An integrative approach to prioritize candidate causal genes for complex traits in cattle

Genome-wide association studies (GWAS) have identified many quantitative trait loci (QTL) associated with complex traits, predominantly in non-coding regions, posing challenges in pinpointing the causal variants and their target genes. Three types of evidence can help identify the gene through which QTL act: (1) proximity to the most significant GWAS variant, (2) correlation of gene expression with the trait, and (3) the gene’s physiological role in the trait. However, there is still uncertainty in the success of these methods in identifying the correct genes. Here we test the ability of these methods in a comparatively simple series of traits associated with the concentration of polar lipids in milk.
We conducted single-trait GWAS for ~14 million imputed variants and 56 individual milk polar lipid (PL) phenotypes in 336 cows. A meta-analysis of multi-trait GWAS identified 10,063 significant SNPs at FDR ≤ 10% (P ≤ 7.15E-5). Transcriptome data from blood (~12.5K genes, 143 cows) and mamm..., , , [https://doi.org/10.5061/dryad.bcc2fqzph](https://doi.org/10.5061/dryad.bcc2fqzph)

## Description of the data and file structure

This dataset is publicly available upon acceptance of the paper titled: \"An integrative approach to prioritize candidate causal genes for complex traits in cattle\". Also, a Read_Me.txt file is included in the zipped data file.

**Genotype File**

The genotype data consists of three PLINK binary files: GenotypesHD.bed, GenotypesHD.bim, and GenotypesHD.fam.

These files include high-density (HD) imputed genotypes for 336 cows, based on Run7 of the 1000 Bull Genomes Project.

**Phenotype File**

The PhenoPLs.csv file contains the phenotypes of 56 milk polar lipid species measured in the 336 cows.

This file includes a header row with information about the group each phenotype belongs to.

The polar lipid groups represented are:

* Phosphatidylcholine (PC)

- Phosphatidylethanolamine (PE)

* Phosphatidylserine (PS)

- Phosphatidylinositol (PI)

* Sphingomyelin...,