Abstract
BackgroundThe 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.ResultsHere, 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.ConclusionsThis 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.
Highlights
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
In tropical regions of Latin America where the high level of relative humidity might be more suitable for rubber development, the climatic conditions are conducive to the infection of rubber tree leaves by the fungus Microcyclus ulei, the causal agent of the South American Leaf Blight
Transcriptome sequencing and assembling In order to capture the H. brasiliensis mass transcriptional profile with reduced sequencing costs, cDNA libraries were prepared from pooled RNA extracts of different tissues
Summary
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 measures for avoiding M. ulei infection takes advantage of the strict high temperature and air humidity conditions for the fungus to reproduce Based on this requirement, two infection avoidance strategies can be proposed: climatic escape, where leaf exchanges occur during the dry season, when weather conditions are not favorable to fungal sporulation or growing rubber trees in sub-optimal areas (with lower average temperatures and air humidity). Two infection avoidance strategies can be proposed: climatic escape, where leaf exchanges occur during the dry season, when weather conditions are not favorable to fungal sporulation or growing rubber trees in sub-optimal areas (with lower average temperatures and air humidity) Both approaches inhibit M. ulei infection, and may reduce rubber tree yield. The RRIM600 Oriental clone is classified as susceptible to SALB, and highly productive over a range of temperatures and relative humidity
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