基于重测序的民猪与大白猪SLAⅠ类基因多态性及抗病潜能差异分析

doi:10.11843/j.issn.0366-6964.2021.07.006

Abstract

Abstract: There are certain differences in the resistance to diseases of different pig breeds, one of the possible reasons for this difference is the diversity of swine leukocyte antigen (SLA) between different pig breeds. The study of SLA gene differences between Chinese indigenous and foreign pig breeds can provide important reference for clarifying the disease resistance mechanism of Chinese indigenous breeds. In this study, 8 healthy Min pigs and 4 Large White pigs were resequenced, and the obtained SNPs were then quality controlled for subsequent analysis. VCFtools and GEVALT softwares were used to analyze the SNP and haplotypes of SLA class I genes, and VEP tool in ENSEMBL was used to annotate SNPs, thus we can expound the diversity of SLA class I genes in two breeds at the global level. Mega software was applied to compare the sequences of nucleotide and coded amino acid of exon 2 and 3 of SLA class I classic genes of the two pig breeds. ProtParam tool and Protscale program on the Expasy server were performed to analyze the protein characteristics, and DnaSP software was used to calculate nucleotide diversity, the differences in antigen presentation ability of SLA class I classic genes between Chinese and foreign pig breeds were analyzed. The results showed that SLA class I genes of Min pigs had more SNPs and shorter haplotype blocks, and the number of missense mutations was more in Min pigs. Two alleles could be identified in exon 2 and 3 of SLA class I classic genes. The nucleotide diversity of alleles in Min pigs was higher than that in Large White pigs in the SLA class I classic genes. Moreover, Min pigs had more nucleotide and amino acid mutations at the antigen-binding site of SLA class I classic genes. The amino acids coded by SLA class Ⅰ classic genes of two pig breeds were hydrophilic, and it was more hydrophilic in Min pigs than that in Large White pigs. In summary, SLA class I genes have more polymorphisms in Min pigs. The number of base and amino acid mutations in the antigen-binding site of SLA class I classic genes of Min pigs are more than those of Large White pigs. The mutations in the ARSs of SLA class I classic gene of Min pigs detected in this study can provide a reference for the selection of pig disease resistance breeding markers.

Key words: Min pigs, Large White pigs, SLA class I genes, antigen-binding site, disease resistance

CLC Number:

S828.2

LI Jingna, SHU Ze, WU Junchao, CHENG Feng, WANG Ligang, WANG Lixian. Analysis of SLA Class Ⅰ Gene Polymorphism and Potential Disease Resistance Difference between Min Pigs and Large White Pigs Based on Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(7): 1820-1830.

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Analysis of SLA Class Ⅰ Gene Polymorphism and Potential Disease Resistance Difference between Min Pigs and Large White Pigs Based on Resequencing

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