Genetic Evaluation of EST-SSRs Derived from Gossypium herbaceum

To investigate contribution of Gossypium herbaceum to the tetraploid genome, expressed sequence tag (EST)-simple sequence repeats (SSRs) were isolated from 247 EST sequences of G. herbaceum documented in GenBank. Twenty-seven perfect SSRs were identified from 25 unique ESTs. These SSRs contained 1 to 6 bp nucleotide motifs with high frequency for 2 bp and 3 bp nucleotide motifs. A total of 25 primers were developed and 22 of them amplified clear bands in 24 cotton accessions (7 diploids of A genome, 11 diploids of D genome, and 6 allotetraploids of AD genome). These primers generated 92 polymorphic bands with an average of 3.64 per primer. The polymorphism information content (PIC) ranged from 0.49 to 0.91 with an average of 0.81. Among the 25 EST-SSR primers, 6 primers revealed polymorphism between Emian 22 and Pima 3–79, and yielded 7 polymorphic loci (5 codominant and 2 dominant) in the BC1 population (Emian 22/Pima 3–79//Emian 22). Only HAU230b showed distorted segregation in the BC1 population. The 6 polymorphic loci were integrated into 6 chromosomes of the interspecific linkage map with BC1 genetic. Among them, 4 loci were mapped on chromosomes 6, 10, 11, and 12 of A subgenome, and 2 loci on chromosomes 19 and 20 of D subgenome.