Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea

Abstract

Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.

Fig 1. First and second principal components based on the genomic relationship matrix of 5 cattle breeds.

The first component separates the European Angus from the East-Asian cattle breeds and explains 26.4% of the variation amongst the individuals. The second component separates the East-Asian breeds and explains 6% of the variation. HW: Hanwoo; BR: Brindle Hanwoo; JB: Jeju Black Hanwoo; YB: Chinese Yanbian; AG: Angus.

Fig 2. Unsupervised hierarchical clustering of individuals genotyped for 38,266 SNP for K = 2, 3 and 4 (best fit K = 3).

Each color depicts the breed proportions per individual and based on allele frequencies of the breeds available for this study. HW: Hanwoo; BR: Brindle Hanwoo; JB: Jeju Black Hanwoo; YB: Chinese Yanbian; AG: Angus.

Fig 3. Genomic regions with selection signals in the Brown Hanwoo vs. a pooled unselected population using Rsb statistic.

Red dots indicate significant markers remaining after FDR correction.

Fig 4

The schematic structure of bovine APP gene in the wild-type (A) and mutated form (B). The bovine protein structure and mutation effects were modelled according to the known template structure of the human gene (PDB code 3KTM). Mutation residue (Ala199Val) is represented by ball and stick.