运用SNP芯片评估马身猪保种群体的遗传结构

旨在研究马身猪保种群体的遗传多样性、亲缘关系和家系结构.本研究利用Illumina CAUPorince 50K SNP芯片检测39头保种马身猪的单核苷酸多态性(single nucleotide polymorphism,SNP);采用Plink软件计算最小等位基因频率、多态信息含量、观察杂合度和期望杂合度,分析保种...

Evaluation of Genetic Structure in Mashen Pigs Conserved Population Based on SNP Chip

The study aimed to explore the genetic diversity, relationship and family structure of Mashen pigs conserved population. Illumina CAUPorince 50 K SNP chip was used to detect the single nucleotide polymorphism (SNP) in 39 Mashen pigs. The minor allele frequency, polymorphism information content, observed heterozygosity and expected heterozygosity were calculated by Plink software to analyze the genetic diversity of conserved population. The identity by state (IBS) distance matrix was constructed and runs of homozygosity (ROH) was analyzed by Plink software. The G matrix was constructed by Gmatix software. IBS, ROH and G matrix were used to analyze the genetic relationship of conserved population. The phylogenetic tree constructed by Mega X software was used to analyze the family structure of conserved population. The result showed that 43 832 SNPs were detected in 39 Mashen pigs, and the average genotype detection rate was 0.980 1. Twenty-eight thousand eight hundred and fifty-nine SNPs met the demand of quality control, and 72.4% of which were polymorphic sites, which indicated that the SNP chip was suitable for analyzing the genetic diversity of Mashen pigs. The effective allele number, polymorphism information content and minor allele frequency were 1.563 4, 0.412, and 0.258, respectively, which indicated that the genetic diversity of Mashen pigs conserved population was abundant. The average observed heterozygosity and expected heterozygosity were 0.354 1 and 0.349 9, which suggested the conserved population of Mashen pigs had differentiated. The IBS genetic distance of 39 Mashen pigs was 0.284 2, and the IBS genetic distance of 20 breeding boars was 0.285 2. The results of IBS distance matrix and G matrix both showed that some breeding pigs had relationship with each other. Eight thousand one hundred and thirty one ROHs were detected in conserved population of Mashen pigs, 46.15% of which were between 400 and 600 Mb in length. The average inbreeding coefficient of conserved population based on ROH was 0.237, which indicated the high degree of inbreeding in conserved population. The result of phylogenetic tree showed that all individuals belonged to 3 families and the number of each family was significantly different. The genetic diversity of conserved population in Mashen pigs is abundant, but the inbreeding coefficient is high, the family of conserved population is few, and the number of individuals in each family varies greatly, which can lead to the loss of genetic diversity. Therefore, importing the new blood from the original conservation farm of Mashen pigs, expanding population size and decreasing inbreeding coefficient are essential ways in the future.