Identification and Validation of Quantitative Trait Loci (QTL) for Canine Hip Dysplasia (CHD) in German Shepherd Dogs

Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA) 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20–32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL) and a novel QTL for CHD in German Shepherd Dogs.     

European domestic horses originated in two holocene refugia

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.     

A one base pair deletion in the canine ATP13A2 gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier

Neuronal ceroid lipofuscinosis (NCL) is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells. Tibetan terriers show a late-onset lethal form of NCL manifesting first visible signs at 5-7 years of age. Genome-wide association analyses for 12 Tibetan-terrier-NCL-cases and 7 Tibetan-terrier controls using the 127K canine Affymetrix SNP chip and mixed model analysis mapped NCL to dog chromosome (CFA) 2 at 83.71-84.72 Mb. Multipoint linkage and association analyses in 376 Tibetan terriers confirmed this genomic region on CFA2. A mutation analysis for 14 positional candidate genes in two NCL-cases and one control revealed a strongly associated single nucleotide polymorphism (SNP) in the MAPK PM20/PM21 gene and a perfectly with NCL associated single base pair deletion (c.1620delG) within exon 16 of the ATP13A2 gene. The c.1620delG mutation in ATP13A2 causes skipping of exon 16 presumably due to a broken exonic splicing enhancer motif. As a result of this mutation, ATP13A2 lacks 69 amino acids. All known 24 NCL cases were homozygous for this deletion and all obligate 35 NCL-carriers were heterozygous. In a sample of 144 dogs from eleven other breeds, the c.1620delG mutation could not be found. Knowledge of the causative mutation for late-onset NCL in Tibetan terrier allows genetic testing of these dogs to avoid matings of carrier animals. ATP13A2 mutations have been described in familial Parkinson syndrome (PARK9). Tibetan terriers with these mutations provide a valuable model for a PARK9-linked disease and possibly for manganese toxicity in synucleinopathies.     

Quantitative assessment of interproximal wear facet outlines for the association of isolated molars

The determination of the minimum number of individuals can be very challenging, especially in an assemblage of fragmentary bones and isolated teeth. Similarities in tooth morphology, degree of wear, and interproximal wear facets (IPWF) are generally used to associate isolated teeth qualitatively. However, no quantitative method has yet been established for an objective identification and matching of isolated tooth crowns. In this study, we analyze the IPWF morphology of adjacent mandibular molars (17 M(1)/M(2) pairs), applying both qualitative and quantitative methods to test a reproducible approach for crown association. The surfaces of distal (for M(1)) and mesial (for M(2)) IPWF were surface-scanned and digitally selected. Three-dimensional (3D) and two-dimensional (2D) outlines of IPWF were analyzed using elliptic Fourier analysis (EFA) and geometric morphometrics methods (GMM). Additionally, teeth were qualitatively associated by visual evaluation of the IPWF outline and by physical matching. Unsatisfactory results with less than 50% of tooth pairs correctly associated were obtained by using both methods, shape analysis (digital approach) and the visual evaluation (qualitative assessment) of the IPWF outline. The physical matching of the crowns showed highly variable accuracy ranging between 53% and 77%. The quantitative form-space analysis of 2D IPWF outlines provided the best results (82% of correctly associated teeth), but no statistically significant differences were recorded when compared with the manual matching. Since three tooth pairs out of 17 could not be quantitatively associated, we suggest that the quantitative analysis of IPWF should be used only in addition with other approaches.     

Plant health and global change – some implications for landscape management

Global change (climate change together with other worldwide anthropogenic processes such as increasing trade, air pollution and urbanization) will affect plant health at the genetic, individual, population and landscape level. Direct effects include ecosystem stress due to natural resources shortage or imbalance. Indirect effects include (i) an increased frequency of natural detrimental phenomena, (ii) an increased pressure due to already present pests and diseases, (iii) the introduction of new invasive species either as a result of an improved suitability of the climatic conditions or as a result of increased trade, and (iv) the human response to global change. In this review, we provide an overview of recent studies on terrestrial plant health in the presence of global change factors. We summarize the links between climate change and some key issues in plant health, including tree mortality, changes in wildfire regimes, biological invasions and the role of genetic diversity for ecosystem resilience. Prediction and management of global change effects are complicated by interactions between globalization, climate and invasive plants and/or pathogens. We summarize practical guidelines for landscape management and draw general conclusions from an expanding body of literature.     

Brief communication: Identification reassessment of the isolated tooth Krapina D58 through occlusal fingerprint analysis

High variability in the dentition of Homo can create uncertainties in the correct identification of isolated teeth. For instance, standard tooth identification criteria cannot determine with absolute certainty if an isolated tooth is a second or third maxillary molar. In this contribution, using occlusal fingerprint analysis, we reassess the identification of Krapina D58 (Homo neanderthalensis), which is catalogued as a third maxillary molar. We have hypothesized that the presence/absence of the distal occlusal wear facets can be used to differentiate second from third maxillary molars. The results obtained confirm our hypothesis, showing a significant difference between second and third maxillary molars. In particular we note the complete absence of Facets 7 and 10 in all third molars included in this analysis. The presence of these facets in Krapina D58 eliminates the possibility that it is a third maxillary molar. Consequently it should be reclassified as a second molar. Although this method is limited by the degree of dental wear (i.e., unworn teeth cannot be analyzed) and to individual molars in full occlusion, it can be used for tooth identification when other common criteria are not sufficient to discriminate between second and third maxillary molars. Am J Phys Anthropol 143:306–312, 2010. © 2010 Wiley‐Liss, Inc.