title: Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection.
abstract: Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Bong-Hwan
authors.initials: BH
authors.lastname: Choi
authors.affiliation: Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305-764, Korea.
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Lee
authors.affiliation: Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An 331-808, Korea.
authors.forename: Seung-Soo
authors.initials: SS
authors.lastname: Lee
authors.affiliation: Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea.
authors.forename: Hyeong-Cheol
authors.initials: HC
authors.lastname: Kim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Dayeong
authors.initials: D
authors.lastname: Yu
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Han-Ha
authors.initials: HH
authors.lastname: Chai
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Cho
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000145:classification* / Q000235:genetics*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000662:veterinary; D043263:Myosin-Light-Chain Phosphatase / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000662:veterinary
chemical_list: D043263:Myosin-Light-Chain Phosphatase
keywords: Hanwoo; SNP; Signature of selection; Whole-genome sequencing; Yanbian cattle