Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs. This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

Sujiang pigs are a synthetic breed derived from Jiangquhai, Fengjing, and Duroc pigs. In this study, we sequenced the genome of 62 pigs with a coverage depth of 10× to 20×, including 27 Sujiang and 35 founder breed pigs, and we collected 360 global pigs' genome sequence data from public databases including 39 Duroc pigs. We obtained a high-quality variant dataset of 365 Sujiang pigs by imputing the porcine 80 K single nucleotide polymorphism (SNP) Beadchip to the whole-genome scale with a total of 422 pigs as a reference panel. A dataset of 365 imputated Sujiang pigs was used to perform single-trait genome-wide association study (GWAS) and meta-analyses for growth and fatness traits. Single-trait GWAS identified 1 907, 18, and 14 SNPs surpassing the suggestively significant threshold for backfat thickness, chest circumference, and chest width, respectively. Meta-analyses identified 2 400 genome-wide significant SNPs and 520 suggestively significant SNPs for backfat thickness and chest circumference, and 719 genome-wide significant SNPs and 1 225 suggestively significant SNPs for all seven traits. According to the meta-analysis of backfat thickness and chest circumference, a remarkable region of 2.69 Mb on Sus scrofa chromosome 4 containing FAM110B, IMPAD1, LYN, MOS, PENK, PLAG1, SDR16C5 and XKR4 was identified as a candidate region. The haplotype heat map of the 2.69 Mb region verified that Sujiang pigs were derived from Duroc and Chinese indigenous pigs, especially Jiangquhai pigs. The Kruskal-Wallis test showed that haplotypes of the 2.69 Mb region significantly affected backfat thickness and chest circumference traits. We then focused on PLAG1, an important growth-related gene, and identified two synonymous SNPs with obvious differences among different breeds in the PLAG1 gene. We then performed genotyping of 365 Sujiang, 150 Duroc, 95 Jiangquhai, and 100 Fengjing pigs to confirm the above result and verified that the two variants significantly affected phenotypes of growth and fatness traits. Our findings not only provide insights into the genetic architecture of porcine growth and fatness traits but also provide potential markers for selective breeding of these traits in Sujiang pigs.

Introduction: Diarrhea after weaning of piglets is one of the most serious diseases in pig herds, which brings huge economic losses to the pig industry. Diarrhea in piglets after weaning has a significant impact on the composition of gut microbiota, which leads to the disturbance of normal metabolic processes.Method: To investigate the effects of weaning diarrhea on gut microbiota and its metabolites, 84 samples were collected from 42 piglets pre-weaning and post-weaning, including 17 samples from post-weaning diarrheal piglets. The samples were sequenced for 16S rRNA and untargeted metabolites.Results: A total of 3,192 ASVs, 20 phyla, and 286 genera were identified. A total of 32 genera were detected by difference analysis between healthy post-weaning piglets and diarrhea post-weaning piglets. It was observed that post-weaning diarrhea led to a reduction in the relative abundance of Bacteroides, UCG-002, Christensenellaceae_R-7_group, Escherichia-Shigella, Pyramidobacter, Lactobacillus and a substantial increase in the relative abundance of Prevotellaceae_NK3B31_group, Muribaculaceae, Prevotella, Holdemanella, Collinsella, Blautia. A total of 360 differential metabolites were detected between healthy and diarrheal weaned piglets. 5-Hydroxyferulic acid methyl ester, D-Saccharic acid 1,4-lactone, 3-Methylhistidine were significantly enriched in post-weaning diarrheal piglets. These differential metabolites were enriched in the Nucleotide metabolism, ABC transporters, Biosynthesis of amino acids, Nicotinate and nicotinamide metabolism, Valine, leucine and isoleucine biosynthesis, Pyrimidine metabolism, Alanine, aspartate and glutamate metabolism, Purine metabolism, Caffeine metabolism, Butanoate metabolism pathways.Discussion: Taken together, this study systematically reveals the dynamic succession and structure of the gut microbiota and metabolites in diarrhea and healthy piglets pre-weaning and post-weaning. Our findings provide a reference for the microbiological and metabolite etiology associated with post-weaning diarrhea.

Endothelin Receptor Type B (EDNRB) is expressed in a variety of cells during embryonic stage, including melanocyte precursors cells. Our previous studies found that 11 bp deletion of EDNRB caused the two-end black (TEB) coat color in Chinese pigs. In this study, we aimed to explore the mutant EDNRB on the formation of TEB coat color in Chinese pigs. We constructed recombinant plasmid for wild and mutant EDNRB and EDN1, respectively, and transfected the recombinant plasmid into mouse B16 melanoma cells in groups. Real-time fluorescent quantitative PCR (RT-qPCR) was performed to detect expression of genes that participate in melanin pathway, including PLCγ, Raf, MITF. Comparing to the wild-type EDNRB cells, expression of the three genes in the cell line expressing mutant EDNRB cells was significantly reduced. We measured the melanin content produced by transfected recombinant granulocytes of wild and mutant EDNRB and found that the amount of melanin in mutant EDNRB cells was significantly lower than that of the wild. Wound-healing assay confirmed that the migration and mobility rate of mutant EDNRB cells were significantly lower than the wild. Co-immunoprecipitation further confirmed that mutant EDNRB could not interact with the EDN1 protein. In conclusion, this study revealed that the 11 bp deletion of EDNRB reduced the melanin production, which may be caused by inhibiting the expression of PLCγ, Raf, and MITF. The mutant EDNRB reduced melanocyte migration and could not interact with the EDN1 protein. We explored the effect of mutant EDNRB in Chinese pigs with TEB coat color, and the results provided a reference for exploring molecular mechanism of mutant EDNRB on the formation of TEB coat color pigs.