Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs f...Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs for cotton gene map- ping, 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 se- quences containing 2818 EST-SSRs, which amoun- ted 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 identi- fied 1554 EST-SSRs primer pair sequences. 300 of them were randomly selected to screen the poly- morphisms between the mapping parents G· hirsutum acc. TM-1 and G· barbadense cv. Hai7124, to con- struct linkage groups in cultivated allotetraploid cot- ton. 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.展开更多
基金supported in part by the National Natural Science Foundation of China(Grant Nos.30471104&30270806)Programs for Changjiang Scholars and Innovative Research Team in University and for New Century Excellent Talents in Ministry of Education(Grant No.NCET-04-0500)+1 种基金Program for Excellent Talents in Jiangsu Province(Grant No.BK2003414)Jiangsu High-Tech Project(Grant No.BG2004305).
文摘Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs for cotton gene map- ping, 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 se- quences containing 2818 EST-SSRs, which amoun- ted 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 identi- fied 1554 EST-SSRs primer pair sequences. 300 of them were randomly selected to screen the poly- morphisms between the mapping parents G· hirsutum acc. TM-1 and G· barbadense cv. Hai7124, to con- struct linkage groups in cultivated allotetraploid cot- ton. 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.
