Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map.

Abstract

     To obtain more information of the H. brasiliensis genome, we sequenced the transcriptome from 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 EST-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 published SSRs were used for 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, covered 842.9 cM with mean interval of 11.9 cM and approximately 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 previous map indicated that the F1 map in this study is appropriate to further study in Marker-assisted selection (MAS).

Reference :

Kanokporn Triwitayakorn1, Pornsupa Chatkulkawin1, Supanath Kanjanawattanawong1,2, Supajit Sraphet1, Thippawan Yoocha3, Duangjai Sangsrakru3, Juntima Chanprasert3, Chumpol Ngamphiw3, Nukoon Jomchai3, Kanikar Therawattanasuk4 and Sithichoke Tangphatsornruang3*
1 Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170 Thailand
2 Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok 10400 Thailand
3 National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
4 Rubber Research Institute of Thailand (RRIT), Department of Agriculture, Ministry of Agriculture, Thailand

* Contact

Sithichoke Tangphatsornruang

National Center for Genetic Engineering and Biotechnology

113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand

Tel.: +66-2-5646700

Fax: +66-2-5646707

Email: sithichoke.tan@biotec.or.th  



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