Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.

Background: Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). Results: A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10^− 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. Conclusions: The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.

Zhaotong pig (ZTP) is a Chinese indigenous pig breed in Yunnan Province, known for its unique body shape and appearance, good meat quality, strong foraging ability, and adaptability. However, there is still a lack of research on its genome. In order to investigate the genetic diversity, population structure, and selection signatures of the breed, we conducted a comprehensive analysis by resequencing on 30 ZTPs and comparing them with genomic data from 10 Asian wild boars (AWBs). A total of 45,514,452 autosomal SNPs were detected in the 40 pigs, and 23,649,650 SNPs were retained for further analysis after filtering. The H_E, H_O, P_N, MAF, π, and Fis values were calculated to evaluate the genetic diversity, and the results showed that ZTPs had higher genetic diversity and lower inbreeding coefficient compared with AWBs. Population structure was analyzed using NJ tree, PCA, ADMIXTURE, and LD methods. It was found that ZTPs were population independent of AWBs and had a lower LD decay compared to AWBs. Moreover, the results of the IBS genetic distance and G matrix showed that most of the individuals had large genetic distances and distant genetic relationships in ZTPs. Selection signatures were detected between ZTPs and AWBs by using two methods, F_ST and π ratio. Totals of 1104 selected regions and 275 candidate genes were identified. Finally, functional enrichment analysis identified some annotated genes that might affect fat deposition (NPY1R, NPY5R, and NMU), reproduction (COL3A1, COL5A2, GLRB, TAC3, and MAP3K12), growth (STAT6 and SQOR), tooth development (AMBN, ENAM, and ODAM), and immune response (MBL2, IL1A, and DNAJA3). Our results will provide a valuable basis for the future effective protection, breeding, and utilization of ZTPs.

Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding.

Introduction: Kele pig (KLP) is a valuable Chinese indigenous pig breed, renowned for its strong adaptability, high intramuscular fat content, and excellent meat quality. However, the genomic characteristics of KLPs are still unknown. This study aims to investigate the genetic diversity, population structure, and trait-related selection signatures of KLPs based on whole-genome resequencing. Methods: The genomes of 30 KLPs were resequenced and analyzed alongside genomic data from 90 pigs of three commercial breeds, comprising 30 Duroc (DUPs), 30 Landrace (LRPs), and 30 Yorkshire pigs (YRPs). To evaluate their genetic diversity, we calculated the expected heterozygosity, observed heterozygosity, polymorphic marker ratio, minor allele frequency, nucleotide diversity (π), runs of homozygosity (ROH), and inbreeding coefficient (F _ROH ). Meanwhile, a neighbor-joining tree, principal component analysis, ADMIXTURE analysis, linkage disequilibrium (LD) analysis, genetic distance and relationship matrices were constructed to analyze the population structure. In addition, selection signatures between KLPs and DUPs, LRPs, and YRPs were detected using fixation index (Fst) and π ratio methods. Results and Discussion: A total of 66,204,339 autosomal single nucleotide polymorphisms (SNPs) were detected in the 120 pigs, and 21,738,497 SNPs were retained for further analysis after filtering. The results showed that KLPs had higher genetic diversity, along with the smallest F _ROH value compared to DUPs, LRPs, and YRPs. Moreover, KLPs displayed a relatively unique genetic structure with a higher LD decay, and the majority of individuals within the KLPs exhibited distant genetic distances and relationships. Totals of 688 selected regions were identified, including 723 published QTLs. Within the selected regions, 192 candidate genes were annotated, and seven genes were found to be functionally involved in coat color ( KIT ), immune response ( JAK2 and SOCS1 ), heart development ( NTRK3 and SRF ), muscle growth and development ( VDR ), and fat deposition ( KDR ). These findings will provide valuable insights for the future conservation, breeding, and utilization of KLPs.

Psoas major muscle (PMM) is different from longissimus dorsi muscle (LDM) and semimembranosus (SM) and is a representative red muscle in pig’s carcass. However, scarce researches focus on the mechanism of pork quality of PMM, especially by multi-omics analysis. In this study, we investigated the mechanisms underlying the meat quality differences between PMM and LDM, SM in Chinese indigenous Saba pigs, integrating physicochemical characteristics, transcriptomics, and proteomics analyses. The results showed that PMM had appropriately lower fat content, better amino acid (AA) compositions, and greater tenderness compared to LDM and SM. Totals of 2,320 differentially expressed genes (DEGs) and 1,562 differentially expressed proteins (DEPs) were identified, of which 22 DEGs/DEPs were co-expression in both PMM vs. LDM and PMM vs. SM groups at the two-omics levels. Some identified AAs and lipids metabolism-related pathways played a crucial role in the meat quality differences among muscles from different parts. Ten genes, including ACADM, ETFB, MYL3, COX5A, CS, HADH, DLD, NDUFS8, NDUFS3, and NDUFAB1 were identified as potential key genes specific to the regulation of synthesis and metabolism of AAs and lipids in skeletal muscle. These findings provide holistic insights into the molecular mechanisms of pork quality, and serve as beneficial foundation for the genetic improvement of pork quality and pork grading.