Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich

Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed sequence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs for cotton gene mapping, we selected and characterized functional markers in Gossypium raimondii, which consisted of 58906 non-redundant EST sequences from NCBI. Among them there were 2620 microsatellite sequences containing 2818 EST-SSRs, which amounted to 4.45% of the non-redundant starting sequence population. This incidence was equivalent to one EST-SSR in every 14.8 kb of G. raimondii genetic material. Among the different motifs ranging from 1 to 6 bp, trinucleotide repeats were most abundant (38.31%), followed by dinucleotide repeats (24.09%) and mononucleotide repeats (23.35%). Among all identified motif types, A/T had the highest frequency (18.67%), followed by AT/TA (14.83%). Among the compound motifs, tandem trinucleotides occurred with the highest frequency (48.65%). In all, we identified 1554 EST-SSRs primer pair sequences. 300 of them were randomly selected to screen the polymorphisms between the mapping parents G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124, to construct linkage groups in cultivated allotetraploid cotton. Among them, 129 (43%) primer pairs were found to have polymorphisms. Using these EST-SSRs we can compare EST-SSR distributions among different cotton species and various chromosomal locations.