Artículos de revistas
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers
Fecha
2014-03-26Registro en:
BMC Genomics. 2014 Mar 26;15(1):236
10.1186/1471-2164-15-236
Autor
Salgado, Leonardo Rippel
Koop, Daniela Martins
Pinheiro, Daniel Guariz
Rivallan, Ronan
Le Guen, Vincent
Nicolás, Marisa Fabiana
Almeida, Luiz Gonzaga Paula de
Rocha, Viviani Ribeiro
Magalhães, Milena
Gerber, Alexandra Lehmkuhl
Figueira, Antonio
Cascardo, Júlio Cézar de Mattos
Vasconcelos, Ana Tereza Ribeiro de
Silva Junior, Wilson Araújo
Coutinho, Luiz Lehmann
Garcia, Dominique
Institución
Resumen
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.