Study of Candidate Genes for production and carcass traits in Italian Heavy Pigs: identification of a new DNA Markers, Expression Studies and Association Analysis using Different Experimental Design

Heavy pig breeding in Italy is mainly oriented for the production of high quality processed products. Of particular importance is the dry cured ham production, which is strictly regulated and requires specific carcass characteristics correlated with green leg characteristics. Furthermore, as pigs are slaughtered at about 160 kg live weight, the Italian pig breeding sector faces severe problems of production efficiency that are related to all biological aspects linked to growth, feed conversion, fat deposition and so on. It is well known that production and carcass traits are in part genetically determined. Therefore, as a first step to understand genetic basis of traits that could have a direct or indirect impact on dry cured ham production, a candidate gene approach can be used to identify DNA markers associated with parameters of economic importance. In this thesis, we investigated three candidate genes for carcass and production traits (TRIB3, PCSK1, MUC4) in pig breeds used for dry cured ham production, using different experimental approaches in order to find molecular markers associated with these parameters.

Amphibian biodiversity in Taita Hills, Kenya

Species richness varies greatly across geographical regions. Eastern Arc Mountains (EAM) of Kenya and Tanzania is one of the global biodiversity hotspots. Despite this, high species diversity the explanatory factors have remained largely unexplored. Herein, this study first investigated amphibian species richness patterns in the EAM and particularly the reasons for the low richness in Taita Hills. It tested the hypothesis that the low richness is due to past forest loss or other factors. The results demonstrated that the regional species richness pattern was influenced largely by mean annual rainfall and not forest area. Secondly, using the 26 currently recorded amphibians in the Taita Hills, it investigated the relationship between amphibian species composition along anthropogenic habitat disturbance and elevation gradients. It tested the hypothesis that sites with similar environmental characteristics (temperature, rainfall and elevation), in close proximity and with similar disturbance levels (habitat types) harbour similar species composition. It was found that amphibian species composition differed in terms of elevation and was explained by both temperature and rainfall. Therefore sites with similar environmental characteristics, disturbance levels and in close proximity geographically have similar amphibian composition. Thirdly, diagnostic characters, distribution, basic life history characteristics and conservation status of all currently known amphibians in the Taita Hills were provided. Finally, first long term life history and ecological characteristics of a brevicipitid frog (Callulina sp) was provided. The results showed that this frog abundance and distribution is influenced mainly by mean monthly temperature, breeds during the long dry season and exhibit parental care. Results of this study strongly recommend increasing indigenous forest cover in order to enhance the conservation of the endemic indigenous forest associated amphibians such as Callulina sp, Boulengerula taitana and Boulengerula niedeni.

Studio di alcuni tratti del temperamento nel cane

Il temperamento può essere definito come l’attitudine che un cane esprime verso le persone e verso altri animali, la combinazione di tratti fisici e mentali, acquisiti e non, che determinano il comportamento del cane. Tale parametro delinea perciò il carattere di un individuo, inclinazioni e tendenze, eccitabilità, tristezza, rabbia e il modo caratteristico di comportarsi di un individuo, con particolare riferimento alle interazioni sociali. La presente tesi di Dottorato rappresenta uno studio su alcuni tratti del temperamento nel cane domestico elaborato in 3 progetti sperimentali. Nei primi due progetti sono state analizzate le differenze attitudinali tra alcune razze canine attraverso l’applicazione di un test di temperamento in cuccioli di 60 giorni e in cani adulti, per valutare e confrontarne il temperamento, la socialità ed identificare profili tipici di razza. Nel terzo progetto un campione di cani morsicatori di canile e di proprietà è stato confrontato con due rispettivi gruppi di controllo. Analizzando i risultati è stato possibile mettere in evidenza caratteristiche di razza omogenee nell’interazione con stimoli inanimati, nelle interazioni sociali e in relazione alla possessività e sono stati delineati profili di razza sia nei cuccioli sia negli adulti. Si sono tuttavia, osservate variabilità individuali, intra-razza e intra-cucciolata, a testimonianza dell’influenza complessa e multifattoriale delle componenti genetica e ambientale sul comportamento dei cani. Il confronto tra cani morsicatori di canile e di proprietà ha messo in luce interessanti differenze tra i soggetti in termini di reattività, socievolezza, propensione all’interazione con il proprietario o con un estraneo, comportamenti di evitamento e velocità di reazione agli stimoli presentati. Il test applicato è risultato un valido strumento per valutare il temperamento di cani dichiarati aggressivi che sono stati sottoposti a situazioni nuove e a stimoli sconosciuti per poter ottenere una migliore visione d’insieme del temperamento del soggetto.

Genomic and proteomic approaches in pig meat quality research field

Pig meat and carcass quality is a complex concept determined by environmental and genetic factors concurring to the phenotypic variation in qualitative characteristics of meat (fat content, tenderness, juiciness, flavor,etc). This thesis shows the results of different investigations to study and to analyze pig meat and carcass quality focusing mainly on genomic; moreover proteomic approach has been also used. The aim was to analyze data from association studies between genes considered as candidate and meat and carcass quality in different pig breeds. The approach was used to detect new SNP in genes functionally associated to the studied traits and to confirm as candidate other genes already known. Five polymorphisms (one new SNP in Calponin 1 gene and four additional polymorphism already known in other genes) were considered on chromosome 2 (SSC2). Calponin 1 (CNN1) was associated to the studied traits and furthermore the results reported confirmed the data already known for Lactate dehydrogenase A (LDHA), Low density lipoprotein receptor (LDLR), Myogenic differentiation 1 (MYOD1) e Ubiquitin-like 5 (UBL5), in Italian Large White pigs. Using an in silico search it was possible to detect on SSC2 a new SNP of Deoxyhypusine synthase (DHPS) gene partially overlapping with WD repeat domain 83 (WDR83) gene and significant for the meat pH variation in Italian Large White (ILW) pigs. Perilipin 1 (PLIN1) mapping on chromosome 7 and Perilipin 2 (PLIN2) mapping on chromosome 1 were studied and the results obtained in Duroc breed have shown significant associations with carcass traits. Moreover a study of protein composition of porcine LD muscle, indicated an effect of temperature treatment of carcass, on proteins of the sarcoplasmic fraction and in particular on PGM1 phosphorylation. Future studies on pig meat quality should be based on the integration of different experimental approaches (genomics, proteomics, transcriptomics, etc).

Swiss warmblood horse with symptoms of hereditary equine regional dermal asthenia without mutation in the cyclophylin B gene (PPIB)

Hereditary equine dermal asthenia (HERDA) is an autosomal recessive skin disease that affects predominantly Quarter Horses and related breeds. Typical symptoms are easy bruising and hyperextensible skin on the back. The prognosis is guarded, as affected horses cannot be ridden normally and are often euthanised. In the Quarter Horse, HERDA is associated with a mutation in cyclophilin B (PPIB), an enzyme involved in triple helix formation of collagen. Here we describe the case of a Swiss Warmblood filly with symptoms of HERDA without PPIB-mutation and in which we also could exclude Ehlers-Danlos syndrome Type IV, VI, VIIA, VIIB and VIIC (dermatosparaxis type) as etiological diseases.

No evidence for a genetic association between female mating preference and male secondary sexual trait in a Lake Victoria cichlid fish

Sexual selection by female mating preference for male nuptial coloration has been suggested as a driving force in the rapid speciation of Lake Victoria cichlid fish. This process could have been facilitated or accelerated by genetic associations between female preference loci and male coloration loci. Preferences, as well as coloration, are heritable traits and are probably determined by more than one gene. However, little is known about potential genetic associations between these traits. In turbid water, we found a population that is variable in male nuptial coloration from blue to yellow to red. Males at the extreme ends of the phenotype distribution resemble a reproductively isolated species pair in clear water that has diverged into one species with blue-grey mates and one species with bright red males. Females of the turbid water population vary in mating preference coinciding with the male phenotype distribution. For the current study, these females were mated to blue males. We measured the coloration of the sires and male offspring. Parents-offspring regression showed that the sires did not affect male offspring coloration, which confirms earlier findings that the blue species breeds true. In contrast, male offspring coloration was determined by the identity of the dams, which suggests that there is heritable variation in male color genes between females. However, we found that mating preferences of the dams were not correlated with male offspring coloration. Thus, there is no evidence for strong genetic linkage between mating preference and the preferred trait in this population [Current Zoology 56 (1): 57-64 2010].

Conserving indigenous animal genetic resources as a coping strategy to adapt to climate change: the Azikheli Buffalo in Northern Mountains of Pakistan

There are clear signs that the agro-pastoralists in the Himalayan and Hindu-Kush mountain ranges will have less cropping opportunities due to reduced possibilities for irrigated agriculture as a result of climate change. The importance of extensive livestock production based on well adapted livestock species may once again increase. This calls for a better documentation and understanding of the adaptation capabilities of indigenous breeds considering a changing environment. The current study investigates the adaptive traits of the Azikheli buffalo to mountain environments through calculating mean, standard error and percentages for different variables. Results from this study suggest that the brown coat color, the small body size and the high fertility are adaptive traits of the Azikheli buffalo that may well suit harsh mountainous environment conditions with greater climate variability. Local farmers find it hard to sustain the Azikheli buffalo’s key adaptive traits because of a low bull to buffalo ratio, possibility of insemination with semen from imported breeds and a lack of institutional support to conserve the Azikheli breed. The breed is crucial for sustaining custodian communities in these mountains and thus needs to be conserved.

A nonsense mutation in the optic atrophy 3 gene (OPA3) causes dilated cardiomyopathy in Red Holstein cattle

Cardiomyopathies are severe degenerative disorders of the myocardium that lead to heart failure. During the last three decades bovine dilated cardiomyopathy (BDCMP) was observed worldwide in cattle of Holstein-Friesian origin. In the Swiss cattle population BDCMP affects Fleckvieh and Red Holstein breeds. The heart of affected animals is enlarged due to dilation of both ventricles. Clinical signs are caused by systolic dysfunction and affected individuals die as a result of severe heart insufficiency. BDCMP follows an autosomal recessive pattern of inheritance and the disease-causing locus was mapped to bovine chromosome 18 (BTA18). In the present study we describe the successful identification of the causative mutation in the OPA3 gene located on BTA18 that was previously reported to cause 3-methylglutaconic aciduria type III in Iraqi-Jewish patients. We demonstrated conclusive genetic and functional evidence that the nonsense mutation c.343C>T in the bovine OPA3 gene causes the late-onset dilated cardiomyopathy in Red Holstein cattle.

[Reproductive performance in Herens cows from 2003 to 2007]

Herens cows have been treated at the Clinic for Ruminants, University of Berne, more frequently for fertility problems than other breeds. The aim of the study was to overview the reproductive performance of the Herens breed by analyzing data sets of the Herens Breeding Book and of the Animal Traffic Database of Switzerland. In addition, a questionnaire was sent to the breeders concerning aspects of management and care to identify a possible influence on the reproductive performance of the animals. Based on 4988 lactations starting in 2003, an average interval of calving to first insemination of 86 days a calving to conception interval of 146 days and an inter calving period of 431 days could be calculated. Conception rate resulted in 39.1%, the fertility index was 1.87 and 6.5% of all cows were culled because of fertility problems. Half of the breeders owned 4 or less cows. The most important reason for keeping Herens cows was cow fighting. Traditional alpine pasturing and cow fight rules resulted in a seasonal calving with 80% of the births taking place between October and December. The calving month and seasonal calving were the most important reasons for a prolonged calving to conception interval.

Use of a 1.5 mm butterfly locking plate for stabilization of atlantoaxial pathology in three toy breed dogs

The objective of this study was to describe the use of a titanium 1.5 mm locking plate in the stabilization of atlantoaxial pathology in three toy breed dogs. Two dogs with atlantoaxial subluxation and another dog with an axial fracture, confirmed by diagnostic imaging, were stabilized via a ventral approach with a 1.5 mm titanium 5-hole locking butterfly-plate. Surgical reduction and stabilization were assessed by computed tomography and radiography after surgery. Follow-up evaluation for resolution of neurological signs and possible complications was performed in all three dogs. For long-term assessment, a telephone follow-up was performed. A considerable improvement of neurological signs occurred within two to four weeks after surgery. An excellent clinical outcome was identified in all three patients. Adequate stabilization and resolution of neurological signs in all three dogs was achieved. The stabilization of atlantoaxial surgical conditions in toy breeds with the 1.5 mm titanium 5-hole butterfly locking plate appears to be an effective means of surgical treatment.

Topographic and age-dependent distribution of subchondral bone density in the elbow joints of clinically normal dogs

OBJECTIVE: To investigate topographic and age-dependent adaptation of subchondral bone density in the elbow joints of healthy dogs by means of computed tomographic osteoabsorptiometry (CTOAM). Animals-42 elbow joints of 29 clinically normal dogs of various breeds and ages. PROCEDURES: Subchondral bone densities of the humeral, radial, and ulnar joint surfaces of the elbow relative to a water-hydroxyapatite phantom were assessed by means of CTOAM. Distribution patterns in juvenile, adult, and geriatric dogs (age, < 1 year, 1 to 8 years, and > 8 years, respectively) were determined and compared within and among groups. RESULTS: An area of increased subchondral bone density was detected in the humerus distomedially and cranially on the trochlea and in the olecranon fossa. The ulna had maximum bone densities on the anconeal and medial coronoid processes. Increased bone density was detected in the craniomedial region of the joint surface of the radius. A significant age-dependent increase in subchondral bone density was revealed in elbow joint surfaces of the radius, ulna, and humerus. Mean subchondral bone density of the radius was significantly less than that of the ulna in paired comparisons for all dogs combined and in adult and geriatric, but not juvenile, dog groups. CONCLUSIONS AND CLINICAL RELEVANCE: An age-dependent increase in subchondral bone density at the elbow joint was revealed. Maximal relative subchondral bone densities were detected consistently at the medial coronoid process and central aspect of the humeral trochlea, regions that are commonly affected in dogs with elbow dysplasia.

Role of the environment in the development of canine atopic dermatitis in Labrador and golden retrievers

Canine and human atopic dermatitis are multifaceted diseases whose clinical development may be influenced by several factors, such as genetic background, environment, secondary infections, food and psychological effects. The role of the environment has been extensively examined in humans but remains unclear in dogs. The aim of this study was to examine environmental factors in two genetically close breeds, Labrador and golden retrievers. Using standard criteria, atopic dogs in Switzerland and Germany were selected and compared with healthy individuals. Information on environmental factors was collected using a 46-question survey encompassing date and place of birth, way of life at the breeder's and owner's home, food and treatments. Univariate and multivariate logistic regression were used to assess the association between potential risk factors and disease status. The following parameters were associated with an increased risk of disease development: living in a shed during puppyhood, adoption at the age of 8-12 weeks and washing the dog regularly. In contrast, the following factors were associated with a lower risk: living in a rural environment, living in a household with other animals and walking in a forest. These associations do not prove causality but support the primary hypothesis that certain environmental factors may influence the development of canine atopic dermatitis. Further studies are warranted to confirm these results and conclusions.

Management effects on colostrogenesis in small ruminants: a review

Colostrum feeding in small ruminants is crucial during the first hours after birth due to the lack of Ig transfer during pregnancy via the placenta. In addition the immature immune system of the neonate is slow to produce its own Ig during the first weeks of life. Colostrogenesis, i.e. the transfer of Ig from blood into mammary secretions, starts several weeks prepartum. In goat plasma, immunoglobulin G (IgG) concentration decreases by around 38% from the third month of gestation until partum, which coincides with the dry period. Thus, management during the dry period is crucial for the course of colostrogenesis. The colostrum synthesis is determined by the nutrition during the prepartum period, but the transfer of Ig is obviously independent of nutritional influences. The administration of conjugated linoleic acid during the dry period to dairy goats causes a less pronounced decrease of blood plasma IgG concentration (6%) but it did not change colostral IgG levels. In cattle, IgG1 is transported from blood into colostrum by an IgG1 specific receptor located on the surface of alveolar epithelial cells during colostrogenesis, and this is most likely similar in small ruminants. Via inactivation of this receptor, the Ig transfer is downregulated by increasing prolactin (PRL) during lactogenesis. It was recently observed in goats treated with PGF2 alpha, in order to induce parturition, lower colostrum IgG concentrations occurred concomitantly with an earlier increase of plasma PRL as compared to untreated animals. The effect of litter size and number of lactations on colostral IgG concentration in small ruminants has not been made fully clear until now most likely due to the different breeds used in the published studies.

Genetic diversity in an indigenous horse breed: implications for mating strategies and the control of future inbreeding

The Franches-Montagnes is an indigenous Swiss horse breed, with approximately 2500 foalings per year. The stud book is closed, and no introgression from other horse breeds was conducted since 1998. Since 2006, breeding values for 43 different traits (conformation, performance and coat colour) are estimated with a best linear unbiased prediction (BLUP) multiple trait animal model. In this study, we evaluated the genetic diversity for the breeding population, considering the years from 2003 to 2008. Only horses with at least one progeny during that time span were included. Results were obtained based on pedigree information as well as from molecular markers. A series of software packages were screened to combine best the best linear unbiased prediction (BLUP) methodology with optimal genetic contribution theory. We looked for stallions with highest breeding values and lowest average relationship to the dam population. Breeding with such stallions is expected to lead to a selection gain, while lowering the future increase in inbreeding within the breed.

LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. Humans share many diseases with our canine companions, making dogs an ideal model organism for comparative disease genetics. Using newly developed resources, genome-wide association studies in dog breeds are proving to be exceptionally powerful. Towards this aim, veterinarians and geneticists from 12 European countries are collaborating to collect and analyse the DNA from large cohorts of dogs suffering from a range of carefully defined diseases of relevance to human health. This project, named LUPA, has already delivered considerable results. The consortium has collaborated to develop a new high density single nucleotide polymorphism (SNP) array. Mutations for four monogenic diseases have been identified and the information has been utilised to find mutations in human patients. Several complex diseases have been mapped and fine mapping is underway. These findings should ultimately lead to a better understanding of the molecular mechanisms underlying complex diseases in both humans and their best friend.