Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip

Melka, Hailu Dadi; Jeon, Eun Kyeong; Kim, Sang Wook; Han, James Bond; Yoon, Duhak; Kim, Kwan‐Suk

doi:10.5808/gi.2011.9.2.69

Cited by 6 publications

(4 citation statements)

References 15 publications

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“…The overall MAF in the present finding for indigenous Ethiopian cattle breeds is higher than an earlier report for indicine breeds but lower than the average value reported for most taurine breeds [ 3 ]. The value found for Hanwoo cattle was comparable with the previous results for taurine breeds but higher than the reported average for the same breed [ 10 , 12 ]. This could be attributed to the different marker density used, and a higher density marker (Illumina Bovine 50K SNP BeadChip) was used in the previous study.…”

Section: Resultssupporting

confidence: 88%

“…The distribution of MAFs revealed that nearly 34.08% of the markers in Ethiopian cattle populations and 53% in Hanwoo cattle displayed a high degree of polymorphisms (0.3 ≤ MAF ≤ 0.5). Yet, this value was higher than an earlier report both for Hanwoo (25%) and Holstein (28%) [ 12 ]. Much higher MAFs were detected in Bos taurus breeds than in Bos indicus breeds [ 3 ].…”

Section: Resultscontrasting

confidence: 79%

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

et al. 2012

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Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing 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), 3 zebu (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.

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Section: Resultssupporting

confidence: 88%

Section: Resultscontrasting

confidence: 79%

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

et al. 2012

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“…For each breed, 50 samples were collected and DNA was extracted according to the laboratory procedure. Technical details of the experiment were previously described by Melka et al (2011) . Additionally, the available SNPs frequency data of Charolais, Angus, Simmental and Limousine breeds were obtained from Decker et al (2009) .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Single Nucleotide Polymorphisms (SNPs) Genotyped by the Illumina Bovine SNP50K in Cattle Focusing on Hanwoo Breed

Dadi

Kim

Yoon³

et al. 2011

Asian Australas. J. Anim. Sci

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In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

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“…According to increasing interest in the genomic selection of cattle based on SNP arrays (especially BovineSNP50 BeadChip, Illumina) there is a huge amount of genomic information concerning the most popular cattle breeds (HARRIS et al 2008;HAYES et al 2009). However, there is only limited information about the performance of currently available genomic tools in native or rare cattle breeds (MATUKUMALLI et al 2009;MELKA et al 2011). Despite the fact that genomic selection does not concern preserved cattle breeds, with low population sizes, these breeds may be the subject of population genetics and phylogenetic studies.…”

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confidence: 99%

The Evaluation of Bovine SNP50 BeadChip Assay Performance in Polish Red Cattle Breed

Gurgul¹,

Żukowski²,

Pawlina³

et al. 2013

folia biol (krakow)

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According to increasing interest in the use of high density SNP (single nucleotide polymorphism) genotyping assays for genome-wide genetic studies in farm animals, there is a need to assess the usefulness of currently available genomic tools for application in different breeds. The performance of the assays may differ between the breeds because of discrepancies in allele frequencies of the polymorphisms or differences in linkage disequilibrium patterns. In this study we attempted to test the performance of the Bovine SNP50 v2 genotyping assay (Illumina) for population genetic and other applications in the Polish Red cattle breed. We found that 37,977 of the 53,438 autosomal markers included in the assay give high quality genomic information and can be used for different applications concerning this breed. The remaining markers were denoted as "of limited use" or redundant because of their weak performance, deviation from Hardy-Weinberg equilibrium, low minor allele frequency, high linkage disequilibrium with other neighboring markers or location on sex chromosomes.

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Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip

Cited by 6 publications

References 15 publications

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

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

Evaluation of Single Nucleotide Polymorphisms (SNPs) Genotyped by the Illumina Bovine SNP50K in Cattle Focusing on Hanwoo Breed

The Evaluation of Bovine SNP50 BeadChip Assay Performance in Polish Red Cattle Breed

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