Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBL...

Understanding non-additive effects in the expression of quantitative traits is very important in genotype selection, especially in species where the commercial products are clones or hybrids. The use of molecular markers has allowed the study of non-additive genetic effects on a genomic level, in addition to a better understanding of its importance in quantitative traits. Thus, the purpose of t...

BACKGROUND Five main methods, commonly applied in genomic selection, were used to estimate the GEBV on the 15th QTLMAS workshop dataset: GBLUP, LASSO, Bayes A and two Bayes B type of methods (BBn and BBt). GBLUP is a mixed model approach where GEBV are obtained using a relationship matrix calculated from the SNP genotypes. The remaining methods are regression-based approaches where the SNP effe...

BACKGROUND With the availability of high throughput genotyping, genomic selection, the evaluation of animals based on dense SNP genotyping, is receiving more and more attention. Several statistical methods have been suggested for genomic selection. Compared to traditional selection, genomic selection can be more accurate which can lead to higher efficiency in terms of time and cost. Herein we a...

Machine learning (ML) is perhaps the most useful tool for interpretation of large genomic datasets. However, performance a single machine method in selection (GS) currently unsatisfactory. To improve predictions, we constructed stacking ensemble framework (SELF), integrating three methods, to predict estimated breeding values (GEBVs). The present study evaluated prediction ability SELF by analy...

Plant breeding populations exhibit varying levels of structure and admixture; these features are likely to induce heterogeneity of marker effects across subpopulations. Traditionally, structure has been dealt with as a potential confounder, and various methods exist to “correct” for population stratification. However, these methods induce a mean correction that does not account for heterogeneit...

Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain ...

Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-s...