The impact of truncating data on the predictive ability for single‐step genomic best linear unbiased prediction

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single‐step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively removed 1 year at a time based on the year an animal was born. For the swine data sets, correlations between corrected phenotypes (Cp) and EBV were used to evaluate the predictive ability on young animals born in 2016–2017. In the simulated data set, keeping data two generations back or greater resulted in no statistical difference (p‐value > 0.05) in the reduction in the true breeding value at generation 15 compared to utilizing all available data. Across swine data sets, removing phenotypes from animals born prior to 2011 resulted in a negligible or a slight numerical increase in the correlation between Cp and EBV. Truncating data is a method to alleviate computational issues without negatively impacting the predictive ability of selection candidate EBV.     

Evaluation of intravenous T-61 as a euthanasia method for birds

The use of T-61 as a sole euthanasia agent for birds was investigated. Nine broiler chickens (Gallus gallus domesticus) were euthanized by intravenous T-61 and assessed for insensibility [brainstem reflexes: nictitating membrane reflex (NIC), palpebral blink reflex (PAL)], brain death [isoelectric electroencephalogram activity (EEG)], cessation of audible heartbeat, and abnormal electrocardiogram. Birds were considered dead when the heart rate was less than 180 beats/minute with an isoelectric EEG. No vocalization or wing flapping occurred. Both NIC and PAL were lost 10.5 s from start of injection and audible heartbeat ceased at 24.5 s. Latency to isoelectric activity was 16.6 s. All but 1 bird died within 60 s. Rapid induction of insensibility meant birds did not experience pain and distress within 10.5 s from start of injection and birds were not conscious during cardiac and circulatory arrest. Intravenous injection of T-61 is an effective and efficient euthanasia method for birds.     

Antimicrobial resistance and recovery of Salmonella,Campylobacter, and Escherichia coli from chicken egg layer flocks in Canadian sentinel surveillance sites using 2 types of sample matrices

Eggs are important to the diet of Canadians. This product is one of the supply-managed commodities in Canada, but unlike other commodities, where food safety risks are extensively explored and reported, information on the prevalence of enteric organisms (e.g., Salmonella, Campylobacter) and antimicrobial resistance (AMR) in layers in Canada are limited. This study was conducted to determine the prevalence of select bacteria and the associated AMR patterns in layer flocks using 2 sample matrices. Farms were located within FoodNet Canada and the Canadian Integrated Program for Antimicrobial Resistance Surveillance sentinel sites (SS). Fecal samples (Ontario: ON_SS1a, ON_SS1b) and environmental sponge swabs (British Columbia: BC_SS2a) were collected. Salmonella prevalence was 29% and 8% in ON_SS1a and ON_SS1b, respectively, and 7% in BC_SS2a. S. Kentucky and S. Livingstone were the most frequently isolated serovars and no S. Enteritidis was detected. Campylobacter was not detected in the BC sponge swabs but was isolated from 89% and 53% of Ontario fecal samples (ON_SS1a and ON_SS1b, respectively). Seven C. jejuni from Ontario were ciprofloxacin-resistant. Escherichia coli prevalence was high in both sample types (98%). Overall, tetracycline resistance among E. coli ranged from 26% to 69%. Resistance to ceftiofur (n = 2 isolates) and gentamicin (n = 2) was relatively low. There were diverse resistance patterns (excludes susceptible isolates) observed among E. coli in Ontario (10 patterns) and British Columbia (14 patterns). This study revealed that fecal samples are more informative for farm-level monitoring of pathogen and AMR prevalence. Without further validation, sponge swabs are limited in their utility for Campylobacter detection and thus, for public health surveillance.     

Prognostic factors in cats with chronic kidney disease

BACKGROUND: Chronic kidney disease (CKD) is a common cause of morbidity and mortality in cats. HYPOTHESIS: Some baseline variables are associated with shorter survival times in cats with CKD. ANIMALS: Client-owned cats. METHODS: Cats with CKD with initial plasma creatinine concentration > or =2.0 mg/dL and urine specific gravity (USG) < or = 1.025 were recruited into a prospective clinical trial that compared benazepril with a placebo. We describe baseline variables in 190 cats and their influence on renal survival time in the placebo group (95 cats), which was followed for up to 1,097 days. Renal survival time was defined as the time from initiation of therapy to the need for parenteral fluid therapy, euthanasia, or death related to renal failure. RESULTS: Of the 95 cats treated with a placebo, 58 were censored and 37 reached the renal survival end point (died, n = 0; euthanized, n = 17; parenteral fluids, n = 12; parenteral fluids followed by euthanasia, n = 8). Increased plasma creatinine concentration, increased urine protein-to-creatinine ratio (UPC), and increased blood leukocyte count were significantly (P < .01) associated with a shorter renal survival time and were independent risk factors. Increased concentrations of plasma phosphate or urea, and lower blood hemoglobin concentration or hematocrit were significantly (P < .01) associated with a shorter renal survival time and were dependent risk factors, because they also were significantly (P < .01) correlated with plasma creatinine concentration at baseline. CLINICAL IMPORTANCE: Several variables were significantly associated with a shorter renal survival time in cats with CKD.     

Growth rates and survival of western rock lobster (Panulirus cygnus) at two temperatures (ambient and 23 °C) and two feeding frequencies

Wild caught post-pueruli, year one and year two post settlement juvenile western rock lobster, Panulirus cygnus, were held at ambient temperatures (15.6 °C to 23.1 °C; mean 19.0 ± 0.07 °C) or at 23 °C, and fed the same ration of a formulated pellet diet either once per night, or 3 times per night, over 12 months, to determine whether elevated temperatures and multiple feeds per night would stimulate growth through increased metabolism and feed utilisation without significant negative impacts on survival. Survival of post-pueruli (mean 63%) did not differ between ambient and 23 °C. Survival of year 1 and 2 juveniles was higher at ambient temperatures (p < 0.01 ambient: year 1 juveniles, 68%; year 2 juveniles, 88%; 23 °C: 57% and 74%, respectively). Feeding frequency did not affect survival of post-pueruli and year 2 juveniles (mean 63%, 81% respectively), but survival was 9% higher for year 1 juveniles fed three times per night (58% versus 67%; p < 0.01). All lobsters grew faster at 23 °C than at ambient temperatures (p < 0.05), with the growth of post-pueruli almost doubled at 23 °C (weight gain at 23 °C versus ambient: post-pueruli, 18 438 % versus 9 915 %; year 1 juveniles 259% versus 165%; year 2 juveniles 23% versus 21%). Feed frequency did not influence the growth of year 1 and 2 juveniles. However, there was an interaction effect of temperature and feed frequency on post-pueruli where weight and carapace length were significantly higher at ambient temperatures when post-pueruli were fed three times a day, whereas at 23 °C weight and carapace length were significantly greater when fed once per day (p < 0.05). Feed intake (g pellet dry matter lobster^− 1 day^− 1) of pellet was higher at 23 °C for all lobsters (p < 0.05), but was the same between lobsters fed 3 times per night versus once per night. This study has shown that increasing temperatures to 23 °C significantly improved the growth of P. cygnus post-pueruli without any adverse effects on survival. The faster growth rates exhibited by year 1 and 2 juveniles at 23 °C may potentially offset their lower survival by significantly reducing culture period. There is no benefit of feeding P. cygnus multiple times at night in terms of growth and survival. The implications for P. cygnus culture are that temperatures should be maintained close to 23 °C during the entire growout period, with due care taken to minimise mortalities through adequate provision of food and shelter. Feeding P. cygnus once daily to excess just prior to dusk to co-incide with nocturnal feeding behaviour is recommended.     

Genomic Prediction of Arsenic Tolerance and Grain Yield in Rice: Contribution of Trait-Specific Markers and Multi-Environment Models

Many rice-growing areas are affected by high concentrations of arsenic(As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability(PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic(1600 K SNPs) and phenotypic(grain As content, grain yield and days to flowering) data of the Bengal and Assam Aus Panel. Under the base-line single-environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As content, respectively; the three prediction methods(Bayesian Lasso, genomic best linear unbiased prediction and reproducing kernel Hilbert spaces) were considered to perform similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17 K, without negative effect on PA of genomic predictions. Single-environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for genotype × environment interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest predictive ability(0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the Bengal and Assam Aus Panel. Genomic prediction can also be applied to breeding for other complex traits under multiple environments.