scholarly journals Loci Controlling Adaptation to Heat Stress Occurring at the Reproductive Stage in Durum Wheat

2019 ◽  
Author(s):  
Khaoula El Hassouni ◽  
Bouchra Belkadi ◽  
Amadou Tidiane Sall ◽  
Abdelkarim Filali-Maltouf ◽  
Ayed Al-Abdallat ◽  
...  
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Durum Wheat ◽  
Genome Wide Association Study ◽  
Reproductive Stage ◽  
Polymorphic Snps ◽  
Positive Allele ◽  
Core Set ◽  
Tolerance Indices ◽  
Genomic Regions

Heat stress occurring during the reproductive stage of wheat has a detrimental effect on productivity. A durum wheat core set was exposed to simulated terminal heat stress by applying plastic tunnels at the time of flowering over two seasons. Mean grain yield was reduced by 54% compared to control conditions, and grain number was the most critical trait for tolerance to this stress. The combined use of tolerance indices and grain yield identified five elites: Kunmiki, Berghouata1, Margherita2, IDON37-141, and Ourgh. The core set was also subjected to genome wide association study using 7,652 polymorphic SNPs markers. The most critical genomic regions were identified in association with spike fertility and tolerance indices on chromosome 1A, 5B and 6B. Haplotype analysis on a set of 208 elites confirmed that lines that carried the positive allele at all three QTLs resulted in a yield advantage of 8% when field tested under daily temperatures above 31° C. Two of the QTLs were successfully validated into KASP markers and explained >10% of the phenotypic variation for an independent elite germplasm set. These genomic regions can now be readily deployed via breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

scholarly journals Loci Controlling Adaptation to Heat Stress Occurring at the Reproductive Stage in Durum Wheat

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 414 ◽  
Author(s):  
Khaoula El Hassouni ◽  
Bouchra Belkadi ◽  
Abdelkarim Filali-Maltouf ◽  
Amadou Tidiane-Sall ◽  
Ayed Al-Abdallat ◽  
...  
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Durum Wheat ◽  
Genome Wide Association Study ◽  
Reproductive Stage ◽  
Specific Pcr ◽  
Positive Allele ◽  
Core Set ◽  
Tolerance Indices ◽  
Genomic Regions

Heat stress occurring during the reproductive stage of wheat has a detrimental effect on productivity. A durum wheat core set was exposed to simulated terminal heat stress by applying plastic tunnels at the time of flowering over two seasons. Mean grain yield was reduced by 54% compared to control conditions, and grain number was the most critical trait for tolerance to this stress. The combined use of tolerance indices and grain yield identified five top performing elite lines: Kunmiki, Berghouata1, Margherita2, IDON37-141, and Ourgh. The core set was also subjected to genome wide association study using 7652 polymorphic single nucleotide polymorphism (SNPs) markers. The most significant genomic regions were identified in association with spike fertility and tolerance indices on chromosomes 1A, 5B, and 6B. Haplotype analysis on a set of 208 elite lines confirmed that lines that carried the positive allele at all three quantitative trait loci (QTLs) had a yield advantage of 8% when field tested under daily temperatures above 31° C. Three of the QTLs were successfully validated into Kompetitive Allele Specific PCR (KASP) markers and explained >10% of the phenotypic variation for an independent elite germplasm set. These genomic regions can now be readily deployed via breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

scholarly journals Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

2020 ◽  
Author(s):  
Aditi Bhandari ◽  
Nitika Sandhu ◽  
Jérôme Bartholome ◽  
Tuong-Vi Cao-Hamadoun ◽  
Nourollah Ahmadi ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Reproductive Stage ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Close Proximity ◽  
Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production globally. Conventional and marker-assisted breeding strategies for developing drought tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles and understanding their interactions with genetic backgrounds for contributing to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage drought. A diverse set of 280 indica-aus accessions was phenotyped for grain yield and nine yield-related traits under normal condition and under two managed drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 220 significant MTAs and candidate gene analysis within 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 47 genes, 4 earlier reported major grain yield QTLs and 8 novel QTLs for 10 traits. The significant MTAs were majorly located on chromosomes 1, 2, 5, 6, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related traits, except flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding program targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex-genetic architecture of grain yield under reproductive-stage drought under different environments. Validation of major genomic regions reported in the study can be effectively used to develop drought tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

scholarly journals Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

2020 ◽  
Author(s):  
Aditi Bhandari ◽  
Nitika Sandhu ◽  
Jérôme Bartholome ◽  
Tuong-Vi Cao-Hamadoun ◽  
Nourollah Ahmadi ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Reproductive Stage ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

scholarly journals Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

2020 ◽  
Author(s):  
Aditi Bhandari ◽  
Nitika Sandhu ◽  
Jérôme Bartholome ◽  
Tuong-Vi Cao-Hamadoun ◽  
Nourollah Ahmadi ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Reproductive Stage ◽  
Phenotypic Variance ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Close Proximity ◽  
Genomic Regions

Abstract Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for grain yield and nine yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 220 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centered from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related traits, except flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

scholarly journals Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

2020 ◽  
Vol 21 (19) ◽  
pp. 7021 ◽  
Author(s):  
Osvin Arriagada ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta ◽  
Andrés R. Schwember
Keyword(s):  
Grain Yield ◽  
Durum Wheat ◽  
Genome Wide Association Study ◽  
Molecular Mapping ◽  
Grain Filling ◽  
Kernel Weight ◽  
Arid Environments ◽  
A Genome ◽  
Grain Filling Period ◽  
Genomic Regions

Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.

scholarly journals GWAS revealed effect of genotype × environment interactions for grain yield of Nebraska winter wheat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shamseldeen Eltaher ◽  
P. Stephen Baenziger ◽  
Vikas Belamkar ◽  
Hamdy A. Emara ◽  
Ahmed A. Nower ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Winter Wheat ◽  
Grain Yield ◽  
Genome Wide Association Study ◽  
Phenotypic Selection ◽  
Wheat Breeding ◽  
Wheat Genotypes ◽  
Genome Wide ◽  
Genomic Regions ◽  
Significant Linkage

Abstract Background Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of wheat genotypes in different environments. Selecting high yielding genotypes that can be used for a target set of environments is needed. Phenotypic selection can be misleading due to the environmental conditions. Incorporating information from phenotypic and genomic analyses can be useful in selecting the higher yielding genotypes for a group of environments. Results A set of 270 F3:6 wheat genotypes in the Nebraska winter wheat breeding program was tested for grain yield in nine environments. High genetic variation for grain yield was found among the genotypes. G × E interaction was also highly significant. The highest yielding genotype differed in each environment. The correlation for grain yield among the nine environments was low (0 to 0.43). Genome-wide association study revealed 70 marker traits association (MTAs) associated with increased grain yield. The analysis of linkage disequilibrium revealed 16 genomic regions with a highly significant linkage disequilibrium (LD). The candidate parents’ genotypes for improving grain yield in a group of environments were selected based on three criteria; number of alleles associated with increased grain yield in each selected genotype, genetic distance among the selected genotypes, and number of different alleles between each two selected parents. Conclusion Although G × E interaction was present, the advances in DNA technology provided very useful tools and analyzes. Such features helped to genetically select the highest yielding genotypes that can be used to cross grain production in a group of environments.

scholarly journals Genomic Regions Associated with the Control of Flowering Time in Durum Wheat

2020 ◽  
Author(s):  
Priyanka Gupta ◽  
Hafssa Kabbaj ◽  
Khaoula El Hassouni ◽  
Marco Maccaferri ◽  
Miguel Sabchez-Garcia ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Strong Association ◽  
Triticum Aestivum L ◽  
Day Length ◽  
Significant Qtls ◽  
A Genome ◽  
Days To Heading ◽  
Genomic Regions

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperatures, day length and other climatic variables. Genotyping with 35K Axiom array generated 7,652 polymorphic SNPs in addition to 3 KASP markers associated to known flowering genes. In total, 34 significant QTLs were identified in both landraces and modern lines. Some QTLs had strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B and vernalization genes Vrn-A1, and Vrn3. However, these loci explained only 5 to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-17 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-11 and Q.ICD.Ppd-12 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.)

scholarly journals Genetic Dissection of Grain Yield Component Traits Under High Nighttime Temperature Stress in a Rice Diversity Panel

2021 ◽  
Vol 12 ◽  
Author(s):  
Anuj Kumar ◽  
Chirag Gupta ◽  
Julie Thomas ◽  
Andy Pereira
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Candidate Genes ◽  
Significant Snps ◽  
The United States ◽  
Yield Component ◽  
Reproductive Stage ◽  
Venn Diagram ◽  
Rice Grain ◽  
Diversity Panel

To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies Oryza sativa ssp. Indica and ssp. Japonica. Under HNT stress, the Japonica ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, Indica, and Japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major GY component quantitative trait loci (QTLs) under heat stress. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the Japonica population, with 20 putative candidate genes being common in the Combined, Indica and Japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.

scholarly journals Genetic variations, heritability, heat tolerance indices and correlations studies for traits of bread wheat genotypes under high temperature

2019 ◽  
Vol 11 (5) ◽  
pp. 672-686
Author(s):  
Elfadil Mohamed Elbashier ◽  
Elfadil Mohammed Eltayeb Elbashier ◽  
Siddig Esa Idris2 ◽  
Wuletaw Tadesse ◽  
Izzat S.A. Tahir ◽  
...  
Keyword(s):  
Heat Stress ◽  
High Temperature ◽  
Grain Yield ◽  
Bread Wheat ◽  
Heat Tolerance ◽  
Agricultural Research ◽  
Canopy Temperature ◽  
Content Type ◽  
Wheat Genotypes ◽  
Tolerance Indices

PurposeThe purpose of this paper was to study the genetic variability, heritability, heat tolerance indices and phenotypic and genotypic correlation studies for traits of 250 elite International Center for Agricultural Research in the Dry Areas (ICARDA) bread wheat genotypes under high temperature in Wad Medani, Center in Sudan.Design/methodology/approachBread wheat is an important food on a global level and is used in the form of different products. High temperature associated with climate change is considered to be a detrimental stress in the future on world wheat production. A total of 10,250 bread wheat genotypes selected from different advanced yield trials introduction from ICARDA and three checks including were grown in two sowing dates (SODs) (1st and 2nd) 1st SOD heat stress and 2nd SOD non-stress at the Gezira Research Farm, of the Agricultural Research Corporation, Wad Medani, Sudan.FindingsAn alpha lattice design with two replications was used to assess the presence of phenotypic and genotypic variations of different traits, indices for heat stress and heat tolerance for 20 top genotypes and phenotypic and genotypic correlations. Analysis of variance revealed significant differences among genotypes for all the characters. A wide range, 944-4,016 kg/ha in the first SOD and 1,192-5,120 kg/ha in the second SOD, was found in grain yield. The average yield on the first SOD is less than that of the secondnd SOD by 717.7 kg/ha, as the maximum and minimum temperatures were reduced by 3ºC each in the second SOD when compared to the first SOD of the critical stage of crop growth shown.Research limitations/implicationsSimilar wide ranges were found in all morpho-physiological traits studied. High heritability in a broad sense was estimated for days to heading and maturity. Moderate heritability estimates found for grain yield ranged from 44 to 63.6 per cent, biomass ranged from 37.8 to 49.1 per cent and canopy temperature (CT) after heading ranged from 44.2 to 48 per cent for the first and secondnd SODs. The top 20 genotypes are better than the better check in the two sowing dates and seven genotypes (248, 139, 143, 27, 67, 192 and 152) were produced high grain yield under both 1st SOD and 2nd SOD.Practical implicationsThe same genotypes in addition to Imam (check) showed smaller tolerance (TOL) values, indicating that these genotypes had a smaller yield reduction under heat-stressed conditions and that they showed a higher heat stress susceptibility index (SSI). A smaller TOL and a higher SSI are favored. Both phenotypic and genotypic correlations of grain yield were positively and significantly correlated with biomass, harvest index, number of spikes/m2, number of seeds/spike and days to heading and maturity in both SODs and negatively and significantly correlated with canopy temperature before and after heading in both SODs.Originality/valueGenetic variations, heritability, heat tolerance indices and correlation studies for traits of bread wheat genotypes under high temperature

17 Genome-wide Association Study for Heat Stress Tolerance in Swine Using Weighted Single-step GBLUP

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 8-8
Author(s):  
Gabriella R Dodd ◽  
Breno O Fragomeni ◽  
Kent A Gray ◽  
Yijian Huang
Keyword(s):  
Heat Stress ◽  
Association Study ◽  
Stress Tolerance ◽  
Genetic Correlation ◽  
Genome Wide Association Study ◽  
Single Step ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Heat Stress Tolerance ◽  
Genomic Regions

Abstract The purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine as well as analyze the accuracy of prediction. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri. Individuals were a commercial cross of a Duroc sire and a dam resulting from a Landrace and Large White cross. Genotypic information was available for 8,232 animals with 33,581 SNP. The pedigree file contained 553,448 animals. A 78 on the Temperature Humidity Index (THI) was used as a threshold for heat stress. A two-trait analysis was used with the phenotypes heat stress (trait one) and non-heat stress (trait two). Variance components were calculated via AIREML and breeding values were calculated using single step GBLUP (ssGBLUP). The heritability for trait one and two were calculated at 0.25 and 0.20, respectively, and the genetic correlation was calculated as 0.63. Validation was calculated for 163 genotyped sires with progeny in the last generation. The GEBV of complete data was used as the benchmark, and the accuracy was determined as the correlation between the GEBV of the reduced and complete data for the validation sires. Weighted ssGBLUP did not increase the accuracies, both methods showed a maximum accuracy of 0.32 for trait one and 0.54 for trait two. Manhattan Plots for trait one, trait two, and the difference between the two were created from the results of the two-trait analysis. Windows explaining around 1% of the genetic variance were identified. The only difference between the two traits was a peak at chromosome 14. The genetic correlation suggests different mechanisms for growth under heat stress. The GWAS results show that both traits are highly polygenic, with few genomic regions explaining more than 1% of variance.

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