Inbreeding levels in an open-registry pedigreed dog breed: The Australian working kelpie

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Cerebellar Abiotrophy in Australian Working Kelpies Is Associated with Two Major Risk Loci

An autosomal recessive form of inherited cerebellar abiotrophy (CA) that is characterized by a degeneration of Purkinje and granule cells in the cerebellar cortex occurs in the Australian working kelpie dog breed. The clinical signs of CA include ataxia, head tremor, motor in-coordination, wide-based stance, and high-stepping gait. Investigation of clinical and pathological features indicated two closely related diseases with differences in age of onset. A genome-wide association study on 45 CA affected and 290 normal healthy Kelpies identified two significantly associated loci, one on CFA9 and a second on CFA20. Dogs homozygous for the risk haplotype on CFA20 (23 dogs) show clinical signs before ten weeks of age. Missense variants in the sixth exon of disruptor of telomeric silencing 1-like (DOT1Lp.R200Q) and in the only exon of Leucine Rich Repeat And Ig Domain Containing 3 (LINGO3p.R359C), both on CFA20, segregate with the associated risk marker which has incomplete penetrance (42%). Affected dogs homozygous for the risk haplotype on CFA9 have later onset ataxia. A missense variant in exon 5 of Vacuole Membrane Protein 1 (VMP1 p.P160Q) on CFA9 segregates as a fully penetrant Mendelian recessive with later-onset CA. Across mammals, the variety of causative loci so far identified as influencing cerebellar disorders reinforces the complexity of the pathways that contribute to cerebellar development and function, and to the pathophysiological mechanisms that may lead to cerebellar ataxia.

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Simple Summary

Deutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔF_i = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.

Abstract

Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔF_i) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔF_i. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.