Transcriptomic Insights into Muscle and Fat Traits in Deccani and Nellore Sheep

This study investigated breed-specific differences in muscle growth and intramuscular fat (IMF) accumulation between Nellore (meat type) and Deccani (dual-purpose) sheep from the Deccan plateau. Carcass evaluation showed significantly higher hot and cold carcass weights and yields in Nellore sheep, along with larger myofibrillar cross-sectional areas (p = 0.012), indicating enhanced musculature. In contrast, Deccani sheep exhibited higher IMF content (p = 0.006), suggesting improved meat flavor and juiciness. Total RNA was extracted from longissimus dorsi muscle and liver tissues using TRIzol reagent, and only RNA samples with RNA Integrity Numbers (RIN) between 5.0 and 7.0 were selected for transcriptome analysis. Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 platform using paired-end reads (2 x 150 bp). Transcriptomic profiling identified differentially expressed genes (DEGs) associated with muscle growth in Nellore and lipid metabolism in Deccani sheep. Functional enrichment analysis revealed 46 significantly enriched Gene Ontology (GO) terms (p < 0.05), providing new insights into the genetic regulation of carcass traits in Indian sheep breeds.