As our knowledge about the genetic factors affecting economically important traits increases, application of such information may add to the efficiency of pig improvement programs through extra response to selection. Commercial DNA tests have recently become available for use by US independent purebred seedstock producers. GeneSeek Inc., a commercial genotyping company in Lincoln, Nebraska has licensed the testing of numerous markers implicated to impact production efficiency of commercial pork production systems. However, the phenotypic effects of many of these markers have been evaluated in commercial crossbred populations with vastly different genetic backgrounds than that of purebred animals within US purebred seedstock herds.

The objective of this study is to examine the potential use of commercially available genetic markers in marker-assisted selection schemes employed by independent purebred seedstock producers, accomplished by the characterization of the allele segregation of commercially available markers in US purebred Duroc, Landrace, and Yorkshire populations as well as verification of the effects of commercially available DNA tests within the US purebred population. Phenotypic data and DNA samples were utilized from three different repositories representing purebred pigs. Growth performance, carcass composition, and meat quality data from the National Barrow Show Sire Progeny Test (N = 522) as well as the National Swine Registry (NSR) Pork Quality Alliance Program (N = 364) were used to evaluate associated DNA tests. Maternal records from purebred Landrace and Yorkshire females (N = 885) from the NSR national performance database were utilized to evaluate maternal DNA tests.
The potential impact of selecting for a genetic marker depends on both the magnitude of its effect and its frequency in the population. Thus, the allele frequencies provide useful information suggesting to the potential application of available DNA markers. The two maternal markers tested within the current study (ESR and EPOR) are fixed for the unfavorable allele within the Duroc breed. Therefore, these DNA tests do not provide a useful avenue for improvement of maternal performance in Durocs.
In the present study, an advantage in number born alive was observed for first-parity Yorkshire females that carry two copies of the favorable form of the ESR marker (GG). Also, a significant advantage in number born alive was also detected within Landrace females at parity 1 for the EPOR marker. Sows that inherit two copies of the C-variant of the EPOR marker were associated with approximately 2 more pigs per litter when compared to sows homozygous for the T allele. The observed litter size differences in first-parity females for each maternal marker provides an opportunity for genetic improvement of litter size within the US purebred Yorkshire and Landrace populations.
Selection for the G-variant of the MC4R marker may prove to be a useful tool for Duroc populations aimed at increased carcass leanness, as a 0.07 in. advantage in leanness was observed for pigs that carry two copies of the favorable MC4R allele in the current study. For an additional DNA marker, HMGA1, a significant difference between HMGA1 genotype classes was observed for backfat within the Duroc breed (difference between homozygote classes = 0.05 in.). The effect of HMGA1 genotype was not significant for backfat in the remaining two breeds. The CCKAR marker was also evaluated for its potential application to improvement of growth performance. The Duroc breed was fixed for the favorable CCKAR allele and was not included in the analysis. However, a significant effect was estimated within the Landrace breed for both measures of growth performance, and may prove to be a useful tool in selection programs.
Two different DNA tests were evaluated for their effects on meat and eating quality traits. The favorable form of the PRKAG3 marker was only abundant enough to effectively evaluate the DNA test within the Duroc breed. In general, PRKAG3 genotype was not found to be a significant source of variation for the meat quality measures evaluated in this study. A second DNA-based meat quality test (CAST) was also evaluated within all three breeds. Two separate markers of the same gene are currently available. Within the current study, both markers were evaluated together as a single test (haplotype). Evaluated as the number of inherited copies of the favorable allele across markers, the CAST haplotype did not significantly contribute to enhanced meat or eating quality within the current study. However, a significant difference among haplotype classes was observed for juiciness score within the Yorkshire breed, where pigs with a greater number of A alleles corresponded to increased juiciness as detected by a sensory taste panel.
As is the case with populations where maker tests are discovered, the findings of validation studies are largely dependent on the specific characteristics of the populations under evaluation, which may lead to differing results from separate populations. Therefore, before marker-assisted selection is initiated, DNA markers found to be associated with an advantage for a trait of interest need to validated within the population where selection will be conducted. In the current study, several DNA tests currently available for testing and use have been confirmed to provide significant opportunity to gain additional selection accuracy and genetic progress. On the other hand, some DNA markers implicated to have effects on economically relevant characters in previous studies were not confirmed within the present study. It is important to note, however, that lack of statistically significant associations should not be interpreted as a marker effect equal to zero. As was observed in the current study, minor allele frequencies may be so small that there is no real opportunity to effectively evaluate the DNA test.

Contact: Clint R. Schwab, Ph.D.
National Swine Registry
P.O. Box 2417
West Lafayette, IN 47996
Phone: 765-463-3594""