Mixed inheritance of equine recurrent airway obstruction

BACKGROUND: Mode of inheritance of equine recurrent airway obstruction (RAO) is unknown. HYPOTHESIS: Major genes are responsible for RAO. ANIMALS: Direct offspring of 2 RAO-affected Warmblood stallions (n = 197; n = 163) and a representative sample of Swiss Warmbloods (n = 401). METHODS: One environmental and 4 genetic models (general, mixed inheritance, major gene, and polygene) were tested for Horse Owner Assessed Respiratory Signs Index (1-4, unaffected to severely affected) by segregation analyses of the 2 half-sib sire families, both combined and separately, using prevalences estimated in a representative sample. RESULTS: In all data sets the mixed inheritance model was most likely to explain the pattern of inheritance. In all 3 datasets the mixed inheritance model did not differ significantly from the general model (P= .62, P= 1.00, and P= .27) but was always better than the major gene model (P < .01) and the polygene model (P < .01). The frequency of the deleterious allele differed considerably between the 2 sire families (P= .23 and P= .06). In both sire families the displacement was large (t= 17.52 and t= 12.24) and the heritability extremely large (h(2)= 1). CONCLUSIONS AND CLINICAL RELEVANCE: Segregation analyses clearly reveal the presence of a major gene playing a role in RAO. In 1 family, the mode of inheritance was autosomal dominant, whereas in the other family it was autosomal recessive. Although the expression of RAO is influenced by exposure to hay, these findings suggest a strong, complex genetic background for RAO.

Genetic mapping of the belt pattern in Brown Swiss cattle to BTA3

The white belt pattern of Brown Swiss cattle is characterized by a lack of melanocytes in a stretch of skin around the midsection. This pattern is of variable width and sometimes the belt does not fully circle the body. To identify the gene responsible for this colour variation, we performed linkage mapping of the belted locus using six segregating half-sib families including 104 informative meioses for the belted character. The pedigree confirmed a monogenic autosomal dominant inheritance of the belted phenotype in Brown Swiss cattle. We performed a genome scan using 186 microsatellite markers in a subset of 88 animals of the six families. Linkage with the belt phenotype was detected at the telomeric region of BTA3. Fine-mapping and haplotype analysis using 19 additional markers in this region refined the critical region of the belted locus to a 922-kb interval on BTA3. As the corresponding human and mouse chromosome segments contain no obvious candidate gene for this coat colour trait, the mutation causing the belt pattern in the Brown Swiss cattle might help to identify an unknown gene influencing skin pigmentation.

The equine DNAH3 gene: SNP discovery and exclusion of an involvement in recurrent airway obstruction (RAO) in European Warmblood horses

Recurrent airway obstruction is one of the most common airway diseases affecting mature horses. Increased bronchoalveolar mucus, neutrophil accumulation in airways, and airway obstruction are the main features of this disease. Mucociliary clearance is a key component of pulmonary defense mechanisms. Cilia are the motile part of this system and a complex linear array of dynein motors is responsible for their motility by moving along the microtubules in the axonemes of cilia and flagella. We previously detected a QTL for RAO on ECA 13 in a half-sib family of European Warmblood horses. The gene encoding DNAH3 is located in the peak of the detected QTL and encodes a dynein subunit. Therefore, we analysed this gene as a positional and functional candidate gene for RAO. In a mutation analysis of all 62 exons we detected 53 new polymorphisms including 7 non-synonymous variants. We performed an association study using 38 polymorphisms in a cohort of 422 animals. However, after correction for multiple testing we did not detect a significant association of any of these polymorphisms with RAO (P>0.05). Therefore, it seems unlikely that variants at the DNAH3 gene are responsible for the RAO QTL in European Warmblood horses.

Replication and fine-mapping of a QTL for recurrent airway obstruction in European Warmblood horses.

Recurrent airway obstruction (RAO), or 'heaves', is a common performance-limiting allergic respiratory disease of mature horses. It is related to sensitization and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. In a previous study, we detected a QTL for RAO on ECA 13 in a half-sib family of European Warmblood horses. In this study, we genotyped additional markers in the family and narrowed the QTL down to about 1.5 Mb (23.7-25.2 Mb). We detected the strongest association with SNP BIEC2-224511 (24,309,405 bp). We also obtained SNP genotypes in an independent cohort of 646 unrelated Warmblood horses. There was no genome-wide significant association with RAO in these unrelated horses. However, we performed a genotypic association study of the SNPs on ECA 13 in these unrelated horses, and the SNP BIEC2-224511 also showed the strongest association with RAO in the unrelated horses (p(raw) = 0.00037). The T allele at this SNP was associated with RAO both in the family and the unrelated horses. Thus, the association study in the unrelated animals provides independent support for the previously detected QTL. The association study allows further narrowing of the QTL interval to about 0.5 Mb (24.0-24.5 Mb). We sequenced the coding regions of the genes in the critical region but did not find any associated coding variants. Therefore, the causative variant underlying this QTL is likely to be a regulatory mutation.

Albinism in the American mink (Neovison vison) is associated with a tyrosinase nonsense mutation

Albino phenotypes are documented in various species including the American mink. In other species the albino phenotypes are associated with tyrosinase (TYR) gene mutations; therefore TYR was considered the candidate gene for albinism in mink. Four microsatellite markers were chosen in the predicted region of the TYR gene. Genotypes at the markers Mvi6025 and Mvi6034 were found to be associated with the albino phenotype within an extended half-sib family. A BAC clone containing Mvi6034 was mapped to chromosome 7q1.1-q1.3 by fluorescent in situ hybridization. Subsequent analysis of genomic TYR sequences from wild-type and albino mink samples identified a nonsense mutation in exon 1, which converts a TGT codon encoding cysteine to a TGA stop codon (c.138T>A, p.C46X; EU627590). The mutation truncates more than 90% of the normal gene product including the putative catalytic domains. The results indicate that the nonsense mutation is responsible for the albino phenotype in the American mink.

Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma.

Recurrent airway obstruction (RAO) is a common and potentially debilitating lower airway disease in horses, which shares many similarities with human asthma. In susceptible horses RAO exacerbation is caused by environmental allergens and irritants present in hay dust. The objective of this study was the identification of genes and pathways involved in the pathology of RAO by global transcriptome analyses in stimulated peripheral blood mononuclear cells (PBMCs). We performed RNA-seq on PBMCs derived from 40 RAO affected and 45 control horses belonging to three cohorts of Warmblood horses: two half-sib families and one group of unrelated horses. PBMCs were stimulated with hay dust extract, lipopolysaccharides, a recombinant parasite antigen, or left unstimulated. The total dataset consisted of 561 individual samples. We detected significant differences in the expression profiles between RAO and control horses. Differential expression (DE) was most marked upon stimulation with hay dust extract. An important novel finding was a strong upregulation of CXCL13 together with many genes involved in cell cycle regulation in stimulated samples from RAO affected horses, in addition to changes in the expression of several HIF-1 transcription factor target genes. The RAO condition alters systemic changes observed as differential expression profiles of PBMCs. Those changes also depended on the cohort and stimulation of the samples and were dominated by genes involved in immune cell trafficking, development, and cell cycle regulation. Our findings indicate an important role of CXCL13, likely macrophage or Th17 derived, and the cell cycle regulator CDC20 in the immune response in RAO.

Análisis, desarrollo y optimización de un sistema para el diseño de redes topográficas valorando el modelo digital del terreno

El presente trabajo tiene como objetivo general el análisis de las técnicas de diseño y optimización de redes topográficas, observadas mediante topografía convencional (no satelital) el desarrollo e implementación de un sistema informático capaz de ayudar a la definición de la geometría más fiable y precisa, en función de la orografía del terreno donde se tenga que ubicar. En primer lugar se realizará un estudio de la metodología del ajuste mediante mínimos cuadrados y la propagación de varianzas, para posteriormente analizar su dependencia de la geometría que adopte la red. Será imprescindible determinar la independencia de la matriz de redundancia (R) de las observaciones y su total dependencia de la geometría, así como la influencia de su diagonal principal (rii), números de redundancia, para garantizar la máxima fiabilidad interna de la misma. También se analizará el comportamiento de los números de redundancia (rii) en el diseño de una red topográfica, la variación de dichos valores en función de la geometría, analizando su independencia respecto de las observaciones así como los diferentes niveles de diseño en función de los parámetros y datos conocidos. Ha de señalarse que la optimización de la red, con arreglo a los criterios expuestos, está sujeta a los condicionantes que impone la necesidad de que los vértices sean accesibles, y además sean visibles entre sí, aquellos relacionados por observaciones, situaciones que dependen esencialmente del relieve del terreno y de los obstáculos naturales o artificiales que puedan existir. Esto implica la necesidad de incluir en el análisis y en el diseño, cuando menos de un modelo digital del terreno (MDT), aunque lo más útil sería la inclusión en el estudio del modelo digital de superficie (MDS), pero esta opción no siempre será posible. Aunque el tratamiento del diseño esté basado en un sistema bidimensional se estudiará la posibilidad de incorporar un modelo digital de superficie (MDS); esto permitirá a la hora de diseñar el emplazamiento de los vértices de la red la viabilidad de las observaciones en función de la orografía y los elementos, tanto naturales como artificiales, que sobre ella estén ubicados. Este sistema proporcionaría, en un principio, un diseño óptimo de una red constreñida, atendiendo a la fiabilidad interna y a la precisión final de sus vértices, teniendo en cuenta la orografía, lo que equivaldría a resolver un planteamiento de diseño en dos dimensiones y media1; siempre y cuando se dispusiera de un modelo digital de superficie o del terreno. Dado que la disponibilidad de obtener de manera libre el MDS de las zonas de interés del proyecto, hoy en día es costoso2, se planteará la posibilidad de conjuntar, para el estudio del diseño de la red, de un modelo digital del terreno. Las actividades a desarrollar en el trabajo de esta tesis se describen en esta memoria y se enmarcan dentro de la investigación para la que se plantean los siguientes objetivos globales: 1. Establecer un modelo matemático del proceso de observación de una red topográfica, atendiendo a todos los factores que intervienen en el mismo y a su influencia sobre las estimaciones de las incógnitas que se obtienen como resultado del ajuste de las observaciones. 2. Desarrollar un sistema que permita optimizar una red topográfica en sus resultados, aplicando técnicas de diseño y simulación sobre el modelo anterior. 3. Presentar una formulación explícita y rigurosa de los parámetros que valoran la fiabilidad de una red topográfica y de sus relaciones con el diseño de la misma. El logro de este objetivo se basa, además de en la búsqueda y revisión de las fuentes, en una intensa labor de unificación de notaciones y de construcción de pasos intermedios en los desarrollos matemáticos. 4. Elaborar una visión conjunta de la influencia del diseño de una red, en los seis siguientes factores (precisiones a posteriori, fiabilidad de las observaciones, naturaleza y viabilidad de las mismas, instrumental y metodología de estacionamiento) como criterios de optimización, con la finalidad de enmarcar el tema concreto que aquí se aborda. 5. Elaborar y programar los algoritmos necesarios para poder desarrollar una aplicación que sea capaz de contemplar las variables planteadas en el apartado anterior en el problema del diseño y simulación de redes topográficas, contemplando el modelo digital de superficie. Podrían considerarse como objetivos secundarios, los siguientes apartados: Desarrollar los algoritmos necesarios para interrelacionar el modelo digital del terreno con los propios del diseño. Implementar en la aplicación informática la posibilidad de variación, por parte del usuario, de los criterios de cobertura de los parámetros (distribución normal o t de Student), así como los grados de fiabilidad de los mismos ABSTRACT The overall purpose of this work is the analysis of the techniques of design and optimization for geodetic networks, measured with conventional survey methods (not satellite), the development and implementation of a computational system capable to help on the definition of the most liable and accurate geometry, depending on the land orography where the network has to be located. First of all, a study of the methodology by least squares adjustment and propagation of variances will be held; then, subsequently, analyze its dependency of the geometry that the network will take. It will be essential to determine the independency of redundancy matrix (R) from the observations and its absolute dependency from the network geometry, as well as the influence of the diagonal terms of the R matrix (rii), redundancy numbers, in order to ensure maximum re liability of the network. It will also be analyzed first the behavior of redundancy numbers (rii) in surveying network design, then the variation of these values depending on the geometry with the analysis of its independency from the observations, and finally the different design levels depending on parameters and known data. It should be stated that network optimization, according to exposed criteria, is subject to the accessibility of the network points. In addition, common visibility among network points, which of them are connected with observations, has to be considered. All these situations depends essentially on the terrain relief and the natural or artificial obstacles that should exist. Therefore, it is necessary to include, at least, a digital terrain model (DTM), and better a digital surface model (DSM), not always available. Although design treatment is based on a bidimensional system, the possibility of incorporating a digital surface model (DSM) will be studied; this will allow evaluating the observations feasibility based on the terrain and the elements, both natural and artificial, which are located on it, when selecting network point locations. This system would provide, at first, an optimal design of a constrained network, considering both the internal reliability and the accuracy of its points (including the relief). This approach would amount to solving a “two and a half dimensional”3 design, if a digital surface model is available. As the availability of free DSM4 of the areas of interest of the project today is expensive, the possibility of combining a digital terrain model will arise. The activities to be developed on this PhD thesis are described in this document and are part of the research for which the following overall objectives are posed: 1. To establish a mathematical model for the process of observation of a survey network, considering all the factors involved and its influence on the estimates of the unknowns that are obtained as a result of the observations adjustment. 2. To develop a system to optimize a survey network results, applying design and simulation techniques on the previous model. 3. To present an explicit and rigorous formulation of parameters which assess the reliability of a survey network and its relations with the design. The achievement of this objective is based, besides on the search and review of sources, in an intense work of unification of notation and construction of intermediate steps in the mathematical developments. 4. To develop an overview of the influence on the network design of six major factors (posterior accuracy, observations reliability, viability of observations, instruments and station methodology) as optimization criteria, in order to define the subject approached on this document. 5. To elaborate and program the algorithms needed to develop an application software capable of considering the variables proposed in the previous section, on the problem of design and simulation of surveying networks, considering the digital surface model. It could be considered as secondary objectives, the following paragraphs: To develop the necessary algorithms to interrelate the digital terrain model with the design ones. To implement in the software application the possibility of variation of the coverage criteria parameters (normal distribution or Student t test) and therefore its degree of reliability.

Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Mérino ewes

Ewes from the Booroola strain of Australian Mérino sheep are characterized by high ovulation rate and litter size. This phenotype is due to the action of the FecBB allele of a major gene named FecB, as determined by statistical analysis of phenotypic data. By genetic analysis of 31 informative half-sib families from heterozygous sires, we showed that the FecB locus is situated in the region of ovine chromosome 6 corresponding to the human chromosome 4q22–23 that contains the bone morphogenetic protein receptor IB (BMPR-IB) gene encoding a member of the transforming growth factor-β (TGF-β) receptor family. A nonconservative substitution (Q249R) in the BMPR-IB coding sequence was found to be associated fully with the hyperprolificacy phenotype of Booroola ewes. In vitro, ovarian granulosa cells from FecBB/FecBB ewes were less responsive than granulosa cells from FecB+/FecB+ ewes to the inhibitory effect on steroidogenesis of GDF-5 and BMP-4, natural ligands of BMPR-IB. It is suggested that in FecBB/FecBB ewes, BMPR-IB would be inactivated partially, leading to an advanced differentiation of granulosa cells and an advanced maturation of ovulatory follicles.

Lethal chondrodysplasia in a family of Holstein cattle is associated with a de novo splice site variant of COL2A1

Background Lethal chondrodysplasia (bulldog syndrome) is a well-known congenital syndrome in cattle and occurs sporadically in many breeds. In 2015, it was noticed that about 12 % of the offspring of the phenotypically normal Danish Holstein sire VH Cadiz Captivo showed chondrodysplasia resembling previously reported bulldog calves. Pedigree analysis of affected calves did not display obvious inbreeding to a common ancestor, suggesting the causative allele was not a rare recessive. The normal phenotype of the sire suggested a dominant inheritance with incomplete penetrance or a mosaic mutation. Results Three malformed calves were examined by necropsy, histopathology, radiology, and computed tomography scanning. These calves were morphologically similar and displayed severe disproportionate dwarfism and reduced body weight. The syndrome was characterized by shortening and compression of the body due to reduced length of the spine and the long bones of the limbs. The vicerocranium had severe dysplasia and palatoschisis. The bones had small irregular diaphyses and enlarged epiphyses consisting only of chondroid tissue. The sire and a total of four affected half-sib offspring and their dams were genotyped with the BovineHD SNP array to map the defect in the genome. Significant genetic linkage was obtained for several regions of the bovine genome including chromosome 5 where whole genome sequencing of an affected calf revealed a COL2A1 point mutation (g.32473300 G > A). This private sequence variant was predicted to affect splicing as it altered the conserved splice donor sequence GT at the 5’-end of COL2A1 intron 36, which was changed to AT. All five available cases carried the mutant allele in heterozygous state and all five dams were homozygous wild type. The sire VH Cadiz Captivo was shown to be a gonadal and somatic mosaic as assessed by the presence of the mutant allele at levels of about 5 % in peripheral blood and 15 % in semen. Conclusions The phenotypic and genetic findings are comparable to a previously reported COL2A1 missense mutation underlying lethal chondrodysplasia in the offspring of a mosaic French Holstein sire (Igale Masc). The identified independent spontaneous splice site variant in COL2A1 most likely caused chondrodysplasia and must have occurred during the early foetal development of the sire. This study provides a first example of a dominant COL2A1 splice site variant as candidate causal mutation of a severe lethal chondrodysplasia phenotype. Germline mosaicism is a relatively frequent mechanism in the origin of genetic disorders and explains the prevalence of a certain fraction of affected offspring. Paternal dominant de novo mutations are a risk in cattle breeding, especially because the ratio of defective offspring may be very high and be associated with significant animal welfare problems.

Genetic analysis of resistance to root-lesion nematode (Pratylenchus thornei) in wheat

The inheritance of resistance to root-lesion nematode was investigated in five synthetic hexaploid wheat lines and two bread wheat lines using a half-diallel design of F-1 and F-2 crosses. The combining ability of resistance genes in the synthetic hexaploid wheat lines was compared with the performance of the bread wheat line 'GS50a', the source of resistance to Pratylenchus thornei used in Australian wheat breeding programmes. Replicated glasshouse trials identified P. thornei resistance as polygenic and additive in gene action. General combining ability (GCA) of the parents was more important than specific combining ability (SCA) effects in the inheritance of P. thornei resistance in both F-1 and F-2 populations. The synthetic hexaploid wheat line 'CPI133872' was identified as the best general combiner, however, all five synthetic hexaploid wheat lines possessed better GCA than 'GS50a'. The synthetic hexaploid wheat lines contain novel sources of P. thornei resistance that will provide alternative and more effective sources of resistance to be utilized in wheat breeding programmes.

Determining the effective dimensionality of the genetic variance-covariance matrix

Determining the dimensionality of G provides an important perspective on the genetic basis of a multivariate suite of traits. Since the introduction of Fisher's geometric model, the number of genetically independent traits underlying a set of functionally related phenotypic traits has been recognized as an important factor influencing the response to selection. Here, we show how the effective dimensionality of G can be established, using a method for the determination of the dimensionality of the effect space from a multivariate general linear model introduced by AMEMIYA (1985). We compare this approach with two other available methods, factor-analytic modeling and bootstrapping, using a half-sib experiment that estimated G for eight cuticular hydrocarbons of Drosophila serrata. In our example, eight pheromone traits were shown to be adequately represented by only two underlying genetic dimensions by Amemiya's approach and factor-analytic modeling of the covariance structure at the sire level. In, contrast, bootstrapping identified four dimensions with significant genetic variance. A simulation study indicated that while the performance of Amemiya's method was more sensitive to power constraints, it performed as well or better than factor-analytic modeling in correctly identifying the original genetic dimensions at moderate to high levels of heritability. The bootstrap approach consistently overestimated the number of dimensions in all cases and performed less well than Amemiya's method at subspace recovery.

Numerical simulation of magnetic field design for damping thermocapillary convection in a floating half-zone

The magnetic fields produced by electrical coils are designed for damping the the thermocapillary convection in a floating half-zone in microgravity. The fields are designed specially to reduce the flow near the free surface and then in the melt zone by adjusting the longitudinal coil positions close to the melt zone. The effects of the designed magnetic fields on reducing the flow velocity and temperature distribution non-uniformity in the melt zone are stronger than those of the case of an uniform longitudinal magnetic field obtained by numerical simulation, particularly at the melt-rod interface. It brings fundamental insights into the heat and mass transfer control at the solidification interface by the magnetic field design for crystal growth by the floating full-zone method.

Design of a half ton dehydrator for fish

A half-ton capacity artificial dryer has been designed at the Central Institute of Fisheries Technology for drying fish like Mackerel, Sardine, White bait etc. The dryer is a hot air recirculation type. 80 KW thermostatically controlled heating coils are made use of for heating the air. The air is circulated by means of an axial flow pattern fan. Drying takes place at a temperature of 115 degrees F. The structure of the dryer comes to about Rs. 20,000.

Half-bridge SIC inverter for hybrid electric vehicles: Design, development and testing at higher operating temperature

In recent years, Silicon Carbide (SiC) semiconductor devices have shown promise for high density power electronic applications, due to their electrical and thermal properties. In this paper, the performance of SiC JFETs for hybrid electric vehicle (HEV) applications is investigated at heatsink temperatures of 100 °C. The thermal runaway characteristics, maximum current density and packaging temperature limitations of the devices are considered and the efficiency implications discussed. To quantify the power density capabilities of power transistors, a novel 'expression of rating' (EoR) is proposed. A prototype single phase, half-bridge voltage source inverter using SiC JFETs is also tested and its performance at 25 °C and 100 °C investigated.