Development of a Comprehensive High Resolution SLA-1 Genotyping Method Using PCR with Genomic DNA and Characterization of New Alleles in Various Breed Pigs

The importance of swine leukocyte antigen (SLA) polymorphisms for disease resistance and susceptibility, possible association to pig production traits and implications for swine animal models has been addressed in a number of studies. Although there have been progresses in SLA typing methods, the current DNA-based typing methods still requires further improvement in the level of resolution of the typing result and usability for large scale typing. We tried to develop the gDNA-direct sequencing method for SLA-1 to replace the cDNA based typing which is relatively cumbersome to use. We designed the locus-specific PCR primers in promoter and exon 4 regions and sequencing primers in the introns 2 and 3 of SLA-1 and performed PCR amplification. The amplified products were analyzed by direct sequencing after purification. We successfully typed 432 pigs including the Korean native breed, NIH minipigs and others. From the typing, we identified a total of 52 alleles which consists of 26 previously reported and 26 newly identified. New alleles were confirmed using RT-PCR for their validity. The typing accuracy was evaluated by comparing results between previously reported cDNA- and our gDNA-based methods. The results were also confirmed by checking the pedigree segregation of alleles and heterozygote simulation test for evaluating allelic dropout. As a result, we developed a method for the specific amplification of SLA-1. The gDNA-based direct sequencing methods can be adopted as a new method for rapid typing of SLA-1 with high resolution.