Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding
Identifieur interne : 000452 ( Pmc/Curation ); précédent : 000451; suivant : 000453Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding
Auteurs : Osval A. Montesinos-L Pez [Mexique] ; Abelardo Montesinos-L Pez [Mexique] ; Paulino Pérez-Rodríguez [Mexique] ; Gustavo De Los Campos [États-Unis] ; Kent Eskridge [États-Unis] ; José Crossa [Mexique]Source :
- G3: Genes|Genomes|Genetics [ 2160-1836 ] ; 2014.
Abstract
Categorical scores for disease susceptibility or resistance often are recorded in plant breeding. The aim of this study was to introduce genomic models for analyzing ordinal characters and to assess the predictive ability of genomic predictions for ordered categorical phenotypes using a threshold model counterpart of the Genomic Best Linear Unbiased Predictor (
Url:
DOI: 10.1534/g3.114.016188
PubMed: 25538102
PubMed Central: 4321037
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000452
Links to Exploration step
PMC:4321037Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding</title>
<author><name sortKey="Montesinos L Pez, Osval A" sort="Montesinos L Pez, Osval A" uniqKey="Montesinos L Pez O" first="Osval A." last="Montesinos-L Pez">Osval A. Montesinos-L Pez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1">Facultad de Telemática, Universidad de Colima, Avenida Universidad 333, Colima, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Facultad de Telemática, Universidad de Colima, Avenida Universidad 333, Colima</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Montesinos L Pez, Abelardo" sort="Montesinos L Pez, Abelardo" uniqKey="Montesinos L Pez A" first="Abelardo" last="Montesinos-L Pez">Abelardo Montesinos-L Pez</name>
<affiliation wicri:level="1"><nlm:aff id="aff2">Departamento de Estadística, Centro de Investigación en Matemáticas (CIMAT), Guanajuato, Guanajuato, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Departamento de Estadística, Centro de Investigación en Matemáticas (CIMAT), Guanajuato, Guanajuato</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Perez Rodriguez, Paulino" sort="Perez Rodriguez, Paulino" uniqKey="Perez Rodriguez P" first="Paulino" last="Pérez-Rodríguez">Paulino Pérez-Rodríguez</name>
<affiliation wicri:level="1"><nlm:aff id="aff3">Colegio de Postgraduados, Edo. de México, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Colegio de Postgraduados, Edo. de México</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<affiliation wicri:level="2"><nlm:aff id="aff4">Department of Biostatistics, University of Alabama at Birmingham, 443, Birmingham, Alabama 35294</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Alabama</region>
</placeName>
<wicri:cityArea>Department of Biostatistics, University of Alabama at Birmingham, 443, Birmingham</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Eskridge, Kent" sort="Eskridge, Kent" uniqKey="Eskridge K" first="Kent" last="Eskridge">Kent Eskridge</name>
<affiliation wicri:level="2"><nlm:aff id="aff5">Department of Statistics, University of Nebraska, Lincoln, Nebraska</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nebraska</region>
</placeName>
<wicri:cityArea>Department of Statistics, University of Nebraska, Lincoln</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Crossa, Jose" sort="Crossa, Jose" uniqKey="Crossa J" first="José" last="Crossa">José Crossa</name>
<affiliation wicri:level="1"><nlm:aff id="aff6">Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), México, D.F., México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), México, D.F.</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25538102</idno>
<idno type="pmc">4321037</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321037</idno>
<idno type="RBID">PMC:4321037</idno>
<idno type="doi">10.1534/g3.114.016188</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000452</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000452</idno>
<idno type="wicri:Area/Pmc/Curation">000452</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000452</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding</title>
<author><name sortKey="Montesinos L Pez, Osval A" sort="Montesinos L Pez, Osval A" uniqKey="Montesinos L Pez O" first="Osval A." last="Montesinos-L Pez">Osval A. Montesinos-L Pez</name>
<affiliation wicri:level="1"><nlm:aff id="aff1">Facultad de Telemática, Universidad de Colima, Avenida Universidad 333, Colima, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Facultad de Telemática, Universidad de Colima, Avenida Universidad 333, Colima</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Montesinos L Pez, Abelardo" sort="Montesinos L Pez, Abelardo" uniqKey="Montesinos L Pez A" first="Abelardo" last="Montesinos-L Pez">Abelardo Montesinos-L Pez</name>
<affiliation wicri:level="1"><nlm:aff id="aff2">Departamento de Estadística, Centro de Investigación en Matemáticas (CIMAT), Guanajuato, Guanajuato, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Departamento de Estadística, Centro de Investigación en Matemáticas (CIMAT), Guanajuato, Guanajuato</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Perez Rodriguez, Paulino" sort="Perez Rodriguez, Paulino" uniqKey="Perez Rodriguez P" first="Paulino" last="Pérez-Rodríguez">Paulino Pérez-Rodríguez</name>
<affiliation wicri:level="1"><nlm:aff id="aff3">Colegio de Postgraduados, Edo. de México, México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Colegio de Postgraduados, Edo. de México</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="De Los Campos, Gustavo" sort="De Los Campos, Gustavo" uniqKey="De Los Campos G" first="Gustavo" last="De Los Campos">Gustavo De Los Campos</name>
<affiliation wicri:level="2"><nlm:aff id="aff4">Department of Biostatistics, University of Alabama at Birmingham, 443, Birmingham, Alabama 35294</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Alabama</region>
</placeName>
<wicri:cityArea>Department of Biostatistics, University of Alabama at Birmingham, 443, Birmingham</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Eskridge, Kent" sort="Eskridge, Kent" uniqKey="Eskridge K" first="Kent" last="Eskridge">Kent Eskridge</name>
<affiliation wicri:level="2"><nlm:aff id="aff5">Department of Statistics, University of Nebraska, Lincoln, Nebraska</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Nebraska</region>
</placeName>
<wicri:cityArea>Department of Statistics, University of Nebraska, Lincoln</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Crossa, Jose" sort="Crossa, Jose" uniqKey="Crossa J" first="José" last="Crossa">José Crossa</name>
<affiliation wicri:level="1"><nlm:aff id="aff6">Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), México, D.F., México</nlm:aff>
<country xml:lang="fr" wicri:curation="lc">Mexique</country>
<wicri:regionArea>Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), México, D.F.</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">G3: Genes|Genomes|Genetics</title>
<idno type="eISSN">2160-1836</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Categorical scores for disease susceptibility or resistance often are recorded in plant breeding. The aim of this study was to introduce genomic models for analyzing ordinal characters and to assess the predictive ability of genomic predictions for ordered categorical phenotypes using a threshold model counterpart of the Genomic Best Linear Unbiased Predictor (<italic>i.e.</italic>
, TGBLUP). The threshold model was used to relate a hypothetical underlying scale to the outward categorical response. We present an empirical application where a total of nine models, five without interaction and four with genomic × environment interaction (G×E) and genomic additive × additive × environment interaction (G×G×E), were used. We assessed the proposed models using data consisting of 278 maize lines genotyped with 46,347 single-nucleotide polymorphisms and evaluated for disease resistance [with ordinal scores from 1 (no disease) to 5 (complete infection)] in three environments (Colombia, Zimbabwe, and Mexico). Models with G×E captured a sizeable proportion of the total variability, which indicates the importance of introducing interaction to improve prediction accuracy. Relative to models based on main effects only, the models that included G×E achieved 9–14% gains in prediction accuracy; adding additive × additive interactions did not increase prediction accuracy consistently across locations.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Atkinson, L" uniqKey="Atkinson L">L. Atkinson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brier, G W" uniqKey="Brier G">G. W. Brier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Burgue O, J" uniqKey="Burgue O J">J. Burgueño</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Weigel, K" uniqKey="Weigel K">K. Weigel</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Burgue O, J" uniqKey="Burgue O J">J. Burgueño</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Mahuku, G" uniqKey="Mahuku G">G. Mahuku</name>
</author>
<author><name sortKey="Dreisigacker, S" uniqKey="Dreisigacker S">S. Dreisigacker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Beyene, Y" uniqKey="Beyene Y">Y. Beyene</name>
</author>
<author><name sortKey="Kassa, S" uniqKey="Kassa S">S. Kassa</name>
</author>
<author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="Hickey, J M" uniqKey="Hickey J">J. M. Hickey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="Hickey, J" uniqKey="Hickey J">J. Hickey</name>
</author>
<author><name sortKey="Burgue O, J" uniqKey="Burgue O J">J. Burgueño</name>
</author>
<author><name sortKey="Ornella, L" uniqKey="Ornella L">L. Ornella</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Naya, H" uniqKey="Naya H">H. Naya</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Legarra, A" uniqKey="Legarra A">A. Legarra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Rosa, G J M" uniqKey="Rosa G">G. J. M. Rosa</name>
</author>
<author><name sortKey="Weigel, K" uniqKey="Weigel K">K. Weigel</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Garthwaite, P H" uniqKey="Garthwaite P">P. H. Garthwaite</name>
</author>
<author><name sortKey="Kadane, J B" uniqKey="Kadane J">J. B. Kadane</name>
</author>
<author><name sortKey="O Agan, A" uniqKey="O Agan A">A. O’Hagan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Foulley, J L" uniqKey="Foulley J">J. L. Foulley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gonzalez Camacho, J M" uniqKey="Gonzalez Camacho J">J. M. González-Camacho</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Cairns, J E" uniqKey="Cairns J">J. E. Cairns</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gonzalez Recio, O" uniqKey="Gonzalez Recio O">O. González-Recio</name>
</author>
<author><name sortKey="Forni, S" uniqKey="Forni S">S. Forni</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heffner, E L" uniqKey="Heffner E">E. L. Heffner</name>
</author>
<author><name sortKey="Sorrells, M E" uniqKey="Sorrells M">M. E. Sorrells</name>
</author>
<author><name sortKey="Jannink, J L" uniqKey="Jannink J">J.-L. Jannink</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heffner, E L" uniqKey="Heffner E">E. L. Heffner</name>
</author>
<author><name sortKey="Lorenz, A J" uniqKey="Lorenz A">A. J. Lorenz</name>
</author>
<author><name sortKey="Jannink, J L" uniqKey="Jannink J">J.-L. Jannink</name>
</author>
<author><name sortKey="Sorrells, M E" uniqKey="Sorrells M">M. E. Sorrells</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heslot, N" uniqKey="Heslot N">N. Heslot</name>
</author>
<author><name sortKey="Yang, H P" uniqKey="Yang H">H.-P. Yang</name>
</author>
<author><name sortKey="Sorrells, M E" uniqKey="Sorrells M">M. E. Sorrells</name>
</author>
<author><name sortKey="Jannink, J L" uniqKey="Jannink J">J.-L. Jannink</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jarquin, D" uniqKey="Jarquin D">D. Jarquín</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Lacaze, X" uniqKey="Lacaze X">X. Lacaze</name>
</author>
<author><name sortKey="Cheyron, P" uniqKey="Cheyron P">P. Cheyron</name>
</author>
<author><name sortKey="Daucourt, J" uniqKey="Daucourt J">J. Daucourt</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kizilkaya, K" uniqKey="Kizilkaya K">K. Kizilkaya</name>
</author>
<author><name sortKey="Tait, R G" uniqKey="Tait R">R. G. Tait</name>
</author>
<author><name sortKey="Garrick, D J" uniqKey="Garrick D">D. J. Garrick</name>
</author>
<author><name sortKey="Fernando, R L" uniqKey="Fernando R">R. L. Fernando</name>
</author>
<author><name sortKey="Reecy, J M" uniqKey="Reecy J">J. M. Reecy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kneib, T" uniqKey="Kneib T">T. Kneib</name>
</author>
<author><name sortKey="Baumgartner, B" uniqKey="Baumgartner B">B. Baumgartner</name>
</author>
<author><name sortKey="Steiner, W J" uniqKey="Steiner W">W. J. Steiner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Littell, R C" uniqKey="Littell R">R. C. Littell</name>
</author>
<author><name sortKey="Stroup, W" uniqKey="Stroup W">W. Stroup</name>
</author>
<author><name sortKey="Freund, R J" uniqKey="Freund R">R. J. Freund</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Meuwissen, T H E" uniqKey="Meuwissen T">T. H. E. Meuwissen</name>
</author>
<author><name sortKey="Hayes, B J" uniqKey="Hayes B">B. J. Hayes</name>
</author>
<author><name sortKey="Goddard, M E" uniqKey="Goddard M">M. E. Goddard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="De Los Campos, G" uniqKey="De Los Campos G">G. de los Campos</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perez Rodriguez, P" uniqKey="Perez Rodriguez P">P. Pérez-Rodríguez</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Gonzalez Camacho, J M" uniqKey="Gonzalez Camacho J">J. M. González-Camacho</name>
</author>
<author><name sortKey="Crossa, J" uniqKey="Crossa J">J. Crossa</name>
</author>
<author><name sortKey="Manes, Y" uniqKey="Manes Y">Y. Manes</name>
</author>
<author><name sortKey="Dreisigacker, S" uniqKey="Dreisigacker S">S. Dreisigacker,</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Sorensen, D A" uniqKey="Sorensen D">D. A. Sorensen</name>
</author>
<author><name sortKey="Andersen, S" uniqKey="Andersen S">S. Andersen</name>
</author>
<author><name sortKey="Gianola, D" uniqKey="Gianola D">D. Gianola</name>
</author>
<author><name sortKey="Korsgaard, I" uniqKey="Korsgaard I">I. Korsgaard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stroup, W" uniqKey="Stroup W">W. Stroup</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Villanueva, B" uniqKey="Villanueva B">B. Villanueva</name>
</author>
<author><name sortKey="Fernandez, J" uniqKey="Fernandez J">J. Fernandez</name>
</author>
<author><name sortKey="Garcia Cortes, L A" uniqKey="Garcia Cortes L">L. A. Garcia-Cortes</name>
</author>
<author><name sortKey="Varona, L" uniqKey="Varona L">L. Varona</name>
</author>
<author><name sortKey="Daetwyler, H D" uniqKey="Daetwyler H">H. D. Daetwyler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, C L" uniqKey="Wang C">C. L. Wang</name>
</author>
<author><name sortKey="Ding, X D" uniqKey="Ding X">X. D. Ding</name>
</author>
<author><name sortKey="Wang, J Y" uniqKey="Wang J">J. Y. Wang</name>
</author>
<author><name sortKey="Liu, J F" uniqKey="Liu J">J. F. Liu</name>
</author>
<author><name sortKey="Fu, W X" uniqKey="Fu W">W. X. Fu</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">G3 (Bethesda)</journal-id>
<journal-id journal-id-type="iso-abbrev">Genetics</journal-id>
<journal-id journal-id-type="hwp">G3: Genes, Genomes, Genetics</journal-id>
<journal-id journal-id-type="pmc">G3: Genes, Genomes, Genetics</journal-id>
<journal-id journal-id-type="publisher-id">G3: Genes, Genomes, Genetics</journal-id>
<journal-title-group><journal-title>G3: Genes|Genomes|Genetics</journal-title>
</journal-title-group>
<issn pub-type="epub">2160-1836</issn>
<publisher><publisher-name>Genetics Society of America</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25538102</article-id>
<article-id pub-id-type="pmc">4321037</article-id>
<article-id pub-id-type="publisher-id">GGG_016188</article-id>
<article-id pub-id-type="doi">10.1534/g3.114.016188</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Genomic Selection</subject>
</subj-group>
</article-categories>
<title-group><article-title>Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Montesinos-López</surname>
<given-names>Osval A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Montesinos-López</surname>
<given-names>Abelardo</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pérez-Rodríguez</surname>
<given-names>Paulino</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>de los Campos</surname>
<given-names>Gustavo</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Eskridge</surname>
<given-names>Kent</given-names>
</name>
<xref ref-type="aff" rid="aff5">**</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Crossa</surname>
<given-names>José</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>††</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>1</sup>
</xref>
</contrib>
<aff id="aff1"><label>*</label>
Facultad de Telemática, Universidad de Colima, Avenida Universidad 333, Colima, México</aff>
<aff id="aff2"><label>†</label>
Departamento de Estadística, Centro de Investigación en Matemáticas (CIMAT), Guanajuato, Guanajuato, México</aff>
<aff id="aff3"><label>‡</label>
Colegio de Postgraduados, Edo. de México, México</aff>
<aff id="aff4"><label>§</label>
Department of Biostatistics, University of Alabama at Birmingham, 443, Birmingham, Alabama 35294</aff>
<aff id="aff5"><label>**</label>
Department of Statistics, University of Nebraska, Lincoln, Nebraska</aff>
<aff id="aff6"><label>††</label>
Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), México, D.F., México</aff>
</contrib-group>
<author-notes><corresp id="cor1"><label>1</label>
Corresponding author: Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México, D.F., México. E-mail: <email>j.crossa@cgiar.org</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>23</day>
<month>12</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><month>2</month>
<year>2015</year>
</pub-date>
<volume>5</volume>
<issue>2</issue>
<fpage>291</fpage>
<lpage>300</lpage>
<history><date date-type="received"><day>31</day>
<month>10</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>19</day>
<month>12</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2015 Montesinos-López <italic>et al</italic>
.</copyright-statement>
<copyright-year>2015</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="291.pdf"></self-uri>
<abstract><p>Categorical scores for disease susceptibility or resistance often are recorded in plant breeding. The aim of this study was to introduce genomic models for analyzing ordinal characters and to assess the predictive ability of genomic predictions for ordered categorical phenotypes using a threshold model counterpart of the Genomic Best Linear Unbiased Predictor (<italic>i.e.</italic>
, TGBLUP). The threshold model was used to relate a hypothetical underlying scale to the outward categorical response. We present an empirical application where a total of nine models, five without interaction and four with genomic × environment interaction (G×E) and genomic additive × additive × environment interaction (G×G×E), were used. We assessed the proposed models using data consisting of 278 maize lines genotyped with 46,347 single-nucleotide polymorphisms and evaluated for disease resistance [with ordinal scores from 1 (no disease) to 5 (complete infection)] in three environments (Colombia, Zimbabwe, and Mexico). Models with G×E captured a sizeable proportion of the total variability, which indicates the importance of introducing interaction to improve prediction accuracy. Relative to models based on main effects only, the models that included G×E achieved 9–14% gains in prediction accuracy; adding additive × additive interactions did not increase prediction accuracy consistently across locations.</p>
</abstract>
<kwd-group><kwd>prediction accuracy</kwd>
<kwd>threshold model</kwd>
<kwd>disease resistance</kwd>
<kwd>GBLUP</kwd>
<kwd>genotype × environment interaction</kwd>
<kwd>GenPred</kwd>
<kwd>shared data resource</kwd>
</kwd-group>
<counts><page-count count="10"></page-count>
</counts>
<custom-meta-group><custom-meta><meta-name> DJS Export </meta-name>
<meta-value>v1</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/TelematiV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000452 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000452 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= TelematiV1 |flux= Pmc |étape= Curation |type= RBID |clé= PMC:4321037 |texte= Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:25538102" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \ | NlmPubMed2Wicri -a TelematiV1
![]() | This area was generated with Dilib version V0.6.31. | ![]() |