Phylogenetic relationships among Oryza species revealed by AFLP markers
The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species five related genera, and three out-group taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP p...
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| Veröffentlicht in: | Theoretical and applied genetics 1999-06, Vol.98 (8), p.1320-1328 |
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| description | The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species five related genera, and three out-group taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta/O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms. |
| doi_str_mv | 10.1007/s001220051198 |
| format | Article |
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Seventy-seven accessions of 23 Oryza species five related genera, and three out-group taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta/O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s001220051198</identifier><identifier>CODEN: THAGA6</identifier><language>eng</language><publisher>Heidelberg: Springer</publisher><subject>amplified fragment length polymorphism ; Biochemistry ; Biological and medical sciences ; chemotaxonomy ; Classical genetics, quantitative genetics, hybrids ; cluster analysis ; DNA fingerprinting ; Fundamental and applied biological sciences. Psychology ; Genetic aspects ; genetic distance ; Genetic diversity ; genetic markers ; genetic variation ; Genetics of eukaryotes. Biological and molecular evolution ; genome ; Genomes ; genomics ; Oryza ; Oryza alta ; Oryza brachyantha ; Oryza eichingeri ; Oryza grandiglumis ; Oryza indandamanica ; Oryza malampuzhaensis ; Oryza meyeriana ; Oryza minuta ; Oryza officinalis ; Oryza punctata ; Oryza ridleyi ; Oryza sativa ; Phylogenetics ; Phylogeny ; Physiological aspects ; Plant genetics ; Poaceae ; Polymorphism ; Pteridophyta, spermatophyta ; Quantitative genetics ; Rice ; Vegetals ; wild relatives</subject><ispartof>Theoretical and applied genetics, 1999-06, Vol.98 (8), p.1320-1328</ispartof><rights>1999 INIST-CNRS</rights><rights>COPYRIGHT 1999 Springer</rights><rights>Springer-Verlag Berlin Heidelberg 1999</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c446t-865767570b95b626cbcf9f05a3887bf04196ff986f17bb5d090f8bbacf801a4a3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,27929,27930</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1860245$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Aggarwal, R.K</creatorcontrib><creatorcontrib>Brar, D.S</creatorcontrib><creatorcontrib>Nandi, S</creatorcontrib><creatorcontrib>Huang, N</creatorcontrib><creatorcontrib>Khush, G.S</creatorcontrib><title>Phylogenetic relationships among Oryza species revealed by AFLP markers</title><title>Theoretical and applied genetics</title><description>The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species five related genera, and three out-group taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta/O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms.</description><subject>amplified fragment length polymorphism</subject><subject>Biochemistry</subject><subject>Biological and medical sciences</subject><subject>chemotaxonomy</subject><subject>Classical genetics, quantitative genetics, hybrids</subject><subject>cluster analysis</subject><subject>DNA fingerprinting</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genetic aspects</subject><subject>genetic distance</subject><subject>Genetic diversity</subject><subject>genetic markers</subject><subject>genetic variation</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>genome</subject><subject>Genomes</subject><subject>genomics</subject><subject>Oryza</subject><subject>Oryza alta</subject><subject>Oryza brachyantha</subject><subject>Oryza eichingeri</subject><subject>Oryza grandiglumis</subject><subject>Oryza indandamanica</subject><subject>Oryza malampuzhaensis</subject><subject>Oryza meyeriana</subject><subject>Oryza minuta</subject><subject>Oryza officinalis</subject><subject>Oryza punctata</subject><subject>Oryza ridleyi</subject><subject>Oryza sativa</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Plant genetics</subject><subject>Poaceae</subject><subject>Polymorphism</subject><subject>Pteridophyta, spermatophyta</subject><subject>Quantitative genetics</subject><subject>Rice</subject><subject>Vegetals</subject><subject>wild relatives</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpd0M1rFDEUAPAgCq7Vo2cHEcHD6MubfM1xKbYWFlqsPYckTaZTZydr3qy4_vWmbEH08HiX3_tk7DWHjxxAfyIAjgggOe_NE7biosMWUeBTtgIQ0Eot8Tl7QXQPACihW7Hzq7vDlIc4x2UMTYmTW8Y80924o8Zt8zw0l-Xw2zW0i2GMVMXP6KZ42_hDsz7bXDVbV77HQi_Zs-Qmiq8e8wm7Ofv87fRLu7k8vzhdb9oghFpao6RWWmrwvfQKVfAh9Qmk64zRPoHgvUqpNypx7b28hR6S8d6FZIA74boT9v7Yd1fyj32kxW5HCnGa3BzznizXqBC0qPDtf_A-78tcd7NGSF2jx4o-HNFQb7LjHPK8xF_L4PZE9uL6q113wDuDxjzY9mhDyUQlJrsrY73-YDnYh__bf_5f_bvHBRwFN6Xi5jDS3yKjAIWs7M2RJZetG0olN9dYpwL2Hdcauz-qCouW</recordid><startdate>19990601</startdate><enddate>19990601</enddate><creator>Aggarwal, R.K</creator><creator>Brar, D.S</creator><creator>Nandi, S</creator><creator>Huang, N</creator><creator>Khush, G.S</creator><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</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></search><sort><creationdate>19990601</creationdate><title>Phylogenetic relationships among Oryza species revealed by AFLP markers</title><author>Aggarwal, R.K ; Brar, D.S ; Nandi, S ; Huang, N ; Khush, G.S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c446t-865767570b95b626cbcf9f05a3887bf04196ff986f17bb5d090f8bbacf801a4a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><topic>amplified fragment length polymorphism</topic><topic>Biochemistry</topic><topic>Biological and medical sciences</topic><topic>chemotaxonomy</topic><topic>Classical genetics, quantitative genetics, hybrids</topic><topic>cluster analysis</topic><topic>DNA fingerprinting</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genetic aspects</topic><topic>genetic distance</topic><topic>Genetic diversity</topic><topic>genetic markers</topic><topic>genetic variation</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>genome</topic><topic>Genomes</topic><topic>genomics</topic><topic>Oryza</topic><topic>Oryza alta</topic><topic>Oryza brachyantha</topic><topic>Oryza eichingeri</topic><topic>Oryza grandiglumis</topic><topic>Oryza indandamanica</topic><topic>Oryza malampuzhaensis</topic><topic>Oryza meyeriana</topic><topic>Oryza minuta</topic><topic>Oryza officinalis</topic><topic>Oryza punctata</topic><topic>Oryza ridleyi</topic><topic>Oryza sativa</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Plant genetics</topic><topic>Poaceae</topic><topic>Polymorphism</topic><topic>Pteridophyta, spermatophyta</topic><topic>Quantitative genetics</topic><topic>Rice</topic><topic>Vegetals</topic><topic>wild relatives</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Aggarwal, R.K</creatorcontrib><creatorcontrib>Brar, D.S</creatorcontrib><creatorcontrib>Nandi, S</creatorcontrib><creatorcontrib>Huang, N</creatorcontrib><creatorcontrib>Khush, G.S</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>Gale In Context: Science</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 (ProQuest)</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><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Aggarwal, R.K</au><au>Brar, D.S</au><au>Nandi, S</au><au>Huang, N</au><au>Khush, G.S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic relationships among Oryza species revealed by AFLP markers</atitle><jtitle>Theoretical and applied genetics</jtitle><date>1999-06-01</date><risdate>1999</risdate><volume>98</volume><issue>8</issue><spage>1320</spage><epage>1328</epage><pages>1320-1328</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><coden>THAGA6</coden><abstract>The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species five related genera, and three out-group taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta/O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms.</abstract><cop>Heidelberg</cop><cop>Berlin</cop><pub>Springer</pub><doi>10.1007/s001220051198</doi><tpages>9</tpages></addata></record> |
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| subjects | amplified fragment length polymorphism Biochemistry Biological and medical sciences chemotaxonomy Classical genetics, quantitative genetics, hybrids cluster analysis DNA fingerprinting Fundamental and applied biological sciences. Psychology Genetic aspects genetic distance Genetic diversity genetic markers genetic variation Genetics of eukaryotes. Biological and molecular evolution genome Genomes genomics Oryza Oryza alta Oryza brachyantha Oryza eichingeri Oryza grandiglumis Oryza indandamanica Oryza malampuzhaensis Oryza meyeriana Oryza minuta Oryza officinalis Oryza punctata Oryza ridleyi Oryza sativa Phylogenetics Phylogeny Physiological aspects Plant genetics Poaceae Polymorphism Pteridophyta, spermatophyta Quantitative genetics Rice Vegetals wild relatives |
| title | Phylogenetic relationships among Oryza species revealed by AFLP markers |
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