Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.

Background: Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. Results: We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Conclusions: In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

As one of the most widely used animal models for human disease research, pigs play a critical role in elucidating disease pathogenesis. However, the genetic characteristics of experimental pig breeds remain underexplored. This study employed whole-genome resequencing to investigate three representative Chinese indigenous pig breeds and two commercial European breeds. Our analysis revealed that indigenous breeds harbor 16.3 million genetic variants (88.3% SNPs), with higher nucleotide diversity compared to commercial breeds. Selective sweep analysis using Fst and π identified key genes under strong selection, including immune regulators (BTK, IL2RG, RASGRP1), metabolic gene MED12, and neuro-associated SDR16C5, with five genes exhibiting significant allele frequency divergence between populations (P < 0.05). Notably, two signature selective regions on chromosome 6 (181,025–182,387 bp and 144,185,871–144,313,689 bp) were identified, containing fixed missense mutations in coat color gene MC1R (p.T305C/p.G283A) and vision-related gene RPE65 (p.G1503A), indicating strong artificial selection for phenotypic traits. This work systematically characterizes the high genetic diversity of Chinese indigenous pigs and their genomic advantages as disease models, providing critical insights for developing precision biomedical animal models.