ArticleBMC proceedings2012
Comparison of analyses of the XVth QTLMAS common dataset III: Genomic Estimations of Breeding Values.
Article in BMC proceedings, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed, 2 citations in OpenAlex.
- A novel genomic selection method combining GBLUP and LASSO.Genetica · 2015Article
- The importance of phenotypic data analysis for genomic prediction - a case study comparing different spatial models in rye.BMC genomics · 2014Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe QTLMAS XVth dataset consisted of pedigree, marker genotypes and quantitative trait performances of animals with a sib family structure. Pedigree and genotypes concerned 3,000 progenies among those 2,000 were phenotyped. The trait was regulated by 8 QTLs which displayed additive, imprinting or epistatic effects. The 1,000 unphenotyped progenies were considered as candidates to selection and their Genomic Estimated Breeding Values (GEBV) were evaluated by participants of the XVth QTLMAS workshop. This paper aims at comparing the GEBV estimation results obtained by seven participants to the workshop.
methodsFrom the known QTL genotypes of each candidate, two "true" genomic values (TV) were estimated by organizers: the genotypic value of the candidate (TGV) and the expectation of its progeny genotypic values (TBV). GEBV were computed by the participants following different statistical methods: random linear models (including BLUP and Ridge Regression), selection variable techniques (LASSO, Elastic Net) and Bayesian methods. Accuracy was evaluated by the correlation between TV (TGV or TBV) and GEBV presented by participants. Rank correlation of the best 10% of individuals and error in predictions were also evaluated. Bias was tested by regression of TV on GEBV.
resultsLarge differences between methods were found for all criteria and type of genetic values (TGV, TBV). In general, the criteria ranked consistently methods belonging to the same family.
conclusionsBayesian methods - A<B<C<Cπ - were the most efficient whatever the criteria and the True Value considered (with the notable exception of the MSEP of the TBV). The selection variable procedures (LASSO, Elastic Net and some adaptations) performed similarly, probably at a much lower computing cost. The TABLUP, which combines BayesB and GBLUP, generally did well. The simplest methods, GBLUP or Ridge Regression, and even worst, the fixed linear model, were much less efficient.
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