近交陆川猪的遗传稳定性研究

旨在探讨高度近交陆川猪的遗传稳定性。本试验采集20头近交和6头非近交陆川猪的耳组织样品进行个体基因组重测序，通过扫描全基因组SNPs分析近交陆川猪群体的遗传多样性，并基于基因组纯合度挖掘近交陆川猪群体中特异的纯合区域（region of homozygosity，ROHs）及相关基因。结果表明，近交陆川猪群体的观察杂合度（0.373）小于期望杂合度（0.491），推测其发生了选择或者近交；系统进化树和群体遗传结构分析发现，近交陆川猪群体在近交过程中分化成为两个近交家系，且230、236、239、132、130及126号个体亲缘关系最近；在近交群体中，基因组纯合度和基因组长纯合片段比例的均值分别为59.64%和0.12，都极显著高于非近交群体53.18%和0.05（P<0.01），说明该近交陆川猪群体已达到高度近交；近交群体和非近交群体中分别有1 250和633个ROHs，重叠分析结果显示，特异存在于近交群体中的阳性纯合区域（positive region of homozygosity，pROHs）有224个，其中由于近交产生的纯合突变可能影响参与激素合成过程、胰液分泌、膜脂代谢过程、IgA产生的肠道免疫网络及纹肌细胞分化等相关的1 322个基因。结果提示，近交陆川猪群体的遗传多样性低、基因组纯合度高且已达到高度近交，说明该群体的遗传稳定性高。此外，近交陆川猪群体在近交过程中产生的纯合突变可能与机体的免疫、生长等生产性状相关。

Genetic Stability of Inbreeding Luchuan Pig

The aim of this study was to explore the genetic stability of high-inbreeding Luchuan pig. Ear samples were collected from 20 inbreeding and 6 non-inbreeding Luchuan pigs and genomic re-sequencing was performed for each samples. Genetic diversity of inbreeding Luchuan pig population was analyzed by scanning the whole genome SNPs. The specific ROHs and associated genes existed in inbreeding Luchuan pig population were detected based on genomic homozygosity. The results showed that observed heterozygosity was 0.373 in inbreeding Luchuan pig population, which was less than expected heterozygosity (0.491), indicating that selection or inbreeding might happen in the population. The analysis of phylogenetic trees and population's genetic structure indicated that two inbred lines were generated during the inbreeding process of Luchuan pig and the number 230, 236, 239, 132, 130 and 126 individuals had closer relationship. In inbreeding population, the average of genomic homozygosity and ratio of genomic run of homozygosity were 59.64% and 0.12, respectively, which were extremely significantly higher than 53.18% and 0.05 in non-inbreeding Luchuan pig population (P<0.01), which indicated that the inbreeding Luchuan pig population had reached a high level of inbreeding. One thousand two hundred and fifty and 633 ROHs were found in inbreeding and non-inbreeding Luchuan pig populations, respectively. The results of overlapping analysis suggested that 224 pROHs were specifically existed in inbreeding population. Among them, homozygous mutations generated from inbreeding process might affect 1 322 genes, which involved in hormone biosynthetic process, pancreatic secretion, membrane lipid metabolic process, intestinal immune network for IgA production and Striated muscle cell differentiation. These results indicate that the inbreeding Luchuan pig population has lower genetic diversity, higher genomic homozygosity and reaches a high inbreeding level, which illustrate that the population has high genetic stability. Moreover, the homozygous mutations generated from inbreeding process might be associated with immune, growth and other production traits.