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

[https://doi.org/10.5061/dryad.vmcvdnd3q](https://doi.org/10.5061/dryad.vmcvdnd3q)

## Description of the data and file structure

## Overview

This repository contains supplementary data and fine-mapping summary statistics from a comprehensive genome-wide association study (GWAS) and Bayesian fine-mapping analysis of 30 complex dairy traits in 50,309 Holstein bulls. The study utilized 11,292,243 quality-controlled, imputed sequence variants to identify genetic associations and prioritize candidate genes through statistical fine-mapping.

#### File: Supplemental_Tables.xlsx

**Description:** Supplementary tables referenced in the main manuscript.

**Contents:**

* **Supplemental Table S1:** Trait definitions and corresponding trait names from Cattle QTLdb used for comparison with previously reported associations across all 30 analyzed dai...,