title: SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome.
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.
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Shearman
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Duangjai
authors.initials: D
authors.lastname: Sangsrakru
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Nukoon
authors.initials: N
authors.lastname: Jomchai
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Panthita
authors.initials: P
authors.lastname: Ruang-Areerate
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Chutima
authors.initials: C
authors.lastname: Sonthirod
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Chaiwat
authors.initials: C
authors.lastname: Naktang
authors.affiliation: Rubber Research Institute of Thailand (RRIT), Department of Agriculture, Ministry of Agriculture and Cooperatives, 50 Phaholyothin Road, Chatuchack, Bangkok, 10900, Thailand.
authors.forename: Kanikar
authors.initials: K
authors.lastname: Theerawattanasuk
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Somvong
authors.initials: S
authors.lastname: Tragoonrung
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
mesh_terms: D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D028482:Hevea / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D018749:RNA, Plant
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