Development of molecular markers from Indian genotypes of two Gossypium L. species

Two genotypes of Gossypium hirsutum and four genotypes of G. herbaceum have been used to develop large-scale molecular markers, especially SSRs and SNPs for their use in various molecular breeding programmes of cotton. A total of 1440 expressed SSRs and 2608 SNPs were identified from transcriptome of two genotypes of G. hirsutum. In addition, 10 971 SNPs were also developed from transcriptome of G. herbaceum, of which 4059 SNPs were transition and 6912 were transversion and there were 238 indels. This study added a total of 334 novel SSRs and 1847 novel SNPs in G. hirsutum and 10 947 novel SNPs in G. herbaceum to the public domain. We also validated a subset of 25 novel SSRs and 12 SNPs with five genotypes of G. hirsutum.