Multi-omics integration characterizes meat quality differences between duroc × wujin × yorkshire and duroc × landrace × yorkshire pigs

Improving pork quality is a core objective in modern pig breeding programs, and the introduction of Chinese indigenous pig lineage represents a significant strategy for enhancing meat quality. Building on the well-established consensus that meat quality traits exhibit distinct phenotypic differences between lean-type and fat-type pig breeds, we hypothesized that incorporating Wujin pig lineages into DWY (Duroc × Wujin × Yorkshire) pigs can improve meat quality traits to a certain extent via the regulation of lipid metabolism networks, compared with DLY (Duroc × Landrace × Yorkshire) pigs. To explore this, integrated transcriptomic and proteomic analyses were conducted to systematically identify key regulators underlying these variances. Phenotypic evaluations revealed that DWY pigs exhibited significantly higher intramuscular fat content (IMF), enhanced water-holding capacity (WHC), and improved meat color relative to DLY pigs. Furthermore, fatty acid profiling revealed elevated levels of oleic acid (C18:1n9) and linoleic acid (C18:2n6c) in DWY pigs. Transcriptomic analysis showed that up-regulated differentially expressed genes in DWY pigs were primarily enriched in pathways related to lipid metabolism and cytoskeletal organization. Proteomic analysis further identified differentially accumulated proteins associated with the skeletal muscle cytoskeleton. Key candidate genes, including PLIN1 , SCD , ADIPOQ , THBS2 , and ACTC1 , were identified as crucial regulators of these traits. From co-expression network analysis, LIMK1 and ATP2A are closely correlated with WHC. These multi-omics findings suggest a potential molecular basis through which Chinese indigenous pig lineage influences pork quality and support the rational utilization of Chinese indigenous pig breeds in commercial breeding strategies.