China has rich genetic resources of local pig breeds. In this study, whole-genome resequencing was performed on five Shanghai local pig breeds, aiming to analyze their population genetic structure and unique genomic characteristics. Tens of millions of single nucleotide variants were obtained through the resequencing of a total of 150 individual pigs from five local pig breeds (Meishan, Fengjing, Shawutou, Pudong White, and Shanghai White) after mapping them with the pig reference genome of Sus scrofa 11.1. The results of admixture structure analysis also clearly demonstrated the genetic differences between the Shanghai local pig breeds and the three commercial pig breeds (Duroc, Landrace, and Yorkshire). The genetic infiltration of Landrace and Yorkshire pig breeds in the SHW breed was detected, which is consistent with the early history of crossbreeding in this breed. Selective sweep analysis between four indigenous Shanghai pig breed populations and three commercial pig breed populations identified 270 and 224 genes with selective signatures in the commercial and indigenous Shanghai pig populations, respectively. Six genes (TGS1, PLAG1, CHCHD7, LCORL, TMEM68, and TMEM8B) were found to be associated with animal growth in the commercial pig population through gene enrichment and protein–protein interaction analysis. In contrast, the MSRB3 gene in the indigenous Shanghai pig population was significantly under selection, which correlated with the long pendulous ear phenotype of the indigenous Shanghai pig population. In conclusion, this study is the first genomic profiling of five representative local pig breeds in Shanghai, which provides molecular genetic data and foundations for better conservation and utilization of local pig breed resources in Shanghai, China.

BACKGROUND: Cryopreservation of goat sperm is important for goat breeding and population expansion. However, goat spermatozoa are generally less resistant to freezing and the fertilization rate of spermatozoa is lower than that of fresh semen. OBJECTIVE: To investigate the effect of different concentrations of Angelica sinensis Polysaccharide (ASP; 0, 150, 300, 600, and 1200 μg/mL) on post-thaw quality, motility characteristics, and oxidative markers of Chongming white goat sperm. MATERIALS AND METHODS: Fresh semen from Chongming white goat (n=8; mean age, 3‐5 years of age) was collected, evaluated, and divided into five treatment groups corresponding to different ASP concentrations. Post-thaw sperm motility kinematics, plasma and acrosomal membrane integrity, and mitochondrial activity were evaluated. Additionally, this study evaluated markers of antioxidant defense, including malondialdehyde (MDA), reactive oxygen species (ROS), superoxide dismutase (SOD), glutathione peroxidase (GSH‐Px), nitric oxide (NO) content, total antioxidant capacity (T‐AOC), as well as 5‐methylcytosine (5‐MC) level. RESULTS: The addition of 600 μg/mL ASP enhanced sperm viability and sperm kinematic parameters, improved integrities of acrosome and plasma membrane, and increased mitochondrial activity as compared with the control. Regarding oxidative markers, ASP‐added groups had reduced ROS, MDA, and NO levels in semen compared to controls. The ASP 600 μg/mL group had the lowest levels of oxidative markers, and adding 600 μg/mL ASP significantly increased SOD, catalase (CAT), and GSH-Px activities in semen. There were significant increases in T‐AOC levels in all ASP‐added groups versus the control group. Additionally, the 300 and 600 g/mL ASP‐groups showed significantly lower levels of DNA methylation 5‐MC than the control groups. CONCLUSION: Adding 600 μg/mL ASP to the Chongming white goat low-temperature diluent improves the motility characteristics and antioxidant markers of Chongming white goat semen.

Cryopreservation of porcine blastocysts remains a significant challenge due to their high lipid content, which can lead to cryoinjury and reduced developmental competence. While liquid nitrogen (LN) vitrification causes significant molecular damage, LHe vitrification enhances oocyte viability, reduces cryoinjury, and better preserves ultrastructure and gene expression. Despite these advantages, the specific effects of LHe vitrification on porcine blastocysts are still underexplored. LHe vitrification significantly improved post-thaw survival rates (96.53 ± 4.27%) compared to conventional LN (71.20 ± 6.82%) and modified LN protocols (90.77 ± 7.88%). scRNA-seq and scWGBS achieved mapping rates of 83.70% and 33.69%, respectively, and a bisulfite conversion efficiency of 99.27%, ensuring high-quality data for gene expression and methylation analysis. Vitrification significantly altered gene expression and epigenetic regulation, with hypermethylation and downregulation of genes associated with energy metabolism (ARG2, AUH, IDH3A, NDUFV1), immune function (CD53), and protein processing (B4GALT5, OSTC, DPM3, EXT1), resulting in mitochondrial and immune dysfunction, as well as protein instability. KEGG pathway analysis revealed disruptions in the TCA cycle, pentose phosphate pathway, homologous recombination, and fatty acid biosynthesis, which impaired blastocyst viability, ATP availability, immune responses, and cellular communication. Conversely, hypomethylation and upregulation of genes regulating energy metabolism (GPAM, AICDA), oxidative stress response (ITGAV), and cell adhesion (PLAU, MRAP2) suggest an adaptive response to mitigate cellular stress and damage. However, excessive upregulation following vitrification may lead to metabolic strain, oxidative stress accumulation, lipotoxicity, and an increased risk of apoptosis. Our findings demonstrate that LHe offers superior metabolic and epigenetic preservation compared to LN, thereby reducing molecular damage and enhancing post-thaw development. These results establish LHe vitrification as an effective method that increases blastocyst viability and reproductive biotechnology applications. The online version contains supplementary material available at 10.1186/s12864-026-12752-5.

As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, F_ST (fixation index) and XP–EHH (cross–population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., SIRPA, FRS2, and GRIN2B) and habitat temperature adaptability (e.g., MITF, PI3KC2A, and FRS2). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., TNR, NOCT, and SPATA5) and strong artificial selection pressure in commercial breeds (e.g., ITPR2, HSD17B12, and UGP2) were identified in this study. Specifically, some MHC–related genes (e.g., ZRTB12, TRIM26, and C7H6orf15) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.