Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins
Currently, the USDA uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for US Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type da...
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| description | Currently, the USDA uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for US Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with ST and MT models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The R2 for parent averages ranged from 10 to 34% for ST models and from 12 to 35% for MT models. The average R2 for all G were 34 and 37% for ST and MT models, respectively. All of the regression coefficients were |
| doi_str_mv | 10.3168/jds.2011-4256 |
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In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with ST and MT models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The R2 for parent averages ranged from 10 to 34% for ST models and from 12 to 35% for MT models. The average R2 for all G were 34 and 37% for ST and MT models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls’ parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for ST and MT models, respectively. When the weight for the inverse of the numerator relationship matrix (A−1) for genotyped animals was reduced from 1 to 0.7, R2 remained almost identical while the regression coefficients increased by 0.11–0.26 and 0.12–0.23 for ST and MT models, respectively. The ST models required about 5s per iteration, whereas MT models required 3 (6) min per iteration for the regular (genomic) model. The MT single-step approach is feasible for 18 linear type traits in US Holstein cattle. Accuracy for genomic evaluation increases when switching ST models to MT models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A−1 for genotyped bulls.</description><identifier>ISSN: 0022-0302</identifier><identifier>EISSN: 1525-3198</identifier><identifier>DOI: 10.3168/jds.2011-4256</identifier><identifier>PMID: 21787955</identifier><identifier>CODEN: JDSCAE</identifier><language>eng</language><publisher>New York, NY: Elsevier Inc</publisher><subject>Animal productions ; Animals ; Biological and medical sciences ; body conformation ; Breeding - methods ; breeding value ; bulls ; Cattle - genetics ; daughters ; Food industries ; Fundamental and applied biological sciences. Psychology ; gene frequency ; Genetic Association Studies - veterinary ; Genetic Variation - genetics ; Genome - genetics ; genomic evaluation ; genomics ; Genotype ; genotyping ; Holstein ; inflation ; linear type trait ; Milk and cheese industries. Ice creams ; Models, Genetic ; parents ; Phenotype ; prediction ; Quantitative Trait, Heritable ; single nucleotide polymorphism ; Terrestrial animal productions ; United States ; US Holstein ; USDA ; Vertebrates</subject><ispartof>Journal of dairy science, 2011-08, Vol.94 (8), p.4198-4204</ispartof><rights>2011 American Dairy Science Association</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c433t-9300731bd702440dd19e9e3313a2a297fb32433860ddb2f2b71dd3f489a50bb43</citedby><cites>FETCH-LOGICAL-c433t-9300731bd702440dd19e9e3313a2a297fb32433860ddb2f2b71dd3f489a50bb43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.3168/jds.2011-4256$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24362295$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21787955$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tsuruta, S.</creatorcontrib><creatorcontrib>Misztal, I.</creatorcontrib><creatorcontrib>Aguilar, I.</creatorcontrib><creatorcontrib>Lawlor, T.J.</creatorcontrib><title>Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins</title><title>Journal of dairy science</title><addtitle>J Dairy Sci</addtitle><description>Currently, the USDA uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for US Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with ST and MT models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The R2 for parent averages ranged from 10 to 34% for ST models and from 12 to 35% for MT models. The average R2 for all G were 34 and 37% for ST and MT models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls’ parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for ST and MT models, respectively. When the weight for the inverse of the numerator relationship matrix (A−1) for genotyped animals was reduced from 1 to 0.7, R2 remained almost identical while the regression coefficients increased by 0.11–0.26 and 0.12–0.23 for ST and MT models, respectively. The ST models required about 5s per iteration, whereas MT models required 3 (6) min per iteration for the regular (genomic) model. The MT single-step approach is feasible for 18 linear type traits in US Holstein cattle. Accuracy for genomic evaluation increases when switching ST models to MT models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A−1 for genotyped bulls.</description><subject>Animal productions</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>body conformation</subject><subject>Breeding - methods</subject><subject>breeding value</subject><subject>bulls</subject><subject>Cattle - genetics</subject><subject>daughters</subject><subject>Food industries</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>gene frequency</subject><subject>Genetic Association Studies - veterinary</subject><subject>Genetic Variation - genetics</subject><subject>Genome - genetics</subject><subject>genomic evaluation</subject><subject>genomics</subject><subject>Genotype</subject><subject>genotyping</subject><subject>Holstein</subject><subject>inflation</subject><subject>linear type trait</subject><subject>Milk and cheese industries. Ice creams</subject><subject>Models, Genetic</subject><subject>parents</subject><subject>Phenotype</subject><subject>prediction</subject><subject>Quantitative Trait, Heritable</subject><subject>single nucleotide polymorphism</subject><subject>Terrestrial animal productions</subject><subject>United States</subject><subject>US Holstein</subject><subject>USDA</subject><subject>Vertebrates</subject><issn>0022-0302</issn><issn>1525-3198</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10U1v1DAQBmALgei2cOQKvqCeUvwRb5IjqoAiFXEoe7Ym9mRx5bWD7VTqv8dhl3LiZI38aOx5h5A3nF1Jvu0_3Nt8JRjnTSvU9hnZcCVUI_nQPycbxoRomGTijJznfF9LLph6Sc4E7_puUGpD3LfFFzd7bEoCV-geQzw4Q_EB_ALFxUDjRL0LCImWxxnpH5fpkl3YP3EIls4_a1FJLS0UoC7Q3R29iT4XdCG_Ii8m8Blfn84Lsvv86cf1TXP7_cvX64-3jWmlLM0gGeskH23HRNsya_mAA0rJJQgQQzeNUlTYb-vVKCYxdtxaObX9AIqNYysvyOWx75zirwVz0QeXDXoPAeOSdR28rbMPvMrmKE2KOSec9JzcAdKj5kyv4eoarl7D1Wu41b89dV7GA9on_TfNCt6fAGQDfkoQjMv_XCu3Qgyre3d0E0QN-1TN7q6-o1hdUaf4OkR3FFiTenCYdDYOg0HrEpqibXT_-eRvrTmeUA</recordid><startdate>20110801</startdate><enddate>20110801</enddate><creator>Tsuruta, S.</creator><creator>Misztal, I.</creator><creator>Aguilar, I.</creator><creator>Lawlor, T.J.</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>IQODW</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>7X8</scope></search><sort><creationdate>20110801</creationdate><title>Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins</title><author>Tsuruta, S. ; Misztal, I. ; Aguilar, I. ; Lawlor, T.J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c433t-9300731bd702440dd19e9e3313a2a297fb32433860ddb2f2b71dd3f489a50bb43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Animal productions</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>body conformation</topic><topic>Breeding - methods</topic><topic>breeding value</topic><topic>bulls</topic><topic>Cattle - genetics</topic><topic>daughters</topic><topic>Food industries</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>gene frequency</topic><topic>Genetic Association Studies - veterinary</topic><topic>Genetic Variation - genetics</topic><topic>Genome - genetics</topic><topic>genomic evaluation</topic><topic>genomics</topic><topic>Genotype</topic><topic>genotyping</topic><topic>Holstein</topic><topic>inflation</topic><topic>linear type trait</topic><topic>Milk and cheese industries. Ice creams</topic><topic>Models, Genetic</topic><topic>parents</topic><topic>Phenotype</topic><topic>prediction</topic><topic>Quantitative Trait, Heritable</topic><topic>single nucleotide polymorphism</topic><topic>Terrestrial animal productions</topic><topic>United States</topic><topic>US Holstein</topic><topic>USDA</topic><topic>Vertebrates</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tsuruta, S.</creatorcontrib><creatorcontrib>Misztal, I.</creatorcontrib><creatorcontrib>Aguilar, I.</creatorcontrib><creatorcontrib>Lawlor, T.J.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of dairy science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tsuruta, S.</au><au>Misztal, I.</au><au>Aguilar, I.</au><au>Lawlor, T.J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins</atitle><jtitle>Journal of dairy science</jtitle><addtitle>J Dairy Sci</addtitle><date>2011-08-01</date><risdate>2011</risdate><volume>94</volume><issue>8</issue><spage>4198</spage><epage>4204</epage><pages>4198-4204</pages><issn>0022-0302</issn><eissn>1525-3198</eissn><coden>JDSCAE</coden><abstract>Currently, the USDA uses a single-trait (ST) model with several intermediate steps to obtain genomic evaluations for US Holsteins. In this study, genomic evaluations for 18 linear type traits were obtained with a multiple-trait (MT) model using a unified single-step procedure. The phenotypic type data on up to 18 traits were available for 4,813,726 Holsteins, and single nucleotide polymorphism markers from the Illumina BovineSNP50 genotyping Beadchip (Illumina Inc., San Diego, CA) were available on 17,293 bulls. Genomic predictions were computed with several genomic relationship matrices (G) that assumed different allele frequencies: equal, base, current, and current scaled. Computations were carried out with ST and MT models. Procedures were compared by coefficients of determination (R2) and regression of 2004 prediction of bulls with no daughters in 2004 on daughter deviations of those bulls in 2009. Predictions for 2004 also included parent averages without the use of genomic information. The R2 for parent averages ranged from 10 to 34% for ST models and from 12 to 35% for MT models. The average R2 for all G were 34 and 37% for ST and MT models, respectively. All of the regression coefficients were <1.0, indicating that estimated breeding values in 2009 of 1,307 genotyped young bulls’ parents tended to be biased. The average regression coefficients ranged from 0.74 to 0.79 and from 0.75 to 0.80 for ST and MT models, respectively. When the weight for the inverse of the numerator relationship matrix (A−1) for genotyped animals was reduced from 1 to 0.7, R2 remained almost identical while the regression coefficients increased by 0.11–0.26 and 0.12–0.23 for ST and MT models, respectively. The ST models required about 5s per iteration, whereas MT models required 3 (6) min per iteration for the regular (genomic) model. The MT single-step approach is feasible for 18 linear type traits in US Holstein cattle. Accuracy for genomic evaluation increases when switching ST models to MT models. Inflation of genomic evaluations for young bulls could be reduced by choosing a small weight for the A−1 for genotyped bulls.</abstract><cop>New York, NY</cop><pub>Elsevier Inc</pub><pmid>21787955</pmid><doi>10.3168/jds.2011-4256</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animal productions Animals Biological and medical sciences body conformation Breeding - methods breeding value bulls Cattle - genetics daughters Food industries Fundamental and applied biological sciences. Psychology gene frequency Genetic Association Studies - veterinary Genetic Variation - genetics Genome - genetics genomic evaluation genomics Genotype genotyping Holstein inflation linear type trait Milk and cheese industries. Ice creams Models, Genetic parents Phenotype prediction Quantitative Trait, Heritable single nucleotide polymorphism Terrestrial animal productions United States US Holstein USDA Vertebrates |
| title | Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins |
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