Research progress and applications of genome-wide association study in farm animals

Exploring the genetic loci underlying economic traits is foundational for innovation in modern animal breeding technology. Genome-wide association studies (GWAS) have been valid and commonly used tools to dissect the genomic variants associated with phenotypes for the past ∼20 years and have contributed to our understanding of genetic and molecular bases of various traits. Here, we comprehensively review the recent research progress on GWAS methods. We highlight the methodological advancements enabled by the combination of new proteome, transcriptome, epigenome, and metagenome information and multi-omics analysis algorithms. The advances in GWAS investigations of chickens, pigs, cattle, and other animals during the last 5 years are also described. Finally, we discuss the current applications of GWAS in cutting-edge breeding technologies and overall future perspectives of the post-GWAS era.