Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP.
ABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compat...
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2023
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| Online Access: | https://ainfo.inia.uy/consulta/busca?b=pc&id=63528&biblioteca=vazio&busca=63528&qFacets=63528 |
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| _version_ | 1868889998996013056 |
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| author | MCWHORTER, T.M. |
| author2 | BERMANN, M. GARCIA, A.L.S. LEGARRA, A. AGUILAR, I. MISZTAL, I. LOURENCO, D. |
| author2_role | author author author author author author |
| author_browse | AGUILAR, I. BERMANN, M. GARCIA, A.L.S. LEGARRA, A. LOURENCO, D. MCWHORTER, T.M. MISZTAL, I. |
| author_facet | MCWHORTER, T.M. BERMANN, M. GARCIA, A.L.S. LEGARRA, A. AGUILAR, I. MISZTAL, I. LOURENCO, D. |
| author_role | author |
| collection | AINFO |
| dc.creator.none.fl_str_mv | MCWHORTER, T.M. BERMANN, M. GARCIA, A.L.S. LEGARRA, A. AGUILAR, I. MISZTAL, I. LOURENCO, D. |
| dc.date.none.fl_str_mv | 2023 2025-06-23T18:24:27Z 2025-06-23T18:24:27Z 2025-06-23T18:24:27Z |
| dc.identifier.none.fl_str_mv | https://ainfo.inia.uy/consulta/busca?b=pc&id=63528&biblioteca=vazio&busca=63528&qFacets=63528 |
| dc.language.none.fl_str_mv | en eng |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Acceso abierto |
| dc.source.none.fl_str_mv | reponame:AINFO instname:Instituto Nacional de Investigación Agropecuaria instacron:Instituto Nacional de Investigación Agropecuaria |
| dc.subject.none.fl_str_mv | Genetic base Indirect predictions Residual polygenic effect Scaling of genomic matrices Single-step genomic best linear unbiased prediction |
| dc.title.none.fl_str_mv | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| dc.type.none.fl_str_mv | Article PublishedVersion info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | ABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_30566204b1a10fa0ef8bfe03be07b044 |
| instacron_str | Instituto Nacional de Investigación Agropecuaria |
| institution | Instituto Nacional de Investigación Agropecuaria |
| instname_str | Instituto Nacional de Investigación Agropecuaria |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/4224 |
| publishDate | 2023 |
| publishDateSort | 2023 |
| reponame_str | AINFO |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Acceso abierto |
| spelling | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP.MCWHORTER, T.M.BERMANN, M.GARCIA, A.L.S.LEGARRA, A.AGUILAR, I.MISZTAL, I.LOURENCO, D.Genetic baseIndirect predictionsResidual polygenic effectScaling of genomic matricesSingle-step genomic best linear unbiased predictionABSTRACT.- Single-step genomic BLUP (ssGBLUP) relies on the combination of the genomic ((Formula presented.)) and pedigree relationship matrices for all ((Formula presented.)) and genotyped ((Formula presented.)) animals. The procedure ensures (Formula presented.) and (Formula presented.) are compatible so that both matrices refer to the same genetic base (?tuning?). Then (Formula presented.) is combined with a proportion of (Formula presented.) (?blending?) to avoid singularity problems and to account for the polygenic component not accounted for by markers. This computational procedure has been implemented in the reverse order (blending before tuning) following the sequential research developments. However, blending before tuning may result in less optimal tuning because the blended matrix already contains a proportion of (Formula presented.). In this study, the impact of ?tuning before blending? was compared with ?blending before tuning? on genomic estimated breeding values (GEBV), single nucleotide polymorphism (SNP) effects and indirect predictions (IP) from ssGBLUP using American Angus Association and Holstein Association USA, Inc. data. Two slightly different tuning methods were used; one that adjusts the mean diagonals and off-diagonals of (Formula presented.) to be similar to those in (Formula presented.) and another one that adjusts based on the average difference between all elements of (Formula presented.) and (Formula presented.). Over 6 million Angus growth records and 5.9 million Holstein udder depth records were available. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Average realized relationship estimates among groups of animals were similar across scenarios. Scatterplots show that GEBV, SNP effects and IP did not noticeably change for all animals in the evaluation regardless of the order of computations and when using blending parameter of 0.05. Formulas were derived to determine the blending parameter that maximizes changes in the genomic relationship matrix and GEBV when changing the order of blending and tuning. Algebraically, the change is maximized when the blending parameter is equal to 0.5. Overall, tuning (Formula presented.) before blending, regardless of blending parameter used, had a negligible impact on genomic predictions and SNP effects in this study. © 2022 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.2025-06-23T18:24:27Z2025-06-23T18:24:27Z20232025-06-23T18:24:27ZArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://ainfo.inia.uy/consulta/busca?b=pc&id=63528&biblioteca=vazio&busca=63528&qFacets=63528reponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación Agropecuariaenenginfo:eu-repo/semantics/openAccessAcceso abiertooai:redi.anii.org.uy:20.500.12381/42242026-02-10T17:35:44Z |
| spellingShingle | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. MCWHORTER, T.M. Genetic base Indirect predictions Residual polygenic effect Scaling of genomic matrices Single-step genomic best linear unbiased prediction |
| status_str | publishedVersion |
| title | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| title_full | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| title_fullStr | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| title_full_unstemmed | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| title_short | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| title_sort | Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. |
| topic | Genetic base Indirect predictions Residual polygenic effect Scaling of genomic matrices Single-step genomic best linear unbiased prediction |
| url | https://ainfo.inia.uy/consulta/busca?b=pc&id=63528&biblioteca=vazio&busca=63528&qFacets=63528 |