Association mapping analysis of fber yield and quality traits in Upland cotton (Gossypium hirsutum L.)

Abstract

t Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fber quality genes are the prime concern of researchers in cotton breeding. Association mapping ofers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed signifcant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at

2 = 0.1, and decreased to ~1 to 2 cM at r 2 = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 signifcant (p < 0.01) marker–trait associations, including seven associations for fber length, ten for fber micronaire, nine for fber strength, eight for fber elongation, fve for fber uniformity index, fve for fber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker–trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identifed QTLs/genes. The QTLs identifed in this study will potentially facilitate improvement of fber yield and quality in the future cotton molecular breeding programs.