Transcriptome-metabolome analysis reveals how sires affect meat quality in hybrid sheep populations

Abstract

Crossbreeding improves and enhances meat quality and is widely used in sheep production; however, the molecular mechanisms underlying the meat quality of various crossbred sheep remain unknown. In this study, male Southdown, Suffolk and Hu sheep were crossbred with female Hu sheep, and the transcriptomes and metabolomes of the longissimus dorsi muscle of the F1 generation were sequenced to explore how different sire breeds affect meat quality. The results showed that 631 differentially expressed genes and 119 significantly altered metabolites contributed to muscle development characteristics and meat quality-related diversity (P < 0.05). These genes and metabolites were significantly enriched in lipid metabolism pathways, including arachidonic acid metabolism and PPAR signaling. Several candidate genes were associated with muscle growth, such as MYLK3, MYL10, FIGN, MYH8, MYOM3, LMCD1, and FLRT1. Among these, MYH8 and MYL10 participated in regulating muscle growth and development and were correlated with meat quality-related fatty acid levels (|r| > 0.5 and p < 0.05). We selected mRNA from four of these genes to verify the accuracy of the sequencing data via qRT-PCR. Our findings provide further insight into the key genes and metabolites involved in muscle growth and meat quality in hybrid sheep populations.

Keywords: hybridization; meat quality; metabolomics; sheep; transcriptomics.

FIGURE 1

Transcriptomic comparisons of the longissimus dorsi for the HH, SH and NH sheep. (A) Volcano plots of the DEGs, non-diff: non-differentially expressed genes. (B) Statistical map of the DEGs. (C) Cluster heatmap of the DEGs, red: upregulated genes; blue: downregulated genes.

FIGURE 2

Functional enrichment analysis of the longissimus dorsi samples of the HH, SH an NH sheep. (A) GO analysis of the DEGs in the three groups. The ordinate indicates the GO terms. (B) Bubble diagram of the top 20 KEGG pathway enrichments for the HH-NH, HH-SH, and SH-NH comparisons. The ordinate indicates the pathways.

FIGURE 3

LC-MS/MS analysis longissimus dorsi metabolic profiles for the HH, SH and NH sheep. (A) PCA score plots of positive mode; (B) Number of up/down-regulated metabolites of different compared groups in POS and NEG modes; (C) OPLS-DA of HH-SH, HH-NH and SH-NH comparisons in positive mode.

FIGURE 4

Bubble diagram of top 20 KEGG pathway enrichment in HH-SH, HH-NH, and SH-NH comparisons. The ordinate indicates the pathways.

FIGURE 5

GC-MS/MS analysis longissimus dorsi metabolic profiles for the HH, SH and NH sheep. (A) OPLS-DA of HH-SH, HH-NH and SH-NH comparisons; (B) Number of up/down-regulated metabolites of different compared groups; red: up-regulated genes; blue: down-regulated genes.

FIGURE 6

Bubble diagram of top 20 KEGG pathway enrichment in HH-SH, HH-NH, and SH-NH comparisons. The ordinate indicates the pathways.

FIGURE 7

Correlation and pathway analysis of significant differential compounds and verification of the associated DEGs. (A) Correlation analysis of the significant differential metabolites and the DEGs; (B) Cytoscape representation of candidate gene TM7SF2 and co-expressed differential metabolites involved in lipid metabolism. Hub gene TM7SF2 is in red; related differential metabolites are in blue circles, and the three trait-related metabolites are in green.

FIGURE 8

Confirmation of expression patterns of the four selected genes via qRT-PCR. The qRT-PCR results were consistent with the RNA-seq data. (A) MYBPH; (B) TMP3; (C) TNNT1; (D) MYLK2.