bluuebunny/crossref_metadata_2025_split huggingface dataset:
35 Applying GGP-F250 genotypes to elucidate the biochemical basis for animal variation in meat quality attributes
Authors: King Andy , Shackelford Steven , Wheeler Tommy 
Published: July 2019

Abstract
Understanding the biological factors regulating animal variation in meat quality traits continues to challenge meat scientists. Meat scientists have studied the impacts of numerous intrinsic and extrinsic variables on meat quality traits. Often, component traits, known to directly contribute to the trait of interest, have been utilized to determine the mechanisms by which these impacts are made. However, only a limited amount of the variation in these traits is explained by component traits, indicating that a significant knowledge gap exists. The rise of genotyping assays for functional alleles provides an opportunity to further understanding of the biological basis of meat quality traits. For example, lean color is the primary factor utilized by consumers in making purchasing decisions. Cuts from some carcasses discolor rapidly and must be discounted or discarded. Component traits (reducing ability and oxygen consumption) generally explains a total 30 to 40% of the variation in lean color stability. A genome-wide association study (GWAS) was conducted using GGP-F250 genotypes from 2,476 steers representing crosses of 18 beef breeds that had been phenotyped for lean color change during simulated retail display. The GWAS identified 417 single nucleotide polymorphisms (SNP) explaining the heritable variation (0.45). Identified genes included genes coding for reductases and cytochromes as well as mitochondrial genes, which are consistent with conventional wisdom regarding lean color stability. However, other genes identified are related to muscle contraction, action potential mediation, calcium binding, actin binding, stress response, and apotosis. In addition, gene ontology analysis indicates 128 genes contributing to metabolic processes, with 74 being associated with nucleobase containing compound metabolic processes. Thus, these results suggest novel mechanisms, which have not been previously studied in detail in relation to lean color stability. This approach provides a means to increase understanding of the biological regulation of meat quality traits.
36 A large multi-breed reference panel and maximizes genotype imputation accuracy in cattle
Authors: Rowan Troy , Hoff Jesse L , Crum Tamar , Taylor Jerry F , Schnabel Robert , Decker Jared E 
Published: July 2019

Abstract
The use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context of genomic prediction, they are less useful in mapping and causal variant discovery. This project focuses on maximizing imputation accuracies to the marker set of two high-density research assays, the Illumina Bovine HD, and the GGP-F250 which contains a large proportion of rare and potentially functional variants (~850,000 total SNPs). This 850K SNP set is well-suited for both imputation to sequence-level genotypes and direct downstream analysis. For testing, 310 animals from multiple breeds, all with observed HD and F250 genotypes, were downsampled to various commercial chip densities ranging from 8K–130K markers. We use both well-established and novel measures of imputation accuracy to categorize precisely where, why, and how imputation errors are made. These metrics provide insights into downstream interpretation and identify situations where caution should be exercised when analyzing imputed variants. We find that a large multi-breed composite imputation reference comprised of 36,131 samples with either HD and F250 genotypes significantly increases imputation accuracy compared to a standard within-breed reference panel, particularly at low minor allele frequencies. Breed composition information for each animal in our testing panel allowed us to identify how a breed’s representation in the reference panel affects the imputation accuracy of both purebred and admixed animals. Starting chip density also impacts imputation accuracy, but gains appear to plateau at around 50,000 markers. The addition of the F250’s rare variation to the reference panel increased the imputation accuracy of rare variants from the HD assay by an average of 4.32%. We expect this low MAF content from the F250 to have a similar positive impact on rare variant imputation at the sequence level. Early work using 850K imputed data in genomic predictions has shown substantial increases in both chip heritability and prediction accuracies. Using a large multi-breed reference and the best practices identified through this work will maximize imputation accuracies in virtually all cattle populations, particularly ones that are highly admixed with little or no available pedigree information.
37 Opportunities for using a functional chip in beef
Authors: John Pollack E 
Published: July 2019

Abstract
Adoption of DNA technology in the beef industry has experienced an accelerating trajectory. The well-accepted and adopted applications are now parentage testing and, more recently, the inclusion of marker data into genetic evaluation systems to produce “genomic enhanced EPDs” (GE-EPD). Neither of these applications requires the markers to be functional variants; however, to produce GE-EPD’s does require the traits (or correlated traits) be in the suite of traits for which EPDs are produced. This does not allow for expansion of the use of the technology to several novel, economically important characteristics. To do so requires discovery populations closely related to the target population if typical marker panels are used and would require retraining as the target population moves away from the discovery population in its degree of relatedness. Knowledge of functional mutations is hypothesized to eliminate the necessity of a closely related population to the point of potentially universal application (across breeds) of the variant contribution to the phenotype(s) of interest. Applications that would then represent significant contribution to the genetic and management programs in beef production would be in the segments of the industry “downstream” of the seedstock industry. Breed independent predictive panels for commercial heifer replacement selection, for feedlot animal management and for product characteristics are fertile ground for the use of functional variants. These applications would target predicting animal performance, and as such would also allow for non-additive effects to be considered. If the variant tool is built as one panel including traits of interest to each segment of the industry, then valuable information becomes available each time ownership of the animal, or products derived from harvesting that animal, occurs.
33 Young Scholar Presentation: Expression quantitative trait loci and allele-specific expression exhibiting joint association with polygenic trait phenotypes in pigs
Authors: Velez-Irizary Deborah , Casiro Sebastian , Daza Kaitlyn R , Bates Ronald O , Raney Nancy E , Steibel Juan P , Ernst Catherine 
Published: July 2019

Abstract
Advancements in sequencing technology, improvements in genome annotation, and development of quantitative genetic models have been instrumental to the significant genetic gains achieved in pork production. Several quantitative trait loci (QTL) have been identified for growth, meat quality and carcass composition (GMC) phenotypes, however, the biological mechanisms underlying most QTL remain unknown. Functional genomic analysis can reveal insights on the genetic architecture of complex traits, and transcriptomic profiling of skeletal muscle during the conversion of muscle to meat can identify critical regulators of GMC phenotypes. Gene transcripts obtained with RNA-seq of longissimus muscle from 168 pigs were used to estimate gene expression variation subject to genetic control by mapping expression QTL (eQTL) and allele-specific expression (ASE). A total of 334 eQTL were mapped (FDR≤0.01) and joint association of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for GMC phenotypes. ASE analysis facilitates the identification of cis-acting regulation of transcript abundance. We tested for ASE in 69,502 coding SNP (cSNP) and a total of 18,234 cSNP with significant ASE were identified (FDR≤0.01). A gene-wise conditional analysis fitting all ASE cSNP per gene for each phenotype identified 60 genes associated with GMC phenotypes. A comparison of eQTL with ASE cSNP showed an overlap of 136 genes. Pearson correlations of peak eQTL SNP with ASE cSNP was significant for 51% of these genes. The ASE analysis showed more precision in the identification of cis-acting effects than the genome-wide eQTL analysis; however, both approaches provide valuable information on the regulation of transcript abundance. For instance, we observed 24 genes associated with distant eQTL (trans effects) and exhibiting ASE. This study provides new information on the complex regulation of the pig longissimus muscle transcriptome and associations with measurable differences in economically important phenotypic traits.
42 Advancements in silage management and technology for beef and dairy cattle
Authors: Ramirez Hugo , Branstad Emily , King Layla 
Published: July 2019

Abstract
In 2017, 2.6 million ha of American farmland were destined for corn silage production, which was estimated at 116.5 million tons. Data for 2018 are yet to be compiled but field observations provide insight of a difficult year for growing and harvesting conditions. In recent years, there has been a renewed interest in making the most efficient use of forage resources. Since corn silage is a predominant forage for beef and dairy cattle, most advances have focused on improving harvesting, storage and feeding methods of this crop. The harvesting process has been modified with the introduction of various designs of kernel processors; commercial laboratory data show a trend towards greater and more uniform processing score since 2010. Furthermore, the degree of processing can now be objectively evaluated by combining hydrodynamic separation and image processing software to obtain a kernel processing score in real time in field conditions. Applications of plastic film technology, such as oxygen barriers, to seal and maintain an anaerobic environment, have aroused interest due to the possibility of reducing spoilage with a concomitant increase in recovery of dry matter from the uppermost layer of a silage pile. Throughout the storage phase, it has been recognized that starch digestibility increases over time due to prolamin solubilization. Recent work with reconstituted high-moisture corn demonstrated that bacterial proteolytic activity contributes 60% to protein solubilization and that fermentation acids play a minor role in this process. The field of inoculants has also seen innovations in terms of application equipment and species and strain selection, with Lactobacillus buchneri becoming relevant for certain conditions that require longer aerobic stability. During feed-out, dry matter monitoring can be done with instant measurements using NIR technology in various applications ranging from tractor-mounted instruments to hand-held devices. Even though silage making has been a longstanding practice, specific aspects of the process have evolved over time and are worthy of consideration to improve forage management and quality in support of ruminant nutrition.
45 Opportunity with functional role of supplemental amino acids
Authors: Shen Yanbin , Kim Sung Woo 
Published: July 2019

Abstract
The technological advancement in production of crystalline amino acids has driven the cost of crystalline amino acids down significantly and facilitated the wide use of crystalline amino acids in food animal production. The primary reason of use of crystalline amino acids in am animal’s diet is to provide dietary essential nutrients for protein synthesis and to balance the diet and reduce dietary cost. Extensive researches with amino acids have greatly enabled such use. As a result, most swine diets today are formulated with 3 or 4 supplemental amino acids. However, the economical return on including beyond 4 supplemental amino acids becomes low and thus discourages the use of more than 4 supplemental amino acids for dietary saving purpose. The use of the functional role of amino acids might bear the new opportunity for amino acids. Tryptophan has unique physiological functions involving synthesize serotonin in the body. Increasing tryptophan intake is shown to elevate serotonin synthesis in the brain of pigs and reduce stress and improve performance of pigs under social stress. Research shows that methionine is used as a precursor of glutathione to protect intestinal mucosa from oxidative damages during weaning stress. Arginine, glutamine, and glutamate are shown to have functions in cell proliferation, potentially improving intestinal and immune function of nursery pigs and preventing loss of lean body mass in the sow. Leucine is a ketogenic amino acid. The carbon skeleton of leucine is converted to acetylCoA, which could be used for fatty acid synthesis in muscle tissue. Research showed that intramuscular fat was increased by feeding high dietary leucine levels. Overall, the different functions of individual AA beyond their roles as the building blocks for proteins give additional opportunities of amino acid application in animal production.
49 Fat metabolism and utilization in growing dairy calves and heifers: What do we know and what still needs to be researched?
Authors: Anderson Jill L , Schossow Chelsea R , Rodriguez-Hernandez Karla , Lawrence Rhea D , Senevirathne Nirosh D 
Published: July 2019

Abstract
The objective of this presentation is to discuss and review research on lipid and fatty acid metabolism in growing calves and heifers. The majority of research related to fat metabolism in dairy cattle has been conducted with lactating or transition cows evaluating the effects of diet on milk fat synthesis, energy status, and reproduction. Despite the biological activities of lipids beyond serving as an energy source and their importance in maintaining normal biological function, there is limited understanding of how they are utilized by developing dairy calves and heifers. Additionally, there is limited understanding on the potential impacts of changes in blood concentrations on development and performance of the growing replacements. In recent research studies we have observed that concentrations of circulating lipid metabolites and plasma fatty acids change as calves and heifers develop and mature. Some of these changes are related to the dietary transitions that occur during the first year of life as a calf moves from milk to a concentrate-based diet, followed by a more forage-based diet at several months of age. Additionally, there are major shifts in lipid metabolism as a calf transitions through key developmental changes such as from a pre-ruminant to ruminant and through the critical reproductive stage around the onset of puberty. A better understanding of lipid metabolism and the impacts of supplementation of dietary fats or manipulations of energy sources may offer new ways to enhance development and improve performance of growing replacement heifers through nutritional strategies.
Reducing phosphorus excretion by horses
Authors: Fowler Ashley , Lawrence Laurie M 
Published: July 2019

Abstract
Phosphorus is both a limited, non-renewable resource and also a major factor in water eutrophication. Therefore, dietary P intakes should only provide what an animal requires, reducing unnecessary addition of P to diets and excretion into the environment. Equine feeding programs commonly include inorganic P in excess of requirements, because organic P (e.g. phytate-P) is thought to be poorly digested by the horse. We have observed that 95% of phytate is degraded by the time it reaches the feces, suggesting that phytate-P availability, and thus true P digestibility, may be greater than believed. In other species but not in horses, it is recognized that fecal P excretion is important for maintaining P homeostasis, but can result in low estimates of P digestibility and subsequently greater P requirements. Ideally, P digestibility values used to calculate requirements should only reflect dietary P availability and not fecal P excreted as part of maintaining homeostasis. This research evaluated two factors that could affect P excretion, a change in physiological state (from lactation to post-lactation) and weight loss. We found that post-lactational mares tended to excrete more P than control mares (P = 0.082), but fecal P excretion exceeded P intake for both groups of mares, and mares also lost weight during the study. In the following study, horses fed to lose weight tended to excrete more P than horses fed to gain weight (P = 0.085), suggesting fecal P excretion can be altered by physiological state independent of dietary P availability and is likely the main homeostatic mechanism for P. Previous studies that have not accounted for homeostatic P excretion may have underestimated P digestibility. Thus, requirements could be revised, resulting in a significant reduction in the amount of inorganic P added to equine diets and in the amount of P excreted into the environment. This research suggests that fecal P excretion can be altered due to physiological changes in the horse independent of actual dietary P digestibility and is likely the main homeostatic mechanism for P. Previous studies that have overfed P or failed to account for homeostatic fecal P excretion may have underestimated dietary P availability.
55 Building a production nutrition department in an integrated production company: critical pillars for our success
Authors: Coble Kyle F 
Published: July 2019

Abstract
From an outsider’s perspective, internalizing a nutrition department may seem straight forward, although the true pillars for success are not as obvious. While formulating rations is certainly an important function, developing the trust of an entire production team has more direct implication on one’s success than the perfect diet. This is highlighted when describing responsibilities of a production nutritionist which consist of 20% formulation and 80% execution. Getting the right feed, in the right bin, at the right time consists of many moving parts and people, striving to work in harmony. You often see this process overcomplicated and unintentionally driving production in the wrong way due to managing to a level above which is executable. The execution leads to the successful implementation of your perfect diet, and ultimately to the trust and respect of your colleagues on the production team. Gaining their trust and respect is paramount to being successful, as production systems today are complex, and nothing can be accomplished in isolation. Keeping this approach as a nutritionist will instill a positive culture, which is even more relevant today as the industry faces challenges in recruiting and keeping talented teammates. This cannot be accomplished by sitting at the desk, it requires you to be present and seen in the field. People need to know you are accountable. Not being afraid to reach out to others for help is also important, especially to those whom have more specialization in a particular area than yourself. There are great people in our industry willing to help and offering to pass on their teachings. Finally, being disciplined about your time can mean the difference between getting many things done in a day and none. While people all desire a portion of your time, being selective is critical to your output. Being a production nutritionist has been a rewarding career, but it has been necessary to study, find, and act on these important pillars that are proven to work.
56 Observations on pre-weaning piglet mortality
Authors: Ellis Michael , Vande Pol Katherine D , Cooper Naomi , Shull Caleb M 
Published: July 2019

Abstract
Pre-weaning piglet mortality (PWM) is a substantial economic loss and a welfare concern. It is not a new issue; however, there is evidence that levels are increasing in US herds. Genetic improvements in prolificacy have been accompanied with lower average piglet birth weights, increased within-litter variation in birth weight, and an increasing proportion of low birth weight piglets. Low birth weight is a major pre-disposing factor for PWM. In a survey involving over 11,000 piglets (average birth weight 1.44 ± 0.390 kg), PWM for piglets weighing 1.5 kg was 44, 15, and 8%, respectively. However, the percentage of total mortality from these 3 weight groupings was 35, 42, and 23%, respectively. This suggests that efforts to reduce PWM should mainly focus on lightest 50% of piglets in a population. The major causes and timing of PWM have not changed over time. Crushing and starvation are predominant; the majority of losses occur in the first few days after birth. A substantial proportion of dead piglets have empty stomachs. Pre-weaning mortality is multifactorial in origin; reducing levels requires attention to all factors, starting with farrowing accommodation design and basic facility hygiene programs. Minimizing piglet body temperature decline after birth, and encouraging early colostrum and milk intake are critical. Strategies to reduce competition between piglets for access to the udder and/or supplementary feeding programs are important. Cross-fostering is central to maximizing piglet survival; however, there is a dearth of research-based information to use to design the optimum strategy. The potential influence of gestation nutrition on PWM requires clarification. Pre-weaning mortality is strongly influenced by the people managing the farrowing facilities; developing approaches for early identification of at risk pigs would have benefit. Ultimately, minimizing PWM requires systems-based approaches involving all components from genetic selection for survival through to facility and animal management practices.
65 Using 3D images and deep learning to predict feeder occupancy in grow-finish pigs
Authors: Han Junjie , Chewning Sarah K , Wurtz Kaitlin E , Siegford Janice , Steibel Juan P 
Published: July 2019

Abstract
A common source of outlying data in automatic feed recording systems used with grow-finish pigs is multiple pig occupancy of a single space feeder. Tracking these events is difficult and may require continuous observation or time-consuming manual decoding of video recordings. An alternative to manual decoding is use of algorithms for automatic image classification. The aim of this work was to build a hierarchical model to classify images from automatic feeders to discern if the feeder is empty, occupied by one pig, or occupied by more than one pig. An experimental pen was equipped with a ceiling-mounted Intel RealSense D435 camera above an automatic feeder. Images were recorded for 3 consecutive days. Randomly selected Images from d 1 were used for model training (n = 414 and n = 238 for models 1 and 2, respectively). Images from subsequent days were used to test the models (n = 196 and n = 427 for models 1 and 2, respectively). Images were manually labeled as “empty feeder,” “one pig inside the feeder,” or “more than one pig inside the feeder.” Pixel intensity data from depth images were used as predictors of feeder occupancy using a two-step decision tree that consisted of fitting two binary outcome models to a) predict if the feeder was occupied and b) predict if there was more than one pig in the occupied feeder. Both models consisted of a feed-forward artificial neural network. The transfer functions used were the reflected linear unit for deep layers and softmax for the outcome layer. The loss function was the binary cross entropy and the optimizer was the stochastic gradient descent. Accuracy, sensitivity, and specificity were 100% for model 1. For model 2, accuracy=97.7%, sensitivity=97.2% and specificity=98.1%. The proposed models allow accurate, continuous, real-time monitoring of feeder occupancy by no pig, one pig, or more than one pig.