Wild species of cotton represent a significant genetic repository for potential exploitation by cotton breeders, who have long recognized the beneficial effects of exotic genes [4]. The introduction of alien genetic variation into upland cotton from the chromosomes of wild species is a valuable and proven technique for cotton improvement. The most successful examples of the use of wild species during the history of cotton breeding history include Gossypium harknessii as a source of cytoplasmic male sterility [5] and Gossypium thurberi as a source of fiber quality [6] and [7].

More recently, other important traits, such as nematode resistance and the low- and high-gossypol plant traits, were successfully introduced from diploid species into upland cotton using various

strategies [8] and [9]. Despite these successes, most learn more of the genetic variation in wild Gossypium species remains to be exploited. G. anomalum (2n = 2x = 26, B1) is a wild species belonging to the B1 genome group. G. anomalum grows in Southwest Africa and along the southern fringes of the Sahara, almost from the Atlantic to the Red Sea [1]. As a member of subsection Anomala Todaro, G. anomalum possesses several desirable characters such as extremely fine fibers, good strength, low fiber weight, resistance to insect pests, immunity see more to the diseases black arm and bacterial blight and tolerance to water deficit, as this species is endemic to relatively dry areas [10]. Some efforts have been made to introduce desirable characters from G. anomalum to cultivated cotton [11] and [12]. G. anomalum represents an inestimable source of genes that can potentially be transferred to the cultivated cotton gene pool. However, the genomic differences between tetraploid cultivated cotton (A1A1D1D1) and the diploid G. anomalum (B1B1) represent serious interspecific reproductive barriers, which limit gene transfer between the species. In a previous study, we obtained triploid hybrids with the genome composition A1D1Bl by crossing

G. hirsutum (A1A1D1D1) with G. anomalum (B1B1) [11]. Hybrid seedling plants were then treated with 0.15% colchicine and a putative fertile hexaploid (A1A1D1D1B1B1) was obtained. This putative hexaploid produced flowers and set bolls normally. The objectives of this study were: (1) to confirm Regorafenib in vitro the hexaploid nature of the plants using morphological, cytological and molecular methods; (2) to compare EST-SSR transferability from other species to G. anomalum; and (3) to obtain a set of informative G. anomalum-specific SSR markers to monitor G. anomalum-specific chromosome segments. Seedling plants of triploid hybrids from the cross between G. hirsutum (A1A1D1D1) var. 86-1 and G. anomalum (B1B1) were treated with 0.15% colchicine [11]. A putative fertile hexaploid (A1A1D1D1B1B1) was selfed and the resulting hexaploid seeds were stored in a − 20 °C freezer. In 2009, all experimental materials, including the putative hexaploid, G.