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Multi-ancestry genome-wide association meta-analysis identifies candidate genes for computed tomography-based carcass
He Han1,2, Pengfei Yu1,2, Zhenyang Zhang1,2
1Zhejiang Key Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
Genetics, Selection, Evolution : GSE
|December 17, 2025
Summary
This study used computed tomography and genome-wide association analysis to uncover genetic factors influencing pig carcass traits. Identified genes offer targets for improving meat quality through molecular breeding.
Area of Science:
- Animal Genetics
- Genomics
- Quantitative Trait Loci (QTL) Analysis
Background:
- Carcass composition traits (lean meat, bone percentage, rib number) are vital for pig production profitability.
- Traditional methods for measuring these traits are invasive and labor-intensive.
- Computed tomography (CT) offers non-invasive in vivo phenotyping for extensive data collection, but genetic underpinnings are underexplored.
Purpose of the Study:
- To identify genetic loci associated with CT-based porcine carcass composition traits.
- To enhance genomic prediction accuracy for these traits using identified genetic variants.
- To pinpoint candidate genes influencing carcass composition.
Main Methods:
- Multi-ancestry genome-wide association meta-analysis (MA-GWAMA) on low-coverage whole-genome sequencing data from four pig breeds.
- Meta-analysis identified 11 independent genome-wide significant loci.
- Integration of MA-GWAMA results with public eQTL and single-cell data.
Main Results:
- Identified 11 independent genome-wide significant loci associated with carcass composition traits.
- Weighting MA-GWAMA significant SNPs improved genomic prediction accuracy by up to 79.4% in an independent population.
- Prioritized candidate genes: ALPK2 for lean meat percentage, ABCD4 and SLC8A3 for number of ribs.
Conclusions:
- CT phenotyping combined with multi-omics effectively dissects the genetic architecture of porcine carcass traits.
- Prioritized variants and genes serve as valuable targets for molecular breeding programs.
- This research advances efforts to enhance pig meat quality through genetic selection.
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