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Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: May 4, 2026

Sampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models

Sampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models

Published on: March 6, 2018

Integrating Multi-Omics Data to Identify Key Functional Variants Affecting Feed Efficiency in Large White Boars.

Yue Xiang^1,2, Jiahui Sun², Guojian Ma²

¹Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.

|August 29, 2024

Summary

Improving pig feed efficiency (FCR) is key for sustainability. Multi-omics data revealed genetic variants in carbohydrate digestion pathways, highlighting CTSD as a potential target for breeding more efficient pigs.

Keywords:

ATAC-seq GWAS duodenum feed efficiency muscle pigs

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Last Updated: May 4, 2026

Sampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models

Sampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models

Published on: March 6, 2018

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

Area of Science:

Animal Genetics
Nutritional Genomics
Livestock Science

Background:

Optimizing feed conversion ratio (FCR) is crucial for the economic viability and sustainability of pig farming.
Understanding the genetic underpinnings of feed efficiency is essential for developing improved breeding strategies.

Purpose of the Study:

To identify key functional genetic variants associated with feed efficiency in pigs.
To integrate multi-omics data (RNA-seq, ATAC-seq, GWAS) for a comprehensive analysis of feed efficiency traits.

Main Methods:

RNA-sequencing (RNA-seq) to analyze gene expression in duodenal and muscle tissues.
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to identify regulatory regions.
Genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs).

Main Results:

Differential gene expression in duodenal and muscle tissues linked to carbohydrate digestion pathways.
ATAC-seq identified regulatory regions associated with glycolytic and fatty acid metabolism.
GWAS identified 211 significant SNPs, with candidate genes including PPP1R14C, TH, and CTSD.
Integration of ATAC-seq and GWAS data pinpointed six functional variants on chromosome 2, with CTSD showing high expression in high-FCR pigs.

Conclusions:

Multi-omics data integration provides deep insights into the genetic architecture of pig feed efficiency.
Specific genetic variants and the CTSD gene are identified as potential targets for improving feed efficiency in pigs.
Findings support the development of targeted breeding programs for enhanced livestock production.