Approximation of reliabilities for random-regression single-step genomic best linear unbiased predictor models
Status PubMed-not-MEDLINE Language English Country United States Media electronic-ecollection
Document type Journal Article
PubMed
39650030
PubMed Central
PMC11624375
DOI
10.3168/jdsc.2023-0513
PII: S2666-9102(24)00078-4
Knihovny.cz E-resources
- Publication type
- Journal Article MeSH
Random-regression models (RRM) are used in national genetic evaluations for longitudinal traits. The outputs of RRM are an index based on random-regression coefficients and its reliability. The reliabilities are obtained from the inverse of the coefficient matrix of mixed model equations (MME). The reliabilities must be approximated for large datasets because it is impossible to invert the MME. There is no extensive literature on methods to approximate the reliabilities of RRM when genomic information is included by single-step GBLUP. We developed an algorithm to approximate such reliabilities. Our method combines the reliability of the index without genomic information with the reliability of a GBLUP model in terms of effective record contributions. We tested our algorithm in the 3-lactation model for milk yield from the Czech Republic. The data had 30 million test-day records, 2.5 million animals in the pedigree, and 54,000 genotyped animals. The correlation between our approximation and the reliabilities obtained from the inversion of the MME was 0.98, and the slope and intercept of the regression were 0.91 and 0.02, respectively. The elapsed time to approximate the reliabilities for the Czech data was 21 min.
Czech Moravian Breeders' Corporation Benešovská 123 252 09 Hradištko Czech Republic
Department of Animal and Dairy Science University of Georgia Athens GA 30602
Instituto Nacional de Investigación Agropecuaria 11500 Montevideo Uruguay
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Aguilar I., Misztal I., Johnson D.L., Legarra A., Tsuruta S., Lawlor T.J. Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score. J. Dairy Sci. 2010;93:743–752. doi: 10.3168/jds.2009-2730. 20105546. PubMed DOI
Alkhoder H., Liu Z., Segelke D., Reents R. Application of a single-step SNP BLUP random regression model to test-day yields and somatic cell scores in German Holsteins. Interbull Bull. 2022;57:74–83.
Bauer J., Přibyl J., Vostrý L. Short communication: Reliability of single-step genomic BLUP breeding values by multi-trait test-day model analysis. J. Dairy Sci. 2015;98:4999–5003. doi: 10.3168/jds.2015-9371. 25935244. PubMed DOI
Ben Zaabza H., Taskinen M., Mäntysaari E.A., Pitkänen T., Aamand G.P., Strandén I. Breeding value reliabilities for multiple-trait single-step genomic best linear unbiased predictor. J. Dairy Sci. 2022;105:5221–5237. doi: 10.3168/jds.2021-21016. 35400498. PubMed DOI
Ben Zaabza H., Van Tassell C.P., Vandenplas J., VanRaden P., Liu Z., Eding H., McKay S., Haugaard K., Lidauer M.H., Mäntysaari E.A., Strandén I. Invited review: Reliability computation from the animal model era to the single-step genomic model era. J. Dairy Sci. 2023;106:1518–1532. doi: 10.3168/jds.2022-22629. 36567247. PubMed DOI
Bermann M., Lourenco D., Cesarani A., Misztal I. Proceedings of the World Congress on Genetics Applied to Livestock Production. Rotterdam 2022. Wageningen Academic Publishers; 2022. ACCF90GS2: Software for fast approximation of reliabilities of estimated breeding values in single-step GBLUP; pp. 1523–1525.
Bermann M., Lourenco D., Misztal I. Efficient approximation of reliabilities for single-step genomic best linear unbiased predictor models with the Algorithm for Proven and Young. J. Anim. Sci. 2021;100 doi: 10.1093/jas/skab353. 34877603. PubMed DOI PMC
Boerner V., Nguyen T.T.T., Nieuwhof G.J. Integration of Interbull's multiple across-country evaluation approach breeding values into the multiple-trait single-step random regression test-day genetic evaluation for yield traits of Australian Red breeds. J. Dairy Sci. 2023;106:1159–1167. 10.3168/jds.2022-21816 PubMed DOI
Edel C., Pimentel E., Erbe M., Emmerling R., Götz K.U. Short communication: Calculating analytical reliabilities for single-step predictions. J. Dairy Sci. 2019;102:3259–3265. doi: 10.3168/jds.2018-15707. 30738687. PubMed DOI
Emamgholi Begli H., Vaez Torshizi R., Masoudi A.A., Ehsani A., Jensen J. Genomic dissection and prediction of feed intake and residual feed intake traits using a longitudinal model in F2 chickens. Animal. 2018;12:1792–1798. doi: 10.1017/S1751731117003354. PubMed DOI
Harris B., Johnson D. Approximate reliability of genetic evaluations under an animal model. J. Dairy Sci. 1998;81:2723–2728. doi: 10.3168/jds.S0022-0302(98)75829-1. 9812277. PubMed DOI
Harris B.L., Johnson D.L. Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation. J. Dairy Sci. 2010;93:1243–1252. doi: 10.3168/jds.2009-2619. 20172244. PubMed DOI
Henderson C.R. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics. 1976;32:69–83. doi: 10.2307/2529339. DOI
Interbull National genetic evaluation forms provided by countries. 2022. https://interbull.org/ib/geforms
Jamrozik J., Schaeffer L., Jansen G. Approximate accuracies of prediction from random regression models. Livest. Prod. Sci. 2000;66:85–92. doi: 10.1016/S0301-6226(00)00158-5. DOI
Kang H., Zhou L., Mrode R., Zhang Q., Liu J.F. Incorporating the single-step strategy into a random regression model to enhance genomic prediction of longitudinal traits. Heredity. 2017;119:459–467. doi: 10.1038/hdy.2016.91. 28029150. PubMed DOI PMC
Koivula M., Strandén I., Pösö J., Aamand G.P., Mäntysaari E.A. Single-step genomic evaluation using multitrait random regression model and test-day data. J. Dairy Sci. 2015;98:2775–2784. doi: 10.3168/jds.2014-8975. 25660739. PubMed DOI
Legarra A., Aguilar I., Misztal I. A relationship matrix including full pedigree and genomic information. J. Dairy Sci. 2009;92:4656–4663. doi: 10.3168/jds.2009-2061. 19700729. PubMed DOI
Liu Z., Reinhardt F., Bünger A., Reents R. Derivation and calculation of approximate reliabilities and daughter yield-deviations of a random regression test-day model for genetic evaluation of dairy cattle. J. Dairy Sci. 2004;87:1896–1907. doi: 10.3168/jds.S0022-0302(04)73348-2. 15453507. PubMed DOI
Liu Z., VanRaden P.M., Lidauer M.H., Calus M.P., Benhajali H., Jorjani H., Ducrocq V. Approximating genomic reliabilities for national genomic evaluation. Interbull Bull. 2017;51:75–85.
Lourenco D., Tsuruta S., Masuda Y., Bermann M., Legarra A., Misztal I. Proceedings of the World Congress on Genetics Applied to Livestock Production. Rotterdam 2022. Wageningen Academic Publishers; 2022. Recent updates in the BLUPF90 software suite; pp. 1530–1533.
Meyer K. Random regression analyses using B-splines to model growth of Australian Angus cattle. Genet. Sel. Evol. 2005;37:473–500. doi: 10.1186/1297-9686-37-6-473. 16093011. PubMed DOI PMC
Misztal I. Inexpensive computation of the inverse of the genomic relationship matrix in populations with small effective population size. Genetics. 2016;202:401–409. doi: 10.1534/genetics.115.182089. 26584903. PubMed DOI PMC
Misztal I., Lawlor T., Short T. Implementation of single- and multiple-trait animal models for genetic evaluation of Holstein type traits. J. Dairy Sci. 1993;76:1421–1432. doi: 10.3168/jds.S0022-0302(93)77473-1. DOI
Misztal I., Tsuruta S., Aguilar I., Legarra A., VanRaden P., Lawlor T. Methods to approximate reliabilities in single-step genomic evaluation. J. Dairy Sci. 2013;96:647–654. doi: 10.3168/jds.2012-5656. 23127903. PubMed DOI
Oliveira H.R., Brito L.F., Lourenco D., Silva F.F., Jamrozik J., Schaeffer L.R., Schenkel F.S. Advances and applications of random regression models: From quantitative genetics to genomics. J. Dairy Sci. 2019;102:7664–7683. doi: 10.3168/jds.2019-16265. 31255270. PubMed DOI
Oliveira H.R., Lourenco D., Masuda Y., Misztal I., Tsuruta S., Jamrozik J., Brito L.F., Silva F.F., Schenkel F.S. Application of single-step genomic evaluation using multiple-trait random regression test-day models in dairy cattle. J. Dairy Sci. 2019;102:2365–2377. doi: 10.3168/jds.2018-15466. 30638992. PubMed DOI
Pocrnic I., Lourenco D.A., Masuda Y., Misztal I. Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species. Genet. Sel. Evol. 2016;48:82. doi: 10.1186/s12711-016-0261-6. 27799053. PubMed DOI PMC
Quaas R.L. Computing the diagonal elements and inverse of a large numerator relationship matrix. Biometrics. 1976;32:949–953. doi: 10.2307/2529279. DOI
Schaeffer L.R. Application of random regression models in animal breeding. Livest. Prod. Sci. 2004;86:35–45. doi: 10.1016/S0301-6226(03)00151-9. DOI
Strabel T., Misztal I., Bertrand J.K. Approximation of reliabilities for multiple-trait model with maternal effects. J. Anim. Sci. 2001;79:833–839. doi: 10.2527/2001.794833x. 11325187. PubMed DOI
Tier B., Meyer K. Approximating prediction error covariances among additive genetic effects within animals in multiple-trait and random regression models. J. Anim. Breed. Genet. 2004;121:77–89. doi: 10.1111/j.1439-0388.2003.00444.x. DOI
Wang Y., Diao C., Kang H., Hao W., Mrode R., Chen J., Liu J., Zhou L. A Random regression model based on a single-step method for improving the genomic prediction accuracy of residual feed intake in pigs. Front. Genet. 2022;12 doi: 10.3389/fgene.2021.769849. 35178070. PubMed DOI PMC