Development of novel locus specific SCAR (sequence characterized amplified region) marker for cotton (Gossypium spp.)

The fifteen cotton cultivars belonging to four species viz. G. hirsutum, G. herbaceum, G. arboretum and G. barbadense were screened through 21 RAPD primers for the development of unique band pattern. The RAPD primer OPB-11 amplified a unique band of around 900bp in all G. arboretum cultivars. This segment was cloned and sequenced in genetic analyzer. Alignment of forward and reverse sequence generated a 914bp segment and primer was designed which will give 297bp segment to confirm the presence of that in the screened cultivars. Then the sequence was submitted in NCBI genebank with the accession number HM 490146 and there were no matched sequences in any genebank, so it was considered as a novel gene sequence for cotton.