Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton |
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Authors: | Zhiguo Han Changbiao Wang Xianliang Song Wangzhen Guo Jinying Gou Chunhong Li Xiaoya Chen Tianzhen Zhang |
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Institution: | (1) National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, P. R. China;(2) National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P. R. China |
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Abstract: | In order to construct a saturated genetic map and facilitate marker-assisted selection (MAS) breeding, it is necessary to
enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants (Kantety et al., Plant
Mol Biol 48:501–510, 2002). Many ESTs are publicly available now and represent a good tool in developing EST-SSRs. From 13,505
ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or
more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by
dinucleotides (30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most
frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC (4.5%). One hundred
and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our
two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross (TM-1×Hai7124)TM-1].
EST-SSR markers were distributed over 20 chromosomes and 6 linkage groups in the map. These EST-SSR markers can be used in
genetic mapping, identification of quantitative trait loci (QTLs), and comparative genomics studies of cotton.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.
Zhiguo Han and Changbiao Wang contributed equally to this work. |
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