Genomewide association for a dominant pigmentation gene in sheep

Most published genomewide association studies (GWAS) in sheep have investigated recessively inherited monogenic traits. The objective here was to assess the feasibility of performing GWAS for a dominant trait for which the genetic basis was already known. A total of 42 Manchega and Rasa Aragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP50 BeadChip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC1R gene, setting an a priori expectation for GWAS. Multiple methods were used to identify and quantify the strength of population substructure between black and white animals, before allelic association testing was performed for 49 034 SNPs. Following correction for substructure, GWAS identified the most strongly associated SNP (s26449) was also the closest to the MC1R gene. The finding was strongly supported by the permutation tree-based random forest (RF) analysis. Importantly, GWAS identified unlinked SNP with only slightly lower p-values than for s26449. Random forest analysis indicated these were false positives, suggesting interpretation based on both approaches was beneficial. The results indicate that a combined analytical approach can be successful in studies where a modest number of animals are available and substantial population stratification exists.

Inheritance of ectopic ureters in Entlebucher Mountain Dogs

To test the hypothesis of a heritable base of ectopic ureters (EU) in Entlebucher Mountain Dogs (EMD) and to elucidate associated risk factors and mode of inheritance of the disease, 565 EMD were clinically investigated and population genetic analyses performed. Based on the location of the most caudal termination of the ureteral openings, 552 EMD were classified into three phenotype groups trigone, intravesically and extravesically ectopic based on results of abdominal sonography, urethra-cystoscopy and/or contrast-enhanced computed tomography. One-third (32.9%) of the phenotyped animals had normal terminations of both ureters in the bladder trigone, 47.3% had at least one intravesicular ectopic termination and 19.8% had at least one extravesicular ectopic termination. Multivariate mixed logistic regression revealed gender as a risk factor associated with EU as males were more often affected than females. Complex segregation analysis indicated a hereditary basis for EU in EMD and the involvement of a major gene in the occurrence of the extravesicular EU phenotype.

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.

Pollen profile from sediment core Höllerer See

(expanded by Eberhard Grüger, Göttingen) The site "Höllerer See" is a lake in the northern foreland of the Alps, about 30 km north of the city of Salzburg/Austria, situated in the south-western part of Oberösterreich/Austria. A 2 m long piston core from this locality, consisting entirely of calcareous gyttja, was studied by pollen analysis. The three lowermost samples (1.98, 1.95 and 1.92 m) were deposited during the Preboreal when Pinus and Betula were still the dominating forest trees. High pollen values of thermophilous woody species (mainly Corylus and Quercus, but also Ulmus, Tilia, Fraxinus) prove the Boreal age of the next younger sample (1.91 m). The following two pollen spectra attest that Alnus (1.89 m) and - later (1.88 m) - Fagus had become important members of the local (Alnus) and the regional (Fagus) vegetation. From this level up to the top of the profile these two tree taxa contribute - together with Betula - always 50 to 80 % to the arboreal pollen sum. The upper 1.89 m of sediment of the Höllerer See core evidently date from the Subboreal and the Subatlantic. As Preboreal sediment was stated at the base of the profile it must be concluded that most of the Boreal and the Atlantic is - for whatever reason - not represented by sediment in this core. As no radiocarbon dates are available age estimates of the distinguished pollen zones can be achieved only by correlating major changes of the former vegetation with historical events which probably influenced the then contemporary vegetation. The pollen grains of the Triticum and Hordeum type found in samples of zone 2.1 might indicate the growing of cereals in the region during the Late Bronze Age. The first pollen grains of Secale date from the boundary Hallstatt/Latène Age (zone 2.2). The cereal curves become continuous in Bavarian times (Bajuwarenzeit, Middle Ages, zone 3.3). The Plantago laceolata curve, continuous since 1.7 m depth (zone 2.1), points to animal breeding since the Early Subatlantic (Hallstattzeit). This curve reaches its absolute maximum in Roman time (zone 3.1). Roman time forest clearance caused a drastic decrease of tree pollen curves (start of zone 3.1). Values of anthropogenic indicators as high as in zone 3.1 are found again - after a distinct decrease in zone 3.2 - not till the Bavarians settled in the region (6th century). Maximal Fagus values and the simultaneous total lack of anthropogenic indicators mark the Migration Period (zone 3.2). The Younger Subatlantic (zone 4) is characterized by a decrease of deciduous forests due to medieval forest clearance. At the same time the conifers Pinus and Picea gained in importance. The lake was probably used for retting hemp in Medieval times. The distinction of the pollen grains of Cannabis and Humulus might not be certain in all cases. It is known that hemp as well as hop was cultivated in the study area. Markers were added to the samples at the beginning of pollen preparation (13500 Lycopodium spores, sample volume 0.5 cm**3) and counted together with the pollen grains. Therefore pollen concentrations can be calculated: Concentration = C * F / V (with C = number of grains of a particular pollen type, V = volume of the untreated pollen sample, F = marker added/marker counted). F ranges from 39 to 1688. Factors that large are not suited to produce reliably interpretable pollen concentrations. Consequently no use was made of the pollen concentrations in this thesis, although a concentration diagram is added.

Influências genéticas nas características da carcaça e carne em bovinos

Tese de Doutoramento em Ciências Veterinárias - Especialidade de Produção Animal

Factor analysis applied to genome prediction for high-dimensional phenotypes in pigs.

The aim of the present study was to propose and evaluate the use of factor analysis (FA) in obtaining latent variables (factors) that represent a set of pig traits simultaneously, for use in genome-wide selection (GWS) studies. We used crosses between outbred F2 populations of Brazilian Piau X commercial pigs. Data were obtained on 345 F2 pigs, genotyped for 237 SNPs, with 41 traits. FA allowed us to obtain four biologically interpretable factors: ?weight?, ?fat?, ?loin?, and ?performance?. These factors were used as dependent variables in multiple regression models of genomic selection (Bayes A, Bayes B, RR-BLUP, and Bayesian LASSO). The use of FA is presented as an interesting alternative to select individuals for multiple variables simultaneously in GWS studies; accuracy measurements of the factors were similar to those obtained when the original traits were considered individually. The similarities between the top 10% of individuals selected by the factor, and those selected by the individual traits, were also satisfactory. Moreover, the estimated markers effects for the traits were similar to those found for the relevant factor.

Linkage disequilibrium and effective population size in a paternal broiler line.

2016

Implementação de algoritmo para avaliação genética de grandes populações de animais de interesse agropecuário.

Apresentamos uma versão inicial da solução em desenvolvimento para estimação dos efeitos desejados através do modelo animal univariado, utilizando duas abordagens distintas para a obtenção do melhor estimador linear não viesado (BLUP) dos parâmetros do modelo.

Genes diferencialmente expressos em músculo de novilhos Nelore divergentes para eficiência parcial de crescimento.

2016

Lipid quality and oxidative stability in food products from animal origin, as affected by breeding factor

Nowadays it is requested more investigations on alternative rearing systems that are able to improve poultry welfare and to warrant high-quality and safe meat products. This thesis work was focused on the evaluation of the oxidative stability of poultry meats, obtained with different rearing systems, diets (supplemented with bioactive compounds), and packaging conditions. The thesis work was divided into the following parts: - Evaluation of the effects of different rearing systems on the quality, fatty acid composition and oxidative stability of poultry thigh and breast meat belonging to different product categories (“rotisserie” and “cut-up” carcasses); - Evaluation of the effects of different rearing systems and packaging conditions on the shelf-life of poultry thigh meat stored at 4°C for 14 days, and the effects of feed supplementation with thymol (control diet and diet with 2 different concentration of thymol) and packaging conditions on lipid oxidation of poultry thigh meat shelf-life (stored at 4°C for 14 days). The oxidative stability of poultry meat was studied by means of the spectrophotometric determinations of peroxide value and thiobarbituric acid reactive substances. - Evaluation of anti-inflammatory effects of different flavonoids (thymol, luteolin, tangeretin, sulforaphane, polymethoxyflavones, curcumin derivates) to detect their biological activity in LPS-stimulated RAW 264.7 macrophage cells in vitro, in order to study more in depth their action mechanisms. It was evaluated the cell vitality (MTT assay), nitrite concentration and protein profile. The study was focused on the identification of potential dietary bioactive compounds in order to investigate their biological activity and possible synergic effects, and to develop new suitable strategies for long-term promotion of human health, in particular against cancer.

Animal production. Livestock; Breeding herd size; Meat production; Civil year balance sheets. 1968-1977. 1978

"This booklet, published by the Statistical Office of the European Communities, updates the publication 'Statistics of Animal Production' of 1976. The statistics apply to the nine Member States of the Community. This publication is divided into four sections as follows: — Animal population (categories of animals, regions) (1973-1978) — Structure of breeding establishments (cattle and pigs) (1973, 1975, 1977) — Meat production (1968-1977) 'Meat' balance sheet and 'livestock' balance sheet (1976, 1977)"

Animals imported for breeding purposes for which certificates of pure breeding have been issued by the Bureau of Animal Industry.

Mode of access: Internet.