Kim, Seungchang
(Animal Genetic Resources Center, National Institute of Animal Science, RDA)
,
Cheong, Hyun Sub
(Department of Genetic Epidemiology, SNP Genetics, Inc.)
,
Shin, Hyoung Doo
(Department of Genetic Epidemiology, SNP Genetics, Inc.)
,
Lee, Sung-Soo
(Animal Genetic Resources Center, National Institute of Animal Science, RDA)
,
Roh, Hee-Jong
(Animal Genetic Resources Center, National Institute of Animal Science, RDA)
,
Jeon, Da-Yeon
(Animal Genetic Resources Center, National Institute of Animal Science, RDA)
,
Cho, Chang-Yeon
(Animal Genetic Resources Center, National Institute of Animal Science, RDA)
Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping arr...
Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.
Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.
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문제 정의
The aim of the present study was to compare the genetic diversity and divergence of Korean cattle breeds using a Bovine HD chip. Understanding the diversity in Korean cattle populations will enable researchers to develop better strategies for the breeding and conservation of these cattle.
To our Knowledge this study is the first to investigate the genome of a BRH cattle population for signatures of positive selection using high density genome-wide SNPs. Here, we have shown that a coat color-related gene (MC1-R) region is one of the selection signatures.
제안 방법
The quantity and quality of the extracted DNA were evaluated using a spectrophotometer (NanoDrop 1000; Thermo Scientific, Waltham, MA, USA). The SNP genotyping was performed using the Illumina BovineHD SNP 777K Bead chip (Illumina, San Diego, CA, USA) [16]. This protocol was approved by the Committee on the Ethics of Animal Experiments of the National Institute of Animal Science.
There were no significant loci in the genomic region for iHS analysis of BH and JB. Therefore, in order to clarify the genetic characteristics of BRH, we analyzed the selection signatures using Fst of single SNPs. The SNP criteria showing significant difference between two populations were considered to be a significant SNP when it had a Bonferroni correction p-value threshold (8.
대상 데이터
Blood of BH was collected by Animal Genetic Resources Research Center of National Institute of Animal Science. Blood of BRH was sampled from two local institutes (Gangwon Provincial Livestock Research Center and Chungbuk Veterinary Service Center). And, blood of JB was collected from Jeju special Self-Governing Provincial Livestock Institute.
Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). Blood of BH was collected by Animal Genetic Resources Research Center of National Institute of Animal Science.
이론/모형
3 [18] was used to phase the genotyped SNPs into the corresponding haplotypes. The fixation index (Fst) was estimated on the basis of the Wright F statistic [19] with use of SVS8. Candidate SNPs were defined as passing the Fst threshold 0.
성능/효과
The SNP criteria showing significant difference between two populations were considered to be a significant SNP when it had a Bonferroni correction p-value threshold (8.77×10–8) of iHS and Rsb analyses, and Fst threshold level is ≥0.25.
The analysis of decay corresponding to the HD chip shows that for the three breeds, r2 levels start at 0.568, 0.551, and 0.557 for BH, BRH, and JB, respectively, when using the 2 kb bin of SNPs.
Using the Illumina BovineHD SNP 777K Bead chip, 99.4% of markers were genotyped in 95% of the samples in the three breeds, which indicates the suitability of the chip for genotyping the breeds studied (Table 1). The BH and BRH were calculated using 24 randomly selected samples to match JB samples.
후속연구
An analysis of differentiation based on high-density SNP chip analysis showed the various differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic region in which they are evolving. Further studies will be necessary in order to determine the association between these genetic variations and various phenotypic traits.
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