Molecular markers and candidate genes of plant height traits in upland cotton identified by single-locus and multi-locus genome-wide association study

With the increasing demands for crop yield and production mechanization, improvement of plant architecture is getting more imperative in cotton. In the present study, we investigated the plant height (PH) and the node of first fruiting branch (NFFB) of 719 upland cotton accessions in six different environments. We used the 10,511 high-quality single nucleotide polymorphisms (SNPs) to perform single-locus and multi-locus genome-wide association study (GWAS). As many as 278 associated SNPs were identified, 142 by the mixed linear model (MLM) in the single-locus model and 192 by six multi-locus models. A total of 42 SNPs were identified in at least four environment-traits or methods, of which 28 SNPs were significantly associated with PH, 22 were significantly associated with NFFB, and eight were co-associated with the two traits. Notably, most of loci were novel besides i33922Gh located in the reported QTL for PH. Furthermore, we identified nine promising candidate genes, among which the three genes Gh_D03G0738, Gh_D10G2028, and Gh_D05G3600 contained non-synonymous SNP mutation. The accessions with alleles of the mutations resulted in significant phenotypic differences. The expression of these genes showed significant differences between short-PH and high-PH varieties. Moreover, overexpression of Gh_D03G0738 led to reduction of PH in Arabidopsis. These results provided insights into genetic basis of plant architecture in cotton.