Supplemental material for: Genome-wide association study and fine-mapping using imputed sequences to prioritize candidate genes for 30 complex traits in 50,309 Holstein bulls

Identifying causal genetic variants underlying economically important traits in dairy cattle is essential for understanding their genetic basis and optimizing breeding programs. The growing availability of sequenced reference genomes and individuals with both phenotypic and genotypic data notably enhances our ability to detect genetic associations and further pinpoint causal effects. This comprehensive genome-wide association study of dairy cattle utilized de-regressed breeding values as phenotypes and analyzed 11,292,243 quality-controlled, imputed DNA sequence variants from 50,309 Holstein bulls. The number of bulls with available phenotypes ranged from 23,121 to 50,309 across 30 complex traits categorized into production and yield, type, and longevity and health. We performed GWAS using our SLEMM-GWA approach, which accounts for the varying reliability of de-regressed breeding values across individuals and demonstrates computational efficiency for large sample sizes and sequence data. This analysis identified 381 significant association peaks (P AOPEP, GC, E2F6, MGST1, VPS13B, ZNF652, ASPH, SFMBT1, and MAPRE2. These findings enhance the understanding of the genetic architecture of these complex dairy traits and provide valuable insights for the refinement of genomic selection strategies and breeding programs in Holstein cattle.