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SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft Genome
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Document Title
SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft Genome
Author
Shearman JR, Sangsrakru D, Jomchai N, Ruang-Areerate P, Sonthirod C, Naktang C, Theerawattanasuk K, Tragoonrung S, Tangphatsornruang S
Name from Authors Collection
Scopus Author ID
36059124300
Scopus Author ID
56030033100
Affiliations
National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC); Ministry of Agriculture & Cooperatives - Thailand
Type
Article
Source Title
PLOS ONE
ISSN
1932-6203
Year
2015
Volume
10
Issue
4
Open Access
gold, Green Published, Green Submitted
Publisher
PUBLIC LIBRARY SCIENCE
DOI
10.1371/journal.pone.0121961
Format
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.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Rubber Research Institute of Thailand (RRIT)
License
CC-BY
Rights
Authors
Publication Source
WOS
Document
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SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft GenomeDownload