High resolution genome-wide association study identified genomic regions and candidate genes for important agronomic traits in wheat

Authors: PANG, YUNLONG - Kansas State University; LIU, CHUNXIA - Kansas State University; WANG, DANFENG - Kansas State University; St Amand, Paul; Bernardo, Amy; LI, WENHUI - Shangdong Agricultural University; HE, FENG - Shangdong Agricultural University; LI, LINZHI - Yantai University; WANG, LIMING - Henan Institute Of Science And Technology; YUAN, XIUFANG - Shangdong Agricultural University; Bai, Guihua

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2020
Publication Date: 7/20/2020
Citation: Pang, Y., Liu, C., Wang, D., St Amand, P.C., Bernardo, A.E., Li, W., He, F., Li, L., Wang, L., Yuan, X., Bai, G., et al. 2020. High resolution genome-wide association study identified genomic regions and candidate genes for important agronomic traits in wheat. Molecular Plant. https://doi.org/10.1016/j.molp.2020.07.008.
DOI: https://doi.org/10.1016/j.molp.2020.07.008

Interpretive Summary: Understanding the genetics of important agronomic traits is essential for improvement of wheat cultivars. We conducted a genome-wide association study (GWAS) using 768 wheat cultivars and more than 300,000 DNA markers. We detected 395 quantitative trait loci (QTLs) for 12 important wheat traits. Among them, 273 QTL regions were precisely mapped to relatively short chromosome regions. Eight candidate genes were identified in three QTL regions for enhanced spike seed-setting and grain size. Protein sequence analysis identified 33 putative wheat genes that have high identity with rice genes affecting similar traits. Large GWAS population size and high marker density greatly improved detection and identification of candidate genes underlying a QTL.

Technical Abstract: Wheat (Triticum aestivum L.) 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 (QTL) for 12 traits under seven environments. Among them, 273 QTL were delimited to = 1.0 Mb intervals and seven of them are either known genes (Rht-D, Vrn-B1 and Vrn-D1) that have been cloned or known QTL (TaGA2ox8, APO1, TaSus1-7B, Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTL that enhance spike seed-setting and grain size using gene expression data and were validated in three bi-parental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes affecting similar traits in other QTL. Large r2 values for additive effects observed among the QTL for most traits indicated that the phenotypes of these identified QTL 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 of large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.