bluuebunny/crossref_metadata_2025_split huggingface dataset:
219 Relationship between host-genetics and the vaginal microbiome in commercial gilts
Authors: Sanglard Leticia , Schmitz-Esser Stephan , Gray Kent , Linhares Daniel C L , Yeoman Carl J , Dekkers Jack C , Niederwerder Megan C , Serão Nick V 
Published: December 2019

Abstract
The objective of this study was to investigate host-genetic contributions to the vaginal microbiome of commercial gilts vaccinated for Porcine Reproductive and Respiratory Syndrome (PRRS). Vaginal swab samples (n = 576) from 308 F1 gilts (183±12 days old) were collected on day 4 (D4) and 52 (D52) post-vaccination with a commercial modified live virus PRRS vaccine. Samples were used to profile the vaginal microbiome by 16S rRNA gene sequencing, with sequences clustered into operational taxonomic units (OTUs) and taxonomically classified. All animals were genotyped for 45,536 SNPs. Arcsine of the square root-transformed OTUs abundance data were analyzed using a linear mixed animal model with age at vaccination as a covariate and animal (random) for estimation of genetic parameters. The same model was used for GWAS for the 100 most abundant OTUs but with addition of genotype of SNPs as a covariate, one at a time. For D4, heritability estimates ranged from &lt; 0.001±0.01(13 OTUs) to 0.60±0.13 (Fusobacterium), with OTUs corresponding to the genera Fusobacterium, Pasteurellaceae, Clostridiales, Prevotellaceae, and Lactobacillus having high estimates (0.41±0.13 to 0.60±0.13). For D52, heritability estimates ranged from &lt; 0.001±0.01 (10 OTUs) to 0.63±0.12 (Terrisporobacter), with OTUs corresponding to Clostridium, Terrisporobacter, Romboutsia, Turicibacter, Phascolarctobacterium, Muribaculaceae, and Ruminococcaceae having high estimates (0.42±0.14 to 0.63±0.12). Forty-six QTLs were significantly (P &lt; 0.00001) associated with OTU across days. Among these, one main QTL on chromosome 12 (20–23Mb), a gene-rich region with previously identified QTL for immune-related traits, was identified for 5 and 6 OTUs on D4 and D52, respectively. These OTUs were mainly of the phyla Proteobacteria and Firmicutes on D4 and D52, respectively. In conclusion, there is evidence of substantial host genetic variation for vaginal microbiome in commercial PRRS-vaccinated gilts, including the identification of many QTLs. Additional research is needed to investigate the genetic relationship between vaginal microbiome, health, and production in pigs.
214 Correlation among host gut microbiome and their relationship with meat quality and carcass composition traits of swine
Authors: Khanal Piush , Maltecca Christian , Schwab Clint , Fix Justin , Tiezzi Francesco 
Published: December 2019

Abstract
Study on correlation among host gut microbiome and their relationship with meat quality and carcass composition traits remains limited. The objectives of this study were 1) to estimate the microbial correlation between meat quality and carcass traits; and 2) to estimate the genetic correlation between microbial alpha diversity, and meat quality and carcass traits in commercial swine population. Data were collected from Duroc sired three-way cross individuals (n = 1,123) genotyped with 60K SNP chips. Fecal 16S microbial sequences for all individuals were obtained at three different stages: weaning (WEAN: 18.64 ± 1.09 days); week 15 (W_15: 118.2 ± 1.18 days); and off test (OT: 196.4 ± 7.80 days). Alpha diversity was measured at each stage [WEAN (alpha_w), W_15 (alpha_15) and OT (alpha_off)] using the Shannon index, which was computed as: ∑ ni=1piln(pi) where pi was the proportional abundance of ith operational taxonomic unit. Microbial correlations were estimated using multi-trait model, which included fixed effects of dam line, contemporary group and sex, as well as random effects of pen, additive genetic and microbiome. Bivariate analyses were conducted between different traits and alpha_w, alpha_15 and alpha_off with the same fixed effects and random pen and additive genetic effect. Analyses were conducted in ASREML v.4. Microbial correlations ranged from -0.93 ± 0.11 between firmness and slice shear force to 0.97 ± 0.02 between carcass average daily gain (CADG) and loin weight. For meat quality traits, correlations were weak, except for alpha_15 with Minolta a* (-0.45±0.19). Alpha_15 showed weak correlations except with CADG (-0.43±0.19). All correlations between alpha_ot and growth, carcass and meat quality traits were weak. These results may establish a newer approach of genetic evaluation process by utilizing gut microbiome information.
216 Contribution of host gut microbiome in prediction of meat quality and carcass composition traits in swine
Authors: Khanal Piush , Maltecca Christian , Schwab Clint , Fix Justin , Tiezzi Francesco 
Published: December 2019

Abstract
The objective of this study was to assess the improvement in predictive ability (PA) for meat quality and carcass composition traits by including the effect of host gut microbiome. Data were collected from Duroc sired three-way crossbred individuals (n = 1,123) genotyped from 60k SNP chips. Fecal 16S microbial sequences for all individuals were obtained at three different stages: weaning (WEAN: 18.64±1.09 days); week 15 (W_15: 118.2±1.18 days); and off test (OT: 196.4±7.80 days). A 4-fold cross validation was used, with animals grouped based on sire relatedness. Analysis was conducted in “BGLR” package in R. The first model included the fixed effect of dam line, contemporary group, and sex, as well as random pen and additive genetic effect (with genomic relationship matrix). The second model included same fixed and random effects with the addition of the microbiome effect (with microbiome relationship matrix). With the inclusion of microbiome, the PA increased for majority of traits. For carcass traits, the increase in PA was greatest for belly weight which changed from 0.22±0.06 to 0.32±0.06 at OT and lowest for loin depth and ham weight which changed from 0.14±0.06 to 0.15 ±0.06 and 0.12±0.02 to 0.13 ±0.03 at WEAN respectively. For meat quality traits, the increase in PA was greatest for subjective firmness score which changed from 0.16±0.04 to 0.19±0.04 at OT and lowest for marbling score and intramuscular fat which changed from 0.27±0.09 to 0.28±0.08 and 0.39±0.05 to 0.40±0.05 at WEAN respectively. Higher predictive ability was observed at OT rather than at WEAN and W_15 microbiome information. The results may lead to a newer approach to the genetic evaluation program of swine.
333 Animal –GRIN a platform for animal genetic information
Authors: Blackburn Harvey D , Manahan Ted , Wilson Carrie S , Fu Wenkai , Cajueiro Eduardo , Thomas Milton G , Paiva Samuel 
Published: December 2019

Abstract
An information system, Animal-GRIN, has been constructed as part of the U.S., Brazilian, and Canadian livestock genetic resource programs. It is designed to provide information to gene bank managers, the research community, and livestock producers about livestock breeds and subpopulations acquired in gene bank collections. The system was developed using a range of free software tools, including: MySQL, Ruby on Rails, Java Script, etc. The system is dynamic and publically accessible (https://nrrc.ars.usda.gov/A-GRIN). Exemplary information in Animal-GRIN consists of: animal identifiers, number and type of samples in the collection, pedigrees, coefficients of genetic relationships between animals within a breed, breeding values, phenotypes, and geographic source. To meet the national need for the long term archiving of genomic information developed with public funds, Animal-GRIN was expanded to store and make publically available genomic information (SNP) from any SNP chip, including custom products. Researchers are encouraged to submit their data upon completion of their publically funded projects. With the drill down concept, users can search the database for genomic information, physical samples associated with the genomic information, and phenotypic information on specific animals. Once animals of interest are found, on-line tools enable users to request either germplasm samples or genomic data. Progress in meeting genetic security for a breed’s collection can also be viewed. To date the U.S. collection has 52,639 animals with almost a million samples representing 36 species, 167 breeds, and 331 subpopulations and these have been entered into Animal-GRIN. Genomic data has been acquired on 1,899 animals representing 36 breeds. The next phase of Animal-GRIN development will be development of landscape genomics components. Acquisition of germplasm samples and associated genomic information are a continuing effort.
47 Genomic selection and gene editing in plant breeding – an industry perspective
Authors: Geha Makram 
Published: December 2019

Abstract
The world population is on an inevitable growth trajectory presenting the challenge of feeding nearly 9 billion people within the next couple of decades. This anticipated population surge is projected to require a 50% increase in agricultural output by 2050 in comparison to the current decade’s output levels (FAO, 2017). This increase in output needs to occur in an environment that is witnessing foreseeable declines in farming operations and availability of agricultural land in addition to an increase in consumer’s demand for high quality sustainable food products. At Corteva Agriscience, we build upon our strong pillars of seeds and traits platform, crop protection and seed treatment solutions as well as advanced digital technologies to continuously provide innovative and sustainable solutions to our customers, helping farmers maximize the value of their investment by providing them with high-performing genetics and effective science-based solutions that optimize yield and crop quality. We capitalize on the use of state of the art technologies and applications in the fields of genomics, phenomics, chemistry, and the like, to drive our industry leading product pipelines. Following the conceptual introduction of genomic selection (Meuwissen et al., 2001) and the increased affordability of genotyping, incorporation of genomic information, via genomic selection, whole genome prediction or more recently gene editing into our breeding pipeline has helped us improve the efficiency and output of our breeding systems and present our customers with innovative and sustainable seed product solutions. This presentation will focus first on introducing some common plant breeding industry practices related to population and product development before providing an overview of genomic selection and its applications in an industrial plant breeding context and finally discuss how new seed product development tools like CRISPR-Cas gene editing could be used to further improve breeding and selection.
227 Leveraging on high-throughput phenotyping technologies to optimize livestock genetic improvement and husbandry
Authors: Rosa Guilherme J M , Dorea João R R , Fernandes Arthur Francisco Araujo , Passafaro Tiago L 
Published: December 2019

Abstract
The advent of fully automated data recording technologies and high-throughput phenotyping (HTP) systems has opened up a myriad of opportunities to advance breeding programs and livestock husbandry. Such technologies allow scoring large number of animals for novel phenotypes and indicator traits to boost genetic improvement, as well as for real-time monitoring of animal behavior and development for optimized management decisions. HTP tools include, for example, image analysis and computer vision, sensor technology for motion, sound and chemical composition, and spectroscopy. Applications span from health surveillance, precision nutrition, and control of meat and milk composition and quality. However, the application of HTP requires sophisticated statistical and computational approaches for efficient data management and appropriate data mining, as it involves large datasets with many covariates and complex relationships. In this talk we will discuss some of the challenges and potentials of HTP in livestock. Some examples to be presented include the utilization of automated feeders to record feed intake and to monitor feeding behavior in broilers, milk-spectra information to predict dairy cattle feed intake, and image analysis and computer vision to monitor growth and body condition in pigs and cattle. HTP and big data will become an essential component of modern livestock operations in the context of precision animal agriculture, boosting animal welfare, environmental footprint, and overall sustainability of animal production.
226 Genomics in animal agriculture: current technologies and applications
Authors: Smith Timothy P 
Published: December 2019

Abstract
The early impact of genomic research on animal agriculture was relatively modest, as it proved difficult to translate quantitative trait loci mapping to industrial application. Fortunately, developments in technology have facilitated the application of genomics to animal agriculture, which has led to more substantial impacts on many commercially produced animal species. A brief look back on the history of genomic research will be presented, followed by an overview of recent developments in genomic technologies. Examples of application of genomic research, focusing on beef cattle and comparative genomics with other bovinae specie, and the current status of some new genomic resources emerging for sheep, pigs, and goats, will also be presented.
228 ASAS-EAAP Exchange Speaker Talk: Big data and the development of resilience indicators for animal breeding
Authors: Mulder Han A , Poppe Marieke , Berghof Tom V L 
Published: December 2019

Abstract
In their lifetime, animals experience various environmental perturbations, such as heat stress, a disease or a change in feed, which require a response. Animals differ in their capacity to respond to various perturbations; this is called resilience, which is the capacity of animals to be minimally affected by perturbations or to rapidly return to the state before exposure to perturbations. The main obstacle in research on genetics of resilience is how to define and quantify resilience. Big data offers great opportunities because longitudinal profiles of animals, such as feed intake, body weight, milk yield or egg production, contain information about how animals respond to perturbations. The objectives of our research were to define resilience indicators and estimate heritable variation in resilience indicators and to estimate associations with existing health and longevity traits to assess the utility of resilience indicators to improve resilience by breeding. The resilience indicators studied were log-transformed variance of deviations (LnVar), lag-1 autocorrelation (Auto) of deviations and skewness of deviations (Skew) based on daily milk yield in dairy cattle and four-weekly body weight measures in laying hens. In dairy cattle, we estimated a heritability of 0.20–0.24 for LnVar, a heritability of 0.08–0.10 for Auto, and a heritability of 0.01 for Skew. The strongest genetic correlations between a resilience indicator and existing health and longevity traits were found for LnVar with udder health (-0.22 to -0.33), ketosis (-0.27 to -0.33) and longevity (-0.29 to -0.34). In laying hens, we estimated similar heritabilities for the three resilience indicators: 0.10 for LnVar, 0.11 for Auto, and 0.09 for Skew. We found predictive value of LnVar breeding values for lesion scores after challenge with an E-coli infection. These results show that especially the variance of deviations is a promising resilience indicator to improve resilience and health in animals by genetic selection.
231 Structure and mechanism of CRISPR/Cas9
Authors: Taylor David W 
Published: December 2019

Abstract
Recent advances in genome editing using CRISPR-Cas9 and related technologies have revolutionized the ability to manipulate genes in a rapid, precise, and flexible manner. These advances have spurred an explosion of interest in the possible ways in which genome editing can improve human health. I will provide an overview of CRISPR-Cas systems, the structure and function of CRISPR-Cas9, and the repurposing of CRISPR-Cas9 for genome engineering.
54 The Heat is On: Heat stress induces radical changes in skeletal muscle
Authors: Selsby Josh , Ganesan Shanthi , Rhoads Robert , Baumgard Lance H 
Published: December 2019

Abstract
Heat stress continues to undermine efficient meat production and meat quality. It also jeopardizes human and animal health and wellbeing, regionalizes animal production, and threatens food security. Environmental models predict more frequent and severe heat waves, even in areas previously considered temperate indicating this problem will continue to have a progressively expanding, deleterious impact on agricultural productivity. Despite the broad, negative impact of heat stress little is known about underlying mechanisms leading to phenotypic outcomes. Because of its mass and energetic demands, skeletal muscle contributes greatly to regulation of systemic metabolism. We have discovered heat stress causes robust but transient oxidative stress and activation of apoptotic signaling in skeletal muscle in as little as two hours. Interestingly, these declined linearly through six hours concomitant with markers of increased autophagy and mitophagy, which would facilitate the removal of damaged mitochondria. Continued heating through 24 h causes a resumption of oxidative stress and autophagic dysfunction with an accumulation of autophagosomes and mitochondria. As mitochondrial injury and autophagic dysregulation appear to be key mediators of hyperthermic muscle dysfunction we propose a model that posits progressive mitochondrial injury leads to production of free radicals that overwhelms antioxidant systems and impairs autophagy facilitating accumulation of damaged, pro-oxidant mitochondria. Ultimately, these aforementioned changes may reduce efficient protein accretion. Our current work is focused on stimulating autophagy and protecting mitochondria during heat stress in an effort to maintain efficient muscle growth.
243 Digestibility, fecal characteristics, and blood parameters of adult dogs fed high fat diets
Authors: Kilburn Logan R 
Published: December 2019

Abstract
The objective was to evaluate the effects of feeding adult dogs increasing levels of fat in low carbohydrate diets on apparent digestibility, fecal characteristics, and health status. Eight adult beagles were used in a 4x4 replicated Latin square design. Dogs were randomly assigned to 1 of 4 fat levels within a phase: 32% (T1), 37% (T2), 42% (T3), and 47% (T4). Fat levels were adjusted with inclusion of canola oil to a commercial diet. Each dog was fed to exceed their energy requirement based on NRC recommendation. Dogs were fed their respective diet twice daily for 15 days. Total fecal collections were done d 11–15 and blood samples were taken on d 15. Data were analyzed using PROC MIXED of SAS (diet and room as fixed effects; period and dog were random). Covariates of baseline, initial body weight, and/or initial body condition score were dependent on trait. Digestibility improved linearly with fat level for dry matter (P = 0.021), organic matter (P = 0.019), and fat (P = 0.001). Fecal output decreased as levels of fat increased in the diet (P = 0.002). There was no effect of fat level on stool quality or short chain fatty acid and ammonia concentrations in fecal samples (P &gt; 0.1). Blood samples were analyzed for complete blood counts and chemistry profiles. All parameters remained within normal reference intervals. Blood urea nitrogen levels decreased with increased fat level (P = 0.03). No significant differences were seen in canine pancreatic lipase immunoreactivity. In addition, serum metabolomics were analyzed among T1 and T4. Metabolite data were log2-transformed and changes among diets were detected using a linear mixed model, the metabolomic profile among diets was characterized using linear discriminant analysis. 19 metabolites, primarily phosphatidylcholines, were statistically significant among treatments. Increase of dietary fat improved digestibility, did not disrupt fecal characteristics, and maintained the health status of each dog.
237 Evaluation of cooked and raw garbanzo beans as main plant protein sources in extruded feline diets
Authors: Reilly Lauren M , He Fei , Mangian Heather , Hoke Jolene , Davenport Gary , Godoy Maria R C de 
Published: December 2019

Abstract
Garbanzo beans (GB; Cicer arietinum) are a readily available pulse crop that have gained popularity as a plant-based protein source in the pet food industry. However, raw GB contain anti-nutritional factors that can reduce digestibility and cause effects in pets that are undesirable to owners. The objective of this study was to determine GB effects on digestibility, gastrointestinal tolerance, and fermentative end-products in cats fed extruded diets containing raw or cooked GB. Five diets were formulated to have either raw GB at 0%, 7.5%, 15%, or 30% or cooked GB at 30% inclusion. Ten, adult, male cats (mean age: 1.0 ± 0.0 years, mean BW: 4.7 ± 0.4 kg) were used in a replicated 5x5 Latin square design. Each period consisted of 14 d, with 10 d of diet adaptation followed by 4 d of total fecal and urine collection. At the end of each period, 4 mL of blood was collected and analyzed for a serum chemistry and complete blood count to ensure all animals remained healthy throughout the study. Cats were fed twice daily and food intake was calculated to maintain body weight. Food intake was highest (P &lt; 0.05) for cats fed 0% raw GB (72.2 g/d, DMB) compared to higher GB inclusions (average 70.3 g/d, DMB). Dry matter and organic matter apparent total tract digestibility (ATTD) were lowest (P &lt; 0.05) among all treatments for the cats consuming the 30% cooked GB diet (77.3% and 81.7%, respectively). Cats fed 7.5% raw GB had higher (P &lt; 0.05) crude protein ATTD (86.2%) than cats fed 15% raw GB (82.3%) or 30% cooked GB (81.6%). In conclusion, all inclusion levels of raw GB showed high digestibility (average &gt;80%) and ideal fecal scores (average 2.9) demonstrating their adequacy as the primary protein source in feline diets up to 30% inclusion levels.
61 Nutritive feed ingredients that pose toxicological potential
Authors: Matulka Ray A 
Published: December 2019

Abstract
A variety of different substances can promote adverse effects on livestock and companion animals, varying from a decrease in overall growth, to frank toxicological response and death. Many substances that are the cause of adverse effects are either components in feed, part of the forage landscape for grazing animals, or even a part of the nutritive feed composition for pets. It has been well-known that vitamin D intake increases bone mineralization, but methionine consumption may also positively impact bone density. Excess consumption of other nutrients may lead to adverse effects, as current research found that excess tryptophan consumption in weaned pigs adversely affects intestinal morphology and tight junction proteins in other species. However, some studies have found that different animals can have opposing effects from consuming the same substances. For example, a study in mice has found that consumption of chitosan impairs intestinal barrier integrity, while twice the intake by weaned piglets improved the average daily gain. This presentation will discuss examples of nutrients and other substances that may adversely impact the growth and reproductive capacity of companion animals and livestock, underscoring the need for the completion of safety studies of potentially new ingredients to evaluate their long-term use in commercial feed formulations.