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Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)
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Document Title
Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)
Author
Pootakham W., Ruang-Areerate P., Jomchai N., Sonthirod C., Sangsrakru D., Yoocha T., Theerawattanasuk K., Nirapathpongporn K., Romruensukharom P., Tragoonrung S., Tangphatsornruang S.
Name from Authors Collection
Scopus Author ID
56030033100
Scopus Author ID
36059124300
Affiliations
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand; Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
Type
Article
Source Title
Frontiers in Plant Science
ISSN
1664462X
Year
2015
Volume
6
Issue
MAY
Page
44531
Open Access
All Open Access, Gold, Green
Publisher
Frontiers Research Foundation
DOI
10.3389/fpls.2015.00367
Format
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species. © 2015 Pootakham, Ruang-Areerate, Jomchai, Sonthirod, Sangsrakru.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
License
N/A
Rights
N/A
Publication Source
Scopus