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. 2019 Jun 6;14(6):e0217461.
doi: 10.1371/journal.pone.0217461. eCollection 2019.

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

Reena Arora  1 , Naveen Kumar S  2 , Sudarshan S  2 , Mohamed Nadeem Fairoze  2 , Mandeep Kaur  1 , Anju Sharma  1 , Yashila Girdhar  1 , Sreesujatha R M  2 , Suresh K Devatkal  3 , Sonika Ahlawat  1 , Ramesh Kumar Vijh  1 , Manjunatha S S  2
Affiliations

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

Reena Arora et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Functional classification of DE genes in Bandur and local sheep.
Fig 2
Fig 2
Gene Ontology terms for different categories for (a) up-regulated and (b) down-regulated DE genes in Bandur sheep.
Fig 3
Fig 3. The co-expression network of 99 DE genes based on GeneMANIA.
Fig 4
Fig 4. Subnetwork of core DE genes with ≥5.0 degree and a fold change of ≥2.0 (50 nodes and 97 edges).
Colour intensity of top 20 genes decreases with increasing order of rank (from light orange to red).
Fig 5
Fig 5. Comparison of fold-change (log10) between RNAseq and qRT-PCR data, for selected genes across Bandur and local sheep.
qRT-PCR data was normalized by GAPDH and B2M genes.
See this image and copyright information in PMC

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