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.
Highlights
Hanwoo is an indigenous cattle breed of Korea that has been maintained with minimal introduction of other germplasm for >2,000 years [1]
This could suggest that YB either had some unaccounted intercrossing with European cattle breeds, or genetic artefacts of the same domestication origin as European taurine remain in this unselected population [20]
By comparing a selected population of brown Hanwoo with three closely related and unselected populations we identified 16 genomic regions suggesting recent selection in Hanwoo
Summary
Hanwoo is an indigenous cattle breed of Korea that has been maintained with minimal introduction of other germplasm for >2,000 years [1]. The brown Hanwoo have been subjected to intensive artificial selection over the past four decades to improve meat production traits such as carcass weight, eye muscle area, marbling (intramuscular fat), and meat tenderness [2, 3]. Outside of the breeding program for HW, two closely related but unselected varieties survived in Korea: Brindle Hanwoo (BR) and Jeju Black Hanwoo (JB) [4, 5]. These two strains have small populations with around 4,000 BR individuals and 1,000 JB. Yanbian are mainly used as draft animals and remained unselected for production traits [6]
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