Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

Jagdeep Singh Sidhu; Dilkaran Singh; Harsimardeep Singh Gill; Navreet Kaur Brar; Yeyan Qiu; Jyotirmoy Halder; Rami Al Tameemi; Brent Turnipseed; Sunish Kumar Sehgal

doi:10.3389/fgene.2019.01345

Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

Front Genet. 2020 Feb 5:10:1345. doi: 10.3389/fgene.2019.01345. eCollection 2019.

Authors

Jagdeep Singh Sidhu¹, Dilkaran Singh², Harsimardeep Singh Gill¹, Navreet Kaur Brar¹, Yeyan Qiu¹, Jyotirmoy Halder¹, Rami Al Tameemi¹, Brent Turnipseed¹, Sunish Kumar Sehgal¹

Affiliations

¹ Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States.
² Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States.

Abstract

Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, understanding the genetic basis of coleoptile length is necessary and important for wheat breeding. We conducted a genome-wide association study (GWAS) using a diverse panel of 298 winter wheat genotypes to dissect the genetic architecture of coleoptile length. We identified nine genomic regions associated with the coleoptile length on seven different chromosomes. Of the nine genomic regions, five have been previously reported in various studies, including one mapped to previously known Rht-B1 region. Three novel quantitative trait loci (QTLs), QCL.sdsu-2AS, QCL.sdsu-4BL, and QCL.sdsu-5BL were identified in our study. QCL.sdsu-5BL has a large substitution effect which is comparable to Rht-B1's effect and could be used to compensate for the negative effect of Rht-B1 on coleoptile length. In total, the nine QTLs explained 59% of the total phenotypic variation. Cultivars 'Agate' and 'MT06103' have the longest coleoptile length and interestingly, have favorable alleles at nine and eight coleoptile loci, respectively. These lines could be a valuable germplasm for longer coleoptile breeding. Gene annotations in the candidate regions revealed several putative proteins of specific interest including cytochrome P450-like, expansins, and phytochrome A. The QTLs for coleoptile length linked to single-nucleotide polymorphism (SNP) markers reported in this study could be employed in marker-assisted breeding for longer coleoptile in wheat. Thus, our study provides valuable insights into the genetic and molecular regulation of the coleoptile length in winter wheat.

Keywords: SNP (Single-nucleotide polymorphism); Triticum aestivum; coleoptile length; genome-wide association study; marker-assisted selection; quantitative trait loci; semi-dwarf wheat.