| Summary: | Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregulated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. <i>PPAPA</i>, <i>FOXO3</i>, <i>FASN</i>, <i>PNPLA2</i>, <i>FKBP5</i>, <i>TCF7L2</i>, <i>BMP2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>ZBTB16</i>, <i>SIRT</i>, <i>GYG2</i>, <i>NCOR1,</i> and <i>NR3C1</i> were involved in the regulation of abdominal fat deposition. <i>PNPLA2</i>, <i>TCF7L2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>BMP2</i>, <i>FKBP5</i>, <i>GYG2</i>, and <i>ZBTB16</i> were regulated by the lncRNAs TCONS_00038080, TCONS_0033547, TCONS_00066773, XR_001190174.3, XR_003492471.1, XR_003493494.1, XR_001192142.3, XR_002405656.2, XR_002401822.2, XR_003497063.1, and so on. This study lays foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks.
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