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

Rippel Salgado Leonardo, Martins Koop Daniela, Guariz Pinheiro Daniel, Rivallan Ronan, Le Guen Vincent, Nicolás Marisa Fabiana, De Almeida Luiz Gonzaga Paula, Ribeiro Rocha Viviani, Magalhaes Milena, Gerber Alexandra Lehmkuhl, Figueira Antonio, De Mattos Cascardo Julio Cézar, Ribeiro de Vasconcelos Ana Tereza, Araújo Silva Wilson, Coutinho Luiz Lehmann, Garcia Dominique. 2014. De novo transcriptome analysis of Hevea brasiliensis# tissues by RNA-seq and screening for molecular markers. BMC Genomics, 15 (236), 15 p.

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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : GENETICS & HEREDITY

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. (Résumé d'auteur)

Mots-clés Agrovoc : Hevea brasiliensis, Marqueur génétique, Génétique moléculaire, Séquence nucléotidique, Transcription

Mots-clés géographiques Agrovoc : Mato Grosso, Bahia

Mots-clés complémentaires : Séquencage

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Rippel Salgado Leonardo, Universidade de São Paulo (BRA)
  • Martins Koop Daniela, UESC (BRA)
  • Guariz Pinheiro Daniel, Universidade de São Paulo (BRA)
  • Rivallan Ronan, CIRAD-BIOS-UMR AGAP (FRA)
  • Le Guen Vincent, CIRAD-BIOS-UMR AGAP (FRA)
  • Nicolás Marisa Fabiana, LNCC (BRA)
  • De Almeida Luiz Gonzaga Paula, LNCC (BRA)
  • Ribeiro Rocha Viviani, LNCC (BRA)
  • Magalhaes Milena, LNCC (BRA)
  • Gerber Alexandra Lehmkuhl, LNCC (BRA)
  • Figueira Antonio, CENA (BRA)
  • De Mattos Cascardo Julio Cézar, UESC (BRA)
  • Ribeiro de Vasconcelos Ana Tereza, LNCC (BRA)
  • Araújo Silva Wilson, Universidade de São Paulo (BRA)
  • Coutinho Luiz Lehmann, Universidade de São Paulo (BRA)
  • Garcia Dominique, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/573216/)

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