bluuebunny/crossref_metadata_2025_split huggingface dataset:
29 Conditional GWAS using sequence-based genotypes for susceptibility to Mycobacterium avium subsp paratuberculosis infection in Canadian Holstein
Authors: Bissonnette Nathalie , Marete Andrew , Kelton Dave , Schenkel Flavio , Ibeagha-Awemu Eveline M , Fecteau Gilles , Miglior Filippo 
Published: November 2020

Abstract
Paratuberculosis is an incurable disease caused by Mycobacterium avium spp. paratuberculosis (MAP). Variability in the definition of a true infection could explain the lack of consensus in published results on host genetic susceptibility to MAP. The objective of this study was to identify quantitative trait loci (QTL) for susceptibility to paratuberculosis in Canadian Holstein with an accurately defined status. Cows with known parentage were recruited from 23 Canadian dairy herds and enrolled in a longitudinal study. Blood and feces were collected semi-annually over a 3-5-yr period. Serum samples were analyzed by ELISA (IDEXX) and feces by qPCR. Cows were labelled based on positive ELISA (&gt; 45%) and on at least two consecutive fecal excretion of MAP (n = 382). Control cows (n = 669) did not excrete MAP nor have MAP antibodies (&lt; 10%) over the 3–5 year period. Their genotypes (GGP Bovine 50K chip) were imputed to HD-SNP (within-breed), then to WGS using FImpute software and Run6 of 1,000 Bulls’ genome project as a multi-breed reference. Using GCTA software, heritability (h2) was estimated and conditional GWAS was performed to define multiple true causal mutations in QTL regions from those caused by linkage disequilibrium. The h2(se) was 0.52 (0.01) and after FDR correction, 1,357 variants presented significant effects (-log10 P &gt; 6), grouped within 7 QTL located on chromosome BTA7, BTA16, BTA20, and BTA23. The most significant variant was on BTA20 (-log10 P =12.39). Functional annotation showed that 76% of all the variants of the QTL were intergenic, with the rest being mostly intronic. Of interest was variant located on BTA7 with effect size (se) of -0.77 (0.02). In conclusion, using accurate phenotypes, chromosomal regions and candidate genes that could be functionally related to MAP infection were uncovered. The significant variants found in this study could contribute to the enhancement of genomic evaluation for MAP resistance.
12 Genetic and phenotypic parameters for Aleutian disease tests and their correlations with growth and pelt quality traits in American mink
Authors: Hu Guoyu , Do Duy Ngoc , Gray Janine , Karimi Karim , Miar Younes 
Published: November 2020

Abstract
Aleutian disease brings tremendous financial losses to the mink industry. The ineffective immunoprophylaxis, medication, and culling strategies have urged the mink industry to select mink with low quantitative enzyme-linked immunosorbent assay (qELISA) score or negative counterimmunoelectrophoresis (CIEP) test result. However, little is known about the heritabilities of qELISA and CEIP as well as their relationships with growth and pelt quality traits. The traits, including qELISA, CIEP, body length at harvest (HLEN), the size of dried pelt (SIZE), the overall quality of dried pelt (QUA), and the nap length of dried pelt (NAP), were measured on 1,683 American mink from the Canadian Center for Fur Animal Research (Nova Scotia, Canada) and Millbank Fur Farm (Ontario, Canada). Significance (P &lt; 0.05) of fixed effects (sex, farm, age, and color) and random effects (common litter, permanent environment, and dam) were determined by univariate analyses, while genetic and phenotypic parameters for all traits were estimated under bivariate analyses using ASREML 4.1. Estimated heritabilities (±SE) were 0.41±0.07 for qELISA, 0.06±0.06 for CIEP, 0.39±0.06 for HLEN, 0.46±0.07 for SIZE, 0.25±0.06 for QUA, and 0.46±0.08 for NAP. The qELISA showed non-significant (P &gt; 0.05) genetic correlations with HLEN (0.05±0.13) and dried pelt traits (0.02±0.18 with SIZE, -0.21±0.20 with QUA, and -0.13±0.16 with NAP). The CIEP only showed a significant (P &lt; 0.05) negative genetic correlation with SIZE (-0.85±0.33). The moderate-to-high heritabilities of qELISA, HLEN, SIZE, QUA, and NAP indicated that these traits can be genetically improved through a genetic/genomic selection. The low and non-significant heritability of CIEP indicated the ineffectiveness of direct selection for this trait. The estimated genetic parameters for qELISA suggested that selection for lower qELISA scores may not interfere with the selection of pelt size and quality in the genetic improvement programs of American mink.
296 Awardee Talk: The Genetics of Sow Longevity
Authors: Stalder Kenneth J 
Published: November 2020

Abstract
Sow longevity is a key productivity indicator trait that has real economic and welfare importance for commercial swine farms globally. The average parity at culling is 3.8 parities. Reports indicate that it takes 3 to 4 parities before a sow “pays for herself.” Research groups around the world have reported heritabilities estimates for sow longevity traits ranging from 0.05 to 0.35. Estimate differences result from the animal population under evaluation, the trait being evaluated, and the methodology employed to obtain the genetic parameter estimate. Because sow longevity is measured at the end of the sow’s productive life, indicator traits like age at first farrowing, leg conformation, and other traits are utilized in gilt selection programs. The genetic correlations between sow longevity and lifetime production traits range have been reported to range from 0.64 to 0.94, suggesting that selection will improve sow longevity. Genetic markers have been identified that affect both sow longevity and other indicator traits. Selection to improved sow longevity still requires phenotypes. Future technologies, e.g. CT scans, digital images, and automated disease detection, will provide additional phenotypes. Continued hardware, software, and molecular developments will improve selection accuracy for sow longevity traits and related traits. Research is needed to evaluate the impact that non-additive genetic effects have on sow longevity and other fitness-related traits. Sow longevity seems to be an ideal trait to employ genomic selection in order to make more rapid trait improvements because it is measured late in life, it is sex-limited, and the trait is not directly measured on nucleus animals. In conclusion, sow longevity and related traits have sufficient heritability and variation to improve through traditional and genomic enhanced selection methods. Selection programs employing effective genomic selection programs will be more effective in improving sow longevity trait and related traits and ultimately economical return.
299 Genetic analysis of temperament and its correlation with production, reproduction, type, health and longevity in Chinese Holstein
Authors: Chang Yao , Wang Yachun 
Published: November 2020

Abstract
The objectives of this study were to estimate genetic parameters for temperament via three approaches and to examine associations of temperament with other economically important traits in Chinese Holstein. Records for temperament score (TS) on 6,586 lactating cows from 2015 to 2017 were obtained. Temperament assessed during rectal temperature measurements was recorded on a 3-point scale (1 = quiet; 2 = average; 3 = nervous). TS was treated as a ternary trait or a binary trait in different scenarios. The genetic parameters were estimated by: 1) a linear model using AI-REML; 2) a Generalized Linear Mixed Model (GLMM); or 3) a Bayesian threshold model via Gibbs sampling. Each record was partitioned into the fixed effects of herd-scorer and parity, an additive genetic effect and a residual effect. Then approximate genetic correlation between TS with production traits [milk yield (MY), fat and protein percentage (FP and PP)], fertility traits [age at first service (AFS), age at first calving (AFC), stillbirth (SB)], overall type, health traits [somatic cell score (SCS), udder diseases (UD) claw and leg diseases (CLD) metabolic disorders (MD)] and productive life (PL) were estimated. Estimates of heritability and accuracy of EBV for TS were listed in Table 1. Low to moderate genetic correlation between TS and above-mentioned traits were found. There was a favorable genetic correlation between TS and FP (-0.35), PP (-0.42), AFC (0.31), UD (0.58) and PL (-0.24); however, undesirable genetic correlation existed between TS and the other traits (-0.43~0.27). Current results suggested that a Bayesian threshold model can be the most recommended algorithm for analyzing temperament since it brought a relatively higher heritability and consequently EBV with higher accuracy, and selection for calmer individuals will translate into increased fat and protein yields, a lower age at first calving, better resistance to udder diseases and a longer functional longevity.
300 ASAS-EAAP Talk: Towards an increasing number and complexity of breeding goal traits in dairy cattle
Authors: Krattenmacher Nina , Seidel Anita , Thaller Georg 
Published: November 2020

Abstract
Worldwide, dairy cattle breeding companies and farmers face several challenges, including concerns about climatic impact of milk production, increasing scarcity of natural resources and feed, and concerns about animal welfare and health. The recording of accurate and comprehensive phenotypic data for these new issues is important for both management and breeding. Technological developments play a key role in this context. An increasing spectrum of traits with relevance to the breeding goal has become available (e.g. behavioral traits from sensor-derived activity patterns, milk metabolites reflecting the metabolic status, direct or indirect measurements of methane emissions). The biological background and genetic architecture of many of the evolving novel traits as well as their relationship with other traits of interest is not yet well understood, which hinders appropriate implementation in breeding programs. Especially for traits that are difficult or expensive to measure, such as feed intake or methane emissions, phenotypes are scarce. Interdisciplinary research and across-country data pooling can be enormously helpful to ensure a fast progress. Hence, the development of universal guidelines for recording is a crucial step, also with regard to a successful application of genomic selection, which enables the improvement of difficult-to-measure traits by transferring genomic knowledge from estimates within comparatively small reference populations to the population level. Furthermore, some traits (e.g. feed intake) show a lactation-stage specific genetic architecture. This highlights the importance of repeated measurements as well as knowledge on genetic correlations among all relevant traits across days in milk, the latter being an important prerequisite for designing balanced breeding strategies. With more traits, especially more complex traits, increasing data sources and volumes, setting up reasonable breeding goals becomes much more sophisticated and often requires innovative approaches.
297 GWAS for complex models accounting for populations structure with GBLUP and ssGBLUP
Authors: Steibel Juan P , Aguilar Ignacio 
Published: November 2020

Abstract
Genomic Best Linear Unbiased Prediction (GBLUP) is the method of choice for incorporating genomic information into the genetic evaluation of livestock species. Furthermore, single step GBLUP (ssGBLUP) is adopted by many breeders’ associations and private entities managing large scale breeding programs. While prediction of breeding values remains the primary use of genomic markers in animal breeding, a secondary interest focuses on performing genome-wide association studies (GWAS). The goal of GWAS is to uncover genomic regions that harbor variants that explain a large proportion of the phenotypic variance, and thus become candidates for discovering and studying causative variants. Several methods have been proposed and successfully applied for embedding GWAS into genomic prediction models. Most methods commonly avoid formal hypothesis testing and resort to estimation of SNP effects, relying on visual inspection of graphical outputs to determine candidate regions. However, with the advent of high throughput phenomics and transcriptomics, a more formal testing approach with automatic discovery thresholds is more appealing. In this work we present the methodological details of a method for performing formal hypothesis testing for GWAS in GBLUP models. First, we present the method and its equivalencies and differences with other GWAS methods. Moreover, we demonstrate through simulation analyses that the proposed method controls type I error rate at the nominal level. Second, we demonstrate two possible computational implementations based on mixed model equations for ssGBLUP and based on the generalized least square equations (GLS). We show that ssGBLUP can deal with datasets with extremely large number of animals and markers and with multiple traits. GLS implementations are well suited for dealing with smaller number of animals with tens of thousands of phenotypes. Third, we show several useful extensions, such as: testing multiple markers at once, testing pleiotropic effects and testing association of social genetic effects.
304 Educational tools promoting biosecurity through discovery learning
Authors: McDonald Jeannette , Kerr Susan R , Rankin Jeanne M , Smith Julia M 
Published: November 2020

Abstract
Education is the most important component in creating and sustaining a healthy national agriculture industry. As part of a large USDA NIFA Coordinated Agricultural Project, we created education products for youth and an online resource, the Healthy Farms Healthy Agriculture (HFHA) website, to help existing and future farmers and ranchers discover how to create and implement a biosecurity plan for their livestock farms. A national team of three subject matter experts, led by a distance education expert, created a series of six biosecurity modules designed for youth audiences between 6thand 12thgrade. Four modules cover biosecurity basics, disease transmission risks, and biosecurity strategies while the last two prepare youth to be biosecurity advocates by helping them create and deliver a persuasive presentation. We used discovery learning to engage students and improve comprehension and retention. In the process of development and deployment of the modules we employed a thorough review process with peer reviews and pilot testing of each of the modules. Peer-reviewers were asked to evaluate the modules on multiple aspects of five dimensions: content, interactivity, effectiveness, usability, and versatility. Modifications were made based on these reviews and the low-end of the target audience was increased from 3rdto 6thgrade. FFA and 4-H youth and adult leaders piloted the revised modules for various parameters including content, effectiveness, and recommendations for improvement. Feedback was used to finalize the modules which were then published on the HFHA website. A summative evaluation plan has been created. We will demonstrate all the products and share formative and summative evaluation tools and results for the biosecurity educational series. All evaluation procedures have the approval of the Institutional Review Board at Washington State University. Funding for this effort is partially supported by the National Institute of Food and Agriculture, US Department of Agriculture, under award number 2015-69004-23273.
312 Statistical graphics and interactive visualization in animal science
Authors: Morota Gota 
Published: November 2020

Abstract
Statistical graphics has advanced significantly in recent years with the development of statistical computing tools that allow us to create reports dynamically, facilitate reproducible research, and explore data interactively. In particular, data visualization is a fundamental aspect of big data analysis in animal science. However, the static nature of standard visualization limits the information that can be displayed and extracted. The objectives of this hands-on workshop are to learn how to utilize interactive visualization and investigate both global and local structures of graphs with useful zooming in and zooming out capabilities. We will use the Shiny R package, which is a web application framework for R. A Shiny application has great potential to deliver interactive data analysis and visualization in a web browser. Yet there is limited application of this type of tool in agricultural science. We will learn the capabilities of R Shiny and its use with example applications in animal science and how to aid scientific discoveries and decision-making processes using interactive data exploration tools. After taking this workshop, the participants will be able to understand the concept of R Shiny and develop a web-based interactive visualization tool. The interactive and integrative data visualization features embedded in Shiny applications offer a new resource for users to readily extract extensive information from complex data.
77 Chemical composition, texture and color analyses, and true metabolizabile energy of green banana flour in retorted diets for domestic cats
Authors: Hsu Clare , He Fei , Mangian Heather , White Brittany , Lambrakis Leah , de Godoy Maria R C 
Published: November 2020

Abstract
Green banana flour (GBF) has gained popularity for its health-promoting properties, since it is nutrient-rich, gluten-free, low in free sugars, and high in fiber, particularly resistant starch type 2 and pectin. Resistant starch helps promote gut health, and pectin could act as a natural thickening agent for manufacturing. Also, GBF may contribute a natural brown color to finished products. The objective of this pilot study was to determine the chemical composition of four commercially available GBFs and the effects of inclusion of these ingredients on texture, color and water binding characteristics in wet pet food products. Four types of GBF were analyzed to determine their nutritional composition. Canned foods containing four sources of green banana flour in different amounts were tested for their effects on texture and/or color of the products. For the chemical composition, all four GBF had high resistant starch concentration, ranging from 28.4% to 40.9%, and low free sugar concentration (1.8% to 7.5%). Crude protein and acid hydrolyzed fat concentrations were below 6% and 4% for all GBF tested, respectively. Texture analyses showed that hardness, adhesiveness, springiness, resilience, and firmness/toughness of canned foods containing GBF were similar to at least one of the commercial diets tested (P &gt;0.05). Using CIE L*a*b* for color parameter, lightness was variable among commercial diets (L* ranged from 24.55 to 36.75) and canned food containing GBF (35.60 to 63.41) (P &lt; 0.05). Redness and yellowness of experimental diets were similar to those of commercial food (P &gt;0.05), with a* ranging from 4.67 to 11.29 and b* from 13.58 to 24.26. Overall, GBF has potential to be a functional ingredient for pet food due to its high resistant starch and low free sugar content, and the resulting product is similar in texture and color to commercial wet pet foods.
330 The use of lactoferrin and lactoperoxidase for oral health
Authors: Nakano Manabu , Tanaka Miyuki , Abe Fumiaki 
Published: November 2020

Abstract
Lactoferrin (LF) and lactoperoxidase (LPO) are known as host defense factors in milk and saliva. LF has antibacterial and biofilm-inhibitory effects against periodontopathic bacteria. LPO catalyzes the formation of hypothiocyanite and exhibits bactericidal activity within a short time. Our research group developed LF- and LPO-containing powders, and examined their applications for oral hygiene. In this presentation, we review the clinical efficacies of LF- and LPO-containing tablets on oral malodor and oral microbiota in humans. We performed a randomized clinical trial to assess the effects of the single ingestion of LF- and LPO-containing tablets on malodor. The main components causing oral malodor are volatile sulfur compounds (VSCs). Subjects with oral malodor ingested a test or placebo tablet in two crossover phases. The concentrations of total VSCs at 10 min after ingestion were significantly lower in the test group than in the placebo group. The effects of LF- and LPO-containing tablets on oral microbiota were also investigated. Elderly subjects ingested test or placebo tablets for 8 weeks. The test group exhibited a significant reduction in Porphyromonas gingivalis compared with the placebo group. Microbiota analysis using next-generation sequencing of the bacterial 16S rRNA genes revealed that the LF- and LPO-containing tablets suppressed the relative abundance of periodontal bacteria, but not that of indigenous bacteria such as Streptococcus. Another trial suggested that the regular intake of LF- and LPO-containing tablets can improve gingival inflammation and oral health-related quality of life in healthy adults. Our findings suggest the potential of LF- and LPO-containing tablets as a daily treatment to maintain good oral health and prevent progression to periodontitis. We consider these effects of LF and LPO to also be applicable to pet food for oral health.
367 Role of skeletal muscle satellite cells in the broiler chicken Wooden Breast myopathy
Authors: Starkey Jessica D 
Published: November 2020

Abstract
To meet the huge global demand for chicken meat, the commercial broiler industry has placed tremendous genetic selection pressure on breast meat yield, growth rate, and feed efficiency traits and has made remarkable improvements over the last 30 years. Unfortunately, along with those tremendous improvements has come a severe meat quality defect whose cause has yet to be elucidated. The Wooden (or Woody) Breast (WB) meat quality defect is characterized by visible bulging of the breast fillet with extreme hardness to the touch. The WB phenotype has been characterized by histopathologists as a degenerative myopathy in which excessive fibrotic tissue infiltration occurs. Skeletal muscle stem cells, also called satellite cells (MSC), play a critical role in post-hatch broiler skeletal muscle growth, repair, and maintenance. Yet the relationship between MSC function in high-yielding broilers and the development of the WB myopathy is still not well understood. Recent work using in vivo cell labeling, cryohistology, and immunofluorescence techniques demonstrates that the relative size and mitotic activity of the various MSC and macrophage populations and collagen deposition are altered in WB-affected muscle. Alterations in myogenic regulatory factor, collagen, and pro- and anti-inflammatory cytokine protein expression in WB-affected muscles have also been observed using quantitative fluorescent Western blotting. These data suggest the involvement of aberrant MSC function in the development of WB myopathy. Future work aimed at determining whether the apparent MSC dysfunction in WB-affected broilers is due to an issue with the MSC themselves and/or their environment will be accomplished using a combination of MSC isolation, labeling, transplant, and tracking strategies. Further exploration will also be required to understand how the local cell signaling mechanisms and cell population kinetics are related to the severity and timing of the development of the WB myopathy in today’s fast-growing, high-yielding broilers.
364 Branded Beef Program Response to COVID-19
Authors: Clark Diana 
Published: November 2020

Abstract
Travel halted. Consumer habits changed. Marketing strategies adjusted. Restaurants closed. Future projections deleted. All of this occurred in the food industry, and many others like it, once COVID-19 spread. As the leading brand of Angus beef, it shifted what it needed to in order to offer more support to its foodservice distribution, retail, restaurant and international partners. The Certified Angus Beef ® brand’s purpose has always been to promote high-quality beef brought to tables by family farmers and ranchers. While that still rings true, the pandemic has shed a light on how every link in the chain strengthens what those cattle caregivers do and what consumers have come to expect.