ArticleGenetics2010
A two-stage approximation for analysis of mixture genetic models in large pedigrees.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Contributions of linkage disequilibrium and co-segregation information to the accuracy of genomic prediction.Genetics, selection, evolution : GSE · 2016Article
- A class of Bayesian methods to combine large numbers of genotyped and non-genotyped animals for whole-genome analyses.Genetics, selection, evolution : GSE · 2014Article
- Article
- Association mapping in an elite maize breeding population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
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3 authors.
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Abstract
Information from cosegregation of marker and QTL alleles, in addition to linkage disequilibrium (LD), can improve genomic selection. Variance components linear models have been proposed for this purpose, but accommodating dominance and epistasis is not straightforward with them. A full-Bayesian analysis of a mixture genetic model is favorable in this respect, but is computationally infeasible for whole-genome analyses. Thus, we propose an approximate two-step approach that neglects information from trait phenotypes in inferring ordered genotypes and segregation indicators of markers. Quantitative trait loci (QTL) fine-mapping scenarios, using high-density markers and pedigrees of five generations without genotyped females, were simulated to test this strategy against an exact full-Bayesian approach. The latter performed better in estimating QTL genotypes, but precision of QTL location and accuracy of genomic breeding values (GEBVs) did not differ for the two methods at realistically low LD. If, however, LD was higher, the exact approach resulted in a slightly higher accuracy of GEBVs. In conclusion, the two-step approach makes mixture genetic models computationally feasible for high-density markers and large pedigrees. Furthermore, markers need to be sampled only once and results can be used for the analysis of all traits. Further research is needed to evaluate the two-step approach for complex pedigrees and to analyze alternative strategies for modeling LD between QTL and markers.
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