Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds

Abstract

Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.

Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color

“…ADMIXTURE ancestry composition analysis showed that the Chinese and Western pig breeds had two differentiated clusters when K = 2, indicating different ancestral lineages. This is consistent with previous reports indicating that European and Chinese pig breeds have different ancestral origins [ 8 , 20 ]. Wang et al [ 8 ] used a 60 K SNP chip to study three pig breeds in Jiangxi province and found that Chinese and European pigs were clustered into two independent branches, whereas the Chinese–European hybrid breed (Sutai) was located in the middle between the European and Chinese branches in the NJ tree; the obvious difference between Chinese and European pig breeds was also reflected in the PCA diagram.…”

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

“…Despite the increasing evidence highlighting introgression between Asian and European pigs (Bosse, Megens, Frantz, et al 2014; Peng et al 2023), the extent and relative contributions of introgressed variants in pig domestication remain inadequately explored. A comprehensive catalog of variants from a diverse set of animals enabled us to reveal significant signals of genetic introgression between Chinese and European pig breeds (Fig.…”

“…Within the Chinese indigenous pigs, we further classified the pigs based on their geographical origins proposed in previous studies (Zheng et al 2022; Peng et al 2023), resulting in the following subgroups: Southern Chinese (SCN, n = 18), Eastern Chinese (ECN, n = 55), Northern Chinese (NCN, n = 42), and Southwestern Chinese indigenous pigs (SWCN, n = 45). Supplementary Table S1 provides the detailed information of the samples, including the sequencing platforms, accession numbers, sample sizes, and average sequencing coverage.…”

“…This integration is particularly pronounced in Northern Chinese indigenous breeds, including Laiwu, Min, and Lichahei pigs, which exhibit notable hybridization with European commercial breeds (Wang et al 2021; Meng et al 2022; Xie et al 2023). Previous population genetics studies based on single-nucleotide polymorphism (SNP) data were largely concentrated on one-way introgression (Bosse, Megens, Frantz, et al 2014; Chen et al 2020; Peng et al 2023). However, the introgression pattern, which can be observed in both directions between Chinese and European pigs, has not been thoroughly investigated.…”

“…Additionally, sequences for 201 animals were downloaded from the Sequence Read Archive (TableS1, Supporting information). In total, we utilized 418 samples in this study, including European domestic pigs (EDOM, n = 217), Duroc × Landrace × Yorkshire pigs (DLY, n = 19), European wild boar graphical origins proposed in previous studies(Zheng et al 2022;Peng et al 2023), resulting in the following subgroups: Southern Chinese (SCN, n = 18), Eastern Chinese (ECN, n = 55), (http://broadinstitute.github.io/picard/) were used for data sorting and duplicates marked, respectively. Variant calling of SNP was performed using GATK v4.1.8.1 (McKenna et al…”