The Value of Information from Commercial Livestock in Genetic Improvement Programmes

Abstract

<p>The importance of extending trait measurement to commercial operations to improve rates of genetic improvement in breeding schemes is of increasing research interest due to the improved ability to identify and record animals using new technologies. In integrated multitiered breeding schemes, selection of commercial ewes and multiplier rams is frequently driven by soundness and overall condition of selected animals and sometimes, based on whether or not the replacement candidate was born in a multiple litter. In breeder flocks, selection is usually supported by knowledge of the genetic merit of candidates. In breeding schemes forming a part of a multi-tier integrated production system, genetic progress is disseminated from the nucleus to the commercial tier through the transfer of males. The opportunity to increase the rate of progress and reduce the genetic lag between tiers in integrated production systems might be exploited by using information from lower tiers to reduce generation interval through candidates’ selection in these tiers and to increase prediction accuracy in individuals from the nucleus.</p> <p>Through deterministic simulation this study estimated the economic benefits that can be generated in multi-tier breeding schemes by implementing performance recording in conjunction with either DNA pedigree assignment or genomic selection. The overall economic benefits of improved performance in the commercial tier, brought about by higher merit multiplier rams, offset the costs of recording the multiplier tier. The net cumulative benefit per commercial ewe over a period of 40 years ranges from $117 to $249 of additional genetic progress depending on the level of GxE and breeding objective of the production system. Applying genomic selection was the most beneficial strategy if testing costs can be reduced or by genotyping only a proportion of the selection candidates. When the cost of genotyping was reduced, i.e. from $50 to $25 per test, scenarios that combined performance recording with genomic selection were more profitable and reached breakeven point at about 10 years, as opposed to 20 years. This gain however, does not have the permanent and cumulative properties of genetic progress achieved in the nucleus flock, and so needs to be continued each year for the benefits to be maintained. Also, the strategies in which recorded multiplier ewes and rams were selected as replacements for the nucleus flock did modestly increase profitability by 2 to 5% when compared to a closed nucleus structure.</p> <p>The opportunity to expand the benefits of data recorded on commercial farm animals in livestock industries was then estimated if these data were used to improve selection accuracy of breeding nucleus individuals. In multi-tiered breeding schemes, the top tier is frequently maintained under different conditions to that of the commercial tier, which may lead to a genotype by environment interaction (GxE) that affects performance in target environments. If there is a genotype by environment interaction such that the expression of traits in the nucleus is not fully transmitted to the commercial tier, there will be an additional advantage to using commercial information for genomic prediction. With multi trait selection, both ranking and scale-type GxE may lead to significant re-ranking for overall economic merit, which can be exacerbated when economic values are different between different environments. </p> <p>The findings of our study indicate minimal evidence of significant sire re-ranking for most traits. Nevertheless, based on relatively limited data, correlations among nucleus and commercial flocks were low for weaning weight (0.79 or less) and dag score (0.85 or less). Also, the spread of EBVs and heritability estimates on other economically important traits differed significantly across environments, which infers distinct responses to selection.</p> <p>The inclusion of phenotypic and genomic data from lower tiers led to increased accuracy of prediction in the breeding tier. When trait phenotypes and genomic information from related commercial individuals were available for genetic evaluations, these could be used as training animals in genomic prediction and link a wider range of selection candidates. Our results indicate that for a genetic correlation of 0.75 between the nucleus and the commercial environment, the accuracy of prediction increased from 0.28 to 0.77 when the number of commercial individuals recorded per year increased from 0 to 2,000. This has potential to benefit larger numbers of individuals across tiers, as it allows accurate selection of candidates that perform well across environments. The extent of genomic relationships between nucleus and commercial individuals was critical to predict the improved accuracy contributed by the commercial information, as was the number of commercial individuals tested. In the presence of a substantial GxE between the nucleus and commercial tiers, the value of the commercial phenotypic records and genotypes was further enhanced.</p> <p>The objective of the final chapter was to model the potential impact of using commercial information on the additional genetic gain, relative to a typical scenario without commercial individual’s performance records, pedigree or genotype information, nor accounting of GxE. Greatest impacts were found to arise from the use of trait measurement and genotype data from commercial operations to more accurately select nucleus sires. Benefits from shortening the genetic lag between commercial and nucleus flocks through improved selection of males for use in the multiplier and commercial tiers were more modest, and the cost effectiveness was very dependent on low genotyping costs. In practice, performance records and genotypes from commercial individuals may strengthen the links between breeders and commercial farmers leading to more relevant genetic progress although novel business agreements will be required for implementation in situations where commercial tiers are separate business entities to the nucleus and/or multiplier tiers. </p>