bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSXI-4 Genome-Wide association study for muscle visual score in Nellore cattle raised in pasture-based systems
Authors: Pedrosa Victor B , Machado Pamela , Martins Rafaela , Silva Marcio , Pinto Luis Fernando , Brito Luiz F 
Published: October 2021

Abstract
Visual scoring traits have been proposed as an alternative to evaluate body composition of Zebu cattle near the slaughter season when phenotyping technologies are not available. Considering the increased demand for high-quality animal protein in developing countries, there is a need to genetically improve body muscle (MUSC) in Zebu cattle (Bos taurus indicus), especially in animals raised in pasture-based systems. Therefore, our main objectives were to estimate genetic parameters, perform a genome-wide association study based on the single-step GBLUP approach (ssGWAS), and identify candidate genes and metabolic pathways related to MUSC in Nellore cattle. A total of 20,808 Nellore animals born between 2009 and 2018 were visually score at 18 months of age and 2,775 of these animals were also genotyped using the GGP-Indicus 35K SNP panel (33,247 SNPs after quality control). Heritability was estimated based on the REML approach and the model included the effects of age at measurement as covariable and the contemporary group (farm, birth season, management group and sex). The ssGWAS was performed using the BLUPF90 family programs. The identification of candidate genes was performed through the Ensembl database incorporated in the BioMart tool. MUSC is heritable (0.38) and can be improved through selection. Nineteen genomic regions (explaining 38.12% of the total additive genetic variance) located on BTA1, BTA7, BTA9, BTA16, and BTA21 and harboring 19 candidate genes were identified. The main genes identified were SEMA6A, TIAM2, UNC5A, and UIMC1, which are related to the metabolism of energy, growth, homeostasis and axonogenesis, and therefore, muscle development. These findings contribute to a better understanding of the molecular mechanisms over the gene expression of muscle visual score in Nellore cattle, and the polymorphisms located in these genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for body and carcass traits.
PSXI-1 Influence of concentrations of essential and toxic elements in semen on qualitative characteristics of sperm of Holstein bulls
Authors: Platonov Stanislav , Zavyalov Oleg , Frolov Alexey , Kharlamov Anatoly , Kurilkina Marina 
Published: October 2021

Abstract
Many studies show that an excess or deficiency of chemical elements in an animal’s body can lead to a number of reproductive disorders. In this regard, the aim of this study was to assess the influence of concentrations of essential and toxic elements in semen on qualitative characteristics of semen of sire bulls. The studies were carried out on Holstein bulls at the age of 3–4 years (n = 65). Sperm concentration (billions) was estimated using a digital photometer (IMV Technologies). Sperm activity (score) was studied using a phase contrast microscope (Nikon ECLIPSE E400, Tokyo, Japan). The elemental composition of the semen was determined by 25 chemical elements (Al, As, B, Ca, Cd, Co, Cr, Cu, Fe, I, K, Li, Mg, Mn, Na, Ni, P, Pb, Se, Si, Sn, Hg, Sr, V, Zn) by ICP-AES and ICP-MS. Coefficients were calculated according to Spearman’s correlation. As a result of the research, it was found that sperm activity negatively correlated (r = -0.47; P ≤ 0.05) with the Pb content in semen and had a positive correlation with Zn concentrations (r = 0.55; P ≤ 0.05); Se (r = 0.64; P ≤ 0.05); P (r = 0.67; P ≤ 0.05). Sperm concentration was positively correlated with Cu levels (r = 0.55; P ≤ 0.05); P (r = 0.76; P ≤ 0.05); Se (r = 0.66; P ≤ 0.05). Thus, the results of the carried out studies indicate a high degree of relationship between the content of essential and toxic elements in semen and main qualitative characteristics of sperm. A deeper study of the role of chemical elements in reproductive function can be useful in overcoming the problem of low reproductive capacity of sires. The studies were carried out in accordance with the research plan for 2019–2021. FSBSI Federal Research Centre BST RAS (No. 0761-2019-0006)
PSXII-6 Landscape genetics used to identify gene bank beef cattle collection completeness and gaps
Authors: Blackburn Harvey D , Paiva Samuel R , Hermuche Potira , McManus Concepta 
Published: October 2021

Abstract
Gene banks (GB) primary goal is to capture genetic diversity among livestock breeds. Genetic diversity assessments by US GB have used pedigrees and genetic markers. Landscape genetics (LG), is a third approach for evaluating germplasm collections and genetic resources. We evaluated the GB’s beef collection using LG for the purpose of assessing collection gaps/completeness by using geographic information systems. The current beef cattle collection contains 3,916 animals from 11 Bos indicus (including composite, BI), and 40 Bos taurus British (BTB) and Bos taurus continental (BTC) breeds. Each GB animal was georeferenced by latitude and longitude. In addition, county level satellite imagery of the continental US was obtained and included: temperature, humidity, precipitation, and normalized difference vegetation index (NDVI). Temperature–humidity index (THI) was computed from temperature and humidity by county. In addition, USDA beef cattle statistics by county were used in mapping overlays. There was a high correspondence between in-situ cattle density and GB collection throughout the mid-west and extending to both borders. Evaluating genetic groups demonstrated that BI were derived from the Gulf Coast region, while BTB and BTC shared a distribution throughout the mid-west. The collection’s BTB were also sourced from the inter-mountain west. All environmental parameters were combined to identify similar environmental conditions where germplasm had already been collected. Through this process future geographies for sampling genetic groups were apparent. New collection areas should include the Great Basin, west Texas, New Mexico and Arizona. Further BI collections should be performed in low THI score areas and BTB and BTC collections in high THI areas is needed. Using GIS/LG adds a new perspective and resolution for future collections to ensure cattle that are adapted to a particular environment are added to the collection.
PSXII-10 Non-invasive measurements of woody and normal condition in broiler breast meat
Authors: OH Sang-Hyon , NOH Euyeon , MIN Byungrok R , YOON Soobin , SHIN Seungjun 
Published: October 2021

Abstract
Woody Breast (WB) defines a quality issue resulting from a muscle abnormality in chicken meat, which makes the breast meat more rigid and sometimes pale in color with inferior texture. The frequency of this defect in Europe is over 30% and some have argued that similar levels may exist in the United States. Given that chicken with WB are of poor economic value and are discriminated by the consumers, producers face significant economic hardship under the current production paradigm. One of the problems in identifying the biological mechanism responsible for WB is that the occurrence and severity of WB can be only identified after harvest. This study is to investigate the physical characteristics of WB and normal breast (NB) in live chicken using a non-invasive, digital palpation device named as “MyotonPRO®”. This technology provides the measurements of superficial muscles regarding dynamic stiffness (100–1500 N/m; DS), elasticity (0.3–2.5), mechanical stress relaxation time (5–40 ms; MSRT) and ratio of deformation and relaxation time (0.3–2.5; RDRT). One hundred breast meat samples were used in this analysis (WB: 50; NB: 50), which were obtained from a local processing plant one day after harvest and sorted based on WB scoring with the naked eye (0, 1 for NB; 2, 3 for WB). One way ANOVA was used to analyze the data as a statistical model. The least squares means of the following variables were significantly different between WB and NB (P &lt; 0.01): DS (603.4 vs 565.8; N/m), and elasticity (1.40 vs 1.55). However, MSRT and RDRT were not significantly different (P &gt; 0.05). These results collectively show that the non-invasive measurements of WB differ from NB. The degree of muscle hardness in WB can be considered as a trait to be selected, and utilized for the genetic/genomic selection program collecting the measurements before harvest.
PSXII-12 Partitioning direct and maternal genetic effects into additive and non-additive components for growth and maternal traits in Yorkshire pigs
Authors: Jiang Jicai , O’Neill Shauneen , Maltecca Christian , Fix Justin , Crum Tamar , Schwab Clint , Tiezzi Francesco 
Published: October 2021

Abstract
This study investigates how much direct and maternal non-additive genetic effects contribute to growth and maternal traits in swine. We analyzed a sample of 19,475 genotyped Yorkshire pigs from Acuity Ag Solutions, LLC (Carlyle, IL). Approximately 50K SNPs were kept after quality control, and missing genotypes were then imputed using findhap.f90. The genotypes were used to construct genomic relationship matrices (GRMs) corresponding to additive (A), dominance (D), and additive-by-additive epistasis (E) effects for both direct and maternal effects. The GRMs were subsequently employed as covariance structure matrices in a linear mixed model consisting of eight random components, namely three direct genetic effects (Ad, Dd, and Ed), three maternal genetic effects (Am, Dm, and Em), maternal environmental effect, and common litter environmental effect. We estimated these variance components (VCs) for six growth traits (birth weight, average daily gain, back fat, and loin area) and six maternal traits of a sow (total number of piglets born, number of piglets born alive, average weight of piglets at birth, average weight of piglets weaned) using REML in MMAP (https://mmap.github.io/). As shown in Table 1, we found significant (P&lt; 0.05) direct dominance and epistasis VCs for all six growth traits. Additionally, direct epistasis effects explained a larger proportion of phenotypic variation than direct dominance for all growth traits (0.04–0.12 vs. 0.01–0.04). In contrast, direct non-additive VCs were not significant for any maternal trait except for epistasis in average weight of piglets weaned. As for maternal non-additive effects, we only discovered significant additive VC in birth weight and average daily gain and significant epistasis VC in back fat (P&lt; 0.05). Other maternal genetic VCs were largely negligible. In summary, direct dominance and epistasis effects play a prominent role in growth traits of Yorkshire pigs.
PSXII-7 Milk somatic cells monitoring in Russian Holstein cattle population as a base for determining genetic and genomic variability
Authors: Lashneva Irina , Sermyagin Alexander A , Ignatieva Larisa P , Gladyr Elena , Ermilov Alexander , Zinovieva Natalia A 
Published: October 2021

Abstract
Health traits in dairy cattle have crucial meaning to produce high quality milk. Despite of fertility problems and metabolic disorders in cows, the mastitis has a bigger economic losses influence to include it as selection criteria in cattle breeding. Somatic cell count (SCC) in that case are the good predictor for monitoring udder health cows under whole population level or separate herd. The aim of our study was to assess genetic and genomic components for SCC and their scores (SCS) using experimental dataset by seven herds with the subsequent QTL identification. For six-month observation the 5824 cows with 19786 test-day records were included into analysis. Then EBVs by offspring assessing of 139 genotyped Holstein sires were calculated trough TD Model (BLUPF90) and then it adopted as pseudo-phenotypes for GWAS. After quality control using Plink 1.90, we used ≈39K SNP (Illumina 50K). The average values for SCC and SCS were 351±7 thousands cells/ml and 2.86±0.02 score respectively. Heritability coefficients revealed low genetic variation for SCC – 0.119 and moderate for SCS – 0.211. Daily yield for cows with SCC &gt;1000×103 cells/ml was low by -4.0 kg milk to compare individuals with SCC &lt; 100×103 cells/ml. At the same time lactose content and freezing point were decreasing by 4.93 to 4.69% and -0.635 to -0.618°C. By Cattle QTLdb we identified some causal genes for SCC on BTA3 (ROR1), BTA9 (EZR), BTA13 (OSBPL2,DNAJC5,ZBTB46,MTG2), BTA14 (KHDRBS3) and BTA22 (RBMS3). But more relevant GWAS calls were found for SCS by BTA14 (KCNB2, ZFAT) as QTL associated to the milking speed that has unfavorable genetic correlation with clinical mastitis or SCS. Thereby, genes detected under experimental study, are the valuable and informative markers to implementation genomic selection methods for cattle health in creating Russian bulls’ reference population. The study was funded by RFBR within project No. 20-316-90050
PSXIV-23 Polymorphism of the LCORL gene in the reindeer
Authors: Krutikova Anna , Dementieva Natalia , Nikitkina Elena 
Published: October 2021

Abstract
Reindeer are one of the main representatives of the ecosystem of the Arctic zone and the only possible object of economic activity of the indigenous peoples of the polar regions of Russia. Reindeer meat is a valuable source of complete protein in the diet of the Evenks, Nenets, Yakuts and other peoples of the Far North. Four breeds of reindeer have been bred in Russia - Nenets, Evenk, Chukchi and Even. Evenk and Nenets are the most numerous. They live in different climatic zones and differ significantly in phenotypic characteristics (size and body weight). Populations of wild reindeer are also widespread. The problem of increasing the meat productivity of the main breeds of domesticated reindeer can be solved by searching for casual polymorphisms in candidate genes responsible for the growth and development of muscle tissue. Thus, polymorphism of the LCORL gene (mRNA ligand-dependent nuclear receptor of the corepressor type, which is a transcription factor) is associated with body weight and size in many mammals. We sequenced exon 7 of the LCORL gene and found seven SNPs, six of which are nonsynonymous and lead to a change in the amino acid composition of the protein. There was a significant difference in the occurrence of wild and mutant alleles in the three analyzed populations (wild reindeer, Nenets breed, Evenk breed), which indicates the presence of selection pressure on the LСORL gene region, and also indirectly confirms the significance of the polymorphism of this locus for phenotypic variability in height and size of the reindeer. Studies of associations of LCORL gene polymorphisms on live weight and growth in other animal species suggest that some of the found SNPs may be true causal quantitative trait loci (QTL) in domestic reindeer breeds. Project No. 0045-2021-0010.
PSXIV-25 Search for the association of SNP in GRM8 gene with sperm quality in stallions
Authors: Nikitkina Elena , Krutikova Anna , Musidray Artem 
Published: October 2021

Abstract
The formation and functioning of the animal reproductive system occurs as a result of the coordinated interaction of a wide range of genes. To search for causal mutations, work was carried out to search for polymorphic variants in the marker regions detected using GWAS. The four single-nucleotide substitutions in the exon of the GRM8 gene identified during the studies and the association of these SNPs with sperm quality was carried out. Semen from 22 stallions was collected. Sperm volume, concentration and progressive motility were assessed. Sequencing of the sections of the candidate GRM8 gene was carried out using an Applied Biosystems 3500 genetic analyzer. For the rs1138419111 genotype, no significant differences were found in the studied parameters. According to the identified single nucleotide substitution rs1147388106, the highest ejaculate volume was in stallions with the GG genotype (55.9±26.5 ml) compared to stallions with the GA genotypes (32.5±13.9 ml) and AA (18.0±33,6) (p &lt; 0.05). When analyzing data on SNP rs395286150, stallions with a heterozygous CT genotype had the best sperm quality. Thus, the cell concentration was 317.0±66.5 million/ml in stallions with the CT genotype, 209.6±58.2 and 189.5±74.9 % with the CC and TT genotypes, respectively (P &lt; 0.05). The progressive sperm motility of stallions with the CT genotype was 65.5±20.5% versus 48.7±22.0% in stallions with the TT genotype and 48.4±18.6% with CC. Analysis of data on SNP rs394524550 revealed a significant effect of the genotype on progressive motility. Stallions with the AG genotype had a progressive motility of 64.6±16.3%, and those with GG and AA 32.7±15.7 and 49.6±18.1%, respectively (P &lt; 0.05). Thus, as a result four single nucleotide polymorphisms were identified in the exon of the GRM gene. Three of them were significantly associated with such indicators of sperm quality as ejaculate volume, concentration and progressive motility. Project No. 0445-2021-0011.
PSIX-15 Assessment of machine learning algorithms for prediction of Aleutian disease in American mink
Authors: Do Duy Ngoc , Hu Guoyu , Miar Younes 
Published: October 2021

Abstract
American mink (Neovison vison) is the major source of fur for the fur industries worldwide and Aleutian disease (AD) is causing severe financial losses to the mink industry. Different methods have been used to diagnose the AD in mink, but the combination of several methods can be the most appropriate approach for the selection of AD resilient mink. Iodine agglutination test (IAT) and counterimmunoelectrophoresis (CIEP) methods are commonly employed in test-and-remove strategy; meanwhile, enzyme-linked immunosorbent assay (ELISA) and packed-cell volume (PCV) methods are complementary. However, using multiple methods are expensive; and therefore, hindering the corrected use of AD tests in selection. This research presented the assessments of the AD classification based on machine learning algorithms. The Aleutian disease was tested on 1,830 individuals using these tests in an AD positive mink farm (Canadian Centre for Fur Animal Research, NS, Canada). The accuracy of classification for CIEP was evaluated based on the sex information, and IAT, ELISA and PCV test results implemented in seven machine learning classification algorithms (Random Forest, Artificial Neural Networks, C50Tree, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) using the Caret package in R. The accuracy of prediction varied among the methods. Overall, the Random Forest was the best-performing algorithm for the current dataset with an accuracy of 0.89 in the training data and 0.94 in the testing data. Our work demonstrated the utility and relative ease of using machine learning algorithms to assess the CIEP information, and consequently reducing the cost of AD tests. However, further works require the inclusion of production and reproduction information in the models and extension of phenotypic collection to increase the accuracy of current methods.
PSIX-18 Effect of chicory silage and se-yeast on peripartum ewes: Immune status via complete blood cell count
Authors: Ford Hunter , Bionaz Massimo , Ates Serkan , Hasan Daniella , Klopfenstein Joe , Park Shelby , Quinones Tyler , Pearce Carolyn , Ness Kate , Torres Mariangel Aleman 
Published: October 2021

Abstract
Immune status is critical for peripartum animals. Immune cells are highly affected by the oxidative status and level of Se. The use of forages with high content of antioxidants in combination with Se-yeast can improve the immune status in peripartum ruminants. The objective of this study was to test the possibility of improving the immune system of peripartum ewes by feeding a combination of chicory silage and Se-yeast. Approximately one month prior to lambing, 36 pregnant Polypay sheep were moved into single pens and randomly assigned to one of four groups to be fed either grass or chicory silage and supplemented or not with 3.6 mg Se/day (DiaMune, Diamond V). Blood was collected throughout the study to assess the complete blood count (VetScan HM5). Secondary compounds in silages were analyzed via LC-MS/MS. Data were analyzed using GLIMMIX (SAS) with day, silage type, Se and their interactions as fixed effects and ewe as random effect with significance declared at P≤0.05. Compared to grass silage, among measured secondary compounds only resveratrol was larger in chicory vs. grass. Total white blood cell count was larger in animals fed grass vs. chicory silage. Silage type and Se-yeast supplementation had little effects on the other measured parameters. The average hemoglobin inside red blood cells was larger in animals fed grass vs. chicory silage. Only tendencies (P between 0.08 and 0.09) were observed for the effects of Se supplementation, including increased hematocrit and number of circulating monocytes but, the latter, only in grass-fed ewes, and decreased red blood cell volume. Platelet size distribution tended (P=0.08) to increase in grass-fed ewes supplemented with Se but the opposite was observed in ewes fed chicory silage. Together, these data indicate a minimum-to-no effect of the type of silage or Se supplementation on complete blood cell count on peripartum ewes.
PSIX-11 Bacterial clinical mastitis associated with abortion in dairy cows
Authors: Artemyeva Olga , Nikanova Daria A , Kolodina Evgenia , Romanova Varvara , Zinovieva Natalia A , Brovko Fedor 
Published: October 2021

Abstract
Within the period from 20.04.2020 to 15.02.2021 the state of 2087 pregnant cows was studied to identify the connection between abortions and the occurrence of mastitis. During the study period 97 cases of clinical mastitis and 149 cases of abortion were identified. Abortions were observed in 42 out of 97 cows with registered clinical mastitis. It was found that cows that had a clinical form of mastitis during the first 45 days of pregnancy (in the embryonic period of development) subsequently had the maximum number of abortions - 27 heads or 64.28% of abortions of cows with mastitis. Among cows that had mastitis in the period of 46–150 days of pregnancy 13 cases of abortion were revealed (30.9% of abortions of cows with mastitis). Among cows that had mastitis during pregnancy for more than 150 days 2 cases of abortion were detected (4.7% of abortions of cows with mastitis). On the basis of bacteriological analysis, Staphylococcus spp., Streptococcus spp. and Enterobacteriaceae were isolated from milk of 15 aborted cows with the diagnosis of clinical mastitis. To identify species the conventional biochemical methods were applied together with the API 20 E, API Staph, API 20 Strep test (bioMerieux SA, France). In total, 18 species of pathogens were identified, including Ps. aeruginosa (n = 5), E. coli (n = 4), S. aureus (n = 1), S. saprophyticus (n = 8). Ps. aeruginosa, E. coli, S. aureus were isolated both from the organs of the reproductive system and from the milk of the cows who had had abortions after suffering from mastitis, whereas no relationship was found between the microflora of the reproductive system and the udder of the cows whose abortions are not associated with mastitis. The study was supported by the Russian Science Foundation, project No.20-16-00106