Simple sequence repeats as useful resources to study transcribed genes of cotton

Microsatellites or Simple Sequence Repeats (SSRs) are informative molecular genetic markers in many crop species. SSRs are PCR-based, highly polymorphic, abundant, widely distributed throughout the genome and inherited in a co-dominant manner in most cases. Here we describe the presence of SSRs in cDNAs of cotton. Thirty one SSR primer pairs of 220 (~ 14%) tested led to PCR amplification of discrete fragments using cotton leaf cDNA as template. Sequence analysis showed 25% of 24 randomly selected cDNA clones amplified with different SSR primer pairs contained repeat motifs. We further showed that sequences from the SSR-containing cDNAs were conserved across G. barbadenseand G. hirsutum, revealing the importance of the SSR markers for comparative mapping of transcribed genes. Data mining for plant SSR-ESTs from the publicly available databases identified SSRs motifs in many plant species, including cotton, in a range of 1.1 to 4.8% of the submitted ESTs for a given species.