High-Density SNP-Based Mapping and MULTI-TRAIT QTL Analysis of Isogenic Chromosome- Specific CS-B17 Rils in Upland Cotton (GOSSYPIUM HIRSUTUM L.)

We have examined the feasibility of linkage mapping and agronomic/fiber trait quantitative locus detection and localization using a set of ~50 chromosome-specific CS-B17 RILs, each theoretically homozygous for a unique array of chromosome-17 segments from the two homozygous lines -- G. hirsutum line ‘TM-1’ and G. barbadense line ‘3–79’.  TM-1 was crossed with an isogenic BC5Sn inbred derivative CS-B17 that is homozygous for chromosome-17 Pima 3-79 in a TM-1-like genetic background.  The F1 was iteratively selfed to create a population of 50 RILs.  The RILs were phenotyped for 13 traits across two years; at four locations using RCBD.  Initial efforts aimed at quantitative analysis with low numbers of markers proved difficult, so we ultimately resorted to using the CottonSNP63K Array.  This yielded ~500 high quality SNP markers across chromosome 17 for the genotyping, linkage mapping and QTL analysis of the traits.  Several programs were used for linkage mapping, JoinMap, and R – “OneMap” package. “qtl” package in R was mainly applied for QTL mapping analysis and QTL cartographer were also used for comparison.  A condensed bin map from the 500 SNP markers was also tested with the phenotype datasets across four distinct locations.  Zero to two QTLs were detected in chromosome-17 for various fiber quality traits. The results underscore the value of isogenic chromosome substitution lines and chromosome-specific RILs to interspecific cotton breeding, genetic diversification and genetic improvement of cotton.