Genome-Wide Association Studies to Identify Loci and Candidate Genes Controlling Kernel Weight and Length in a Historical United States Wheat Population

Daba, Sintayehu; Tyagi, Priyanka; Brown‐Guedira, Gina; Mohammadi, Mohsen

doi:10.3389/fpls.2018.01045

Cited by 23 publications

(17 citation statements)

References 86 publications

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“…tauschii, the D genome donor of hexaploid wheat, the total of 7,243 (47.2%) of shared SNPs between the diploid and hexaploid datasets also agrees with the gene flow between these species. Mapping against the CS exome sequence and subsequent comparison with exome capture data identified 9,570 SNPs, from which the B (45.1%), A (36.6%) and D (17.3%) sub-genome distribution compared to several previous reports (Wang et al, 2014;Daba et al, 2018;Pont et al, 2019).…”

Section: Genetic Diversitymentioning

confidence: 78%

Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics

et al. 2020

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Leaf rust caused by Puccinia triticina is the most widespread rust disease of wheat. As pathogen populations are constantly evolving, identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead of this plant-pathogen evolutionary arms race. The wild genepool of wheat is a rich source of genetic diversity, accounting for 44% of the Lr genes identified. Here we performed a genome-wide association study (GWAS) on a diverse germplasm of 385 accessions, including 27 different Triticum and Aegilops species. Genetic characterization using the wheat 90 K array and subsequent filtering identified a set of 20,501 single nucleotide polymorphic (SNP) markers. Of those, 9,570 were validated using exome capture and mapped onto the Chinese Spring reference sequence v1.0. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the T. aestivum and T. turgidum species. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3–4 years at 2–3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related loci associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known Lr genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Isolation of these candidate genes will contribute to the elucidation of their role in leaf rust resistance and promote their usefulness in marker-assisted selection and introgression.

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Section: Genetic Diversitymentioning

confidence: 78%

Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics

et al. 2020

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“…Great progress has been made in identifying major QTLs for kernel size and shape [ 17 , 18 , 19 , 20 , 21 , 22 ], and several candidate genes were identified in wheat. For instance, cytokinin oxidase (encoded by TaCKX ) reversibly inactivates cytokinin and increases kernel weight [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses

Elhadi

Kamal

Gorafi

et al. 2021

IJMS

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Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat–drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin–protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.

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“…Association mapping has been proven to be successful in identifying markertrait associations in plant [27]. Recent study has identified 26 quantitative trait loci (QTL) for kernel width and 27 QTL for kernel length in a historical United States wheat population [28]. A comprehensive genome-wide analysis using microsatellite markers and 90K iSELECT array identified TaGW-6A underlying thousand grain weight in a panel of European winter wheat varieties [29].…”

Section: Introductionmentioning

confidence: 99%

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

et al. 2020

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Durum wheat, genetic resource with favorable alleles is considered as natural gene pool for wheat breeding. Kernel size and weight are important factors affecting grain yield in crops. Here, association analysis was performed to dissect the genetic constitution of kernelrelated traits in 150 lines collected from 46 countries and regions using a set of EST-derived and genome-wide SNP markers with five consecutive years of data. Total 109 significant associations for eight kernel-related traits were detected under a mix linear model, generating 54 unique SNP markers distributed on 13 of 14 chromosomes. Of which, 19 marker-trait associations were identified in two or more environments, including one stable and pleiotropic SNP BE500291_5_A_37 on chromosome 5A correlated with six kernel traits. Although most of our SNP loci were overlapped with the previously known kernel weight QTLs, several novel loci for kernel traits in durum were reported. Correlation analysis implied that the moderate climatic variables during growth and development of durum are needed for the large grain size and high grain weight. Combined with our previous studies, we found that chromosome 5A might play an important role in durum growth and development.

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Genome-Wide Association Studies to Identify Loci and Candidate Genes Controlling Kernel Weight and Length in a Historical United States Wheat Population

Cited by 23 publications

References 86 publications

Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics

Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics

Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

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