Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci
The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 mi...
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| Veröffentlicht in: | The New phytologist 2010-10, Vol.188 (1), p.242-253 |
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| creator | Li, Ying-Hui Li, Wei Zhang, Chen Yang, Liang Chang, Ru-Zhen Gaut, Brandon S Qiu, Li-Juan |
| description | The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China. |
| doi_str_mv | 10.1111/j.1469-8137.2010.03344.x |
| format | Article |
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In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/j.1469-8137.2010.03344.x</identifier><identifier>PMID: 20618914</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Agriculture ; Alleles ; Bayes Theorem ; Cluster Analysis ; Datasets ; diversity pattern ; domestication ; Evolutionary genetics ; Genetic diversity ; Genetic loci ; Genetic Loci - genetics ; Genetic Variation ; Genetics, Population ; Geographic regions ; geographic variation ; geographical variation ; Geography ; Glycine max ; Glycine max - genetics ; Glycine soja ; introgression ; Minisatellite Repeats - genetics ; Phylogeny ; Plant domestication ; Polymorphism, Single Nucleotide - genetics ; Population Dynamics ; Population parameters ; Population structure ; Soybeans</subject><ispartof>The New phytologist, 2010-10, Vol.188 (1), p.242-253</ispartof><rights>2010 New Phytologist Trust</rights><rights>The Authors (2010). Journal compilation © New Phytologist Trust (2010)</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5944-30145468d0a47fe6356873de2e86703f4913af7ab18f8fcacfbc0b714f0f30a3</citedby><cites>FETCH-LOGICAL-c5944-30145468d0a47fe6356873de2e86703f4913af7ab18f8fcacfbc0b714f0f30a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/40856396$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/40856396$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,1411,1427,27901,27902,45550,45551,46384,46808,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20618914$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Ying-Hui</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><creatorcontrib>Zhang, Chen</creatorcontrib><creatorcontrib>Yang, Liang</creatorcontrib><creatorcontrib>Chang, Ru-Zhen</creatorcontrib><creatorcontrib>Gaut, Brandon S</creatorcontrib><creatorcontrib>Qiu, Li-Juan</creatorcontrib><title>Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.</description><subject>Agriculture</subject><subject>Alleles</subject><subject>Bayes Theorem</subject><subject>Cluster Analysis</subject><subject>Datasets</subject><subject>diversity pattern</subject><subject>domestication</subject><subject>Evolutionary genetics</subject><subject>Genetic diversity</subject><subject>Genetic loci</subject><subject>Genetic Loci - genetics</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Geographic regions</subject><subject>geographic variation</subject><subject>geographical variation</subject><subject>Geography</subject><subject>Glycine max</subject><subject>Glycine max - genetics</subject><subject>Glycine soja</subject><subject>introgression</subject><subject>Minisatellite Repeats - genetics</subject><subject>Phylogeny</subject><subject>Plant domestication</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Population Dynamics</subject><subject>Population parameters</subject><subject>Population structure</subject><subject>Soybeans</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFu1DAURSMEokPhEwDvoIsMduzYzoIFqsoUqQIkisTOcpznwaMkTu0MnXwOf4rTlGFZvLH13r3X9jtZhghek7Te7daE8SqXhIp1gVMVU8rY-vAoWx0bj7MVxoXMOeM_TrJnMe4wxlXJi6fZSYE5kRVhq-z3BnoYnUGN-wUhunFCrkeN7yCmqh6hQdFPNegevd20k3E9oE4fzpDuG-TGiG5d26Ah-C30bvThnyr6nT5DNpWi64Y2FeBmD70BFGAAPd4lRNdvW8j7vWnBj64BNPh26nwYfrrYodYb9zx7YnUb4cX9fppdf7y4Pr_Mr75sPp1_uMpNWTGWU0xYybhssGbCAqcll4I2UIDkAlPLKkK1Fbom0kprtLG1wbUgzGJLsaan2ZslNv0lvTOOqnPRQNvqHvw-KllyUUrM-cPKggjKhCgeVIqyJDLxqpJSLkoTfIwBrBqC63SYFMFqRq52aiarZrJqRq7ukKtDsr66v2Rfd9AcjX8ZJ8H7RZBQwfTfwerz18v5lPwvF_8uJsBHP8NpJLSa5_F66Vvtld4GF9X3bykpEZGSUULpHzw8z5g</recordid><startdate>201010</startdate><enddate>201010</enddate><creator>Li, Ying-Hui</creator><creator>Li, Wei</creator><creator>Zhang, Chen</creator><creator>Yang, Liang</creator><creator>Chang, Ru-Zhen</creator><creator>Gaut, Brandon S</creator><creator>Qiu, Li-Juan</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing</general><general>Blackwell Publishing Ltd</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>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7TM</scope></search><sort><creationdate>201010</creationdate><title>Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci</title><author>Li, Ying-Hui ; Li, Wei ; Zhang, Chen ; Yang, Liang ; Chang, Ru-Zhen ; Gaut, Brandon S ; Qiu, Li-Juan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5944-30145468d0a47fe6356873de2e86703f4913af7ab18f8fcacfbc0b714f0f30a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Agriculture</topic><topic>Alleles</topic><topic>Bayes Theorem</topic><topic>Cluster Analysis</topic><topic>Datasets</topic><topic>diversity pattern</topic><topic>domestication</topic><topic>Evolutionary genetics</topic><topic>Genetic diversity</topic><topic>Genetic loci</topic><topic>Genetic Loci - genetics</topic><topic>Genetic Variation</topic><topic>Genetics, Population</topic><topic>Geographic regions</topic><topic>geographic variation</topic><topic>geographical variation</topic><topic>Geography</topic><topic>Glycine max</topic><topic>Glycine max - genetics</topic><topic>Glycine soja</topic><topic>introgression</topic><topic>Minisatellite Repeats - genetics</topic><topic>Phylogeny</topic><topic>Plant domestication</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Population Dynamics</topic><topic>Population parameters</topic><topic>Population structure</topic><topic>Soybeans</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Ying-Hui</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><creatorcontrib>Zhang, Chen</creatorcontrib><creatorcontrib>Yang, Liang</creatorcontrib><creatorcontrib>Chang, Ru-Zhen</creatorcontrib><creatorcontrib>Gaut, Brandon S</creatorcontrib><creatorcontrib>Qiu, Li-Juan</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>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Nucleic Acids Abstracts</collection><jtitle>The New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Ying-Hui</au><au>Li, Wei</au><au>Zhang, Chen</au><au>Yang, Liang</au><au>Chang, Ru-Zhen</au><au>Gaut, Brandon S</au><au>Qiu, Li-Juan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2010-10</date><risdate>2010</risdate><volume>188</volume><issue>1</issue><spage>242</spage><epage>253</epage><pages>242-253</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>The study of genetic diversity between a crop and its wild relatives may yield fundamental insights into evolutionary history and the process of domestication. In this study, we genotyped a sample of 303 accessions of domesticated soybean (Glycine max) and its wild progenitor Glycine soja with 99 microsatellite markers and 554 single-nucleotide polymorphism (SNP) markers. The simple sequence repeat (SSR) loci averaged 21.5 alleles per locus and overall Nei's gene diversity of 0.77. The SNPs had substantially lower genetic diversity (0.35) than SSRs. A SSR analyses indicated that G. soja exhibited higher diversity than G. max, but SNPs provided a slightly different snapshot of diversity between the two taxa. For both marker types, the primary division of genetic diversity was between the wild and domesticated accessions. Within taxa, G. max consisted of four geographic regions in China. G. soja formed six subgroups. Genealogical analyses indicated that cultivated soybean tended to form a monophyletic clade with respect to G. soja. G. soja and G. max represent distinct germplasm pools. Limited evidence of admixture was discovered between these two species. Overall, our analyses are consistent with the origin of G. max from regions along the Yellow River of China.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>20618914</pmid><doi>10.1111/j.1469-8137.2010.03344.x</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Agriculture Alleles Bayes Theorem Cluster Analysis Datasets diversity pattern domestication Evolutionary genetics Genetic diversity Genetic loci Genetic Loci - genetics Genetic Variation Genetics, Population Geographic regions geographic variation geographical variation Geography Glycine max Glycine max - genetics Glycine soja introgression Minisatellite Repeats - genetics Phylogeny Plant domestication Polymorphism, Single Nucleotide - genetics Population Dynamics Population parameters Population structure Soybeans |
| title | Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci |
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