Hendrix Genetics (Canada)

Abstract Although an organism’s genetic information is predominantly identical among most of its cell types, the epigenome regulates the expression of the genome in a cell type- and context-dependent manner. In mammals, DNA methylation in regulatory regions, such as promoters, primarily regulates gene expression by inducing transcriptional inactivation. With genome-wide approaches came the realization that DNA methylation patterns underlying mammalian development are considerably more dynamic than previously recognized. This realization highlights the need for methodological approaches capable of capturing this phenomenon. In this study, we investigated the feasibility of modeling DNA methylation networks by jointly estimating regularized precision matrices from time- and tissue-specific omics data derived from the pig genome. For that, we utilized RNA-Seq and RRBS data that span seven pig tissues at three developmental stages: early organogenesis, late organogenesis, and newborn. Our analysis focused on 61, 48, and 74 genes — differentially expressed across developmental stages and CpG-methylated in promoter regions, from endoderm-, mesoderm-, and ectoderm-derived tissues, respectively. Using a joint fused ridge approach, we were able to borrow information across tissues and time points, enabling more robust network inference. This analytical framework advances exploratory methods for studying organism development using pig as a model species. Our results highlight the importance of fetal-maternal immunity and the circulatory system in early development, and shed light on dynamic interactions across tissues, organ systems, and germ layers. We anticipate that this flexible framework can be extended to other omics data and species, facilitating future research. Author summary This study explores how gene activity is controlled during pig fetal development using networks. The epigenome can turn genes on and off, depending on, e.g. the cell’s function and the organism’s growth stage. This process includes chemical changes to DNA, such as methylation. We focused on DNA methylation patterns during pig fetal development by analyzing samples from several organs at three stages of fetal growth. We combined gene activity data with DNA methylation data by using a network-based method that allows us to visualize and study how genes interact across different tissues and developmental stages. We discovered that the immune and circulatory systems are critical during early development. We have also observed complex interactions across tissues and organ systems. Our study provides a flexible toolbox with clear, step-by-step explanations. This analytical framework can be used to explore developmental patterns at the genomic scale in other species and can be adapted to different types of biological data.

Abstract Count traits are usually explored in livestock breeding programs and it usually does not fit into Normal distribution, requiring alternatives to adjust the phenotype to estimate accurate genetic parameters and breeding values. Alternatively, distribution such as Poisson can be used to evaluate count traits. This study aimed to compare and discuss the genetic evaluation for oocyte and embryo counts considering Gaussian (untransformed variable – LIN, transformed by logarithm – LOG, transformed by Anscombe – ANS) and Poisson (POI) distributions. The data comprised 11343 total oocytes, viable oocytes, cleaved embryos, viable embryos records of ovum pick-up from 1740 dairy Gir heifers and cows. The genetic parameters and breeding values were estimated by the MCMCglmm package of the R software. The posterior means of heritability varied from 0.40 (LIN) to 0.49 (POI) for TO; 0.39 (LIN) to 0.49 (POI) for VO; 0.30 (LOG) to 0.41 (POI) for CE; 0.19 (LIN) to 0.32 (POI) for VE, respectively. The posterior means of repeatability varied from 0.56 (LIN) to 0.65 (POI) for TO; 0.53 (LOG) to 0.63 (POI) for VO; 0.44 (LOG) to 0.60 (POI) for CE; 0.36 (LOG) to 0.56 (POI) for VE, respectively. Deviance information criterion and mean squared residuals indicated that POI model should be used for genetic evaluation of embryo and oocytes count traits. The Spearman rank correlation between estimated breeding value (EBV) for embryo and oocytes count traits computed by POI, LOG, and ANS models was high (ranging from 0.77 to 0.99), indicating little reordering among the best animals. The POI model is the most adequate for genetic evaluation, resulting in more reliable EBV for Dairy Gir cattle of oocyte and embryo counts traits.

Abstract The biological role of kisspeptin in the reproduction of swine has been far less studied than in other species. In the porcine hypothalamus, kisspeptin is coexpressed with neurokinin B and dynorphin in KNDy neurons. Although kisspeptin-stimulated secretion of gonadotropin hormones in gilts was established early, increased expression of hypothalamic KISS1 was only recently confirmed to be associated with puberty and cyclicity in pigs. Gene knockout (KO) models to study kisspeptin in livestock did not exist until TALEN gene editing technology was used to knockout KISS1R in pigs, resulting in a hypogonadotropic-hypogonadal (HH) phenotype that caused pubertal failure. Little is known about the reproductive physiology of KISS1R KO pigs, except that exogenous follicle-stimulating hormone and gonadotropin-releasing hormone only partially restored gonadal development in boars. To further explore the biological function of kisspeptin and its receptor in swine, we recently used CRISPR/cas9-ribonucleoproteins to knockout KISS1 in pigs (10.3389/fgene.2022.1078991). A total of 684 zygotes were injected resulting in 69 piglets with 58% bearing KISS1 KO alleles (KISS1-/-). The proportion of KISS1-/- alleles did not affect BW or ADG in these mosaic founder pigs. Two boars and 2 gilts with complete KISS1 KO exhibited HH and failed to become pubertal. Germ and Sertoli cells were disorganized in small seminiferous tubules. Mating mosaic F0 pigs (frequency of KISS1-/-, 35 to 88%) resulted in 170 F1 piglets with KISS1-/- alleles observed in a Mendelian frequency. These KISS1-/- pigs displayed normal BW growth during development but were also HH. Ovarian development of KISS1-/- gilts was arrested at a juvenile state, although antral follicles were present. The KISS1-/- boars lacked testicular development and had dramatically reduced concentrations of androgens and skatole, suggesting the lack of boar taint in their meat. Importantly, KISS1 and KISS1R are expressed in ovarian, uterine and testicular tissue; however, the direct role of kisspeptin in these reproductive organs remains unknown in livestock. These KISS1-/- pigs provide a unique animal model that opens new avenues for understanding the role of kisspeptin and gonadotropin hormones in regulation of reproductive development and function in pigs as well as livestock in general. These animals facilitate our ability to explore questions such as: 1) how KNDy neurons function and control gonadotropin pulses or 2) what role does KISS1 play in the development and function of the ovary, uterus and testis in domestic animals. Some of these questions have heretofore only been addressable with difficult surgical modifications, and therefore, KISS1-/- pigs represent an alternative to painful procedures in livestock research. Pursuing these fundamental studies is expected to lead to methods that restore fertility in KISS1-/- pigs. This, in turn, could provide new possibilities for the elimination of surgical castration from pork production. The USDA is an equal opportunity provider and employer.

Abstract Infectious diseases impact the swine industry through increased morbidity and mortality, leading to large economic losses and reduced animal welfare. Disease resilience is the ability of an animal to maintain production performance under pathogen exposure and has gained traction as an approach to help reduce the impact of infectious disease. For this purpose, a wean-to-finish polymicrobial natural disease challenge model was set up, in which, using a continuous flow system, batches of 60 or 75 young healthy Landrace × Yorkshire barrows from one of seven breeding companies of PigGen Canada were entered into a quarantine nursery before their entry in a nursery/finisher that was seeded with multiple pathogens. The objective of this study was to evaluate phagocytosis assays that can be conducted on blood from young healthy pigs as potential indicator traits to select for disease resilience in high-health nucleus breeding herds. Immune cell proportions and their phagocytic activity were evaluated in blood collected at ~26 days of age in the quarantine nursery on 985 pigs. Genetic parameters, including heritabilities and genetic correlations with disease resilience phenotypes collected on these pigs and an additional 2,220 pigs from the same companies in the polymicrobial challenge were estimated using GBLUP in ASReml 4.2, with the fixed effect of batch, the covariate of entry age, and random effects of pen by batch, litter, and additive genetics, using a genomic relationship matrix derived from genotypes of 650K single nucleotide polymorphisms. Results showed moderate heritability estimates for immune cell proportions (average = 0.36; range = 0.22-0.42) and the % of phagocytizing cells for each cell type (0.32; 0.19-0.48), but low estimates for mean fluorescence intensity (MFI) of the phagocytizing cells of each type (0.2; 0.05-0.3). Estimates of genetic correlations with disease resilience traits ranged from -0.93 to 0.72, but had substantial standard errors. Granulocyte % had a high positive genetic correlation with number of health treatments across the challenge nursery and finisher (0.72 ± 0.5), while a greater % phagocytizing eosinophils was genetically correlated with decreased growth rate in the challenge nursery (-0.26 ± 0.2) but greater growth rate (0.33 ± 0.2) and reduced mortality in the finisher (-0.78 ± 0.6) and across the challenge nursery and finisher (-0.50 ± 0.4). Greater MFI of phagocytizing eosinophils was also genetically correlated with reduced mortality across the challenge nursery and finisher (-0.93 ± 0.5). These results provide insights into potential indicator traits that can be used to select for disease resilience without the need to subject animals to disease, with the overall aim to improve animal welfare and increase production performance in herds that are subject to hard-to-manage infectious pathogens. This project was supported by Genome Canada, Genome Alberta, PigGen Canada, and USDA-NIFA grant #2017-67007-26144.

Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis in poultry, an economically important disease worldwide. In Ontario, Canada, early and late systemic bacterial infections due to APEC were the most commonly reported diseases in broiler chickens. In 2016, Ontario poultry veterinarians submitted samples from 331 cases of broiler and broiler breeder chickens with a high suspicion of colibacillosis to the Animal Health Laboratory (Guelph, Ontario, Canada) for bacterial culture. Escherichia coli isolates from those samples were tested with multiplex PCR to detect the presence of 13 virulence-associated genes. The most common genes identified were sitA (detected in 93% of isolates), iss (88%), iroN (85%), iutA (79%), ompT (77%), and etsB (67%). In 94% of isolates, at least three virulence-associated genes were detected. Antimicrobial susceptibility testing of isolates by using the disk diffusion method revealed high frequencies of resistance to tetracycline (57% of isolates), gentamicin (50%), spectinomycin (46%), and ampicillin (44%). Relatively fewer isolates were resistant to trimethoprim-sulfamethoxazole (18%), ceftiofur (15%), kanamycin (11%), and apramycin (3%). A high proportion (46%) of the isolates were multidrug resistant (≥3 antimicrobial classes). On the basis of multivariable, mixed effects logistic regression models, statistically significant associations ( P ≤ 0.05) were identified between the following: ampicillin resistance and the presence of kpsII (odds ratio [OR] = 1.88), tsh (OR = 0.46), and ireA (OR = 0.32); ceftiofur resistance and etsB (OR = 2.98) and kpsII (OR = 2.61); gentamicin resistance and ompT (OR = 3.89) and sitA (OR = 3.54); kanamycin resistance and papC (OR = 50.10); spectinomycin resistance and ireA (OR = 2.50) and iutA (OR = 3.15); trimethoprim-sulfamethoxazole resistance and ompT (OR = 0.14) and tsh (OR = 0.31); and tetracycline resistance and cvaC (OR = 2.12), eitA (OR = 2.15), and papC (OR = 8.27). On the basis of a multivariable, mixed effects Poisson regression model, the number of antimicrobials to which an isolate was resistant increased with the presence of eitA (risk ratio [RR] = 1.37), iroN (RR = 1.24), papC (RR = 1.34), and sitA (RR = 1.77) and decreased with the presence of tsh (RR = 0.79). On the basis of bivariable logistic regression models, age group and time of sample collection were not significantly associated with resistance to individual antimicrobials, the presence of multidrug resistance, or the presence of virulence-associated genes. Our results provide information on antimicrobial resistance and virulence gene patterns currently present on Ontario broiler chicken and broiler breeder farms that can be used as a benchmark from which to measure changes.

Acute bronchitis is a predominantly viral illness and, according to clinical practice guidelines, should not be treated with antibiotics. Despite clear guidelines, acute bronchitis continues to be the most common acute respiratory illness for which antibiotics are incorrectly prescribed. Although the national benchmark for antibiotic prescribing for adults with acute bronchitis is 0%, a preliminary record review before implementing the intervention at the project setting showed that 96% (N = 30) of adults with acute bronchitis in this setting were prescribed an antibiotic. This quality improvement project utilized a single-group, pre-post design. The setting for this project was a large urgent care network with numerous locations in central North Carolina. The purpose was to determine whether nurse practitioners and physician assistants, after participating in a multifaceted provider education session, would reduce inappropriate antibiotic prescribing for healthy adults with acute uncomplicated bronchitis. Twenty providers attended 1 of 4 training sessions offered in October and November 2015. The face-to-face interactive training sessions focused on factors associated with inappropriate antibiotic prescribing, current clinical practice guidelines, and patient communication skills. Retrospective medical record review of 217 pretraining and 335 posttraining encounters for acute bronchitis by 19 eligible participating providers demonstrated a 61.9% reduction in immediate antibiotic prescribing from 91.7% to 29.8%. Delayed prescribing, which accounted for a small percentage of the total prescriptions given, had a small but significant increase of 9.3% after training. Overall, this multifaceted, interactive provider training resulted in significant reductions in inappropriate prescriptions.

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

This article documents the activities and discussions of the ICC discussion group A4D comparing the performance of TRXLPE and XLPE insulation material used in medium voltage underground power cables. It was not possible at the time to use water tree growth tests, carried out according to ASTM 6097-97, to provide a definition of a water tree retardant material. This was due to the relatively small number of tests carried out, the large scatter in the data of repeat tests on the same material, and the overlap in the data observed between XLPE and TRXLPE insulations.