Meat production traits in pigs are critical economic characteristics, primarily influenced by the formation and development of skeletal muscle. Skeletal muscle development is regulated by a complex transcriptional network, which partly relies on chromatin accessibility for initiation. Ningxiang pigs, a renowned Chinese indigenous breed, are highly valued for their tender meat. However, studies focusing on skeletal muscle development in Ningxiang pigs, particularly from the perspective of chromatin accessibility, have not yet been reported. Based on this, the present study selected several key time points in the skeletal muscle development of Ningxiang pigs to perform Transposase-Accessible Chromatin Sequencing (ATAC-seq) and RNA sequencing (RNA-seq). This was carried out to identify key open chromatin regions and genes during different growth stages, which could influence skeletal muscle development in Ningxiang pigs. We collected longissimus dorsi muscle samples at postnatal days 14 (D14), 28 (D28), 85 (D85), 165 (D165), and 250 (D250). For each age, three individuals were collected for ATAC-seq and RNA-seq. After initial differential analysis among different ages, we identified 6412 differentially accessible chromatin peaks and 1464 differentially expressed genes. To clarify the key candidate transcription factors affecting the development of skeletal muscle in Ningxiang pigs, motif analysis of differential peaks revealed potential cis-regulatory elements with binding sites for transcription factors, including Fosl2 and JunB. Correlation analysis identified 56 overlapping genes and a significant positive correlation (r = 0.73, p = 1 × 10⁻¹⁴) between gene expression and chromatin accessibility. Key candidate genes such as HOXA10, closely related to skeletal muscle development, were specifically examined. These results enhance our understanding of the genetic and epigenetic regulatory mechanisms of porcine skeletal muscle development, providing a robust foundation for future molecular studies.

In the context of modern pig farming, the central role of boars is underscored by large-scale centralized breeding and the widespread application of artificial insemination techniques. However, previous studies and breeding programs have focused mainly on product efficiency traits, such as growth rate, lean meat yield, and litter size, often neglecting boar semen traits. In this study, we estimated the genetic parameters and assessed the genomic prediction accuracy of boar semen traits with phenotypes evaluated from 274,332 ejections in a large population consisting of 2467 Duroc boars. Heritability of sperm morphological abnormality rate (ABN), fresh semen volume (VOL), sperm concentration (DEN), and motility (MOT) were estimated to be 0.43, 0.22, 0.23, and 0.16, respectively. GBLUP achieved a moderate predictive ability of semen traits, with a range of 0.32–0.50. Incorporating gene interactions indicated by the KEGG pathways (biBLUP) significantly improved predictive accuracy over the classical additive model (GBLUP) and epistatic model (RKHS). Moreover, biBLUP showed an improvement from 9.50% to 20.10% among the studied traits compared with GBLUP, with the greatest improvement (0.40 vs. 0.48) observed in sperm morphological abnormality rate. In conclusion, moderate to low heritability was estimated for the Duroc boar semen traits. Genomic prediction was able to achieve moderate accuracy, with a range from 0.32 to 0.56, for the studied traits. Considering gene interactions within KEGG pathways enhanced the predictive ability of boar semen traits.

The Ningxiang pig, one of the well-known Chinese native pig breeds, has the advantages of tender meat, high intramuscular fat (IMF) content, and roughage tolerance, compared to the commercial lean pig breeds. The genetic basis for complex traits in Ningxiang pigs has been previously studied through other genetic markers, such as Single Nucleotide Polymorphism (SNP), while the characteristics of copy number variation (CNV) and the selection signal have not been investigated yet. In this study, GGP 50 k genotyping data of 2242 Ningxiang pigs (NX) and 1137 Duroc pigs (Duroc) were involved in CNV atlas construction and selection signals identification. Annotations of genes and quantitative trait locus (QTLs) were performed on the target candidate regions, as follows: (1) 162 CNVs were detected in Ningxiang pigs, while 326 CNVs were detected in Duroc pigs, and there are 21 copy number variation regions (CNVRs) shared between them; (2) The CNVRs of Duroc are more abundant, with 192 CNVRs, accounting for 1.61% of the entire genome, while those of Ningxiang pigs only have 98 CNVRs, accounting for 0.49%; (3) The QTLs annotated on CNVs and selected regions of Ningxiang pigs were mainly associated with meat quality and fertility. In contrast, the Duroc QTLs’ notes relate primarily to the carcass and immunity, and explain why they have a higher slaughter rate and immunity; (4) There is a presence of high-frequency acquired CNVs, specifically in Ningxiang pigs, with 24 genes significantly enriched in the sensory receptor-related pathway in this region; (5) Based on the CNVs atlas, candidate genes such as 3 inositol 1,4,5-triphosphate receptor, type 3 (ITPR3), forkhead box protein K2 (FOXK2), G-protein coupled estrogen receptor 1 (GPER1), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), triosephosphate isomerase 1 (TPI1), and other candidate genes related to fat deposition and differentiation were screened. In general, this study improved our knowledge about copy number variation and selection signal information of Ningxiang pigs, which can not only further explain the genetic differences between Chinese native and Western commercial pig breeds, but also provide new materials for the analysis of the genetic basis of complex traits.

To unravel the genetic basis of economically critical reproductive traits in swine, we genotyped 839 sows from three commercial breeds (Duroc, Landrace, Yorkshire) using the Porcine Breeding Chip_plus 50K SNP array, and analyzed three key traits: total number born (TNB), number born alive (NBA), and number of healthy piglets (NHP). We integrated principal component analysis (PCA) for population structure, runs of homozygosity (ROH) detection, genome-wide association studies (GWAS), and GO/KEGG enrichment analysis. Phenotypically, Yorkshire sows exhibited superior and persistent reproductive capacity across parities 1–7 (peak TNB: 14.17 ± 2.82 at parity 4 based on N ≥ 3 data), Duroc sows had limited data with only parity 1 available (TNB: 9.44 ± 2.13), and Landrace sows showed moderate to high performance across parities 1–4 and 7, with peak TNB at parity 4 (17.08 ± 4.61). ROH analysis further revealed that short ROH fragments (1–5 Mb) were the most abundant category across breeds, while the majority of detected ROH were under 10 Mb in length. GWAS identified significant SNPs concentrated on chromosomes 1 and 2, and annotated candidate genes including AMH (ovarian reserve), IZUMO4 (embryo implantation), ACSBG2 (steroid synthesis), RFX2 (follicular maturation), and DOT1L (embryonic development). GO/KEGG enrichment highlighted pathways such as “histone methyltransferase activity” and “fatty acid biosynthesis”, which are critical for reproductive processes. This study clarifies breed-specific reproductive patterns and identifies key genetic loci/genes for porcine reproductive traits, providing molecular markers and a theoretical basis for improving swine reproductive performance via molecular breeding.