Intraspecific linkage map construction and QTL mapping of yield and fiber quality of Gossypium babardense

Gossypium barbadense, famous for the superior quality of its fibers, is the second most cultivated cotton in the world. In order to determine the genetic basis of its agronomic traits, a linkage map was constructed and QTLs were analyzed. A total of 15,971 markers, including gSSRs, EST-SSRs, SRAPs, and SSCP-SNPs, were used to construct an intraspecific linkage map of G. barbadense with 124 F2 individuals derived from the cross (Hai7124 × 3-79). In the F2 population, 412 loci showed polymorphism, giving a polymorphic rate of 2.58%. Three hundred and thirty-seven loci were mapped on 52 linkage groups, and 35 groups were assigned to 20 chromosomes. The full length of the linkage map was 2108.34 cM, and the mean distance between adjacent loci was 6.26 cM. Fifty-two loci (12.62%) showed segregation distortion (P<0.01), including 34 loci (65.38%) towards the maternal genotype, 15 (28.85%) towards the paternal genotype, and 3 (5.78%) towards the heterozygote genotype. A total of 33 QTLs for yield and fiber quality traits were detected with three repeats in 2010, including 21 QTLs for yield components and 12 QTLs for fiber quality traits. LOD value ranged from 2.52 to 4.63, and the explanation rates for trait variation ranged from 6.93% to 34.52%. Marker interval of MON_CGR5376 and NAU2575 was linked to seed cotton weight per boll, lint weight per boll, hundred seeds weight, fiber elongation, and seed index. The main gene action of QTLs was over-dominance.