Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs
The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the ident...
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| Veröffentlicht in: | PloS one 2018-03, Vol.13 (3), p.e0194398-e0194398 |
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| creator | Deperi, Sofía I Tagliotti, Martín E Bedogni, M Cecilia Manrique-Carpintero, Norma C Coombs, Joseph Zhang, Ruofang Douches, David Huarte, Marcelo A |
| description | The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here. |
| doi_str_mv | 10.1371/journal.pone.0194398 |
| format | Article |
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The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0194398</identifier><identifier>PMID: 29547652</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Andigena ; Biodiversity ; Biology and Life Sciences ; Breeding ; Cloning ; Cluster Analysis ; Cultivars ; Deoxyribonucleic acid ; Discriminant Analysis ; DNA ; Ecology and Environmental Sciences ; Gene polymorphism ; Genetic analysis ; Genetic diversity ; Genetic structure ; Genetic Variation ; Genetics, Population ; Genomes ; Genotype ; Genotypes ; Methods ; Multiculturalism & pluralism ; Pedigree ; Plant Breeding ; Ploidy ; Polymorphism ; Polymorphism, Single Nucleotide ; Population ; Population genetics ; Population structure ; Potatoes ; Principal Component Analysis - methods ; Research and Analysis Methods ; Single-nucleotide polymorphism ; Solanum ; Solanum tuberosum ; Solanum tuberosum - classification ; Solanum tuberosum - genetics ; Species diversity ; Taxonomy ; Tetraploidy ; Variability ; Vegetables</subject><ispartof>PloS one, 2018-03, Vol.13 (3), p.e0194398-e0194398</ispartof><rights>2018 Deperi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://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>2018 Deperi et al 2018 Deperi et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c577t-f6527178c7fa10517929133f709dc9e8097c5aadadc491db71d729cccc2efbcb3</citedby><cites>FETCH-LOGICAL-c577t-f6527178c7fa10517929133f709dc9e8097c5aadadc491db71d729cccc2efbcb3</cites><orcidid>0000-0001-6314-494X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856401/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5856401/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29547652$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Deperi, Sofía I</creatorcontrib><creatorcontrib>Tagliotti, Martín E</creatorcontrib><creatorcontrib>Bedogni, M Cecilia</creatorcontrib><creatorcontrib>Manrique-Carpintero, Norma C</creatorcontrib><creatorcontrib>Coombs, Joseph</creatorcontrib><creatorcontrib>Zhang, Ruofang</creatorcontrib><creatorcontrib>Douches, David</creatorcontrib><creatorcontrib>Huarte, Marcelo A</creatorcontrib><title>Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.</description><subject>Andigena</subject><subject>Biodiversity</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Cloning</subject><subject>Cluster Analysis</subject><subject>Cultivars</subject><subject>Deoxyribonucleic acid</subject><subject>Discriminant Analysis</subject><subject>DNA</subject><subject>Ecology and Environmental Sciences</subject><subject>Gene polymorphism</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic structure</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Methods</subject><subject>Multiculturalism & pluralism</subject><subject>Pedigree</subject><subject>Plant Breeding</subject><subject>Ploidy</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Potatoes</subject><subject>Principal Component Analysis - methods</subject><subject>Research and Analysis Methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Solanum</subject><subject>Solanum tuberosum</subject><subject>Solanum tuberosum - classification</subject><subject>Solanum tuberosum - genetics</subject><subject>Species diversity</subject><subject>Taxonomy</subject><subject>Tetraploidy</subject><subject>Variability</subject><subject>Vegetables</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptkt9uFSEQxjdGY2v1DYySeOPNOcLCLsuNSVP_NWnURL0mc4BdOWFhBbbJeRZfVtY9bVojNxD4zTczH1NVzwneEsrJm32Yowe3nYI3W0wEo6J7UJ0SQetNW2P68M75pHqS0h7jhnZt-7g6qUXDeNvUp9XvdzapaEfrwWcERfCQbEKhR1O0XtkJHFJhXJL4nAqg0WS0HaIxCFIyKY3lYeEH4022Cml7bWKy-bDCYZodZBs8SjnOKs_RIOsRoGxyhMkFu0AZckATeOPQnKwf0LfPX9PT6lEPLplnx_2s-vHh_feLT5urLx8vL86vNqrhPG_60ggnvFO8B4IbwkUtCKU9x0IrYTosuGoANGjFBNE7TjSvhSqrNv1O7ehZ9XLVLdUkefQ1yRoTxgRtO1GIy5XQAfayODNCPMgAVv69CHGQEEvzzkiuatJQCkoRwtpegTI9xSWZZlp0WhWtt8ds8240WhX7Irh7ovdfvP0ph3Atm65pGSZF4PVRIIZfs0lZjuUPjXPFvjCvdQsmcMcL-uof9P_dsZVSMaQUTX9bDMFymbWbKLmMgTzOWgl7cbeR26Cb4aJ_ABVU2G4</recordid><startdate>20180316</startdate><enddate>20180316</enddate><creator>Deperi, Sofía I</creator><creator>Tagliotti, Martín E</creator><creator>Bedogni, M Cecilia</creator><creator>Manrique-Carpintero, Norma C</creator><creator>Coombs, Joseph</creator><creator>Zhang, Ruofang</creator><creator>Douches, David</creator><creator>Huarte, Marcelo A</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><orcidid>https://orcid.org/0000-0001-6314-494X</orcidid></search><sort><creationdate>20180316</creationdate><title>Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs</title><author>Deperi, Sofía I ; Tagliotti, Martín E ; Bedogni, M Cecilia ; Manrique-Carpintero, Norma C ; Coombs, Joseph ; Zhang, Ruofang ; Douches, David ; Huarte, Marcelo A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c577t-f6527178c7fa10517929133f709dc9e8097c5aadadc491db71d729cccc2efbcb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Andigena</topic><topic>Biodiversity</topic><topic>Biology and Life Sciences</topic><topic>Breeding</topic><topic>Cloning</topic><topic>Cluster Analysis</topic><topic>Cultivars</topic><topic>Deoxyribonucleic acid</topic><topic>Discriminant Analysis</topic><topic>DNA</topic><topic>Ecology and Environmental Sciences</topic><topic>Gene polymorphism</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic structure</topic><topic>Genetic Variation</topic><topic>Genetics, Population</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Methods</topic><topic>Multiculturalism & pluralism</topic><topic>Pedigree</topic><topic>Plant Breeding</topic><topic>Ploidy</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Population genetics</topic><topic>Population structure</topic><topic>Potatoes</topic><topic>Principal Component Analysis - 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The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29547652</pmid><doi>10.1371/journal.pone.0194398</doi><orcidid>https://orcid.org/0000-0001-6314-494X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Andigena Biodiversity Biology and Life Sciences Breeding Cloning Cluster Analysis Cultivars Deoxyribonucleic acid Discriminant Analysis DNA Ecology and Environmental Sciences Gene polymorphism Genetic analysis Genetic diversity Genetic structure Genetic Variation Genetics, Population Genomes Genotype Genotypes Methods Multiculturalism & pluralism Pedigree Plant Breeding Ploidy Polymorphism Polymorphism, Single Nucleotide Population Population genetics Population structure Potatoes Principal Component Analysis - methods Research and Analysis Methods Single-nucleotide polymorphism Solanum Solanum tuberosum Solanum tuberosum - classification Solanum tuberosum - genetics Species diversity Taxonomy Tetraploidy Variability Vegetables |
| title | Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs |
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