Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system

Abstract

Next-generation sequencing (NGS) is a powerful tool to study DNA or RNA samples. New methods and protocols based on NGS have been developed to carry out the analysis of genetic variation for animal parentage testing, disease screening and trait detection. Targeted NGS is aimed at achieving targeted enrichment of genome subregions to reduced significantly the sequencing of genomic loci of interest, as well as costs and efforts, compared with whole-genome sequencing (WGS). We generated genotyping information of 387 targets from 95 clinical canine samples (76 Doberman and 19 Toy Poodle dogs) and 3 control samples using AgriSeq Targeted GBS. Based on these data, we calculated the exclusion power of 228 parentage markers with Cervus 3.0 software. Furthermore, we detected disease/trait markers presenting polymorphism and calculated their allele frequencies within each breed. In the case of parentage markers, the assigned parents showed a higher LOD score (>1.22 x1016), and the available pedigree data of offspring agreed with the assigned parent information. Interestingly, full siblings were also assigned like parents. On the other hand, we found 19 polymorphic disease/trait markers in the total sample, 3 of which (progressive rod-cone degeneration, von Willebrand disease 1 and dilated cardiomyopathy) were validated by pyrosequencing with 100% concordance. The mutant allele for cone-rod dystrophy3 (CRD3) was found in both groups, a variant which had not been reported in either breed to date. Sequencing of genomic loci of interest, costs and efforts can be reduced significantly with targeted NGS as compared with WGS. The AgriSeq Targeted GBS is a very good alternative for the massive genetic evaluation of animal populations.