The practical use of genome sequencing data in the management of a feline colony pedigree

Abstract

BackgroundA higher prevalence of inherited disorders among companion animals are often rooted in their historical restricted artificial selection for a variety of observed phenotypes that eventually decreased genetic diversity. Cats have been afflicted with many inherited diseases due to domestication and intense breed selection. Advances in sequencing technology have generated a more comprehensive way to access genetic information from an individual, allowing identification of putative disease-causing variants and in practice a means to avoid their spread and thus better pedigree management. We examine variants in three domestic shorthair cats and then calculated overall genetic diversity to extrapolate the benefits of this data for breeding programs within a feline colony.ResultsWe generated whole genome sequence (WGS) data for three related cats that belong to a large feline pedigree colony. Genome-wide coverage ranged from 27-32X, from which we identified 18 million variants in total. Previously known disease-causing variants were screened in our cats, but none carry any of these known disease alleles. Loss of function (LoF) variants, that are in genes associated with a detrimental phenotype in human or mice were chosen for further evaluation on the comparative impact inferred. A set of LoF variants were observed in four genes, each with predicted detrimental phenotypes as a result. However, none of our cats displayed the expected disease phenotypes. Inbreeding coefficients and runs of homozygosity were also evaluated as a measure of genetic diversity. We find low inbreeding coefficients and total runs of homozygosity, thus suggesting pedigree management of genetic relatedness is acceptable.ConclusionsThe use of WGS of a small sampling among a large feline colony has enabled us to identify possible disease-causing variants, their genotype state and measure pedigree management of genetic diversity. We contend a limited but strategic sampling of feline colony individuals using WGS can inform veterinarians of future health anomalies and guide breeding practices to ensure healthy genetic diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-017-1144-y) contains supplementary material, which is available to authorized users.

Identification of selection signatures involved in performance traits in a paternal broiler line

“…We suggest that the reasons for identifying shorter ROH relies on the higher resolution of WGS data in comparison with SNPchip data. This difference in ROH calling was also observed in another study with feline that used both types of dataset for the same individuals [46].…”

Identification of selection signatures involved in performance traits in a paternal broiler line

“…We suggest that the reasons for identifying shorter ROH relies on the higher resolution of WGS data in comparison with SNPchip data, leading to an identification of two or more ROH (using WGS data) as a unique ROH. This difference in ROH calling was also observed in another study with feline that used both types of dataset of the same individuals[46].It is also important to highlight that low coverage WGS data may present higher error rate of variant calling in comparison with SNPchip data and that it may lead to inaccuracy of ROH calling[29]. Thus, we followed parameters based on Ceballos et al[29], which demonstrated equivalent results to SNPchip data's results, when dealing with low coverage WGS, considering the differences of error rate in variant calling in both types of data.…”