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RNA-seq and ATAC-seq data from pig jejunum with high and low feed efficiency

ABSTRACT: RNA-seq and ATAC-seq data from pig jejunum with high and low feed efficiency

PROVIDER: PRJNA1186677 | ENA |

REPOSITORIES: ENA

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RNA-seq and ATAC-seq data from pig jejunum with high and low feed efficiency

Project description:Feed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how pigs process and utilize feed. To explore the genetic and regulatory mechanisms behind FE, we conducted an integrative multi-omics study using RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on pigs with high and low FE. By comparing gene expression and chromatin accessibility profiles in the jejunum, we identified key differentially expressed genes (DEGs) and differentially accessible regions (DARs) associated with lipid metabolism and immune function, both of which are critical pathways for efficient growth. Notably, we identified transcription factors such as GATA4 and EHF and genes like SCARB1 and GRXCR1 that may play regulatory roles in FE. Our findings provide novel insights into the molecular mechanisms governing FE in pigs, offering potential targets for genetic selection and nutritional interventions to enhance feed efficiency and sustainability in pig production.

2025-01-29 | GSE282017 | GEO

Integrating multi-omics data to identify key functional variants affecting feed efficiency in pigs

Project description:Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.

2024-09-30 | GSE270124 | GEO

RNA-seq of muscle from pigs divergent in feed efficiency and product quality

Project description:Feed efficiency (FE) is an indicator of efficiency in converting energy from feed into a tissue that is of major environmental and economic significance.This study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE.

2018-10-10 | E-MTAB-6174 | biostudies-arrayexpress

Ileal transcriptome profiles of pigs divergent in feed efficiency

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Caecal transcriptome profiles of pigs divergent in feed efficiency

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Hypothalamic transcriptome profiles of pigs divergent in feed efficiency

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Ileal transcriptome profiles of pigs divergent in feed efficiency

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Jejunal transcriptome profiles of pigs divergent in feed efficiency

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Duodenal transcriptome profiles of pigs divergent in feed efficiency

Project description:in vivo microarray study of transcriptional changes of duodenum scratchings (mucosa) obtained from pigs divergent in feed efficiency.

2018-12-21 | GSE109331 | GEO

Liver transcriptome profile associated with feed efficiency in Nellore Cattle (Bos indicus)

Project description:8 animals of high feed efficiency and 8 animals of low feed efficiency, selected by the measure of residual intake and body weight gain at the end of a feeding trial, had their liver samples collected by biopsy and sequenced in a Illumina HiSeq2500 plataform

2015-03-16 | E-MTAB-3376 | biostudies-arrayexpress

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