Vasu, Mahanthi, Ahlawat, Sonika, Choudhary, Vikas, Kaur, Rashmeet, Arora, Reena, Sharma, Rekha, Sharma, Upasna, Chhabra, Pooja, Mir, MA, and Kumar Singh, Manoj
• A systematic assessment of 18 potential reference genes (RGs) in 10 different ovine tissues was carried out to identify internal control genes for qPCR analysis. • Four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), were employed to rank the stability of these RGs. • RefFinder was used for a comprehensive ranking, identifying ACTB, PPIB, BACH1 , and B2M as the most stable RGs. • RPS9, RPS15 , and PGK1 showed variable expression across different tissues. • Validation was performed using qPCR analysis of four target genes in the skin from two sheep breeds. Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB , BACH1 , B2M , GAPDH , HMBS , HPRT1 , PGK1 , PPIA , PPIB , RPLP0 , RPL19 , RPS9 , RPS15 , RPS28 , SDHA , TBP , UXT , and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1 , and B2M emerged as the most stable RGs, while RPS9, RPS15 , and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1 , and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1 , and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues. [ABSTRACT FROM AUTHOR]