title: De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers.
abstract: 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.
authors.affiliation: 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. lrippel@usp.br.
authors.forename: Leonardo Rippel
authors.initials: LR
authors.lastname: Salgado
authors.forename: Daniela Martins
authors.initials: DM
authors.lastname: Koop
authors.forename: Daniel Guariz
authors.initials: DG
authors.lastname: Pinheiro
authors.forename: Ronan
authors.initials: R
authors.lastname: Rivallan
authors.forename: Vincent
authors.initials: V
authors.lastname: Le Guen
authors.forename: Marisa Fabiana
authors.initials: MF
authors.lastname: Nicolás
authors.forename: Luiz Gonzaga Paula
authors.initials: LG
authors.lastname: de Almeida
authors.forename: Viviani Ribeiro
authors.initials: VR
authors.lastname: Rocha
authors.forename: Milena
authors.initials: M
authors.lastname: Magalhães
authors.forename: Alexandra Lehmkuhl
authors.initials: AL
authors.lastname: Gerber
authors.forename: Antonio
authors.initials: A
authors.lastname: Figueira
authors.forename: Júlio Cézar de Mattos
authors.initials: JC
authors.lastname: Cascardo
authors.forename: AnaTereza Ribeiro
authors.initials: AR
authors.lastname: de Vasconcelos
authors.forename: Wilson Araújo
authors.initials: WA
authors.lastname: Silva
authors.forename: Luiz Lehmann
authors.initials: LL
authors.lastname: Coutinho
authors.forename: Dominique
authors.initials: D
authors.lastname: Garcia
mesh_terms: D016000:Cluster Analysis; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D005838:Genotype; D028482:Hevea / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers