A genome-wide association study of highly heritable agronomic traits in durum wheat

Authors: WANG, SHUBIN - Shandong University; Xu, Steven; Chao, Shiaoman; SUN, QUN - North Dakota State University; LIU, SHUWEI - Shandong University; XIA, GUANGMIN - Shandong University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/28/2019
Publication Date: 7/17/2019
Citation: Wang, S., Xu, S.S., Chao, S., Sun, Q., Liu, S., Xia, G. 2019. A genome-wide association study of highly heritable agronomic traits in durum wheat. Frontiers in Plant Science. 10:919. https://doi.org/10.3389/fpls.2019.00919.
DOI: https://doi.org/10.3389/fpls.2019.00919

Interpretive Summary: Durum wheat is an important cereal specifically for making pasta products. Improvement of the durum wheat crop for enhanced productivity and tolerance to unfavorable environments such as drought is an important target in durum wheat breeding. However, effective improvement of durum wheat is highly dependent on identification of the genes controlling key agronomic traits. This study was conducted with an aim to identify the genes for 18 agronomically important traits including plant height, heading date, head and seed morphology, and tolerance to drought in durum wheat. By evaluating 493 durum wheat lines in the multiple field environments and analyzing them with DNA markers, we identified 44 chromosomal regions in which the genes controlling these traits were possibly located in the durum wheat genome. Based on the genome sequence of bread wheat, we identified 14 putative candidate genes, including one gene on chromosome 4B associating with both drought tolerance and reduced plant stature. The results from this study are relevant in the context of durum wheat improvement and the isolation of genes controlling some important traits in durum wheat.

Technical Abstract: Uncovering the genetic basis of key agronomic traits, and particularly of drought tolerance, addresses an important priority for durum wheat improvement. Here, a genome-wide association study (GWAS) in 493 durum wheat accessions representing a worldwide collection was employed to address the genetic basis of 17 agronomically important traits and a drought wilting score. Using a linear mixed model with 4 inferred subpopulations and a kinship matrix, we identified 90 marker-trait-associations (MTAs) defined by 78 markers. These markers could be merged into 44 genomic loci by linkage disequilibrium (r2 > 0.2). Based on sequence alignment of the markers to the reference genome of bread wheat, we identified 14 putative candidate genes involved in enzymes, hormone-response, and transcription factors. The GWAS in durum wheat and a previous quantitative trait locus (QTL) analysis in bread wheat identified a consensus QTL locus.4B.1 conferring drought tolerance, which was further scanned for the presence of potential candidate genes. A haplotype analysis of this region revealed that two minor haplotypes were associated with both drought tolerance and reduced plant stature, thought to be the effect of linkage with the semi-dwarfing gene Rht-B1. Haplotype variants in the key chromosome 4B region were informative regarding evolutionary divergence among durum, emmer and bread wheat. Over all, the data are relevant in the context of durum wheat improvement and the isolation of genes underlying variation in some important quantitative traits.