Population Genomic Survey of Dongliao Black and Jilin Spotted Pigs and Their Genetic Relationships With Northeastern Asian Breeds.

Abstract

In this study, we conducted a population genomic survey of two local pig breeds in Jilin Province, Dongliao Black (DLB) and Jilin Spotted (JLS) pigs, and evaluated their genetic relationships with 23 Northeastern Asian pig breeds, comprising 46 wild boars, 211 Chinese local pigs, 69 Russian pigs, 13 Korean pigs, and 107 commercial pigs. The results will be helpful for the conservation and utilization of these rare germplasm resources. The minor allele frequency of DLB and JLS pigs was 0.24 and 0.22, respectively. Both DLB and JLS pigs exhibited higher observed heterozygosity than expected values. Moreover, JLS pigs displayed the lowest excess of homozygosity inbreeding coefficient (-0.12 ± 0.07) among all studied populations. Additionally, population structure analyses indicated that DLB and JLS pigs possess admixed ancestries intermediate between Chinese and Western pigs, with DLB being closely related to Min pigs and both breeds showing admixture signals with neighboring Northeastern Chinese breeds, reflecting their distinct hybrid histories. Furthermore, 16 and 19 genes were identified as putative candidate genes in DLB and JLS pigs using Fst analyses, respectively. All these findings are consistent with a history of crossbreeding and with low levels of inbreeding in DLB and JLS pig populations. Additionally, it is hypothesized that DLB and JLS pig breeds may carry putative candidate genes during their breeding programs, which are associated with meat quality, reproduction, production, immunity, and environmental adaptation. Therefore, strengthening conservation and promotion efforts for DLB and JLS pigs is of great significance.