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To provide a resource for cotton genetics and breeding, an interspecific hybridization between  Gossypium hirsutum  cv. Emian22 and  G .  barbadense  acc. 3–79 was made. A population of 54 BILs (backcross inbred lines, BC 1 F 8 ) was developed with the aim of transferring  G .  barbadense  genes into  G .  hirsutum  in order to genetically analyze these genes’ function in a  G .  hirsutum  background and create new germplasms for breeding. Preliminary investigation of the morphological traits showed that the BILs had diverse variations in plant architecture, seed size, and fuzz color; the related traits of yield and fiber quality evaluated in 4 environments also showed abundant phenotypic variation. In order to explore the molecular diversity of the BIL population, 446 SSR markers selected at an average genetic distance of 10 cM from our interspecific linkage map were used to genotype the BIL population. A total of 393 polymorphic loci accounting for 84.4% MAF (major allele frequency) > 0.05 and 922 allele loci were detected, and the Shannon diversity index (I) was 0.417 per locus. The average introgression segment length was 16.24 cM, and an average of 29.53 segments were introgressed in each BIL line with an average background recovery of 79.8%. QTL mapping revealed 58 QTL associated with fiber quality and yield traits, and 47 favored alleles derived from the donor parent were discovered. This study demonstrated that the interspecific BIL population was enriched with much phenotypic and molecular variation which could be a resource for cotton genetics and breeding.

A BIL Population Derived from G. hirsutum and G. barbadense Provides a Resource for Cotton Genetics and Breeding