Development of a large SNP genotyping array and generation of high-density genetic maps in tomato
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We develope...
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| creator | Sim, Sung-Chur Durstewitz, Gregor Plieske, Jörg Wieseke, Ralf Ganal, Martin W Van Deynze, Allen Hamilton, John P Buell, C Robin Causse, Mathilde Wijeratne, Saranga Francis, David M |
| description | The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions. |
| doi_str_mv | 10.1371/journal.pone.0040563 |
| format | Article |
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We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0040563</identifier><identifier>PMID: 22802968</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Accuracy ; Agriculture ; Bins ; Biology ; Chromosome Mapping - methods ; Chromosomes ; Corn ; Crop science ; Density ; DNA, Plant - genetics ; Euchromatin ; Gene expression ; Gene mapping ; Gene sequencing ; Genes ; Genetic aspects ; Genetic Linkage ; Genetic markers ; Genetic research ; Genome, Plant ; Genomes ; Genomics ; Genotype ; Genotyping ; Germplasm ; Horticulture ; Interspecific ; Inversions ; Life Sciences ; Markers ; Nucleotide sequence ; Plant biology ; Polymorphism ; Polymorphism, Single Nucleotide ; Population ; Quality control ; R&D ; Recombination ; Research & development ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Solanum lycopersicum ; Solanum lycopersicum - genetics ; Solanum pennellii ; Solanum pimpinellifolium ; Tomatoes ; Vegetal Biology</subject><ispartof>PloS one, 2012-07, Vol.7 (7), p.e40563-e40563</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Sim et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>Sim et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c792t-22b42b429db0ed5cdea6a7f778c9c27f47ec405a9ee028b2645afb9a4b8d27083</citedby><cites>FETCH-LOGICAL-c792t-22b42b429db0ed5cdea6a7f778c9c27f47ec405a9ee028b2645afb9a4b8d27083</cites><orcidid>0000-0002-0407-4985</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393668/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393668/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22802968$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02650989$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Yin, Tongming</contributor><creatorcontrib>Sim, Sung-Chur</creatorcontrib><creatorcontrib>Durstewitz, Gregor</creatorcontrib><creatorcontrib>Plieske, Jörg</creatorcontrib><creatorcontrib>Wieseke, Ralf</creatorcontrib><creatorcontrib>Ganal, Martin W</creatorcontrib><creatorcontrib>Van Deynze, Allen</creatorcontrib><creatorcontrib>Hamilton, John P</creatorcontrib><creatorcontrib>Buell, C Robin</creatorcontrib><creatorcontrib>Causse, Mathilde</creatorcontrib><creatorcontrib>Wijeratne, Saranga</creatorcontrib><creatorcontrib>Francis, David M</creatorcontrib><title>Development of a large SNP genotyping array and generation of high-density genetic maps in tomato</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.</description><subject>Accuracy</subject><subject>Agriculture</subject><subject>Bins</subject><subject>Biology</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes</subject><subject>Corn</subject><subject>Crop science</subject><subject>Density</subject><subject>DNA, Plant - genetics</subject><subject>Euchromatin</subject><subject>Gene expression</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Linkage</subject><subject>Genetic markers</subject><subject>Genetic research</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Germplasm</subject><subject>Horticulture</subject><subject>Interspecific</subject><subject>Inversions</subject><subject>Life Sciences</subject><subject>Markers</subject><subject>Nucleotide sequence</subject><subject>Plant biology</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Quality control</subject><subject>R&D</subject><subject>Recombination</subject><subject>Research & development</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Solanum lycopersicum</subject><subject>Solanum lycopersicum - genetics</subject><subject>Solanum pennellii</subject><subject>Solanum pimpinellifolium</subject><subject>Tomatoes</subject><subject>Vegetal Biology</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk12L1DAUhoso7rr6D0QLgrgXM6ZJmzQ3wrB-7MDgiqvehtM2bTO0STdpB-ffm-50l-myF9JCw8nznpzzNicIXkdoGREWfdyawWpolp3RcolQjBJKngSnESd4QTEiT4_WJ8EL57YIJSSl9HlwgnGKMKfpaQCf5U42pmul7kNThhA2YCsZXn__EVZSm37fKV2FYC3sQ9DFGJQWemX0iNeqqheF1E71-9utXuVhC50LlQ5700JvXgbPSmicfDV9z4LfX7_8urhcbK6-rS9Wm0XOOO4XGGfx-PIiQ7JI8kICBVYyluY8x6yMmcx9j8ClRDjNMI0TKDMOcZYWmKGUnAVvD3m7xjgxueNERHASE4Z55In1gSgMbEVnVQt2LwwocRswthJgfQONFCgrOEuzokwxxAhkmsU0BpT5AliWA_a5Pk2nDVkri9zbZ6GZJZ3vaFWLyuwEIZxQOpZ7fkhQP5BdrjZijCFME8RTvhsL_zAdZs3NIF0vWuVy2TSgpRl8j55NaYIJ9ei7B-jjTkxUBb5ZpUvja8zHpGIVMxZFJOZjictHKP8UslW5v3al8vGZ4Hwm8Ewv__YVDM6J9fXP_2ev_szZ90dsLaHpa2eaYbyFbg7GBzC3xjkry3tnIyTGqblzQ4xTI6ap8bI3xz_zXnQ3JuQfyuQRpQ</recordid><startdate>20120710</startdate><enddate>20120710</enddate><creator>Sim, Sung-Chur</creator><creator>Durstewitz, Gregor</creator><creator>Plieske, Jörg</creator><creator>Wieseke, Ralf</creator><creator>Ganal, Martin W</creator><creator>Van Deynze, Allen</creator><creator>Hamilton, John P</creator><creator>Buell, C Robin</creator><creator>Causse, Mathilde</creator><creator>Wijeratne, Saranga</creator><creator>Francis, David M</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-0407-4985</orcidid></search><sort><creationdate>20120710</creationdate><title>Development of a large SNP genotyping array and generation of high-density genetic maps in tomato</title><author>Sim, Sung-Chur ; Durstewitz, Gregor ; Plieske, Jörg ; Wieseke, Ralf ; Ganal, Martin W ; Van Deynze, Allen ; Hamilton, John P ; Buell, C Robin ; Causse, Mathilde ; Wijeratne, Saranga ; Francis, David M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c792t-22b42b429db0ed5cdea6a7f778c9c27f47ec405a9ee028b2645afb9a4b8d27083</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Accuracy</topic><topic>Agriculture</topic><topic>Bins</topic><topic>Biology</topic><topic>Chromosome Mapping - 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Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sim, Sung-Chur</au><au>Durstewitz, Gregor</au><au>Plieske, Jörg</au><au>Wieseke, Ralf</au><au>Ganal, Martin W</au><au>Van Deynze, Allen</au><au>Hamilton, John P</au><au>Buell, C Robin</au><au>Causse, Mathilde</au><au>Wijeratne, Saranga</au><au>Francis, David M</au><au>Yin, Tongming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of a large SNP genotyping array and generation of high-density genetic maps in tomato</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-07-10</date><risdate>2012</risdate><volume>7</volume><issue>7</issue><spage>e40563</spage><epage>e40563</epage><pages>e40563-e40563</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22802968</pmid><doi>10.1371/journal.pone.0040563</doi><tpages>e40563</tpages><orcidid>https://orcid.org/0000-0002-0407-4985</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2012-07, Vol.7 (7), p.e40563-e40563 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1325437291 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Accuracy Agriculture Bins Biology Chromosome Mapping - methods Chromosomes Corn Crop science Density DNA, Plant - genetics Euchromatin Gene expression Gene mapping Gene sequencing Genes Genetic aspects Genetic Linkage Genetic markers Genetic research Genome, Plant Genomes Genomics Genotype Genotyping Germplasm Horticulture Interspecific Inversions Life Sciences Markers Nucleotide sequence Plant biology Polymorphism Polymorphism, Single Nucleotide Population Quality control R&D Recombination Research & development Single nucleotide polymorphisms Single-nucleotide polymorphism Solanum lycopersicum Solanum lycopersicum - genetics Solanum pennellii Solanum pimpinellifolium Tomatoes Vegetal Biology |
| title | Development of a large SNP genotyping array and generation of high-density genetic maps in tomato |
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