Evaluation of marker assisted selection in pig enterprises

The profitability of using DNA markers linked to quantitative trait loci (QTL) in a pig enterprise in marker assisted selection (MAS) was evaluated, using a computer simulation of a pig population with segregating QTL and markers. The starting point for MAS was a population of pigs evolved for a large number of generations. Mutation, drift and natural selection affected both the size and frequency of segregating QTL. The QTL affected four independent traits, growth index (GI), net food intake (NFI), pigs born alive (PBA) and a meat quality index (MQI). A genome scan was conducted in the population, using a genome-wide (GW), chromosome-wide (CW) or point-wise (PW) threshold as criteria for taking QTL from the genome scan to MAS. MAS with the significant markers was conducted in a small nucleus population of 20 sows, and selection was on an index of the four quantitative traits. The extra dollar returns from the additional genetic gain from MAS 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). Returns were largest with MAS schemes using QTL detected with CW and PW thresholds. However, when the cost of genotyping per animal per marker was $4, profit (extra returns from MAS−cost of genotyping) were greatest with the GW criteria, as for this criteria the fewest markers needed to be genotyped. MAS as described in this study may be difficult to implement in commercial herds, as markers and QTL were not closely linked, and linkage phase between QTL and markers had to be established within every family. If markers could be found in linkage disequilibrium with QTL, such that marker–QTL allele associations persist across the whole population, the profitability of MAS could be increased.