Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)
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 construct...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-05-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00367/full |
| _version_ | 1811300410314457088 |
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| author | Wirulda ePootakham Panthita eRuang-areerate Nukoon eJomchai Chutima eSonthirod Duangjai eSangsrakru Thippawan eYoocha Kanikar eTheerawattanasuk Kanlaya eNirapathpongporn Phayao eRomruensukharom Somvong eTragoonrung Sithichoke eTangphatsornruang |
| author_facet | Wirulda ePootakham Panthita eRuang-areerate Nukoon eJomchai Chutima eSonthirod Duangjai eSangsrakru Thippawan eYoocha Kanikar eTheerawattanasuk Kanlaya eNirapathpongporn Phayao eRomruensukharom Somvong eTragoonrung Sithichoke eTangphatsornruang |
| author_sort | Wirulda ePootakham |
| collection | DOAJ |
| description | 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 1,704 and 1,719 markers and encompassed 2,041 cM and 1,874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23 - 1.25 cM. A total of 1,114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2,321 markers and spanned the cumulative length of 2,052 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. |
| first_indexed | 2024-04-13T06:51:47Z |
| format | Article |
| id | doaj.art-dfa18cdc69de4bbf89dd9e558c2e1e20 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T06:51:47Z |
| publishDate | 2015-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-dfa18cdc69de4bbf89dd9e558c2e1e202022-12-22T02:57:24ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-05-01610.3389/fpls.2015.00367137209Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)Wirulda ePootakham0Panthita eRuang-areerate1Nukoon eJomchai2Chutima eSonthirod3Duangjai eSangsrakru4Thippawan eYoocha5Kanikar eTheerawattanasuk6Kanlaya eNirapathpongporn7Phayao eRomruensukharom8Somvong eTragoonrung9Sithichoke eTangphatsornruang10National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)Rubber Research Institute of Thailand (RRIT)Rubber Research Institute of Thailand (RRIT)Rubber Research Institute of Thailand (RRIT)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA)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 1,704 and 1,719 markers and encompassed 2,041 cM and 1,874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23 - 1.25 cM. A total of 1,114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2,321 markers and spanned the cumulative length of 2,052 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00367/fullSNP genotypingsingle nucleotide polymorphism (SNP)rubber treeHevea brasiliensisgenotyping-by-sequencing (GBS)Genetic linkage map |
| spellingShingle | Wirulda ePootakham Panthita eRuang-areerate Nukoon eJomchai Chutima eSonthirod Duangjai eSangsrakru Thippawan eYoocha Kanikar eTheerawattanasuk Kanlaya eNirapathpongporn Phayao eRomruensukharom Somvong eTragoonrung Sithichoke eTangphatsornruang Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) Frontiers in Plant Science SNP genotyping single nucleotide polymorphism (SNP) rubber tree Hevea brasiliensis genotyping-by-sequencing (GBS) Genetic linkage map |
| title | Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) |
| title_full | Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) |
| title_fullStr | Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) |
| title_full_unstemmed | Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) |
| title_short | Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS) |
| title_sort | construction of a high density integrated genetic linkage map of rubber tree hevea brasiliensis using genotyping by sequencing gbs |
| topic | SNP genotyping single nucleotide polymorphism (SNP) rubber tree Hevea brasiliensis genotyping-by-sequencing (GBS) Genetic linkage map |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00367/full |
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