Whole-genome scan identifies quantitative trait loci for chronic pastern dermatitis in German draft horses

Chronic pastern dermatitis (CPD), also known as chronic progressive lymphedema (CPL), is a skin disease that affects draft horses. This disease causes painful lower-leg swelling, nodule formation, and skin ulceration, interfering with movement. The aim of this whole-genome scan was to identify quantitative trait loci (QTL) for CPD in German draft horses. We recorded clinical data for CPD in 917 German draft horses and collected blood samples from these horses. Of these 917 horses, 31 paternal half-sib families comprising 378 horses from the breeds Rhenish German, Schleswig, Saxon-Thuringian, and South German were chosen for genotyping. Each half-sib family was constituted by only one draft horse breed. Genotyping was done for 318 polymorphic microsatellites evenly distributed on all equine autosomes and the X chromosome with a mean distance of 7.5 Mb. An across-breed multipoint linkage analysis revealed chromosome-wide significant QTL on horse chromosomes (ECA) 1, 9, 16, and 17. Analyses by breed confirmed the QTL on ECA1 in South German and the QTL on ECA9, 16, and 17 in Saxon-Thuringian draft horses. For the Rhenish German and Schleswig draft horses, additional QTL on ECA4 and 10 and for the South German draft horses an additional QTL on ECA7 were found. This is the first whole-genome scan for CPD in draft horses and it is an important step toward the identification of candidate genes.     

A rare form of persistent right aorta arch in linkage disequilibrium with the DiGeorge critical region on CFA26 in German Pinschers

Persistent right aortic arch (PRAA) is a congenital vascular ring anomaly common in several dog breeds. In German Pinscher, the disorder is characterized by a left retroesophageal subclavian artery in combination with a ligamentum arteriosum originating at the aberrant left subclavian artery (PRAA-SA-LA). In this study, we genotyped 38 microsatellite markers on canine chromosome 26 (CFA26) in German Pinschers and tested them for linkage and association. We found a chromosome-wide significantly linked genomic region on CFA26, which corresponds to the human DiGeorge syndrome critical region (DGCR). Therefore, we analyzed sequences from 13 genes of DGCR and the canine t-box gene TBX1. We identified a total of 26 polymorphisms in German Pinschers. Three of these SNPs located within TBX1 and one in the mitochondrial ribosomal protein L40 gene (MRPL40) were associated with the PRAA-SA-LA phenotype in German Pinscher. Despite linkage and association between PRAA-SA-LA and the canine DGCR, none of these mutations appeared responsible for PRAA-SA-LA. As the orthologue human region on HSA22q11.2 is known for high susceptibility to genomic rearrangements, we suspect that in German Pinschers, chromosomal aberrations might cause PRAA-SA-LA.     

No biogeographical pattern for a root‐associated fungal species complex

Aim The biogeography of microbes is poorly understood and there is an open debate regarding if and how microbial biodiversity is structured. At the beginning of the 20th century, Baas Becking laid the foundations for the biogeography of microbes by stating that ‘Everything is everywhere, but the environment selects’ (the EisE hypothesis). This hypothesis remained dogma for almost a century. However, the recognition that microbial ‘species’ are often assemblages of reproductively isolated lineages challenged the EisE hypothesis, leading to the now common assumption that microbial communities possess cryptic biogeographic structures. We tested the presence of a cryptic biogeographical structure for a well‐characterized fungal species complex (the Phialocephala fortinii s.l.–Acephala applanata species complex, PAC) using precise molecular species resolution. In addition, we analysed factors that could govern PAC community assembling. Locations Forty‐four study sites in temperate and boreal forests across the Northern Hemisphere were included. Methods (1) The distance–decay relationship among PAC communities was calculated and a resampling procedure was applied to analyse the effect of sampling intensity and geographic distances among PAC communities. (2) Factors shaping PAC communities (e.g. climatic factors and tree species composition) were studied. (3) We tested PAC communities for random composition. Results We found that the similarity of species assemblages did not decrease with increasing geographical distance. Moreover, species diversity did not increase by expanding the area sampled. Instead, species diversity increased by increasing the sampling effort. Community composition correlated neither with tree species composition nor climate, and no association among species was observed. Main conclusions We could not discover any cryptic biogeographic structure even after applying refined species assignment but we demonstrate the importance of sampling effort for understanding the biogeography of microorganisms. Moreover, we show that primarily stochastic effects are responsible for the species composition of PAC communities.     

Meeting report: Signal transduction meets systems biology

ABSTRACT: In the 21st century, systems-wide analyses of biological processes are getting more and more realistic. Especially for the in depth analysis of signal transduction pathways and networks, various approaches of systems biology are now successfully used. The EU FP7 large integrated project SYBILLA (Systems Biology of T-cell Activation in Health and Disease) coordinates such an endeavor. By using a combination of experimental data sets and computational modelling, the consortium strives for gaining a detailed and mechanistic understanding of signal transduction processes that govern T-cell activation. In order to foster the interaction between systems biologists and experimentally working groups, SYBILLA co-organized the 15th meeting "Signal Transduction: Receptors, Mediators and Genes" together with the Signal Transduction Society (STS). Thus, the annual STS conference, held from November 7 to 9, 2011 in Weimar, Germany, provided an interdisciplinary forum for research on signal transduction with a major focus on systems biology addressing signalling events in T-cells. Here we report on a selection of ongoing projects of SYBILLA and how they were discussed at this interdisciplinary conference.     

Behavioral responses to food odor in juvenile marine fish: Acuity varies with species and fish length

This study tested the hypothesis that acuity of behavioral responses to food odor in three commercially important species of marine fish would increase as juvenile length increased. Swimming activity among two size groups of fish was measured in the presence of a series of squid extract dilutions. Increased swimming activity in juvenile Pacific halibut Hippoglossus stenolepis Schmidt, walleye pollock Theragra chalcogramma Pallas, and sablefish Anoplopoma fimbria Pallas was stimulated above threshold concentrations of squid extract, expressed as dilution from full strength. Maximum chemosensory acuity was observed in smaller (8-14 cm total length, TL) Pacific halibut and walleye pollock, while larger sablefish (15-23 cm TL) continued to develop acuity. Response thresholds were highest (10^− 3 dilution) in Pacific halibut, at intermediate levels (10^− 4-10^− 6 dilution) in walleye pollock and smaller sablefish and reached the lowest levels (10^− 13 dilution) in larger sablefish. The widely held view that dissolved free amino acids (DFAA) are the primary chemosensory stimulants for fish food searching may not be valid for sablefish, as they detected squid extract at dilutions containing DFAA that appeared to be far below ambient sea water DFAA concentrations.     

Identification of Quantitative Trait Loci (QTL) for Canine Hip Dysplasia and Canine Elbow Dysplasia in Bernese Mountain Dogs

A genome-wide association study for canine hip dysplasia (CHD) and canine elbow dysplasia (CED) using the Illumina canine high density bead chip had been performed for 174 Bernese mountain dogs. General and mixed linear model analysis identified two different regions with single nucleotide polymorphisms (SNPs) on dog chromosome (CFA) 14 significantly associated with CHD and a further significantly CHD-associated region on CFA37. For CED, four SNPs on CFA11 and 27 were significantly associated. The identified SNPs of four associated regions included nearby candidate genes. These possible positional candidates were the genes PON2 on CFA14 and FN1 on CFA37 for CHD and the genes LMNB1 on CFA11 and WNT10B on CFA27 for CED.