scholarly journals Evaluation of Zoetis GeneMax Advantage genomic predictions in commercial Bos taurus Angus cattle

2020 ◽  
Author(s):  
Brian. C. Arisman ◽  
Troy N. Rowan ◽  
Jordan M. Thomas ◽  
Harly J. Durbin ◽  
David J. Patterson ◽  
...  
Keyword(s):  
Linear Models ◽  
Bos Taurus ◽  
Carcass Weight ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Weaning Weight ◽  
University Of Missouri ◽  
Angus Cattle ◽  
Effective Selection ◽  
Genomic Predictions

ABSTRACTThe GeneMax (GMX) Advantage test, developed by Zoetis, uses approximately 50,000 single nucleotide polymorphisms (SNP) to predict the genomic potential of a commercial Angus heifer. Genetic predictions are provided for Calving Ease Maternal, Weaning Weight, Heifer Pregnancy, Milk, Mature Weight, Dry Matter Intake, Carcass Weight, Marbling, and Yield. Indices of economically important traits are estimated on an index score (1-100 scale) and are divided into three indices; Cow Advantage index, Feeder Advantage index, and Total Advantage index. The indices provide a genomic prediction of the profitability of the cow’s calves. Therefore, test results can inform selection and culling decisions made by commercial beef cattle producers. To measure the accuracy of the trait predictions, data from commercial Angus females and their progeny at the University of Missouri Thompson Research Center was utilized to analyze weaning weight, milk, marbling, fat, ribeye area, and carcass weight. Progeny phenotypic data was matched to the respective dam, then the cow’s genomic predictions were compared to the calf’s age-adjusted phenotypes using correlation and linear models. All tested GeneMax scores of the dam were significantly correlated with and predicted calf performance. Our predicted effect sizes, except for fat thickness, were similar to those reported by Zoetis. In conclusion, the GeneMax Advantage test accurately ranks animals based on their genetic merit and is an effective selection tool in commercial cowherds.

scholarly journals 101 National Center for Applied Reproduction and Genomics (NCARG) evaluates accuracy of genomic prediction in commercial Angus cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 84-84
Author(s):  
Jared E Decker ◽  
David J Patterson ◽  
Brian Arisman ◽  
Troy N Rowan ◽  
Jordan M Thomas ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Linear Models ◽  
New Technologies ◽  
Random Effect ◽  
Carcass Weight ◽  
P Value ◽  
Phenotypic Data ◽  
Weaning Weight ◽  
Angus Cattle ◽  
Genomic Predictions

Abstract One of the goals of the National Center of Applied Reproduction and Genomics (NCARG) is to demonstrate in real-world settings the potential of new technologies. To this end, we evaluated the predictive ability of the Zoetis GeneMax Advantage genomic prediction. The GeneMax Advantage test analyzes tens of thousands of single nucleotide polymorphisms (SNP) to predict the genetic potential of a commercial Angus female. Genetic predictions are provided for Calving Ease Maternal, Weaning Weight, Heifer Pregnancy, Milk, Mature Weight, Dry Matter Intake, Carcass Weight, Marbling, and Yield. Indices of economically important traits are estimated on an index score (1–100 scale) and are reported in three indices; Cow Advantage Index, Feeder Advantage Index, and Total Advantage Index. Producers can use the scores and indices to make selection, culling, and mating decisions. To measure the accuracy of the trait predictions, data from commercial Angus females and their progeny at the University of Missouri Thompson Research Center was utilized to analyze Weaning Weight, Milk, Marbling, Fat Thickness, Ribeye Area and Carcass Weight. Progeny phenotypic data was matched to the respective dam, and the genomic predictions were then compared to the phenotypic data using correlation and linear models in R software. Linear models accounted for differences in sex, birth year, and the random effect of sire. Interestingly, all genomic predictions had correlations with progeny phenotypes that were significantly different from zero (P-value < 0.05). Likewise in the linear models, genomic predictions for all analyzed traits were significantly associated with calf performance (Table 1). Academics, farmers and ranchers, and extension professionals can trust the effectiveness of GeneMax Advantage genomic predictions in commercial Angus cattle.

The area of eye muscle of beef cattle carcasses

1963 ◽  
Vol 3 (10) ◽  
pp. 249
Author(s):  
RM Seebeck
Keyword(s):  
Beef Cattle ◽  
Cross Sectional Area ◽  
Carcass Weight ◽  
Sectional Area ◽  
Muscle Area ◽  
Cross Sectional ◽  
Eye Muscle ◽  
Angus Cattle ◽  
The Cross

Variations in the cross-sectional area of eye muscle of carcasses cut between the tenth and eleventh ribs were investigated, using 105 Hereford and 51 Angus steers aged 20 months. These cattle consisted of three groups, born in successive years. At constant carcass weight, statistically significant differences in eye muscle area were found between breeds and between years. Breed and year differences were also found in eye muscle area with width and depth of eye muscle constant, so that there are limitations to the estimation of eye muscle area from width and depth measurements. A nomograph is given for estimating eye muscle area from width and depth for Hereford and Angus cattle, when all animals are reared in the same year and environment. The use of eye muscle area as an indicator of weight of carcass muscle is discussed.

scholarly journals Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires

2022 ◽  
Author(s):  
Gabriel Soares Campos ◽  
Fernando Flores Cardoso ◽  
Claudia Cristina Gulias Gomes ◽  
Robert Domingues ◽  
Luciana Correia de Almeida Regitano ◽  
...  
Keyword(s):  
Reference Population ◽  
Single Step ◽  
Linear Regression Method ◽  
Effective Population ◽  
Genetic Progress ◽  
Angus Cattle ◽  
Improvement Programs ◽  
Snp Panels ◽  
Estimate Variance ◽  
Genomic Predictions

Abstract Genomic prediction has become the new standard for genetic improvement programs, and currently, there is a desire to implement this technology for the evaluation of Angus cattle in Brazil. Thus, the main objective of this study was to assess the feasibility of evaluating young Brazilian Angus (BA) bulls and heifers for 12 routinely recorded traits using single-step genomic BLUP (ssGBLUP) with and without genotypes from American Angus (AA) sires. The second objective was to obtain estimates of effective population size (Ne) and linkage disequilibrium (LD) in the Brazilian Angus population. The dataset contained phenotypic information for up to 277,661 animals belonging to the Promebo® breeding program, pedigree for 362,900, of which 1,386 were genotyped for 50k, 77k, and 150k SNP panels. After imputation and quality control, 61,666 SNP were available for the analyses. In addition, genotypes from 332 American Angus (AA) sires widely used in Brazil were retrieved from the AA Association database to be used for genomic predictions. Bivariate animal models were used to estimate variance components, traditional EBV, and genomic EBV (GEBV). Validation was carried out with the linear regression method (LR) using young-genotyped animals born between 2013 and 2015 without phenotypes in the reduced dataset and with records in the complete dataset. Validation animals were further split into progeny of BA and AA sires to evaluate if their progenies would benefit by including genotypes from AA sires. The Ne was 254 based on pedigree and 197 based on LD, and the average LD (±SD) and distance between adjacent SNPs across all chromosomes was 0.27 (±0.27) and 40743.68 bp, respectively. Prediction accuracies with ssGBLUP outperformed BLUP for all traits, improving accuracies by, on average, 16% for BA young bulls and heifers. The GEBV prediction accuracies ranged from 0.37 (total maternal for weaning weight and tick count) to 0.54 (yearling precocity) across all traits, and dispersion (LR coefficients) fluctuated between 0.92 and 1.06. Inclusion of genotyped sires from the AA improved GEBV accuracies by 2%, on average, compared to using only the BA reference population. Our study indicated that genomic information could help to improve GEBV accuracies and hence genetic progress in the Brazilian Angus population. The inclusion of genotypes from American Angus sires heavily used in Brazil just marginally increased the GEBV accuracies for selection candidates.

scholarly journals Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0198419 ◽  
Author(s):  
Bartosz Czech ◽  
Magdalena Frąszczak ◽  
Magda Mielczarek ◽  
Joanna Szyda
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bos Taurus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour

2009 ◽  
Vol 49 (8) ◽  
pp. 675 ◽  
Author(s):  
N. L. Feeley ◽  
K. A. Munyard
Keyword(s):  
Mus Musculus ◽  
Bos Taurus ◽  
Receptor Gene ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Pcr Products ◽  
Phenotypic Variations

The aim of this study was to determine if any correlation exists between melanocortin-1 receptor (MC1R) polymorphisms and skin and fibre colour in alpacas. Primers capable of amplifying the entire alpaca MC1R gene were designed from a comparative alignment of Bos taurus and Mus musculus MC1R gene sequences. The complete MC1R gene of 41 alpacas exhibiting a range of fibre colours, and which were sourced from farms across Australia, was sequenced from PCR products. Twenty-one single nucleotide polymorphisms were identified within MC1R. Two of these polymorphisms (A82G and C901T) have the potential to reduce eumelanin production by disrupting the activity of MC1R. No agreement was observed between fibre colour alone and MC1R genotype in the 41 animals in this study. However, when the animals were assigned to groups based on the presence or absence of eumelanin in their fibre and skin, only animals that had at least one allele with the A82/C901 combination expressed eumelanin. We propose that A82/C901 is the wild-type dominant ‘E’ MC1R allele, while alpacas with either G82/T901 or G82/Y901 are homozygous for the recessive ‘e’ MC1R allele and are therefore unable to produce eumelanin.

scholarly journals Longitudinal Phenotypes Improve Genotype Association for Hyperketonemia in Dairy Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1059 ◽  
Author(s):  
Francisco A. Leal Yepes ◽  
Daryl V. Nydam ◽  
Sabine Mann ◽  
Luciano Caixeta ◽  
Jessica A. A. McArt ◽  
...  
Keyword(s):  
Linear Models ◽  
Association Studies ◽  
Genetic Selection ◽  
Area Under The Curve ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Mixed Linear Models ◽  
Biological Insight ◽  
Group 2 ◽  
Genomic Regions

The objective of our study was to identify genomic regions associated with varying concentrations of non-esterified fatty acid (NEFA), β-hydroxybutyrate (BHB), and the development of hyperketonemia (HYK) in longitudinally sampled Holstein dairy cows. Our study population consisted of 147 multiparous cows intensively characterized by serial NEFA and BHB concentrations. To identify individuals with contrasting combinations in longitudinal BHB and NEFA concentrations, phenotypes were established using incremental area under the curve (AUC) and categorized as follows: Group (1) high NEFA and high BHB, group (2) low NEFA and high BHB), group (3) low NEFA and low BHB, and group (4) high NEFA and low BHB. Cows were genotyped on the Illumina Bovine High-density (777 K) beadchip. Genome-wide association studies using mixed linear models with the least-related animals were performed to establish a genetic association with HYK, BHB-AUC, NEFA-AUC, and the comparisons of the 4 AUC phenotypic groups using Golden Helix software. Nine single-nucleotide polymorphisms were associated with high longitudinal concentrations of BHB and further investigated. Five candidate genes related to energy metabolism and homeostasis were identified. These results provide biological insight and help identify susceptible animals thus improving genetic selection criteria thereby decreasing the incidence of HYK.

scholarly journals Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Harly J. Durbin ◽  
Duc Lu ◽  
Helen Yampara-Iquise ◽  
Stephen P. Miller ◽  
Jared E. Decker
Keyword(s):  
Heat Stress ◽  
Beef Cattle ◽  
Tall Fescue ◽  
The United States ◽  
Genetic Evaluation ◽  
Functional Enrichment ◽  
Fescue Toxicosis ◽  
Weaning Weight ◽  
Angus Cattle ◽  
Genetic Evaluations

Abstract Background Heat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States and cost the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in temperate or subtropical parts of the world. Furthermore, research suggests that early-summer hair shedding may reflect tolerance to fescue toxicosis, since vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Both heat stress and fescue toxicosis reduce profitability partly via indirect maternal effects on calf weaning weight. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle, and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA). Results Hair shedding score was moderately heritable (h2 = 0.34 to 0.40), with different repeatability estimates between cattle grazing versus not grazing endophyte-infected tall fescue. Our results suggest modestly negative genetic and phenotypic correlations between a dam’s hair shedding score (lower score is earlier shedding) and the weaning weight of her calf, which is one metric of performance. Together, these results indicate that economic gains can be made by using hair shedding score breeding values to select for heat-tolerant cattle. GWAA identified 176 variants significant at FDR < 0.05. Functional enrichment analyses using genes that were located within 50 kb of these variants identified pathways involved in keratin formation, prolactin signalling, host-virus interaction, and other biological processes. Conclusions This work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. Our results will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

Cutaneous Melanocytomas in 10 Young Cattle

1995 ◽  
Vol 32 (5) ◽  
pp. 479-484 ◽  
Author(s):  
M. A. Miller ◽  
A. D. Weaver ◽  
P. L. Stogsdill ◽  
J. R. Fischer ◽  
J. M. Kreeger ◽  
...  
Keyword(s):  
Coat Color ◽  
Surgical Excision ◽  
Histopathologic Examination ◽  
Diagnostic Laboratory ◽  
University Of Missouri ◽  
Angus Cattle ◽  
Biopsy Specimens ◽  
Medical Diagnostic ◽  
Young Cattle ◽  
Mitotic Figures

Ten melanocytomas from 10 cattle were diagnosed by histopathologic examination of biopsy specimens submitted to the Veterinary Medical Diagnostic Laboratory, University of Missouri, between 1 January 1986 and 31 December 1993. One tumor was congenital; the others were first noticed between 2 months and 2 years of age (x = 9.9 months). Six tumors occurred in purebred (3) or crossbred (3) Angus cattle; one tumor each occurred in a Holstein, a Shorthorn, a Simmental, and a beef calf of unrecorded breed or coat color. Five calves were female, and five were male. Five tumors occurred in truncal dermis or subcutis (three in abdominal skin), four occurred on a limb, and one occurred on the jaw. Tumors varied in histologic appearance, but all were pigmented and all had few mitotic figures. Outcome was known for 8/10 cattle. In four cattle followed for at least 1 year, the tumor did not recur after surgical excision. Another heifer had residual gray tissue at the tumor site after surgery but remained in the herd without regrowth of the tumor 30 months after excision. Three other calves were slaughtered within 6 months of excision without apparent recurrence of the tumor.

Genetic and phenotypic parameters for pre-weaning growth and weaning conformation of Angus cattle

1978 ◽  
Vol 29 (2) ◽  
pp. 373
Author(s):  
R Barlow ◽  
EB Dettmann
Keyword(s):  
Least Squares ◽  
New South ◽  
New South Wales ◽  
Genetic Correlations ◽  
Components Of Variance ◽  
Weaning Weight ◽  
Environmental Correlations ◽  
Angus Cattle ◽  
South Wales

Weaning weight (WW) and conformation score (CS) records on Angus calves from four New South Wales herds were analysed by least-squares procedures. Paternal half-sib components of variance and covariance were used to obtain estimates of heritabilities of various measures of growth and cs, as well as genetic, phenotypic and environmental correlations. Estimates of the heritabilities of measures of growth ranged from 0.20 (all data) to 0.24 when derived from heifer data only. The heritability of cs was 0.24 when the data were adjusted for ww, and 0.19 when no covariate was included in the analysis. All correlations among different measures of growth were positive and close to unity. There were small positive phenotypic and environmental correlations (0.19 to 0.36) and small negative genetic correlations between ww and cs (–0.02 to –0.41).

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