BPI基因生物信息学分析及其在不同猪群体中的遗传变异情况

Bioinformatics analysis of pig BPI gene and its genetic variation in different populations

【目的】明确猪杀菌性/通透性增加蛋白(BPI)基因中可能存在的SNP位点,并探讨BPI基因外显子10在上海地区5个猪群体中的多态性及其与抗病相关的优势基因型,为揭示BPI基因在仔猪腹泻抗病机制中的作用及开展猪抗病育种提供理论依据。【方法】采用在线生物信息学软件分别从碱基序列、SNP位点和蛋白氨基酸序列等角度比对分析猪BPI基因全长cDNA序列与电子克隆序列的差异,采用PCR-RFLP检测分析猪BPI基因外显子10的多态性,并检测BPI基因外显子10在杜洛克、长白、大白、申农和梅山猪群体中的基因型及基因频率。【结果】猪BPI基因电子克隆编码区(CDS)序列长度1452 bp,编码483个氨基酸,存在44个SNP位点,其中22个为同义SNP位点、22个为非同义SNP位点。猪BPI基因全长cDNA序列(EF436278.1和FJ810853.1)与电子克隆序列相比存在14处碱基差异,而对应的翻译蛋白序列存在4处氨基酸差异。猪BPI基因外显子10存在AA、BB和AB 3种基因型,各基因型在杜洛克猪、长白猪、大白猪、申农猪和梅山猪群体中的分布情况各不相同。在杜洛克猪群体中AA基因型和AB基因型呈中度多态分布(0.404和0.416),BB基因型检出比例较低(0.180);在长白猪和申农猪群体中均未检测出AA基因型,BB基因型检出比例较高,而AB基因型检出比例较低;在大白猪和梅山猪群体中均以BB基因型检出比例较高,AB基因型次之,AA基因型检出比例最低。总体来看,除了杜洛克猪群体的A等位基因频率较高外,其他4个猪群体均以B等位基因频率较高。【结论】猪BPI基因外显子10 AA基因型频率在杜洛克猪群体中最高,在大白猪和梅山群体中较低,在长白猪和申农猪群体中未检出,即AA基因型在杜洛克猪群体中比例高与其仔猪腹泻发病率低的情况一致。因此,在大白猪和梅山猪育种过程中需提高AA基因型比例,而在长白猪和申农猪育种过程中需引进AA基因型个体,降低BB和AB基因型比例,以增加仔猪的抗病能力。

【Objective】To clarify the possible SNP loci in pig bactericidal/permeability-increasing protein(BPI)gene and to explore the polymorphism of exon 10 of BPI gene in five pig populations in Shanghai and its dominant genotype related to disease resistance,so as to provide theoretical basis for function of BPI gene in diarrhea disease resistance of piglets and disease resistant pig breeding.【Method】Online bioinformatics software was used to analyze the difference between the full-length cDNA sequence of pig BPI gene and the electronic clone sequence,and the comparative analysis was conducted from the perspectives of base sequence,SNP loci and protein amino acid sequence,etc.The polymorphism of exon 10 of pig BPI gene was analyzed by PCR-RFLP,and the genotypes and gene frequencies of BPI gene in Duroc pig,Landrace pig,Large White pig,Shennongpig and Meishan pig populations were detected.【Result】The sequence length of the electronic clone sequence coding region(CDS)of pig BPI gene was 1452 bp,encoding 483 amino acids.It has been reported that there were 44 SNP loci,including 22 mutations of synonym and 22 non-synonymous mutations.The full-length cDNA sequence of pig BPI gene(EF436278.1 and FJ810853.1)showed 14 base differences compared with the electronic clone sequence,and the corresponding translation protein sequence showed four amino acid differences.The exon 10 of BPI gene in pig had three genotypes(AA,BB and AB),the distribution of them were different in Duroc pig,Landrace pig,Large White pig,Shennong pig and Meishan pig populations.AA genotype and AB genotype in Duroc pig showed moderate polymorphic distribution(0.404 and 0.416),while the proportion of BB genotype was low(0.180).AA genotype was not detected in Landrace pig and Shennong pig,BB genotype was highly detected,and AB genotype proportion was low.The proportion of BB genotype was high in Large White pig and Meishan pig,while the proportion of AB genotype was lower and the proportion of AA genotype was the lowest.In general,except for the high proportion of A allele in Durocpig,the high proportion of B allele in other four pig populations were observed.【Conclusion 】There are three genotypes of AA,BB and AB in exon 10 of pig BPI gene,the frequency of AA genotype is the highest in Duroc pig,the proportion of AA genotype in Large White pig and Meishan groups is low,and no AA genotypeis detected in Landrace pig and Shennong pig.This indicates that the high proportion of AA genotype in Duroc pig is consistent with the low incidence of diarrhea in Duroc pig.Therefore,in the process of Large White pig and Meishan pig breeding,the proportion of AA genotype should be increased,and in the process of Landrace pig and Shennong pig breeding,the AA genotype should be added into the population,which reduces the AB and BB genotypes,so as to increase the disease resistance of piglets.