# Transcriptomic Exploration of Muscle Development and Fat Deposition Trait Diversity in Selected Indian Sheep Breeds: Implications for Meat Quality and Yield

## TL;DR

This study compares muscle and fat traits in two Indian sheep breeds using gene activity and tissue analysis to improve meat quality and yield.

## Contribution

The first comparative transcriptomic and histological analysis of muscle and fat traits in Nellore and Deccani sheep breeds in India.

## Key findings

- Nellore sheep showed enhanced musculature with higher carcass weight and yield.
- Deccani sheep exhibited elevated intramuscular fat deposition linked to better meat flavor.
- Transcriptomic analysis identified breed-specific genes related to muscle development and lipid metabolism.

## Abstract

This study aimed to explore the muscle development and fat deposition trait diversity in Nellore (meat-type) and Deccani (wool-meat type) sheep breeds of India by integrating transcriptomics profiling, carcass characteristics, and histological analysis of longissimus dorsi muscle and liver tissues. Differential gene expression analysis revealed the genes that are associated with muscle development and fat deposition, while the functional enrichment analysis unveiled the underlying molecular mechanisms involved in lipid storage, triglyceride synthesis, muscle development, mitochondrial oxidation, etc. As the first comparative investigation of transcriptomics profiles, carcass characteristics and histological analysis of myofibrillar cross-sectional area between Nellore and Deccani breeds of India, it not only enhances our understanding of genotype–phenotype relationships in the selected Indian sheep but also lays the foundation for genomic selection strategies aimed at improving meat production and quality.

Sheep’s meat production and quality are influenced by genetic and physiological factors that affect muscle development, growth, and fat deposition metabolism. However, the breed-specific transcriptional landscapes driving these traits in Indian sheep breeds, especially in Nellore (meat-type) and Deccani (wool-meat type) breeds are remain unexplored. Therefore, this study aimed to investigate the differences in muscle growth and fat deposition between Nellore and Deccani breeds by integrating transcriptomic profiling, carcass characteristics, and histological analysis of longissimus dorsi muscle and liver tissues. Carcass assessment revealed higher Hot Carcass Weight (HCW), Cold Carcass Weight (CCW), Hot Carcass Yield (HCY) and Cold Carcass Yield (CCY), and larger myofibrillar cross-sectional area (p < 0.05), indicating enhanced musculature, which was observed in Nellore. Deccani showed elevated Intramuscular Fat (IMF) deposition (p < 0.05), indicating improved meat flavour/juiciness. Transcriptomic profiling revealed several Differentially Expressed Genes (DEGs) associated with meat quality and quantity traits. In Nellore, the genes WFIKKN2, FGFRL1, FKBP4, and IRF1 were upregulated, while the gene TAS1R2 was downregulated, leading to enhanced muscle development, superior carcass traits, thermotolerance, and immunity. While Deccani showed higher expression of lipid metabolism genes PLA2G4F, ACSL1, ACOX1, CPT1A, and PLIN1, which are linked to higher IMF content. Functional enrichment analysis revealed 46 significantly enriched GO terms for the DEGs (p < 0.05), including oxidoreductase activity, muscle development, etc. These outcomes demonstrate novel genetic markers and key biological insights into the regulation of muscle development, thermotolerance, immunity, and IMF for future validation in Indian sheep breeds.