ArticleBMC genomics2014
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 79 citations in OpenAlex.
- Genetic variation and structure of endemic and endangered wild celery (Frontiers in plant science · 2024Article
- Development of Novel Markers for Yield in Hevea brasiliensis Muell. Arg. Based on Candidate Genes from Biosynthetic Pathways Associated with Latex Production.Biochemical genetics · 2022Article
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- Transcriptome dataset from bark and latex tissues of threeData in brief · 2020Article
- Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis).BMC genomics · 2019Article
- Biosynthesis of Natural Rubber: Current State and Perspectives.International journal of molecular sciences · 2018Review
- QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions.BMC plant biology · 2018Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches.BMC genomics · 2018Article
- Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Frontiers in plant science · 2018Article
- High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits ofFrontiers in plant science · 2018Article
- Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses.Molecules (Basel, Switzerland) · 2017Article
- Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids.Scientific reports · 2016Article
- De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology.Molecular genetics and genomics : MGG · 2016Article
- Molecular mechanism of ethylene stimulation of latex yield in rubber tree (Hevea brasiliensis) revealed by de novo sequencing and transcriptome analysis.BMC genomics · 2016Article
- Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis).Scientific reports · 2016Article
- Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes.BMC genomics · 2016Article
- Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture.Tropical life sciences research · 2016Article
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Authors and funding
16 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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