High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

Abstract

Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to %1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three biparental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r 2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.

Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat

“…In such cases, projection onto a genetic map serves as a complementary approach. Owing to the increasing number of different types of genetic markers, a high-density consensus genetic map that compiles 7352 markers has been reported [130] and is used here for the projection of kernel hardness-associated QTLs ( Figure S1, Table S2). While the QTLs subjected to fewer studies can be located on the consensus genetic map, both QTL locations on the genetic and genome maps are consistent.…”

Adapting Cereal Grain Crops to Drought Stress: 2020 and Beyond

“…Through advances in next generation sequencing, identification of major QTLs regulating specific drought responses has been made possible, via the development of large numbers of genetic markers such as single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels), thereby opening the doors for an efficient way to improving drought tolerance in cereal crops [89]. Additionally, large-scale genome-wide association studies (GWAS) have been conducted to detect genomic regions and candidate genes for various agronomic traits, including drought tolerance in cereals [13,136,137]. Resultantly, hundreds of studies reporting thousands of major drought-responsive genes and QTLs in cereal grain crops can be found in the literature, including those for maize [13,[138][139][140], rice [12,13,105,138,141,142], wheat [13,31,137,138,143], sorghum [138,144,145], barley [138,146], and pearl millet [136,147,148].…”

“…Going forward, MAS remains a useful tool for major QTL, whereas QTL cloning is increasingly becoming a more routine activity. This has been necessitated by increased use of high-throughput sequencing, precise phenotyping and identification of appropriate candidate genes through omics approaches [89,136,137]. Cloned QTL facilitate a more targeted search for novel alleles and will offer novel insights for genetic engineering of drought resilient cereal crops [13].…”

Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection

“…Using the genome browser of IWGSC RefSeq v1.0, we found that the SNP is located ~255 kb upstream of the major STB resistance gene Stb6. Linkage disequilibrium (LD) in wheat is large in comparison to other cereals due to its self-pollinating nature (Cavanagh et al 2013;Wang et al 2014;Pang et al 2020). Pang et al (2020) showed that the average genome-wide LD block size in wheat is around 4.2 Mb.…”