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dc.contributor.authorBosse, Mirte
dc.contributor.authorMegens, Hendrik-Jan
dc.contributor.authorMadsen, Ole
dc.contributor.authorCrooijmans, Richard P. M. A.
dc.contributor.authorRyder, Oliver A.
dc.contributor.authorAusterlitz, Frédéric
dc.contributor.authorGroenen, Martien A. M.
dc.contributor.authorCara, M. Angeles R. de
dc.date.accessioned2020-06-29T17:56:51Z
dc.date.available2020-06-29T17:56:51Z
dc.date.issued2015
dc.identifier.issn1088-9051, 1549-5469
dc.identifier.doi10.1101/gr.187039.114
dc.identifier.urihttp://hdl.handle.net/20.500.12634/449
dc.description.abstractConservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.
dc.language.isoen
dc.relation.urlhttp://genome.cshlp.org/content/25/7/970
dc.rights© 2015 Bosse et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/bync/ 4.0/.
dc.rights.urihttp://creativecommons.org/licenses/bync/ 4.0/
dc.subjectPIGS
dc.subjectPHILIPPINES
dc.subjectGENOMICS
dc.subjectCONSERVATION GENETICS
dc.subjectWILDLIFE CONSERVATION
dc.titleUsing genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
dc.typeArticle
dc.source.journaltitleGenome Research
dc.source.volume25
dc.source.issue7
dc.source.beginpage970
dc.source.endpage981
refterms.dateFOA2020-06-29T17:56:51Z
html.description.abstractConservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.


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© 2015 Bosse et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/bync/ 4.0/.
Except where otherwise noted, this item's license is described as © 2015 Bosse et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/bync/ 4.0/.