Comprehensive Identification of miRNAs and circRNAs in the Regulation of Intramuscular and Subcutaneous Fat Deposition in Meat Ducks

Fat deposition is an important factor that affects meat production and its quality in livestock animals, including poultry. Non-coding RNAs (ncRNAs) play an important role in duck fat deposition. This study aims to systematically identify key regulatory molecules involved in fat deposition in 8-day-old Cherry Valley ducks through transcriptomic sequencing across four sample groups: intramuscular pre-adipocytes (IMP-0), intramuscular adipocytes after 4 days of induction (IMP-4), subcutaneous pre-adipocytes (SCP-0), and subcutaneous adipocytes after 4 days of induction (SCP-4). Differential expression analysis preliminarily identified several circRNAs and miRNAs differentially expressed during adipocyte differentiation, including novel_circ_000012, novel_circ_000037, novel_circ_000089, as well as miR-501-y, miR-378-y, and miR-3968-y. Further co-expression network analysis revealed that the network constructed during intramuscular adipocyte differentiation comprised 17 nodes and 39 edges, while the network constructed during subcutaneous adipocyte differentiation was larger, containing 39 nodes and 50 edges. Based on connectivity screening, we identified several key miRNAs, such as novel-m0630-5p, novel-m0485-5p, novel-m0672-5p, miR-5126-y, and miR-1408-y. Notably, this study uncovered several novel ceRNA regulatory axes during intramuscular and subcutaneous adipocyte differentiation, including novel_circ_001327/miR-141-y/<i>Zdhhc1</i>, novel_circ_002268/miR-2478-y/<i>ACLY</i>, and novel_circ_002268/miR-3963-x/<i>ACLY</i>. These findings provide crucial molecular insights into the specific deposition mechanisms of intramuscular versus subcutaneous fat in meat ducks, offering valuable targets for molecular breeding programs aimed at improving meat quality.