Identification of cotton hybrid through the combination of PCR based RAPD, ISSR and microsatellite markers

Hybrid cotton H '6' and its parents G.Cot.10 (male) and G.Cot.100 (female) were studied for identification with three PCR based molecular markers, RAPID, ISSR and microsatellite. Twenty RAPID primers, nineteen ISSR primers and twenty-five JESPR cotton microsatellite loci were used. RAPD primer OPA 11 was found to be useful in differentiating parents and hybrid. Two ISSR primers, IS4 and IS7 showed polymorphism in the parents. IS4 identified a female-specific amplicon of about 500bp and IS7 identified two female-specific amplicons of about 500 and 1200bp in the hybrid H W. Microsatellite loci JESPR-2 and JESPR-17 were found to be heteroallelic for parents. JESPR-2 identified one male-specific repeat of about 850bp, while JESPR-17 detected two male-specific repeats of about 800bp and 700bp in the hybrid H W. Results indicated that using all three markers - RAPD, ISSR and SSR - in combination is faster and more reliable than using the three in isolation, for the identification of cotton hybrid.