Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.).

To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron-exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F-2:7 recombinant inbred lines derived from an upland cotton cross (T586 x Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0\\%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6\\% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1\\% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20\\% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.