bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSI-B-27 Association of multiple SNP in the LRP4 gene with features of the cattle elemental status
Authors: Tarasova Ekaterina , Notova Svetlana , Markova Irina , Kataev Vladimir , Plotnikov Andrey 
Published: October 2021

Abstract
Bovine syndactyly is an autosomal monogenic recessive trait associated with multiple mutations in the LRP4 gene encoding low-density lipoprotein receptor-related protein 4. This protein is a specific facilitator of sclerostin-mediated inhibition of both Wnt1/ β-catenin signaling and osteocyte-secreted bone formation. It is assumed that sclerostin induces a decrease in extracellular pH and promotes the release of calcium ions from mineralized substrates. Therefore, mutations in the LRP4 gene might be associated with changes in the elemental status. The aim of this research was to evaluate the elemental composition of serum in cattle carrying multiple SNP in the LRP4 gene (16 trial animals) compared to animals without such mutations (62 control animals). DNA samples from 78 Black Pied cattle were sequenced with a TruSeq Bovine Parentage Sequencing Panel (Illumina, USA) on a MiSeq Illumina platform following by SNP analysis. The elemental composition of the serum was determined using ICP-AES and ICP-MS. The levels of Ca and P, crucial bone elements, were higher in trial cattle than in control group by 12.9% (P = 0.004) and 22.5% (P = 0.008), respectively. The level of V affecting the uniform distribution of calcium salts in bones, was higher in trial group than in control one by 34.5% (P = 0.001). The concentrations of Mn and Mg were higher in trial group than in control one by 23.6% (P = 0.026) and 10.0% (P = 0.044), respectively. The Sr level in trial cattle was higher by 18.8% (P = 0.04) that may indicate the rickets-like state. A similar trend was observed for toxic metals As and Li. This study demonstrates the association of the LRP4 multiple SNP and the changes in cattle elemental status. Moreover, such heterozygous animals have a higher risk of mineral metabolism disorders. This research was supported by The Ministry of Science and Higher Education of the Russian Federation (Project No. 0526-2019-0001).
PSI-B-21 Alternative SNP weighting for multi-step and single-step genomic BLUP in the presence of causative variants
Authors: Santana Bruna , Riser Molly , Fragomeni Breno O 
Published: October 2021

Abstract
This study aimed to evaluate the accuracy of genomic prediction with simulated data, using SNP markers, causal quantitative trait nucleotide (QTN), and the combination of both. The methods used were the best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP), with alternative SNP weights. Data were simulated using the package AlphasimR. Trait heritability of 0.3 was assumed, and genetic variance was fully accounted for by 100 or 1000 QTNs. A population with an effective size of 200 was selected, and 20 generations were simulated. The genomic information mimicked the 29 bovine chromosomes and included 50k SNP markers evenly distributed across the genome. Approximately 16800 genotypes were available from selected sires and dams in generations 16–19, and 2000 animals in generation 20. Phenotypes for young animals were not included in the analysis, as they were used in the validation. For GBLUP, three pseudo-phenotypes were considered: the raw phenotype, the true breeding value, and the true breeding value with noise added. The genomic relationship matrix was weighted using quadratic weights, calculated based on the SNP variance, and non-linear A, following different equation parameters. The scenario with exclusively causal variants presented accuracies close to 1 for 100 QTL, and slightly lower in the 1000 QTL. For the SNP + QTN scenario, quadratic weights promoted higher accuracy gains than the SNPs alone, especially in the 100 QTN trait. Accuracies converged at higher values for both quadratic and non-linear A weights in the 100 QTN scenario. For the 1000 QTN trait, quadratic weights diverged and reduced accuracy, while non-linear A maintained accuracy at their peaks, depending on the equation parameters. Parameters of non-linear A for highest accuracy were different in each scenario and type of analysis. Proportionally, gains in accuracy were more prominent with GBLUP than with ssGBLUP.
PSVII-27 Genetic analysis of disease resilience of nursery-to-finish pigs under a natural disease challenge model using reaction norms
Authors: Cheng Jian , Lim KyuSang , Putz Austin , Wolc Anna , Harding John , Dyck Michael , Fortin Frederic , Plastow Graham , Dekkers Jack C 
Published: October 2021

Abstract
Disease resilience is the ability of an animal to maintain performance across environments with different disease challenge loads (CL) and can be quantified using random regression reaction norm models that describe phenotype as a function of CL. Objectives of this study were to: 1) develop measures of CL using growth rate and clinical disease phenotypes under a natural disease challenge; 2) evaluate genetic variation in disease resilience. Data used were late nursery and finisher growth rates and clinical disease phenotypes, including medical treatment and mortality rates, and subjective health scores, collected on 50 batches of 60/75 crossbred (LRxY) barrows under a polymicrobial natural disease challenge. All pigs were genotyped using a 650K SNP panel. Different CL were derived from estimates of contemporary group effects and used as environmental covariates in reaction norm analyses of average daily gain (ADG) and treatment rate (TRT). The CL were compared based on model loglikelihoods and estimates of genetic variance, using both linear and cubic spline reaction norm models. Linear reaction norm models fitted the data significantly better than the standard genetic model and the cubic spline models fitted the data significantly better than the linear reaction norm model for most traits. CL based on early finisher ADG provided the best fit for nursery ADG, while CL based on clinical disease phenotypes was best for finisher ADG and TRT. With increasing CL, estimates of heritability for ADG initially decreased and then increased, while estimates of heritability for TRT generally increased with CL. Genetic correlations were low between ADG or TRT at high versus low CL but high for close CLs. Results can be used to select more resilient pigs across different CL levels, or high-performance animals at a given CL level, or a combination of these. Funded by Genome Canada, Genome Alberta, USDA-NIFA, and PigGenCanada.
PSXV-12 What 30 years of accumulated pregnancy data taught us about the Bos indicus influence on reproductive performance of beef cattle
Authors: Martins Thiago , Rocha Cecilia Constantino , Driver Joseph D , Rae Owen , Elzo Mauricio A , Mateesku Raluca , Binelli Mario 
Published: October 2021

Abstract
Bos taurus X Bos indicus crossbreeding is commonly used in tropical and subtropical regions to enhance beef production. The effect of Bos indicus genetics on pregnancy to AI (P/AI) and AI + natural service (P/AI+NS) is understudied. We measured the indicus effect from a 30-year dataset of the University of Florida multibreed herd (MBH; n= 7105 animals). The MBH is composed of six breed groups, according to the following proportion of Brahman: 0–19%, 20–34%, 37% (Brangus), 40–59%, 60%-78% and 79%-100%. Estrus of all animals was synchronized using mainly the SelectSynch+CIDR protocol, followed by three-day AI based on heat or timed-AI (TAI) for non-heat animals. After TAI, animals were bred by NS. Breeding seasons lasted 91±18d. Pregnancy was diagnosed by rectal palpation and/or ultrasonography 30d after AI and 30d after removal of bulls. P/AI was affected negatively (P &lt; 0.001) by the proportion of Brahman, regardless of parity, but P/AI+NS was similar across breeding groups (Table 1). By logistic regression, each 1/32nd increment of Brahman influence reduced odds of P/AI by 0.5% (0/32nd = 51.4% to 32/32nd = 35.3%). The variables of body condition score (BCS), days post-partum (DPP) and body weight at the beginning of synchronization protocol did not explain the negative effect of indicus genetics on P/AI. However, indicus genetics were associated negatively with the proportion of animals AIed in heat (P &lt; 0.001). AI in heat resulted in twice as great (P &lt; 0.001) P/AI (65.4%; n = 984) than no-heat TAI (30.9%; n = 829). In conclusion, indicus genetics did not influence overall pregnancy rates at the end of a 90d breeding season. Nevertheless, indicus influence dampened estrus responses to protocols based solely on GnRH-PGF and progestin/progesterone, resulting on suboptimal P/AI (&lt; 40%).
PSVII-28 Genetic analysis of frame score and performance traits in Nellore cattle–growth, carcass and efficiency traits
Authors: Negreiros Maria Paula , Peripolli Elisa , Magnabosco Claudio U , Guimarães Nayanny , Lôbo Raysildo , Baldi Fernando S , Sainz Roberto D 
Published: October 2021

Abstract
We evaluated a novel frame score system for Nellore cattle raised on pasture (Guimarães et al., 2020 J, Anim. Sci. 98 (Suppl. 4)). Growth traits included age-adjusted weights (kg) at birth (W0), 120 (W120), 210 (W210) and 450 (W450) days of age, and adult weight (AW). Carcass traits (by ultrasound) included ribeye area (REA, cm2), 12th-13th rib backfat (BF, mm), rump fat (RF, mm), and intramuscular fat (IMF, %). Feed efficiency traits included residual feed intake (RFI, kg of DM/d) and DM intake (DMI, kg/d). We applied the previously developed equations (that also include hip height (HH, cm) and age to 12,049 records from the National Association of Breeders and Researchers (ANCP) database:FSmales= -20.35 + 0.1305*REA + 0.2633*BF - 0.5901*RF+ 0.1139*HH + 0.0056*AGEFSfemales = -11.87 + 0.1316*REA - 0.2457*BF - 0.6218*RF + 0.1139*HH + 0.0009507*AGEThe (co)variance components and genetic parameters were estimated using a linear animal model or a threshold animal model depending on the trait. The heritability estimate for frame score was moderate (0.30). Estimated genetic correlations were moderate for growth traits (W0, 0.51; W120, 0.41; W210, 0.35; W450, 0.29; AW, 0.39). Estimated genetic correlations for carcass and efficiency traits ranged from low to high (REA, 0.50; BF, -0.25; RF, -0.84; IMF, -0.15; DMI, 0.29; RFI, 0.10). The estimates support the notion that larger frame animals are heavier, leaner and later maturing, and less feed efficient. The new frame score may be a useful tool for genetic selection of animals that are best suited to their environment.
PSVIII-5 Genetic parameters of thrombin as a proxy for horn fly abundance in beef cattle
Authors: Ling Ashley S , Krause Taylor , Warner Amanda , Duggin Jason , Heins Bradley , Hinkle Nancy , Aggrey Samuel E , Pringle Dean , Rekaya Romdhane 
Published: October 2021

Abstract
Horn flies (Haematobia irritans) are a major nuisance to cattle, especially in warm, humid regions, and are estimated to cause economic losses in excess of $1 billion annually to the U.S. beef cattle industry. Variation in horn fly tolerance has been reported within and across breeds, and heritability estimates ranging between 10 and 80% show a clear genetic basis. However, collecting fly abundance phenotypes is costly and logistically demanding, which precludes large-scale implementation. Consequently, finding correlated phenotypes and endo-phenotypes that are heritable and relatively easy to measure would facilitate implementation of horn fly tolerance genetic improvement programs. Thrombin (TH), a blood coagulation precursor, has a reported association with horn fly count variation within and across cattle breeds. In this study, the genetic basis of thrombin in beef cattle was investigated. Blood samples and horn fly count were collected on 360 cows and heifers twice during the summer of 2019 (June and August). Due to uncertainty associated with assessment of horn fly abundance and thrombin and the fact that economic losses occur only when fly abundance exceeds a certain threshold, thrombin was categorized into 4 classes (1=TH &gt; 500 ng/ml; 2=250&lt; TH&lt; 500 ng/ml; 3=100&lt; TH&lt; 250 ng/ml; and 4=TH&lt; 100 ng/ml). The trait was analyzed using linear (continuous) and threshold (discrete) mixed models. Both models included farm, pregnancy status, and cow age as fixed effects and additive and permanent environment random effects. The pedigree included 642 animals. Estimates of heritability were 0.24 and 0.29 using linear and threshold models, respectively. Estimates of repeatability were slightly higher using the threshold model (0.21 vs 0.19). Despite the small data size, all estimates were non-zero based on their respective highest posterior density intervals. These results indicate reasonable genetic variation for thrombin that could be harnessed for improvement of horn fly tolerance in cattle.
PSXI-5 Genome-wide association study of feed efficiency in Russian Duroc boars
Authors: Belous Anna A , Sermyagin Alexander A , Zinovieva Natalia A 
Published: October 2021

Abstract
The cost of fodder is the major part in expenditure in pork industry. In this regard, improving the feed efficiency is the main goal of breeding programs for the most of pig breeds. Residual feed intake (RFI) is an alternative measure for feed efficiency, which is accepted in different livestock species including pigs. RFI is defined as the difference between the observed and predicted feed intake based on average daily gain and (additionally) back fat thickness. Our aim was to find the candidate genes responsible for RFI in Russian Duroc boars. RFI values for individual boars (n = 766) were calculated using linear regression of daily feed intake on metabolic mid-test weight and average daily gain. The SNP genotyping was carried out using Porcine GGP HD BeadChip (GeneSeek/Neogene). After data quality control, performed in PLINK 1.9, 43,199 SNPs were selected for genome-wide association studies (GWAS). The average daily gain in studied boars was 957 g with variation in individual animals from 424 to 1508 g. Feed conversion rates averaged to 2.21 kg/kg with variation from 1.8 to 3.7 kg/kg. GWAS results showed the presence of 48 SNPs, which were significantly (P &lt; 0.00001) associated with RFI, including 15 SNPs on SSC2, 9 SNP – SSC4, 2 SNPs – SSC6, 21 SNPs – SSC9, and 1 SNP – SSC17. A search for genes located within 0.4 Mb window (0.2 Mb down-stream to 0.2 Mb up-stream from identified SNP) revealed several putative candidates. Functional annotation of the obtained candidates showed the presence of genes involved in protein metabolism (ADAMTS2,UIMC1 on SSC2; NTNG1 on SSC4), regulation of glucose and bile acid metabolism (FGFR4 on SSC2), neuronal development (ENC1 on SSC2; NTRK1, MEF2D on SSC4), vitamin D and K pathways (BGLAP on SSC4). The study was funded by the Russian Ministry of Science and Higher Education No.0445-2019-0029.
PSXII-4 Impact of delayed processing time on total RNA quality and quantitation of transcript abundance
Authors: Wilson Chace , Wege Dias Nicholas W , Pancini Stefania , Mercadante Vitor R G , Biase Fernando 
Published: October 2021

Abstract
Critical biological information related to economically important traits is present in the blood transcriptome in cattle. Following a sample collection, however, RNA molecules containing this valuable information are prone to degradation affecting transcript abundance. Thus, proper sample handling and storage is essential when working with RNA. Here, we hypothesized that delayed time between sample collection and processing would lead to RNA degradation and alter gene transcript quantification. We aimed to determine the effect of delayed processing of whole blood on transcriptomic profiles in peripheral white blood cells (PWBC). We collected blood samples (10ml) in tubes containing anticoagulant (K2EDTA) from estrus synchronized beef heifers (n = 5). The tubes remained chilled on ice until processing time. From each heifer, we collected five samples from the jugular vein. We processed one sample from each animal within one hour of collection, and we delayed the processing time of the remaining samples to three, six, eight, and 24 hours post collection. We extracted total RNA from PWBCs, measured yield and assessed quality. We also quantified transcript abundance of 12,724 genes by RNA-sequencing. Samples processed 24 hours post collection had lower RNA integrity number (RIN) compared to samples processed withing one hour of collection (RIN24h=8.00±0.37, RIN1h=8.52±0.37, P = 0.03). There were four and 504 genes with differential transcript abundance (FDR&lt; 0.05) when comparing eight and 24 hours of delayed processing with samples processed within one hour of collection, respectively. Notably, several genes had &gt;1.4-fold greater transcript abundance when samples were stored on ice for eight or 24 hours. Our results indicate that RNA degradation and cellular activity of PWBCs have critical impact on transcript abundance when blood samples are stored for 24 hours under refrigeration. As the development of RNA-based biomarkers gain importance in cattle production systems, timely handling of samples is critical for accurate results.
PSXV-9 Transgenerational epigenetic variance for production and reproduction traits in maternal-line pigs
Authors: Graham Jason R , Johnson Jay S , Araujo Andre C , Howard Jeremy T , Brito Luiz F 
Published: October 2021

Abstract
Modeling epigenetic factors impacting phenotypic expression of economically important traits has become a hot-topic in the field of animal breeding due to the variability in genetic expression caused by environmental stressors (e.g., heat stress). This variability may be due, in part, to in-utero epigenomic remodeling, which has been reported to be passed from parent to offspring. We aimed to estimate transgenerational epigenetic variance for various production and reproduction traits measured in a maternal-line pig population, using a Bayesian approach. The phenotypes for production [n = 10,862; i.e., weaning weight (WW), birth weight (BW) and ultrasound-backfat thickness (BF)] and reproduction [n = 5,235, i.e., number of piglets born alive (NBA) and total number of piglets born (TB)] traits from a purebred Landrace population were provided by Smithfield Premium Genetics (NC, USA). The pedigree information traced back to 10 generations. Single-trait genetic analyses were performed using mixed models that included additive genetic, common environmental, and epigenetic random effects. The Gibbs sampler algorithm based on Markov chain Monte Carlo was used to estimate the variance components. The epigenetic relationship matrix was constructed using a recursive parameter (λ) related to the transmissibility coefficient of epigenetic markers. A grid search approach was used to define the optimal λ value (λ values ranged from 0.1 to 0.5, with an interval of 0.1). The optimal λ value was determined based on the deviance information criterion, and it was used to estimate the additive and epigenetic variances. For instance, based on preliminary results, the optimal λ value estimated for TB was 0.3 with an additive genetic variance of 0.94 (0.19 PSD) and epigenetic variance of 0.67 (0.18 PSD). The additive genetic heritability was 0.076 (0.015 PSD) and the estimated epigenetic heritability was 0.053 (0.015 PSD). This preliminary result suggests that epigenetics contribute to the non-Mendelian variability in pigs.
PSXV-3 The influence of the dams genotype on the indicators of the breeding value of offspring
Authors: Lapshina Alexandra , Gabidulin Vyacheslav , Alimova Svetlana , Kizaev Mikhail , Ruchay Aleksey 
Published: October 2021

Abstract
Aberdeen Angus cattle of Australian breeding is a new ecological and genetic genotype and it is currently in the process of formation and differentiation, the genealogy of the breeding stock is represented by the leading related groups of bulls-leaders of domestic and imported breeding. The aim of this work was to study the breeding value of Bismarck5682bovine cows of Australian selection (n = 20) and Design1015 (n = 20) of domestic reproduction of the Aberdeen-Angus breeding and their influence on the selection and genetic parameters of the productivity of heifers-daughters. It was revealed that the representatives of the Design line had an advantage in live weight (615.4 kg,lim-705-495kg) by 9.8% (P &lt; 0.001), milk productivity (219.7 kg,lim-241-184kg) by 2.4% (P &gt; 0.05) and height insacrum (134.5 cm,lim-140cm-128cm) by 4.1% (P &lt; 0.001) compared to peers of Bismarck line.The ability of animals to realize their breeding potential is determined by many factors. So, it was revealed that the heifers of Design lineexceeded their peers from Bismarck group in live weight in 15 months (359.8 kg, Cv-5.24%) by 5.2%, (P &gt;0.05), average daily gain (652.8 g, Cv-7.86%) - 10.6% (P&lt; 0.001), body conformation score (19.7 points, Cv-3.72)- 14.5% (P&lt; 0.01). It should be noted that heifers – daughters of the Bismarck genealogical line gave in sacrum height but had a better estimate of meat forms by 2.9% with reliable values. These results allow us to conclude that the offspring of the Bismarck 5682 genealogical line of Australian breeding are more affected by the negative factors of the new breeding zone. Thus, a step-by-step selection evaluation of the breeding stock will allow more reliable identification of breeding bulls with a better ability to improve valuable distinguishing features in the generations of cows during their linear breeding. The research was carried out within the framework of RAS 0526-2021-0001.
PSXV-1 Genetic evaluation of longevity of cows culled due to fertility-related problems using random regression models and censored data
Authors: Oliveira Hinayah R , Miller Stephen P , Brito Luiz F , Schenkel Flavio S 
Published: October 2021

Abstract
A recent study showed that longevity based on different culling reasons should be considered as different traits in genetic evaluations. However, it is still necessary to create a pipeline that avoid including/excluding animals culled for different reasons in every genetic evaluation run. This study aimed to: 1) perform a genetic evaluation of the longevity of cows culled due to fertility-related problems including records of animals culled for other reasons (i.e., age, structural problems, disease, and performance) as censored records; and, 2) identify the impact of censored data in the genetic parameters and breeding values estimated. Two longevity indicators were evaluated: traditional (TL; time from first calving to culling) and functional (FL; time period in which the cow was alive and also calving after its first calving) longevity. Both TL and FL were evaluated from 2 to 15 years-old, and codified as binary traits for each age (0 = culled and 1 = alive/calved). Both trait definitions were analyzed using a Bayesian random regression linear model. Animals culled for reasons other than fertility were either excluded from the data (standard) or had their records censored after the culling date reported in the dataset (censored). After the quality control, 154,419 and 450,124 animals had uncensored and censored records, respectively. Heritabilities estimated for TL over the ages ranged from 0.02 to 0.13 for standard, and from 0.01 to 0.12 for censored datasets. Heritabilities estimated for FL ranged from 0.01 to 0.14 (standard), and from 0.01 to 0.13 (censored). Average (SD) correlation of breeding values predicted over all ages, using the standard and censored datasets, was 0.77 (0.16) for TL, and 0.83 (0.11) for FL. Our findings suggest that including censored data in the analyses might impact the genomic evaluations and further work is need to determine the optimal predictive approach.