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

Date Published: June 6, 2019

Publisher: Public Library of Science

Author(s): Reena Arora, Naveen Kumar S., Sudarshan S., Mohamed Nadeem Fairoze, Mandeep Kaur, Anju Sharma, Yashila Girdhar, Sreesujatha R. M., Suresh K. Devatkal, Sonika Ahlawat, Ramesh Kumar Vijh, Manjunatha S. S., Juan J. Loor.


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.

Partial Text

India possesses 6% of the world’s sheep population [1], with 42 registered breeds & several lesser known ones [2]. The economic potential of this ovine biodiversity remains underutilized due to lack of knowledge of their genetic characteristics. Sheep contribute to 7.6% of the total meat production in India [1]. Bandur is a famous mutton type sheep breed of India which is preferred by consumers for its palatability. It fetches a higher price than mutton from other breeds in the same area [3]. It is a registered breed, also known as Mandya or Bannur, mainly distributed in Mandya district of Karnataka. The Bandur animals have a compact body, white coat and a typical reversed U-shaped conformation from the rear [4]. Another population of sheep found in the same area, which is not registered is referred as the local sheep.The local sheep are medium built, heavier than Bandur, with a light brown coat colour. The geographical and management conditions as well as available feed and fodder are similar for both populations. Mutton from Bandur sheep is favoured over local sheep by consumers. The specific organoleptic quality of Bandur meat are attributed to the intramuscular fat content, climate and feed, however, such claims have not been substantiated with scientific studies. The Bandur breed is used for genetic improvement of local sheep population [3]. Despite the local popularity and market potential, no scientific information is available on the uniqueness of its meat quality or muscle traits. Some information is available on the carcass traits for Bandur sheep [5,6,7], but genetic analysis is still lacking.

The present study investigated the gene differences in skeletal muscles of phenotypically diverse sheep populations. The animals compared in the study were of similar age, sex and reared under similar environment as well as management conditions. Our results revealed differences in the physico-chemical traits of meat from both local and Bandur sheep. A total of 99 highly significant DE genes with fold change ≥ ±2.0 and p<0.05, were identified in our study. Most of the genes identified in our study were related to muscle development or differentiation, fat metabolism and to a lesser extent to energy metabolism, cellular stress and immune response. Molecular events that occur during muscle development, fat deposition, post-mortem proteolysis and energy metabolism are important for underpinning genes underlying meat quality. Therefore, in this study we focused the analysis on genes and pathways that are known to be associated with muscle development, lipid metabolism, tenderness of muscles and postmortem proteolysis.   Source: