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 ◽  
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 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 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 Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Niranjan Baisakh ◽  
Jonalyn Yabes ◽  
Andres Gutierrez ◽  
Venkata Mangu ◽  
Peiyong Ma ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Grain Yield ◽  
Drought Resistance ◽  
Quantitative Trait ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Yield Traits ◽  
Rice Varieties ◽  
Drought Tolerant ◽  
Trait Loci

Improving drought resistance in crops is imperative under the prevailing erratic rainfall patterns. Drought affects the growth and yield of most modern rice varieties. Recent breeding efforts aim to incorporate drought resistance traits in rice varieties that can be suitable under alternative irrigation schemes, such as in a (semi)aerobic system, as row (furrow-irrigated) rice. The identification of quantitative trait loci (QTLs) controlling grain yield, the most important trait with high selection efficiency, can lead to the identification of markers to facilitate marker-assisted breeding of drought-resistant rice. Here, we report grain yield QTLs under greenhouse drought using an F2:3 population derived from Cocodrie (drought sensitive) × Nagina 22 (N22) (drought tolerant). Eight QTLs were identified for yield traits under drought. Grain yield QTL under drought on chromosome 1 (phenotypic variance explained (PVE) = 11.15%) co-localized with the only QTL for panicle number (PVE = 37.7%). The drought-tolerant parent N22 contributed the favorable alleles for all QTLs except qGN3.2 and qGN5.1 for grain number per panicle. Stress-responsive transcription factors, such as ethylene response factor, WD40 domain protein, zinc finger protein, and genes involved in lipid/sugar metabolism were linked to the QTLs, suggesting their possible role in drought tolerance mechanism of N22 in the background of Cocodrie, contributing to higher yield under drought.

scholarly journals Evaluation of yield performance and establishment methods of drought tolerant rice genotypes under rainfed condition in drought prone areas of Bangladesh

2020 ◽  
Vol 5 (2) ◽  
pp. 97-104
Author(s):  
M.M. Islam ◽  
M.I. Ali ◽  
M.S. Islam ◽  
A.B.M.S. Alam ◽  
M.H. Rahman ◽  
...  
Keyword(s):  
Grain Yield ◽  
Field Experiments ◽  
Block Design ◽  
Direct Seeding ◽  
Rice Varieties ◽  
Rainfed Condition ◽  
Local Cultivar ◽  
Drought Tolerant ◽  
Seeding Method ◽  
Randomized Complete Block Design

Two field experiments were carried out at farmer’s field of Rajshahi and Chapainawabgonj under the Department of Agronomy, BINA during aman season of 2017 and 2018 consecutively to evaluate the drought tolerant rice varieties under different establishment methods in rain fed condition. First experiment (E1) was conducted to find out the performance of varieties and second experiment (E2) was to find out the suitability of method of transplanting/sowing in combination with short duration aman varieties. Different methods were as direct seeding, puddled and un-puddled transplanting and cultivars were used to cultivate BRRI dhan56, Binadhan-7, Binadhan-17 (except in second experiment) and Huttra (local cultivar). The experiment was laid out in a randomized complete block design with three replications. The recommended fertilizer doses applied for the experiment were 80 kg N ha-1, 15 kg P ha-1, 50 kg K ha-1, 20 kg S ha-1 and 2 kg Zn ha-1. Nitrogen, phosphorus, potassium, sulphur and zinc were supplied from urea, TSP, MoP, gypsum and zinc sulphate monohydrate respectively while urea was applied in three equal splits. Among the cultivar Binadhan-17 produced statistically higher grain yield (5.62 t ha-1) at Chapainawabgonj. Among methods Binadhan-7 statistically higher grain yield 5.32 t ha-1 and 5.21 t ha-1, respectively) in puddle transplanting method both Chapainawabgonj and Rajshahi region during 2017. Among the cultivar Huttra (local) produced statistically higher grain yield (5.43 t ha-1) at Chapainawabgonj. Among methods, BRRI dhan56 statistically higher grain yield 6.37 t ha-1 and 6.19 t ha-1, respectively) in puddle transplanting method bothat Rajshahi and Chapainawabgonj during 2018. Overall results indicates that BRRI dhan56, Binadhan-7, Binadhan-17 performed better in puddled transplanting, Huttra (local) in direct seeding method in drought prone region of Bangladesh.

scholarly journals Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

2018 ◽  
Vol 19 (10) ◽  
pp. 3011 ◽  
Author(s):  
Madhav Bhatta ◽  
Alexey Morgounov ◽  
Vikas Belamkar ◽  
P. Baenziger
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Association Study ◽  
Hexaploid Wheat ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Synthetic Hexaploid Wheat ◽  
Phenotypic Variance ◽  
Genome Wide ◽  
Synthetic Hexaploid

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.

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 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 Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Xin ◽  
Jingguo Wang ◽  
Jia Li ◽  
Hongwei Zhao ◽  
Hualong Liu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Negative Impact ◽  
Genome Wide Association ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Genome Wide ◽  
A Genome

Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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