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Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

ABSTRACT: Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

PROVIDER: PRJNA638286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11964160.fastq.gz	Fastqsanger.gz
	SRR11964161.fastq.gz	Fastqsanger.gz
	SRR11964162.fastq.gz	Fastqsanger.gz
	SRR11964163.fastq.gz	Fastqsanger.gz
	SRR11964164.fastq.gz	Fastqsanger.gz

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Project description:Fat deposition is a prominent economic trait and complex process in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Histological analysis of backfat tissue showed that adipocyte area increased and adipocyte number decreased with the development of backfat tissue in different stages (60d, 120d, 180d, 240d, 300d, and 360d). Meanwhile, a total of 1024 differentially expressed genes were identified in five comparison groups (120d vs 60d, 180d vs 120d, 240d vs 180d, 300d vs 240d, and 360d vs 300d). And then strongly co-expressed genes in modules were clustered by Weighted gene co-expression network analysis (WGCNA). Among these modules, turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had close correlation with 60d, 120d, 180d, 240d, 300d, and 360d developmental stage, respectively, while tan, black and turquoise module had intimate relation with backfat thickness, adipocyte area and adipocyte number, respectively. Furthermore, GO and KEGG enrichment were analyzed in each module, the gene co-expression network was constructed, and the hub genes were described. According to the co-expression network, 13 genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized as hub genes. Further analysis revealed that ACSL1 and ACOX1 might perform considerable function in early developmental stage of backfat tissue before 60d. FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position around 120d developmental stage. Besides, the functional relevance associated with SELP and backfat thickness, DNM1 and adipocyte area needs to be elucidated. In addition, QCR analysis validated the strong consistency of genes expressions with RNA-seq data, manifesting the reliability and accuracy of our study. The present research preliminarily depicted the gene co-expression network for each period of backfat developmental stage in Ningxiang pigs, which not only help to understand the integrated mechanism underlying backfat tissue development and lipid metabolism, but also promotes the progress of genetic improvement in pigs.

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.

Dataset Information

Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

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