Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population
KEY MESSAGE : Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimat...
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| Veröffentlicht in: | Theoretical and applied genetics 2014-04, Vol.127 (4), p.981-994 |
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| creator | Cros, David Sánchez, Leopoldo Cochard, Benoit Samper, Patrick Denis, Marie Bouvet, Jean-Marc Fernández, Jesús |
| description | KEY MESSAGE : Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657–1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (0.9) and a low RMSE (0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0. |
| doi_str_mv | 10.1007/s00122-014-2273-3 |
| format | Article |
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Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657–1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy–Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-014-2273-3</identifier><identifier>PMID: 24504554</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>Agricultural research ; Agriculture ; Algorithms ; Arecaceae - genetics ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Breeding ; Computer Simulation ; computer software ; data collection ; Elaeis guineensis ; Estimates ; Flowers & plants ; founder effect ; Gene expression ; Genealogy ; Genetic aspects ; Genetic Markers ; Genetic research ; Genetics, Population ; hermaphroditism ; Life Sciences ; linkage disequilibrium ; Linkage Disequilibrium - genetics ; microsatellite repeats ; Microsatellite Repeats - genetics ; monoecy ; new methods ; Oil palm ; Original Paper ; Palm Oil ; Pedigree ; Phylogeny ; Plant Biochemistry ; plant breeding ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plant Oils - metabolism ; Plant reproduction ; Population ; population size ; Self-Fertilization - genetics ; selfing ; Vegetal Biology</subject><ispartof>Theoretical and applied genetics, 2014-04, Vol.127 (4), p.981-994</ispartof><rights>Springer-Verlag Berlin Heidelberg 2014</rights><rights>COPYRIGHT 2014 Springer</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c564t-f5fe2c5f807d6dec0ecfd427f7e8798319f5103b7a00c92007c93eb7c881f8153</citedby><cites>FETCH-LOGICAL-c564t-f5fe2c5f807d6dec0ecfd427f7e8798319f5103b7a00c92007c93eb7c881f8153</cites><orcidid>0000-0002-8285-0441</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-014-2273-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-014-2273-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24504554$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01268542$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Cros, David</creatorcontrib><creatorcontrib>Sánchez, Leopoldo</creatorcontrib><creatorcontrib>Cochard, Benoit</creatorcontrib><creatorcontrib>Samper, Patrick</creatorcontrib><creatorcontrib>Denis, Marie</creatorcontrib><creatorcontrib>Bouvet, Jean-Marc</creatorcontrib><creatorcontrib>Fernández, Jesús</creatorcontrib><title>Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>KEY MESSAGE : Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657–1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy–Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.</description><subject>Agricultural research</subject><subject>Agriculture</subject><subject>Algorithms</subject><subject>Arecaceae - genetics</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Breeding</subject><subject>Computer Simulation</subject><subject>computer software</subject><subject>data collection</subject><subject>Elaeis guineensis</subject><subject>Estimates</subject><subject>Flowers & plants</subject><subject>founder effect</subject><subject>Gene expression</subject><subject>Genealogy</subject><subject>Genetic aspects</subject><subject>Genetic Markers</subject><subject>Genetic research</subject><subject>Genetics, Population</subject><subject>hermaphroditism</subject><subject>Life Sciences</subject><subject>linkage disequilibrium</subject><subject>Linkage Disequilibrium - genetics</subject><subject>microsatellite repeats</subject><subject>Microsatellite Repeats - genetics</subject><subject>monoecy</subject><subject>new methods</subject><subject>Oil palm</subject><subject>Original Paper</subject><subject>Palm Oil</subject><subject>Pedigree</subject><subject>Phylogeny</subject><subject>Plant Biochemistry</subject><subject>plant breeding</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Oils - metabolism</subject><subject>Plant reproduction</subject><subject>Population</subject><subject>population size</subject><subject>Self-Fertilization - genetics</subject><subject>selfing</subject><subject>Vegetal Biology</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</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>eNqNks1u1DAUhSMEosPAA7ABS2zoIsW_42Q5qgqtNBISpWvL49ipKycOdoLoc_DC3DSl6iCEkBeWr79zpHvuLYrXBJ8QjOWHjDGhtMSEl5RKVrInxYpwRuHF6dNihTHHpZCCHhUvcr7BGFOB2fPiiHKBuRB8Vfw8y6Pv9Ohjj6JDre2tDrH1Rgdkou6NzWO6Rb5HQ9D9iPJgjbcZTdn3LdJosI1vk7UoWRN7YCdz56VDG5Mfrzuk-wbpYQhgefczRiih6AMadOjQHsTN7DXEYQp3yMvimdMh21f397q4-nj29fS83H3-dHG63ZVGbPhYOuEsNcJVWDabxhpsjWs4lU7aStYVI7UTBLO91BibmkJgpmZ2L01VEVcRwdbF8eJ7rYMaEsSQblXUXp1vd2quQbqbSnD6nQD7fmGHFL9NEIrqfDY2QCg2TlkRQTaSi039XyjMhUgYxbp49wd6E6fUQ9NA4VpUDJNHVKuDVb53cUzazKZqyza1EFjQmTr5CwWnsZ2H2VjnoX4gOD4QADPaH2Orp5zVxeWXQ5YsrEkx52TdQ14Eq3kX1bKLEBlX8y4qBpo3981N-842D4rfywcAXYAMX31r06Pu_-H6dhE5HZVuk8_q6pICANstCJEV-wVHoPCS</recordid><startdate>20140401</startdate><enddate>20140401</enddate><creator>Cros, David</creator><creator>Sánchez, Leopoldo</creator><creator>Cochard, Benoit</creator><creator>Samper, Patrick</creator><creator>Denis, Marie</creator><creator>Bouvet, Jean-Marc</creator><creator>Fernández, Jesús</creator><general>Springer-Verlag</general><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><general>Springer Verlag</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>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>RC3</scope><scope>7X8</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0002-8285-0441</orcidid></search><sort><creationdate>20140401</creationdate><title>Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population</title><author>Cros, David ; Sánchez, Leopoldo ; Cochard, Benoit ; Samper, Patrick ; Denis, Marie ; Bouvet, Jean-Marc ; Fernández, Jesús</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c564t-f5fe2c5f807d6dec0ecfd427f7e8798319f5103b7a00c92007c93eb7c881f8153</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Agricultural research</topic><topic>Agriculture</topic><topic>Algorithms</topic><topic>Arecaceae - genetics</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Breeding</topic><topic>Computer Simulation</topic><topic>computer software</topic><topic>data collection</topic><topic>Elaeis guineensis</topic><topic>Estimates</topic><topic>Flowers & plants</topic><topic>founder effect</topic><topic>Gene expression</topic><topic>Genealogy</topic><topic>Genetic aspects</topic><topic>Genetic Markers</topic><topic>Genetic research</topic><topic>Genetics, Population</topic><topic>hermaphroditism</topic><topic>Life Sciences</topic><topic>linkage disequilibrium</topic><topic>Linkage Disequilibrium - genetics</topic><topic>microsatellite repeats</topic><topic>Microsatellite Repeats - genetics</topic><topic>monoecy</topic><topic>new methods</topic><topic>Oil palm</topic><topic>Original Paper</topic><topic>Palm Oil</topic><topic>Pedigree</topic><topic>Phylogeny</topic><topic>Plant Biochemistry</topic><topic>plant breeding</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Oils - metabolism</topic><topic>Plant reproduction</topic><topic>Population</topic><topic>population size</topic><topic>Self-Fertilization - genetics</topic><topic>selfing</topic><topic>Vegetal Biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cros, David</creatorcontrib><creatorcontrib>Sánchez, Leopoldo</creatorcontrib><creatorcontrib>Cochard, Benoit</creatorcontrib><creatorcontrib>Samper, Patrick</creatorcontrib><creatorcontrib>Denis, Marie</creatorcontrib><creatorcontrib>Bouvet, Jean-Marc</creatorcontrib><creatorcontrib>Fernández, Jesús</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>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</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>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cros, David</au><au>Sánchez, Leopoldo</au><au>Cochard, Benoit</au><au>Samper, Patrick</au><au>Denis, Marie</au><au>Bouvet, Jean-Marc</au><au>Fernández, Jesús</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2014-04-01</date><risdate>2014</risdate><volume>127</volume><issue>4</issue><spage>981</spage><epage>994</epage><pages>981-994</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><abstract>KEY MESSAGE : Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657–1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy–Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>24504554</pmid><doi>10.1007/s00122-014-2273-3</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-8285-0441</orcidid></addata></record> |
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| ispartof | Theoretical and applied genetics, 2014-04, Vol.127 (4), p.981-994 |
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| language | eng |
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| source | MEDLINE; SpringerNature Journals |
| subjects | Agricultural research Agriculture Algorithms Arecaceae - genetics Biochemistry Biomedical and Life Sciences Biotechnology Breeding Computer Simulation computer software data collection Elaeis guineensis Estimates Flowers & plants founder effect Gene expression Genealogy Genetic aspects Genetic Markers Genetic research Genetics, Population hermaphroditism Life Sciences linkage disequilibrium Linkage Disequilibrium - genetics microsatellite repeats Microsatellite Repeats - genetics monoecy new methods Oil palm Original Paper Palm Oil Pedigree Phylogeny Plant Biochemistry plant breeding Plant Breeding/Biotechnology Plant Genetics and Genomics Plant Oils - metabolism Plant reproduction Population population size Self-Fertilization - genetics selfing Vegetal Biology |
| title | Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
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