农业生物技术学报2024，Vol.32Issue(8)：1869-1877,9.DOI:10.3969/j.issn.1674-7968.2024.08.014
基于SNP芯片检测皖南花猪保种群遗传结构
Detection of Genetic Structure of Conservation Population in Wannanhua Pig(Sus scrofa domesticus)Based on SNPs Chip
摘要
Abstract
The Wannanhua pig(Sus scrofa domesticus)is an indispensable valuable pig breed resource in Anhui province and even in China.Studying the genetic diversity,kinship relationships,and pedigree structure of the Wannanhua pig population is crucial for revealing the current population status.The SNP of 32 Wannanhua pigs was detected using Chinese Chip-1 BeadChip.PLINK software was used to calculate the observed heterozygosity(Ho),expected heterozygosity(He)and polymorphic information content(PIC),and to analyse the runs of homozygosity(ROH)of the Wannanhua pig population;Constructing G-matrix using GCTA software to analyze the genetic relationship of Wannanhua pig population.A colony evolutionary tree was built using MEGA X software to analyze the family structure of the Wannanhua pig population.The findings indicated that 42 662 SNP loci were identified,with 21 317 of them passing the quality control assessment;The polymorphism marker ratio(PN)was 0.500;The effective population size(Ne)was 3,the observed heterozygosity(Ho)was 0.372,the expected heterozygosity(He)was 0.348.The average relationship coefficient was 0.11.The G matrix results all indicated that most of the Wannanhua pigs were moderately related.There were 884 ROH fragments in the results,the average ROH length of(12.35±2.17)Mb and the individual ROH length of(341.19±139.58)Mb;The mean inbreeding coefficient based on ROH was 0.139±0.056,indicating that the inbreeding degree of the conserved population was not severe;The results of the cluster analysis showed that the Wannanhua pigs were derived from 5 bloodlines.In summary,the population of the Wannanhua pig conservancy herd had a low effective content,medium genetic diversity,medium degree of inbreeding,and might contain a small amount of foreign blood.This study provides scientific basis for the conservation and utilization of genetic resources of the southern Wannanhua pig.关键词
皖南花猪/SNP芯片/遗传结构/亲缘关系/家系结构Key words
Wannanhua pig/SNP chip/Genetic structure/Genetic relationship/Family structure分类
农业科技引用本文复制引用
王静琳,吴旭东,何志兵,刘阳光,王小芬,丁月云,郑先瑞,张晓东,殷宗俊..基于SNP芯片检测皖南花猪保种群遗传结构[J].农业生物技术学报,2024,32(8):1869-1877,9.基金项目
国家自然科学基金(31972531) （31972531）
安徽省生猪产业技术体系项目(AHCYJSTX-05-01) （AHCYJSTX-05-01）
