Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Evaluation of different doses of propofol in xylazine pre-medicated horses

Objective To characterize responses to different doses of propofol in horses pre‐medicated with xylazine. Animals Six adult horses (five females and one male). Methods Each horse was anaesthetized four times with either ketamine or propofol in random order at 1‐week intervals. Horses were pre‐medicated with xylazine (1.1 mg kg^?1 IV over a minute), and 5 minutes later anaesthesia was induced with either ketamine (2.2 mg kg^?1 IV) or propofol (1, 2 and 4 mg kg^?1 IV; low, medium and high doses, respectively). Data were collected continuously (electrocardiogram) or after xylazine administration and at 5, 10 and 15 minutes after anaesthetic induction (arterial pressure, respiratory rate, pH, PaO₂, PaCO₂ and O₂ saturation). Anaesthetic induction and recovery were qualitatively and quantitatively assessed. Results Differences in the quality of anaesthesia were observed; the low dose of propofol resulted in a poorer anaesthetic induction that was insufficient to allow intubation, whereas the high dose produced an excellent quality of induction, free of excitement. Recorded anaesthesia times were similar between propofol at 2 mg kg^?1 and ketamine with prolonged and shorter recovery times after the high and low dose of propofol, respectively (p < 0.05; ketamine, 38 ± 7 minutes; propofol 1 mg kg^?1, 29 ± 4 minutes; propofol 2 mg kg^?1, 37 ± 5 minutes; propofol 4 mg kg^?1, 50 ± 7 minutes). Times to regain sternal and standing position were longest with the highest dose of propofol (32 ± 5 and 39 ± 7 minutes, respectively). Both ketamine and propofol reversed bradycardia, sinoatrial, and atrioventricular blocks produced by xylazine. There were no significant alterations in blood pressure but respiratory rate, and PaO₂ and O₂ saturation were significantly decreased in all groups (p < 0.05). Conclusion The anaesthetic quality produced by the three propofol doses varied; the most desirable effects, which were comparable to those of ketamine, were produced by 2 mg kg^?1 propofol.     

Anatomy,Morphometry and Radiography in the thoracic limb bones of the Patagonian Huemul Deer (Hippocamelus bisulcus)

The aim of this study was to provide morphometric, anatomic and radiographic data of the thoracic limb bones of the Patagonian Huemul (Hippocamelus bisulcus) including a functional interpretation of this, as a reference for clinical use, biomedical research and teaching purposes. Currently, the Patagonian huemul deer is in danger of becoming extinct due to multiple causes. Research carried out for its conservation has focused mainly on its ecology and pathology, leaving gaps in biological knowledge, which is basic and important for its comprehension. This study was conducted to reveal the gross osteology and radiology features of the thoracic limb bones of the Patagonian huemul deer. The osteological findings suggest the presence of powerful flexor muscles in the scapulohumeral and elbow joints, useful to cushion the jumps. Also, the principal nutrient foramen of Patagonian huemul differs in position with respect to domestic ungulates, which may be important to consider during surgical procedures. Finally, the radiographic data can provide new information about the tissue loading conditions in Patagonian huemul, so that this new knowledge can be of great importance for a better understanding of mechanically induced or adaptive changes in bone produced by habitat or other ecological phenomena.     

Dairy goat production systems

Goat production concentrated in developing countries (tropics, dry areas), contributes largely to the livelihoods of low and medium income farmers. Farming systems in these areas have evolved to cope with the formidable constraints imposed by harsh natural and economic conditions by adapting integrated crop/livestock production strategies. In Asia, Africa and Latin America, due to its almost exclusive extensive nature, goat production relies mainly on grazing on communal lands that hardly provide the minimum nutrient requirements due to overstocking and degradation. While some of these production systems are becoming semi-intensive, appropriate breeding strategies should be designed to promote conservation and improvement of their unique attributes, such as adaptability, water use efficiency and suitability under harsh climatic conditions. In Europe, dairy goat production is more common around the Mediterranean basin, where it is important from an economic, environmental and sociological perspective to the Mediterranean countries: Spain, France, Italy and Greece. Europe owns only 5.1 % of the world’s dairy goat herds, but produces 15.6 % of the world’s goat milk; this is the only continent where goat milk has such an economic importance and organization. In developing countries the dairy goat sector requires a systemic approach, whereby nutrition, animal health, breeding, know-how, inputs and technologies must be assembled. This would allow the optimization of natural and local resources and would promote the transition from a risk reduction strategy towards an increased productivity strategy. Such an increase would privilege production efficiency based on clean, green and ethical practices for responsible innovation.     

Molecular identification of a 16SrIII-B phytoplasma associated with cassava witches’ broom disease

Since its arrival in the British Isles in 1845 Phytophthora infestans has remained the most destructive pathogen of potato. In the ensuing period, the British and Irish P. infestans populations have undergone major displacements following the immigration of novel strains. Here we report the re-emergence of the Ib mitochondrial DNA haplotype in the British and Irish P. infestans populations associated with the 6_A1 genotype. Historically associated with the previously panglobally distributed clonal lineage US-1, the Ib haplotype has not been detected (with the exception of a single isolate in the mid 1990s) in the British or Irish P. infestans populations since the early 1980s. The 6_A1 isolates analysed possessed mtDNA Ib, but were otherwise quite unlike US-1, having the Pep allozyme genotype 96/96 and novel RG57 and SSR fingerprints. These genetic characteristics strongly suggest that the appearance of the 6_A1 genotype in these populations has resulted from migration (possibly after a recombination event elsewhere). This study highlights the advantages of utilising a range of different markers in pathogen monitoring.     

Multiply-primed rolling-circle amplification (MPRCA) of PCV2 genomes: Applications on detection, sequencing and virus isolation

Multiply-primed rolling-circle amplification (MPRCA) was used to amplify porcine circovirus type 2 (PCV2) genomes isolated from tissues of pigs with signs of post-weaning multisystemic wasting syndrome (PMWS). Two of the amplified PCV2 genomes were cloned in prokaryotic plasmids and sequenced. Both were nearly identical (1767 nt) except for one silent substitution in the region coding for the capsid protein (ORF2). In addition, they showed high nucleotide sequence similarity with PCV2 isolates from others countries (93–99%). To investigate whether the MPRCA amplified PCV2 genomes could be used to produce infectious virus, the cloned genomes were isolated from the plasmids, recircularized and used for transfection in PK-15 cells. This procedure led to the production of infectious virus to titres up to 10^5.55 TCID₅₀/mL. It was concluded that MPRCA is a useful tool to amplify PCV2 genomes aiming at sequencing and virus isolation strategies, where particularly useful is the fact that it allows straightforward construction of PCV2 infectious clones from amplified genomes. However, it was less sensitive than PCR for diagnostic purposes.     

Thermal comfort indices assessed in integrated production systems in the Brazilian savannah

The objective was to evaluate the animal thermal comfort indices from two integrated crop-livestock-forestry (ICLF) systems. For this, temperature–humidity index (THI), black globe temperature and humidity index (BGHI), and the radiant thermal load (RTL) were assessed. Two ICLF (ICLF-1 and ICLF-2) systems and one control system were established. On the ICLF systems, the arboreal component was the eucalyptus tree (Eucalyptus grandis × Eucalyptus urophylla; H13 clone), planted in simple wide-spaced rows. The ICLF-1 system had a tree spacing of 14 × 2 m with 357 trees per hectare, and the ICLF-2 had a tree spacing of 22 × 2 m with 227 trees per hectare. The control system had five scattered native trees per hectare, pertaining to Gochnatia and Dipteryx species. The forage component in all three systems was piatã-grass (Brachiaria brizantha cv. BRS Piatã). The experimental design was a randomized block in a sub-subplot design scheme with four replications. The presence of shade provided by the trees offered better conditions of animal comfort when compared with the condition of full sun. The ICLF-1 system, with higher tree density, provided better indicators for thermal comfort, THI, BGHI, and RTL when compared with the condition of full sun, while ICLF-2 was no different than ICLF-1 for BGHI.     

Development of an appropriate breeding scheme for tolerance to Empoasca kraemeri in common bean

Summary Significant advances in increasing tolerance to the leafhopper Empoasca kraemeri Ross & Moore in common bean have been obtained using a new breeding scheme where yield under leafhopper attack is the principal selection criterion in the evaluation of progenies. However, to further refine this breeding scheme, a study was conducted to determine whether selection for nonprotected yield would be more effective in early versus late generations. Two selection strategies were compared. In Strategy I, early generation selections in the F₂ and F₃ were compared to Strategy II where late generation selections were made in the F₄ and F₅, with the F₂ and F₃ generations advanced using single pod descent and bulk practices, respectively. Yield trials of the F₆ lines from both selection strategies were conducted under nonprotected and insecticide protected treatments. No significant differences were detected between the two selection strategies. However, Strategy II did produce advanced lines with greater nonprotected yields than did Strategy I, with the best F₆ line, in three out of four crosses, coming out of Strategy II. Late generation selection is recommended over early generation selection. Results of the new leafhopper breeding scheme, based on yield, are compared to the old breeding scheme where selections were made using visual selection practices in early generations.     

Chemical speciation of copper and manganese in solution of a copper-contaminated soil and young grapevine growth with amendment application

Copper(Cu)-based fungicide application to control foliar diseases in grapevine(Vitis vinifera L.) can increase soil Cu availability. Brazilian soils have high natural Cu and manganese(Mn) concentrations, increasing the potential for toxicity to grapevine plants. Application of amendment substances can reduce the concentrations of toxic chemical species of Cu and Mn in soil solution, especially for the soils grown with young plants. We evaluated the chemical speciation of Cu and Mn in soil soluti...     

Corneal endothelium of the Magellanic penguin (Spheniscus magellanicus) by scanning electron microscopy.

The corneal endothelium is essential for the maintenance of the corneal transparency. The aim of this study was to examine the morphology of the endothelial surface and perform morphometric analysis of the normal corneal endothelial cells of the Magellanic penguin (Spheniscus magellanicus) using scanning electron microscopy. The present work demonstrates that the corneal endothelium of the Magellanic penguin is similar to those described in other vertebrates.