Selection indexes using principal component analysis for reproductive, beef and milk traits in Simmental cattle

Selection indexes in dual-purpose cattle should include beef, milk and reproductive traits. The principal component analysis is a multivariate technique that allows researchers to explore relationships between explanatory variables and traits of interest. The objective of this study was to construct selection indexes for tropical dual-purpose Simmental cattle based on principal components. The evaluated traits were weight at 8 months of age; age at first calving; cumulative first-lactation milk yield at 60, 150, 210 and 305 days; and first calving interval. The selection indexes were estimated as the sum of the products of the estimated breeding values for the seven traits times their respective eigenvectors for the first three principal components. The three selection indexes from principal components analysis generated favourable expected genetic progress for all the traits. However, a selection index with a high expected genetic progress for all traits could not be obtained. The principal component analysis allows breeders to have a selection index that simultaneously improves milk, beef and reproductive traits in dual-purpose Simmental cattle. Because a selection index yielding high expected genetic progress for all traits could not be achieved, the decision to use a specific selection index will depend on the specific conditions of the market, the local needs and the farmer preference.

Genomic prediction based on data from three layer lines: a comparison between linear methods

Background

The prediction accuracy of several linear genomic prediction models, which have previously been used for within-line genomic prediction, was evaluated for multi-line genomic prediction.

Methods

Compared to a conventional BLUP (best linear unbiased prediction) model using pedigree data, we evaluated the following genomic prediction models: genome-enabled BLUP (GBLUP), ridge regression BLUP (RRBLUP), principal component analysis followed by ridge regression (RRPCA), BayesC and Bayesian stochastic search variable selection. Prediction accuracy was measured as the correlation between predicted breeding values and observed phenotypes divided by the square root of the heritability. The data used concerned laying hens with phenotypes for number of eggs in the first production period and known genotypes. The hens were from two closely-related brown layer lines (B1 and B2), and a third distantly-related white layer line (W1). Lines had 1004 to 1023 training animals and 238 to 240 validation animals. Training datasets consisted of animals of either single lines, or a combination of two or all three lines, and had 30 508 to 45 974 segregating single nucleotide polymorphisms.

Results

Genomic prediction models yielded 0.13 to 0.16 higher accuracies than pedigree-based BLUP. When excluding the line itself from the training dataset, genomic predictions were generally inaccurate. Use of multiple lines marginally improved prediction accuracy for B2 but did not affect or slightly decreased prediction accuracy for B1 and W1. Differences between models were generally small except for RRPCA which gave considerably higher accuracies for B2. Correlations between genomic predictions from different methods were higher than 0.96 for W1 and higher than 0.88 for B1 and B2. The greater differences between methods for B1 and B2 were probably due to the lower accuracy of predictions for B1 (~0.45) and B2 (~0.40) compared to W1 (~0.76).

Conclusions

Multi-line genomic prediction did not affect or slightly improved prediction accuracy for closely-related lines. For distantly-related lines, multi-line genomic prediction yielded similar or slightly lower accuracies than single-line genomic prediction. Bayesian variable selection and GBLUP generally gave similar accuracies. Overall, RRPCA yielded the greatest accuracies for two lines, suggesting that using PCA helps to alleviate the “n ≪ p” problem in genomic prediction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0057-5) contains supplementary material, which is available to authorized users.