A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with
Igor Ricardo Savoldi1, Adriana Mércia Guaratini Ibelli2,3, Maurício Egídio Cantão2
1Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Chapecó, SC, 89815-630, Brazil.
BMC Genomics
|November 14, 2021
Summary
This study identified genetic variants associated with umbilical hernia (UH) in pigs using exome and transcriptome sequencing. These findings shed light on the genetic basis of UH, potentially aiding in diagnosis and prevention strategies.
Area of Science:
- Genomics
- Molecular Biology
- Veterinary Science
Background:
- Umbilical hernia (UH) involves intestinal protrusion through the umbilical canal.
- Causes include infections, management, and genetic factors, with genetic components poorly understood.
- This study focuses on identifying genetic variants linked to UH in pigs.
Purpose of the Study:
- To identify genetic polymorphisms and genes associated with umbilical hernia in pigs.
- To investigate the genetic underpinnings of umbilical hernia using a case-control design.
- To leverage exome and transcriptome sequencing for comprehensive genetic analysis.
Main Methods:
- Exome sequencing of normal and UH-affected pigs.
- Transcriptome sequencing of umbilical ring tissue.
- Comparative analysis of exome and transcriptome data to identify concordant variants.
Main Results:
- Identified 119 variants in 58 genes from exome sequencing and 46 variants in 27 genes from transcriptome sequencing.
- Found 34 concordant variants in 17 genes between both methods.
- Highlighted biological processes including cell adhesion, embryonic morphogenesis, and muscle contraction involved in UH.
Conclusions:
- Generated the first exome sequencing data for normal and UH-affected pigs.
- Identified numerous variants potentially involved in UH development, with RNA-Seq confirming DNA variants.
- Combined sequencing approaches provide insights into UH molecular mechanisms in pigs and other mammals.
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