Estimates of the actual relationship between half‐sibs in a pig population
Summary Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at th...
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| Veröffentlicht in: | Journal of animal breeding and genetics (1986) 2017-04, Vol.134 (2), p.109-118 |
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| container_title | Journal of animal breeding and genetics (1986) |
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| creator | García‐Baccino, C.A. Munilla, S. Legarra, A. Vitezica, Z.G. Forneris, N.S. Bates, R.O. Ernst, C.W. Raney, N.E. Steibel, J.P. Cantet, R.J.C. |
| description | Summary
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half‐sibs from a cross‐bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half‐sibs. |
| doi_str_mv | 10.1111/jbg.12236 |
| format | Article |
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Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half‐sibs from a cross‐bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half‐sibs.</description><identifier>ISSN: 0931-2668</identifier><identifier>EISSN: 1439-0388</identifier><identifier>DOI: 10.1111/jbg.12236</identifier><identifier>PMID: 27670252</identifier><language>eng</language><publisher>Germany: Blackwell Publishing Ltd</publisher><subject>Actual relationships ; Animal reproduction ; Animals ; Breeding of animals ; Crosses, Genetic ; Estimates ; estimation methods ; Female ; Gene loci ; genomic selection ; Genotype ; Hogs ; identity by descent ; Life Sciences ; Male ; Pedigree ; Polymorphism, Single Nucleotide ; Siblings ; Sus scrofa - genetics</subject><ispartof>Journal of animal breeding and genetics (1986), 2017-04, Vol.134 (2), p.109-118</ispartof><rights>2016 Blackwell Verlag GmbH</rights><rights>2016 Blackwell Verlag GmbH.</rights><rights>Copyright © 2017 Blackwell Verlag GmbH</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4206-ab4d83f517415c39ca74e370405e2767ff0c1ba056babeb9b12694ebe37aabc33</citedby><cites>FETCH-LOGICAL-c4206-ab4d83f517415c39ca74e370405e2767ff0c1ba056babeb9b12694ebe37aabc33</cites><orcidid>0000-0001-8893-7620 ; 0000-0002-3162-7258</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjbg.12236$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjbg.12236$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,780,784,885,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27670252$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01603844$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>García‐Baccino, C.A.</creatorcontrib><creatorcontrib>Munilla, S.</creatorcontrib><creatorcontrib>Legarra, A.</creatorcontrib><creatorcontrib>Vitezica, Z.G.</creatorcontrib><creatorcontrib>Forneris, N.S.</creatorcontrib><creatorcontrib>Bates, R.O.</creatorcontrib><creatorcontrib>Ernst, C.W.</creatorcontrib><creatorcontrib>Raney, N.E.</creatorcontrib><creatorcontrib>Steibel, J.P.</creatorcontrib><creatorcontrib>Cantet, R.J.C.</creatorcontrib><title>Estimates of the actual relationship between half‐sibs in a pig population</title><title>Journal of animal breeding and genetics (1986)</title><addtitle>J Anim Breed Genet</addtitle><description>Summary
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half‐sibs from a cross‐bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half‐sibs.</description><subject>Actual relationships</subject><subject>Animal reproduction</subject><subject>Animals</subject><subject>Breeding of animals</subject><subject>Crosses, Genetic</subject><subject>Estimates</subject><subject>estimation methods</subject><subject>Female</subject><subject>Gene loci</subject><subject>genomic selection</subject><subject>Genotype</subject><subject>Hogs</subject><subject>identity by descent</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Pedigree</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Siblings</subject><subject>Sus scrofa - genetics</subject><issn>0931-2668</issn><issn>1439-0388</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1Kw0AUhQdRtFYXvoAMuNFFdP4yySyrqFUKbnQ9zKQ3dkqaxExicecj-Iw-iVNTRQTBu7lw-Ticcw9CB5Sc0jBnc_t4ShnjcgMNqOAqIjxNN9GAKE4jJmW6g3a9nxMS7onaRjsskQlhMRugyaVv3cK04HGV43YG2GRtZwrcQGFaV5V-5mpsoV0ClHhmivz99c0767ErscG1e8R1VXc9u4e2clN42F_vIXq4ury_GEeTu-ubi9EkygQjMjJWTFOexzQRNM64ykwigCdEkBhWzvKcZNQaEktrLFhlKZNKgA2MMTbjfIhOet3gR9dN8N-86Mo4PR5N9OpGqAxRhXimgT3u2bqpnjrwrV44n0FRmBKqzmuapjSRiqXqH2iskvBlSgJ69AudV11ThtCBChFYytUPn1lTed9A_m2WEr1qTofm9GdzgT1cK3Z2AdNv8quqAJz1wNIV8PK3kr49v-4lPwBSKqC4</recordid><startdate>201704</startdate><enddate>201704</enddate><creator>García‐Baccino, C.A.</creator><creator>Munilla, S.</creator><creator>Legarra, A.</creator><creator>Vitezica, Z.G.</creator><creator>Forneris, N.S.</creator><creator>Bates, R.O.</creator><creator>Ernst, C.W.</creator><creator>Raney, N.E.</creator><creator>Steibel, J.P.</creator><creator>Cantet, R.J.C.</creator><general>Blackwell Publishing Ltd</general><general>Wiley</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>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0001-8893-7620</orcidid><orcidid>https://orcid.org/0000-0002-3162-7258</orcidid></search><sort><creationdate>201704</creationdate><title>Estimates of the actual relationship between half‐sibs in a pig population</title><author>García‐Baccino, C.A. ; Munilla, S. ; Legarra, A. ; Vitezica, Z.G. ; Forneris, N.S. ; Bates, R.O. ; Ernst, C.W. ; Raney, N.E. ; Steibel, J.P. ; Cantet, R.J.C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4206-ab4d83f517415c39ca74e370405e2767ff0c1ba056babeb9b12694ebe37aabc33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Actual relationships</topic><topic>Animal reproduction</topic><topic>Animals</topic><topic>Breeding of animals</topic><topic>Crosses, Genetic</topic><topic>Estimates</topic><topic>estimation methods</topic><topic>Female</topic><topic>Gene loci</topic><topic>genomic selection</topic><topic>Genotype</topic><topic>Hogs</topic><topic>identity by descent</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Pedigree</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Siblings</topic><topic>Sus scrofa - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>García‐Baccino, C.A.</creatorcontrib><creatorcontrib>Munilla, S.</creatorcontrib><creatorcontrib>Legarra, A.</creatorcontrib><creatorcontrib>Vitezica, Z.G.</creatorcontrib><creatorcontrib>Forneris, N.S.</creatorcontrib><creatorcontrib>Bates, R.O.</creatorcontrib><creatorcontrib>Ernst, C.W.</creatorcontrib><creatorcontrib>Raney, N.E.</creatorcontrib><creatorcontrib>Steibel, J.P.</creatorcontrib><creatorcontrib>Cantet, R.J.C.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Journal of animal breeding and genetics (1986)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>García‐Baccino, C.A.</au><au>Munilla, S.</au><au>Legarra, A.</au><au>Vitezica, Z.G.</au><au>Forneris, N.S.</au><au>Bates, R.O.</au><au>Ernst, C.W.</au><au>Raney, N.E.</au><au>Steibel, J.P.</au><au>Cantet, R.J.C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Estimates of the actual relationship between half‐sibs in a pig population</atitle><jtitle>Journal of animal breeding and genetics (1986)</jtitle><addtitle>J Anim Breed Genet</addtitle><date>2017-04</date><risdate>2017</risdate><volume>134</volume><issue>2</issue><spage>109</spage><epage>118</epage><pages>109-118</pages><issn>0931-2668</issn><eissn>1439-0388</eissn><abstract>Summary
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half‐sibs from a cross‐bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half‐sibs.</abstract><cop>Germany</cop><pub>Blackwell Publishing Ltd</pub><pmid>27670252</pmid><doi>10.1111/jbg.12236</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-8893-7620</orcidid><orcidid>https://orcid.org/0000-0002-3162-7258</orcidid></addata></record> |
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| source | MEDLINE; Wiley Online Library All Journals |
| subjects | Actual relationships Animal reproduction Animals Breeding of animals Crosses, Genetic Estimates estimation methods Female Gene loci genomic selection Genotype Hogs identity by descent Life Sciences Male Pedigree Polymorphism, Single Nucleotide Siblings Sus scrofa - genetics |
| title | Estimates of the actual relationship between half‐sibs in a pig population |
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