Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing

PLoS One. 2014 Jul 3;9(7):e101127. doi: 10.1371/journal.pone.0101127. eCollection 2014.

Abstract

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding*
  • Cattle / genetics*
  • DNA Copy Number Variations
  • Genome
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing
  • Homozygote
  • INDEL Mutation
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Republic of Korea

Grant support

This research was supported by the grant from the BioGreen 21 Program (No. PJ008196), the Cooperative Research Program for Agriculture Science & Technology Development, Rural Development Administration (No. PJ009153012014, PJ006405), Animal Promotion Resource Institute, Jeju and Kangwon National University (No. 120131448), Republic of Korea. Xiaoping Liao was funded by the Genome Canada project entitled "Whole Genome Selection Through Genome Wide Imputation in Beef Cattle". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.