Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase (GmNFR1α)
The rj1 mutation of soybean is a simple recessive allele in a single line that arose as a spontaneous mutation in a population; it exhibits non-nodulation with virtually all Bradyrhizobium and Sinorhizobium strains. Here, we described fine genetic and physical mapping of the rj1 locus on soybean chr...
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| Veröffentlicht in: | Theoretical and applied genetics 2011-03, Vol.122 (5), p.875-884 |
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| creator | Lee, Woo Kyu Jeong, Namhee Indrasumunar, Arief Gresshoff, Peter M Jeong, Soon-Chun |
| description | The rj1 mutation of soybean is a simple recessive allele in a single line that arose as a spontaneous mutation in a population; it exhibits non-nodulation with virtually all Bradyrhizobium and Sinorhizobium strains. Here, we described fine genetic and physical mapping of the rj1 locus on soybean chromosome 2. The initial mapping of the rj1 locus using public markers indicated that A343.p2, a sequence-based marker that contains sequence similar to a part of the LjNFR1 gene regulating nodule formation as a member of lysin motif-type receptor-like kinase (LYK) family, maps very close to or cosegregates with the rj1 locus. The sequence of A343.p2 is 100% identical to parts of two BAC clone sequences (GM_WBb0002O19 and GM_WBb098N11) that contain three members of the LYK family. We analyzed the sequence contig (262 kbp) of the two BAC clones by resequencing and subsequent fine genetic and physical mapping. The results indicated that rj1 is located in a gene-rich region with a recombination rate of 120 kbp/cM: several fold higher than the genome average. Among the LYK genes, NFR1α is most likely the gene encoded at the Rj1 locus. The non-nodulating rj1 allele was created by a single base-pair deletion that results in a premature stop codon. Taken together, the fine genetic and physical mapping of the Rj1-residing chromosomal region, combined with the unexpected observation of a putative recombination hotspot, allowed us to demonstrate that the Rj1 locus most likely encodes the NFR1α gene. |
| doi_str_mv | 10.1007/s00122-010-1493-4 |
| format | Article |
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Here, we described fine genetic and physical mapping of the rj1 locus on soybean chromosome 2. The initial mapping of the rj1 locus using public markers indicated that A343.p2, a sequence-based marker that contains sequence similar to a part of the LjNFR1 gene regulating nodule formation as a member of lysin motif-type receptor-like kinase (LYK) family, maps very close to or cosegregates with the rj1 locus. The sequence of A343.p2 is 100% identical to parts of two BAC clone sequences (GM_WBb0002O19 and GM_WBb098N11) that contain three members of the LYK family. We analyzed the sequence contig (262 kbp) of the two BAC clones by resequencing and subsequent fine genetic and physical mapping. The results indicated that rj1 is located in a gene-rich region with a recombination rate of 120 kbp/cM: several fold higher than the genome average. Among the LYK genes, NFR1α is most likely the gene encoded at the Rj1 locus. The non-nodulating rj1 allele was created by a single base-pair deletion that results in a premature stop codon. Taken together, the fine genetic and physical mapping of the Rj1-residing chromosomal region, combined with the unexpected observation of a putative recombination hotspot, allowed us to demonstrate that the Rj1 locus most likely encodes the NFR1α gene.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-010-1493-4</identifier><identifier>PMID: 21104396</identifier><language>eng</language><publisher>Berlin/Heidelberg: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Agriculture ; Alleles ; Amino Acid Motifs ; bacterial artificial chromosomes ; Base Sequence ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Bradyrhizobium ; Chromosome Mapping ; Chromosomes, Plant ; clones ; DNA, Plant - genetics ; Gene Expression Regulation, Plant ; Gene loci ; Genes, Recessive ; Genetic Loci ; genetic markers ; Genomes ; Genotype ; Glycine max ; Glycine max - genetics ; Kinases ; Legumes ; Life Sciences ; loci ; lysine ; Lysine - genetics ; Molecular Sequence Data ; Mutation ; nodulation ; Original Paper ; Phosphotransferases - metabolism ; physical chromosome mapping ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide ; protein kinases ; Recombination, Genetic ; Sequence Analysis, DNA ; single nucleotide polymorphism ; Sinorhizobium ; Soybeans ; stop codon</subject><ispartof>Theoretical and applied genetics, 2011-03, Vol.122 (5), p.875-884</ispartof><rights>Springer-Verlag 2010</rights><rights>Springer-Verlag 2011</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c492t-957a423a56ec4c909ef5923e8a47f5de071db6968f43a19a72810a142f29ad1c3</citedby><cites>FETCH-LOGICAL-c492t-957a423a56ec4c909ef5923e8a47f5de071db6968f43a19a72810a142f29ad1c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-010-1493-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-010-1493-4$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21104396$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Woo Kyu</creatorcontrib><creatorcontrib>Jeong, Namhee</creatorcontrib><creatorcontrib>Indrasumunar, Arief</creatorcontrib><creatorcontrib>Gresshoff, Peter M</creatorcontrib><creatorcontrib>Jeong, Soon-Chun</creatorcontrib><title>Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase (GmNFR1α)</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>The rj1 mutation of soybean is a simple recessive allele in a single line that arose as a spontaneous mutation in a population; it exhibits non-nodulation with virtually all Bradyrhizobium and Sinorhizobium strains. Here, we described fine genetic and physical mapping of the rj1 locus on soybean chromosome 2. The initial mapping of the rj1 locus using public markers indicated that A343.p2, a sequence-based marker that contains sequence similar to a part of the LjNFR1 gene regulating nodule formation as a member of lysin motif-type receptor-like kinase (LYK) family, maps very close to or cosegregates with the rj1 locus. The sequence of A343.p2 is 100% identical to parts of two BAC clone sequences (GM_WBb0002O19 and GM_WBb098N11) that contain three members of the LYK family. We analyzed the sequence contig (262 kbp) of the two BAC clones by resequencing and subsequent fine genetic and physical mapping. The results indicated that rj1 is located in a gene-rich region with a recombination rate of 120 kbp/cM: several fold higher than the genome average. Among the LYK genes, NFR1α is most likely the gene encoded at the Rj1 locus. The non-nodulating rj1 allele was created by a single base-pair deletion that results in a premature stop codon. Taken together, the fine genetic and physical mapping of the Rj1-residing chromosomal region, combined with the unexpected observation of a putative recombination hotspot, allowed us to demonstrate that the Rj1 locus most likely encodes the NFR1α gene.</description><subject>Agriculture</subject><subject>Alleles</subject><subject>Amino Acid Motifs</subject><subject>bacterial artificial chromosomes</subject><subject>Base Sequence</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Bradyrhizobium</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Plant</subject><subject>clones</subject><subject>DNA, Plant - genetics</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene loci</subject><subject>Genes, Recessive</subject><subject>Genetic Loci</subject><subject>genetic markers</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Glycine max</subject><subject>Glycine max - genetics</subject><subject>Kinases</subject><subject>Legumes</subject><subject>Life Sciences</subject><subject>loci</subject><subject>lysine</subject><subject>Lysine - genetics</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>nodulation</subject><subject>Original Paper</subject><subject>Phosphotransferases - metabolism</subject><subject>physical chromosome mapping</subject><subject>Plant Biochemistry</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>protein kinases</subject><subject>Recombination, Genetic</subject><subject>Sequence Analysis, DNA</subject><subject>single nucleotide polymorphism</subject><subject>Sinorhizobium</subject><subject>Soybeans</subject><subject>stop codon</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</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><recordid>eNqFkc1u1DAUhS0EotPCA7CBiA2wMNzrnyRmhyo6IFUFUbq2PIkz8jSxBzuRmG3fiBfhmXBIAYkFrOxrf-f4Xh9CHiG8RIDqVQJAxiggUBSKU3GHrFBwRhkT7C5ZAQigspLsiByntAMAJoHfJ0cMEQRX5YrcrPtD47wtBvO18MFTH9qpN6MLvuhDM6Ui7vB1YYpomzBsnA9b612Ty-2MWJ9P9yYl57cZurz4WDifN_0h_TQNo-tmqd2PIdLeXdvi2nmTbPF8PVycfcLv3148IPc60yf78HY9IVdnbz-fvqPnH9bvT9-c00YoNlIlKyMYN7K0jWgUKNtJxbitjag62VqosN2Uqqw7wQ0qU7EawaBgHVOmxYafkGeL7z6GL5NNox5camzfG2_DlLQCxkVd5w_8H1lLLkpZlSqTT_8id2GKPo-RoRJRyZpnCBeoiSGlaDu9j24w8aAR9BykXoLUMNc5SD238PjWeNoMtv2t-JVcBtgCpHzltzb-eflfrk8WUWeCNtvokr66ZIAcUAleY8V_AI1rsOY</recordid><startdate>20110301</startdate><enddate>20110301</enddate><creator>Lee, Woo Kyu</creator><creator>Jeong, Namhee</creator><creator>Indrasumunar, Arief</creator><creator>Gresshoff, Peter M</creator><creator>Jeong, Soon-Chun</creator><general>Berlin/Heidelberg : Springer-Verlag</general><general>Springer-Verlag</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>7SS</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20110301</creationdate><title>Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase (GmNFR1α)</title><author>Lee, Woo Kyu ; Jeong, Namhee ; Indrasumunar, Arief ; Gresshoff, Peter M ; Jeong, Soon-Chun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c492t-957a423a56ec4c909ef5923e8a47f5de071db6968f43a19a72810a142f29ad1c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Agriculture</topic><topic>Alleles</topic><topic>Amino Acid Motifs</topic><topic>bacterial artificial chromosomes</topic><topic>Base Sequence</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Bradyrhizobium</topic><topic>Chromosome Mapping</topic><topic>Chromosomes, Plant</topic><topic>clones</topic><topic>DNA, Plant - genetics</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene loci</topic><topic>Genes, Recessive</topic><topic>Genetic Loci</topic><topic>genetic markers</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Glycine max</topic><topic>Glycine max - genetics</topic><topic>Kinases</topic><topic>Legumes</topic><topic>Life Sciences</topic><topic>loci</topic><topic>lysine</topic><topic>Lysine - genetics</topic><topic>Molecular Sequence Data</topic><topic>Mutation</topic><topic>nodulation</topic><topic>Original Paper</topic><topic>Phosphotransferases - metabolism</topic><topic>physical chromosome mapping</topic><topic>Plant Biochemistry</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>protein kinases</topic><topic>Recombination, Genetic</topic><topic>Sequence Analysis, DNA</topic><topic>single nucleotide polymorphism</topic><topic>Sinorhizobium</topic><topic>Soybeans</topic><topic>stop codon</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, Woo Kyu</creatorcontrib><creatorcontrib>Jeong, Namhee</creatorcontrib><creatorcontrib>Indrasumunar, Arief</creatorcontrib><creatorcontrib>Gresshoff, Peter M</creatorcontrib><creatorcontrib>Jeong, Soon-Chun</creatorcontrib><collection>AGRIS</collection><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>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech 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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</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>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, Woo Kyu</au><au>Jeong, Namhee</au><au>Indrasumunar, Arief</au><au>Gresshoff, Peter M</au><au>Jeong, Soon-Chun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase (GmNFR1α)</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2011-03-01</date><risdate>2011</risdate><volume>122</volume><issue>5</issue><spage>875</spage><epage>884</epage><pages>875-884</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><abstract>The rj1 mutation of soybean is a simple recessive allele in a single line that arose as a spontaneous mutation in a population; it exhibits non-nodulation with virtually all Bradyrhizobium and Sinorhizobium strains. Here, we described fine genetic and physical mapping of the rj1 locus on soybean chromosome 2. The initial mapping of the rj1 locus using public markers indicated that A343.p2, a sequence-based marker that contains sequence similar to a part of the LjNFR1 gene regulating nodule formation as a member of lysin motif-type receptor-like kinase (LYK) family, maps very close to or cosegregates with the rj1 locus. The sequence of A343.p2 is 100% identical to parts of two BAC clone sequences (GM_WBb0002O19 and GM_WBb098N11) that contain three members of the LYK family. We analyzed the sequence contig (262 kbp) of the two BAC clones by resequencing and subsequent fine genetic and physical mapping. The results indicated that rj1 is located in a gene-rich region with a recombination rate of 120 kbp/cM: several fold higher than the genome average. Among the LYK genes, NFR1α is most likely the gene encoded at the Rj1 locus. The non-nodulating rj1 allele was created by a single base-pair deletion that results in a premature stop codon. Taken together, the fine genetic and physical mapping of the Rj1-residing chromosomal region, combined with the unexpected observation of a putative recombination hotspot, allowed us to demonstrate that the Rj1 locus most likely encodes the NFR1α gene.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>21104396</pmid><doi>10.1007/s00122-010-1493-4</doi><tpages>10</tpages></addata></record> |
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| ispartof | Theoretical and applied genetics, 2011-03, Vol.122 (5), p.875-884 |
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| subjects | Agriculture Alleles Amino Acid Motifs bacterial artificial chromosomes Base Sequence Biochemistry Biomedical and Life Sciences Biotechnology Bradyrhizobium Chromosome Mapping Chromosomes, Plant clones DNA, Plant - genetics Gene Expression Regulation, Plant Gene loci Genes, Recessive Genetic Loci genetic markers Genomes Genotype Glycine max Glycine max - genetics Kinases Legumes Life Sciences loci lysine Lysine - genetics Molecular Sequence Data Mutation nodulation Original Paper Phosphotransferases - metabolism physical chromosome mapping Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Polymorphism, Single Nucleotide protein kinases Recombination, Genetic Sequence Analysis, DNA single nucleotide polymorphism Sinorhizobium Soybeans stop codon |
| title | Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase (GmNFR1α) |
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