Detection of Genetic Structure of Conservation Population in Wannanhua Pig (Sus scrofa domesticus) Based on SNPs Chip
WANG Jing-Lin1, WU Xu-Dong2, HE Zhi-Bing1, LIU Yang-Guang1, WANG Xiao-Fen1, DING Yue-Yun1, ZHENG Xian-Rui1, ZHANG Xiao-Dong1,*, YIN Zong-Jun1,*
1 College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; 2 Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Medicine, Hefei 230031, China
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.
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