Polymorphism and haplotype analyses of swine leukocyte antigen DQA exons 2, 3, 4, and their associations with piglet diarrhea in Chinese native pig

Abstract

ABSTRACT. In this study, 290 Chinese native Yantai black pig piglets were investigated to identify gene polymorphisms, for haplotype reconstruction, and to determine the association between piglet diarrhea and swine leukocyte antigen (SLA) class II DQA exons 2, 3, and 4 by polymerase chain reaction-single stranded conformational polymorphism and cloning sequencing. The results showed that the 5, 8, and 7 genotypes were identified from SLA-DQA exon 2, 3, and 4, respectively, based on the single-stranded conformational polymorphism banding patterns and found a novel allele D in exon 2 and 2 novel mutational sites of allele C (c.4828T>C) and allele F (c.4617T>C) in exon 3. Polymorphism information content testing showed that exon 2 was moderately polymorphic and that exons-3 and -4 loci were highly polymorphic. The piglet diarrhea scores for genotypes AB (1.40 ± 0.14) and AC (1.54 ± 0.17) in exon 2, AA (1.22 ± 0.32), BC (1.72 ± 0.13), DD (2015) (1.67 ± 0.35), and CF (1.22 ± 0.45) in exon 3, and AD (2.35 ± 0.25) in exon 4 were significantly higher than those for the other genotypes (P ≤ 0.05) in DQA exons. There were 14 reconstructed haplotypes in the 3 exons from 290 individuals and Hap12 may be the diarrhea-resistant gene. Haplotype distribution was extremely uneven, and the SLA-DQA gene showed genetic linkage. In this study, we identified molecular genetic markers and provided a theoretical foundation for future pig anti-disease resistance breeding.

Effect of swine leukocyte antigen‐DQA gene variation on diarrhea in Large White, Landrace, and Duroc piglets

“…This is in agreement with a previous result in Yantai Black pigs (Huang et al . ), but differs from a previous study in Bamei, Juema, and Gansu Black pigs. (Liu L.X., Gun S.B., Zhao S.G., Lu H.N., Yang Q.L., Wei T., Xie D.Q.…”

“…Huang et al . () identified six alleles (GenBank accession nos –) in 290 Yantai Black pigs, with one novel SNP (c.4617T>C) and seven SNPs that are identical to those found by (Liu L.X., Gun S.B., Zhao S.G., Lu H.N., Yang Q.L., Wei T., Xie D.Q. and Ye L.X., unpublished data).…”

“…S2a) and detected in four alleles ( DQA*wb0301 , *wb04 , *wb05 and *lw02 ), which contribute to a greater number of SLA‐DQA alleles in Large White, Landrace and Duroc pigs than those identified in local pig breeds (Huang et al . ; Liu et al . unpublished data).…”

Genetic association of sequence variation in exon 3 of the swine leukocyte antigen-DQA gene with piglet diarrhea in Large White, Landrace, and Duroc piglets

“…Liu et al (Liu LX, Gun SB, Zhao SG, Lu HN, et al, unpublished results) identified four nucleotide variants (c.4618T>C, c.4635A>G, c.4673G>A, and c.4760G>A) and three nucleotide deletions (c.4727-4729 CAG) that formed only three alleles in 471 Bamei, Juema, and Gansu Black pigs (GenBank accession Nos. KP324797-KP324799), while Huang et al (2015) identified seven polymorphic sites identical to those found by Liu et al (Liu LX, Gun SB, Zhao SG, Lu HN, et al, unpublished results) and one additional novel mutation (c.4617T>C) that formed six alleles in 290 Yantai Black pigs (GenBank accession Nos. KM485555-KM485560).…”

“…This gene contains four exons and three introns: exon 1 encodes a signal peptide, exons 2 and 3 encode corresponding external cellular a1 and a2 domains, and exon 4 encodes both the transmembrane and cytoplasmic domains. Although recent study has increased our knowledge of the association between DQA exon 2 genetic variation and piglet diarrhea (Yang et al, 2013;Huang et al, 2015;Liu et al, 2015b), it is widely accepted that polymorphic loci do not act alone in determining disease resistance, but rather as part of an intrinsic network (Stumpf, 2004;Bahlo et al, 2006). As both SLA-DRA and SLA-DRA-DQA haplotypes are linked to diarrhea resistance in Large White, Landrace, Duroc, and Yantai Black piglets (Yang et al, 2014, it is probable that variants in additional SLA-DQA exon coding regions act as a linked intrinsic network to contribute to diarrhea disease.…”