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Vinícius Silva Junqueira Daniela Lourenco Yutaka Masuda Fernando Flores Cardoso Paulo Svio Lopes Fabyano Fonseca e Silva Ignacy Misztal 《Journal of animal science》2022,100(5)
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 () 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 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. 相似文献
3.
Ignacy Misztal Ignacio Aguilar Daniela Lourenco Li Ma Juan Pedro Steibel Miguel Toro 《Journal of animal science》2021,99(6)
Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface. 相似文献
4.
Paraskevas Koumpiadis Daniela E. Sganga Sebastian N. Politis Victor Gallego Ian A. E. Butts Juan F. Asturiano Ioannis E. Batjakas Jonna Tomkiewicz 《Reproduction in domestic animals》2021,56(12):1497-1505
Aquaculture production relies on controlled management of gametogenesis, especially in species where assisted reproduction is needed for obtaining gametes in captivity. The present study used human chorionic gonadotropin (hCG) treatments to induce and sustain spermatogenesis in European eel (Anguilla anguilla). The aim was to evaluate effects of strip-spawning timing (12 vs. 24 hr) after weekly administration of hCG and the necessity of a primer dose (in addition to weekly hormonal treatment) prior to strip spawning (primer vs. no-primer) on sperm quality parameters. Sperm parameters included milt production (weight), density and sperm kinematics at Week 9, 11 and 13 after onset of treatment. Spermiation commenced in 11.5% of males in Week 5 and by Week 9, and all males produced milt. Male weight, milt production, sperm density and spermatocrit did not differ among hormonal treatments during the experimental period. Overall, male weight decreased from 106.3 to 93.0 g, milt weight increased from 3.5 to 5.4 g, sperm density counts decreased from 11.7 × 109 to 10.5 × 109 cells/ml, and spermatocrit decreased from 46.5% to 40.5%. Furthermore, spermatocrit was positively related to haemocytometer counts (R2 = .86, p < .001), providing a reliable indicator of sperm density. Differences in sperm kinematics were observed depending on strip-spawning timing after hormonal injection (12 vs. 24 hr) but with no consistent pattern. These sperm quality parameters also did not consistently differ between the no-primer and primer treatments. Considering that each male may be stripped 4–5 times over the 2–3 months spawning season, omitting the primer would reduce animal handling, material costs and labour intensity, while sustaining high-quality sperm production. 相似文献
5.
Julia P.P. Rangel Eduardo R. Monteiro Flavia S. Bitti Juarez S.N. Junior Daniela Campagnol 《Veterinary anaesthesia and analgesia》2021,48(2):167-173
ObjectiveTo evaluate the effects of incremental doses of acepromazine on hemodynamics in isoflurane-anesthetized dogs.Study designProspective, experimental study.AnimalsHealthy, adult, mixed-breed dogs (two male and four female) weighing 16.8 ± 5.1 kg (mean ± standard deviation).MethodsDogs were anesthetized with propofol (7 mg kg–1) intravenously (IV) and isoflurane. Thermodilution and arterial catheters were placed for hemodynamic monitoring and arterial blood sampling for blood gas analysis. Baseline measurements were performed with stable expired concentration of isoflurane (Fe′Iso) at 1.8%. Each dog was then administered four incremental acepromazine injections (10, 15, 25 and 50 μg kg–1) IV, and measurements were repeated 20 minutes after each acepromazine injection with Fe′Iso decreased to 1.2%. The four acepromazine injections resulted in cumulative doses of 10, 25, 50 and 100 μg kg–1 (time points ACP10, ACP25, ACP50 and ACP100, respectively).ResultsCompared with baseline, cardiac index (CI) increased significantly by 34%, whereas systemic vascular resistance index (SVRI) decreased by 25% at ACP50 and ACP100. Arterial oxygen content (CaO2) was significantly lower than baseline after all acepromazine injections (maximum decreases of 11%) and was lower at ACP50 and ACP100 than at ACP10. No significant change was found in heart rate, stroke index, oxygen delivery index and systolic, mean and diastolic blood pressures. Hypotension (mean arterial pressure < 60 mmHg) was observed in one dog at baseline, ACP10, ACP25 and ACP100, and in two dogs at ACP50.Conclusions and clinical relevanceCompared with isoflurane alone, anesthesia with acepromazine–isoflurane resulted in increased CI and decreased SVRI and CaO2 values. These effects were dose-related, being more pronounced at ACP50 and ACP100. Under the conditions of this study, acepromazine administration did not change blood pressure. 相似文献
6.
Edgar G. GUTIÉRREZ Isabela VIVAS-TORO Daniela CARMONA-RUÍZ David VILLALOBOS-CHAVES Bernal RODRÍGUEZ-HERRERA Melina Del REAL-MONROY Gloria LEÓN-AVILA Jorge ORTEGA 《Integrative zoology》2021,16(5):646-658
Ectophylla alba is a tent-making bat that roosts in mixed-sex clusters comprising adults and offspring. Our goal was to determine the genetic identity of individuals belonging to different roosting groups. We tested the hypothesis of kin selection as a major force structuring group composition. We used 9 microsatellites designed for E. alba to determine the genetic identity and probability of parentage of individuals. We analyzed parentage and kinship using the software ML-Relate, GenAIEx, and Cervus. The obtained relationship probabilities (0.5) revealed a clear maternal relationship between female adults and offspring with allele compatibility, and at least 5 relationships between male adults and pups. We found a low degree of relatedness within roosting groups. Between roosting groups at different sites, the mean probability of a half-sibling relationship ranged from 0.214 to 0.244 and, for full-sibling relationship, from 0.383 to 0.553. Genetically, adult individuals were poorly related within clusters, and kinship as an evolutionary force could not explain group membership. 相似文献
7.
Amália Turner Giannico Elaine Mayumi Ueno Gil Daniela Aparecida Ayres Garcia Marlos Gonçalves Sousa Tilde Rodrigues Froes 《Veterinary research communications》2016,40(1):11-19
The aim of this study was to develop regression models for correlation of canine fetal heart development with body size to characterize normal development or suggest cardiac anomalies. Twenty clinically healthy pregnant bitches, either brachycephalic and non-brachycephalic, were examined ultrasonographically. Transabdominal fetal echocardiography was conducted every 4 days from the beginning of cardiac chambers differentiation until parturition. Ten cardiac parameters were measured: length, width and diameter of the heart; heart area; left and right ventricular dimensions; left and right atrial dimensions; and aortic and pulmonary artery diameter. Femoral length, biparietal diameter and abdominal cross-sectional area were also recorded. Regression equations were developed for each parameter of fetal body size, and linear and logarithmic models were compared. The model with the highest correlation coefficient was chosen to produce equations to calculate relative dimensions based on the correlations. Only the left-ventricular chamber differed between the two racial groups. Biparietal diameter was the independent parameter that produced the highest correlation coefficient for the most fetal cardiac dimensions, although good correlations were also observed using femoral length and abdominal cross-sectional area. Heart width and heart diameter were used as surrogates of cardiac development, as these measurements showed the best statistical correlation. Quantitative evaluation of fetal cardiac structures can be used to monitor normal and abnormal cardiac development. 相似文献
8.
Ana Regueiras lvaro Huguet Tiago Conde Daniela Couto Pedro Domingues Maria Rosrio Domingues Ana Margarida Costa Joana Laranjeira da Silva Vitor Vasconcelos Ralph Urbatzka 《Marine drugs》2022,20(1)
Microalgae are known as a producer of proteins and lipids, but also of valuable compounds for human health benefits (e.g., polyunsaturated fatty acids (PUFAs); minerals, vitamins, or other compounds). The overall objective of this research was to prospect novel products, such as nutraceuticals from microalgae, for application in human health, particularly for metabolic diseases. Chlorella vulgaris and Chlorococcum amblystomatis were grown autotrophically, and C. vulgaris was additionally grown heterotrophically. Microalgae biomass was extracted using organic solvents (dichloromethane, ethanol, ethanol with ultrasound-assisted extraction). Those extracts were evaluated for their bioactivities, toxicity, and metabolite profile. Some of the extracts reduced the neutral lipid content using the zebrafish larvae fat metabolism assay, reduced lipid accumulation in fatty-acid-overloaded HepG2 liver cells, or decreased the LPS-induced inflammation reaction in RAW264.7 macrophages. Toxicity was not observed in the MTT assay in vitro or by the appearance of lethality or malformations in zebrafish larvae in vivo. Differences in metabolite profiles of microalgae extracts obtained by UPLC-LC-MS/MS and GNPS analyses revealed unique compounds in the active extracts, whose majority did not have a match in mass spectrometry databases and could be potentially novel compounds. In conclusion, microalgae extracts demonstrated anti-obesity, anti-steatosis, and anti-inflammatory activities and could be valuable resources for developing future nutraceuticals. In particular, the ultrasound-assisted ethanolic extract of the heterotrophic C. vulgaris significantly enhanced the anti-obesity activity and demonstrated that the alteration of culture conditions is a valuable approach to increase the production of high-value compounds. 相似文献
9.
Clayton T Larue Joel E Ream Xuefeng Zhou Farhard Moshiri Arlene Howe Michael Goley Oscar C Sparks Steven T Voss Erin Hall Christine Ellis Janice Weihe Qungang Qi Daniela Ribeiro Xiaoping Wei Shirley Guo Artem G Evdokimov Marguerite J Varagona James K Roberts 《Pest management science》2020,76(3):1031-1038
10.
Robson RV Alves Tatiana Soares Elinaldo FL Bento Ricardo S Roldan‐Filho Brbara SS Souza Marcele KN Lima Jssica S Nascimento Luana CBB Coelho Roberto A S Thmarah A Lima Gabriel GA Gonalves Fbio A Brayner Luiz C Alves Daniela MAF Navarro Thiago H Napoleo Patrícia MG Paiva 《Pest management science》2020,76(2):730-736