Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich
Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich
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DOI：
10.1007/s11434-006-0557-y
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发表时间：
2006
影响因子：
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通讯作者：
Changbiao Wang;Wangzhen Guo;Caiping Cai;Tianzhen Zhang
中科院分区：
文献类型：
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作者：
Changbiao Wang;Wangzhen Guo;Caiping Cai;Tianzhen Zhang
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 inGossypium 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 ofG. raimondiigenetic 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 parentsG. hirsutumacc. TM-1 andG. barbadensecv. 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.
