Using a very low-density SNP panel for genomic selection in a breeding program for sheep.
Identifieur interne : 000073 ( PubMed/Checkpoint ); précédent : 000072; suivant : 000074Using a very low-density SNP panel for genomic selection in a breeding program for sheep.
Auteurs : Jérôme Raoul [France] ; Andrew A. Swan [Australie] ; Jean-Michel Elsen [France]Source :
- Genetics, selection, evolution : GSE [ 1297-9686 ] ; 2017.
Abstract
Building an efficient reference population for genomic selection is an issue when the recorded population is small and phenotypes are poorly informed, which is often the case in sheep breeding programs. Using stochastic simulation, we evaluated a genomic design based on a reference population with medium-density genotypes [around 45 K single nucleotide polymorphisms (SNPs)] of dams that were imputed from very low-density genotypes (≤ 1000 SNPs).
DOI: 10.1186/s12711-017-0351-0
PubMed: 29065868
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using a very low-density SNP panel for genomic selection in a breeding program for sheep.</title><author><name sortKey="Raoul, Jerome" sort="Raoul, Jerome" uniqKey="Raoul J" first="Jérôme" last="Raoul">Jérôme Raoul</name><affiliation wicri:level="1"><nlm:affiliation>Institut de l'Elevage, Castanet-Tolosan, France. Jerome.raoul@inra.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut de l'Elevage, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Swan, Andrew A" sort="Swan, Andrew A" uniqKey="Swan A" first="Andrew A" last="Swan">Andrew A. Swan</name><affiliation wicri:level="1"><nlm:affiliation>Animal Genetics and Breeding Unit, University of New England, Armidale, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Animal Genetics and Breeding Unit, University of New England, Armidale</wicri:regionArea><wicri:noRegion>Armidale</wicri:noRegion></affiliation></author><author><name sortKey="Elsen, Jean Michel" sort="Elsen, Jean Michel" uniqKey="Elsen J" first="Jean-Michel" last="Elsen">Jean-Michel Elsen</name><affiliation wicri:level="1"><nlm:affiliation>GenPhySE, INRA, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>GenPhySE, INRA, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29065868</idno><idno type="pmid">29065868</idno><idno type="doi">10.1186/s12711-017-0351-0</idno><idno type="wicri:Area/PubMed/Corpus">000357</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000357</idno><idno type="wicri:Area/PubMed/Curation">000355</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000355</idno><idno type="wicri:Area/PubMed/Checkpoint">000355</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000355</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Using a very low-density SNP panel for genomic selection in a breeding program for sheep.</title><author><name sortKey="Raoul, Jerome" sort="Raoul, Jerome" uniqKey="Raoul J" first="Jérôme" last="Raoul">Jérôme Raoul</name><affiliation wicri:level="1"><nlm:affiliation>Institut de l'Elevage, Castanet-Tolosan, France. Jerome.raoul@inra.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut de l'Elevage, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Swan, Andrew A" sort="Swan, Andrew A" uniqKey="Swan A" first="Andrew A" last="Swan">Andrew A. Swan</name><affiliation wicri:level="1"><nlm:affiliation>Animal Genetics and Breeding Unit, University of New England, Armidale, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Animal Genetics and Breeding Unit, University of New England, Armidale</wicri:regionArea><wicri:noRegion>Armidale</wicri:noRegion></affiliation></author><author><name sortKey="Elsen, Jean Michel" sort="Elsen, Jean Michel" uniqKey="Elsen J" first="Jean-Michel" last="Elsen">Jean-Michel Elsen</name><affiliation wicri:level="1"><nlm:affiliation>GenPhySE, INRA, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>GenPhySE, INRA, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genetics, selection, evolution : GSE</title><idno type="eISSN">1297-9686</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Building an efficient reference population for genomic selection is an issue when the recorded population is small and phenotypes are poorly informed, which is often the case in sheep breeding programs. Using stochastic simulation, we evaluated a genomic design based on a reference population with medium-density genotypes [around 45 K single nucleotide polymorphisms (SNPs)] of dams that were imputed from very low-density genotypes (≤ 1000 SNPs).</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">29065868</PMID><DateCreated><Year>2017</Year><Month>10</Month><Day>25</Day></DateCreated><DateRevised><Year>2017</Year><Month>11</Month><Day>01</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1297-9686</ISSN><JournalIssue CitedMedium="Internet"><Volume>49</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Oct</Month><Day>24</Day></PubDate></JournalIssue><Title>Genetics, selection, evolution : GSE</Title><ISOAbbreviation>Genet. Sel. Evol.</ISOAbbreviation></Journal><ArticleTitle>Using a very low-density SNP panel for genomic selection in a breeding program for sheep.</ArticleTitle><Pagination><MedlinePgn>76</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12711-017-0351-0</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Building an efficient reference population for genomic selection is an issue when the recorded population is small and phenotypes are poorly informed, which is often the case in sheep breeding programs. Using stochastic simulation, we evaluated a genomic design based on a reference population with medium-density genotypes [around 45 K single nucleotide polymorphisms (SNPs)] of dams that were imputed from very low-density genotypes (≤ 1000 SNPs).</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">A population under selection for a maternal trait was simulated using real genotypes. Genetic gains realized from classical selection and genomic selection designs were compared. Genomic selection scenarios that differed in reference population structure (whether or not dams were included in the reference) and genotype quality (medium-density or imputed to medium-density from very low-density) were evaluated.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The genomic design increased genetic gain by 26% when the reference population was based on sire medium-density genotypes and by 54% when the reference population included both sire and dam medium-density genotypes. When medium-density genotypes of male candidates and dams were replaced by imputed genotypes from very low-density SNP genotypes (1000 SNPs), the increase in gain was 22% for the sire reference population and 42% for the sire and dam reference population. The rate of increase in inbreeding was lower (from - 20 to - 34%) for the genomic design than for the classical design regardless of the genomic scenario.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We show that very low-density genotypes of male candidates and dams combined with an imputation process result in a substantial increase in genetic gain for small sheep breeding programs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Raoul</LastName><ForeName>Jérôme</ForeName><Initials>J</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3140-4433</Identifier><AffiliationInfo><Affiliation>Institut de l'Elevage, Castanet-Tolosan, France. Jerome.raoul@inra.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>GenPhySE, INRA, Castanet-Tolosan, France. Jerome.raoul@inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Swan</LastName><ForeName>Andrew A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Animal Genetics and Breeding Unit, University of New England, Armidale, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Elsen</LastName><ForeName>Jean-Michel</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>GenPhySE, INRA, Castanet-Tolosan, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>10</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>France</Country><MedlineTA>Genet Sel Evol</MedlineTA><NlmUniqueID>9114088</NlmUniqueID><ISSNLinking>0999-193X</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections 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