Comparison of SNP Variation and Distribution in Indigenous Ethiopian and Korean Cattle (Hanwoo) Populations

다국어 초록 (Multilingual Abstract)

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genomesequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals,representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3zebu (Borana, Arsi and Ambo), and 1 zebu × Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22,0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p ＜ 0.001). Across the Ethiopian cattle populations, a common variant MAF (≥0.10 and ≤0.5) accounted for an overall estimated 73.79% of the 7,045 SNPs.
The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.

참고문헌 (Reference)

1 Li MH, "Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis" 98 : 214-221, 2007

2 Dadi H, "Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations" 39 : 425-431, 2008

3 Hailu Dadi Melka, "Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip" 한국유전체학회 9 (9): 69-73, 2011

4 Lin BZ, "Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers" 81 : 281-289, 2010

5 Gautier M, "Genetic and haplotypic structure in 14 European and African cattle breeds" 177 : 1059-1070, 2007

6 Peakall R, "GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research" 6 : 288-295, 2006

7 Hailu Dadi Melka, "Evaluation of Single Nucleotide Polymorphisms (SNPs) Genotyped by the Illumina Bovine SNP50K in Cattle Focusing on Hanwoo Breed" 아세아·태평양축산학회 25 (25): 28-32, 2012

8 Kemp S, "Domestic animal genetic resources information system" International Livestock Research Institute,

9 Williams JL, "Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality" 40 : 486-491, 2009

10 Boichard D, "Design of a bovine low-density SNP array optimized for imputation" 7 : 34130-, 2012

11 Carruthers CR, "Comparison of Angus cattle populations using gene variants and microsatellites" 91 : 81-85, 2011

12 McKay SD, "An assessment of population structure in eight breeds of cattle using a whole genome SNP panel" 9 : 37-, 2008

13 Payne WJA, "An Introduction to Animal Husbandry in the Tropics" Blackwell Science Ltd 1999

14 Kijas JW, "A genome wide survey of SNP variation reveals the genetic structure of sheep breeds" 4 : 4668-, 2009