Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness

Summary The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EB...

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Veröffentlicht in:Animal genetics 2014-10, Vol.45 (5), p.745-749
Hauptverfasser: Schiavo, G., Dolezal, M. A., Scotti, E., Bertolini, F., Calò, D. G., Galimberti, G., Russo, V., Fontanesi, L.
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container_end_page 749
container_issue 5
container_start_page 745
container_title Animal genetics
container_volume 45
creator Schiavo, G.
Dolezal, M. A.
Scotti, E.
Bertolini, F.
Calò, D. G.
Galimberti, G.
Russo, V.
Fontanesi, L.
description Summary The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P 
doi_str_mv 10.1111/age.12180
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A. ; Scotti, E. ; Bertolini, F. ; Calò, D. G. ; Galimberti, G. ; Russo, V. ; Fontanesi, L.</creator><creatorcontrib>Schiavo, G. ; Dolezal, M. A. ; Scotti, E. ; Bertolini, F. ; Calò, D. G. ; Galimberti, G. ; Russo, V. ; Fontanesi, L.</creatorcontrib><description>Summary The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P &lt; 0.10, and seven were significant at P &lt; 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.</description><identifier>ISSN: 0268-9146</identifier><identifier>EISSN: 1365-2052</identifier><identifier>DOI: 10.1111/age.12180</identifier><identifier>PMID: 24961592</identifier><identifier>CODEN: ANGEE3</identifier><language>eng</language><publisher>England: Blackwell Publishing Ltd</publisher><subject>Adipose Tissue ; Animals ; copy number variants ; DNA Copy Number Variations ; fat deposition ; heavy pigs ; obesity ; Polymorphism, Single Nucleotide ; single nucleotide polymorphisms ; Sus scrofa - genetics ; ZPLD1</subject><ispartof>Animal genetics, 2014-10, Vol.45 (5), p.745-749</ispartof><rights>2014 Stichting International Foundation for Animal Genetics</rights><rights>2014 Stichting International Foundation for Animal Genetics.</rights><rights>Copyright © 2014 Stichting International Foundation for Animal Genetics</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4590-98d438fe7d3e2054d34ac6047456e3e39b6c639bc6e7092d791368fc7cbed4193</citedby><cites>FETCH-LOGICAL-c4590-98d438fe7d3e2054d34ac6047456e3e39b6c639bc6e7092d791368fc7cbed4193</cites></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.12180$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fage.12180$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24961592$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schiavo, G.</creatorcontrib><creatorcontrib>Dolezal, M. A.</creatorcontrib><creatorcontrib>Scotti, E.</creatorcontrib><creatorcontrib>Bertolini, F.</creatorcontrib><creatorcontrib>Calò, D. G.</creatorcontrib><creatorcontrib>Galimberti, G.</creatorcontrib><creatorcontrib>Russo, V.</creatorcontrib><creatorcontrib>Fontanesi, L.</creatorcontrib><title>Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness</title><title>Animal genetics</title><addtitle>Anim Genet</addtitle><description>Summary The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P &lt; 0.10, and seven were significant at P &lt; 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.</description><subject>Adipose Tissue</subject><subject>Animals</subject><subject>copy number variants</subject><subject>DNA Copy Number Variations</subject><subject>fat deposition</subject><subject>heavy pigs</subject><subject>obesity</subject><subject>Polymorphism, Single Nucleotide</subject><subject>single nucleotide polymorphisms</subject><subject>Sus scrofa - genetics</subject><subject>ZPLD1</subject><issn>0268-9146</issn><issn>1365-2052</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1uEzEUhUcIRENhwQsgS2xgMa09_hsvq1BCpQgkBCo7y2PfybiZn2B7KHkVnhaHtF0gIeHFtez7nSPde4riJcFnJJ9zs4EzUpEaPyoWhApeVphXj4sFrkRdKsLESfEsxhuMcU0keVqcVEwJwlW1KH4tp90ejfPQQEA_TPBmTBH5EV0l0-cHWpuwAXTd-QRo5zcROUhgEzg0Rz9uUOc3XelgjD7t0eGnh2xne5iSd1ky9fthCrvOxyEiMzqUOvABmRgn603y04hufepQY-wWtSblvrfbEWJ8XjxpTR_hxd19Wnx9f_ll-aFcf1pdLS_WpWVc4VLVjtG6Beko5LmZo8xYgZlkXAAFqhphRa5WgMSqclLlFdWtlbYBx4iip8Wbo-8uTN9niEkPPlroezPCNEdNuBA1Z5LW_4HyvFhZKZzR13-hN9McxjzIgaq5UJjxTL09UjZMMQZo9S74wYS9JlgfstU5W_0n28y-unOcmwHcA3kfZgbOj8Ct72H_byd9sbq8tyyPCh8T_HxQmLDVQlLJ9fXHlX73DUv2ebnUlP4GMmi-Aw</recordid><startdate>201410</startdate><enddate>201410</enddate><creator>Schiavo, G.</creator><creator>Dolezal, M. A.</creator><creator>Scotti, E.</creator><creator>Bertolini, F.</creator><creator>Calò, D. G.</creator><creator>Galimberti, G.</creator><creator>Russo, V.</creator><creator>Fontanesi, L.</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</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>7TK</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>201410</creationdate><title>Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness</title><author>Schiavo, G. ; Dolezal, M. A. ; Scotti, E. ; Bertolini, F. ; Calò, D. G. ; Galimberti, G. ; Russo, V. ; Fontanesi, L.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4590-98d438fe7d3e2054d34ac6047456e3e39b6c639bc6e7092d791368fc7cbed4193</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adipose Tissue</topic><topic>Animals</topic><topic>copy number variants</topic><topic>DNA Copy Number Variations</topic><topic>fat deposition</topic><topic>heavy pigs</topic><topic>obesity</topic><topic>Polymorphism, Single Nucleotide</topic><topic>single nucleotide polymorphisms</topic><topic>Sus scrofa - genetics</topic><topic>ZPLD1</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schiavo, G.</creatorcontrib><creatorcontrib>Dolezal, M. A.</creatorcontrib><creatorcontrib>Scotti, E.</creatorcontrib><creatorcontrib>Bertolini, F.</creatorcontrib><creatorcontrib>Calò, D. G.</creatorcontrib><creatorcontrib>Galimberti, G.</creatorcontrib><creatorcontrib>Russo, V.</creatorcontrib><creatorcontrib>Fontanesi, L.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><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><collection>Nucleic Acids Abstracts</collection><jtitle>Animal genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schiavo, G.</au><au>Dolezal, M. A.</au><au>Scotti, E.</au><au>Bertolini, F.</au><au>Calò, D. G.</au><au>Galimberti, G.</au><au>Russo, V.</au><au>Fontanesi, L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness</atitle><jtitle>Animal genetics</jtitle><addtitle>Anim Genet</addtitle><date>2014-10</date><risdate>2014</risdate><volume>45</volume><issue>5</issue><spage>745</spage><epage>749</epage><pages>745-749</pages><issn>0268-9146</issn><eissn>1365-2052</eissn><coden>ANGEE3</coden><abstract>Summary The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P &lt; 0.10, and seven were significant at P &lt; 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.</abstract><cop>England</cop><pub>Blackwell Publishing Ltd</pub><pmid>24961592</pmid><doi>10.1111/age.12180</doi><tpages>5</tpages><oa>free_for_read</oa></addata></record>
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source MEDLINE; Wiley Online Library All Journals
subjects Adipose Tissue
Animals
copy number variants
DNA Copy Number Variations
fat deposition
heavy pigs
obesity
Polymorphism, Single Nucleotide
single nucleotide polymorphisms
Sus scrofa - genetics
ZPLD1
title Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness
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