Population Genomics and Haplotype Analysis in Bread Wheat Identify a Gene Regulating Glume Pubescence

Abstract

Glume hairiness or pubescence is an important morphological trait with high heritability to distinguish/characterize wheat and is related to the resistance to biotic and abiotic stresses. <i>Hg1</i> (formerly named <i>Hg</i>) on chromosome arm 1AS controlled glume hairiness in wheat. Its genetic analysis and mapping have been widely studied, yet more useful and accurate information for fine mapping of <i>Hg1</i> and identification of its candidate gene is lacking. The cloning of this gene has not yet been reported for the large complex wheat genome. Here, we performed a GWAS between SNP markers and glume pubescence (Gp) in a wheat population with 352 lines and further demonstrated the gene expression and haplotype analysis approach for isolating the <i>Hg1</i> gene. One gene, <i>TraesCSU02G143200</i> (<i>TaELD1-1A</i>), encoding glycosyltransferase-like ELD1/KOBITO 1, was identified as the most promising candidate gene of <i>Hg1</i>. The gene annotation, expression pattern, function SNP variation, haplotype analysis, and co-expression analysis in floral organ (spike) development indicated that it is likely to be involved in the regulation of glume pubescence. Our study demonstrates the importance of high-quality reference genomes and annotation information, as well as bioinformatics analysis, for gene cloning in wheat.