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

Abstract

The study presents the miRNA profiles of two Indian sheep populations with divergent carcass and muscle traits. The RNA sequencing of longissimus thoracis muscles from the two populations revealed a total of 400 known miRNAs. Myomirs or miRNAs specific to skeletal muscles identified in our data included oar-miR-1, oar-miR-133b, oar-miR-206 and oar-miR-486. Comparison of the two populations led to identification of 100 differentially expressed miRNAs (p < 0.05). A total of 45 miRNAs exhibited a log2 fold change of ≥ ( ±) 3.0. Gene Ontology analysis revealed cell proliferation, epithelial to mesenchymal transition, apoptosis, immune response and cell differentiation as the most significant functions of the differentially expressed miRNAs. The differential expression of some miRNAs was validated by qRT-PCR analysis. Enriched pathways included metabolism of proteins and lipids, PI3K-Akt, EGFR and cellular response to stress. The microRNA-gene interaction network revealed miR-21, miR-155, miR-143, miR-221 and miR-23a as the nodal miRNAs, with multiple targets. MicroRNA-21 formed the focal point of the network with 42 interactions. The hub miRNAs identified in our study form putative regulatory candidates for future research on meat quality traits in Indian sheep. Our results provide insight into the biological pathways and regulatory molecules implicated in muscling traits of sheep.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

“…On the other hand, DP had an almost significant signal on BTA1: the gene closest to the SNP was SIM2 , already known to be associated with carcass quality, differentiation of longissimus, and semimembranosus muscle ( De Las Heras-Saldana et al, 2019 ; Edea et al, 2020 ). To conclude, the strongest of the remaining suggestively associated signals for DP came from BTA4, within LOC112446424 , a non-coding RNA close to candidate gene SLC13A4 , a cationic canal important both for muscle traits in sheep and growth and development in cattle ( Carvalho et al, 2020 ; Kaur et al, 2020 ).…”

Muscle transcriptome provides the first insight into the dynamics of gene expression with progression of age in sheep

“…It is interesting to note that this activity is in turn dependent on MAPK and NFκβ signaling 27 . Recent studies on Bandur sheep have also reported the enrichment of the PI3K-Akt and MAPK pathways that are associated with hypertrophy as well muscle differentiation 12 , 13 . These pathways were enriched in the young animals.…”

“…Consumer preferences for Bandur sheep in India led to the investigation that established tenderness and higher backfat content in muscles of Bandur sheep as compared to local sheep found in the same area 12 . Our previous studies have attempted to understand the regulatory molecular mechanisms underlying the muscle traits in Bandur sheep breed in comparison to the local sheep 12 , 13 . These studies have identified the genes and pathways that may be associated with the muscling traits.…”

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

“…A miRNA, miR-192, was reported to regulate the myogenic differentiation and proliferation of skeletal muscle sheep satellite cells [ 44 ], which are responsible for producing myoblasts in skeletal muscle [ 118 ], through regulating the repression of retinoblastoma 1, which is a known regulator of myogenesis [ 119 ]. Additionally, miR-1, miR-133b, miR-206, and miR-486 were also reported to be differential expressed in the skeletal muscle of sheep and predicted to correlate with the development of skeletal muscle [ 120 ].…”