ArticlePloS one2015
SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 44 citations in OpenAlex.
- Genetic analysis of agronomic and physiological traits associated with latex yield revealed complex genetic bases inHeliyon · 2024Article
- Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.).Scientific reports · 2019Article
- Genetic Mapping of Prince Rupprecht's Larch (Genes · 2019Article
- 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
- High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits ofFrontiers in plant science · 2018Article
- Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Frontiers in plant science · 2018Article
- Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm.Scientific reports · 2017Article
- De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species.Scientific reports · 2017Article
- Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids.Scientific reports · 2016Article
- Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS).Frontiers in plant science · 2015Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.