Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain

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.

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Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Plants ◽

10.3390/plants10030559 ◽

2021 ◽

Vol 10 (3) ◽

pp. 559

Author(s):

Ashutosh Kumar Yadav ◽

Aruna Kumar ◽

Nitasha Grover ◽

Ranjith Kumar Ellur ◽

Haritha Bollinedi ◽

...

Keyword(s):

Salt Tolerance ◽

Association Study ◽

Salinity Tolerance ◽

Genome Wide Association Study ◽

Genomic Region ◽

Seedling Stage ◽

Genome Wide Association ◽

High Yield ◽

Genome Wide ◽

Trait Associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

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Genome-wide association study of rice grain width variation

Genome ◽

10.1139/gen-2017-0106 ◽

2018 ◽

Vol 61 (4) ◽

pp. 233-240 ◽

Cited By ~ 5

Author(s):

Xiao-Ming Zheng ◽

Tingting Gong ◽

Hong-Ling Ou ◽

Dayuan Xue ◽

Weihua Qiao ◽

...

Keyword(s):

Association Study ◽

Seed Size ◽

Large Scale ◽

Genome Wide Association Study ◽

Rice Variety ◽

Genome Wide Association ◽

Grass Species ◽

Rice Grain ◽

Genome Wide ◽

Grain Width

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

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Genome Wide Association Study of Resistance to PstS2 and Warrior Races of Stripe (Yellow) Rust in Bread Wheat Landraces

10.1101/2020.02.09.940775 ◽

2020 ◽

Author(s):

Muhammad Massub Tehseen ◽

Fatma Aykut Tonk ◽

Muzaffer Tosun ◽

Ahmed Amri ◽

Carolina P. Sansaloni ◽

...

Keyword(s):

Association Study ◽

Resistance Genes ◽

Genome Wide Association Study ◽

Snp Markers ◽

Genome Wide Association ◽

Adult Plant ◽

Mapping Panel ◽

Genome Wide ◽

Genomic Regions ◽

Trait Associations

ABSTRACTStripe rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and new emerging aggressive races of stripe rusts are causing serious concerns in all main wheat growing areas of the world. To search for new sources of resistance genes and associated QTL for effective utilization in future breeding programs an association mapping panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the association mapping panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study are far away from any previously reported Yr gene or QTL hence, tagging novel genomic regions. The In-silico analysis of the novel QTL regions identified candidate resistance genes encoding proteins putative to plants disease resistance and defense mechanism.

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