title: 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.
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW Australia.
authors.forename: Eva M
authors.initials: EM
authors.lastname: Strucken
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Bong Hwan
authors.initials: BH
authors.lastname: Choi
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Han Ha
authors.initials: HH
authors.lastname: Chai
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Yong Min
authors.initials: YM
authors.lastname: Cho
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Gul Won
authors.initials: GW
authors.lastname: Jang
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW Australia.
authors.forename: Cedric
authors.initials: C
authors.lastname: Gondro
authors.affiliation: Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305-764, Republic of Korea.
authors.forename: Seung Hwan
authors.initials: SH
authors.lastname: Lee
mesh_terms: D016564:Amyloid beta-Protein Precursor / Q000737:chemistry / Q000235:genetics; D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D016000:Cluster Analysis; D005787:Gene Frequency / Q000235:genetics; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D008460:Meat; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D056910:Republic of Korea; D012641:Selection, Genetic
chemical_list: D016564:Amyloid beta-Protein Precursor