Exploitation of favorable gene resource by a synthetic hexaploid derived from an interspecific hybrid between Gossypium hirsutum and G. anomalum

Wild species of Gossypium present an impressive range of variation in many characters, all of which can potentially be exploited in cotton improvement programs. G. anomalum possesses several desirable characters such as extremely fine fibers, immunity to black arm and bacterial blight disease and tolerance to water deficit, as this species is endemic to relatively dry areas. To effectively introgression desirable traits into cultivated cotton from G. anomalum, we made crosses between G. hirsutum (A1A1D1D1) and G. anomalum (B1B1) and obtained triploid hybrids with the genome composition A1D1Bl. Then we treated triploid hybrids with 0.15% colchicine and obtained a putative fertile hexaploid (A1A1D1D1B1B1) in order to resolve interspecific hybrid sterility problems. We demonstrated the hybridity and doubled status of a (G. anomalum × G. hirsutum)2 hexaploid using morphological, cytological and molecular marker methods. To effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72 % of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48 % of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86 % of the recombination events on all chromosomes. By successive backcrosses and selfing combined with marker assisted selection, about 60 chromosome segment substitution lines (CSSLs) were developed. Genomic regions that affect fiber quality, plant height and boll size were identified. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum.