title: Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.
abstract: 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.
authors: Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.
authors: Joaquim Manoel
authors: JM
authors: da Silva
authors: Laboratório Multiusuário de Bioinformática (LMB)-Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
authors: Poliana Fernanda
authors: PF
authors: Giachetto
authors: Embrapa Gado de Corte, Campo Grande, Mato Grosso do Sul, Brazil.
authors: Luiz Otávio Campos
authors: LO
authors: da Silva
authors: Laboratório Multiusuário de Bioinformática (LMB)-Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
authors: Leandro Carrijo
authors: LC
authors: Cintra
authors: Embrapa-Secretaria de Relações Internacionais, Brasília, Distrito Federal, Brazil.
authors: Samuel Rezende
authors: SR
authors: Paiva
authors: Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.
authors: Alexandre Rodrigues
authors: AR
authors: Caetano
authors: Laboratório Multiusuário de Bioinformática (LMB)-Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
authors: Michel Eduardo Beleza
authors: ME
authors: Yamagishi
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics; D063990:Gene Ontology; D005819:Genetic Markers; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
chemical_list: D005819:Genetic Markers