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

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

不同中外猪种对疾病的抵抗能力有一定差异,原因之一是不同猪种猪白细胞抗原(swine leukocyte antigen,SLA)分子的多样性不同。本研究旨在探究中外猪种的SLA基因差异,为阐明地方猪的抗病机理提供重要参考。本研究首先对健康的8头民猪以及4头大白猪进行基因组重测序,并对所获得的SNP进一步质控用于后续分析。使用VCFtools、GEVALT软件分析SLAⅠ类基因的SNP以及单倍型,并将SNP利用ENSEMBL中的VEP工具进行注释,在全局层面阐述两个猪种的SLAⅠ类基因多样性。通过Mega软件比对两猪种的经典SLAⅠ类基因外显子2和3的核苷酸及编码氨基酸序列,利用Expasy服务器上的ProtParam工具和Protscale程序分析蛋白质特性,并利用DnaSP软件计算核苷酸多样性,分析两个猪种经典SLAⅠ类基因抗原递呈能力的差异。结果表明,民猪的SLAⅠ类基因具有更多的SNPs和长度较短的单倍型块,并且错义突变的碱基数量较多。在经典SLAⅠ类基因的外显子2和3可分别鉴定出2个等位基因,民猪在等位基因上的核苷酸多样性要明显高于大白猪,并且民猪具有更多的碱基突变以及位于抗原结合位点上的氨基酸突变。两个猪种的经典SLAⅠ类基因氨基酸表现为亲水性,民猪的亲水性要强于大白猪。综上所述,SLAⅠ类基因在民猪上有更强的多态性。民猪经典SLAⅠ类基因的碱基突变数量和抗原结合位点上氨基酸突变的数量都要多于大白猪。本研究所检测到的民猪在经典SLAⅠ类基因ARSs上的变异可为猪抗病育种标记的筛选提供参考。

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 classⅠclassic 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.