Segregation analysis of blood oxygen saturation in broilers suggests a major gene influence on ascites

1. Blood oxygen saturation (SaO) is a potential indicator trait for resistance to ascites in chickens. 2. The objective of the study was to investigate the genetic architecture of SaO in a meat-type chicken line reared in commercial conditions. 3. Data were collected over 15 generations of selection and were divided into two data sets on the basis of a change in recording age from 6 to 5 weeks of age, approximately halfway through the period. The resulting pedigrees comprised in excess of 90,000 birds each and, on average, 12% of these birds had SaO records. 4. Segregation analyses of SaO were carried out assuming a mixed inheritance model that included a major locus segregating in a polygenic background. 5. The analyses suggest that a major gene is involved in the genetic control of SaO in this line. The putative gene acts in a dominant fashion and has an additive effect of around 0.90 sigma(p), equivalent to a predicted difference in SaO between the two homozygous classes of more than 10%. The frequency of the allele that increases SaO changed from 0.53 to 0.65 from the first to the second set of data, consistent with selection on SaO scores. 6. Using estimated genotype probabilities at the putative major locus, we inferred that it acts in an overdominant fashion on body weight and fleshing score. If the low SaO allele leads to susceptibility to ascites, its combined effects are consistent with it being maintained in the population by a balance of natural selection on fitness nad artificial selection on growth and carcase traits. 7. Even with selection on both SaO and growth traits, the combined genotypic effects would make it difficult to remove the unfavourable low-SaO allele by means of traditional selection without the use of genetic markers.     

Full pedigree quantitative trait locus analysis in commercial pigs using variance components

In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method, as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650 tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI.     

Association between in-transit loss, internal trailer temperature, and distance traveled by Ontario market hogs

An observational study was conducted from July to October 2004 to determine the association between in-transit losses of swine and internal trailer temperature after controlling for loading density, trip distance, herd size, and random trip effect. A convenience sample of 3 trucking companies was used to collect temperature, relative humidity, and global positioning data for 104 trips that delivered 21 834 pigs from 371 producers to Ontario abattoirs. The association between in-transit loss and trailer temperature was determined using the 90th percentiles of internal temperature for each trip. Average loading density was 0.36 m²/100 kg pig (range 0.28 to 0.50 m²/100 kg pig). Average in-transit loss was 0.12%; however, 94% of producers experienced no losses. As the 90th percentile of internal trailer temperature increased from a range of 8.6°C to 23.3°C to a range of 23.4°C to 26.1°C, average in-transit loss ratio increased approximately 3-fold, with an additional 2-fold increase as the range increased from 26.2°C to 28.9°C to 29.0°C to 30.5°C. As the 90th percentile of temperature increased by 1°C over the full range of temperatures in this study, in-transit loss was expected to increase 1.26 times. The in-transit loss was expected to decrease 0.81 times for each 50-km increase in distance traveled between the farm and the abattoir.     

The effects of weaning beef calves in two stages on their behavior and growth rate

Four trials were conducted to explore possible advantages of weaning beef calves in two stages compared with the traditional method of weaning by abrupt separation. In the two-stage treatment, calves were prevented from nursing their dam for a period (Stage 1) before their separation (Stage 2). Control calves nursed from their dams until they were separated. Calf weights and behavior were recorded before and after the separation of cows and calves. Following separation, calves weaned in two stages vocalized 96.6% less (P = 0.001) and spent 78.9% less time walking (P = 0.001), 23.0% more time eating (P = 0.001), and 24.1% more time resting (P = 0.001) than control calves. Compared with controls, two-stage calves had lower (P < 0.001) ADG when nursing was deprived (Stage 1), but greater (P < 0.001) ADG during the 7 d following separation. In Trial 3, calves weaned by the two-stage method had greater (P = 0.05) growth rates than control calves for 7 wk after separation, but no treatment effects on ADG were detected (P > 0.38) in Trials 1 and 2. Over the entire study period (before and after separation), ADG did not differ (P > 0.10) for both treatments. In Trial 4, calves weaned in two stages walked 1.3 km/d more (P < 0.05) during the 4-d period when nursing was prevented (Stage 1) and 5.8 km/d less (P < 0.05) during the 4-d period after separation than controls. Differences between treatments were the greatest in the 2 d after separation. On the first day after separation, two-stage calves walked 5.2 +/- 0.5 km/ d, whereas control calves walked 16.7 +/- 3.1 km/d. Calves weaned in two stages were less distressed than calves weaned by the traditional method of abrupt separation based on behavioral data, but overall calf ADG did not differ for either method in this study. Nutritional management of two-stage weaned calves during the nursing-deprived period should be evaluated in future research because poor pasture conditions may have decreased gains by calves weaned by the two-stage method in this study.     

Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland,USA (2011–2015)

Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty‐one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6′)‐Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.     

“Arte et Labore”—A Blackburn Rovers fan's legacy in human complex trait genetics

Through his own research contributions on the modelling and genetic analysis of quantitative traits and through his former students and postdocs, Robin Thompson has indirectly left a major legacy in human genetics. In this short note, we highlight examples of the long‐lasting relevance and impact of Robin's work in human genetics. A lone early study of marker‐assisted selection developed many of the tools and approaches later exploited (often after reinvention) by the human genetics community in GWAS studies and for prediction. Furthermore, a particularly clear example of the pervasive impact of Robin's work is that REML has become the default method to estimate variance components and that genetic predictions exploiting linkage disequilibrium in the population are starting to become used in precision medicine applications.     

Seroprevalence of and Risk Factors for Toxoplasma gondii in the US Swine Herd Using Sera Collected During the National Animal Health Monitoring Survey (Swine 2006)

The United States Department of Agriculture (USDA) initiated the National Animal Health Monitoring System (NAHMS) in 1983 to collect, analyse and disseminate data on animal health, management and productivity in US domestic livestock populations, including swine. The programme includes an on‐farm serological sampling component which can be used to monitor seroprevalence of various pathogens, including Toxoplasma gondii. The purpose of this study was to determine the seroprevalence of T. gondii in grower/finisher pigs using sera collected during NAHMS Swine 2006 and to determine farm level factors associated with differences in seroprevalence on farms where sera was collected during the Swine 2006 survey. Sera and data on management practices for this study were collected from 185 grower/finisher swine production sites located in 16 states accounting for >90% of US swine production (Arkansas, Colorado, Iowa, Illinois, Indiana, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Carolina, Ohio, Pennsylvania, South Dakota, Texas and Wisconsin). A total of 6238 sera were tested for T. gondii antibodies using a commercial ELISA assay (Vet. Parasitol. 128 , 2005, 177). Seroprevalence in this study, as determined by ELISA, was 2.6%, with a herd prevalence of 21.6% and a mean within‐herd prevalence of 2.7%. Analysis of swine management practices indicated that rodent control methods and carcass disposal methods were associated with differences in the number of T. gondii positive samples on farm. These results are consistent with current epidemiological knowledge of the transmission of Toxoplasma on the farm (ingestion of organic matter containing oocysts, or ingestion of infected animal tissues). Production practices which eliminate these sources of exposure can reduce the risk of Toxoplasma infection in pigs, and reduce the likelihood of human infection from consumption of infected pork.