Reliability of pedigree-based and genomic evaluations in selected populations

Background: Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations. Methods: Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified. Results: The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account. Conclusions: For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidere

The evolution of genomic imprinting:Theories, predictions and empirical tests

The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues’ kinship theory; Day and Bonduriansky’s sexual antagonism theory; and Wolf and Hager’s maternal–offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal and patrilineal relatives. The sexual antagonism and maternal–offspring coadaptation theories view genomic imprinting as a mechanism to modify the resemblance of an individual to its two parents, with imprinting evolving to increase the probability of expressing the fitter of the two alleles at a locus. In an effort to stimulate further empirical work on the topic, we carefully detail the logic and assumptions of all three theories, clarify the specific predictions of each and suggest tests to discriminate between these alternative theories for why particular genes are imprinted

HETEROSIS FOR PREWEANING TRAITS IN DEVON-HEREFORD CROSSES UNDER TEMPERATE RANGE CONDITIONS

Heterosis for gestation length. birth weight. suckling stimulus. weaning weight and preweaning growth was estimated from the first years data of a complete two-breed diallel with the Devon and Hereford breeds. involving 119 calves by 29 sires grown together under temperate grazing conditions at Gunnedah. New South Wales. Australia. Estimates of heterosis (and average mid-parent values) for gestation length were 0.2% (282.9 days); birth weight 6.5% (32.6kg); suckling stimulus 22.9% (3.51/day); weaning weight 5.9% (155.1kg); and average daily gain to weaning 7.0% (0.6kg/day)

An Efficient Method to Calculate Genomic Prediction Accuracy for New Individuals

Diagonal elements of the coefficient matrix are necessary to calculate the genomic prediction accuracy. Here an improved methodology is described, to update the inverse of the coefficient matrix (C) for new individuals with a genotype, with and without phenotypes. Computational performance is significantly improved by re-using parts of the coefficient matrix inverse calculations that do not change from one animal to another, in combination with updated calculations for those that do change. This method expedites calculation of accuracy for new individuals with genotypes, without re-doing the whole population, by using the previously calculated matrices