Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India

Abstract

This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep. The longissimus thoracis transcriptome profiles of Bandur and local sheep were obtained using RNA sequencing (RNA Seq). The animals were male, non-castrated, with uniform age and reared under similar environment, as well as management conditions. We could identify 568 significantly up-regulated and 538 significantly down-regulated genes in Bandur sheep (p≤0.05). Among these, 181 up-regulated and 142 down-regulated genes in Bandur sheep, with a fold change ≥1.5, were considered for further analysis. Significant Gene Ontology terms for the up-regulated dataset in Bandur sheep included transporter activity, substrate specific transmembrane, lipid and fatty acid binding. The down-regulated activities in Bandur sheep were mainly related to RNA degradation, regulation of ERK1 and ERK2 cascades and innate immune response. The MAPK signaling pathway, Adipocytokine signaling pathway and PPAR signaling pathway were enriched for Bandur sheep. The highly connected genes identified by network analysis were CNOT2 , CNOT6 , HSPB1 , HSPA6 , MAP3K14 and PPARD , which may be important regulators of energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. These key genes affect the CCR4-NOT complex, PPAR and MAPK signaling pathways. The highly connected genes identified in this study, form interesting candidates for further research on muscle traits in Bandur sheep.

Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits

“…Our results indicate that the differentially expressed miRNAs in Bandur and local sheep were mainly implicated in myogenesis and lipid metabolism. These observations are consistent with our previous study on mRNAs of the same animals 24 . Even though the shear force estimates between the two sheep populations under investigation were significantly different, we did not find miR-182, miR-183 and miR-338 to be differentially expressed.…”

“…The key pathways known to be involved in muscle metabolism and development were observed to be enriched in our study. The enrichment of cellular response to stress and fatty acid metabolism pathways corroborate our previous results on mRNA expression in Bandur sheep 24 .…”

“…All the up-regulated miRNAs in Bandur sheep were used for gene target prediction and genes associated with tenderness/meat quality (identified from published literature) were filtered from the dataset. The genes list was then compared with our previous data on mRNA of Bandur sheep 24 and only those genes that were differentially expressed were selected. A total of 32 miRNAs were identified as potential candidates for regulating meat tenderness (Table S2).…”

“…The phenotypes, carcass measurements and muscle tenderness of the animals used in this study have been previously described 24 . The animals were slaughtered according to standard commercial 'halal' procedures.…”

Integrating a Genome-Wide Association Study With Transcriptome Analyses to Identify Candidate Genes and Pathways for Feed Conversion Ratio in Yorkshire Pigs

“…CNOT2 is an important regulator for energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. The heterozygous intragenic deletion of CNOT2 displayed disordered phenotypes of learning disability, developmental delay, and hypothyroidism [65,66]. TRHDE is an extracellular peptidase that specifically degrades the TRH to regulate appetite and metabolism [67,68].…”