Publication: Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map
Accepted Date
2011-08-29
Issued Date
2011
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Language
eng
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Mahidol University
Bibliographic Citation
DNA Research. Vol.18, No.6 (2011), 471-482
Suggested Citation
Kanokporn Triwitayakorn, Pornsupa Chatkulkawin, Supanath Kanjanawattanawong, Supajit Sraphet, Thippawan Yoocha, Duangjai Sangsrakru, Juntima Chanprasert, Chumpol Ngamphiw, Nukoon Jomchai, Kanikar Therawattanasuk, Sithichoke Tangphatsornruang Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Research. Vol.18, No.6 (2011), 471-482. doi:10.1093/dnares/dsr034 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/1828
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Title
Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map
Abstract
To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ∼4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection.