Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

Abstract

Carcass weight, meat quality and muscle components are important traits economically and they underpin most of the commercial return to goat producers. In this study, the Longissimus dorsi muscle tissues were collected from five Liaoning cashmere (LC) goats and five Ziwuling black (ZB) goats with phenotypic difference in carcass weight, some meat quality traits and muscle components. The histological quantitative of collagen fibers and the transcriptome profiles in the Longissimus dorsi muscle tissues were investigated using Masson-trichrome staining and RNA-Seq, respectively. The percentage of total collagen fibers in the Longissimus dorsi muscle tissues from ZB goats was less than those from LC goats, suggesting that these ZB goats had more tender meat. An average of 15,919 and 15,582 genes were found to be expressed in Longissimus dorsi muscle tissues from LC and ZB goats, respectively. Compared to LC goats, the expression levels of 78 genes were up-regulated in ZB goats, while 133 genes were down-regulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in GO terms related to the muscle growth and development and the deposition of intramuscular fat and lipid metabolism, hippo signaling pathway and Jak-STAT signaling pathway. The results provide an improved understanding of the genetic mechanisms regulating meat production performance in goats, and will help us improve the accuracy of selection for meat traits in goats using marker-assisted selection based on these differentially expressed genes obtained.

Keywords: Liaoning cashmere goats; RNA-Seq; Ziwuling black goats; differentially expressed gene; skeletal muscle.

FIGURE 1

The percentage of collagen fibers in the Longissimus dorsi muscle (%). (A) The micrographs (400×) of the Longissimus dorsi muscle from LC rams. (B) The micrographs (400×) of the Longissimus dorsi muscle from ZB rams. The collagen fibers and muscle fibers in the Longissimus dorsi muscle tissues were stained with blue and red, respectively. (C) Comparison of the percentage of collagen fibers in the Longissimus dorsi muscle tissues from LC rams, with those from ZB rams; ^∗p < 0.05.

FIGURE 2

Volcano plot comparing the change in gene expression of the LC goats and ZB goats. The red and blue dots represent the up-regulated and down-regulated genes in the Longissimus dorsi muscle tissues of ZB goats compared to the Longissimus dorsi muscle tissues of LC goats, respectively (FDR < 0.05). The black dots represent genes that are not significantly different in the two caprine breeds (FDR > 0.05).

FIGURE 3

The classification of Gene Ontology (GO) terms for up-regulated genes (A) and down-regulated genes (B) in ZB goats compared to LC goats. The most enriched biological process, cellular component and molecular function GO terms are shown.

FIGURE 4

KEGG pathway analysis for the up-regulated genes (A) and down-regulated genes (B) in ZB goats compared to LC goats.

FIGURE 5

Comparison of gene expression levels obtained by RNA-Seq, with those measured using RT-qPCR for 20 randomly selected DEGs. These contained ten up-regulated genes and ten down-regulated genes in ZB goats compared to LC goats. The expression level values for the RT-qPCR were normalized by GAPDH and β-actin genes. The error bars represent the variation in the five separate goats studied per breed.