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.

Genetic and phenotypic characterization of the novel mouse substrain C57BL/6N Korl with increased body weight

“…Because missing genotypes were found exclusively in all of the Korl samples, the possibility that this was due to a simple technical sequencing error can be ruled out. In recent studies, invariably missing genotypes could be explained by structural variations that prevent intact sequencing 26 , 27 . Therefore, regions of high-missing genotypes in chromosome 14 would be indicative of a Korl-specific genomic region with unusual structural variation.…”