Cow genotyping strategies for genomic selection in a small dairy cattle population.

This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can improve the accuracy of genomic EBV. The Guernsey breed is a small dairy cattle breed with approximately 14,000 recorded individuals worldwide. Predictions of phenotypes of milk yield, fat yield, protein yield, and calving interval were made for Guernsey cows from England and Guernsey Island using genomic EBV, with training sets including 197 de-regressed proofs of genotyped bulls, with cows selected from among 1,440 genotyped cows using different genotyping strategies. Accuracies of predictions were tested using 10-fold cross-validation among the cows. Genomic EBV were predicted using 4 different methods: (1) pedigree BLUP, (2) genomic BLUP using only bulls, (3) univariate genomic BLUP using bulls and cows, and (4) bivariate genomic BLUP. Genotyping cows with phenotypes and using their data for the prediction of single nucleotide polymorphism effects increased the correlation between genomic EBV and phenotypes compared with using only bulls by 0.163±0.022 for milk yield, 0.111±0.021 for fat yield, and 0.113±0.018 for protein yield; a decrease of 0.014±0.010 for calving interval from a low base was the only exception. Genetic correlation between phenotypes from bulls and cows were approximately 0.6 for all yield traits and significantly different from 1. Only a very small change occurred in correlation between genomic EBV and phenotypes when using the bivariate model. It was always better to genotype all the cows, but when only half of the cows were genotyped, a divergent selection strategy was better compared with the random or directional selection approach. Divergent selection of 30% of the cows remained superior for the yield traits in 8 of 10 folds.

Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey.

As of December 2015, 2,376 Guernsey bulls and cows had genotypes from collaboration between the United States, Canada, the United Kingdom, and the Isle of Guernsey. Of those, 439 bulls and 504 cows had traditional US evaluations, which provided sufficient data to justify investigation of the possible benefits of genomic evaluation for the Guernsey breed. Evaluation accuracy was assessed using a traditional 4-yr cutoff study. Twenty-two traits were analyzed (5 yield traits, 3 functional traits, and 14 conformation traits). Mean reliability gain over that for parent average was 16.8 percentage points across traits, which compares with 8.2, 18.5, 20.0, and 32.6 percentage points reported for Ayrshires, Brown Swiss, Jerseys, and Holsteins, respectively. Highest Guernsey reliability gains were for rump width (44.5 percentage points) and dairy form (40.5 percentage points); lowest gains were for teat length (1.9 percentage points) and rear legs (side view) (2.3 percentage points). Slight reliability losses (1.5 to 4.5 percentage points) were found for udder cleft, final score, and udder depth as well as a larger loss (13.6 percentage points) for fore udder attachment. Twenty-one single nucleotide polymorphisms were identified for Guernsey breed determination and can be used in routine genotype quality control to confirm breed and identify crossbreds. No haplotypes that affect fertility were identified from the current data set. Principal component analysis showed some divergence of US and Isle of Guernsey subpopulations. However, the overlap of US, Canadian, UK, and Isle of Guernsey subpopulations indicated the presence of gene flow, and the similarities in the subpopulations supports a common genomic evaluation system across the regions.

Producing more pigs per sow per year--genetic contributions.

This review paper summarizes available knowledge on the genetic manipulation of litter size in pigs. Selection among breeds permits the exploitation of existing variation and this has already proceeded much further in Europe than in the United States. Crossbreeding strategies are available to enable the commercial herd to maximize sow productivity while ensuring carcasses acceptable to each particular market demand. These involve either the regular purchase of both replacement gilts and boars, or a high standard of management of the herd breeding program. Selection within purebred lines to increase further prolificacy seems possible, in spite of some contrary results from initial experiments. Success will only be achieved in well-designed and carefully executed programs with adequate population size that are continued for many generations. It is likely that breeders can continue to improve the potential of their stock at the commercial level, and this will be achieved by a degree of specialization between sire and dam lines.

Effectiveness of genetic selection for prolificacy in pigs.

This paper attempts to summarize and discuss the new evidence on the effectiveness of selection for prolificacy. In recent years selection between lines, and the adoption of formal cross-breeding programmes, have led to considerable improvements at a commercial level. Within-line selection has not been tackled seriously except in a few experiments. The mainly negative results from these should not lead to the conclusion that progress is impossible, but rather that it needs larger resources, applied consistently for several generations, to overcome the inherent problems. There are now many estimates of genetic parameters, based on large data sets, and these have helped to clear up some of the confusion resulting from previous inadequate material. A heritability of around 0.1, repeatability of 0.15, and fairly high genetic correlations between successive records seem justified. The negative environmental effect of being reared in a large litter is frequently present, but there is no good reason why this should seriously affect attempts to improve the trait by selection. Information from a candidate's relatives other than its dam can undoubtedly increase the accuracy with which its breeding value is estimated, but the routine use of such data in practical programmes is not straightforward. Prolificacy is only one group of traits contributing to net economic worth. The need to strike a balance between all relevant traits is explored in the particular context of a scheme based on hyperprolific sows. Finally, selection can only have lasting and cumulative effectiveness if it is applied at the top of a pyramid of improvement. Both culling and selection of replacement gilts within the commercial sector are largely irrelevant.