Association mapping seed kernel oil content in upland cotton using genome-wide SSRs and SNPs

Abstract

Cotton is a major fiber and oilseed crop; however, few studies have been focused on oil content in cotton. To dissect the genetic basis of seed oil content (SOC), genome-wide association study was performed by using SOC phenotypic data of 503 upland cotton inbred accessions in eight environments and two sets of genotypic data including 179 simple sequence repeats (SSRs) and 11,975 single-nucleotide polymorphism (SNPs) from our previous study. SOC for a given genotype was fairly stable which was reflected in a broad-sense heritability of H2 = 96.6%. Using the mixed linear model (K + Q), 16 significant SSRs (P < 0.01) and 26 significant SNPs (P < 1/11,975), were detected cross BLUP values and at least one individual environments. Based on the LD block analysis, eight SOC-associated QTL on chromosome 6, 10, 12, 13, 15, 17, and 24 covering more than one significant markers were identified, two QTL of them on chromosome 10 and 13 could be matched between SSR and SNP markers. The confidence interval of candidate genes in each QTL ranged from 0.14 to 1.50 Mb, and 12 to 70 genes were identified in these QTL. According to the gene function annotation and gene FPKM value of the 20~35 days post anther (DPA) cotton ovules, key genes involved in lipid metabolism and transport; tricarboxylic acid cycle which might affect seed oil content were found near the leading markers. These results will facilitate the molecular marker assisted breeding of cotton oil content.