Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle
| Autor: | Michel Eduardo Beleza Yamagishi, Luiz Otávio Campos da Silva, Samuel Rezende Paiva, Joaquim Silva, P. F. Giachetto, L. C. Cintra, Alexandre Rodrigues Caetano |
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| Přispěvatelé: | JOAQUIM MANOEL DA SILVA, Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Bra, POLIANA FERNANDA GIACHETTO, CNPTIA, LUIZ OTAVIO CAMPOS DA SILVA, CNPGC, LEANDRO CARRIJO CINTRA, CNPTIA, SAMUEL REZENDE PAIVA, SRI, ALEXANDRE RODRIGUES CAETANO, CENARGEN, MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA., JOAQUIM MANOEL DA SILVA, Unemat, LUIZ OTÁVIO CAMPOS DA SILVA, CNPGC |
| Rok vydání: | 2015 |
| Předmět: |
Genetic Markers
Genotype Science Population Genotypes Gado de corte Population genetics Bos Indicus Single-nucleotide polymorphism Genome-wide association study Sequenciamento de DNA Biology Breeding Polymorphism Single Nucleotide Open Reading Frames Genetic variation Animals education Indel Cattle Genotyping Base Pairing Genetic association Polimorfismo de nucleotídeo único Genetics education.field_of_study Multidisciplinary Genome Sequence analysis Genetic Variation Molecular Sequence Annotation Chromosomes Mammalian Single nucleotide polymorphism Nelore Gene Ontology Medicine Research Article |
| Zdroj: | PLoS ONE Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice) Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA PLoS ONE, Vol 10, Iss 8, p e0136035 (2015) |
| ISSN: | 1932-6203 |
| Popis: | High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. |
| Databáze: | OpenAIRE |
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