Piglet
diarrhea is one of the most common factors that affects the benefits of the swine industry. Although recent studies have shown that exon 2 of SLA-DQA is associated with piglet resistance to
diarrhea, contributions of genetic variation in the additional exon coding regions of this gene remain unclear. Here, we investigated variation in exons 1, 3 and 4 of the SLA-DQA gene and evaluated their effects on diarrheal
infection in 425 suckling piglets. No variation was identified in exon 1. In exon 3, there were eight alleles detected, generated by 14 single nucleotide polymorphisms (SNPs) and three
nucleotide deletions, eight SNPs being newly identified. Four allele sequences and three SNPs were identified in exon 4, only one SNP being newly identified. Statistical analysis showed that the genotypes of exon 3 are significantly associated with piglet
diarrhea; indeed, genotypes DQA*wb01/wb02 and wb04/wb05 are clearly associated with resistance to piglet
diarrhea, as they have the lowest probabilities of
infection (P < 0.05). However, no significant association was found between the genotypes of exon 4 and
diarrhea (P > 0.05). These results provide important new information concerning the level of genetic diversity at the SLA-DQA locus and suggest that further genetic association studies of piglet
diarrhea resistance should include analyses of both exons 2 and 3 of this locus.