title: Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population.
abstract: Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.
authors.affiliation: Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
authors.forename: Daehwan
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
authors.forename: Minah
authors.initials: M
authors.lastname: Cho
authors.affiliation: Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
authors.forename: Woon-Young
authors.initials: WY
authors.lastname: Hong
authors.affiliation: National Institute of Animal Science, Wanju 55365, Korea.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
authors.affiliation: National Institute of Animal Science, Wanju 55365, Korea.
authors.forename: Hyung-Chul
authors.initials: HC
authors.lastname: Kim
authors.affiliation: National Institute of Animal Science, Wanju 55365, Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Cho
authors.affiliation: National Institute of Animal Science, Wanju 55365, Korea.
authors.forename: Jin-Young
authors.initials: JY
authors.lastname: Jeong
authors.affiliation: National Institute of Animal Science, Wanju 55365, Korea.
authors.forename: Bong-Hwan
authors.initials: BH
authors.lastname: Choi
authors.affiliation: Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul 03722, Korea.
authors.forename: Younhee
authors.initials: Y
authors.lastname: Ko
authors.affiliation: Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
authors.forename: Jaebum
authors.initials: J
authors.lastname: Kim
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea
keywords: Hanwoo; evolutionary analyses; interaction network; resequencing; single nucleotide polymorphism