Break-even cost of genotyping genetic mutations affecting economic traits in Australian pig enterprises

Abstract

If direct tests for genetic mutations affecting economic traits in pig production where available, the tests could be used to increase the accuracy of selection, using gene-assisted selection (GAS). In this paper we evaluated the increased economic returns from using a direct genetic test in the nucleus of a commercial pig enterprise. A pig population with segregating quantitative trait loci (QTL) and markers was simulated. The QTL affected four independent traits, growth index (GI), net food intake (NFI), pigs born alive (PBA) and meat quality index (MQI). A direct genetic test was assumed to be available for the QTL which contributed the greatest proportion of genetic variance for each trait. Four strategies were investigated, GAS-GI, GAS-NFI, GAS-PBA and GAS-MQI, where in each strategy genotyping was available for an identified locus affecting only the trait in the strategy name. The effect of the QTL in each case was assumed to be known without error. For each strategy, GAS was conducted in a small nucleus population of 20 sows, and selection was on an index of the four quantitative traits. Extra dollar returns from the additional genetic gain from GAS schemes were calculated using an economic model of a pig enterprise (with a 100 sow nucleus, 1000 sow multiplier tier and 10 000 sow commercial tier). Over five generations of selection, the extra returns from GAS were calculated as the discounted difference in response from GAS and non-GAS, in dollars. The extra returns were divided by the number of progeny in the nucleus each generation, multiplied by the number of generations required to fix the QTL and a discounting factor, to give the break-even cost of the genetic test. Break-even cost of test per animal were $104 for GAS-GI, $97 for GAS-NFI, $78 for GAS-PBA and $80 for GAS-MQI. While in this study a direct genetic test was assumed to be available for the mutation causing the QTL effect, results should be similar when a haplotype of markers in linkage disequilibrium with the favourable QTL allele is used in MAS.