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Background  The rubber tree,  Hevea brasiliensis , is a species native to the Brazilian Amazon region and it supplies almost all the world’s natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition.    Results  Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of  H. brasiliensis  tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23  Hevea  genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the  in silico  detection of the SNVs.    Conclusions  This is the first study of the  H. brasiliensis  transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of  in silico  detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the  H. brasiliensis  genetic breeding program focused on improving of disease resistance and latex yield.

De novo transcriptome analysis of Hevea brasiliensistissues by RNA-seq and screening for molecular markers