Genome-association analysis of Korean Holstein milk traits using genomic estimated breeding value

Abstract

Objective: Holsteins are known as the world's highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data.

Methods: This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits.

Results: We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein.

Conclusion: This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins.

Keywords: Genome-wide Association Studies (GWAS); Korean Holstein; Milk Fat; Milk Production; Milk Protein.

Figure 1

Manhattan plot of genome-wide association studies (GWAS) result of each milk traits after p-value integration. Each circle indicated each region containing 5 single nucleotide polymorphism (SNP) and circle with ring meant that region contained nearby gene. We provide the gene names which were significant in both GWAS and gene ontology analysis. a) milk production, b) milk fat, and c) milk protein. Grey dot line indicates the threshold of Bonferroni multiple test based on integrated p-values in each milk traits association test (genomic p-value<6.09E-06, equivalent to p-value = 0.05 after Bonferroni multiple correction).

Figure 2

Result of gene ontology analysis using gene sets of significant genetic regions as each genome-wide association studies (GWAS) result of milk production (skyblue), fat (pink), and protein (green).

Figure 3

Clustering based on result of gene ontology analysis using gene set of significant genetic regions as genome-wide association studies (GWAS) result of milk protein. Number in parenthesis means number of genes in each cluster group.