QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L
SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 prim...
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| description | SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots. |
| doi_str_mv | 10.1371/journal.pone.0053541 |
| format | Article |
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DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0053541</identifier><identifier>PMID: 23308250</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>2-Isopropylmalate Synthase - genetics ; 2-Isopropylmalate Synthase - metabolism ; Agriculture ; Aliphatic compounds ; Amino acids ; Arabidopsis ; Arabidopsis - genetics ; Arabidopsis - metabolism ; Arabidopsis thaliana ; Base Sequence ; Biology ; Biosynthesis ; Branched chain amino acids ; Brassica ; Brassica rapa ; Brassica rapa - genetics ; Brassica rapa - metabolism ; Brassicaceae ; Chain branching ; Chromosome Mapping ; Chromosomes, Plant ; Cultivars ; Cytochrome ; Deoxyribonucleic acid ; DNA ; DNA, Plant - genetics ; Expressed Sequence Tags ; Fragments ; Gene expression ; Gene sequencing ; Genes ; Genomes ; Genomics ; Genotype & phenotype ; Glucosinolates ; Glucosinolates - biosynthesis ; High-Throughput Nucleotide Sequencing ; Leucine ; Malate Dehydrogenase - genetics ; Malate Dehydrogenase - metabolism ; Markers ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; Multiplexing ; Nucleotide sequence ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant Roots - genetics ; Plant Roots - metabolism ; Polymerase chain reaction ; Polymorphism, Single Nucleotide ; Quantitative genetics ; Quantitative Trait Loci ; Raphanus ; Raphanus - genetics ; Raphanus - metabolism ; Raphanus sativus ; Roots ; Science ; Seeds ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Synteny ; Transaminases - genetics ; Transaminases - metabolism</subject><ispartof>PloS one, 2013-01, Vol.8 (1), p.e53541</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Zou 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. 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DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. 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genetics</subject><subject>Expressed Sequence Tags</subject><subject>Fragments</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Glucosinolates</subject><subject>Glucosinolates - biosynthesis</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Leucine</subject><subject>Malate Dehydrogenase - genetics</subject><subject>Malate Dehydrogenase - metabolism</subject><subject>Markers</subject><subject>Molecular Sequence Data</subject><subject>Multiplex Polymerase Chain Reaction</subject><subject>Multiplexing</subject><subject>Nucleotide sequence</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - metabolism</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative genetics</subject><subject>Quantitative Trait Loci</subject><subject>Raphanus</subject><subject>Raphanus - genetics</subject><subject>Raphanus - metabolism</subject><subject>Raphanus sativus</subject><subject>Roots</subject><subject>Science</subject><subject>Seeds</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Synteny</subject><subject>Transaminases - genetics</subject><subject>Transaminases - metabolism</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>eNqNU11rFDEUHUSxtfoPRAOCKDhrMsl8vQil-FFYrLbV15BNbnZTs8mazJTuj_Q_mXS3pSt9kDwkJOece3PPvUXxnOAJoS15f-HH4ISdrLyDCcY1rRl5UOyTnlZlU2H68M55r3gS40UGdU3zuNirKMVdVeP94s_38ykSSWcdTURjNG6Ozr5-Q0sRfkGISMElWL8ChWZr5OBqKOfgIIjBeIci_B7ByczRPiCjwA1GG7l59RpJ4ZRRYgCUWRFJ74bgrc0MVi5hWKztsDC-pOVsHMCtLZrbUfqUhreZlglJNCLjUPA-HZJqEMrExTt0KlYL4caIYgp4mfbp0-KRFjbCs-1-UPz49PH86Es5Pfl8fHQ4LWVbd0MJWM8aIhvdEAKYUVY1ZKYbVmmoZE21olAp1bR1r9quVr2Ejkrds7ZWWErC6EHxcqO7sj7yrRORk6rrcdOyPiOONwjlxQVfBZMKuuZeGH594cOcizAYaYG3UhDCRI0FrllXVx1te82EnrWd6lTTJ60P22jjbAlKpoIEYXdEd1-cWfC5v-Q0-V2znMybrUDwybE48KWJEqwVDvyY824pY5ik_jgoXv0Dvf93W9RcpA8Yp32KK7MoP2Rtl6RInVGTe1BpKVia5Cxok-53CG93CNfuXw1zMcbIj89O_x978nMX-_oOdgEiNV30dsxtGneBbAOUwccYQN8WmWCep-6mGjxPHd9OXaK9uGvQLelmzOhfO6Ir7g</recordid><startdate>20130107</startdate><enddate>20130107</enddate><creator>Zou, Zhongwei</creator><creator>Ishida, Masahiko</creator><creator>Li, Feng</creator><creator>Kakizaki, Tomohiro</creator><creator>Suzuki, Sho</creator><creator>Kitashiba, Hiroyasu</creator><creator>Nishio, Takeshi</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>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130107</creationdate><title>QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L</title><author>Zou, Zhongwei ; Ishida, Masahiko ; Li, Feng ; Kakizaki, Tomohiro ; Suzuki, Sho ; Kitashiba, Hiroyasu ; Nishio, Takeshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-e0fb61c6f611e0434261bf642fe2c53fd3e2dd6759d785d9ce83cf9475d0cc143</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>2-Isopropylmalate Synthase - 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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>Zou, Zhongwei</au><au>Ishida, Masahiko</au><au>Li, Feng</au><au>Kakizaki, Tomohiro</au><au>Suzuki, Sho</au><au>Kitashiba, Hiroyasu</au><au>Nishio, Takeshi</au><au>Zhang, Jinfa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-01-07</date><risdate>2013</risdate><volume>8</volume><issue>1</issue><spage>e53541</spage><pages>e53541-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>SNP markers for QTL analysis of 4-MTB-GSL contents in radish roots were developed by determining nucleotide sequences of bulked PCR products using a next-generation sequencer. DNA fragments were amplified from two radish lines by multiplex PCR with six primer pairs, and those amplified by 2,880 primer pairs were mixed and sequenced. By assembling sequence data, 1,953 SNPs in 750 DNA fragments, 437 of which have been previously mapped in a linkage map, were identified. A linkage map of nine linkage groups was constructed with 188 markers, and five QTLs were detected in two F(2) populations, three of them accounting for more than 50% of the total phenotypic variance being repeatedly detected. In the identified QTL regions, nine SNP markers were newly produced. By synteny analysis of the QTLs regions with Arabidopsis thaliana and Brassica rapa genome sequences, three candidate genes were selected, i.e., RsMAM3 for production of aliphatic glucosinolates linked to GSL-QTL-4, RsIPMDH1 for leucine biosynthesis showing strong co-expression with glucosinolate biosynthesis genes linked to GSL-QTL-2, and RsBCAT4 for branched-chain amino acid aminotransferase linked to GSL-QTL-1. Nucleotide sequences and expression of these genes suggested their possible function in 4MTB-GSL biosynthesis in radish roots.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23308250</pmid><doi>10.1371/journal.pone.0053541</doi><tpages>e53541</tpages><oa>free_for_read</oa></addata></record> |
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| language | eng |
| recordid | cdi_plos_journals_1289067494 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | 2-Isopropylmalate Synthase - genetics 2-Isopropylmalate Synthase - metabolism Agriculture Aliphatic compounds Amino acids Arabidopsis Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis thaliana Base Sequence Biology Biosynthesis Branched chain amino acids Brassica Brassica rapa Brassica rapa - genetics Brassica rapa - metabolism Brassicaceae Chain branching Chromosome Mapping Chromosomes, Plant Cultivars Cytochrome Deoxyribonucleic acid DNA DNA, Plant - genetics Expressed Sequence Tags Fragments Gene expression Gene sequencing Genes Genomes Genomics Genotype & phenotype Glucosinolates Glucosinolates - biosynthesis High-Throughput Nucleotide Sequencing Leucine Malate Dehydrogenase - genetics Malate Dehydrogenase - metabolism Markers Molecular Sequence Data Multiplex Polymerase Chain Reaction Multiplexing Nucleotide sequence Plant Proteins - genetics Plant Proteins - metabolism Plant Roots - genetics Plant Roots - metabolism Polymerase chain reaction Polymorphism, Single Nucleotide Quantitative genetics Quantitative Trait Loci Raphanus Raphanus - genetics Raphanus - metabolism Raphanus sativus Roots Science Seeds Single nucleotide polymorphisms Single-nucleotide polymorphism Synteny Transaminases - genetics Transaminases - metabolism |
| title | QTL analysis using SNP markers developed by next-generation sequencing for identification of candidate genes controlling 4-methylthio-3-butenyl glucosinolate contents in roots of radish, Raphanus sativus L |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T18%3A32%3A48IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=QTL%20analysis%20using%20SNP%20markers%20developed%20by%20next-generation%20sequencing%20for%20identification%20of%20candidate%20genes%20controlling%204-methylthio-3-butenyl%20glucosinolate%20contents%20in%20roots%20of%20radish,%20Raphanus%20sativus%20L&rft.jtitle=PloS%20one&rft.au=Zou,%20Zhongwei&rft.date=2013-01-07&rft.volume=8&rft.issue=1&rft.spage=e53541&rft.pages=e53541-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0053541&rft_dat=%3Cgale_plos_%3EA478401154%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1289067494&rft_id=info:pmid/23308250&rft_galeid=A478401154&rft_doaj_id=oai_doaj_org_article_7ca114a50a0548528379f4afb78d8d69&rfr_iscdi=true |