Detection of QTL controlling fiber-related traits in a recombinant inbred lines population from G. hirsutum race punctatum using RTM-GWAS procedure

Detection of quantitative trait loci (QTL) for fiber yield and quality traits would be beneficial to cotton breeding and to understanding the genetic architecture of these economic traits. Here, fiber-related QTL were detected in a recombinant inbred lines (RIL) population developed from a cross between Gossypium hirsutum cultivar and race punctatum. The population was genotyped with specific-locus amplified fragment sequencing (SLAF-Seq), and 13,130 SNP linkage disequilibrium block (SNPLDB) markers were generated. For 2 fiber yield and 5 fiber quality traits, a total of 376 QTL with main-effect and/or QTL-environment interaction (QEI) effect were identified using a relatively innovative procedure restricted two-stage multi-locus genome wide association study (RTM-GWAS). The candidate genes for nine large-contribution QTL were further identified and analyzed. Additionally, 12 lines with elite fiber quality and yield were identified, and 10 potential optimal crosses for each trait were predicted. The findings contributed to a better understanding of the genetic basis of fiber-related traits and helped to breed high-yielding cotton cultivars with superior fiber quality.