SNPs And Haplotypes Of SLA-DQA Gene And Association Of SNPs With Some Production And Immune Traits

The Swine Leucocyte Antigen (SLA) complex is a chromosomal region consisting of series of closely linked loci and locating on chromosome 7, which have highly polymorphism and encode the major histocompatibility antigen, and play a central role in the immune system. In the long time, many researchers regard SLA genes as the candidate genes for disease resistance breeding, and a large number of studies revealed that the SLA complex is associated with the immune response, disease sensitivity and some economic traits. In this research, the polymorphisms of a moderate polymorphic gene, SLA-DQA, were detected using the method of direct sequencing, cloned sequencing and PCR-RFLP in Large White pigs, Landrace pigs, and Tongcheng pigs. Also their association with immune traits and production traits was analyzed. The results are as follows:1. The coding sequence of Tongcheng pigs was cloned using the method of RT-PCR. A novel SNP at the nucleotide 722 were found through comparing the cloned sequence and the sequence of SLA-DQA in GenBank. The nucleotide conversion from A to G in this novel SNP caused the amino acid changed from Gly to Arg and bring the recognition site of restriction endonuclease Taq I.2. Through direct sequencing of RT-PCR products, the polymorphisms of DQA encoding sequnce were studied in Large White pigs, Landrace pigs, and Tongcheng pigs. The results showed that 45 (29P+16S), 39 (25P+14S), and 59 (45P+14S) variant sites were correspondingly detected in Large White pigs, Landrace pigs, and Tongcheng pigs. At the same time, integrating cloning sequence, the condon usage, polymorphism distribution in domain, and the alleles of kinds were analyzed.3. The polymorphic sites which have polymorphism in three breeds, including 46, 169 46, 169, 209, 264, 274, 285, 294, 299, 331, 355, 372, 410, were choosed for association analysis with partial immune traits and production traits. The results are as follows: SNP at the nucleotide 46 (ACC→GCC) polymorphism have significant effect on MCV,DP (P<0.05), and the effect on ABF is also near to significant(P=0.063); SNP at the nucleotide 169(GAA→CAA)have significant effects on LMA, Proportion of lean and bone of the ham; SNP at the nucleotide 274(TTA→GCA/GGA)have effects on DTH, IgG , Percentage of leaf and caul fat, LMA, LFP, Ham, Proportion of lean and bone of the ham; SNP at the nucleotide 285 have effects on DTH, Percentage of leaf and caul fat, LMA, LFP, Ham; SNP at the nucleotide 294 (ATT→ATC) have effects on WBC, IgG, ,LAM, tenderness ; SNP at the nucleotide 299 (ACT→ATT) have effects on DTH,LAM; SNP at the nucleotide 331 (CAG→AAG) have effects on WBC, 6-7BF,tenderness; SNP at the nucleotide 355 (TCO~CCC) have effects on DTH and LAM; SNP at the nucleotide 372 have effects on DTH, Percentage of leaf and caul fat, LAM, LFP, Ham; SNP at the nucleotide 410 have effects on Percentage of leaf and caul fat, LFP, Ham, MCS; no any correlation with immune traits and production traits were detected at position 209 and 264 .4. In the experimental population constructed by our Lab and animal husbandry bureau of Tongcheng, the association was analyzed between the nucleotide 722 Taq /-RFLP polymorphism and production traits, and the result displayed that there are significant differences of different genotypes on percentage of leaf and caul fat, avg. backfat at 3 points and backfat thickness (depth) between 6th and 7th ribs (P<0.05).5. The Taq /-RFLP polymorphism at nucleotide 722 were detected in Lantang pig, Qingping pigs, Tibet pigs, Min pigs, Xiaomeishan pigs, Exi black pigs and Large white pigs. The x 2 test on genotype frequency revealed that there was significant difference between Tibet Pigs and Ming Pigs, Tibet Pigs and Lantang Pigs, and E'xi black pigs and Qingping pigs (P<0.05);The genotype of E'xi black pig were very significant difference with Min Pigs and Qingping Pigs, Xiaomeishan Pigs also showed very significant difference to other five indigenous breeds (P<0.01).