<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-02639642</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-23T23:35:22+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes</title>
            <author role="aut">
              <persName>
                <forename type="first">B.O.</forename>
                <surname>Fragomeni</surname>
              </persName>
              <idno type="halauthorid">1862670-0</idno>
              <affiliation ref="#struct-303339"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">D.A.L.</forename>
                <surname>Lourenco</surname>
              </persName>
              <idno type="halauthorid">1236201-0</idno>
              <affiliation ref="#struct-303339"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Shogo</forename>
                <surname>Tsuruta</surname>
              </persName>
              <idno type="halauthorid">1042448-0</idno>
              <affiliation ref="#struct-303339"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Yutaka</forename>
                <surname>Masuda</surname>
              </persName>
              <idno type="halauthorid">530815-0</idno>
              <affiliation ref="#struct-303339"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Ignacio</forename>
                <surname>Aguilar</surname>
              </persName>
              <idno type="halauthorid">1042449-0</idno>
              <affiliation ref="#struct-360987"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Andres</forename>
                <surname>Legarra</surname>
              </persName>
              <email type="md5">9b7503eeb1eabcdc91ddff2db0dc6455</email>
              <email type="domain">uscdcb.com</email>
              <idno type="idhal" notation="string">andres-legarra</idno>
              <idno type="idhal" notation="numeric">184398</idno>
              <idno type="halauthorid" notation="string">34277-184398</idno>
              <idno type="ORCID">https://orcid.org/0000-0001-8893-7620</idno>
              <idno type="IDREF">https://www.idref.fr/163703434</idno>
              <orgName ref="#struct-577435"/>
              <affiliation ref="#struct-444812"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">T.J.</forename>
                <surname>Lawlor</surname>
              </persName>
              <idno type="halauthorid">1882090-0</idno>
              <affiliation ref="#struct-1033179"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Ignacy</forename>
                <surname>Misztal</surname>
              </persName>
              <idno type="halauthorid">1042452-0</idno>
              <affiliation ref="#struct-303339"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Migration</forename>
                <surname>ProdInra</surname>
              </persName>
              <email type="md5">9e5ed7d56b52b3d4383123b1ffb42236</email>
              <email type="domain">inrae.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2020-05-28 12:36:55</date>
              <date type="whenModified">2026-03-18 14:22:02</date>
              <date type="whenReleased">2020-05-28 12:36:56</date>
              <date type="whenProduced">2015</date>
              <date type="whenEndEmbargoed">2020-05-28</date>
              <ref type="file" target="https://hal.inrae.fr/hal-02639642v1/document">
                <date notBefore="2020-05-28"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.inrae.fr/hal-02639642v1/file/2015_Fragomeni_JDS_1.pdf" id="file-2639642-2463161">
                <date notBefore="2020-05-28"/>
              </ref>
              <ref type="externalLink" target="http://www.journalofdairyscience.org/article/S0022030215002386/pdf"/>
              <fs>
                <f name="inra_publicVise_local" notation="string" n="SC">
                  <string>Scientists</string>
                </f>
              </fs>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="888556">
                <persName>
                  <forename>Migration</forename>
                  <surname>ProdInra</surname>
                </persName>
                <email type="md5">9e5ed7d56b52b3d4383123b1ffb42236</email>
                <email type="domain">inrae.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-02639642</idno>
            <idno type="halUri">https://hal.inrae.fr/hal-02639642</idno>
            <idno type="halBibtex">fragomeni:hal-02639642</idno>
            <idno type="halRefHtml">&lt;i&gt;Journal of Dairy Science&lt;/i&gt;, 2015, 98 (6), pp.4090-4094. &lt;a target="_blank" href="https://dx.doi.org/10.3168/jds.2014-9125"&gt;&amp;#x27E8;10.3168/jds.2014-9125&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Journal of Dairy Science, 2015, 98 (6), pp.4090-4094. &amp;#x27E8;10.3168/jds.2014-9125&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-2639642-2463161"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="ENSA-TOULOUSE">Ecole Nationale Supérieure Agronomique de Toulouse</idno>
            <idno type="stamp" n="INRA">INRA - Institut national de la recherche agronomique</idno>
            <idno type="stamp" n="AGREENIUM">Archive ouverte en agrobiosciences</idno>
            <idno type="stamp" n="INRAE">Institut National de Recherche en Agriculture, Alimentation et Environnement</idno>
            <idno type="stamp" n="GENETIQUE_ANIMALE">Département GA INRAE</idno>
            <idno type="stamp" n="GENPHYSE">Génétique Physiologie et Systèmes d'Elevage</idno>
            <idno type="stamp" n="INRAEOCCITANIETOULOUSE" corresp="INRAE">INRAE Occitanie Toulouse</idno>
            <idno type="stamp" n="TOULOUSE-INP">Toulouse - INP</idno>
            <idno type="stamp" n="UT3-INP">Université de Toulouse / Toulouse INP</idno>
            <idno type="stamp" n="UT3-TOULOUSEINP">Université de Toulouse / Toulouse INP</idno>
            <idno type="stamp" n="TEST3-HALCNRS">TEST3-HALCNRS</idno>
            <idno type="stamp" n="ENVT">École Nationale Vétérinaire de Toulouse </idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes</title>
                <author role="aut">
                  <persName>
                    <forename type="first">B.O.</forename>
                    <surname>Fragomeni</surname>
                  </persName>
                  <idno type="halauthorid">1862670-0</idno>
                  <affiliation ref="#struct-303339"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">D.A.L.</forename>
                    <surname>Lourenco</surname>
                  </persName>
                  <idno type="halauthorid">1236201-0</idno>
                  <affiliation ref="#struct-303339"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Shogo</forename>
                    <surname>Tsuruta</surname>
                  </persName>
                  <idno type="halauthorid">1042448-0</idno>
                  <affiliation ref="#struct-303339"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Yutaka</forename>
                    <surname>Masuda</surname>
                  </persName>
                  <idno type="halauthorid">530815-0</idno>
                  <affiliation ref="#struct-303339"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Ignacio</forename>
                    <surname>Aguilar</surname>
                  </persName>
                  <idno type="halauthorid">1042449-0</idno>
                  <affiliation ref="#struct-360987"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Andres</forename>
                    <surname>Legarra</surname>
                  </persName>
                  <email type="md5">9b7503eeb1eabcdc91ddff2db0dc6455</email>
                  <email type="domain">uscdcb.com</email>
                  <idno type="idhal" notation="string">andres-legarra</idno>
                  <idno type="idhal" notation="numeric">184398</idno>
                  <idno type="halauthorid" notation="string">34277-184398</idno>
                  <idno type="ORCID">https://orcid.org/0000-0001-8893-7620</idno>
                  <idno type="IDREF">https://www.idref.fr/163703434</idno>
                  <orgName ref="#struct-577435"/>
                  <affiliation ref="#struct-444812"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">T.J.</forename>
                    <surname>Lawlor</surname>
                  </persName>
                  <idno type="halauthorid">1882090-0</idno>
                  <affiliation ref="#struct-1033179"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Ignacy</forename>
                    <surname>Misztal</surname>
                  </persName>
                  <idno type="halauthorid">1042452-0</idno>
                  <affiliation ref="#struct-303339"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">6000</idno>
                <idno type="issn">0022-0302</idno>
                <title level="j">Journal of Dairy Science</title>
                <imprint>
                  <publisher>American Dairy Science Association</publisher>
                  <biblScope unit="volume">98</biblScope>
                  <biblScope unit="issue">6</biblScope>
                  <biblScope unit="pp">4090-4094</biblScope>
                  <date type="datePub">2015</date>
                </imprint>
              </monogr>
              <idno type="doi">10.3168/jds.2014-9125</idno>
              <idno type="prodinra">320906</idno>
              <idno type="pubmed">25864050</idno>
              <idno type="wos">000354634600050</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">single-step method</term>
                <term xml:lang="en">genomic selection</term>
                <term xml:lang="en">genomic recursion</term>
              </keywords>
              <classCode scheme="halDomain" n="sdv">Life Sciences [q-bio]</classCode>
              <classCode scheme="halDomain" n="info">Computer Science [cs]</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>The purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with &gt;5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires + cows (50,000), only cows (27,000), or sires with &gt;5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="institution" xml:id="struct-303339" status="VALID">
          <idno type="ROR">https://ror.org/00te3t702</idno>
          <orgName>University of Georgia [USA]</orgName>
          <desc>
            <address>
              <addrLine>Athens, GA 30602</addrLine>
              <country key="US"/>
            </address>
            <ref type="url">https://www.uga.edu/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-360987" status="VALID">
          <orgName>Instituto Nacional de Investigación Agropecuaria</orgName>
          <orgName type="acronym">INIA</orgName>
          <desc>
            <address>
              <addrLine>Andes 1365 - piso 12 CP. 11100 Montevideo - Uruguay</addrLine>
              <country key="UY"/>
            </address>
            <ref type="url">http://www.inia.uy/</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-444812" status="OLD">
          <orgName>Génétique Physiologie et Systèmes d'Elevage</orgName>
          <orgName type="acronym">GenPhySE</orgName>
          <date type="start">2014-01-01</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <addrLine>INRA Auzeville - 24, chemin de Borde-Rouge -Auzeville Tolosane31326 Castanet Tolosan</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://genphyse.toulouse.inra.fr/</ref>
          </desc>
          <listRelation>
            <relation name="UMR1388" active="#struct-92114" type="direct"/>
            <relation active="#struct-300421" type="direct"/>
            <relation active="#struct-448187" type="indirect"/>
            <relation active="#struct-443875" type="indirect"/>
            <relation active="#struct-301264" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-1033179" status="INCOMING">
          <orgName>Holstein Association USA</orgName>
          <desc>
            <address>
              <country key="US"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-1031275" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-92114" status="OLD">
          <idno type="ROR">https://ror.org/01x3gbx83</idno>
          <orgName>Institut National de la Recherche Agronomique</orgName>
          <orgName type="acronym">INRA</orgName>
          <date type="start">1946-05-18</date>
          <date type="end">2019-12-31</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inra.fr</ref>
          </desc>
        </org>
        <org type="regrouplaboratory" xml:id="struct-300421" status="VALID">
          <idno type="ROR">https://ror.org/03m3gzv89</idno>
          <orgName>École nationale vétérinaire de Toulouse</orgName>
          <orgName type="acronym">ENVT</orgName>
          <desc>
            <address>
              <addrLine>23 chemin des Capelles - 31076 Toulouse Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://envt.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-448187" type="direct"/>
            <relation active="#struct-443875" type="indirect"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-448187" status="VALID">
          <idno type="IdRef">026388820</idno>
          <idno type="ISNI">0000000121766169</idno>
          <idno type="ROR">https://ror.org/033p9g875</idno>
          <orgName>Institut National Polytechnique (Toulouse)</orgName>
          <orgName type="acronym">Toulouse INP</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.inp-toulouse.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-443875" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-443875" status="VALID">
          <idno type="ROR">https://ror.org/017tgbk05</idno>
          <orgName>Communauté d'universités et établissements de Toulouse</orgName>
          <orgName type="acronym">Comue de Toulouse</orgName>
          <desc>
            <address>
              <addrLine>41 Allée Jules Guesde, 31000 Toulouse</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.univ-toulouse.fr/</ref>
          </desc>
        </org>
        <org type="regrouplaboratory" xml:id="struct-301264" status="VALID">
          <idno type="ISNI">0000 0001 2182 8729</idno>
          <idno type="ROR">https://ror.org/03d5w9863</idno>
          <orgName>École nationale supérieure agronomique de Toulouse</orgName>
          <orgName type="acronym">ENSAT, INP-ENSAT, AgroToulouse, INP-AgroToulouse</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.ensat.fr/fr/index.html</ref>
          </desc>
          <listRelation>
            <relation active="#struct-448187" type="direct"/>
            <relation active="#struct-443875" type="indirect"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-1031275" status="INCOMING">
          <orgName>Partenaires INRAE</orgName>
          <desc>
            <address>
              <addrLine>Cette structure regroupe l'ensemble des structures créées pour la reprise des données ProdInra</addrLine>
              <country key="FR"/>
            </address>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>