Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis
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In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.
KeywordsHevea brasiliensis Transcriptome Single-nucleotide polymorphism MVA and MEP pathways
This project is funded by RISDA (304/PBIOLOGI/650728/P137) awarded to Ahmad Sofiman Othman of Universiti Sains Malaysia. We thank Yue Keong Choon (Universiti Sains Malaysia) for collecting the samples used in this work and Mohd Khairul Luqman Mohd Sakaf and Khairul Nasirudin Abu Mangsor (Universiti Sains Malaysia) for assisting in analysis. We also thank MyPhD15 for providing a scholarship to the first author.
SNAR and MFAB carried out the field and laboratory work including data analysis. GVS and SNAR prepared the manuscript. ASO initiated the research and designed the experiment.
Rubber Industry Smallholders Development Authority (Risda) (304/PBIOLOGI/650728/P137).
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
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