Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle
| Autor: | Yoshinobu Inoue, Shouta Nariai, Kanako Yoshinari, Shiyunsuke Moriwaki, Yuuichi Yoshida, Masayuki Takeda, Ryotaro Nakashima, Ryoya Hideshima, Shinji Sasaki, Eiji Muraki, Takatoshi Kojima, Hideki Nikadori, Ryouhei Suezawa, Katsuo Uchiyama |
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| Rok vydání: | 2019 |
| Předmět: |
Genotype
Population Cattle Diseases Single-nucleotide polymorphism Biology Genome Polymorphism Single Nucleotide 03 medical and health sciences Gene Frequency Japan SNP Animals education Allele frequency Online Mendelian Inheritance in Animals 030304 developmental biology Genetics 0303 health sciences education.field_of_study 0402 animal and dairy science Genetic Diseases Inborn 04 agricultural and veterinary sciences General Medicine Genomics 040201 dairy & animal science Cattle General Agricultural and Biological Sciences SNP array |
| Zdroj: | Animal science journal = Nihon chikusan GakkaihoREFERENCES. 90(12) |
| ISSN: | 1740-0929 |
| Popis: | Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position-unassigned SNPs, or "buried SNPs" include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle. |
| Databáze: | OpenAIRE |
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