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Comparative muscle transcriptome associated with carcass traits of Nellore cattle

ABSTRACT: Comparative muscle transcriptome associated with carcass traits of Nellore cattle

PROVIDER: PRJEB19421 | ENA |

REPOSITORIES: ENA

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Project description:Adipose tissue plays a critical role in growth, energy metabolism, and carcass composition in pigs. However, the age-dependent molecular mechanisms underlying backfat development remain poorly characterized, particularly in native breeds such as the Ningxiang pig, which exhibits high fat deposition and distinct growth patterns. This study aimed to characterize the dynamic proteomic changes in backfat tissue across postnatal development and identify molecular pathways and candidate proteins associated with economically important carcass traits. We performed a comprehensive proteomic analysis of backfat tissue collected from Ningxiang pigs across seven postnatal developmental stages (day 60 to 360). Using high-resolution mass spectrometry, we quantified dynamic changes in protein abundance and explored their functional relevance through gene ontology (GO) enrichment and network-based analyses. Principal component analysis revealed clear age-related separation in proteomic profiles, particularly between early (day 60–120) and later developmental stages. GO enrichment analysis of differentially abundant proteins indicated significant overrepresentation of biological processes related to energy metabolism, translation, immune response, and mitochondrial function in older age groups. Further curation of lipid metabolism pathways identified hundreds of proteins involved in lipogenesis and lipolysis, many of which displayed distinct age-dependent expression patterns. To link protein expression to economically important traits, we performed weighted gene co-expression network analysis (WGCNA), identifying four protein modules significantly associated with carcass characteristics such as lean meat percentage, fat content, and carcass weight. From these modules, we identified four key hub proteins— ALDH18A1, FABP4, FBP1, and HADHB—with known roles in lipid transport, gluconeogenesis, amino acid metabolism, and fatty acid oxidation, respectively. This study provides novel insights into the proteomic remodeling of backfat during postnatal development and highlights potential molecular targets for improving carcass quality in pigs. Our findings contribute to a deeper understanding of adipose tissue biology and offer a valuable resource for future genetic and breeding strategies.This study provides the first in-depth proteomic characterization of backfat development across seven postnatal stages in Ningxiang pigs, a native Chinese breed known for high fat deposition. By integrating high-resolution mass spectrometry with gene ontology and co-expression network analyses, we uncovered dynamic, age-dependent changes in protein abundance linked to key biological processes, including energy metabolism, immune function, and mitochondrial activity. Notably, we identified four protein modules significantly associated with carcass traits such as lean meat percentage and fat content, and highlighted four hub proteins (ALDH18A1, FABP4, FBP1, and HADHB) as potential molecular markers for selective breeding. These findings advance our understanding of adipose tissue biology and provide actionable molecular targets for improving carcass composition in pigs. The work also offers a valuable reference dataset for future functional genomics and precision breeding efforts in indigenous and commercial pig populations.

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Comparative muscle transcriptome associated with carcass traits of Nellore cattle

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