Analysis of DNA polymorphisms in the swine major histocompatibility complex (MHC) class I genes

Performance data and blood samples from 70 Duroc and 38 Hampshire boars were collected from the 1986-87 national boar performance test of each breed. These boars represented a total of 97 litters from 73 farms. Few boars were inbred. The objectives of the study were: (1) to characterize the swine MHC class I genes by using restriction fragment length polymorphisms (RFLPs), (2) to determine the genetic variability within and between two breeds based on RFLPs of swine MHC class I genes and (3) to investigate the association between RFLP patterns of swine MHC class I genes and production traits in Duroc and Hampshire boars.;Genomic DNA was isolated from the white blood cells. Southern blotting and hybridization procedures were performed by using three different endonucleases and a swine MHC class I probe (PD1-A). The patterns of RFLPs of the two breeds showed a high degree of polymorphism and very few patterns were identical.;Jaccard coefficients, a similarity index, were used to measure the similarity between two RFLP patterns. Average Jaccard coefficients for each breed indicated that the similarity within breeds was higher than that between the two breeds and that the similarity within the Hampshire breed was higher than within the Duroc breed.;Nucleotide diversity, the average number of nucleotide differences per site between two DNA sequences, was calculated from RFLP patterns to measure the variability between two DNA sequences through RFLP patterns. The nucleotide diversity calculated within breed was lower than that between the two breeds and the diversity of Hampshire boars was lower than that of Duroc boars.;Least squares procedures and stepwise regression methods revealed that the associations exist between certain DNA restriction fragments and the selection index (INDEX), average daily gain (ADG), average backfat thickness (BF), loin muscle area (LEA) and age at 230 pounds (DAY230). These results suggest an association between swine MHC class I genes and performance traits in swine. Their use as genetic markers has potential for improving pig performance.