Open Access Highly Accessed Research article

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

Leonardo Rippel Salgado1*, Daniela Martins Koop2, Daniel Guariz Pinheiro1, Ronan Rivallan3, Vincent Le Guen3, Marisa Fabiana Nicolás4, Luiz Gonzaga Paula de Almeida4, Viviani Ribeiro Rocha4, Milena Magalhães4, Alexandra Lehmkuhl Gerber4, Antonio Figueira5, Júlio Cézar de Mattos Cascardo2, AnaTereza Ribeiro de Vasconcelos4, Wilson Araújo Silva1, Luiz Lehmann Coutinho6 and Dominique Garcia3*

Author Affiliations

1 Departamento de Genética/FMRP/USP, Laboratório de Genética Molecular e Bioinformática, Rua Tenente Catão Roxo, 2501, CEP 14.051- 140 Ribeirão Preto, São Paulo, Brazil

2 Laboratório de Genômica e Biologia Molecular, Universidade Estadual de Santa Cruz, Rod. Ilhéus-Itabuna BR 415, Km 16, Ilhéus, Bahia CEP 45.662-000, Brazil

3 CIRAD, BIOS, UMR-AGAP, TA A96/03, Av. Agropolis, 34398 Montpellier, France

4 Laboratório Nacional de Computação Científica, av. Getulio Vargas, n° 333 Quitandinha, CEP 25.651-075 Petrópolis, Rio de Janeiro, Brazil

5 Centro de Energia Nuclear na Agricultura/Universidade de São Paulo, Piracicaba, Brazil

6 ESALQ/USP, Piracicaba, Brazil

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BMC Genomics 2014, 15:236  doi:10.1186/1471-2164-15-236

Published: 26 March 2014



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.


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.


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.

Next generation sequencing; Molecular markers; KASP genotyping chemistry; Rubber tree