GWAS & Selection signatures

Insights from large-scale GWAS analysis of simple and complex variations in cattle

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Abstract

Genome-wide association studies (GWAS) have revolutionized the study of complex traits by identifying genetic variants associated with phenotypic variation. To date, over 10,000 GWAS studies have revealed more than 500,000 trait-associated loci across a wide range of species and traits. These findings reveal that most complex traits are highly polygenic, influenced by thousands of variants with small individual effects. The majority of associated variants reside in non-coding regions, implicating regulatory mechanisms as key mediators of genetic effects. Integration of GWAS with functional genomics information-such as expression quantitative trait loci (eQTL) chromatin accessibility maps, and single-cell transcriptomics-has begun to identify causal genes and pathways underlying major association signals. Here, leveraging the large genome-phenome database from the US evaluation system, we comprehensively evaluate the genome-phenome links using simple SNP and complex structural variants in cattle. We show that structural variants significantly contribute to complex trait variation after adjusting for SNP effects. Together, GWAS of simple and complex variation have provided a comprehensive framework linking full spectrum of genetic variation to molecular function and economically important traits, enabling more advanced genome editing and genomic selection in the future.

Keywords: 2026

How to Cite:

Yang, L., Cai, J., Wang, J., Cole, J., Jiang, J., Liu, G. & Ma, L., (2026) “Insights from large-scale GWAS analysis of simple and complex variations in cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2277286. doi: https://doi.org/10.31274/wcgalp.23427

Rights: 1