Examining Genotype-phenotype Associations of GRAM Domain Proteins Using GWAS, PheWAS and Literature Review in Cattle, Human, Pig, Mouse and Chicken

Overview

Journal Sci Rep

Specialty Science

Date 2024 Nov 21

PMID 39572677

Authors

Tanja Kunej

Martin Simon

Barbara Lustrek

Simon Horvat

Klemen Potocnik

Affiliations

Soon will be listed here.

Abstract

The GRAMD genes are involved in maintaining cholesterol homeostasis, apoptosis, cancer and production traits in livestock. A lipid-binding GRAM domain is implicated in lipid transport and metabolism. The functions of GRAMD proteins remain incompletely understood. The aim of the present study was therefore to investigate the associations between six GRAMD genes in cattle using data from the international genomic evaluation of the Interbull InterGenomics Centre and to evaluate genotype-phenotype associations in human, cattle, pig, mouse and, chicken. Genotyping of 55,013 bulls was performed using DNA microarrays and 11 SNPs were mapped to the five GRAMD genes. A phenome-wide association study (PheWAS) tested associations between the 11 SNPs and 36 traits. The integrated analysis of SNP effects, rankings, and clustering patterns revealed their potential for improving cattle productivity, health, and robustness, and established a baseline for the targeted improvement of cattle traits. This study lays the groundwork for functional experiments aimed at uncovering the mechanism of action of GRAMD genes and to evaluate the potential of using GRAMD sequence variants for selection programs in dairy cattle. The study presents an example of how the combination of GWAS and the PheWAS offers a promising toolbox for the systematic functional annotation of vertebrate genomes.

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