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Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome. [ABSTRACT FROM AUTHOR]

Longer porcine carcasses may be expected to have more vertebrae. Therefore, vertebrae number in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 578 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study (GWAS) identified 36 significant single nucleotide polymorphisms (SNPs) on the chromosomes SSC1 (294.28–300.32 Mb) and SSC7 (102.22–109.39 Mb). A 6.04-Mb region that contained all 13 significant SNPs on SSC1 also contained the gene NR6A1, previously reported to influence the number of vertebrae in pigs. However, the reported putative casual mutation of NR6A1 c.748C>T showed no genome-wide significant association with the trait, suggesting it was not a causal mutation in our population. The remaining 23 significant SNPs on SSC7 were concentrated in a 7.17-Mb region, which was within a quantitative trait locus interval for number of vertebrae. TMED10 was the closest gene to the most significant SNP and might be a candidate. Haplotype sharing and block analysis refined the QTL to an interval of about 3 Mb containing 29 candidate genes. Of these 29 genes, the previously reported possible casual mutation of VRTN g.19034A>C was not found to be a causal mutation in our population. Exploration of these genes via additional genetic and functional studies in mammals revealed that TGFβ3 could be a good candidate on SSC7. A mutation of TGFβ3 c.1749G>A was detected by GWAS and could be proposed as a candidate causal mutation, or as closely linked to a causal mutation, for the number of vertebrae in pigs.

The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs. [ABSTRACT FROM AUTHOR]

As one of the few animals with variation in the number of rib pairs (RIB), the pig is a good model to study the mechanism of RIB regulation. Quantitative trait loci (QTL) for porcine RIB are present on Sus scrofa chromosome 7 (SSC7). Although several candidate genes exist in this QTL region on SSC7, the causal gene has yet to be verified. Beijing Black pig with 14–17 RIB is a good population for candidate gene mining and 1104 individuals were genotyped using the Illumina Porcine 50K BeadChip. A total of 14 SNPs from 95.49 to 97.78 Mb on SSC7 showed genome‐wide significant association with RIB. On SSC7, a locuszoom plot using pairwise linkage disequilibrium displayed the narrowest linkage region encompassing only two genes, ABCD4 and VRTN. In mice, a transcriptome expression profile was obtained using three embryos at E9.5 (the critical period for rib formation). ABCD4 was highly expressed, but no expression of VRTN was detected. On SSC6, there were four genome‐wide significant SNPs from 106.42 to 106.92 Mb associated with RIB. GREB1L and MIB1, in this region, were regarded as novel candidate genes. These results revealed a crucial candidate causal gene on SSC7 and novel genes on SSC6 for rib number and provided interesting new insights into its genetic basis. [ABSTRACT FROM AUTHOR]

Imprinted genes – exhibiting parent‐specific transcription – play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA‐seq and RNA‐seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single‐nucleotide variations were discovered in the DNA‐seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single‐nucleotide variations were used to determine the allelic‐specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1‐3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1‐3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1‐3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding. [ABSTRACT FROM AUTHOR]

Backfat thickness (BFT) is an important carcass composition trait and regarded as a breeding focus. Our initial transcriptome analysis of pig BFT identified GLI pathogenesis-related 1 (GLIPR1) as one of the promising candidate genes. This study was conducted to identify the expression profiles, polymorphisms, and genetic effects of the GLIPR1 gene on BFT in pigs. The expression of the GLIPR1 gene existed in every detected tissue, and there was a significantly higher expression in spleen and adipose tissue than others (p < 0.05). At the different ages of pig, the expression of the GLIPR1 gene was low at an early age, increased with growth, and reached the highest level at 180 days. Genetic polymorphism analysis was detected in 553 individuals of the Large White × Minzhu F2 population. Four SNPs in the promoter significantly associated with 6–7 rib BFT (p < 0.05) were predicted to alter the transcription factor binding sites (TFBS), and the mutations of g.38758089 T>G and g.38758114 G>C were predicted to change the TFs associated with the regulation of adipogenesis. Haplotypes were formed by the detected SNPs, and one block showed a strong association with BFT (p < 0.05). In summary, our results indicate that the expression profiles and genetic variants of GLIPR1 affected the BFT of pigs. To our knowledge, this study is the first to demonstrate the biological function and genetic effects of the GLIPR1 gene on the BFT of pig and provide genetic markers to optimize breeding for BFT in pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: Copy number variation (CNV) is a type of variant that may influence meat quality of, for example intramuscular fat (IMF). In this study, a genome-wide association study (GWAS) was then performed between CNVs and IMF in a pig F2 resource population. A total of 19 CNVRs were found to be significantly associated with IMF. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings. [ABSTRACT FROM AUTHOR]

RNA editing is an essential post‐transcriptional regulatory mechanism. However, few studies have investigated the functional RNA edits in the economic traits of livestock on a genome‐wide scale. Pigs are one of the most important livestock species and their fat is the principal organ involved in the regulation of adipose deposition. Here, we used three full‐sibling pairs, with each pair comprising a pig with higher backfat (BF) thickness and lower backfat thickness, to identify RNA editing events based on whole‐genome and transcriptome sequencing data. A total of 60,903 non‐redundant RNA editing sites with 59,472 (97.7%) A‐to‐G edits were detected using a revised bioinformatics pipeline. A specific sequence context with G preference was found one base downstream of the edited site, and the editing level was associated with the distribution of nucleotides across nearly sites. Moreover, the A‐to‐G editing sites mostly occurred in the pig‐special short interspersed nuclear elements, Pre0_SS. Comparing the difference between pigs with higher BF and lower BF, we found 211 differentially edited sites (DESites). Functional enrichment analyses revealed a significant enrichment of genes containing DESites in terms of adipose deposition. The DESites located in the six adipose‐related genes (SKP1, GSK3B, COL5A3, MDM4, NT5C2, and DENND2A) were selected as candidate RNA editing sites associated with adipose deposition, and thus require further evaluation. This study mined the potentially functional RNA editing sites in pig adipose tissue and indicated that RNA editing may play an important role in adipose deposition, which provides a new insight into the post‐transcriptionally mediated regulation mechanism of fat development. [ABSTRACT FROM AUTHOR]

Alternative splicing (AS) is a key step in the post-transcriptional regulation of gene expression that can affect intramuscular fat (IMF). In this study, longissimus dorsi muscles from 30 pigs in high- and low- IMF groups were used to perform Oxford Nanopore Technologies (ONT) full-length sequencing and Illumina strand-specific RNA-seq. A total of 43,688 full-length transcripts were identified, with 4,322 novel genes and 30,795 novel transcripts. Using AStalavista, a total of 14,728 AS events were detected in the longissimus dorsi muscle. About 17.79% of the genes produced splicing isoforms, in which exon skipping was the most frequent AS event. By analyzing the expression differences of mRNAs and splicing isoforms, we found that differentially expressed mRNAs with splicing isoforms could participate in skeletal muscle development and fatty acid metabolism, which might determine muscle-related traits. SERBP1 , MYL1 , TNNT3 , and TNNT1 were identified with multiple splicing isoforms, with significant differences in expression. AS events occurring in IFI6 and GADD45G may cause significant differences in gene expression. Other AS events, such as ONT.15153.3, may regulate the function of ART1 by regulating the expression of different transcripts. Moreover, co-expression and protein-protein interaction (PPI) analysis indicated that several genes (MRPL27 , AAR2 , PYGM , PSMD4 , SCNM1 , and HNRNPDL) may be related to intramuscular fat. The splicing isoforms investigated in our research provide a reference for the study of alternative splicing regulation of intramuscular fat deposition. [ABSTRACT FROM AUTHOR]

Residual feed intake (RFI) is defined as the difference between the observed and expected feed intake for maintenance and growth requirements. In this study, the expression profiles of mRNAs and long noncoding RNAs (lncRNAs) from skeletal muscle in Duroc pigs with divergent RFI phenotypes were investigated by Illumina sequencing. Finally, a total of 2195 annotated lncRNAs and 1976 novel lncRNAs were obtained. About 210 mRNAs and 43 lncRNAs were differentially expressed among high and low RFI pigs. The differentially expressed mRNAs were potentially involved in the biological processes of lipid metabolism, extracellular matrix organization, cell proliferation, and cell adhesion. The lipolysis in skeletal muscle was increased in high RFI pigs, suggesting that high RFI pigs might need more energy than low RFI pigs. However, skeletal muscle development was increased in low RFI pigs. These results suggested that low RFI pigs might be more efficient in energy utilization during skeletal muscle growth. The function of lncRNA was also analyzed by target prediction. Nine lncRNAs might be candidate lncRNAs for the determination of RFI phenotype, by the regulation of the biological processes of lipid metabolism, cell proliferation, and cell adhesion. This study should facilitate a further understanding of the molecular mechanism for the determination of RFI phenotype in pigs. [ABSTRACT FROM AUTHOR]

The aim of this research was to screen candidate genes affecting growth traits in pigs by studying the difference expression genes (DEGs) between the longissimus dorsi of Large White (LW) and Mashen (MS) pigs. RNA-sequencing (RNA-seq) technology was applied to analyse the transcriptomes from six longissimus dorsi in two pig breeds (LW and MS). Based on sequencing, the DEGs were screened, and functional annotation and enrichment analysis were performed. The results showed that 697 different significant genes were obtained (p < 0.05, FDR <0.05 and |FC| ≥ 2). The results of Gene Ontology (GO) functional annotation showed that DEGs were mainly related to the growth and development of skeletal muscle, the formation of organelles and the function of protein binding. DEGs were mainly involved in the pathways of Phagosome, Viral myocarditis, Antigen processing and presentation, Allograft rejection, Graft-versus-host disease, Cardiac muscle contraction by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Combined with other livestock genomics studies, SFRP2, KDM6A, OGT may be candidate genes involved in pig growth traits. The results provided a theoretical basis for the improvement of pig growth traits and the study of candidate genes. In this study, three candidate genes (SFRP2, KDM6A, OGT) which affecting growth traits were screened. The experimental animals selected in this study were the local breed Mashen pig and the Western commercial breed Large White pig with obvious growth traits difference. In this study, RNA-Seq technology was applied to analysis the transcriptomes of pig muscle. [ABSTRACT FROM AUTHOR]

The pulmonary surfactant-associated protein ( SFTPA1, SP-A) gene has been studied as a candidate gene for lung disease resistance in humans and livestock. The objective of the present study was to identify polymorphisms of the porcine SFTPA1 gene coding region and its association with acute lung injury ( ALI). Through DNA sequencing and the PCR-single-strand conformation polymorphism method, a novel 9-bp nucleotide insertion (+) or deletion (-) was detected on exon 2 of SFTPA1, which causes a change in three amino acids, namely, alanine ( Ala), glycine ( Gly) and proline ( Pro). Individuals of three genotypes (−/−, +/− and +/+) were divided into equal groups from 60 Rongchang pigs that were genotyped. These pigs were selected for participation in the oleic acid ( OA)- ALI model by 1-h and 3-h injections of OA, and there were equal numbers of pigs in the control and injection groups. The lung water content, a marker for acute lung injury, was measured in this study; there is a significant correlation between high lung water content and the presence of the 9-bp indel polymorphism ( P < 0.01). The lung water content of the OA injection group was markedly higher than that of the control group and lung water content for the +/+ genotype was significantly higher than that of the others in the 1-h group ( P < 0.01). No differences in the expression of the SFTPA1 gene were found among individuals with different SFTPA1 genotypes, indicating that the trait is not caused by a linked polymorphism causing altered expression of the gene. The individuals with the −/− genotype showed lower lung water content than the +/+ genotype pigs, which suggests that polymorphism could be a potential marker for lung disease-resistant pig breeding and that pig can be a potential animal model for human lung disease resistance in future studies. [ABSTRACT FROM AUTHOR]

Simple Summary: The number of thoracic vertebrae (NTV) and number of vertebrae (NV) varies among pig breeds with a high correlation of about 0.8. It is important to discover variants associated with the NTV by considering the effect of the NV in pig. The results suggest that regulation variants on SSC7 might play crucial roles in the NTV and the FOS on SSC7 should be further studied as a critical candidate gene. In addition, BMPR1A was identified as a novel candidate gene affecting the NTV in pigs. The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: Runs of homozygosity (ROH) are the DNA segments that harbor uninterrupted stretches of homozygous genotype segments in the genome that are present in an individual due to the transmission of identical haplotypes from parents to their offspring. ROHs are widely used as predictors of whole-genome inbreeding levels in animals and identify highly selected genomic regions. In this study, we investigated the ROH distributions on the whole genome in three pig populations (Landrace, Songliao black and Yorkshire pigs). Moreover, inbreeding coefficients based on ROH were calculated and genes were annotated in the genomic regions with a high frequency of ROH. Results showed that Songliao black pigs had higher inbreeding in recent generations and ten genes related to economically important traits were located within ROH regions. Our findings provide a reference for developing breeding programs to maintain diversity and fitness in these breeds. Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection. [ABSTRACT FROM AUTHOR]

Simple Summary: Backfat thickness is an important characteristic in pig breeding. In this study, the key microRNAs (miRNAs) and genes associated with pig backfat deposition were detected and characterized using RNA sequencing between adipose tissues of high-backfat and low-backfat pigs. Strong candidate mRNA‒miRNA interaction pairs were identified to affect backfat deposition through the regulation of target genes by miRNAs. These results provide novel insights into the backfat deposition mechanism in pigs. Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (AQP9, DKK3, GLYCTK, GLIPR1, and DUSP2) related to fat deposition were found to be strong candidate genes, and mir-31-5p/AQP9 and mir-31-5p/GLIPR1 may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies. [ABSTRACT FROM AUTHOR]

• Differential metabolites and lipids in muscles were investigated between Laiwu and Yorkshire pigs. • PIs and TGs were related to high IMF content in the Laiwu pigs. • Oxoglutaric acid, fumarate, and l -aspartate contributed to Laiwu pig's better flavor. • The possible biomarkers were supplied to distinguish the two pig breeds. • The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Chinese indigenous pig breeds have higher intramuscular fat content (IMF) and better meat quality than Western commercial pigs. The differential metabolites and lipids in the skeletal muscle associated with IMF contents and meat flavor in Laiwu and Yorkshire pigs were investigated in this study. As a result, 113 differential metabolites and 54 differential lipids were discovered. Lipidomics revealed that the Laiwu pig had a fast lipid droplet formation and contained more triglyceride than the Yorkshire pig, which was corresponded to its high IMF contents. Both the lipidomics and metabolomics results indicated that the Laiwu pig had a higher mitochondrial content and aerobic respiration, due to its larger percentage of oxidative fibers. In addition, differential metabolites, such as oxoglutaric acid, fumarate, and l -aspartate, were thought to be important flavor precursors contributing to the Laiwu pig's improved pork taste. [ABSTRACT FROM AUTHOR]

• The proteome profiles with different quality meats were performed by TMT labeling together with MS. • High quality (HQ) meats had lower level of glycolysis, oxidative stress, and apoptosis compared to low quality (LQ) meats. • The results provided possible target proteins in porcine meat quality prediction. To explore the molecular mechanisms of meat quality, four high-quality (HQ) samples and four low-quality (LQ) samples from longissimus dorsi muscles were chosen, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) were performed to find associations between meat quality and proteome profiles. The LQ meats had lower pH, lighter color, and higher drip loss compared to the HQ meats. About 140 differentially expressed proteins were identified. Functional analysis results of differentially expressed proteins showed that decreased release of Ca2+, lower contents of type II fibers, lower contents of glycogen, and decreased glycogenolysis in HQ meats indicated a lower degree of glycolysis in HQ as compared to LQ meats. Meanwhile, some differentially expressed proteins suggested that the levels of oxidative stress and apoptosis were lower in HQ meats than in LQ meats. This study reveals physiological changes between HQ and LQ meats according to the proteome profiles. [ABSTRACT FROM AUTHOR]