RNA-Seq Analysis of Rubber Tree Bark and SNPs Markers Development for Rubber Biosynthesis Pathways

Rubber tree (Hevea brasiliensis) the major source of natural rubber in the world and is native to the Amazon rainforest. Natural rubber has singular properties that make it superior and competitive to synthetic rubber in several applications. In this study we performed a RNA-seq from rubber tree bark which generated 179,326,804 million raw reads using Illumina GAIIx platform. A de novo assembly were performed and 50,384 contigs longer than 400 bp were obtained. Similarity search against non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hit. The contigs were also annotated through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Pfam database. Futhermore, single nucleotide polymorphisms (SNPs) markers search were performed to discover putative SNPs. In total 404.114 putative SNPs were detected being 242,732 (60%) transition SNPs and 161,382 (40%) transversion SNPs. To validate SNPs markers, we selected sequences annotated by KEGG database into mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are directly related to rubber biosynthesis. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. The observed and expected heterozygosities ranged from 0.0294 to 0.9167 and 0.000 to 0.5394 respectively, and the PIC values ranged between 0.0286 and 0.4402. This RNA-seq data provided a more comprehensive understanding about bark transcripts in H. brasiliensis. . In addition the SNPs markers associated to potentially important genes that can be a powerful resource for rubber tree breeding programs and genetic diversity studies.