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Published on: July 27, 2021
Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in
Zhehong Shen1, Liping Yang1, Yuheng Xue1
1College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
Animals : an Open Access Journal From MDPI
|May 13, 2026
Summary
This study identified 238 mutation loci associated with body measurement traits in Yili horses using genome-wide association studies (GWAS) and machine learning. These findings reveal genetic differences between Yili horse types and offer insights into their development.
Area of Science:
- Animal Genetics
- Genomics
- Equine Science
Background:
- Body measurement traits are crucial for assessing Yili horse growth, production, and breeding value.
- Limited research exists on the genetic loci linked to these traits in Yili horses.
Purpose of the Study:
- To investigate the association between body measurement traits and mutation loci in Yili horses.
- To identify candidate genes influencing these traits and understand genetic variations between Yili horse types.
Main Methods:
- Whole-genome resequencing of 255 Yili mares (152 speed-type, 103 meat-type).
- Phenotypic data collection including four body measurements and body weight.
- Application of mixed linear model (MLM)-based genome-wide association study (GWAS) and a machine learning-based GWAS (ML-GWAS) framework (Lasso regression and Random Forest).
Main Results:
- Identified 238 mutation loci significantly associated with body measurement traits.
- Annotated 277 candidate genes involved in skeletal development, muscle formation, cell growth, energy metabolism, and protein synthesis.
- Detected significant genetic differences at the genomic level between speed-type and meat-type Yili horses.
Conclusions:
- Genetic variations underlie the observed differences in body measurement traits among Yili horse populations.
- Integrating machine learning with GWAS enhances the detection of loci associated with complex traits.
- Provides molecular evidence for understanding the genetic basis of body measurement variations in Yili horses.
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