QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa
Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt t...
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| description | Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits. |
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Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0076059</identifier><identifier>PMID: 24204591</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Arabidopsis ; Bioinformatics ; Brassica ; Brassica oleracea ; Brassica rapa ; Brassica rapa - genetics ; Chinese cabbage ; Chromosome Mapping ; Frequency distribution ; Gene mapping ; Genes ; Genetic Linkage ; Genetic markers ; Genetic Variation ; Genetics ; Genome, Plant ; Genomes ; Genomics ; Genotype ; Genotyping ; Inbreeding ; Laboratories ; Mapping ; Markers ; Markov chains ; Nutrients ; Oryza sativa ; Parents ; Phenotype ; Physiology ; Plant Leaves - genetics ; Polymorphism, Single Nucleotide ; Population ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Recombination ; Recombination, Genetic ; Rice ; Single-nucleotide polymorphism ; Vegetables ; Vitamins</subject><ispartof>PloS one, 2013-10, Vol.8 (10), p.e76059-e76059</ispartof><rights>2013 Yu 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>2013 Yu et al 2013 Yu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c592t-31da7ac38bf31eedf427d9556ba59cf6654a9e6e02d654566b7a653b39a4aa423</citedby><cites>FETCH-LOGICAL-c592t-31da7ac38bf31eedf427d9556ba59cf6654a9e6e02d654566b7a653b39a4aa423</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810141/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810141/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24204591$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Wu, Rongling</contributor><creatorcontrib>Yu, Xiang</creatorcontrib><creatorcontrib>Wang, Han</creatorcontrib><creatorcontrib>Zhong, Weili</creatorcontrib><creatorcontrib>Bai, Jinjuan</creatorcontrib><creatorcontrib>Liu, Pinglin</creatorcontrib><creatorcontrib>He, Yuke</creatorcontrib><title>QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.</description><subject>Arabidopsis</subject><subject>Bioinformatics</subject><subject>Brassica</subject><subject>Brassica oleracea</subject><subject>Brassica rapa</subject><subject>Brassica rapa - genetics</subject><subject>Chinese cabbage</subject><subject>Chromosome Mapping</subject><subject>Frequency distribution</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic Linkage</subject><subject>Genetic markers</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Inbreeding</subject><subject>Laboratories</subject><subject>Mapping</subject><subject>Markers</subject><subject>Markov chains</subject><subject>Nutrients</subject><subject>Oryza sativa</subject><subject>Parents</subject><subject>Phenotype</subject><subject>Physiology</subject><subject>Plant Leaves - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Quantitative Trait Loci</subject><subject>Quantitative Trait, Heritable</subject><subject>Recombination</subject><subject>Recombination, Genetic</subject><subject>Rice</subject><subject>Single-nucleotide polymorphism</subject><subject>Vegetables</subject><subject>Vitamins</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptkluLFDEQhRtR3Iv-A9GAL_syY-49eRF08TIwIMoKvoXqpDLTQ3enTXqE-fd27_Quu-JTiuQ7J1XFKYpXjC6ZKNm7fTykDpplHztcUlpqqsyT4pwZwReaU_H0QX1WXOS8p1SJldbPizMuOZXKsPPi1_ebDWmh7-tuS2IgDUI4kh2Cz6Q6ki12sUWSMOPvA3ZuouqODDskP9Yb0sf-0MBQx27SfkyQc-2AJOjhRfEsQJPx5XxeFj8_f7q5_rrYfPuyvv6wWThl-LAQzEMJTqyqIBiiD5KX3iilK1DGBa2VBIMaKfdjqbSuStBKVMKABJBcXBZvTr59E7Odl5Itk1KLUkizGon1ifAR9rZPdQvpaCPU9vYipq2FNNSuQRu88JSbwB2iND6smHcslFyEMoTA1ej1fv7tULXoHXZDguaR6eOXrt7ZbfxjxYpRJtlocDUbpDhuNA-2rbPDpoEO4-G2b1NqI8WEvv0H_f908kS5FHNOGO6bYdROQblT2Skodg7KKHv9cJB70V0yxF82hbxQ</recordid><startdate>20131028</startdate><enddate>20131028</enddate><creator>Yu, Xiang</creator><creator>Wang, Han</creator><creator>Zhong, Weili</creator><creator>Bai, Jinjuan</creator><creator>Liu, Pinglin</creator><creator>He, Yuke</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>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>5PM</scope><scope>DOA</scope></search><sort><creationdate>20131028</creationdate><title>QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa</title><author>Yu, Xiang ; Wang, Han ; Zhong, Weili ; Bai, Jinjuan ; Liu, Pinglin ; He, Yuke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c592t-31da7ac38bf31eedf427d9556ba59cf6654a9e6e02d654566b7a653b39a4aa423</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Arabidopsis</topic><topic>Bioinformatics</topic><topic>Brassica</topic><topic>Brassica oleracea</topic><topic>Brassica rapa</topic><topic>Brassica rapa - genetics</topic><topic>Chinese cabbage</topic><topic>Chromosome Mapping</topic><topic>Frequency distribution</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic Linkage</topic><topic>Genetic markers</topic><topic>Genetic Variation</topic><topic>Genetics</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotyping</topic><topic>Inbreeding</topic><topic>Laboratories</topic><topic>Mapping</topic><topic>Markers</topic><topic>Markov chains</topic><topic>Nutrients</topic><topic>Oryza sativa</topic><topic>Parents</topic><topic>Phenotype</topic><topic>Physiology</topic><topic>Plant Leaves - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Quantitative Trait Loci</topic><topic>Quantitative Trait, Heritable</topic><topic>Recombination</topic><topic>Recombination, Genetic</topic><topic>Rice</topic><topic>Single-nucleotide polymorphism</topic><topic>Vegetables</topic><topic>Vitamins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Xiang</creatorcontrib><creatorcontrib>Wang, Han</creatorcontrib><creatorcontrib>Zhong, Weili</creatorcontrib><creatorcontrib>Bai, Jinjuan</creatorcontrib><creatorcontrib>Liu, Pinglin</creatorcontrib><creatorcontrib>He, Yuke</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</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>Yu, Xiang</au><au>Wang, Han</au><au>Zhong, Weili</au><au>Bai, Jinjuan</au><au>Liu, Pinglin</au><au>He, Yuke</au><au>Wu, Rongling</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-10-28</date><risdate>2013</risdate><volume>8</volume><issue>10</issue><spage>e76059</spage><epage>e76059</epage><pages>e76059-e76059</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24204591</pmid><doi>10.1371/journal.pone.0076059</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Arabidopsis Bioinformatics Brassica Brassica oleracea Brassica rapa Brassica rapa - genetics Chinese cabbage Chromosome Mapping Frequency distribution Gene mapping Genes Genetic Linkage Genetic markers Genetic Variation Genetics Genome, Plant Genomes Genomics Genotype Genotyping Inbreeding Laboratories Mapping Markers Markov chains Nutrients Oryza sativa Parents Phenotype Physiology Plant Leaves - genetics Polymorphism, Single Nucleotide Population Quantitative Trait Loci Quantitative Trait, Heritable Recombination Recombination, Genetic Rice Single-nucleotide polymorphism Vegetables Vitamins |
| title | QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa |
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