Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip

  • Melka, Hailu Dadi (Department of Animal Science, Chungbuk National University) ;
  • Jeon, Eun-Kyeong (Department of Animal Science, Chungbuk National University) ;
  • Kim, Sang-Wook (Department of Animal Science, Chungbuk National University) ;
  • Han, James-Bond (Department of Animal Science, Chungbuk National University) ;
  • Yoon, Du-Hak (Department of Animal Science, Kyungbook National University) ;
  • Kim, Kwan-Suk (Department of Animal Science, Chungbuk National University)
  • Accepted : 2011.04.26
  • Published : 2011.06.30
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Abstract

The use of genomic information in genomic selection programs for dairy and beef cattle breeds has become a reality in recent years. In this investigation, we analyzed single-nucleotide polymorphisms (SNPs) for Hanwoo (n=50) and Holstein (n=50) breeds using the Illumina Bovine SNP50 BeadChip to facilitate genomic selection and utilization of the Hanwoo breed in Korea. Analysis of the entire genomes showed different spectra of SNP frequencies for Hanwoo and Holstein cattle. The study revealed a highly significant (p<0.001) difference between Hanwoo and Holstein cattle in minor allele frequency (MAF). The average MAFs were $0.19{\pm}0.16$ and $0.22{\pm}0.16$ for Hanwoo and Holstein, respectively. From the total of 52,337 SNPs that were successfully identified, about 72% and 79% were polymorphic in Hanwoos and Holsteins, respectively. Polymorphic and fixed SNPs were not distributed uniformly across the chromosomes within breeds or between the two breeds. The number of fixed SNPs on all chromosomes was higher in Hanwoo cattle, reflecting the genetic uniqueness of the Hanwoo breed. In general, the rate of polymorphisms detected in these two breeds suggests that the SNPs can be used for different applications, such as whole-genome association and comparative genetic studies, and are a helpful tool in developing breed identification genetic markers.

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