Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle
Summary Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree‐based inbreeding and to detect selection signatures using the integrated haplotype score....
Gespeichert in:
| Veröffentlicht in: | Animal genetics 2021-06, Vol.52 (3), p.251-262 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 262 |
|---|---|
| container_issue | 3 |
| container_start_page | 251 |
| container_title | Animal genetics |
| container_volume | 52 |
| creator | Gautason, E. Schönherz, A. A. Sahana, G. Guldbrandtsen, B. |
| description | Summary
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree‐based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH‐based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009–2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P |
| doi_str_mv | 10.1111/age.13058 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2510243517</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2510243517</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3538-3bc68389d215175e226b2024c9f1dc07c2c232af855bf26de43e23e0a02a0a243</originalsourceid><addsrcrecordid>eNp1kD1PwzAURS0EoqUw8AeQJRYY0trPceqOqCqlUiUWOkeO81Jc5aPYiVD_PaYpDEi85S3nHl1dQm45G_NwE73FMRdMqjMy5CKRETAJ52TIIFHRjMfJgFx5v2OMKT7ll2QghIKZ5HJINkusm8oaauvMIea23lJd59Rjiaa1TU293da67Rz6wND2HWnZGF3SXFt3oMcQXRksQypo5rptS7wmF4UuPd6c_ohsnhdv85do_bpczZ_WkRFSqEhkJlFCzXLgkk8lAiQZMIjNrOC5YVMDBgToQkmZFZDkGAsEgUwz0ExDLEbkoffuXfPRoW_TyvrQJZTBpvMpSB50IsgDev8H3TWdq0O7QAFXik2ZCtRjTxnXeO-wSPfOVtodUs7S763TsHV63Dqwdydjl1WY_5I_4wZg0gOftsTD_6b0abnolV-LcIZH</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2521880708</pqid></control><display><type>article</type><title>Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle</title><source>Wiley Online Library Journals Frontfile Complete</source><creator>Gautason, E. ; Schönherz, A. A. ; Sahana, G. ; Guldbrandtsen, B.</creator><creatorcontrib>Gautason, E. ; Schönherz, A. A. ; Sahana, G. ; Guldbrandtsen, B.</creatorcontrib><description>Summary
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree‐based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH‐based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009–2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.</description><identifier>ISSN: 0268-9146</identifier><identifier>EISSN: 1365-2052</identifier><identifier>DOI: 10.1111/age.13058</identifier><identifier>PMID: 33829515</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Animal husbandry ; Bos taurus ; Cattle ; Chromosomes ; Dairy cattle ; Genomics ; Genotypes ; Haplotypes ; Homozygosity ; Inbreeding ; integrated haplotype score ; Livestock breeding ; Pedigree ; Runs of homozygosity ; Signatures ; Single-nucleotide polymorphism</subject><ispartof>Animal genetics, 2021-06, Vol.52 (3), p.251-262</ispartof><rights>2021 Stichting International Foundation for Animal Genetics</rights><rights>2021 Stichting International Foundation for Animal Genetics.</rights><rights>Copyright © 2021 Stichting International Foundation for Animal Genetics</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3538-3bc68389d215175e226b2024c9f1dc07c2c232af855bf26de43e23e0a02a0a243</citedby><cites>FETCH-LOGICAL-c3538-3bc68389d215175e226b2024c9f1dc07c2c232af855bf26de43e23e0a02a0a243</cites><orcidid>0000-0001-7608-7577 ; 0000-0002-7343-0314 ; 0000-0002-5057-9351</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%2Fage.13058$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fage.13058$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27903,27904,45553,45554</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33829515$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gautason, E.</creatorcontrib><creatorcontrib>Schönherz, A. A.</creatorcontrib><creatorcontrib>Sahana, G.</creatorcontrib><creatorcontrib>Guldbrandtsen, B.</creatorcontrib><title>Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle</title><title>Animal genetics</title><addtitle>Anim Genet</addtitle><description>Summary
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree‐based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH‐based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009–2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.</description><subject>Animal husbandry</subject><subject>Bos taurus</subject><subject>Cattle</subject><subject>Chromosomes</subject><subject>Dairy cattle</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Haplotypes</subject><subject>Homozygosity</subject><subject>Inbreeding</subject><subject>integrated haplotype score</subject><subject>Livestock breeding</subject><subject>Pedigree</subject><subject>Runs of homozygosity</subject><subject>Signatures</subject><subject>Single-nucleotide polymorphism</subject><issn>0268-9146</issn><issn>1365-2052</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp1kD1PwzAURS0EoqUw8AeQJRYY0trPceqOqCqlUiUWOkeO81Jc5aPYiVD_PaYpDEi85S3nHl1dQm45G_NwE73FMRdMqjMy5CKRETAJ52TIIFHRjMfJgFx5v2OMKT7ll2QghIKZ5HJINkusm8oaauvMIea23lJd59Rjiaa1TU293da67Rz6wND2HWnZGF3SXFt3oMcQXRksQypo5rptS7wmF4UuPd6c_ohsnhdv85do_bpczZ_WkRFSqEhkJlFCzXLgkk8lAiQZMIjNrOC5YVMDBgToQkmZFZDkGAsEgUwz0ExDLEbkoffuXfPRoW_TyvrQJZTBpvMpSB50IsgDev8H3TWdq0O7QAFXik2ZCtRjTxnXeO-wSPfOVtodUs7S763TsHV63Dqwdydjl1WY_5I_4wZg0gOftsTD_6b0abnolV-LcIZH</recordid><startdate>202106</startdate><enddate>202106</enddate><creator>Gautason, E.</creator><creator>Schönherz, A. A.</creator><creator>Sahana, G.</creator><creator>Guldbrandtsen, B.</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TK</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7608-7577</orcidid><orcidid>https://orcid.org/0000-0002-7343-0314</orcidid><orcidid>https://orcid.org/0000-0002-5057-9351</orcidid></search><sort><creationdate>202106</creationdate><title>Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle</title><author>Gautason, E. ; Schönherz, A. A. ; Sahana, G. ; Guldbrandtsen, B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3538-3bc68389d215175e226b2024c9f1dc07c2c232af855bf26de43e23e0a02a0a243</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animal husbandry</topic><topic>Bos taurus</topic><topic>Cattle</topic><topic>Chromosomes</topic><topic>Dairy cattle</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Haplotypes</topic><topic>Homozygosity</topic><topic>Inbreeding</topic><topic>integrated haplotype score</topic><topic>Livestock breeding</topic><topic>Pedigree</topic><topic>Runs of homozygosity</topic><topic>Signatures</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gautason, E.</creatorcontrib><creatorcontrib>Schönherz, A. A.</creatorcontrib><creatorcontrib>Sahana, G.</creatorcontrib><creatorcontrib>Guldbrandtsen, B.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Animal genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gautason, E.</au><au>Schönherz, A. A.</au><au>Sahana, G.</au><au>Guldbrandtsen, B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle</atitle><jtitle>Animal genetics</jtitle><addtitle>Anim Genet</addtitle><date>2021-06</date><risdate>2021</risdate><volume>52</volume><issue>3</issue><spage>251</spage><epage>262</epage><pages>251-262</pages><issn>0268-9146</issn><eissn>1365-2052</eissn><abstract>Summary
Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree‐based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH‐based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009–2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33829515</pmid><doi>10.1111/age.13058</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0001-7608-7577</orcidid><orcidid>https://orcid.org/0000-0002-7343-0314</orcidid><orcidid>https://orcid.org/0000-0002-5057-9351</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0268-9146 |
| ispartof | Animal genetics, 2021-06, Vol.52 (3), p.251-262 |
| issn | 0268-9146 1365-2052 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2510243517 |
| source | Wiley Online Library Journals Frontfile Complete |
| subjects | Animal husbandry Bos taurus Cattle Chromosomes Dairy cattle Genomics Genotypes Haplotypes Homozygosity Inbreeding integrated haplotype score Livestock breeding Pedigree Runs of homozygosity Signatures Single-nucleotide polymorphism |
| title | Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-25T02%3A53%3A36IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genomic%20inbreeding%20and%20selection%20signatures%20in%20the%20local%20dairy%20breed%20Icelandic%20Cattle&rft.jtitle=Animal%20genetics&rft.au=Gautason,%20E.&rft.date=2021-06&rft.volume=52&rft.issue=3&rft.spage=251&rft.epage=262&rft.pages=251-262&rft.issn=0268-9146&rft.eissn=1365-2052&rft_id=info:doi/10.1111/age.13058&rft_dat=%3Cproquest_cross%3E2510243517%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2521880708&rft_id=info:pmid/33829515&rfr_iscdi=true |