomass and photosynthesis) and WUE in the RIL population. Leaf ABA concentration was associated to the first component (PC1) of the PCA, which explained a 60% of the variance in WUE, while the ethylene precursor ACC and the ratio ACC/ABA were also associated to PC1 but in the opposite direction. Secondly, we selected RILs according to their extreme biomass (high, B, low, b) and water use (high, W, low, w), and studied the differential effect of shoot and root on WUE by reciprocal grafting. In absence of any imposed stress, there were no rootstock effects on vegetative shoot growth and water relations. Finally, we exploited the previously identified root-related hormonal traits by grafting a commercial tomato variety onto the selected RILs to improve WUE. Interestingly, rootstocks that induced low biomass and water use, 'bw', improved fruit yield and WUE (defined as fruit yield/water use) by up to 40% compared to self-grafted plants. Although other hormonal factors appear implicated in this response, xylem ACC concentration seems an important root-derived trait that inhibits leaf growth but does not limit fruit yield. Thus tomato WUE can be improved exploiting rootstock-derived hormonal signals

  15. The contrasting roles of growth traits and architectural traits in diversity maintenance in clonal plant communities.

    PubMed

    Wildová, Radka; Goldberg, Deborah E; Herben, Tomáš

    2012-12-01

    Plant communities often exhibit high diversity, even though pairwise experiments usually result in competitive hierarchies that should result in competitive exclusion. Such experiments, however, do not typically allow expression of spatial traits, despite theoretical studies showing the potential importance of spatial mechanisms of diversity maintenance. Here we ask whether, in a clonal plant model system, spatial trait variation is more likely than growth trait variation to maintain diversity. We used a field-calibrated, spatially explicit model to simulate communities comprising sets of four simulated species differing in only one of a suite of architectural or growth traits at a time, examining their dynamics and long-term diversity. To compare trait manipulation effects across traits measured in different units, we scaled traits to have identical effects on initial productivity. We found that in communities of species differing only in an architectural trait, all species usually persist, whereas communities of species differing only in a growth trait experienced rapid competitive exclusion. To examine the roles of equalizing and stabilizing mechanisms in maintaining diversity, we conducted reciprocal invasion experiments for species pairs differing only in single traits. The results suggest that stabilizing mechanisms cannot account for the observed long-term co-occurrence. Strong positive correlations between diversity and similarity both in monoculture carrying capacity and reciprocal invasion ability suggesting equalizing mechanisms may instead be responsible.

  16. Towards an evolutionary ecology of sexual traits.

    PubMed

    Cornwallis, Charlie K; Uller, Tobias

    2010-03-01

    Empirical studies of sexual traits continue to generate conflicting results, leading to a growing awareness that the current understanding of this topic is limited. Here we argue that this is because studies of sexual traits fail to encompass three important features of evolution. First, sexual traits evolve via natural selection of which sexual selection is just one part. Second, selection on sexual traits fluctuates in strength, direction and form due to spatial and temporal environmental heterogeneity. Third, phenotypic plasticity is ubiquitous and generates selection and responses to selection within and across generations. A move from purely gene-focused theories of sexual selection towards research that explicitly integrates development, ecology and evolution is necessary to break the stasis in research on sexual traits.

  17. A functional trait perspective on plant invasion

    PubMed Central

    Drenovsky, Rebecca E.; Grewell, Brenda J.; D'Antonio, Carla M.; Funk, Jennifer L.; James, Jeremy J.; Molinari, Nicole; Parker, Ingrid M.; Richards, Christina L.

    2012-01-01

    Background and Aims Global environmental change will affect non-native plant invasions, with profound potential impacts on native plant populations, communities and ecosystems. In this context, we review plant functional traits, particularly those that drive invader abundance (invasiveness) and impacts, as well as the integration of these traits across multiple ecological scales, and as a basis for restoration and management. Scope We review the concepts and terminology surrounding functional traits and how functional traits influence processes at the individual level. We explore how phenotypic plasticity may lead to rapid evolution of novel traits facilitating invasiveness in changing environments and then ‘scale up’ to evaluate the relative importance of demographic traits and their links to invasion rates. We then suggest a functional trait framework for assessing per capita effects and, ultimately, impacts of invasive plants on plant communities and ecosystems. Lastly, we focus on the role of functional trait-based approaches in invasive species management and restoration in the context of rapid, global environmental change. Conclusions To understand how the abundance and impacts of invasive plants will respond to rapid environmental changes it is essential to link trait-based responses of invaders to changes in community and ecosystem properties. To do so requires a comprehensive effort that considers dynamic environmental controls and a targeted approach to understand key functional traits driving both invader abundance and impacts. If we are to predict future invasions, manage those at hand and use restoration technology to mitigate invasive species impacts, future research must focus on functional traits that promote invasiveness and invader impacts under changing conditions, and integrate major factors driving invasions from individual to ecosystem levels. PMID:22589328

  18. Relating Stomatal Conductance to Leaf Functional Traits

    PubMed Central

    Kröber, Wenzel; Plath, Isa; Heklau, Heike; Bruelheide, Helge

    2015-01-01

    Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, morphological leaf traits have the potential to summarize plants strategies in terms of water use efficiency, growth pattern and nutrient use. The leaf economics spectrum (LES) is a recognized framework in functional plant ecology and reflects a gradient of increasing specific leaf area (SLA), leaf nitrogen, phosphorus and cation content, and decreasing leaf dry matter content (LDMC) and carbon nitrogen ratio (CN). The LES describes different strategies ranging from that of short-lived leaves with high photosynthetic capacity per leaf mass to long-lived leaves with low mass-based carbon assimilation rates. However, traits that are not included in the LES might provide additional information on the species' physiology, such as those related to stomatal control. Protocols are presented for a wide range of leaf functional traits, including traits of the LES, but also traits that are independent of the LES. In particular, a new method is introduced that relates the plants’ regulatory behavior in stomatal conductance to vapor pressure deficit. The resulting parameters of stomatal regulation can then be compared to the LES and other plant functional traits. The results show that functional leaf traits of the LES were also valid predictors for the parameters of stomatal regulation. For example, leaf carbon concentration was positively related to the vapor pressure deficit (vpd) at the point of inflection and the maximum of the conductance-vpd curve. However, traits that are not included in the LES added information in explaining parameters of stomatal control: the vpd at the point of inflection of the conductance-vpd curve was lower for species with higher stomatal density and higher stomatal index. Overall, stomata and vein traits were more powerful predictors for explaining stomatal regulation than traits used in the LES

  19. Relating Stomatal Conductance to Leaf Functional Traits.

    PubMed

    Kröber, Wenzel; Plath, Isa; Heklau, Heike; Bruelheide, Helge

    2015-10-12

    Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, morphological leaf traits have the potential to summarize plants strategies in terms of water use efficiency, growth pattern and nutrient use. The leaf economics spectrum (LES) is a recognized framework in functional plant ecology and reflects a gradient of increasing specific leaf area (SLA), leaf nitrogen, phosphorus and cation content, and decreasing leaf dry matter content (LDMC) and carbon nitrogen ratio (CN). The LES describes different strategies ranging from that of short-lived leaves with high photosynthetic capacity per leaf mass to long-lived leaves with low mass-based carbon assimilation rates. However, traits that are not included in the LES might provide additional information on the species' physiology, such as those related to stomatal control. Protocols are presented for a wide range of leaf functional traits, including traits of the LES, but also traits that are independent of the LES. In particular, a new method is introduced that relates the plants' regulatory behavior in stomatal conductance to vapor pressure deficit. The resulting parameters of stomatal regulation can then be compared to the LES and other plant functional traits. The results show that functional leaf traits of the LES were also valid predictors for the parameters of stomatal regulation. For example, leaf carbon concentration was positively related to the vapor pressure deficit (vpd) at the point of inflection and the maximum of the conductance-vpd curve. However, traits that are not included in the LES added information in explaining parameters of stomatal control: the vpd at the point of inflection of the conductance-vpd curve was lower for species with higher stomatal density and higher stomatal index. Overall, stomata and vein traits were more powerful predictors for explaining stomatal regulation than traits used in the LES.

  20. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

    PubMed Central

    Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

    2015-01-01

    Abstract In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

  1. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

    PubMed

    Kumar, Anil; Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

    2015-10-01

    In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes.

  2. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

    PubMed

    Kumar, Anil; Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

    2015-10-01

    In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

  3. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bean production is challenged by many limitations with drought being among the top causes of crop failure worldwide. An estimated 60% of common bean production is affected by drought. In this study, we constructed three small red-seeded bean RIL populations (S48M, S94M and S95M) with a common parent...

  4. Allelic variations of a light harvesting chlorophyll A/B protein gene (Lhcb1) associated with agronomic traits in Barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Light-harvesting chlorophyll a/b-binding protein (LHCP) is one of the most abundant chloroplast proteins in plants. Its main function is to collect and transfer light energy to photosynthetic reaction centers. However, the roles of different LHCPs in light-harvesting antenna systems remain obscure. ...

  5. Quantitative trait loci associated with phenological development, low temperature tolerance, grain quality, and agronomic characters in wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant m...

  6. Registration of six soybean germplasm lines selected within the cultivar ‘Haskell’ differing in seed and agronomic traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six soybean [Glycine max (L.) Merr.] germplasm lines were developed by the Georgia Agricultural Experiment Stations and released in 2005: G95-Has339 (Reg. No. 344, PI 644054), G95-Has551 (Reg. No. 345, PI 644055), G95-Has1452 (Reg. No. 346, PI 644056), G95-Has1536 (Reg. No. 347, PI 644057), G95-Has2...

  7. Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea.

    PubMed

    Das, Shouvik; Upadhyaya, Hari D; Bajaj, Deepak; Kujur, Alice; Badoni, Saurabh; Laxmi; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-06-01

    A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R(2) at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the

  8. Sewage sludge fertiliser use: implications for soil and plant copper evolution in forest and agronomic soils.

    PubMed

    Ferreiro-Domínguez, Nuria; Rigueiro-Rodríguez, Antonio; Mosquera-Losada, M Rosa

    2012-05-01

    Fertilisation with sewage sludge may lead to crop toxicity and environmental degradation. This study aims to evaluate the effects of two types of soils (forest and agronomic), two types of vegetation (unsown (coming from soil seed bank) and sown), and two types of fertilisation (sludge fertilisation and mineral fertilisation, with a no fertiliser control) in afforested and treeless swards and in sown and unsown forestlands on the total and available Cu concentration in soil, the leaching of this element and the Cu levels in plant. The experimental design was completely randomised with nine treatments and three replicates. Fertilisation with sewage sludge increased the concentration of Cu in soil and plant, but the soil values never exceeded the maximum set by Spanish regulations. Sewage sludge inputs increased both the total and Mehlich 3 Cu concentrations in agronomic soils and the Cu levels in plant developed in agronomic and forest soils, with this effect pronounced in the unsown swards of forest soils. Therefore, the use of high quality sewage sludge as fertiliser may improve the global productivity of forest, agronomic and silvopastoral systems without creating environmental hazards. PMID:22425275

  9. A survey of the agronomic and end-use characteristics of low phytic acid soybeans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With unique high protein and oil contents, soybean (Glycine max L. merr.) is one of the most widely grown agronomic crops in the United States. Around 98% of those soybeans are used in animal feeds ranging from swine and cattle to domestic animals and aquaculture. This chapter will introduce phytic ...

  10. Agronomic effects of mutations in two soybean Stearoyl-ACP-Desaturases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean [Glycine max (L.) Merr.] oil normally contains 2-4% stearic acid. Oil with higher levels of stearic acid is desired for use in the baking industry, for both its chemical properties and human health benefits. Several lines with increased stearic acid have been identified; however, the agronom...

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

    PubMed Central

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

    2014-01-01

    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. PMID:25185998

  12. Sebacina vermifera: a unique root symbiont with vast agronomic potential.

    PubMed

    Ray, Prasun; Craven, Kelly D

    2016-01-01

    The Sebacinales belong to a taxonomically, ecologically, and physiologically diverse group of fungi in the Basidiomycota. While historically recognized as orchid mycorrhizae, recent DNA studies have brought to light both their pandemic distribution and the broad spectrum of mycorrhizal types they form. Indeed, ecological studies using molecular-based methods of detection have found Sebacinales fungi in field specimens of bryophytes (moss), pteridophytes (fern) and all families of herbaceous angiosperms (flowering plants) from temperate, subtropical and tropical regions. These natural host plants include, among others, liverworts, wheat, maize and Arabidopsis thaliana, the model plant traditionally viewed as non-mycorrhizal. The orchid mycorrhizal fungus Sebacina vermifera (MAFF 305830) was first isolated from the Australian orchid Cyrtostylis reniformis. Research performed with this strain clearly indicates its plant growth promoting abilities in a variety of plants, while demonstrating a lack of specificity that rivals or even surpasses that of arbuscular mycorrhizae. Indeed, these traits thus far appear to characterize a majority of strains belonging to the so-called "clade B" within the Sebacinales (recently re-classified as the Serendipitaceae), raising numerous basic research questions regarding plant-microbe signaling and the evolution of mycorrhizal symbioses. Further, given their proven beneficial impact on plant growth and their apparent but cryptic ubiquity, sebacinoid fungi should be considered as a previously hidden, but amenable and effective microbial tool for enhancing plant productivity and stress tolerance. PMID:26715121

  13. Generalized Latent Trait Models.

    ERIC Educational Resources Information Center

    Moustaki, Irini; Knott, Martin

    2000-01-01

    Discusses a general model framework within which manifest variables with different distributions in the exponential family can be analyzed with a latent trait model. Presents a unified maximum likelihood method for estimating the parameters of the generalized latent trait model and discusses the scoring of individuals on the latent dimensions.…

  14. Reinforcing loose foundation stones in trait-based plant ecology.

    PubMed

    Shipley, Bill; De Bello, Francesco; Cornelissen, J Hans C; Laliberté, Etienne; Laughlin, Daniel C; Reich, Peter B

    2016-04-01

    The promise of "trait-based" plant ecology is one of generalized prediction across organizational and spatial scales, independent of taxonomy. This promise is a major reason for the increased popularity of this approach. Here, we argue that some important foundational assumptions of trait-based ecology have not received sufficient empirical evaluation. We identify three such assumptions and, where possible, suggest methods of improvement: (i) traits are functional to the degree that they determine individual fitness, (ii) intraspecific variation in functional traits can be largely ignored, and (iii) functional traits show general predictive relationships to measurable environmental gradients.

  15. Going underground: root traits as drivers of ecosystem processes.

    PubMed

    Bardgett, Richard D; Mommer, Liesje; De Vries, Franciska T

    2014-12-01

    Ecologists are increasingly adopting trait-based approaches to understand how community change influences ecosystem processes. However, most of this research has focussed on aboveground plant traits, whereas it is becoming clear that root traits are important drivers of many ecosystem processes, such as carbon (C) and nutrient cycling, and the formation and structural stability of soil. Here, we synthesise emerging evidence that illustrates how root traits impact ecosystem processes, and propose a pathway to unravel the complex roles of root traits in driving ecosystem processes and their response to global change. Finally, we identify research challenges and novel technologies to address them. PMID:25459399

  16. Reinforcing loose foundation stones in trait-based plant ecology.

    PubMed

    Shipley, Bill; De Bello, Francesco; Cornelissen, J Hans C; Laliberté, Etienne; Laughlin, Daniel C; Reich, Peter B

    2016-04-01

    The promise of "trait-based" plant ecology is one of generalized prediction across organizational and spatial scales, independent of taxonomy. This promise is a major reason for the increased popularity of this approach. Here, we argue that some important foundational assumptions of trait-based ecology have not received sufficient empirical evaluation. We identify three such assumptions and, where possible, suggest methods of improvement: (i) traits are functional to the degree that they determine individual fitness, (ii) intraspecific variation in functional traits can be largely ignored, and (iii) functional traits show general predictive relationships to measurable environmental gradients. PMID:26796410

  17. Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

    PubMed Central

    Singh, Rajinder; Tan, Soon G; Panandam, Jothi M; Rahman, Rahimah Abdul; Ooi, Leslie CL; Low, Eng-Ti L; Sharma, Mukesh; Jansen, Johannes; Cheah, Suan-Choo

    2009-01-01

    Background Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL

  18. The Trait Psychology Controversy.

    ERIC Educational Resources Information Center

    Morgan, William P.

    1980-01-01

    Arguments associated with trait psychology are reviewed with an application in the field of sport psychology. The role of cognition and perception in sport and physical activities is also discussed. (CJ)

  19. Association mapping of leaf traits in spinach (Spinacia oleracea L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spinach (Spinacia oleracea L.) is an important leafy vegetable crop grown world-wide. Leaf traits, surface texture (smooth vs. savoy or semi-savoy), petiole color (green vs. purple), and edge shape (serrate vs. entire) are important for spinach. Association mapping of the three traits were conducted...

  20. Divergent selection in a maize population for germination at low temperature in controlled environment: study of the direct response, of the trait inheritance and of correlated responses in the field.

    PubMed

    Frascaroli, Elisabetta; Landi, Pierangelo

    2013-03-01

    Improving cold tolerance in maize (Zea mays L.) is an important breeding objective, allowing early sowings which result in many agronomic advantages. Using as source the F(2) population of B73 × IABO78 single cross, we previously conducted four cycles of divergent recurrent selection for high (H) and low (L) cold tolerance level, evaluated as the difference (DG) between germination at 9.5 °C and at 25 °C in the germinator. Then, we pursued the divergent selection in inbreeding from S(1) to S(4). This research was conducted to study (1) the direct response to selection (by testing ten S(4) L and ten S(4) H lines), (2) the trait inheritance (in a complete diallel scheme involving four L and four H lines), (3) the associated responses for cold tolerance in the field (at early and delayed sowings) and (4) the responses for other traits, by testing the ten L and the ten H lines at usual sowing. Selection was effective, leading to appreciable and symmetric responses for DG. Variation among crosses was mainly due to additive effects and the ability to predict hybrid DG based on parental lines DG was appreciable. Associated responses for cold tolerance traits in the field were noticeable, though the relationship between DG and these traits was not outstanding. High tolerance was also associated with early flowering, short plants, less leaves, low kernel moisture, red and thin cob, and flint kernels. These divergently selected lines can represent valuable materials for undertaking basic studies and breeding works concerning cold tolerance. PMID:23178876

  1. Effect of agronomics on production and conversion quality of Napiergrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Napiergrass (Pennisetum purpureum (L) Schum) is being developed as a bioenergy crop for production in the southeastern United States. An important criterion for selecting a crop is establishing a consistent and dependable source of feedstock. In this study, we considered the effects of fertilizer ap...

  2. Morpho-physiolological and qualitative traits of a bread wheat collection spanning a century of breeding in Italy

    PubMed Central

    Laino, Paolo; Limonta, Margherita; Gerna, Davide

    2015-01-01

    Abstract Evaluation and characterization are crucial steps in the exploitation of germplasm collections. The Sant’Angelo Lodigiano unit of the Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) maintains a broad collection of Triticum spp, including more than 4000 genotypes of T. aestivum. Such collection represents a wide source of genetic variability for many agronomic and qualitative traits, extremely useful in modern breeding programs. The collection size, however, makes very difficult its management as a whole. A reduced subset, representing the process of wheat breeding in Italy during the last hundred years, was hence identified for an in-depth characterization. The lines were cropped in two locations over two growing seasons, and analyzed using 16 morpho-agronomic and qualitative descriptors. Most of the analysed characters showed a broad variation throughout the collection, allowing to follow the plant ideotype changes across the breeding progress in Italy during the 20th century. PMID:26379457

  3. Evaluating Callous-Unemotional Traits as a Personality Construct.

    PubMed

    Frick, Paul J; Ray, James V

    2015-12-01

    We evaluate the importance of callous-unemotional (CU) traits as a personality construct in isolation from other facets of psychopathy. Specifically, we review research suggesting that these traits are useful for designating a subgroup of youth with serious conduct problems who differ from other antisocial youth on important biological, emotional, cognitive, and social characteristics. In addition, the temperamental features related to CU traits are risk factors for impairments in conscience development in young children. Thus, these traits could advance theoretical models explaining the development of severe antisocial behavior and psychopathy. CU traits also have important clinical utility because they designate a particularly severe and impaired subgroup of antisocial youth, leading to their inclusion in the DSM-5. As a result of this inclusion in diagnostic classification, there has been an increased focus on how to best assess CU traits, and we discuss several key issues in their assessment, highlighting several limitations in existing measures. Finally, the increased use of CU traits, separately from other facets of psychopathy, makes it important to determine how these traits relate to other personality constructs. Thus, we examine how measures of CU traits relate to the broader construct of psychopathy and to other basic personality dimensions.

  4. Productivity of sodic soils can be enhanced through the use of salt tolerant rice varieties and proper agronomic practices

    PubMed Central

    Singh, Y.P.; Mishra, V.K.; Singh, Sudhanshu; Sharma, D.K.; Singh, D.; Singh, U.S.; Singh, R.K.; Haefele, S.M.; Ismail, A.M.

    2016-01-01

    Regaining the agricultural potential of sodic soils in the Indo-Gangetic plains necessitates the development of suitable salt tolerant rice varieties to provide an entry for other affordable agronomic and soil manipulation measures. Thus selection of high yielding rice varieties across a range of sodic soils is central. Evaluation of breeding lines through on-station and on-farm farmers’ participatory varietal selection (FPVS) resulted in the identification of a short duration (110–115 days), high yielding and disease resistant salt-tolerant rice genotype ‘CSR-89IR-8’, which was later released as ‘CSR43’ in 2011. Several agronomic traits coupled with good grain quality and market value contributed to commercialization and quick adoption of this variety in the sodic areas of the Indo-Gangetic plains of eastern India. Management practices required for rice production in salt affected soils are evidently different from those in normal soils and practices for a short duration salt tolerant variety differ from those for medium to long duration varieties. Experiments were conducted at the Indian Council of Agricultural Research-Central Soil Salinity Research Institute (ICAR-CSSRI), Regional Research Station, Lucknow, Uttar Pradesh, India during 2011 and 2013 wet seasons, to test the hypothesis that combining matching management practices (Mmp) with an improved genotype would enhance productivity and profitability of rice in sodic soils. Mmp were developed on-station by optimizing existing best management practices (Bmp) recommended for the region to match the requirements of CSR43. The results revealed that transplanting 4 seedlings hill−1 at a spacing of 15 × 20 cm produced significantly higher yield over other treatments. The highest additional net gain was US$ 3.3 at 90 kg ha−1 N, and the lowest was US$ 0.4 at 150 kg ha−1 N. Above 150 kg ha−1, the additional net gain became negative, indicating decreasing returns from additional N

  5. Inversion of vegetation canopy reflectance models for estimating agronomic variables. II - Use of angle transforms and error analysis as illustrated by Suits' model

    NASA Technical Reports Server (NTRS)

    Goel, N. S.; Thompson, R. L.; Strebel, D. E.

    1984-01-01

    The technique for inverting a vegetation canopy reflectance model described earlier (Goel and Strebel, 1983) is investigated further. The novel concept of an 'angle transform' is introduced. This concept allows the formation of functions of reflectances at different view zenith and azimuth angles, which are either sensitive or insensitive to a certain agronomic parameter. A proper combination of these functions can allow determination of all the important agronomic and spectral parameters from measured canopy reflectance data. The technique is demonstrated using Suits' (1972) model for homogeneous canopies. It is shown that leaf area index, leaf reflectance and transmittance, and average leaf angle all can be determined from the canopy reflectance at a set of selected view zenith and azimuth angles. A sensitivity analysis of the calculated values to the errors in the data is also carried out. Guidelines are formulated for the number and types of observations required to obtain the values of a particular canopy variable to within a given degree of accuracy for a given level of error in the measurement of canopy reflectance.

  6. Farmyard manures: the major agronomic sources of heavy metals in the Philippi Horticultural Area in the Western Cape Province of South Africa.

    PubMed

    Malan, Marÿke; Müller, Francuois; Raitt, Lincoln; Aalbers, Johannes; Cyster, Lilburne; Brendonck, Luc

    2015-11-01

    Heavy metal toxicity in agro-ecosystems is a global problem. Recently, it has been indicated that the soils used for agriculture and the fresh produce grown on these soils in the Philippi Horticultural Area (PHA) contains heavy metals exceeding the maximum permissible concentrations thereof in South Africa. This study was therefore aimed at evaluating the concentrations of heavy metals in the soils and vegetables produced in the PHA, as well as to determine the major agronomic sources of these metals in this area. Cu, Pb, and Zn concentrations in the soils exceeded the maximum permissible concentrations of 6.6, 6.6, and 46 mg/kg, respectively. Cd, Pb, and Zn concentrations in the vegetables also exceeded the maximum permissible concentrations of 0.1, 0.5, and 40 mg/kg, respectively. The biggest agronomic contributors of these heavy metals to the soils in the PHA were found to be the farmyard manures. Knowing what the major sources of these heavy metals are, it is important to determine ways to mitigate the inputs thereof, as well as to remove existing concentrations from the soils without contaminating the groundwater resources in the area.

  7. Farmyard manures: the major agronomic sources of heavy metals in the Philippi Horticultural Area in the Western Cape Province of South Africa.

    PubMed

    Malan, Marÿke; Müller, Francuois; Raitt, Lincoln; Aalbers, Johannes; Cyster, Lilburne; Brendonck, Luc

    2015-11-01

    Heavy metal toxicity in agro-ecosystems is a global problem. Recently, it has been indicated that the soils used for agriculture and the fresh produce grown on these soils in the Philippi Horticultural Area (PHA) contains heavy metals exceeding the maximum permissible concentrations thereof in South Africa. This study was therefore aimed at evaluating the concentrations of heavy metals in the soils and vegetables produced in the PHA, as well as to determine the major agronomic sources of these metals in this area. Cu, Pb, and Zn concentrations in the soils exceeded the maximum permissible concentrations of 6.6, 6.6, and 46 mg/kg, respectively. Cd, Pb, and Zn concentrations in the vegetables also exceeded the maximum permissible concentrations of 0.1, 0.5, and 40 mg/kg, respectively. The biggest agronomic contributors of these heavy metals to the soils in the PHA were found to be the farmyard manures. Knowing what the major sources of these heavy metals are, it is important to determine ways to mitigate the inputs thereof, as well as to remove existing concentrations from the soils without contaminating the groundwater resources in the area. PMID:26508018

  8. Genetic map construction and quantitative trait loci (QTL) mapping for nitrogen use efficiency and its relationship with productivity and quality of the biennial crop Belgian endive (Cichorium intybus L.).

    PubMed

    Cassan, Laurent; Moreau, Laurence; Segouin, Samuel; Bellamy, Annick; Falque, Mathieu; Limami, Anis M

    2010-10-15

    A genetic study of the biennial crop Belgian endive (Cichorium intybus) was carried out to examine the effect of nitrogen nutrition during the vegetative phase in the control of the productivity and quality of the chicon (etiolated bud), a crop that grows during the second phase of development (forcing process). A population of 302 recombinant inbred lines (RIL) was obtained from the cross between contrasting lines "NS1" and "NR2". A genetic map was constructed and QTLs of several physiological and agronomical traits were mapped under two levels of nitrogen fertilization during the vegetative phase (N- and N+). The agronomical traits showed high broad sense heritability, whereas the physiological traits were characterized by low broad sense heritability. Nitrogen reserves mobilization during the forcing process was negatively correlated with nitrogen reserves content of the tuberized root and common QTLs were detected for these traits. The chicon productivity and quality were not correlated, but showed one common QTL. This study revealed that chicon productivity and quality were genetically associated with nitrogen reserves mobilization that exerts opposite effects on both traits. Chicon productivity was positively correlated with N reserves mobilization under N- and N+ and a common QTL with the same additive effects was detected for both traits. Chicon quality was negatively correlated with N reserves mobilization under N- and N+ and a common QTL with opposite additive effects was detected for both traits. These results lead to the conclusion that N reserves mobilization is a more effective trait than N reserves content in predicting chicon productivity and quality. Finally, this study revealed agronomical and physiological QTLs utilizable by breeders via marker-assisted selection to aid the optimization of chicon quality under adapted N fertilization.

  9. Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.).

    PubMed

    Meng, S; Yang, X L; Dang, P M; Cui, S L; Mu, G J; Chen, C Y; Liu, L F

    2016-01-01

    Peanut is one of the most important oil crops worldwide. We used insertion-deletion (InDel) markers to assess the genetic diversity and population structure in cultivated peanut. Fifty-four accessions from North China were genotyped using 48 InDel markers. The markers amplified 61 polymorphic loci with 1 to 8 alleles and an average of 2.6 alleles per marker. The polymorphism information content values ranged from 0.0364 to 0.9030, with an average of 0.5038. Population structure and neighbor-joining (NJ) tree analyses suggested that all accessions could be divided into four clusters (A1-A4), using the NJ method. Likewise, four subpopulations (G1-G4) were identified using STRUCTURE analysis. A principal component analysis was also used and results concordant with the other analysis methods were found. A multi-linear stepwise regression analysis revealed that 13 InDel markers correlated with five measured agronomical traits. Our results will provide important information for future peanut molecular breeding and genetic research. PMID:27525935

  10. Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.).

    PubMed

    Meng, S; Yang, X L; Dang, P M; Cui, S L; Mu, G J; Chen, C Y; Liu, L F

    2016-08-12

    Peanut is one of the most important oil crops worldwide. We used insertion-deletion (InDel) markers to assess the genetic diversity and population structure in cultivated peanut. Fifty-four accessions from North China were genotyped using 48 InDel markers. The markers amplified 61 polymorphic loci with 1 to 8 alleles and an average of 2.6 alleles per marker. The polymorphism information content values ranged from 0.0364 to 0.9030, with an average of 0.5038. Population structure and neighbor-joining (NJ) tree analyses suggested that all accessions could be divided into four clusters (A1-A4), using the NJ method. Likewise, four subpopulations (G1-G4) were identified using STRUCTURE analysis. A principal component analysis was also used and results concordant with the other analysis methods were found. A multi-linear stepwise regression analysis revealed that 13 InDel markers correlated with five measured agronomical traits. Our results will provide important information for future peanut molecular breeding and genetic research.

  11. Integrating microbial traits into ecosystem models

    NASA Astrophysics Data System (ADS)

    Allison, S. D.

    2012-12-01

    Diverse bacterial and fungal communities control the decomposition of complex organic material, thereby driving important ecosystem functions such as CO2 production and nutrient regeneration. Predicting these functions is challenging because microbial communities and the chemical substrates they metabolize are complex. To address this challenge, I developed a theoretical model of microbial decomposition based on microbial traits involved in substrate degradation, uptake, and growth. The model represents a large number of microbial taxa, each of which possesses a set of trait values drawn at random from empirically-based distributions. The model also includes a large number of chemical substrates that can be degraded by microbial extracellular enzymes and taken up by membrane transporters. Microbes with different trait values for enzyme production and uptake capacity compete for chemical substrates and vary in abundance during model runs. I used the model to predict rates of plant litter decomposition and determine which traits were associated with high microbial abundance under different environmental conditions. The model predicted that optimal traits depend on the level of enzyme production in the whole community, which determines resource availability and decomposition rates. There is also evidence for facilitation and competition among microbial taxa that co-occur on decomposing litter, suggesting that microbial interactions may play a role in determining ecosystem function. These interactions vary with community investment in extracellular enzyme production and the magnitude of tradeoffs affecting biochemical traits such as enzyme kinetic parameters. The model accounted for 69% of the variation in decomposition rates and up to 26% of the variation in enzyme activities in an empirical dataset with 15 types of Hawaiian plant litter. By explicitly representing microbial diversity, trait-based models can predict ecosystem processes based on functional trait

  12. Fates beyond traits: ecological consequences of human-induced trait change

    PubMed Central

    Palkovacs, Eric P; Kinnison, Michael T; Correa, Cristian; Dalton, Christopher M; Hendry, Andrew P

    2012-01-01

    Human-induced trait change has been documented in freshwater, marine, and terrestrial ecosystems worldwide. These trait changes are driven by phenotypic plasticity and contemporary evolution. While efforts to manage human-induced trait change are beginning to receive some attention, managing its ecological consequences has received virtually none. Recent work suggests that contemporary trait change can have important effects on the dynamics of populations, communities, and ecosystems. Therefore, trait changes caused by human activity may be shaping ecological dynamics on a global scale. We present evidence for important ecological effects associated with human-induced trait change in a variety of study systems. These effects can occur over large spatial scales and impact system-wide processes such as trophic cascades. Importantly, the magnitude of these effects can be on par with those of traditional ecological drivers such as species presence. However, phenotypic change is not always an agent of ecological change; it can also buffer ecosystems against change. Determining the conditions under which phenotypic change may promote vs prevent ecological change should be a top research priority. PMID:25568040

  13. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.

    PubMed

    Varshney, Rajeev K; Song, Chi; Saxena, Rachit K; Azam, Sarwar; Yu, Sheng; Sharpe, Andrew G; Cannon, Steven; Baek, Jongmin; Rosen, Benjamin D; Tar'an, Bunyamin; Millan, Teresa; Zhang, Xudong; Ramsay, Larissa D; Iwata, Aiko; Wang, Ying; Nelson, William; Farmer, Andrew D; Gaur, Pooran M; Soderlund, Carol; Penmetsa, R Varma; Xu, Chunyan; Bharti, Arvind K; He, Weiming; Winter, Peter; Zhao, Shancen; Hane, James K; Carrasquilla-Garcia, Noelia; Condie, Janet A; Upadhyaya, Hari D; Luo, Ming-Cheng; Thudi, Mahendar; Gowda, C L L; Singh, Narendra P; Lichtenzveig, Judith; Gali, Krishna K; Rubio, Josefa; Nadarajan, N; Dolezel, Jaroslav; Bansal, Kailash C; Xu, Xun; Edwards, David; Zhang, Gengyun; Kahl, Guenter; Gil, Juan; Singh, Karam B; Datta, Swapan K; Jackson, Scott A; Wang, Jun; Cook, Douglas R

    2013-03-01

    Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

  14. Testing Trait Depression as a Potential Clinical Domain in Schizophrenia

    PubMed Central

    Chiappelli, Joshua; Kochunov, Peter; DeRiso, Katherine; Thangavelu, Kavita; Sampath, Hemalatha; Muellerklein, Florian; Nugent, Katie L.; Postolache, Teodor T.; Carpenter, William T.; Hong, L. Elliot

    2014-01-01

    The DSM-5 includes depression as a dimension of psychosis. We tested whether persistent experience of depression, called ‘trait depression’, is a clinical feature separate from psychosis and several well-known, trait-like deficits of schizophrenia. 126 individuals with schizophrenia and 151 control participants completed the Maryland Trait and State Depression questionnaire, with a subset completing measures of cognition and functional capacity, and diffusion tensor imaging (n=73 patients and 102 controls for imaging analysis). Subjectively experienced, longitudinal trait depression is significantly higher in patients with schizophrenia compared with controls. Higher trait depression scores were associated with more severe psychosis. Surprisingly, individuals with higher trait depression manifested less cognitive and global functioning deficits. In addition, trait depression scores were positively associated with fractional anisotropy of white matter. Trait depression appears to be a highly relevant clinical domain in the care of patients with schizophrenia that also has distinct relationships with some other known traits of the disease. Trait depression may be an important contributor to the clinical heterogeneity of schizophrenia. PMID:25171855

  15. Testing trait depression as a potential clinical domain in schizophrenia.

    PubMed

    Chiappelli, Joshua; Kochunov, Peter; DeRiso, Katherine; Thangavelu, Kavita; Sampath, Hemalatha; Muellerklein, Florian; Nugent, Katie L; Postolache, Teodor T; Carpenter, William T; Hong, L Elliot

    2014-10-01

    The DSM-5 includes depression as a dimension of psychosis. We tested whether persistent experience of depression, called 'trait depression', is a clinical feature separate from psychosis and several well-known, trait-like deficits of schizophrenia. 126 individuals with schizophrenia and 151 control participants completed the Maryland Trait and State Depression questionnaire, with a subset completing measures of cognition and functional capacity, and diffusion tensor imaging (n=73 patients and 102 controls for imaging analysis). Subjectively experienced, longitudinal trait depression is significantly higher in patients with schizophrenia compared with controls. Higher trait depression scores were associated with more severe psychosis. Surprisingly, individuals with higher trait depression manifested less cognitive and global functioning deficits. In addition, trait depression scores were positively associated with fractional anisotropy of white matter. Trait depression appears to be a highly relevant clinical domain in the care of patients with schizophrenia that also has distinct relationships with some other known traits of the disease. Trait depression may be an important contributor to the clinical heterogeneity of schizophrenia.

  16. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species.

    PubMed

    Xu, Jiaxin; Ranc, Nicolas; Muños, Stéphane; Rolland, Sophie; Bouchet, Jean-Paul; Desplat, Nelly; Le Paslier, Marie-Christine; Liang, Yan; Brunel, Dominique; Causse, Mathilde

    2013-03-01

    Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex™ assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0-41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations. PMID:23124430

  17. Contrasting agronomic response of biochar amendment to a Mediterranean Cambisol: Incubation vs. field experiment

    NASA Astrophysics Data System (ADS)

    De la Rosa, José M.; Paneque, Marina; De Celis, Reyes; Miller, Ana Z.; Knicker, Heike

    2015-04-01

    The application of biochar to soil is being proposed as a novel approach to establish a significant long-term sink for atmospheric carbon dioxide in terrestrial ecosystems. In addition, biochars offer a simple, sustainable tool for managing organic wastes and to produce added value products. Numerous research studies pointed out that biochar can act as a soil conditioner enhancing plant growth by supplying and, more importantly, retaining nutrients and by providing other services such as improving soil physical and biological properties [1]. However, the effectiveness of biochar in enhancing plant fertility is a function of soil type, climate, and type of crop [2] but also of the biochar properties. The inherent variability of biochars due to different feedstock and production conditions implies a high variability of their effect on soil properties and productivity. Furthermore, due to the irreversibility of biochar application, it is necessary to perform detailed studies to achieve a high level of certainty that adding biochar to agricultural soils, for whatever reason, will not negatively affect soil health and productivity. The major goals of this research were: i) understanding how the properties of 5 different biochars produced by using different feedstock and pyrolysis conditions are related to their agronomic response, and ii) assessing the agronomic effect of biochar amendment under field conditions of a typical Mediterranean non-irrigated plantation. Four of the used biochars were produced by pyrolysis from wood (2), paper sludge (1) and sewage sludge (1), at temperatures up to 620 °C. The fifth biochar was produced from old grapevine wood by applying the traditional kiln method. Biochars were analysed for elemental composition (C, H, N), pH, WHC and ash contents. The H/C and O/C atomic ratios suggested high aromaticity of all biochars, which was confirmed by 13C solid-state NMR spectroscopy. The FT-IR spectra indicated the presence of lignin residues in

  18. First impressions: gait cues drive reliable trait judgements.

    PubMed

    Thoresen, John C; Vuong, Quoc C; Atkinson, Anthony P

    2012-09-01

    Personality trait attribution can underpin important social decisions and yet requires little effort; even a brief exposure to a photograph can generate lasting impressions. Body movement is a channel readily available to observers and allows judgements to be made when facial and body appearances are less visible; e.g., from great distances. Across three studies, we assessed the reliability of trait judgements of point-light walkers and identified motion-related visual cues driving observers' judgements. The findings confirm that observers make reliable, albeit inaccurate, trait judgements, and these were linked to a small number of motion components derived from a Principal Component Analysis of the motion data. Parametric manipulation of the motion components linearly affected trait ratings, providing strong evidence that the visual cues captured by these components drive observers' trait judgements. Subsequent analyses suggest that reliability of trait ratings was driven by impressions of emotion, attractiveness and masculinity. PMID:22717166

  19. First impressions: gait cues drive reliable trait judgements.

    PubMed

    Thoresen, John C; Vuong, Quoc C; Atkinson, Anthony P

    2012-09-01

    Personality trait attribution can underpin important social decisions and yet requires little effort; even a brief exposure to a photograph can generate lasting impressions. Body movement is a channel readily available to observers and allows judgements to be made when facial and body appearances are less visible; e.g., from great distances. Across three studies, we assessed the reliability of trait judgements of point-light walkers and identified motion-related visual cues driving observers' judgements. The findings confirm that observers make reliable, albeit inaccurate, trait judgements, and these were linked to a small number of motion components derived from a Principal Component Analysis of the motion data. Parametric manipulation of the motion components linearly affected trait ratings, providing strong evidence that the visual cues captured by these components drive observers' trait judgements. Subsequent analyses suggest that reliability of trait ratings was driven by impressions of emotion, attractiveness and masculinity.

  20. Designing an accompanying ecosystem to foster entrepreneurship among agronomic and forestry engineering students. Opinion and commitment of university lecturers

    NASA Astrophysics Data System (ADS)

    Ortiz-Medina, L.; Fernández-Ahumada, E.; Lara-Vélez, P.; Taguas, E. V.; Gallardo-Cobos, R.; del Campillo, M. C.; Guerrero-Ginel, J. E.

    2016-07-01

    In the Higher School of Agronomic and Forestry Engineering of the University of Cordoba, a collective project conceived as an 'ecosystem to support and accompany entrepreneurs' has been proposed. The approach aims to spread and consolidate the entrepreneurial spirit and to respond to the demands of possible stakeholders involved in the whole process of training, as well as the subsequent integration of graduates into the labour market. Putting into practice this initiative, which involves multiple actors, is a complex and difficult task. For this reason, prior to its implementation, the authors considered it necessary to listen to main stakeholders' opinions and evaluate their degree of commitment and the requirements they consider important for the viability and sustainability of the initiative. This paper focuses on the faculty's opinions, gathered by means of a survey conducted with the entire faculty (N = 128, response rate = 45%) and semi-structured interviews held with 20 members of the School board. The results suggest that there is a general consensus on the suitability of this collective project and that there is a core of teachers willing to get involved. Evidently, guidelines need to be produced to facilitate taking on such tasks. However, the main drawbacks are related with the conflict between formal requirements of professor professional profile and the steps needed to establish the ecosystem.

  1. Estimation of genetic parameters for reproductive traits in alpacas.

    PubMed

    Cruz, A; Cervantes, I; Burgos, A; Morante, R; Gutiérrez, J P

    2015-12-01

    One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU. PMID:26490188

  2. Children's Reasoning about Norms and Traits as Motives for Behavior

    ERIC Educational Resources Information Center

    Kalish, Charles W.; Shiverick, Sean M.

    2004-01-01

    Two important sources of information for social judgments are personality dispositions (traits) and social norms. Existing research suggests that young children do not find traits salient. To what extent might they rely on a different source of information? Two experiments explored how information about preferences (what someone likes) and rules…

  3. Two-trait-locus linkage analysis: A powerful strategy for mapping complex genetic traits

    SciTech Connect

    Schork, N.J.; Boehnke, M. ); Terwilliger, J.D.; Ott, J. )

    1993-11-01

    Nearly all diseases mapped to date follow clear Mendelian, single-locus segregation patterns. In contrast, many common familial diseases such as diabetes, psoriasis, several forms of cancer, and schizophrenia are familial and appear to have a genetic component but do not exhibit simple Mendelian transmission. More complex models are required to explain the genetics of these important diseases. In this paper, the authors explore two-trait-locus, two-marker-locus linkage analysis in which two trait loci are mapped simultaneously to separate genetic markers. The authors compare the utility of this approach to standard one-trait-locus, one-marker-locus linkage analysis with and without allowance for heterogeneity. The authors also compare the utility of the two-trait-locus, two-marker-locus analysis to two-trait-locus, one-marker-locus linkage analysis. For common diseases, pedigrees are often bilineal, with disease genes entering via two or more unrelated pedigree members. Since such pedigrees often are avoided in linkage studies, the authors also investigate the relative information content of unilineal and bilineal pedigrees. For the dominant-or-recessive and threshold models that the authors consider, the authors find that two-trait-locus, two-marker-locus linkage analysis can provide substantially more linkage information, as measured by expected maximum lod score, than standard one-trait-locus, one-marker-locus methods, even allowing for heterogeneity, while, for a dominant-or-dominant generating model, one-locus models that allow for heterogeneity extract essentially as much information as the two-trait-locus methods. For these three models, the authors also find that bilineal pedigrees provide sufficient linkage information to warrant their inclusion in such studies. The authors discuss strategies for assessing the significance of the two linkages assumed in two-trait-locus, two-marker-locus models. 37 refs., 1 fig., 4 tabs.

  4. Evolving Trait Concepts.

    ERIC Educational Resources Information Center

    Anastasi, Anne

    1983-01-01

    Redefines intelligence as a useful, comprehensive, and flexible construct that allows its modifiability as a function of age and culture. Reviews theories on two-factor, multiple-factor, facet, and hierarchical models of trait formation based on research in developmental, cross-cultural, learning, and cognitive psychology. (Author/AOS)

  5. Trait emotional intelligence influences on academic achievement and school behaviour.

    PubMed

    Mavroveli, Stella; Sánchez-Ruiz, María José

    2011-03-01

    BACKGROUND. Trait emotional intelligence (trait EI or trait emotional self-efficacy) refers to individuals' emotion-related self-perceptions (Petrides, Furnham, & Mavroveli, 2007). The children's trait EI sampling domain provides comprehensive coverage of their affective personality. Preliminary evidence shows that the construct has important implications for children's psychological and behavioural adjustment. AIMS. This study investigates the associations between trait EI and school outcomes, such as performance in reading, writing, and maths, peer-rated behaviour and social competence, and self-reported bullying behaviours in a sample of primary school children. It also examines whether trait EI scores differentiate between children with and without special educational needs (SEN). SAMPLE. The sample comprised 565 children (274 boys and 286 girls) between the ages of 7 and 12 (M((age)) = 9.12 years, SD= 1.27 years) attending three English state primary schools. METHOD. Pupils completed the Trait Emotional Intelligence Questionnaire-Child Form (TEIQue-CF), the Guess Who peer assessment, the Peer-Victimization Scale, and the Bullying Behaviour Scale. Additional data on achievement and SEN were collected from the school archives. RESULTS. As predicted by trait EI theory, associations between trait EI and academic achievement were modest and limited to Year 3 children. Higher trait EI scores were related to more nominations from peers for prosocial behaviours and fewer nominations for antisocial behaviour as well as lower scores on self-reported bulling behaviours. Furthermore, SEN students scored lower on trait EI compared to students without SEN. CONCLUSIONS. Trait EI holds important and multifaceted implications for the socialization of primary schoolchildren.

  6. Statistical analysis of agronomical factors and weather conditions influencing deoxynivalenol levels in oats in Scandinavia.

    PubMed

    Lindblad, M; Börjesson, T; Hietaniemi, V; Elen, O

    2012-01-01

    The relationship between weather data and agronomical factors and deoxynivalenol (DON) levels in oats was examined with the aim of developing a predictive model. Data were collected from a total of 674 fields during periods of up to 10 years in Finland, Norway and Sweden, and included DON levels in the harvested oats crop, agronomical factors and weather data. The results show that there was a large regional variation in DON levels, with higher levels in one region in Norway compared with other regions in Norway, Finland and Sweden. In this region the median DON level was 1000 ng g⁻¹ and the regulatory limit for human consumption (1750 ng g⁻¹) was exceeded in 28% of the samples. In other regions the median DON levels ranged from 75 to 270 ng g⁻¹, and DON levels exceeded 1750 ng g⁻¹ in 3-8% of the samples. Including more variables than region in a multiple regression model only increased the adjusted coefficient of determination from 0.17 to 0.24, indicating that very little of the variation in DON levels could be explained by weather data or agronomical factors. Thus, it was not possible to predict DON levels based on the variables included in this study. Further studies are needed to solve this problem. Apparently the infection and/or growth of DON producing Fusarium species are promoted in certain regions. One possibility may be to study the species distribution of fungal communities and their changes during the oats cultivation period in more detail.

  7. A highly concentrated diet increases biogas production and the agronomic value of young bull's manure.

    PubMed

    Mendonça Costa, Mônica Sarolli Silva de; Lucas, Jorge de; Mendonça Costa, Luiz Antonio de; Orrico, Ana Carolina Amorim

    2016-02-01

    The increasing demand for animal protein has driven significant changes in cattle breeding systems, mainly in feedlots, with the use of young bulls fed on diets richer in concentrate (C) than in forage (F). These changes are likely to affect animal manure, demanding re-evaluation of the biogas production per kg of TS and VS added, as well as of its agronomic value as a biofertilizer, after anaerobic digestion. Here, we determined the biogas production and agronomic value (i.e., the macronutrient concentration in the final biofertilizer) of the manure of young bulls fed on diets with more (80% C+20% F; 'HighC' diet) or less (65% C+35% F; 'LowC' diet) concentrate, evaluating the effects of temperature (25, 35, and 40°C) and the use of an inoculum, during anaerobic digestion. A total of 24 benchtop reactors were used, operating in a semi-continuous system, with a 40-day hydraulic retention time (HRT). The manure from animals given the HighC diet had the greatest potential for biogas production, when digested with the use of an inoculum and at 35 or 40°C (0.6326 and 0.6207m(3)biogas/kg volatile solids, or VS, respectively). We observed the highest levels of the macronutrients N, P, and K in the biofertilizer from the manure of animals given HighC. Our results show that the manure of young bulls achieves its highest potential for biogas production and agronomic value when animals are fed diets richer in concentrate, and that biogas production increases if digestion is performed at higher temperatures, and with the use of an inoculum.

  8. An agronomic field-scale sensor network for monitoring soil water and temperature variation

    NASA Astrophysics Data System (ADS)

    Brown, D. J.; Gasch, C.; Brooks, E. S.; Huggins, D. R.; Campbell, C. S.; Cobos, D. R.

    2014-12-01

    Environmental sensor networks have been deployed in a variety of contexts to monitor plant, air, water and soil properties. To date, there have been relatively few such networks deployed to monitor dynamic soil properties in cropped fields. Here we report on experience with a distributed soil sensor network that has been deployed for seven years in a research farm with ongoing agronomic field operations. The Washington State University R. J. Cook Agronomy Farm (CAF), Pullman, WA, USA has recently been designated a United States Department of Agriculture (USDA) Long-Term Agro-Ecosystem Research (LTAR) site. In 2007, 12 geo-referenced locations at CAF were instrumented, then in 2009 this network was expended to 42 locations distributed across the 37-ha farm. At each of this locations, Decagon 5TE probes (Decagon Devices Inc., Pullman, WA, USA) were installed at five depths (30, 60, 90, 120, and 150 cm), with temperature and volumetric soil moisture content recorded hourly. Initially, data loggers were wirelessly connected to a data station that could be accessed through a cell connection, but due to the logistics of agronomic field operations, we later buried the dataloggers at each site and now periodically download data via local radio transmission. In this presentation, we share our experience with the installation, maintenance, calibration and data processing associated with an agronomic soil monitoring network. We also present highlights of data derived from this network, including seasonal fluctuations of soil temperature and volumetric water content at each depth, and how these measurements are influenced by crop type, soil properties, landscape position, and precipitation events.

  9. Birth Order Positions and Personality Traits.

    ERIC Educational Resources Information Center

    Tharbe, Ida Hartini Ahmad; Harun, Lily Mastura Hj.

    The growing concern for the development of teenagers has brought up issues regarding the role of the family system in shaping the personality traits of children. Alfred Adler (1870-1937), an Austrian psychiatrist who introduced the psychological/therapeutic model, "Individual Psychology," highlighted the importance of birth order positions in…

  10. Quantitative Field Testing Heterodera glycines from Metagenomic DNA Samples Isolated Directly from Soil under Agronomic Production

    PubMed Central

    Li, Yan; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2014-01-01

    A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil. PMID:24587100

  11. Agronomic characterization of the Argentina Indicator Region. [U.S. corn belt and Argentine pampas

    NASA Technical Reports Server (NTRS)

    Hicks, D. R. (Principal Investigator)

    1982-01-01

    An overview of the Argentina indicator region including information on topography, climate, soils and vegetation is presented followed by a regionalization of crop livestock land use. Corn/soybean production and exports as well as agricultural practices are discussed. Similarities and differences in the physical agronomic scene, crop livestock land use and agricultural practices between the U.S. corn belt and the Argentine pampa are considered. The Argentine agricultural economy is described. Crop calendars for the Argentina indicator region, an accompanying description, notes on crop-livestock zones, wheat production, field size, and agricultural problems and practices are included.

  12. Quantitative field testing Heterodera glycines from metagenomic DNA samples isolated directly from soil under agronomic production.

    PubMed

    Li, Yan; Lawrence, Gary W; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P

    2014-01-01

    A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil.

  13. Agronomic threshold of soil available phosphorus in grey desert soils in Xinjiang, China

    NASA Astrophysics Data System (ADS)

    Wang, B.; Liu, H.; Hao, X. Y.; Wang, X. H.; Sun, J. S.; Li, J. M.; Ma, Y. B.

    2016-08-01

    Based on 23 years of data, yields of maize, wheat and cotton were modelled under different fertilizer management practices and at different levels of available phosphorus (Olsen-P) in soil. Three types of threshold models were used, namely linear-linear (LL), linear- plateau (LP), and Mitscherlich type exponential (Exp). The agronomic thresholds of available phosphorus were 25.4 mgkg-1 for cotton, 14.8 mgkg-1 for wheat, 13.1 mgkg-1 for maize and 25.4 mgkg-1 for the grey desert soil regions of Xinjiang in China as a whole.

  14. Trait stacking via targeted genome editing.

    PubMed

    Ainley, William M; Sastry-Dent, Lakshmi; Welter, Mary E; Murray, Michael G; Zeitler, Bryan; Amora, Rainier; Corbin, David R; Miles, Rebecca R; Arnold, Nicole L; Strange, Tonya L; Simpson, Matthew A; Cao, Zehui; Carroll, Carley; Pawelczak, Katherine S; Blue, Ryan; West, Kim; Rowland, Lynn M; Perkins, Douglas; Samuel, Pon; Dewes, Cristie M; Shen, Liu; Sriram, Shreedharan; Evans, Steven L; Rebar, Edward J; Zhang, Lei; Gregory, Phillip D; Urnov, Fyodor D; Webb, Steven R; Petolino, Joseph F

    2013-12-01

    Modern agriculture demands crops carrying multiple traits. The current paradigm of randomly integrating and sorting independently segregating transgenes creates severe downstream breeding challenges. A versatile, generally applicable solution is hereby provided: the combination of high-efficiency targeted genome editing driven by engineered zinc finger nucleases (ZFNs) with modular 'trait landing pads' (TLPs) that allow 'mix-and-match', on-demand transgene integration and trait stacking in crop plants. We illustrate the utility of nuclease-driven TLP technology by applying it to the stacking of herbicide resistance traits. We first integrated into the maize genome an herbicide resistance gene, pat, flanked with a TLP (ZFN target sites and sequences homologous to incoming DNA) using WHISKERS™-mediated transformation of embryogenic suspension cultures. We established a method for targeted transgene integration based on microparticle bombardment of immature embryos and used it to deliver a second trait precisely into the TLP via cotransformation with a donor DNA containing a second herbicide resistance gene, aad1, flanked by sequences homologous to the integrated TLP along with a corresponding ZFN expression construct. Remarkably, up to 5% of the embryo-derived transgenic events integrated the aad1 transgene precisely at the TLP, that is, directly adjacent to the pat transgene. Importantly and consistent with the juxtaposition achieved via nuclease-driven TLP technology, both herbicide resistance traits cosegregated in subsequent generations, thereby demonstrating linkage of the two independently transformed transgenes. Because ZFN-mediated targeted transgene integration is becoming applicable across an increasing number of crop species, this work exemplifies a simple, facile and rapid approach to trait stacking.

  15. Physiological Traits Associated with Wheat Yield Potential and Performance under Water-Stress in a Mediterranean Environment.

    PubMed

    Del Pozo, Alejandro; Yáñez, Alejandra; Matus, Iván A; Tapia, Gerardo; Castillo, Dalma; Sanchez-Jardón, Laura; Araus, José L

    2016-01-01

    Different physiological traits have been proposed as key traits associated with yield potential as well as performance under water stress. The aim of this paper is to examine the genotypic variability of leaf chlorophyll, stem water-soluble carbohydrate content and carbon isotope discrimination (Δ(13)C), and their relationship with grain yield (GY) and other agronomical traits, under contrasting water conditions in a Mediterranean environment. The study was performed on a large collection of 384 wheat genotypes grown under water stress (WS, rainfed), mild water stress (MWS, deficit irrigation), and full irrigation (FI). The average GY of two growing seasons was 2.4, 4.8, and 8.9 Mg ha(-1) under WS, MWS, and FI, respectively. Chlorophyll content at anthesis was positively correlated with GY (except under FI in 2011) and the agronomical components kernels per spike (KS) and thousand kernel weight (TKW). The WSC content at anthesis (WSCCa) was negatively correlated with spikes per square meter (SM2), but positively correlated with KS and TKW under WS and FI conditions. As a consequence, the relationships between WSCCa with GY were low or not significant. Therefore, selecting for high stem WSC would not necessary lead to genotypes of GY potential. The relationship between Δ(13)C and GY was positive under FI and MWS but negative under severe WS (in 2011), indicating higher water use under yield potential and MWS conditions.

  16. Physiological Traits Associated with Wheat Yield Potential and Performance under Water-Stress in a Mediterranean Environment

    PubMed Central

    del Pozo, Alejandro; Yáñez, Alejandra; Matus, Iván A.; Tapia, Gerardo; Castillo, Dalma; Sanchez-Jardón, Laura; Araus, José L.

    2016-01-01

    Different physiological traits have been proposed as key traits associated with yield potential as well as performance under water stress. The aim of this paper is to examine the genotypic variability of leaf chlorophyll, stem water-soluble carbohydrate content and carbon isotope discrimination (Δ13C), and their relationship with grain yield (GY) and other agronomical traits, under contrasting water conditions in a Mediterranean environment. The study was performed on a large collection of 384 wheat genotypes grown under water stress (WS, rainfed), mild water stress (MWS, deficit irrigation), and full irrigation (FI). The average GY of two growing seasons was 2.4, 4.8, and 8.9 Mg ha−1 under WS, MWS, and FI, respectively. Chlorophyll content at anthesis was positively correlated with GY (except under FI in 2011) and the agronomical components kernels per spike (KS) and thousand kernel weight (TKW). The WSC content at anthesis (WSCCa) was negatively correlated with spikes per square meter (SM2), but positively correlated with KS and TKW under WS and FI conditions. As a consequence, the relationships between WSCCa with GY were low or not significant. Therefore, selecting for high stem WSC would not necessary lead to genotypes of GY potential. The relationship between Δ13C and GY was positive under FI and MWS but negative under severe WS (in 2011), indicating higher water use under yield potential and MWS conditions. PMID:27458470

  17. Physiological Traits Associated with Wheat Yield Potential and Performance under Water-Stress in a Mediterranean Environment.

    PubMed

    Del Pozo, Alejandro; Yáñez, Alejandra; Matus, Iván A; Tapia, Gerardo; Castillo, Dalma; Sanchez-Jardón, Laura; Araus, José L

    2016-01-01

    Different physiological traits have been proposed as key traits associated with yield potential as well as performance under water stress. The aim of this paper is to examine the genotypic variability of leaf chlorophyll, stem water-soluble carbohydrate content and carbon isotope discrimination (Δ(13)C), and their relationship with grain yield (GY) and other agronomical traits, under contrasting water conditions in a Mediterranean environment. The study was performed on a large collection of 384 wheat genotypes grown under water stress (WS, rainfed), mild water stress (MWS, deficit irrigation), and full irrigation (FI). The average GY of two growing seasons was 2.4, 4.8, and 8.9 Mg ha(-1) under WS, MWS, and FI, respectively. Chlorophyll content at anthesis was positively correlated with GY (except under FI in 2011) and the agronomical components kernels per spike (KS) and thousand kernel weight (TKW). The WSC content at anthesis (WSCCa) was negatively correlated with spikes per square meter (SM2), but positively correlated with KS and TKW under WS and FI conditions. As a consequence, the relationships between WSCCa with GY were low or not significant. Therefore, selecting for high stem WSC would not necessary lead to genotypes of GY potential. The relationship between Δ(13)C and GY was positive under FI and MWS but negative under severe WS (in 2011), indicating higher water use under yield potential and MWS conditions. PMID:27458470

  18. Systems genetics approaches to understand complex traits

    PubMed Central

    Civelek, Mete; Lusis, Aldons J.

    2014-01-01

    Systems genetics is an approach to understand the flow of biological information that underlies complex traits. It uses a range of experimental and statistical methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels, in populations that vary for traits of interest. Systems genetics studies have provided the first global view of the molecular architecture of complex traits and are useful for the identification of genes, pathways and networks that underlie common human diseases. Given the urgent need to understand how the thousands of loci that have been identified in genome-wide association studies contribute to disease susceptibility, systems genetics is likely to become an increasingly important approach to understanding both biology and disease. PMID:24296534

  19. Affective Traits in Schizophrenia and Schizotypy

    PubMed Central

    Horan, William P.; Blanchard, Jack J.; Clark, Lee Anna; Green, Michael F.

    2008-01-01

    This article reviews empirical studies of affective traits in individuals with schizophrenia spectrum disorders, population-based investigations of vulnerability to psychosis, and genetic and psychometric high-risk samples. The review focuses on studies that use self-report trait questionnaires to assess Negative Affectivity (NA) and Positive Affectivity (PA), which are conceptualized in contemporary models of personality as broad, temperamentally-based dispositions to experience corresponding emotional states. Individuals with schizophrenia report a pattern of stably elevated NA and low PA throughout the illness course. Among affected individuals, these traits are associated with variability in several clinically important features, including functional outcome, quality of life, and stress reactivity. Furthermore, evidence that elevated NA and low PA (particularly the facet of anhedonia) predict the development of psychosis and are detectable in high-risk samples suggests that these traits play a role in vulnerability to schizophrenia, though they are implicated in other forms of psychopathology as well. Results are discussed in terms of their implications for treatment, etiological models, and future research to advance the study of affective traits in schizophrenia and schizotypy. PMID:18667393

  20. Quantifying hummingbird preference for floral trait combinations: The role of selection on trait interactions in the evolution of pollination syndromes.

    PubMed

    Fenster, Charles B; Reynolds, Richard J; Williams, Christopher W; Makowsky, Robert; Dudash, Michele R

    2015-05-01

    Darwin recognized the flower's importance for the study of adaptation and emphasized that the flower's functionality reflects the coordinated action of multiple traits. Here we use a multitrait manipulative approach to quantify the potential role of selection acting on floral trait combinations underlying the divergence and maintenance of three related North American species of Silene (Caryophyllaceae). We artificially generated 48 plant phenotypes corresponding to all combinations of key attractive traits differing among the three Silene species (color, height, inflorescence architecture, flower orientation, and corolla-tube width). We quantified main and interaction effects of trait manipulation on hummingbird visitation preference using experimental arrays. The main effects of floral display height and floral orientation strongly influenced hummingbird visitation, with hummingbirds preferring flowers held high above the ground and vertically to the sky. Hummingbirds also prefer traits in a nonadditive manner as multiple two-way and higher order interaction effects were important predictors of hummingbird visitation. Contemporary trait combinations found in hummingbird pollinated S. virginica are mostly preferred. Our study demonstrates the likelihood of pollination syndromes evolving due to selection on trait combinations and highlights the importance of trait interactions in understanding the evolution of complex adaptations. PMID:25765062

  1. Quantifying hummingbird preference for floral trait combinations: The role of selection on trait interactions in the evolution of pollination syndromes.

    PubMed

    Fenster, Charles B; Reynolds, Richard J; Williams, Christopher W; Makowsky, Robert; Dudash, Michele R

    2015-05-01

    Darwin recognized the flower's importance for the study of adaptation and emphasized that the flower's functionality reflects the coordinated action of multiple traits. Here we use a multitrait manipulative approach to quantify the potential role of selection acting on floral trait combinations underlying the divergence and maintenance of three related North American species of Silene (Caryophyllaceae). We artificially generated 48 plant phenotypes corresponding to all combinations of key attractive traits differing among the three Silene species (color, height, inflorescence architecture, flower orientation, and corolla-tube width). We quantified main and interaction effects of trait manipulation on hummingbird visitation preference using experimental arrays. The main effects of floral display height and floral orientation strongly influenced hummingbird visitation, with hummingbirds preferring flowers held high above the ground and vertically to the sky. Hummingbirds also prefer traits in a nonadditive manner as multiple two-way and higher order interaction effects were important predictors of hummingbird visitation. Contemporary trait combinations found in hummingbird pollinated S. virginica are mostly preferred. Our study demonstrates the likelihood of pollination syndromes evolving due to selection on trait combinations and highlights the importance of trait interactions in understanding the evolution of complex adaptations.

  2. Integration of agronomic practices with herbicides for sustainable weed management in aerobic rice.

    PubMed

    Anwar, M P; Juraimi, A S; Mohamed, M T M; Uddin, M K; Samedani, B; Puteh, A; Man, Azmi

    2013-01-01

    Till now, herbicide seems to be a cost effective tool from an agronomic view point to control weeds. But long term efficacy and sustainability issues are the driving forces behind the reconsideration of herbicide dependent weed management strategy in rice. This demands reappearance of physical and cultural management options combined with judicious herbicide application in a more comprehensive and integrated way. Keeping those in mind, some agronomic tools along with different manual weeding and herbicides combinations were evaluated for their weed control efficacy in rice under aerobic soil conditions. Combination of competitive variety, higher seeding rate, and seed priming resulted in more competitive cropping system in favor of rice, which was reflected in lower weed pressure, higher weed control efficiency, and better yield. Most of the herbicides exhibited excellent weed control efficiency. Treatments comprising only herbicides required less cost involvement but produced higher net benefit. On the contrary, treatments comprising both herbicide and manual weeding required high cost involvement and thus produced lower net benefit. Therefore, adoption of competitive rice variety, higher seed rate, and seed priming along with spraying different early-postemergence herbicides in rotation at 10 days after seeding (DAS) followed by a manual weeding at 30 DAS may be recommended from sustainability view point.

  3. Waterfowl foraging in winter-flooded ricefields: Any agronomic benefits for farmers?

    PubMed

    Brogi, Anne; Pernollet, Claire A; Gauthier-Clerc, Michel; Guillemain, Matthieu

    2015-12-01

    Winter-flooding of ricefields provides foraging habitat to waterfowl, which in return may bring agronomic benefits to farmers. Our study experimentally tested the effect of mallards (Anas platyrhynchos) on the standing stalks and weed seed bank in the Camargue (France), both of which present major challenges for farmers. Three duck densities were tested: (D1) 5 ducks ha(-1) (historical nocturnal density), (D2) 23 ducks ha(-1) (present nocturnal density), and (D3) 300 ducks ha(-1) (Asian rice-duck farming density). The ducks reduced the stalks significantly: -27 % (D1), -52 % (D2), and -91 % (D3). Conversely, they decreased the number of seeds by only 3 % (D3) and the seed mass by about 21 % (D1 and D3), which was not significant. Besides they had no effect on seed species richness. This study clearly demonstrates that the winter-flooding effect on straw decomposition can be enhanced by waterfowl foraging, hence showing an agronomic benefit from ducks to farmers. However, there was no clear effect in terms of seed bank reduction.

  4. Agronomic Practices for Improving Gentle Remediation of Trace Element-Contaminated Soils.

    PubMed

    Kidd, Petra; Mench, Michel; Álvarez-López, Vanessa; Bert, Valérie; Dimitriou, Ioannis; Friesl-Hanl, Wolfgang; Herzig, Rolf; Janssen, Jolien Olga; Kolbas, Aliaksandr; Müller, Ingo; Neu, Silke; Renella, Giancarlo; Ruttens, Ann; Vangronsveld, Jaco; Puschenreiter, Markus

    2015-01-01

    The last few decades have seen the rise of Gentle soil Remediation Options (GRO), which notably include in situ contaminant stabilization ("inactivation") and plant-based (generally termed "phytoremediation") options. For trace element (TE)-contaminated sites, GRO aim to either decrease their labile pool and/or total content in the soil, thereby reducing related pollutant linkages. Much research has been dedicated to the screening and selection of TE-tolerant plant species and genotypes for application in GRO. However, the number of field trials demonstrating successful GRO remains well below the number of studies carried out at a greenhouse level. The move from greenhouse to field conditions requires incorporating agronomical knowledge into the remediation process and the ecological restoration of ecosystem services. This review summarizes agronomic practices against their demonstrated or potential positive effect on GRO performance, including plant selection, soil management practices, crop rotation, short rotation coppice, intercropping/row cropping, planting methods and plant densities, harvest and fertilization management, pest and weed control and irrigation management. Potentially negative effects of GRO, e.g., the introduction of potentially invasive species, are also discussed. Lessons learnt from long-term European field case sites are given for aiding the choice of appropriate management practices and plant species.

  5. IMPROVING BIOMASS LOGISTICS COST WITHIN AGRONOMIC SUSTAINABILITY CONSTRAINTS AND BIOMASS QUALITY TARGETS

    SciTech Connect

    J. Richard Hess; Kevin L. Kenney; Christopher T. Wright; David J. Muth; William Smith

    2012-10-01

    Equipment manufacturers have made rapid improvements in biomass harvesting and handling equipment. These improvements have increased transportation and handling efficiencies due to higher biomass densities and reduced losses. Improvements in grinder efficiencies and capacity have reduced biomass grinding costs. Biomass collection efficiencies (the ratio of biomass collected to the amount available in the field) as high as 75% for crop residues and greater than 90% for perennial energy crops have also been demonstrated. However, as collection rates increase, the fraction of entrained soil in the biomass increases, and high biomass residue removal rates can violate agronomic sustainability limits. Advancements in quantifying multi-factor sustainability limits to increase removal rate as guided by sustainable residue removal plans, and mitigating soil contamination through targeted removal rates based on soil type and residue type/fraction is allowing the use of new high efficiency harvesting equipment and methods. As another consideration, single pass harvesting and other technologies that improve harvesting costs cause biomass storage moisture management challenges, which challenges are further perturbed by annual variability in biomass moisture content. Monitoring, sampling, simulation, and analysis provide basis for moisture, time, and quality relationships in storage, which has allowed the development of moisture tolerant storage systems and best management processes that combine moisture content and time to accommodate baled storage of wet material based upon “shelf-life.” The key to improving biomass supply logistics costs has been developing the associated agronomic sustainability and biomass quality technologies and processes that allow the implementation of equipment engineering solutions.

  6. Waterfowl foraging in winter-flooded ricefields: Any agronomic benefits for farmers?

    PubMed

    Brogi, Anne; Pernollet, Claire A; Gauthier-Clerc, Michel; Guillemain, Matthieu

    2015-12-01

    Winter-flooding of ricefields provides foraging habitat to waterfowl, which in return may bring agronomic benefits to farmers. Our study experimentally tested the effect of mallards (Anas platyrhynchos) on the standing stalks and weed seed bank in the Camargue (France), both of which present major challenges for farmers. Three duck densities were tested: (D1) 5 ducks ha(-1) (historical nocturnal density), (D2) 23 ducks ha(-1) (present nocturnal density), and (D3) 300 ducks ha(-1) (Asian rice-duck farming density). The ducks reduced the stalks significantly: -27 % (D1), -52 % (D2), and -91 % (D3). Conversely, they decreased the number of seeds by only 3 % (D3) and the seed mass by about 21 % (D1 and D3), which was not significant. Besides they had no effect on seed species richness. This study clearly demonstrates that the winter-flooding effect on straw decomposition can be enhanced by waterfowl foraging, hence showing an agronomic benefit from ducks to farmers. However, there was no clear effect in terms of seed bank reduction. PMID:26121948

  7. Genetic mapping of quantitative trait loci affecting growth and carcass traits in F2 intercross chickens.

    PubMed

    Uemoto, Y; Sato, S; Odawara, S; Nokata, H; Oyamada, Y; Taguchi, Y; Yanai, S; Sasaki, O; Takahashi, H; Nirasawa, K; Kobayashi, E

    2009-03-01

    We constructed a chicken F(2) resource population to facilitate the genetic improvement of economically important traits, particularly growth and carcass traits. An F(2) population comprising 240 chickens obtained by crossing a Shamo (lean, lightweight Japanese native breed) male and White Plymouth Rock breed (fat, heavyweight broiler) females was measured for BW, carcass weight (CW), abdominal fat weight (AFW), breast muscle weight (BMW), and thigh muscle weight (TMW) and was used for genome-wide linkage and QTL analysis, using a total of 240 microsatellite markers. A total of 14 QTL were detected at a 5% chromosome-wide level, and 7 QTL were significant at a 5% experiment-wide level for the traits evaluated in the F(2) population. For growth traits, significant and suggestive QTL affecting BW (measured at 6 and 9 wk) and average daily gain were identified on similar regions of chromosomes 1 and 3. For carcass traits, the QTL effects on CW were detected on chromosomes 1 and 3, with the greatest F-ratio of 15.0 being obtained for CW on chromosome 3. Quantitative trait loci positions affecting BMW and TMW were not detected at the same loci as those detected for BMW percentage of CW and TMW percentage of CW. For AFW, QTL positions were detected at the same loci as those detected for AFW percentage of CW. The present study identified significant QTL affecting BW, CW, and AFW. PMID:19211515

  8. Clines in polygenic traits.

    PubMed

    Barton, N H

    1999-12-01

    This article outlines theoretical models of clines in additive polygenic traits, which are maintained by stabilizing selection towards a spatially varying optimum. Clines in the trait mean can be accurately predicted, given knowledge of the genetic variance. However, predicting the variance is difficult, because it depends on genetic details. Changes in genetic variance arise from changes in allele frequency, and in linkage disequilibria. Allele frequency changes dominate when selection is weak relative to recombination, and when there are a moderate number of loci. With a continuum of alleles, gene flow inflates the genetic variance in the same way as a source of mutations of small effect. The variance can be approximated by assuming a Gaussian distribution of allelic effects; with a sufficiently steep cline, this is accurate even when mutation and selection alone are better described by the 'House of Cards' approximation. With just two alleles at each locus, the phenotype changes in a similar way: the mean remains close to the optimum, while the variance changes more slowly, and over a wider region. However, there may be substantial cryptic divergence at the underlying loci. With strong selection and many loci, linkage disequilibria are the main cause of changes in genetic variance. Even for strong selection, the infinitesimal model can be closely approximated by assuming a Gaussian distribution of breeding values. Linkage disequilibria can generate a substantial increase in genetic variance, which is concentrated at sharp gradients in trait means.

  9. Trait Emotional Intelligence and Personality

    PubMed Central

    Furnham, Adrian; Petrides, K. V.

    2015-01-01

    This study investigated if the linkages between trait emotional intelligence (trait EI) and the Five-Factor Model of personality were invariant between men and women. Five English-speaking samples (N = 307-685) of mostly undergraduate students each completed a different measure of the Big Five personality traits and either the full form or short form of the Trait Emotional Intelligence Questionnaire (TEIQue). Across samples, models predicting global TEIQue scores from the Big Five were invariant between genders, with Neuroticism and Extraversion being the strongest trait EI correlates, followed by Conscientiousness, Agreeableness, and Openness. However, there was some evidence indicating that the gender-specific contributions of the Big Five to trait EI vary depending on the personality measure used, being more consistent for women. Discussion focuses on the validity of the TEIQue as a measure of trait EI and its psychometric properties, more generally. PMID:25866439

  10. The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

    PubMed

    Madin, Joshua S; Anderson, Kristen D; Andreasen, Magnus Heide; Bridge, Tom C L; Cairns, Stephen D; Connolly, Sean R; Darling, Emily S; Diaz, Marcela; Falster, Daniel S; Franklin, Erik C; Gates, Ruth D; Hoogenboom, Mia O; Huang, Danwei; Keith, Sally A; Kosnik, Matthew A; Kuo, Chao-Yang; Lough, Janice M; Lovelock, Catherine E; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M; Pochon, Xavier; Pratchett, Morgan S; Putnam, Hollie M; Roberts, T Edward; Stat, Michael; Wallace, Carden C; Widman, Elizabeth; Baird, Andrew H

    2016-01-01

    Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research. PMID:27023900

  11. The Coral Trait Database, a curated database of trait information for coral species from the global oceans

    PubMed Central

    Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C.L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

    2016-01-01

    Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research. PMID:27023900

  12. The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

    PubMed

    Madin, Joshua S; Anderson, Kristen D; Andreasen, Magnus Heide; Bridge, Tom C L; Cairns, Stephen D; Connolly, Sean R; Darling, Emily S; Diaz, Marcela; Falster, Daniel S; Franklin, Erik C; Gates, Ruth D; Hoogenboom, Mia O; Huang, Danwei; Keith, Sally A; Kosnik, Matthew A; Kuo, Chao-Yang; Lough, Janice M; Lovelock, Catherine E; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M; Pochon, Xavier; Pratchett, Morgan S; Putnam, Hollie M; Roberts, T Edward; Stat, Michael; Wallace, Carden C; Widman, Elizabeth; Baird, Andrew H

    2016-03-29

    Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

  13. Interpersonal Problems Associated with Multidimensional Personality Questionnaire Traits in Women during the Transition to Adulthood

    ERIC Educational Resources Information Center

    Hopwood, Christopher J.; Burt, S. Alexandra; Keel, Pamela K.; Neale, Michael C.; Boker, Steven M.; Klump, Kelly L.

    2013-01-01

    Personality traits are known to be associated with a host of important life outcomes, including interpersonal dysfunction. The interpersonal circumplex offers a comprehensive system for articulating the kinds of interpersonal problems associated with personality traits. In the current study, traits as measured by the Multidimensional Personality…

  14. Traits and Trade-Offs Are an Important Tier

    ERIC Educational Resources Information Center

    Nettle, Daniel

    2007-01-01

    Replies to comments by K. M. Sheldon et al on the author's original article on evolution and personality variation. Sheldon et al concurred with the thrust of that article that the way natural selection shapes or gives rise to interindividual variation is a worthy topic for evolutionary psychologists to consider, so at a broad level Sheldon et al…

  15. Economics of selecting for sex: the most important genetic trait.

    PubMed

    Seidel, G E

    2003-01-15

    Over 20,000 calves have resulted from artificial insemination (AI) of cattle with sexed, frozen/thawed sperm in the course of experimentation in several countries, and from commercial sales in the United Kingdom. This technology likely will become commercially available in many countries within a few years. Accuracy of the process is about 90% for either sex, and resulting calves appear to be no different from non-sexed controls in birthweight, mortality, rate of gain, and incidence of abnormalities. The main determinants of the extent of use of sexed sperm will be pregnancy rate and cost. Fertility of low doses (1.5 x 10(6)-2 x 10(6)) of sexed, frozen sperm for AI of heifers usually has been in the range of 70-80% of unsexed sperm at normal doses (10 x 10(6)-20 x 10(6) sperm) in well managed herds; it has been lower in poorly managed herds, and likely will be lower with lactating dairy cows. It is expected that fertility of sexed sperm will increase significantly due to very recent improvements in the hydrodynamics of the sexing process and potential improvements in cryopreservation procedures. It is unclear how sexed sperm will be priced; the cost of sexed sperm for cattle will likely be more than double the cost of unsexed sperm in most markets. The economic benefit of using sexed sperm also will depend on the baseline fertility of the herd since at lower fertility, it takes more doses of semen per calf produced. It is noted that for a small percentage of elite cattle, the economics of using sexed sperm do not depend primarily on increased production or efficiency of producing meat or milk, but rather on factors such as scarcity, tradition, cattle show winnings, and biosecurity during herd expansion. Until sorting efficiencies improve and costs decline, sales likely will be limited primarily to these niche markets. With near normal fertility and a premium for sexing in the range of US$ 10 per insemination dose, sexed sperm likely would become economically and environmentally beneficial for many, if not most populations of cattle being bred by AI. PMID:12499006

  16. EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multivalent tetraploids that include many plant species, such as potato, sugarcane and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such ...

  17. On the fate of sexual traits under asexuality.

    PubMed

    van der Kooi, Casper J; Schwander, Tanja

    2014-11-01

    Environmental shifts and life-history changes may result in formerly adaptive traits becoming non-functional or maladaptive. In the absence of pleiotropy and other constraints, such traits may decay as a consequence of neutral mutation accumulation or selective processes, highlighting the importance of natural selection for adaptations. A suite of traits are expected to lose their adaptive function in asexual organisms derived from sexual ancestors, and the many independent transitions to asexuality allow for comparative studies of parallel trait maintenance versus decay. In addition, because certain traits, notably male-specific traits, are usually not exposed to selection under asexuality, their decay would have to occur as a consequence of drift. Selective processes could drive the decay of traits associated with costs, which may be the case for the majority of sexual traits expressed in females. We review the fate of male and female sexual traits in 93 animal lineages characterized by asexual reproduction, covering a broad taxon range including molluscs, arachnids, diplopods, crustaceans and eleven different hexapod orders. Many asexual lineages are still able occasionally to produce males. These asexually produced males are often largely or even fully functional, revealing that major developmental pathways can remain quiescent and functional over extended time periods. By contrast, for asexual females, there is a parallel and rapid decay of sexual traits, especially of traits related to mate attraction and location, as expected given the considerable costs often associated with the expression of these traits. The level of decay of female sexual traits, in addition to asexual females being unable to fertilize their eggs, would severely impede reversals to sexual reproduction, even in recently derived asexual lineages. More generally, the parallel maintenance versus decay of different trait types across diverse asexual lineages suggests that neutral traits

  18. A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea.

    PubMed

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-06-10

    We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.

  19. Identification of quantitative trait transcripts for growth traits in the large scales of liver and muscle samples.

    PubMed

    Xiong, Xinwei; Yang, Hui; Yang, Bin; Chen, Congying; Huang, Lusheng

    2015-07-01

    Growth-related traits are economically important traits to the pig industry. Identification of causative gene and mutation responsible for growth-related QTL will facilitate the improvement of pig growth through marker-assisted selection. In this study, we applied whole genome gene expression and quantitative trait transcript (QTT) analyses in 497 liver and 586 longissimus dorsi muscle samples to identify candidate genes and dissect the genetic basis of pig growth in a white Duroc × Erhualian F2 resource population. A total of 20,108 transcripts in liver and 23,728 transcripts in muscle with expression values were used for association analysis between gene expression level and phenotypic value. At the significance threshold of P < 0.0005, we identified a total of 169 and 168 QTTs for nine growth-related traits in liver and muscle, respectively. We also found that some QTTs were correlated to more than one trait. The QTTs identified here showed high tissue specificity. We did not identify any QTTs that were associated with one trait in both liver and muscle. Through an integrative genomic approach, we identified SDR16C5 as the important candidate gene in pig growth trait. These findings contribute to further identification of the causative genes for porcine growth traits and facilitate improvement of pig breeding.

  20. Quantitative trait locus mapping and functional genomics of an organophosphate resistance trait in the western corn rootworm, Diabrotica virgifera virgifera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The western corn rootworm (WCR), Diabrotica virgifera virgifera, is an insect pest of corn, and population suppression with chemical insecticides is an important management tool. Traits conferring organophosphate insecticide resistance have increased in frequency among WCR populations, resulting in...

  1. A database of life-history traits of European amphibians

    PubMed Central

    Moulherat, Sylvain; Calvez, Olivier; Stevens, Virginie M; Clobert, Jean; Schmeller, Dirk S

    2014-01-01

    Abstract In the current context of climate change and landscape fragmentation, efficient conservation strategies require the explicit consideration of life history traits. This is particularly true for amphibians, which are highly threatened worldwide, composed by more than 7400 species, which is constitute one of the most species-rich vertebrate groups. The collection of information on life history traits is difficult due to the ecology of species and remoteness of their habitats. It is therefore not surprising that our knowledge is limited, and missing information on certain life history traits are common for in this species group. We compiled data on amphibian life history traits from literature in an extensive database with morphological and behavioral traits, habitat preferences and movement abilities for 86 European amphibian species (50 Anuran and 36 Urodela species). When it were available, we reported data for males, females, juveniles and tadpoles. Our database may serve as an important starting point for further analyses regarding amphibian conservation. PMID:25425939

  2. Plant functional traits predict green roof ecosystem services.

    PubMed

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services.

  3. Plant functional traits predict green roof ecosystem services.

    PubMed

    Lundholm, Jeremy; Tran, Stephanie; Gebert, Luke

    2015-02-17

    Plants make important contributions to the services provided by engineered ecosystems such as green roofs. Ecologists use plant species traits as generic predictors of geographical distribution, interactions with other species, and ecosystem functioning, but this approach has been little used to optimize engineered ecosystems. Four plant species traits (height, individual leaf area, specific leaf area, and leaf dry matter content) were evaluated as predictors of ecosystem properties and services in a modular green roof system planted with 21 species. Six indicators of ecosystem services, incorporating thermal, hydrological, water quality, and carbon sequestration functions, were predicted by the four plant traits directly or indirectly via their effects on aggregate ecosystem properties, including canopy density and albedo. Species average height and specific leaf area were the most useful traits, predicting several services via effects on canopy density or growth rate. This study demonstrates that easily measured plant traits can be used to select species to optimize green roof performance across multiple key services. PMID:25599106

  4. Functional traits in agriculture: agrobiodiversity and ecosystem services.

    PubMed

    Wood, Stephen A; Karp, Daniel S; DeClerck, Fabrice; Kremen, Claire; Naeem, Shahid; Palm, Cheryl A

    2015-09-01

    Functional trait research has led to greater understanding of the impacts of biodiversity in ecosystems. Yet, functional trait approaches have not been widely applied to agroecosystems and understanding of the importance of agrobiodiversity remains limited to a few ecosystem processes and services. To improve this understanding, we argue here for a functional trait approach to agroecology that adopts recent advances in trait research for multitrophic and spatially heterogeneous ecosystems. We suggest that trait values should be measured across environmental conditions and agricultural management regimes to predict how ecosystem services vary with farm practices and environment. This knowledge should be used to develop management strategies that can be easily implemented by farmers to manage agriculture to provide multiple ecosystem services.

  5. Brain structure links trait creativity to openness to experience.

    PubMed

    Li, Wenfu; Li, Xueting; Huang, Lijie; Kong, Xiangzhen; Yang, Wenjing; Wei, Dongtao; Li, Jingguang; Cheng, Hongsheng; Zhang, Qinglin; Qiu, Jiang; Liu, Jia

    2015-02-01

    Creativity is crucial to the progression of human civilization and has led to important scientific discoveries. Especially, individuals are more likely to have scientific discoveries if they possess certain personality traits of creativity (trait creativity), including imagination, curiosity, challenge and risk-taking. This study used voxel-based morphometry to identify the brain regions underlying individual differences in trait creativity, as measured by the Williams creativity aptitude test, in a large sample (n = 246). We found that creative individuals had higher gray matter volume in the right posterior middle temporal gyrus (pMTG), which might be related to semantic processing during novelty seeking (e.g. novel association, conceptual integration and metaphor understanding). More importantly, although basic personality factors such as openness to experience, extroversion, conscientiousness and agreeableness (as measured by the NEO Personality Inventory) all contributed to trait creativity, only openness to experience mediated the association between the right pMTG volume and trait creativity. Taken together, our results suggest that the basic personality trait of openness might play an important role in shaping an individual's trait creativity.

  6. Brain structure links trait creativity to openness to experience

    PubMed Central

    Huang, Lijie; Kong, Xiangzhen; Yang, Wenjing; Wei, Dongtao; Li, Jingguang; Cheng, Hongsheng; Zhang, Qinglin

    2015-01-01

    Creativity is crucial to the progression of human civilization and has led to important scientific discoveries. Especially, individuals are more likely to have scientific discoveries if they possess certain personality traits of creativity (trait creativity), including imagination, curiosity, challenge and risk-taking. This study used voxel-based morphometry to identify the brain regions underlying individual differences in trait creativity, as measured by the Williams creativity aptitude test, in a large sample (n = 246). We found that creative individuals had higher gray matter volume in the right posterior middle temporal gyrus (pMTG), which might be related to semantic processing during novelty seeking (e.g. novel association, conceptual integration and metaphor understanding). More importantly, although basic personality factors such as openness to experience, extroversion, conscientiousness and agreeableness (as measured by the NEO Personality Inventory) all contributed to trait creativity, only openness to experience mediated the association between the right pMTG volume and trait creativity. Taken together, our results suggest that the basic personality trait of openness might play an important role in shaping an individual’s trait creativity. PMID:24603022

  7. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    PubMed Central

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  8. Designing an accompanying ecosystem for entrepreneurship students of agronomic and forestry engineering. Opinion and commitment of the faculty

    NASA Astrophysics Data System (ADS)

    Ortiz, Leovigilda; Fernández-Ahumada, Elvira; Lara-Vélez, Pablo; Taguas, Encarnación V.; Gallardo-Cobos, Rosa; Campillo, M. Carmen; Guerrero-Ginel, José E.

    2014-05-01

    The current context has called attention to the need of training engineers with new skills beyond the purely technical. Among others, fostering the entrepreneurial spirit has gained special prominence. In the Higher School of Agronomic and Forestry Engineering of the University of Cordoba, a 12-year-experience of an entrepreneurship program for undergraduate students concluded that, for an adequate consolidation and evolution of the program, is important to establish a robust network with active participation of all actors involved. With this antecedent, a collective project conceived as an "ecosystem of support and accompaniment for entrepreneurs" is the approach proposed. The objective is to perform an evaluation of this model in terms of viability, usefulness, actions to be taken and degree of commitment. The key actors identified (undergraduate students, faculty, alumni, local and regional entrepreneurs, enterprises, public administration) have been involved in the evaluation process. This study focuses on the academic staff. For that aim, a survey to the entire faculty (N=128, response rate = 45%) and semi-structured interviews to 20 members have been performed. Data have been treated by means of univariate and multivariate analysis. Results suggest that there exists an agreement concerning the appropriateness of a collective project; there is a critical mass of teachers willing to be engaged; guidelines need to be incorporated in order to facilitate taking on tasks; main restrictions concern the existing asymmetry between formal requirements and those necessary for establishing the ecosystem. ACKNOWLEDGMENT: This research work has been developed in the framework of the ALFA III programme financed by the European Union.

  9. Designing an Accompanying Ecosystem to Foster Entrepreneurship among Agronomic and Forestry Engineering Students. Opinion and Commitment of University Lecturers

    ERIC Educational Resources Information Center

    Ortiz-Medina, L.; Fernández-Ahumada, E.; Lara-Vélez, P.; Taguas, E. V.; Gallardo-Cobos, R.; del Campillo, M. C.; Guerrero-Ginel, J. E.

    2016-01-01

    In the Higher School of Agronomic and Forestry Engineering of the University of Cordoba, a collective project conceived as an 'ecosystem to support and accompany entrepreneurs' has been proposed. The approach aims to spread and consolidate the entrepreneurial spirit and to respond to the demands of possible stakeholders involved in the whole…

  10. Enhanced efficiency fertilizers: A multi-site comparison of the effects on nitrous oxide emissions and agronomic performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The need to understand the effects of enhanced efficiency fertilizers (EEF) for their effect on nitrous oxide emissions and agronomic performance was the motivation underpinning this multi-location study across North America. Research locations participating in this study included Ames, IA; Auburn, ...

  11. EVALUATING THE ROLE OF HABITAT QUALITY ON ESTABLISHMENT OF GM AGROSTIS STOLONIFERA PLANTS IN NON-AGRONOMIC SETTINGS

    EPA Science Inventory

    We compared soil chemistry and plant community data at non-agronomic mesic locations that either did or did not contain genetically modified (GM) Agrostis stolonifera. The best two-variable logistic regression model included soil Mn content and A. stolonifera cover and explained...

  12. Sewage sludge hydrochars: properties and agronomic impact as related to different production conditions

    NASA Astrophysics Data System (ADS)

    Paneque, Marina; María De la Rosa, José; Aragón, Carlos; Kern, Jürgen; Conte, Pellegrino; Knicker, Heike

    2015-04-01

    The huge amount of sewage sludge (SS) generated in wastewater treatment plants all over the world represents an environmental problem. Due to the high concentration of phosphorus and nitrogen in SS as well as other macro and micro nutrients it has been considered a suitable soil amendment. However, before being applied to soil a complete sterilization and elimination of pollutants should be carried out [1]. In this context, thermal treatments appear as a convenient methodology for producing SS byproducts useful for agronomic purposes. Hydrothermal carbonization (HTC) is a kind of pyrolysis characterized by the heating of the biomass in presence of water. This process shows an advantage compared to other thermal treatments for wet residues since dryness of the biomass prior to the thermal transformation is not necessary. The solid product which results from HTC is called hydrochar and it has been suggested to increase soil productivity [2]. However, the agronomic potential of hydrochars depends on the feedstock and production conditions. Additionally, possible toxic and risks have to be carefully evaluated. Thus, SS hydrochars appear as a potential soil amendment but further scientific research is needed to find its real capacity, optimal production conditions as well as possible environmental harmful effects. The aim of this study was to evaluate which are the most suitable production conditions, to transform SS into hydrochar. An additional goal of this work was to relate the hydrochars properties to its agronomic response. Therefore, hydrochars were produced from SS collected from the Experimental Wastewater Treatment plant of CENTA (http://www.centa.es/), located in Carrion de los Cespedes (Seville), under two different temperatures (200 and 260˚C) and residence times (30 min and 1h). With the hydrochars obtained, a greenhouse pot incubation study was carried out for 80 days. The pots contained 250 g of a Calcic Cambisol (IUSS Working Group WRB, 2007) and an

  13. Agronomic, metabolomic and lipidomic characterisation of Sicilian Origanum vulgare (L.) ecotypes.

    PubMed

    Tuttolomondo, Teresa; Martinelli, Federico; Mariotti, Lorenzo; Leto, Claudio; Maggio, Antonella; La Bella, Salvatore

    2016-01-01

    Although Origanum vulgare (L.) has been deeply analysed at phytochemical level, poor knowledge is available regarding non-volatile compounds such as lipids. The aim of this work was to characterise five wild Sicilian Origanum ecotypes from an agronomic, metabolomic and lipidomic perspective. Serradifalco presented higher dry weight and inflorescences/plant than the others while Favara had a significantly higher number of branches per plant and more extensive flowered stratum. Metabolomic analysis, performed with LC-MS-TOF, allowed a preliminary characterisation of the non-volatile metabolome of the five oregano ecotypes Origanum vulgare ssp. hirtum. Twenty-five metabolites were identified belonging to organic acids, amino acids, lysophosphatidylcholines, carnithines, nucleic bases and lysophosphatidylethanolamines. Lipidomic analysis identified 115 polar plant membrane glycerolipid species. Thirteen of them were differentially present in the two chosen ecotypes. The role of these metabolites in plant physiology from a qualitative and pharmacological point of view was discussed.

  14. Foundation species influence trait-based community assembly.

    PubMed

    Schöb, Christian; Butterfield, Bradley J; Pugnaire, Francisco I

    2012-11-01

    Here, we incorporate facilitation into trait-based community assembly theory by testing two mutually compatible facilitative mechanisms: changes in the environmental filter, causing either an increase in the range of trait values (i.e. a range expansion effect) and/or a shift in trait distributions (i.e. a range shift effect); and changes in trait spacing, suggesting an effect on niche differentiation. We analyzed the distribution of three functional traits - leaf dry matter content, specific leaf area and lateral spread - of plant communities dominated by a cushion-forming foundation species at four sites differing in elevation and aspect. We found support for environmental filtering and niche differentiation mechanisms by cushions, with filtering effects (in particular range shifts) increasing with environmental severity at higher elevation. The effect size of cushions on trait distribution was similar to that of environmental gradients caused by elevation and aspect. The consideration of intraspecific trait variability improved the detection of cushion effects on trait distributions. Our results highlight the importance of facilitation in the modification of taxonomic and functional diversity of ecological communities, and indicate that facilitation can occur through combined effects on environmental filtering and niche differentiation, with strong environmental context dependence of each mechanism.

  15. Isolation and Characterization of Endophytic Colonizing Bacteria from Agronomic Crops and Prairie Plants†

    PubMed Central

    Zinniel, Denise K.; Lambrecht, Pat; Harris, N. Beth; Feng, Zhengyu; Kuczmarski, Daniel; Higley, Phyllis; Ishimaru, Carol A.; Arunakumari, Alahari; Barletta, Raúl G.; Vidaver, Anne K.

    2002-01-01

    Endophytic bacteria reside within plant hosts without causing disease symptoms. In this study, 853 endophytic strains were isolated from aerial tissues of four agronomic crop species and 27 prairie plant species. We determined several phenotypic properties and found approximately equal numbers of gram-negative and gram-positive isolates. In a greenhouse study, 28 of 86 prairie plant endophytes were found to colonize their original hosts at 42 days postinoculation at levels of 3.5 to 7.7 log10 CFU/g (fresh weight). More comprehensive colonization studies were conducted with 373 corn and sorghum endophytes. In growth room studies, none of the isolates displayed pathogenicity, and 69 of the strains were recovered from corn or sorghum seedlings at levels of 8.3 log10 CFU/plant or higher. Host range greenhouse studies demonstrated that 26 of 29 endophytes were recoverable from at least one host other than corn and sorghum at levels of up to 5.8 log10 CFU/g (fresh weight). Long-range dent corn greenhouse studies and field trials with 17 wild-type strains and 14 antibiotic-resistant mutants demonstrated bacterial persistence at significant average colonization levels ranging between 3.4 and 6.1 log10 CFU/g (fresh weight) up to 78 days postinoculation. Three prairie and three agronomic endophytes exhibiting the most promising levels of colonization and an ability to persist were identified as Cellulomonas, Clavibacter, Curtobacterium, and Microbacterium isolates by 16S rRNA gene sequence, fatty acid, and carbon source utilization analyses. This study defines for the first time the endophytic nature of Microbacterium testaceum. These microorganisms may be useful for biocontrol and other applications. PMID:11976089

  16. Plastic mulching in agriculture. Trading short-term agronomic benefits for long-term soil degradation?

    PubMed

    Steinmetz, Zacharias; Wollmann, Claudia; Schaefer, Miriam; Buchmann, Christian; David, Jan; Tröger, Josephine; Muñoz, Katherine; Frör, Oliver; Schaumann, Gabriele Ellen

    2016-04-15

    Plastic mulching has become a globally applied agricultural practice for its instant economic benefits such as higher yields, earlier harvests, improved fruit quality and increased water-use efficiency. However, knowledge of the sustainability of plastic mulching remains vague in terms of both an environmental and agronomic perspective. This review critically discusses the current understanding of the environmental impact of plastic mulch use by linking knowledge of agricultural benefits and research on the life cycle of plastic mulches with direct and indirect implications for long-term soil quality and ecosystem services. Adverse effects may arise from plastic additives, enhanced pesticide runoff and plastic residues likely to fragment into microplastics but remaining chemically intact and accumulating in soil where they can successively sorb agrochemicals. The quantification of microplastics in soil remains challenging due to the lack of appropriate analytical techniques. The cost and effort of recovering and recycling used mulching films may offset the aforementioned benefits in the long term. However, comparative and long-term agronomic assessments have not yet been conducted. Furthermore, plastic mulches have the potential to alter soil quality by shifting the edaphic biocoenosis (e.g. towards mycotoxigenic fungi), accelerate C/N metabolism eventually depleting soil organic matter stocks, increase soil water repellency and favour the release of greenhouse gases. A substantial process understanding of the interactions between the soil microclimate, water supply and biological activity under plastic mulches is still lacking but required to estimate potential risks for long-term soil quality. Currently, farmers mostly base their decision to apply plastic mulches rather on expected short-term benefits than on the consideration of long-term consequences. Future interdisciplinary research should therefore gain a deeper understanding of the incentives for farmers

  17. Plastic mulching in agriculture. Trading short-term agronomic benefits for long-term soil degradation?

    PubMed

    Steinmetz, Zacharias; Wollmann, Claudia; Schaefer, Miriam; Buchmann, Christian; David, Jan; Tröger, Josephine; Muñoz, Katherine; Frör, Oliver; Schaumann, Gabriele Ellen

    2016-04-15

    Plastic mulching has become a globally applied agricultural practice for its instant economic benefits such as higher yields, earlier harvests, improved fruit quality and increased water-use efficiency. However, knowledge of the sustainability of plastic mulching remains vague in terms of both an environmental and agronomic perspective. This review critically discusses the current understanding of the environmental impact of plastic mulch use by linking knowledge of agricultural benefits and research on the life cycle of plastic mulches with direct and indirect implications for long-term soil quality and ecosystem services. Adverse effects may arise from plastic additives, enhanced pesticide runoff and plastic residues likely to fragment into microplastics but remaining chemically intact and accumulating in soil where they can successively sorb agrochemicals. The quantification of microplastics in soil remains challenging due to the lack of appropriate analytical techniques. The cost and effort of recovering and recycling used mulching films may offset the aforementioned benefits in the long term. However, comparative and long-term agronomic assessments have not yet been conducted. Furthermore, plastic mulches have the potential to alter soil quality by shifting the edaphic biocoenosis (e.g. towards mycotoxigenic fungi), accelerate C/N metabolism eventually depleting soil organic matter stocks, increase soil water repellency and favour the release of greenhouse gases. A substantial process understanding of the interactions between the soil microclimate, water supply and biological activity under plastic mulches is still lacking but required to estimate potential risks for long-term soil quality. Currently, farmers mostly base their decision to apply plastic mulches rather on expected short-term benefits than on the consideration of long-term consequences. Future interdisciplinary research should therefore gain a deeper understanding of the incentives for farmers

  18. Applied genetic evaluations for production and functional traits in dairy cattle.

    PubMed

    Mark, T

    2004-08-01

    The objective of this study was to review the current status of genetic evaluation systems for production and functional traits as practiced in different Interbull member countries and to discuss that status in relation to research results and potential improvements. Thirty-one countries provided information. Substantial variation was evident for number of traits considered per country, trait definition, genetic evaluation procedure within trait, effects included, and how these were treated in genetic evaluation models. All countries lacked genetic evaluations for one or more economically important traits. Improvement in the genetic evaluation models, especially for many functional traits, could be achieved by closing the gaps between research and practice. More detailed and up to date information about national genetic evaluation systems for traits in different countries is available at www.interbull.org. Female fertility and workability traits were considered in many countries and could be next in line for international genetic evaluations.

  19. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae.

    PubMed

    Narwani, Anita; Alexandrou, Markos A; Herrin, James; Vouaux, Alaina; Zhou, Charles; Oakley, Todd H; Cardinale, Bradley J

    2015-01-01

    Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken. PMID:26348482

  20. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae

    PubMed Central

    Narwani, Anita; Alexandrou, Markos A.; Herrin, James; Vouaux, Alaina; Zhou, Charles; Oakley, Todd H.; Cardinale, Bradley J.

    2015-01-01

    Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken. PMID:26348482

  1. Responses of Crop Water Use Efficiency to Climate Change and Agronomic Measures in the Semiarid Area of Northern China

    PubMed Central

    Zhang, Jingting; Ren, Wei; An, Pingli; Pan, Zhihua; Wang, Liwei; Dong, Zhiqiang; He, Di; Yang, Jia; Pan, Shufen; Tian, Hanqin

    2015-01-01

    It has long been concerned how crop water use efficiency (WUE) responds to climate change. Most of existing researches have emphasized the impact of single climate factor but have paid less attention to the effect of developed agronomic measures on crop WUE. Based on the long-term field observations/experiments data, we investigated the changing responses of crop WUE to climate variables (temperature and precipitation) and agronomic practices (fertilization and cropping patterns) in the semi-arid area of northern China (SAC) during two periods, 1983–1999 and 2000–2010 (drier and warmer). Our results suggest that crop WUE was an intrinsical system sensitive to climate change and agronomic measures. Crops tend to reach the maximum WUE (WUEmax) in warm-dry environment while reach the stable minimum WUE (WUEmin) in warm-wet environment, with a difference between WUEmax and WUEmin ranging from 29.0%-55.5%. Changes in temperature and precipitation in the past three decades jointly enhanced crop WUE by 8.1%-30.6%. Elevated fertilizer and rotation cropping would increase crop WUE by 5.6–11.0% and 19.5–92.9%, respectively. These results indicate crop has the resilience by adjusting WUE, which is not only able to respond to subsequent periods of favorable water balance but also to tolerate the drought stress, and reasonable agronomic practices could enhance this resilience. However, this capacity would break down under impact of climate changes and unconscionable agronomic practices (e.g. excessive N/P/K fertilizer or traditional continuous cropping). Based on the findings in this study, a conceptual crop WUE model is constructed to indicate the threshold of crop resilience, which could help the farmer develop appropriate strategies in adapting the adverse impacts of climate warming. PMID:26336098

  2. Responses of Crop Water Use Efficiency to Climate Change and Agronomic Measures in the Semiarid Area of Northern China.

    PubMed

    Zhang, Jingting; Ren, Wei; An, Pingli; Pan, Zhihua; Wang, Liwei; Dong, Zhiqiang; He, Di; Yang, Jia; Pan, Shufen; Tian, Hanqin

    2015-01-01

    It has long been concerned how crop water use efficiency (WUE) responds to climate change. Most of existing researches have emphasized the impact of single climate factor but have paid less attention to the effect of developed agronomic measures on crop WUE. Based on the long-term field observations/experiments data, we investigated the changing responses of crop WUE to climate variables (temperature and precipitation) and agronomic practices (fertilization and cropping patterns) in the semi-arid area of northern China (SAC) during two periods, 1983-1999 and 2000-2010 (drier and warmer). Our results suggest that crop WUE was an intrinsical system sensitive to climate change and agronomic measures. Crops tend to reach the maximum WUE (WUEmax) in warm-dry environment while reach the stable minimum WUE (WUEmin) in warm-wet environment, with a difference between WUEmax and WUEmin ranging from 29.0%-55.5%. Changes in temperature and precipitation in the past three decades jointly enhanced crop WUE by 8.1%-30.6%. Elevated fertilizer and rotation cropping would increase crop WUE by 5.6-11.0% and 19.5-92.9%, respectively. These results indicate crop has the resilience by adjusting WUE, which is not only able to respond to subsequent periods of favorable water balance but also to tolerate the drought stress, and reasonable agronomic practices could enhance this resilience. However, this capacity would break down under impact of climate changes and unconscionable agronomic practices (e.g. excessive N/P/K fertilizer or traditional continuous cropping). Based on the findings in this study, a conceptual crop WUE model is constructed to indicate the threshold of crop resilience, which could help the farmer develop appropriate strategies in adapting the adverse impacts of climate warming.

  3. Responses of Crop Water Use Efficiency to Climate Change and Agronomic Measures in the Semiarid Area of Northern China.

    PubMed

    Zhang, Jingting; Ren, Wei; An, Pingli; Pan, Zhihua; Wang, Liwei; Dong, Zhiqiang; He, Di; Yang, Jia; Pan, Shufen; Tian, Hanqin

    2015-01-01

    It has long been concerned how crop water use efficiency (WUE) responds to climate change. Most of existing researches have emphasized the impact of single climate factor but have paid less attention to the effect of developed agronomic measures on crop WUE. Based on the long-term field observations/experiments data, we investigated the changing responses of crop WUE to climate variables (temperature and precipitation) and agronomic practices (fertilization and cropping patterns) in the semi-arid area of northern China (SAC) during two periods, 1983-1999 and 2000-2010 (drier and warmer). Our results suggest that crop WUE was an intrinsical system sensitive to climate change and agronomic measures. Crops tend to reach the maximum WUE (WUEmax) in warm-dry environment while reach the stable minimum WUE (WUEmin) in warm-wet environment, with a difference between WUEmax and WUEmin ranging from 29.0%-55.5%. Changes in temperature and precipitation in the past three decades jointly enhanced crop WUE by 8.1%-30.6%. Elevated fertilizer and rotation cropping would increase crop WUE by 5.6-11.0% and 19.5-92.9%, respectively. These results indicate crop has the resilience by adjusting WUE, which is not only able to respond to subsequent periods of favorable water balance but also to tolerate the drought stress, and reasonable agronomic practices could enhance this resilience. However, this capacity would break down under impact of climate changes and unconscionable agronomic practices (e.g. excessive N/P/K fertilizer or traditional continuous cropping). Based on the findings in this study, a conceptual crop WUE model is constructed to indicate the threshold of crop resilience, which could help the farmer develop appropriate strategies in adapting the adverse impacts of climate warming. PMID:26336098

  4. Characterizing psychopathy using DSM-5 personality traits.

    PubMed

    Strickland, Casey M; Drislane, Laura E; Lucy, Megan; Krueger, Robert F; Patrick, Christopher J

    2013-06-01

    Despite its importance historically and contemporarily, psychopathy is not recognized in the current Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revised (DSM-IV-TR). Its closest counterpart, antisocial personality disorder, includes strong representation of behavioral deviance symptoms but weak representation of affective-interpersonal features considered central to psychopathy. The current study evaluated the extent to which psychopathy and its distinctive facets, indexed by the Triarchic Psychopathy Measure, can be assessed effectively using traits from the dimensional model of personality pathology developed for DSM-5, operationalized by the Personality Inventory for DSM-5 (PID-5). Results indicate that (a) facets of psychopathy entailing impulsive externalization and callous aggression are well-represented by traits from the PID-5 considered relevant to antisocial personality disorder, and (b) the boldness facet of psychopathy can be effectively captured using additional PID-5 traits. These findings provide evidence that the dimensional model of personality pathology embodied in the PID-5 provides effective trait-based coverage of psychopathy and its facets.

  5. Causes of male sexual trait divergence in introduced populations of guppies.

    PubMed

    Lindholm, A K; Head, M L; Brooks, R C; Rollins, L A; Ingleby, F C; Zajitschek, S R K

    2014-02-01

    Males from different populations of the same species often differ in their sexually selected traits. Variation in sexually selected traits can be attributed to sexual selection if phenotypic divergence matches the direction of sexual selection gradients among populations. However, phenotypic divergence of sexually selected traits may also be influenced by other factors, such as natural selection and genetic constraints. Here, we document differences in male sexual traits among six introduced Australian populations of guppies and untangle the forces driving divergence in these sexually selected traits. Using an experimental approach, we found that male size, area of orange coloration, number of sperm per ejaculate and linear sexual selection gradients for male traits differed among populations. Within populations, a large mismatch between the direction of selection and male traits suggests that constraints may be important in preventing male traits from evolving in the direction of selection. Among populations, however, variation in sexual selection explained more than half of the differences in trait variation, suggesting that, despite within-population constraints, sexual selection has contributed to population divergence of male traits. Differences in sexual traits were also associated with predation risk and neutral genetic distance. Our study highlights the importance of sexual selection in trait divergence in introduced populations, despite the presence of constraining factors such as predation risk and evolutionary history.

  6. Causes of male sexual trait divergence in introduced populations of guppies

    PubMed Central

    Lindholm, A K; Head, M L; Brooks, R C; Rollins, L A; Ingleby, F C; Zajitschek, S R K

    2014-01-01

    Males from different populations of the same species often differ in their sexually selected traits. Variation in sexually selected traits can be attributed to sexual selection if phenotypic divergence matches the direction of sexual selection gradients among populations. However, phenotypic divergence of sexually selected traits may also be influenced by other factors, such as natural selection and genetic constraints. Here, we document differences in male sexual traits among six introduced Australian populations of guppies and untangle the forces driving divergence in these sexually selected traits. Using an experimental approach, we found that male size, area of orange coloration, number of sperm per ejaculate and linear sexual selection gradients for male traits differed among populations. Within populations, a large mismatch between the direction of selection and male traits suggests that constraints may be important in preventing male traits from evolving in the direction of selection. Among populations, however, variation in sexual selection explained more than half of the differences in trait variation, suggesting that, despite within-population constraints, sexual selection has contributed to population divergence of male traits. Differences in sexual traits were also associated with predation risk and neutral genetic distance. Our study highlights the importance of sexual selection in trait divergence in introduced populations, despite the presence of constraining factors such as predation risk and evolutionary history. PMID:24456226

  7. Causes of male sexual trait divergence in introduced populations of guppies.

    PubMed

    Lindholm, A K; Head, M L; Brooks, R C; Rollins, L A; Ingleby, F C; Zajitschek, S R K

    2014-02-01

    Males from different populations of the same species often differ in their sexually selected traits. Variation in sexually selected traits can be attributed to sexual selection if phenotypic divergence matches the direction of sexual selection gradients among populations. However, phenotypic divergence of sexually selected traits may also be influenced by other factors, such as natural selection and genetic constraints. Here, we document differences in male sexual traits among six introduced Australian populations of guppies and untangle the forces driving divergence in these sexually selected traits. Using an experimental approach, we found that male size, area of orange coloration, number of sperm per ejaculate and linear sexual selection gradients for male traits differed among populations. Within populations, a large mismatch between the direction of selection and male traits suggests that constraints may be important in preventing male traits from evolving in the direction of selection. Among populations, however, variation in sexual selection explained more than half of the differences in trait variation, suggesting that, despite within-population constraints, sexual selection has contributed to population divergence of male traits. Differences in sexual traits were also associated with predation risk and neutral genetic distance. Our study highlights the importance of sexual selection in trait divergence in introduced populations, despite the presence of constraining factors such as predation risk and evolutionary history. PMID:24456226

  8. Genome sequencing and analysis of the whitefly (Bemisia tabaci) MEAM1, one of the most important vectors for plant viruses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Among whiteflies, the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex is particularly important because of its ability to transmit hundreds of plant viruses, resulting in the loss of billions of U.S. dollars on agronomically important crops such as tomato, cucurbits, cassava, and cotton worl...

  9. Leaf Trait-Environment Relationships in a Subtropical Broadleaved Forest in South-East China

    PubMed Central

    Kröber, Wenzel; Böhnke, Martin; Welk, Erik; Wirth, Christian; Bruelheide, Helge

    2012-01-01

    Although trait analyses have become more important in community ecology, trait-environment correlations have rarely been studied along successional gradients. We asked which environmental variables had the strongest impact on intraspecific and interspecific trait variation in the community and which traits were most responsive to the environment. We established a series of plots in a secondary forest in the Chinese subtropics, stratified by successional stages that were defined by the time elapsed since the last logging activities. On a total of 27 plots all woody plants were recorded and a set of individuals of every species was analysed for leaf traits, resulting in a trait matrix of 26 leaf traits for 122 species. A Fourth Corner Analysis revealed that the mean values of many leaf traits were tightly related to the successional gradient. Most shifts in traits followed the leaf economics spectrum with decreasing specific leaf area and leaf nutrient contents with successional time. Beside succession, few additional environmental variables resulted in significant trait relationships, such as soil moisture and soil C and N content as well as topographical variables. Not all traits were related to the leaf economics spectrum, and thus, to the successional gradient, such as stomata size and density. By comparing different permutation models in the Fourth Corner Analysis, we found that the trait-environment link was based more on the association of species with the environment than of the communities with species traits. The strong species-environment association was brought about by a clear gradient in species composition along the succession series, while communities were not well differentiated in mean trait composition. In contrast, intraspecific trait variation did not show close environmental relationships. The study confirmed the role of environmental trait filtering in subtropical forests, with traits associated with the leaf economics spectrum being the most

  10. Leaf trait-environment relationships in a subtropical broadleaved forest in South-East China.

    PubMed

    Kröber, Wenzel; Böhnke, Martin; Welk, Erik; Wirth, Christian; Bruelheide, Helge

    2012-01-01

    Although trait analyses have become more important in community ecology, trait-environment correlations have rarely been studied along successional gradients. We asked which environmental variables had the strongest impact on intraspecific and interspecific trait variation in the community and which traits were most responsive to the environment. We established a series of plots in a secondary forest in the Chinese subtropics, stratified by successional stages that were defined by the time elapsed since the last logging activities. On a total of 27 plots all woody plants were recorded and a set of individuals of every species was analysed for leaf traits, resulting in a trait matrix of 26 leaf traits for 122 species. A Fourth Corner Analysis revealed that the mean values of many leaf traits were tightly related to the successional gradient. Most shifts in traits followed the leaf economics spectrum with decreasing specific leaf area and leaf nutrient contents with successional time. Beside succession, few additional environmental variables resulted in significant trait relationships, such as soil moisture and soil C and N content as well as topographical variables. Not all traits were related to the leaf economics spectrum, and thus, to the successional gradient, such as stomata size and density. By comparing different permutation models in the Fourth Corner Analysis, we found that the trait-environment link was based more on the association of species with the environment than of the communities with species traits. The strong species-environment association was brought about by a clear gradient in species composition along the succession series, while communities were not well differentiated in mean trait composition. In contrast, intraspecific trait variation did not show close environmental relationships. The study confirmed the role of environmental trait filtering in subtropical forests, with traits associated with the leaf economics spectrum being the most

  11. Leaf trait-environment relationships in a subtropical broadleaved forest in South-East China.

    PubMed

    Kröber, Wenzel; Böhnke, Martin; Welk, Erik; Wirth, Christian; Bruelheide, Helge

    2012-01-01

    Although trait analyses have become more important in community ecology, trait-environment correlations have rarely been studied along successional gradients. We asked which environmental variables had the strongest impact on intraspecific and interspecific trait variation in the community and which traits were most responsive to the environment. We established a series of plots in a secondary forest in the Chinese subtropics, stratified by successional stages that were defined by the time elapsed since the last logging activities. On a total of 27 plots all woody plants were recorded and a set of individuals of every species was analysed for leaf traits, resulting in a trait matrix of 26 leaf traits for 122 species. A Fourth Corner Analysis revealed that the mean values of many leaf traits were tightly related to the successional gradient. Most shifts in traits followed the leaf economics spectrum with decreasing specific leaf area and leaf nutrient contents with successional time. Beside succession, few additional environmental variables resulted in significant trait relationships, such as soil moisture and soil C and N content as well as topographical variables. Not all traits were related to the leaf economics spectrum, and thus, to the successional gradient, such as stomata size and density. By comparing different permutation models in the Fourth Corner Analysis, we found that the trait-environment link was based more on the association of species with the environment than of the communities with species traits. The strong species-environment association was brought about by a clear gradient in species composition along the succession series, while communities were not well differentiated in mean trait composition. In contrast, intraspecific trait variation did not show close environmental relationships. The study confirmed the role of environmental trait filtering in subtropical forests, with traits associated with the leaf economics spectrum being the most

  12. Functional traits and root morphology of alpine plants

    PubMed Central

    Pohl, Mandy; Stroude, Raphaël; Buttler, Alexandre; Rixen, Christian

    2011-01-01

    Background and Aims Vegetation has long been recognized to protect the soil from erosion. Understanding species differences in root morphology and functional traits is an important step to assess which species and species mixtures may provide erosion control. Furthermore, extending classification of plant functional types towards root traits may be a useful procedure in understanding important root functions. Methods In this study, pioneer data on traits of alpine plant species, i.e. plant height and shoot biomass, root depth, horizontal root spreading, root length, diameter, tensile strength, plant age and root biomass, from a disturbed site in the Swiss Alps are presented. The applicability of three classifications of plant functional types (PFTs), i.e. life form, growth form and root type, was examined for above- and below-ground plant traits. Key Results Plant traits differed considerably among species even of the same life form, e.g. in the case of total root length by more than two orders of magnitude. Within the same root diameter, species differed significantly in tensile strength: some species (Geum reptans and Luzula spicata) had roots more than twice as strong as those of other species. Species of different life forms provided different root functions (e.g. root depth and horizontal root spreading) that may be important for soil physical processes. All classifications of PFTs were helpful to categorize plant traits; however, the PFTs according to root type explained total root length far better than the other PFTs. Conclusions The results of the study illustrate the remarkable differences between root traits of alpine plants, some of which cannot be assessed from simple morphological inspection, e.g. tensile strength. PFT classification based on root traits seems useful to categorize plant traits, even though some patterns are better explained at the individual species level. PMID:21795278

  13. Personality traits, personality disorders, and migraine: a review.

    PubMed

    Davis, Rachel E; Smitherman, Todd A; Baskin, Steven M

    2013-05-01

    The personality trait of neuroticism has been associated with migraine, although research is needed to clarify potential moderators of this relationship and the extent to which neuroticism reflects a stable disposition or instead is a function of general somatic distress or situational influences. With the possible exception of harm avoidance, research has not consistently identified any other personality trait unique among migraineurs. Personality disorders have been researched less extensively, but existing data suggests that borderline personality disorder, in particular, is associated with increased negative impact of migraine, risk for medication overuse, and poor response to treatment that is likely of greater clinical importance than any personality trait per se.

  14. Variability of Root Traits in Spring Wheat Germplasm

    PubMed Central

    Narayanan, Sruthi; Mohan, Amita; Gill, Kulvinder S.; Prasad, P. V. Vara

    2014-01-01

    Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), regions of origin, and market classes. Plants were grown in 150-cm columns for 61 days in a greenhouse under optimal growth conditions. Rooting depth, root dry weight, root: shoot ratio, and shoot traits were determined for 297 genotypes of the germplasm, Cultivated Wheat Collection (CWC). The remaining root traits such as total root length and surface area were measured for a subset of 30 genotypes selected based on rooting depth. Significant genetic variability was observed for root traits among spring wheat genotypes in CWC germplasm or its subset. Genotypes Sonora and Currawa were ranked high, and genotype Vandal was ranked low for most root traits. A positive relationship (R2≥0.35) was found between root and shoot dry weights within the CWC germplasm and between total root surface area and tiller number; total root surface area and shoot dry weight; and total root length and coleoptile length within the subset. No correlations were found between plant height and most root traits within the CWC germplasm or its subset. Region of origin had significant impact on rooting depth in the CWC germplasm. Wheat genotypes collected from Australia, Mediterranean, and west Asia had greater rooting depth than those from south Asia, Latin America, Mexico, and Canada. Soft wheat had greater rooting depth than hard wheat in the CWC germplasm. The genetic variability identified in this research for root traits can be exploited to improve drought tolerance and/or resource capture in wheat. PMID:24945438

  15. Structural brain MRI trait polygenic score prediction of cognitive abilities

    PubMed Central

    Luciano, Michelle; Marioni, Riccardo E; Hernández, Maria Valdés; Maniega, Susana Munoz; Hamilton, Iona F; Royle, Natalie A.; Scotland, Generation; Chauhan, Ganesh; Bis, Joshua C.; Debette, Stephanie; DeCarli, Charles; Fornage, Myriam; Schmidt, Reinhold; Ikram, M. Arfan; Launer, Lenore J.; Seshadri, Sudha; Bastin, Mark E.; Porteous, David J.; Wardlaw, Joanna; Deary, Ian J

    2016-01-01

    Structural brain magnetic resonance imaging (MRI) traits share part of their genetic variance with cognitive traits. Here, we use genetic association results from large meta-analytic studies of genome-wide association for brain infarcts, white matter hyperintensities, intracranial, hippocampal and total brain volumes to estimate polygenic scores for these traits in three Scottish samples: Generation Scotland: Scottish Family Health Study (GS:SFHS), and the Lothian Birth Cohorts of 1936 (LBC1936) and 1921 (LBC1921). These five brain MRI trait polygenic scores were then used to 1) predict corresponding MRI traits in the LBC1936 (numbers ranged 573 to 630 across traits) and 2) predict cognitive traits in all three cohorts (in 8,115 to 8,250 persons). In the LBC1936, all MRI phenotypic traits were correlated with at least one cognitive measure; and polygenic prediction of MRI traits was observed for intracranial volume. Meta-analysis of the correlations between MRI polygenic scores and cognitive traits revealed a significant negative correlation (maximal r=0.08) between the hippocampal volume polygenic score and measures of global cognitive ability collected in childhood and in old age in the Lothian Birth Cohorts. The lack of association to a related general cognitive measure when including the GS:SFHS points to either type 1 error or the importance of using prediction samples that closely match the demographics of the genome-wide association samples from which prediction is based. Ideally, these analyses should be repeated in larger samples with data on both MRI and cognition, and using MRI GWA results from even larger meta-analysis studies. PMID:26427786

  16. Species identity influences belowground arthropod assemblages via functional traits

    PubMed Central

    Gorman, Courtney E.; Read, Quentin D.; Van Nuland, Michael E.; Bryant, Jessica A. M.; Welch, Jessica N.; Altobelli, Joseph T.; Douglas, Morgan J.; Genung, Mark A.; Haag, Elliot N.; Jones, Devin N.; Long, Hannah E.; Wilburn, Adam D.; Schweitzer, Jennifer A.; Bailey, Joseph K.

    2013-01-01

    Plant species influence belowground communities in a variety of ways, ultimately impacting nutrient cycling. Functional plant traits provide a means whereby species identity can influence belowground community interactions, but little work has examined whether species identity influences belowground community processes when correcting for evolutionary history. Specifically, we hypothesized that closely related species would exhibit (i) more similar leaf and root functional traits than more distantly related species, and (ii) more similar associated soil arthropod communities. We found that after correcting for evolutionary history, tree species identity influenced belowground arthropod communities through plant functional traits. These data suggest that plant species structure may be an important predictor in shaping associated soil arthropod communities and further suggest the importance of better understanding the extended consequences of evolutionary history on ecological processes, as similarity in traits may not always reflect similar ecology.

  17. Exaggerated trait growth in insects.

    PubMed

    Lavine, Laura; Gotoh, Hiroki; Brent, Colin S; Dworkin, Ian; Emlen, Douglas J

    2015-01-01

    Animal structures occasionally attain extreme proportions, eclipsing in size the surrounding body parts. We review insect examples of exaggerated traits, such as the mandibles of stag beetles (Lucanidae), the claspers of praying mantids (Mantidae), the elongated hindlimbs of grasshoppers (Orthoptera: Caelifera), and the giant heads of soldier ants (Formicidae) and termites (Isoptera). Developmentally, disproportionate growth can arise through trait-specific modifications to the activity of at least four pathways: the sex determination pathway, the appendage patterning pathway, the insulin/IGF signaling pathway, and the juvenile hormone/ecdysteroid pathway. Although most exaggerated traits have not been studied mechanistically, it is already apparent that distinct developmental mechanisms underlie the evolution of the different types of exaggerated traits. We suggest this reflects the nature of selection in each instance, revealing an exciting link between mechanism, form, and function. We use this information to make explicit predictions for the types of regulatory pathways likely to underlie each type of exaggerated trait.

  18. Quantitative trait loci analysis of egg and meat production traits in a red junglefowlxWhite Leghorn cross.

    PubMed

    Wright, D; Kerje, S; Lundström, K; Babol, J; Schütz, K; Jensen, P; Andersson, L

    2006-12-01

    Egg and production traits are of considerable economic importance in chickens. Using a White Leghorn x red junglefowl F(2) intercross, standard production measures of liver weight and colour, egg size, eggshell thickness, egg taste and meat quality were taken. A total of 160 markers covering 29 autosomes and the Z chromosome were genotyped on 175-243 individuals, depending on the trait under consideration. A total of nine significant quantitative trait loci (QTL) and three suggestive QTL were found on chicken chromosomes 1, 2, 4, 5, 7, 8, 10, 12, E47W24 and E22C19W28. PMID:17121597

  19. Quantitative trait loci underlying udder morphology traits in dairy sheep.

    PubMed

    Gutiérrez-Gil, B; El-Zarei, M F; Alvarez, L; Bayón, Y; de la Fuente, L F; San Primitivo, F; Arranz, J J

    2008-09-01

    A genome scan was conducted on the basis of the daughter design to detect quantitative trait loci (QTL) influencing udder morphology traits in Spanish Churra dairy sheep. A total of 739 ewes belonging to 11 half-sib families were genotyped for 182 microsatellite markers covering 3,248.2 cM (Kosambi) of the ovine autosomal genome. Phenotypic traits included scores for 5 linear udder traits: udder depth, udder attachment, teat placement, teat size, and udder shape. Quantitative measurements for the QTL analysis were calculated for each trait from evaluation scores using within-family yield deviations corrected for fixed environmental effects. Joint analysis of all families using Haley-Knott regression identified 5 regions that exceeded the 5% chromosome-wise significance threshold on chromosomes 7, 14, 15, 20, and 26. Based on the across-family results, a within-family analysis was carried out to identify families segregated according to the QTL and to estimate the QTL effect. The allelic substitution effect for individual families ranged from 0.47 to 1.7 phenotypic standard deviation units for udder shape on chromosome 15 and udder depth on chromosome 14, respectively. These QTL regions provide a starting point for further research aimed at the characterization of genetic variability involved in udder traits in Churra sheep. This paper presents the first report of a sheep genome scan for udder-related traits in a dairy sheep outbred population.

  20. Quantitative trait loci underlying milk production traits in sheep.

    PubMed

    Gutiérrez-Gil, B; El-Zarei, M F; Alvarez, L; Bayón, Y; de la Fuente, L F; San Primitivo, F; Arranz, J-J

    2009-08-01

    Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits.

  1. Linking Tropical Forest Function to Hydraulic Traits in a Size-Structured and Trait-Based Model

    NASA Astrophysics Data System (ADS)

    Christoffersen, B. O.; Gloor, M.; Fauset, S.; Fyllas, N.; Galbraith, D.; Baker, T. R.; Rowland, L.; Fisher, R.; Binks, O.; Sevanto, S.; Xu, C.; Jansen, S.; Choat, B.; Mencuccini, M.; McDowell, N. G.; Meir, P.

    2015-12-01

    A major weakness of forest ecosystem models is their inability to capture the diversity of responses to changes in water availability, severely hampering efforts to predict the fate of tropical forests under climate change. Such models often prescribe moisture sensitivity using heuristic response functions that are uniform across all individuals and lack important knowledge about trade-offs in hydraulic traits. We address this weakness by implementing a process representation of plant hydraulics into an individual- and trait-based model (Trait Forest Simulator; TFS) intended for application at discrete sites where community-level distributions of stem and leaf trait spectra (wood density, leaf mass per area, leaf nitrogen and phosphorus content) are known. The model represents a trade-off in the safety and efficiency of water conduction in xylem tissue through hydraulic traits, while accounting for the counteracting effects of increasing hydraulic path length and xylem conduit taper on whole-plant hydraulic resistance with increasing tree size. Using existing trait databases and additional meta-analyses from the rich literature on tropical tree ecophysiology, we obtained all necessary hydraulic parameters associated with xylem conductivity, vulnerability curves, pressure-volume curves, and hydraulic architecture (e.g., leaf-to-sapwood area ratios) as a function of the aforementioned traits and tree size. Incorporating these relationships in the model greatly improved the diversity of tree response to seasonal changes in water availability as well as in response to drought, as determined by comparison with field observations and experiments. Importantly, this individual- and trait-based framework provides a testbed for identifying both critical processes and functional traits needed for inclusion in coarse-scale Dynamic Global Vegetation Models, which will lead to reduced uncertainty in the future state of tropical forests.

  2. Row Ratios of Intercropping Maize and Soybean Can Affect Agronomic Efficiency of the System and Subsequent Wheat.

    PubMed

    Zhang, Yitao; Liu, Jian; Zhang, Jizong; Liu, Hongbin; Liu, Shen; Zhai, Limei; Wang, Hongyuan; Lei, Qiuliang; Ren, Tianzhi; Yin, Changbin

    2015-01-01

    Intercropping is regarded as an important agricultural practice to improve crop production and environmental quality in the regions with intensive agricultural production, e.g., northern China. To optimize agronomic advantage of maize (Zea mays L.) and soybean (Glycine max L.) intercropping system compared to monoculture of maize, two sequential experiments were conducted. Experiment 1 was to screening the optimal cropping system in summer that had the highest yields and economic benefits, and Experiment 2 was to identify the optimum row ratio of the intercrops selected from Experiment 1. Results of Experiment 1 showed that maize intercropping with soybean (maize || soybean) was the optimal cropping system in summer. Compared to conventional monoculture of maize, maize || soybean had significant advantage in yield, economy, land utilization ratio and reducing soil nitrate nitrogen (N) accumulation, as well as better residual effect on the subsequent wheat (Triticum aestivum L.) crop. Experiment 2 showed that intercropping systems reduced use of N fertilizer per unit land area and increased relative biomass of intercropped maize, due to promoted photosynthetic efficiency of border rows and N utilization during symbiotic period. Intercropping advantage began to emerge at tasseling stage after N topdressing for maize. Among all treatments with different row ratios, alternating four maize rows with six soybean rows (4M:6S) had the largest land equivalent ratio (1.30), total N accumulation in crops (258 kg ha(-1)), and economic benefit (3,408 USD ha(-1)). Compared to maize monoculture, 4M:6S had significantly lower nitrate-N accumulation in soil both after harvest of maize and after harvest of the subsequent wheat, but it did not decrease yield of wheat. The most important advantage of 4M:6S was to increase biomass of intercropped maize and soybean, which further led to the increase of total N accumulation by crops as well as economic benefit. In conclusion, alternating

  3. Row Ratios of Intercropping Maize and Soybean Can Affect Agronomic Efficiency of the System and Subsequent Wheat

    PubMed Central

    Zhang, Yitao; Liu, Jian; Zhang, Jizong; Liu, Hongbin; Liu, Shen; Zhai, Limei; Wang, Hongyuan; Lei, Qiuliang; Ren, Tianzhi; Yin, Changbin

    2015-01-01

    Intercropping is regarded as an important agricultural practice to improve crop production and environmental quality in the regions with intensive agricultural production, e.g., northern China. To optimize agronomic advantage of maize (Zea mays L.) and soybean (Glycine max L.) intercropping system compared to monoculture of maize, two sequential experiments were conducted. Experiment 1 was to screening the optimal cropping system in summer that had the highest yields and economic benefits, and Experiment 2 was to identify the optimum row ratio of the intercrops selected from Experiment 1. Results of Experiment 1 showed that maize intercropping with soybean (maize || soybean) was the optimal cropping system in summer. Compared to conventional monoculture of maize, maize || soybean had significant advantage in yield, economy, land utilization ratio and reducing soil nitrate nitrogen (N) accumulation, as well as better residual effect on the subsequent wheat (Triticum aestivum L.) crop. Experiment 2 showed that intercropping systems reduced use of N fertilizer per unit land area and increased relative biomass of intercropped maize, due to promoted photosynthetic efficiency of border rows and N utilization during symbiotic period. Intercropping advantage began to emerge at tasseling stage after N topdressing for maize. Among all treatments with different row ratios, alternating four maize rows with six soybean rows (4M:6S) had the largest land equivalent ratio (1.30), total N accumulation in crops (258 kg ha-1), and economic benefit (3,408 USD ha-1). Compared to maize monoculture, 4M:6S had significantly lower nitrate-N accumulation in soil both after harvest of maize and after harvest of the subsequent wheat, but it did not decrease yield of wheat. The most important advantage of 4M:6S was to increase biomass of intercropped maize and soybean, which further led to the increase of total N accumulation by crops as well as economic benefit. In conclusion, alternating

  4. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

  5. Predicting personality traits related to consumer behavior using SNS analysis

    NASA Astrophysics Data System (ADS)

    Baik, Jongbum; Lee, Kangbok; Lee, Soowon; Kim, Yongbum; Choi, Jayoung

    2016-07-01

    Modeling a user profile is one of the important factors for devising a personalized recommendation. The traditional approach for modeling a user profile in computer science is to collect and generalize the user's buying behavior or preference history, generated from the user's interactions with recommender systems. According to consumer behavior research, however, internal factors such as personality traits influence a consumer's buying behavior. Existing studies have tried to adapt the Big 5 personality traits to personalized recommendations. However, although studies have shown that these traits can be useful to some extent for personalized recommendation, the causal relationship between the Big 5 personality traits and the buying behaviors of actual consumers has not been validated. In this paper, we propose a novel method for predicting the four personality traits-Extroversion, Public Self-consciousness, Desire for Uniqueness, and Self-esteem-that correlate with buying behaviors. The proposed method automatically constructs a user-personality-traits prediction model for each user by analyzing the user behavior on a social networking service. The experimental results from an analysis of the collected Facebook data show that the proposed method can predict user-personality traits with greater precision than methods that use the variables proposed in previous studies.

  6. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  7. Model Adequacy and the Macroevolution of Angiosperm Functional Traits.

    PubMed

    Pennell, Matthew W; FitzJohn, Richard G; Cornwell, William K; Harmon, Luke J

    2015-08-01

    Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the model is appropriate for the data and the question being addressed. One way to assess this is to ask whether the model provides a good statistical explanation for the variation in the data. To date, researchers have focused primarily on the explanatory power of a model relative to alternative models. Methods have been developed to assess the adequacy, or absolute explanatory power, of phylogenetic trait models, but these have been restricted to specific models or questions. Here we present a general statistical framework for assessing the adequacy of phylogenetic trait models. We use our approach to evaluate the statistical performance of commonly used trait models on 337 comparative data sets covering three key angiosperm functional traits. In general, the models we tested often provided poor statistical explanations for the evolution of these traits. This was true for many different groups and at many different scales. Whether such statistical inadequacy will qualitatively alter inferences drawn from comparative data sets will depend on the context. Regardless, assessing model adequacy can provide interesting biological insights-how and why a model fails to describe variation in a data set give us clues about what evolutionary processes may have driven trait evolution across time. PMID:26655160

  8. Polytraits: A database on biological traits of marine polychaetes

    PubMed Central

    2014-01-01

    Abstract The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. PMID:24855436

  9. Agronomic Characteristics Related to Grain Yield and Nutrient Use Efficiency for Wheat Production in China.

    PubMed

    Chuan, Limin; He, Ping; Zhao, Tongke; Zheng, Huaiguo; Xu, Xinpeng

    2016-01-01

    In order to make clear the recent status and trend of wheat (Triticum aestivum L.) production in China, datasets from multiple field experiments and published literature were collected to study the agronomic characteristics related to grain yield, fertilizer application and nutrient use efficiency from the year 2000 to 2011. The results showed that the mean grain yield of wheat in 2000-2011 was 5950 kg/ha, while the N, P2O5 and K2O application rates were 172, 102 and 91 kg/ha on average, respectively. The decrease in N and P2O5 and increase in K2O balanced the nutrient supply and was the main reason for yield increase. The partial factor productivity (PFP, kg grain yield produced per unit of N, P2O5 or K2O applied) values of N (PFP-N), P (PFP-P) and K (PFP-K) were in the ranges of 29.5~39.6, 43.4~74.9 and 44.1~76.5 kg/kg, respectively. While PFP-N showed no significant changes from 2000 to 2010, both PFP-P and PFP-K showed an increased trend over this period. The mean agronomic efficiency (AE, kg grain yield increased per unit of N, P2O5 or K2O applied) values of N (AEN), P (AEP) and K (AEK) were 9.4, 10.2 and 6.5 kg/kg, respectively. The AE values demonstrated marked inter-annual fluctuations, with the amplitude of fluctuation for AEN greater than those for AEP and AEK. The mean fertilizer recovery efficiency (RE, the fraction of nutrient uptake in aboveground plant dry matter to the nutrient of fertilizer application) values of N, P and K in the aboveground biomass were 33.1%, 24.3% and 28.4%, respectively. It was also revealed that different wheat ecological regions differ greatly in wheat productivity, fertilizer application and nutrient use efficiency. In summary, it was suggested that best nutrient management practices, i.e. fertilizer recommendation applied based on soil testing or yield response, with strategies to match the nutrient input with realistic yield and demand, or provided with the 4R's nutrient management (right time, right rate, right site and

  10. Agronomic Characteristics Related to Grain Yield and Nutrient Use Efficiency for Wheat Production in China

    PubMed Central

    Zheng, Huaiguo; Xu, Xinpeng

    2016-01-01

    In order to make clear the recent status and trend of wheat (Triticum aestivum L.) production in China, datasets from multiple field experiments and published literature were collected to study the agronomic characteristics related to grain yield, fertilizer application and nutrient use efficiency from the year 2000 to 2011. The results showed that the mean grain yield of wheat in 2000–2011 was 5950 kg/ha, while the N, P2O5 and K2O application rates were 172, 102 and 91 kg/ha on average, respectively. The decrease in N and P2O5 and increase in K2O balanced the nutrient supply and was the main reason for yield increase. The partial factor productivity (PFP, kg grain yield produced per unit of N, P2O5 or K2O applied) values of N (PFP-N), P (PFP-P) and K (PFP-K) were in the ranges of 29.5~39.6, 43.4~74.9 and 44.1~76.5 kg/kg, respectively. While PFP-N showed no significant changes from 2000 to 2010, both PFP-P and PFP-K showed an increased trend over this period. The mean agronomic efficiency (AE, kg grain yield increased per unit of N, P2O5 or K2O applied) values of N (AEN), P (AEP) and K (AEK) were 9.4, 10.2 and 6.5 kg/kg, respectively. The AE values demonstrated marked inter-annual fluctuations, with the amplitude of fluctuation for AEN greater than those for AEP and AEK. The mean fertilizer recovery efficiency (RE, the fraction of nutrient uptake in aboveground plant dry matter to the nutrient of fertilizer application) values of N, P and K in the aboveground biomass were 33.1%, 24.3% and 28.4%, respectively. It was also revealed that different wheat ecological regions differ greatly in wheat productivity, fertilizer application and nutrient use efficiency. In summary, it was suggested that best nutrient management practices, i.e. fertilizer recommendation applied based on soil testing or yield response, with strategies to match the nutrient input with realistic yield and demand, or provided with the 4R’s nutrient management (right time, right rate, right site

  11. Bio-effectors from waste materials as growth promoters, an agronomic and metabolomic study

    NASA Astrophysics Data System (ADS)

    Alwanney, Deaa; Chami, Ziad Al; Angelica De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

    2014-05-01

    Nowadays, improving plant performance by providing growth promoters is a main concern of the organic agriculture. As a consequence of increased food demands, more efficient and alternatives of the current plant nutrition strategies are becoming urgent. Recently, a novel concept "bio-effectors" raised on to describe a group of products that are able to improve plant performance and do not belong to fertilizers or pesticides. Agro-Food processing residues are promising materials as bio-effector. Three plant-derived materials: brewers' spent grain (BSG), fennel processing residues (FPR) and lemon processing residues (LPR) were chosen as bio-effector candidates. Plant-derived materials were characterized in term of total macro and micronutrients content. Green extraction methodology and solvent choice (aqueous; ethanol; and aqueous: ethanol mixture 1:1) was based on the extraction yield as main factor. Optimum extracts, to be used on the tomato test plant, were determined using phytotoxicity test (seed germination test) as main constraint. Thereafter, selected extracts were characterized and secondary metabolites profiling were detected by NMR technique. Selected extracts were applied on tomato in a growth chamber at different doses in comparison to humic-like substances as positive control (Ctrl+) and to a Hoagland solution as negative control (Ctrl-). At the end of the experiment, agronomical parameters were determined and NMR-metabolomic profiling were conducted on tomato seedlings. Results are summarized as follow: (i) raw showed an interesting content, either at nutritional or biological level; (ii) aqueous extraction resulted higher yield than other used solvent; (iii) at high extraction ratio (1:25 for BSG; 1:100 for FPR; and 1:200 for LPR) aqueous extracts were not phytotoxic on the tomato test plant; (iv) all aqueous extract are differently rich in nutrients, aminoacids, sugars and low molecular weight molecules; (v) all extract exhibited a growth promotion at

  12. Multi-taxa trait and functional responses to physical disturbance.

    PubMed

    Pedley, Scott M; Dolman, Paul M

    2014-11-01

    Examining assemblage trait responses to environmental stressors extends our understanding beyond patterns of taxonomic diversity and composition, with results potentially transferable among bioregions. But the degree to which trait responses may be generalized across taxonomic groups remains incompletely understood. We compared trait responses among carabids, spiders and plants to an experimentally manipulated gradient of physical disturbance, replicated in open habitats within a forested landscape. Recolonization of recently disturbed habitats is expected to favour species with traits that promote greater dispersal ability, independent of taxa. We specifically predicted that physical disturbance would increase the representation of carabids with smaller body size, wings or wing dimorphism, spiders able to disperse aerially, and plants with therophyte life-history and wind-dispersed seed. We sampled 197 arthropod species (14,738 individuals) and 164 species of plant. The strength of association between each trait and the disturbance intensity was quantified by correlating matrices of species by traits, species abundance by sites and sites by environment, with significance assessed by comparison with a null model. Responses of biological traits varied among taxa but could be consistently interpreted in terms of dispersal ability. Trait shifts for carabid and plant assemblages were as predicted and correspond to those observed in other disturbance regimes. Assemblages after disturbance comprised smaller and winged carabids, and smaller plants with wind-dispersed seed, consistent with selection for species with better dispersal ability. In contrast, aerial dispersal did not appear important in spider recolonization, instead terrestrial dispersal ability was suggested by the increased abundance of larger-bodied and cursorial species. However, larger spider body size was also associated with an active-hunting strategy, also favoured in the post-disturbance environment

  13. Sickle Cell Trait: An Update

    PubMed Central

    Johnson, Lenworth N.

    1982-01-01

    A review of the literature on sickle cell trait was completed by Sears in 1978. Since that time, several papers have been published concerning the possible health risks of sickle cell trait. Data presented from these studies show that there is no association with sickle cell trait and overall survival, overall mortality, overall morbidity, frequency and length of hospitalization, short-term survival of renal transplant recipient, and inheritance of glucose-6-phosphate dehydrogenase. Association with sickle cell trait is very likely in the following: splenic infarction at high altitudes (over 10,000 feet), in unpressurized airplane flight and mountain climbing, bacteriuria and pyelonephritis in pregnancy, hyposthenuria, hematuria, and delayed resolution of anterior chamber hyphema. Although these conditions have a statistical significant association with sickle cell trait, they occur quite infrequently. Thus, when they are observed, other causes should be sought before attributing them to sickle cell trait. Reduced mortality from Plasmodium falciparum infection also shows significant association with sickle cell trait. PMID:6752430

  14. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus

    PubMed Central

    Yu, Xiaona; Choi, Su Ryun; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Pang, Wenxing; Lee, Ji-Young; Lim, Yong Pyo

    2016-01-01

    Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) “835” and “B2,” including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69–12.6 of the LOD value, and 0.82–16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs. PMID:26973691

  15. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus.

    PubMed

    Yu, Xiaona; Choi, Su Ryun; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Pang, Wenxing; Lee, Ji-Young; Lim, Yong Pyo

    2016-01-01

    Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.

  16. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus.

    PubMed

    Yu, Xiaona; Choi, Su Ryun; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Pang, Wenxing; Lee, Ji-Young; Lim, Yong Pyo

    2016-01-01

    Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs. PMID:26973691

  17. Consumer trait variation influences tritrophic interactions in salt marsh communities

    PubMed Central

    Hughes, Anne Randall; Hanley, Torrance C; Orozco, Nohelia P; Zerebecki, Robyn A

    2015-01-01

    The importance of intraspecific variation has emerged as a key question in community ecology, helping to bridge the gap between ecology and evolution. Although much of this work h