De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

Abstract

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.Citation: Mantello CC, Cardoso-Silva CB, da Silva CC, de Souza LM, Scaloppi Junior EJ, et al. (2014) De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS ONE 9(7): e102665.

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas

“…We obtained 7,588 (21.62 %) unigenes that were longer than 1 kb, a size range that commonly confers a high annotation rate [34, 55]. We also compared the unigene metrics obtained here to the transcriptomes that were obtained from Phytozome (Additional file 1) and found that the observed total contig number, N50 contig length, average contig length and GC content more closely resembled the Phytozome transcriptomes of these species.…”

“…Similar to other perennial species [55], Koronivia grass remains in the early stages of domestication, which increases the difficulty of identifying concentrated gene groups that play specific roles in important agronomic characteristics. The Koronivia grass breeding program has applied selection methods for many decades, and hybrid progenies were obtained in the early 2000s.…”

Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees

“…In this study, we achieved more than 7 Gb of clean reads from each of the four sets of sequencing samples derived from the cambia-containing materials of rubber tree clone CATAS7-33-97. The sequencing depth of each sample was higher than the reported 0.2–6 Gb sequencing depth of bark in rubber tree3031323334 and equivalent to sequencing depth (7–8 Gb) reported by Mantello et al 35. This high sequencing depth is beneficial for global transcriptome assembly.…”

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

“…Fetrina Oktavia et al: IRRDB 1981 Diversity and Population Structure............................................................................. The ability to identify genetic resources having wide genetic distances would be beneficial in the identification of parents for hybridization programs since crossing among those parents' result in in more diverse progenies and prevent the occurrence of the inbreeding depression. Inbreeding depression was the major problem in the current rubber trees breeding program (Lopes & Marques, 2015). Taken together, based on the genetic diversity and the population analysis results using EST-SSR primers, we could summarize that the genetic structure of the evaluated PN'81 rubber accessions was more widely and diverse than that of the Wickham clones.…”

“…Moreover, because of assortative mating, low fruit-set limitation, selection for the high latex yield character, and extensive use of particular clones as parents in rubber breeding programs, further reduce the genetic diversity of the commercial rubber germplasm (Priyadarshan, 2016). Researchers have reported the occurrences of inbreeding depression because the superior genotypes are repeatedly used in rubber tree breeding programs, resulting in low latex yield, high-risk exposures to disease and insects attack (Lopes & Marques, 2015), and low adaptability to environmental changes (Ellstrand & Elam, 1993). Therefore, broadening the genetic basis through the introduction of new germplasm from the natural population is necessary for the breeding program.…”