Outliers often pose problems in analyses of data in plant breeding, but their influence on the performance of methods for estimating predictive accuracy in genomic prediction studies has not yet been evaluated. Here, we evaluate the influence of outliers on the performance of methods for accuracy estimation in genomic prediction studies using simulation. We simulated 1000 datasets for each of 1...

This study investigated the accuracy of imputation from LD (7K) to 54K panel and compared accuracy of genomic prediction with or without the X chromosome information, based on data of Nordic Holstein bulls. Beagle and Findhap were used for imputation. Averaged over two imputation datasets, the allele correct rates of imputation using Findhap were 98.2% for autosomal markers, 89.7% for markers o...

We derive a class of extended one-step methods of order m for solving delay-differential equations. This class includes methods of fourth and fifth order of accuracy. Also, the class of these methods depends on two free parameters. A convergence theorem and convergence factor of these methods are given. In addition, we investigate the stability properties of these methods. The results of the ar...

Although common datasets are an important resource for the scientific community and can be used to address important questions, genomic datasets of a meaningful size have not generally been available in livestock species. We describe a pig dataset that PIC (a Genus company) has made available for comparing genomic prediction methods. We also describe genomic evaluation of the data using methods...

Opportunities exist in beef cattle breeding to significantly increase the rates of genetic gain by increasing the accuracy of selection at earlier ages. Currently, selection of young beef bulls incorporates several economically important traits but estimated breeding values for these traits have a large range in accuracies. While there is potential to increase accuracy through increased levels ...

20 Genomic selection is rapidly becoming the state-of-the-art genetic selection 21 methodology in dairy cattle breeding schemes around the world. The objective of this 22 paper was to explore possibilities to apply genomic selection for traits related to dairy 23 cow robustness. Deterministic simulations indicate that replacing progeny testing with 24 genomic selection may favour genetic respon...

Replacement of the average numerator relationship matrix derived from the pedigree with the realized genomic relationship matrix based on DNA markers might be an attractive strategy in forest tree breeding for predictions of genetic merit. We used genotypes from 3461 single-nucleotide polymorphism loci to estimate genomic relationships for a population of 165 loblolly pine (Pinus taeda L.) indi...

Genomic prediction utilizes single nucleotide polymorphism (SNP) chip data to predict animal genetic merit. It has the advantage of potentially capturing the effects of the majority of loci that contribute to genetic variation in a trait, even when the effects of the individual loci are very small. To implement genomic prediction, marker effects are estimated with a training set, including indi...

Different methods for genomic evaluation were compared for accuracy and feasibility of evaluation using phenotypic, pedigree, and genomic information for a trait influenced by a maternal effect. A simulated population was constructed that included 15,800 animals in 5 generations. Genotypes from 45,000 SNP were available for 1,500 animals in the last 3 generations. Genotyped animals in the last ...