scholarly journals Genome-Wide Association Mapping through 90K SNP Array for Quality and Yield Attributes in Bread Wheat against Water-Deficit Conditions

Agriculture ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 392
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Muhammad Sajjad ◽  
Yawen Zeng ◽  
Muhammad Iqbal ◽  
Sultan Habibullah Khan ◽  
...  
Keyword(s):  
Grain Yield ◽  
Candidate Genes ◽  
Water Deficit ◽  
Bread Wheat ◽  
Genome Wide Association ◽  
Water Deficit Stress ◽  
Yield Attributes ◽  
Yield And Quality ◽  
Isolation And Characterization ◽  
Genome Wide

The decrease in water resources is a serious threat to food security world-wide. In this regard, a genome-wide association study (GWAS) was conducted to identify grain yield and quality-related genes/loci under normal and water-deficit conditions. Highly significant differences were exhibited among genotypes under both conditions for all studied traits. Water-deficit stress caused a reduction in grains yield and an increase in grains protein contents (GPC) and gluten contents (GLC). Population structure divided the 96 genotypes into four sub-populations. Out of 72 significant marker-trait associations (MTAs), 28 and 44 were observed under normal and water-deficit stress conditions, respectively. Pleiotropic loci (RAC875_s117925_244, BobWhite_c23828_341 and wsnp_CAP8_c334_304253) for yield and quality traits were identified on chromosomes 5A, 6B and 7B, respectively, under normal conditions. Under a water-deficit condition, the pleiotropic loci (Excalibur_c48047_90, Tdurum_contig100702_265 and BobWhite_c19429_95) for grain yield per plant (GYP), GPC and GLC were identified on chromosomes 3A, 4A and 7B, respectively. The pleiotropic loci (BS00063551_51 and RAC875_c28721_290) for GPC and GLC on chromosome 1B and 3A, respectively, were found under both conditions. Besides the validation of previously reported MTAs, some new MTAs were identified for flag leaf area (FLA), thousand grain weight (TGW), GYP, GPC and GLC under normal and water-deficit conditions. Twenty SNPs associated with the traits were mapped in the coding DNA sequence (CDS) of the respective candidate genes. The protein functions of the identified candidate genes were predicted and discussed. Isolation and characterization of the candidate genes, wherein, SNPs were mapped in CDS will result in discovering novel genes underpinning water-deficit tolerance in bread wheat.

scholarly journals Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raju Bheemanahalli ◽  
Montana Knight ◽  
Cherryl Quinones ◽  
Colleen J. Doherty ◽  
S. V. Krishna Jagadish
Keyword(s):  
Grain Size ◽  
Candidate Genes ◽  
Gene Network ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Genetic Loci ◽  
Stay Green ◽  
Yield And Quality ◽  
Genome Wide ◽  
Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

scholarly journals Genome-Wide Association Mapping for Stomata and Yield Indices in Bread Wheat under Water Limited Conditions

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1646
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Muhammad Nouman Iqbal ◽  
Muhammad Arslan Iqbal ◽  
Yawen Zeng ◽  
Aziz Ullah ◽  
...  
Keyword(s):  
Grain Yield ◽  
Bread Wheat ◽  
Significant Snps ◽  
Water Shortage ◽  
Genome Wide Association ◽  
Yield Potential ◽  
Strong Positive Correlation ◽  
Leaf Venation ◽  
Genome Wide ◽  
Stomata Size

Genome-wide association study (GWAS) was performed for stomata- and yield-related attributes with high-density Illumina 90 K Infinium SNP (single nucleotide polymorphism) array in bread wheat to determine genetic potential of germplasm for scarce water resources with sustainable yield potential. Major yield and stomata attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water shortage environments during two seasons. Highly significant variations were shown among accessions in both conditions for examined characteristics. Water shortage conditions reduced the overall wheat yield and strong positive correlation existed among stomatal frequency, leaf venation and grain yield per plant. Population structure analyses based on 90,000 SNP data classified the accessions into four sub-populations which indicated the presence of genetic variability. Marker-trait association (MTA) analyses revealed that 422 significant SNPs at p ≤ 10−3, after crossing the false discovery rate (FDR) <0.05 threshold, were linked with examined attributes. Pleiotropic loci (wsnp_Ex_c8913_14881924 and Tdurum_contig10598_304) were associated with flag leaf area (FLA), stomata size (SS), stomata frequency (SF), leaf venation (LV), number of grain per spike (NGS) and grain yield per plant (GYP), which were located on chromosome 4B and 6B at the positions 173.63cM and 229.64cM, respectively, under water shortage conditions. Pleotropic loci wsnp_Ex_c24167_33416760, wsnp_Ex_c5412_9564046 and Tdurum_contig81797_369 on chromosomes 7A, 2A and 4B at the positions 148.26cM, 261.05cM and 173.63cM, respectively, were significantly linked with stomata and yield indices such as FLA, SS, SF, LV, NGS and GYP under normal and water shortage conditions. The current experiment not only validated several MTAs for studied indices reported in other studies but also discovered novel MTAs significant under water shortage environments. Associated and significant SNPs will be useful in discovering novel genes underpinning water shortage tolerance in bread wheat for producing high-yielding and drought tolerant wheat varieties to fulfill the wheat demand for growing populations.

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Genetica ◽  
2016 ◽  
Vol 144 (6) ◽  
pp. 651-664 ◽  
Author(s):  
Gabriel Feresin Pantalião ◽  
Marcelo Narciso ◽  
Cléber Guimarães ◽  
Adriano Castro ◽  
José Manoel Colombari ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Niu ◽  
Tianxiao Chen ◽  
Chunchao Wang ◽  
Kai Chen ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Genes ◽  
Grain Quality ◽  
Genome Wide Association Study ◽  
Grain Shape ◽  
Grain Weight ◽  
Genome Wide Association ◽  
Rice Grain ◽  
Genome Wide

Abstract Background Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape. Results Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided. Conclusions Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.

scholarly journals Genome-Wide Association Study of the Genetic Basis of Effective Tiller Number in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mengmeng Ren ◽  
Minghan Huang ◽  
Haiyang Qiu ◽  
Yan Chun ◽  
Lu Li ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Positive Association ◽  
Tiller Number ◽  
Genome Wide Association ◽  
Favorable Alleles ◽  
Genome Wide ◽  
A Genome

Abstract Background Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. Results In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition from vegetative to reproductive growth of tillers. Conclusions Our results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.

scholarly journals Genome-wide association study reveals the genetic basis of yield- and quality-related traits in wheat

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Le Gao ◽  
Chengsheng Meng ◽  
Tengfei Yi ◽  
Ke Xu ◽  
Huiwen Cao ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Wheat Yield ◽  
Significant Snps ◽  
Wheat Breeding ◽  
Genome Wide Association ◽  
Yield And Quality ◽  
Genome Wide

Abstract Background Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-density 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties. Results A total of 11,140 polymorphic SNPs were distributed on 21 chromosomes, including 270 significant SNPs associated with 25 yield- and quality-related traits. Additionally, 638 putative candidate genes were detected near the significant SNPs based on BLUP data, including three (TraesCS7A01G482000, TraesCS4B01G343700, and TraesCS6B01G295400) related to spikelet number per spike, diameter of the first internode, and grain volume. The three candidate genes were further analyzed using stage- and tissue- specific gene expression data derived from an RNA-seq analysis. These genes are promising candidates for enhancing yield- and quality-related traits in wheat. Conclusions The results of this study provide a new insight to understand the genetic basis of wheat yield and quality. Furthermore, the markers detected in this study may be applicable for marker-assisted selection in wheat breeding programs.

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