Genome-wide association mapping of glyphosate-resistance in Gossypium hirsutum races

Glyphosate resistance is tightly related to the cotton industry. Glyphosate treatments of plants always result in high levels of shikimate accumulation and a sharp reduction in the relative dry weight, severely affecting normal growth. In this study, a broad range of variations were observed for the shikimate contents and relative dry weights in three natural environments, which significantly affected these phenotypic variations, but the genetic effects were the main contributors. Association mapping was applied to dissect the genetic basis of glyphosate-resistance in 202 accessions of Gossypium hirsutum races using 182 simple sequence repeat markers covering all of the cotton chromosomes. Based on the model controlling both population structure and relative kinship, 41 loci were detected as being significantly associated with relative dry weight, ranging from 13 to 70 %, which could explain part of the phenotypic variance, whereas another 48 loci were associated with shikimate accumulation, explaining 10-29 % of the phenotypic variation. Gene sequences, including the associated markers, were searched against the cotton genome project database of G. arboreum L., G. raimondii and G. hirsutum, and adenosine triphosphate-binding cassette transporter, which embodies the associated marker MON_CGR6680, was demonstrated by the Kyoto Encyclopedia of Genes and Genomes to be concerned with shikimate biosynthesis. Our results provide insights into the genetic basis of glyphosate resistance, and the detected loci may be used as candidate markers for the improvement of glyphosate-resistance in cotton breeding.