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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.

 Premise of the study: We demonstrated the application of high-throughput 454 sequencing technology in the identifi cation of single nucleotide polymorphism (SNP) markers in Hevea brasiliensis .  Methods and Results: A total of 5883 putative SNP positions were discovered in silico, and 10 biallelic SNP markers were validated from 454-derived EST sequences. The polymorphism information content ( PIC ) and the observed heterozygosity ( H o ) ranged from 0.0963 – 0.5135 and 0.1071 – 0.4643, respectively.  Conclusions: These markers can be useful for the construction of genetic maps, the identifi cation of quantitative trait loci linked to commercially desirable traits, and the study of genetic structure in H. brasiliensis .