Emerging issues in genomic selection

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.     

Sperm production and quality in European eel (Anguilla anguilla) in relation to hormonal treatment

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.     

Hemodynamic effects of incremental doses of acepromazine in isoflurane-anesthetized dogs

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.     

Socio-spatial organization reveals paternity and low kinship in the Honduran white bat (Ectophylla alba) in Costa Rica

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.     

Canine fetal echocardiography: correlations for the analysis of cardiac dimensions

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.     

Metastatic pericardial tumors in a dog with equivocal pericardial cytological findings

A metastatic tumor associated with pericardial effusion was diagnosed in a 6-year-old, female, mixed-breed dog. Echocardiography identified multiple echogenic masses adherent to both visceral and parietal pericardium, while results of pericardial fluid cytology were non-diagnostic. The distribution pattern of the masses is remarkable in that they protruded from both pericardial surfaces, rather than one, and demonstrated an oscillatory motion during the cardiac cycle. Pathological examination confirmed the diagnosis of multiple metastatic tumors of the pericardium, with the primary tumor being an anaplastic gastric adenocarcinoma.     

Relationships of the Sardinian isolate of tomato yellow leaf curl geminivirus with its whitefly vectorBemisia tabaci Gen

Relationships of an Italian isolate of tomato yellow leaf curl geminivirus from Sardinia (TYLCV-S) with its whitefly vectorBemisia tabaci were studied by means of experimental transmissions from tomato to tomato plants. TYLCV-S was confirmed to be transmitted in a persistent, circulative manner. The minimum latent period in the vector was between 17 and 20 h from the beginning of the acquisition access period (AAP). The maximum retention of infectivity was 8 days from the end of the AAP. Both acquisition and inoculation feeding times influenced the detected proportion of infective insects, with patterns well described by an exponential model. Acquisition was more efficient than inoculation. Males were significantly less efficient vectors than females. Nymphs were as efficient as adults in acquiring the virus. The length of AAP influenced both the retention of infectivity, and the pattern of transmission in serial transfer transmission tests with individual females. No significant difference in transmission efficiency was detected between two colonies ofB. tabaci, one inducing typical silverleaf symptoms on squash, the other inducing only mild symptoms with more than 50 whiteflies per plant. The phenomenon of periodic acquisition was not unequivocally proved for TYLCV-S.Research supported by the National Research Council of Italy, Special Project RAISA, Sub-project N. 2. Paper N. 1961.Supported by a grant from the Istituto Agronomico Mediterraneo, Valenzano (Bari), Italy.