Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/19694
Title: Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea
Contributor(s): Lim, Dajeong (author); Strucken, Eva  (author)orcid ; Choi, Bong Hwan (author); Chai, Han Ha (author); Cho, Yong Min (author); Jang, Gul Won (author); Kim, Tae-Hun (author); Gondro, Cedric  (author)orcid ; Lee, Seung Hwan (author)
Publication Date: 2016
Open Access: Yes
DOI: 10.1371/journal.pone.0151324Open Access Link
Handle Link: https://hdl.handle.net/1959.11/19694
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.
Publication Type: Journal Article
Source of Publication: PLoS One, 11(3), p. 1-18
Publisher: Public Library of Science
Place of Publication: United States of America
ISSN: 1932-6203
Fields of Research (FoR) 2008: 070201 Animal Breeding
Fields of Research (FoR) 2020: 300305 Animal reproduction and breeding
Socio-Economic Objective (SEO) 2008: 830301 Beef Cattle
Socio-Economic Objective (SEO) 2020: 100401 Beef cattle
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Journal Article

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