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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
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Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with
Yuliaxis Ramayo-Caldas1, Maria Ballester2, Juan Pablo Sánchez2
1Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, Spain. yuliaxis.ramayo@irta.cat.
Scientific Reports
|January 12, 2018
Summary
This study identified specific genes and pathways in pig liver and duodenum linked to feed efficiency (FE). Heat shock proteins were key in both tissues, suggesting tissue-specific regulation of FE.
Area of Science:
- Animal Genetics
- Genomics
- Molecular Biology
Background:
- Feed efficiency (FE) is crucial for sustainable animal agriculture.
- Understanding the genetic and molecular basis of FE can improve livestock breeding.
- Residual feed intake (RFI) is a common measure of FE, but its underlying mechanisms are complex.
Purpose of the Study:
- To identify candidate genes and molecular pathways associated with feed efficiency (FE) in pigs.
- To explore tissue-specific transcriptomic differences between pigs with high and low residual feed intake (RFI).
- To uncover potential regulatory mechanisms of FE in liver and duodenum.
Main Methods:
- RNA sequencing (RNA-Seq) of liver and duodenum tissues from 37 gilts with high and low RFI.
- Differential gene expression (DE) analysis to identify significantly altered genes.
- Weighted gene co-expression network analysis (WGCNA) to identify modules of co-expressed genes associated with FE.
Main Results:
- 55 differentially expressed genes (DEGs) in liver and 112 DEGs in duodenum were identified.
- Four gene co-expression modules (one in liver, three in duodenum) were significantly associated with FE indicators.
- Candidate genes and enriched pathways involved oxidative stress, inflammation, immune response, lipid metabolism, and thermoregulation.
- Heat shock proteins were identified as candidate genes associated with FE in both liver and duodenum.
Conclusions:
- Transcriptome analysis reveals tissue-specific regulatory processes underlying feed efficiency in pigs.
- Candidate genes and pathways identified provide insights into the molecular mechanisms of FE.
- Heat shock proteins represent a conserved molecular link to FE across different pig tissues.
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