Selection and validation of reference genes for the normalization of quantitative real-time PCR in different muscle tissues of rabbits

BACKGROUND: In molecular biology studies, the selection of optimal reference genes is of vital importance for accurately quantifying gene expression. The purpose of the present study was to screen the most stable reference genes in different muscle tissues of New Zealand white rabbits and Yufeng yellow rabbits. METHODS AND RESULTS: Results indicated that the most stable reference genes in the muscle tissues of New Zealand white rabbits were HPRT1, ACTB and PPIC, while HPRT1, PPIC, and RPL13A were the most stable reference genes in muscle tissues of Yufeng yellow rabbits. However, in the longissimus dorsi muscle and the abdominal wall muscle of both varieties, the most stable reference genes were HPRT1, RPL13A, and SDHA. In the quadriceps femoris muscle, the most stable reference genes were ACTB, HPRT1, and SDHA. Furthermore, the relative abundance of MYOG, MYH3 and MSTN was used to confirm the suitability and reliability of the selected most stable reference genes and the most unstable reference gene. Results revealed the same expression patterns of these myogenic genes when normalized according to the most stable genes, while normalization against the unstable reference gene altered the observed expression patterns. CONCLUSIONS: Taken together, our results demonstrated that the most stable reference genes varied among different muscle tissues and different breeds of rabbits. However, HPRT1, PPIC and SDHA presented high stability among all examined reference genes; thus, the combined analysis of HPRT1/ PPIC/ SDHA gene provides the best reference for RT-qPCR in muscle tissues of New Zealand white rabbits and Yufeng yellow rabbits, while HPRT1 is a better choice than other reference genes when using a single reference gene to assess target gene expression. Our results provide basic data for better measuring target gene expression profiles in muscle tissues of rabbits. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40850-022-00159-0.