利用SNP标记分析淳安花猪群体遗传多样性和群体结构

Analysis of Genetic Diversity and Genetic Structure in Chun'an Spotted Pigs Conserved Population Based on SNP Chip

利用Illumina CAUPorcine 50K SNP芯片检测54头淳安花猪的单核苷酸多态性(SNP),分析群体遗传多样性和群体结构。结果显示,共检测到44739个SNP位点,个体的平均基因型检出率为98.49%;通过质控的SNP位点有32713个,其中54.3%具有多态性;平均有效等位基因数为1.355,平均多态信息含量为0.193,最小等位基因频率平均为0.143;平均观察杂合度为0.254,平均期望杂合度为0.257;平均IBS(状态同源)遗传距离为0.2129,其中公猪为0.2339;ROH(基因组长度纯合片段)共有2646个,65%的长度在400~700 Mb之间,平均近交系数为0.199;54头淳安花猪可划分为6个家系,各家系的个体数量差异明显。综上所述,淳安花猪保种群体的杂合度低,近交程度高,家系少,各家系的个体数量差异大,容易引起遗传多样性的丢失。在后续保种过程中,应根据划分的家系进行选种选配或引入血统,以确保淳安花猪遗传资源的长期保护。

In order to explore the genetic diversity and family structure of Chun'an spotted pigs conserved population,Illumina CAUPorcine 50K SNP chip was used to detect the single nucleotide polymorphism(SNP)in 54 Chun'an spotted pigs.The result showed that 44739 SNPs were detected in 54 Chun'an spotted pigs,and the average genotype detection rate was 98.49%.32713 SNPs met the demand of quality control,and 54.3%of which were polymorphic sites.The average effective allele number,polymorphic information content and average minor allele frequency were 1.355,0.193 and 0.143,respectively.The average observed heterozygosity and expected heterozygosity were 0.254 and 0.257.The average IBS genetic distance of whole 54 Chun'an spotted pigs was 0.2129,and the IBS genetic distance of breeding boars was 0.2339.2646 ROHs were detected in Chun'an spotted pigs,65%of which were between 400~700 Mb in length.The average inbreeding coefficient of conserved population based on ROH was 0.199.All the individuals belonged to 6 families and the number of each family was significantly different.In conclusion,the heterozygosity of conserved population in Chun'an pigs is low,the inbreeding coefficient is high,the family of conserved population is few,and the number of individuals varies greatly among different families,which can easily lead to the loss of genetic diversity.In order to ensure the long-term protection of genetic resources of Chun'an spotted pigs,it is necessary to select and match the breeds according to the families,and try to introduce new family to the conserved population.