Whole-genome SNP allele frequency differences between Tibetan and Large white pigs reveal genes associated with skeletal muscle growth

Abstract

Background: The skeletal muscle growth rate and body size of Tibetan pigs (TIB) are lower than Large white pigs (LW). However, the underlying genetic basis attributing to these differences remains uncertain. To address this knowledge gap, the present study employed whole-genome sequencing of TIB (slow growth) and LW (fast growth) individuals, and integrated with existing NCBI sequencing datasets of TIB and LW individuals, enabling the identification of a comprehensive set of genetic variations for each breed. The specific and predominant SNPs in the TIB and LW populations were detected by using a cutoff value of 0.50 for SNP allele frequency and absolute allele frequency differences (△AF) between the TIB and LW populations.

Results: A total of 21,767,938 SNPs were retrieved from 44 TIB and 29 LW genomes. The analysis detected 2,893,106 (13.29%) and 813,310 (3.74%) specific and predominant SNPs in the TIB and LW populations, and annotated to 24,560 genes. Further GO analysis revealed 291 genes involved in biological processes related to striated and/or skeletal muscle differentiation, proliferation, hypertrophy, regulation of striated muscle cell differentiation and proliferation, and myoblast differentiation and fusion. These 291 genes included crucial regulators of muscle cell determination, proliferation, differentiation, and hypertrophy, such as members of the Myogenic regulatory factors (MRF) (MYOD, MYF5, MYOG, MYF6) and Myocyte enhancer factor 2 (MEF2) (MEF2A, MEF2C, MEF2D) families, as well as muscle growth inhibitors (MSTN, ACVR1, and SMAD1); KEGG pathway analysis revealed 106 and 20 genes were found in muscle growth related positive and negative regulatory signaling pathways. Notably, genes critical for protein synthesis, such as MTOR, IGF1, IGF1R, IRS1, INSR, and RPS6KA6, were implicated in these pathways.

Conclusion: This study employed an effective methodology to rigorously identify the potential genes associated with skeletal muscle development. A substantial number of SNPs and genes that potentially play roles in the divergence observed in skeletal muscle growth between the TIB and LW breeds were identified. These findings offer valuable insights into the genetic underpinnings of skeletal muscle development and present opportunities for enhancing meat production through pig breeding.

Keywords: Large white pigs; Predominant SNPs; Skeletal muscle growth; Specific SNPs; Tibetan pigs; Whole-genome SNPs.

Fig. 1

Summary of TIB-specific and predominant SNP metrics. (A) TIB specific SNP density for each chromosome; (B) Percentage of TIB-specific SNPs on each chromosome; (C) Allele frequency distribution of TIB-specific SNPs; (D) Location and functional classification of TIB-specific SNPs; (E) Distribution of TIB-predominant SNP △AF between TIB and LW

Fig. 2

Summary of LW-specific and predominant SNP metrics. (A) LW-specific SNP density on each chromosome; (B) Percentage of LW-specific SNPs on each chromosome; (C) Allele frequency distribution of LW-specific SNPs; (D) Location and functional classification of LW-specific SNPs; (E) Distribution of LW-predominant SNP △AF between LW and TIB

Fig. 3

Muscle-related GO terms and genes identified by GO analysis. Muscle development related GO terms for candidate genes (A), and SNP allele frequency of MSTN (B), ACVR1 (C) and SMAD1 (D) genes in TIB and LW populations

Fig. 4

Haplotype blocks of MEF2A, MEF2C, MEF2D, MSTN, MYF5, MYOD, MYOG, MTOR genes in TIB and LW populations

Fig. 5

Genes involved in the mTOR and TGFβ/myostatin/activin/BMP signaling pathways. (A) Ten genes involved in the mTOR signaling pathway harbored missense variations (green box) and 19 genes harbored TIB-specific SNPs with allele frequency > = 0.95 (red box); (B) Genes involved in TGFβ/myostatin/activin/BMP signaling pathway harbored TIB-specific SNPs with allele frequency > = 0.95(red box); (C) SNP allele frequency of RPS6KA6 genes in TIB and LW populations. The mTOR signaling pathway map were downloaded from https://www.kegg.jp/kegg/pathway.html [34], and the TGFβ/myostatin/activin/BMP signaling diagram was adapted from [35]

Fig. 6

Identifying skeletal muscle development related genes by selective sweep analysis. (A) Distribution of F_ST values calculated in 50 kb sliding window size with 10 kb step size between TIB and LW; (B) π-ratio (π_LW/π_TIB) was calculated by π value in LW / π value in TIB in 50 kb window size with 10 kb step size; (C) Overlap genes between PSGs and muscle related genes enriched in 67 muscle related biological process by GO analysis for candidate genes was showed by Venn diagram. Each dot represented 50 kb sliding window size and 10 kb step size, within which the average F_ST value and π-ratio (π_LW/π_TIB) were calculated. The blue line was the top 5% of F_ST (0.58) and π-ratio (π_LW/π_TIB) (1.20) line. Genes visualized in (A) and (B) were the overlap genes