bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSVIII-4 Genetic evaluation of functional heifer longevity in north American angus cattle
Authors: Oliveira Hinayah R , Miller Stephen P , Brito Luiz F , Schenkel Flavio S 
Published: October 2021

Abstract
The goals of this study were to develop a genetic evaluation system for a novel trait called functional heifer longevity (FHL), and determine if this novel trait is heritable. The FHL trait was defined as binary, in which the heifers received the code 1 if they had calved by the end of their third year (n = 377,938), or 0 if they were culled/sold during this period (n = 368,308). Analysis were performed using linear animal models and Bayesian inference. The significant systematic effects included in the statistical models are born by embryo transfer, year-season of birth, and age at calving (in months). Three models, differing according to their random effects (i.e., reduced model, which included only herd-year-season and additive genetic random effects; maternal genetic model, which added maternal genetic effects; and complete model, which further added maternal permanent environmental effects), were compared based on the deviance information criterion (DIC) and the estimates of genetic parameters. The reduced model was preferred according to the DIC values. However, high maternal heritabilities were estimated using the maternal genetic (0.51) and complete (0.36) models, indicating that maternal effects can impact the selection of heifers for breeding. Similar additive genetic heritabilities were estimated among the three models (0.24, 0.27, and 0.25 using the reduced, maternal genetic, and complete models, respectively), and no significant re-ranking of selection candidates were observed based on their additive genetic breeding values. Total heritabilities and correlations estimated between additive genetic and maternal genetic effects were 0.37 and -0.28 for the maternal genetic, and 0.31 and -0.27 for the complete model, respectively. This study shows that FHL is heritable, and that including maternal effects in the statistical models might be important. These results contribute to a larger project studying the genetics of female longevity in Angus cattle.
PSVIII-6 Genetic features of Russian Simmental cattle population different origin derived by assessing milk production and fertility traits
Authors: Ignatieva Larisa P , Sermyagin Alexander A , Nikitin Sergey 
Published: October 2021

Abstract
Since the beginning of the 20th century, over 43 thousand animals of Simmental cattle and related breeds have been imported to Russia from Europe. This had a significant impact on the selection intensity and genetic structure within the pale-motley population. The research included 42 breeding herds from 14 regions of Russia. The EBV using the BLUPF90 program based on the ANIMAL MODEL procedure was calculated. Totally of 1471 bulls by using 61816 daughters were estimated. The heritability coefficients showed moderate variability for milk yield (MY) h2=0.140, fat percentage (FP) h2=0.194, protein percentage (PP) h2=0.184 and live weight h2=0.163, as an indirect predictor for meat production. The variability for fertility features like number of inseminations per conception and days open was h2=0.073 and h2=0.061, respectively. Genetic correlation between MY and FP was rg=0.149, and for MY and PP – rg=0.180, while between FP and PP – rg=0.226. The average bulls’ EBV for milk traits in Red Holsteins consisted +23 kg MY, +0.002% FP and +0.001% PP, by Austrian Simmental +10 kg MY, +0.013% FP and +0.002% PP. For Russian Simmental origin animals was signed negative selection response for MY (-23 kg), FP (-0.001%) and PP (-0.003%). High average EBV for imported Simmental cows were revealed +146 kg MY, +0.009% FP and +0.004% PP, while in Russian Simmental we got negative values for MY -70 kg and PP -0.004% but only for FP was showed positive level +0.001%. Simmental breed improvement strategy in Russia focused not only to increasing milk yield but also to improving milk compositions with stabilizing cows’ reproductive traits using the world gene pool of related breeds from Europe. The study was funded by Ministry of Science and Higher Education No.0445-2021-0016
PSVIII-9 Genome assembly of American mink (Neovison vison) using high-fidelity long reads
Authors: Karimi Karim , Do Duy Ngoc , Miar Younes 
Published: October 2021

Abstract
Development of genome-enabled selection and providing new insights in the genetic architecture of economically important traits are essential parts of mink breeding programs. Availability of a contagious genome assembly would guarantee the fundamental genomic studies in American mink (Neovison vison). Advances in long-read sequencing technologies have provided the opportunity to obtain high quality and free-gaps assemblies for different species. The objective of this study was to generate an accurate genome assembly using Single Molecule High-Fidelity (HiFi) Sequencing for American mink. The whole genome sequences of 100 mink were analyzed to select the most homozygous individual. A black American mink from Millbank Fur Farm (Rockwood, ON, Canada) was selected for PacBio sequencing. The total number of 2,884,047 HiFi reads with the average size of 20 kb were generated using three libraries of PacBio Sequel II System. Three de novo assemblers including wtdbg, Flye and IPA were used to obtain the initial draft of assembly using the long reads. The draft generated using Flye was selected as the final assembly based on the metrics of contiguity and completeness. The final assembly included 3,529 contigs with the N50 of 18.26 Mb and the largest contig of 62.16 Mb. The length of genome assembly was 2.66 Gb with 85 gaps. These results confirmed that high-coverage and accurate long-reads significantly improved the American mink genome assembly and successfully generated more contagious assembly. The chromosome conformation capture data will be integrated to the current draft to obtain a chromosome-level genome assembly for American mink at the next step of the project.
PSVIII-8 Genetic parameters for parasite resistance in an endangered and heritage sheep breed from Florida
Authors: Estrada-Reyes Zaira M , Hidalgo Moreno Jorge A , Diehl Brittany N , Ogunade Ibukun M , Pech-Cervantes Andres A , Terrill Thomas H , Rae Owen 
Published: October 2021

Abstract
The Florida Native Sheep is one of the oldest sheep breeds in the United States. This heritage breed from Florida, naturally adapted to humid and hot climate conditions, is one of the most parasite resistant breeds from the Southern US. However, only approximately 1,000 individuals remain alive in the world. Therefore, conservation efforts and breeding programs are critical for survival of this breed. The objective of this research was to estimate genetic parameters for parasite resistance and body condition score in Florida Native sheep. The pedigree file contained 695 animals born between 2018 and 2020 and included 279 individuals with genotypes (38,429 SNP after quality control). The dataset contained 365 animals with phenotypic records at 38 days post-infection (natural Haemonchus contortus infection) for fecal egg count (FEC), blood packed count volume (PCV), FAMACHA score (FAM), and body condition score (BCS). Genetic parameters were estimated using a multi-trait model with a Bayesian implementation in the GIBBS3F90 program. Heritabilities were 0.38 0.07, 0.47 0.05, 0.27 0.04, and 0.52 0.07 for FEC, PCV, FAM, and BCS. Genetic correlations among parasite resistance traits were high and favorable: -0.82 0.06 (FEC-PCV), 0.83 0.07 (FEC-FAM), and -0.94 0.03 (PCV-FAM). Genetic correlations among parasite resistance traits and BCS were -0.42 0.11 (FEC-BCS), 0.75 0.09 (PCV-BCS), and -0.82 0.05 (FAM-BCS). Genetic progress for parasite resistance is possible in Florida Native sheep. The FAMACHA score is a phenotypic parameter easy to record in sheep; therefore, genetic selection for this trait can be effective to improve the remaining traits.
PSVIII-2 Genetic diversity analysis of hybrid Karachaev goats (Capra hircus) population using microsatellite marker data
Authors: Fomenko Oleg , Petrov Sergey N 
Published: October 2021

Abstract
The Karachaev goat is an indigenous breed that possesses unique features including significantly less fat deposition in the body compared to sheep and cattle, ability to graze at an altitude of up to 1200 meters and to produce fertile hybrids with wild relatives. To understand the genetic diversity and population structure of hybrids between domestic Karachaev goats (Capra hircus) and The West Caucasian tur (Capra caucasica) 143 individuals were analyzed using 10 microsatellites panel. Sample were analyzed according to the manufacturer’s recommendations on an automatic sequencer, ABI 3130XL genetic analyzer (Applied Biosystems). Genetic diversity was calculated using GenAlEx 6.503 software. Genotyping of ten microsatellite loci in hybrid forms of Karachaev goats and turs detected 106 alleles in total. Na values ranged from five (INR063) to seventeen (SRCRSO008), averaging 10.6 alleles per locus across the 10 loci. All loci were polymorphic. The average number of alleles was 10.6 alleles per locus. This is higher than the similar indicator obtained by Kharzinova et al. (2019) in populations of Soviet wool, Tajik wool, Orenburg downy, Alpine and Zaanen dairy breeds of goats, studied using the panel of same 10 STR-markers (9.3 loci). Other key indexes of genetic diversity could be found in table 1. The values of the coefficient FIS suggest the absence of related mating in the herd. Information on genotypic variability of Karachaev goats hybrid forms obtained here will contribute into the breeding programs improvement and to preservation of existing native breeds.
PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed
Authors: Hay El Hamidi , Roberts Andrew 
Published: October 2021

Abstract
Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P &lt; 0.001), 4.67 kg (P &lt; 0.0001), 42.39 kg (P &lt; 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.
PSXI-8 Heritability estimates of antibody- and cell-mediated immune response in north American angus beef cattle
Authors: Beard Shannon , Hodgins Doug C , Schmied Julie , Caswell Jeff , Lohuis Michael M , Miller Steve , Devani Kajal , Schenkel Flavio S , Mallard Bonnie 
Published: October 2021

Abstract
Including immune response traits in breeding programs has been suggested as a solution to improve overall animal health and enhance disease resistance but is not yet available for Angus cattle in North America. One way to measure immune response is to use the High Immune Response (HIR™) technology, which identifies animals with superior heritable immunity by evaluating antibody-mediated (AMIR) and cell-mediated (CMIR) immune response, allowing for the calculation of an estimated breeding value for total adaptive immune response for each animal. Before HIR™ can be included in beef cattle breeding programs, genetic parameters, including heritability, must be estimated for the traits involved. The objective of this study was to estimate a preliminary heritability for AMIR and CMIR in North American Angus beef cattle. On day 0 of the phenotyping protocol, cattle were immunized intramuscularly with a preparation of type 1 (CMIR) and type 2 (AMIR) antigens with adjuvant. On day 14, cattle received an intradermal injection of 0.1 mL of the CMIR test antigen in the right tail fold, and 0.1 mL PBS in the left tail fold. Change in cutaneous double skinfold thickness after 24 hours was used to assess CMIR. Blood was collected on days 0 and 14 to evaluate serum antibody to the type 2 antigen by ELISA to quantify AMIR. Heritability estimates were calculated for Canada and the USA separately, and then for both countries combined using single-trait animal models in ASReml and are presented in Table 1. The results of this study indicate that the heritabilities of AMIR and CMIR are moderate and emphasize the potential for its inclusion into Angus breeding schemes.
PSXI-6 Genome-wide SNP analysis of three Azerbaijani sheep breeds
Authors: Dotsev Arsen V , Deniskova Tatiana E , Bagirov Vugar A , Abilov Ahmed I , Reyer Henry , Wimmers Klaus , Brem Gottfried , Zinovieva Natalia A 
Published: October 2021

Abstract
Azerbaijani sheep breeds are of particular interest since this region is in close proximity to the Fertile Crescent – the proposed place of domestication. Molecular genetic studies of local breeds will help shed light on the history of sheep breeding. Our work was aimed to identify genetic characteristics of three sheep breeds from Azerbaijan: Bozakh (n = 19), Karabakh (n = 16) and Mazekh (n = 19). For genotyping, we used Illumina OvineHD BeadChip (AgResearch) containing around 600 thousand SNPs. PLINK 1.9 was used to perform quality control. Genetic diversity parameters and pairwise FST distances were calculated in R package diveRsity. After all quality control procedures, including LD pruning, 286663 SNPs were selected for subsequent analyses. PCA revealed that, while all the breeds formed their own clusters, only 1.62% of genetic variability was explained by the first component (PC1). Cluster analysis conducted in Admixture 1.3 showed that Bozakh was derived from Karabakh and Mazekh breeds. However, based on CV error, the number of clusters (K) judged to be one. Pairwise FST distances were quite low, with highest value of 0.017 between Karabakh and Mazekh and lowest (0.006) between Mazekh and Bozakh breeds. The global fixation index (FST) was 0.01, which indicated that 99% of genetic variability was due to within breeds differences. Expected heterozygosity was similar in Bozah and Mazeh (0.363±0.000 and 0.360±0.000, respectively) and a slight lower in Karabakh breed (0.353±0.000). We observed neither heterozygotes excess nor deficiency in all of the studied breeds. The inbreeding coefficient (Fis), ranged from 0.001 in Karabakh to 0.011 in Mazekh sheep. Our results demonstrate that the studied Azerbaijani sheep breeds are genetically close, but carry specific genomic components that allows consider them as valuable genetic resources. The study was funded by the RSF 21-66-00007 (genotyping) and the Russian Ministry of Science and Higher Education 0445-2019-0024 (expedition studies).
PSXI-3 Genome-wide association study for MIR-predicted milk fatty acids composition in Russian Holstein cattle population
Authors: Sermyagin Alexander A , Lashneva Irina , Ignatieva Larisa P , Kositsin Alexander , Gladyr Elena , Ermilov Alexander , Yanchukov Ivan , Zinovieva Natalia A 
Published: October 2021

Abstract
Milk fatty acids (FA) derived from infrared spectra are a new type of traits that allow fast and predictability use their in dairy breeding and herd cattle management. The Holstein animals feature are the high milk yield, but milk composition traits can be different according to population or country origin. The purpose of our study was to find out genetic variation for milk FA and detect QTLs associated with Holstein sires’ EBV in Russian cattle population. For this analysis, we used an experimental dataset for 36982 milk test records from 14 breeding herds in the Moscow region. Individual milk samples per animal analyzed routinely by MilkoScan7 for different FA types: C14:0, C16:0, C18:0, C18:1, saturated, mono- and polyunsaturated, short-, medium- and long-chain. Total number of bulls consisted 778 individuals including 222 animals with genotypes (39051 SNP, Illumina 50K). For calculating EBV by Sire Model, we applied BLUPF90. Plink 1.90 performed quality check control and GWAS procedure. Heritability coefficients were 0.071–0.155 for C14:0-C18:0 levels, 0.196 for C18:1, 0.083 for SFA, 0.018 for PUFA, 0.176 for MUFA, 0.114–0.155 for SCFA-LCFA levels. GWAS revealed most significant (P &lt; 0.001-0.00001) frequently QTLs associated with FA content that were cited in articles previously for BTA5 (CHST11,C18:1), BTA6 (KCNIP4,C18:1; PPRAGC1A,C18:0), BTA11 (NRXN1,LPIN1,C18:1; NBAS,C18:0), BTA26 (PCDH15,PUFA; PRKG1,C18:1). These genes were responsible for synthesis milk fat, fertility, udder conformation traits, lauric, myristic, myristoleic, palmatoleic, oleic and other types of FA. In addition, we identified several QTLs for C14:0, C16:0, SFA, MUFA, SCFA, LCFA on BTA1 (137.32 Mb), BTA10 (5.50 Mb, 9.79 Mb), BTA14 (44.35 Mb), BTA19 (17.57–17.89 Mb) and BTA22 (14.02–14.06 Mb, 20.29–20.45 Mb). Our results are the first steps toward to understanding genetic and genomic mechanisms for using FA in selection processes to improve milk quality for Holstein cattle in Russia. The study was funded by RSF (project No. 21-76-20046)
PSXI-2 Genome-Wide association study and possibilities for genomic selection of Simmental cattle breed in Russia
Authors: Ignatieva Larisa P , Sermyagin Alexander A , Nikitin Sergey , Conte Alexander , Naryshkina Elena , Zinovieva Natalia A 
Published: October 2021

Abstract
The implementation of genomic selection methods in dairy cattle is limited due to the size of the reference population, quantitative traits variability and genetic structure of population. The Simmental cattle and related breeds in Russia occupy the third place by registered cows - 87.6 thousand, and are bred from the western borders of central Russia to Yakutia in Siberia. The study aim was to search for QTL using as a pseudo phenotype sires’ EBV to validate the effectiveness of genomic assessments for Simmental cattle in Russia. Reference group based on 358 bulls from different Russian regional populations was formed. By the dataset of 61976 cows, using BLUP Animal Model approach, animals’ EBV were calculated. The GBLUP procedure was used to get genomic prediction (DGV). Genotype quality control selected of 37143 SNPs. GWAS analysis was perform by Plink 1.90. To prove DGV we used verification procedure to comparison with EBV in training population dataset that showed slightly moderate repeatability for 305-milk yield - 37.6%, milk fat - 39.8% and milk protein - 43.6%. Significant SNPs associated with bulls EBV according to milk production and fertility traits revealed for: 305-milk yield on BTA5 (ACO2,p=0.0005), BTA29 (NAP1L4, P = 0.00004; KCNQ1, P = 0.00004); fat percentage on BTA3 (ROR1, P = 0.0003), BTA14 (CRH, P = 0.0003; TRIM55, P = 0.0003; DNAJC5B, P = 0.0003; REX2, P = 0.0020; ZFHX4, P = 0.0020) BTA17 (TLR2, P = 0.0011); days open on BTA1 (TNIK, P = 0.0007; FNDC3B, P = 0.0007), BTA21 (IGF1R, P = 0.0002). Using Cattle QTL Database, the identified genes were associated with milk yield, fat and protein percentage, protein yield, somatic cell score, protein-to-fat ratio, stearic fatty acid content, calving ease, daughter pregnancy rate, stillbirth and inseminations per conception. GWAS results identified significant SNPs associated with milk production and fertility traits that will allow in the nearest future improve reliability for genomic prediction of young bulls and boost genetic trend in the Russian Simmental cattle population. The study was funded by RFBR within project No.17-29-08030
PSXII-8 Mitochondrial DNA diversity within domestic reindeer in Russia
Authors: Kharzinova Veronika R , Dotsev Arsen V , Bardukov Nikolay V , Deniskova Tatiana E , Upadhyay Maulik , Krebs Stefan , Kunz Elisabeth , Medugorac Ivica , Zinovieva Natalia A 
Published: October 2021

Abstract
Domestic reindeer in Russia are a valuable resource of vital importance to the physical and cultural survival of the Northern indigenous minority. During the last decades, the mitochondrial (mt) genetic markers have been widely used as a molecular tool to investigate genetic structure and diversity of livestock species. Here we aimed at the assessing the mtDNA diversity of the domestic reindeer inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east. A complete cytochrome b (cytb) sequences (1,140 bp) from representatives of six populations, including Nenets (NEN, n = 16), Evenk (EVK, n = 12), Even (EVN, n = 6), Chukotka (CHU, n = 6), Chukotka-Khargin (CHUKH, n = 6) and Tuva (TUVA, n = 6) were obtained. Sequences’ alignment was conducted using MUSCLE algorithm in R package msa. In total, 34 haplotypes were identified. Median-joining network, constructed in PopART 1.7, revealed three major groups of haplotypes: the first one joined the samples of all the populations, the second one included NEN, EVN and CHUKH, and the third group was presented by the one sample of CHU. AMOVA, calculated in Arlequin 3.5.2.2, showed that only 9.58% of molecular variance could be explained by the differences between populations and 90.42% - within populations. Genetic diversity parameters calculated in DnaSP 6.12.03, demonstrated that average number of nucleotide differences (K) was highest in CHUKH (28.333) and EVN (27.409) and lowest in TUVA (4.533) and EVK (5.400). Nucleotide diversity (Pi) was 0.01238±0.00559, 0.00474±0.00091, 0.02404±0.00453, 0.01281±0.00464, 0.02485±0.00744, and 0.00398±0.00110 for NEN, EVK, EVN, CHU, CHUKH and TUVA, respectively. Our study demonstrated the lack of clear genetic structure of the studied reindeer populations in relation to cytb sequence. The level of genetic diversity was associated with census size and was lowest in the smallest Tuva population. This study was supported by RSF-21-16-00071 and Russian Ministry of Science and Higher Education-0445-2019-0024.