Isolation, Characterization, and Mapping of Genomic Microsatellite Markers in Sea-Island Cotton (Gossypium barbadense)

For developing novel microsatellite markers from the genome of sea-island cotton (Gossypium barbadense L.), 2 approaches were used to isolate microsatellites from the genetic standard line G. barbadense acc. 3-79, that is, cloning amplified fragments from either inter simple sequence repeat (ISSR) or degenerated primers. A total of 239 unique clones were generated from 1447 recombinants, and 214 unique sequences were obtained. Eighty-six primer pairs were developed from 70 sequences that had flanking regions sufficient for primer design. The 86 microsatellite primer pairs were evaluated with 56 sea-island cotton accessions and 4 upland cotton (G. hirsutum L.) cultivars. Of them, 16 primers had no amplification, 43 primers amplified identical products among all the accessions, 27 primers presented polymorphism between sea-island and upland cotton, and the remaining 19 primers were polymorphic among accessions of the sea-island cotton. On the basis of Jaccard's genetic similarity coefficient detected by the 27 polymorphic microsatellites, sea-island cotton was separated from upland cotton in the phylogentic tree, and all the sea-island cotton accessions were classified into 4 groups. Nine interspecific polymorphic markers were mapped on the cotton genetic map, of which 4 on chromosomes A subgenome and 5 on chromosome of D subgenome.