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.

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 PSX-19 Factors affecting growth and carcass trait performance of Canadian heavy lambs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 457-457
Author(s):  
Erin Massender ◽  
Luiz Brito ◽  
Angela Cánovas ◽  
Delma Kennedy ◽  
Flavio Schenkel
Keyword(s):  
Evaluation System ◽  
Fixed Effects ◽  
Linear Models ◽  
Random Effect ◽  
Growth Trait ◽  
Carcass Trait ◽  
Classification Systems ◽  
Carcass Weight ◽  
Mixed Linear Models ◽  
Factors Affecting

Abstract The profitability of meat lamb production is strongly dependent on growth and carcass trait performance of market lambs. The objective of this research was to test the significance of non-genetic factors on growth, ultrasound, and carcass traits of Canadian heavy lambs. Hot carcass weight (HCW, kg), fat depth at the GR site (FATGR, mm), average carcass conformation score (CONF, points), and total carcass value (PRICE, $CAD) were measured for 8,865 purebred lambs marketed through Quebec’s Heavy Lamb Sales Agency. Corresponding management information and growth trait records for over 19,000 animals with carcass records and their relatives were extracted from the Canadian Sheep Genetic Evaluation System. Single-trait mixed linear models in SAS were used to test the significance (P < 0.05) of various non-genetic effects, after a Scheffe adjustment for multiple comparisons. All models included categorical fixed effects of sex (male or female), breed (Hampshire, HA; Suffolk, SU; Canadian Arcott, CD; Polled Dorset, DP; Rideau Arcott, RI; Polypay, PO), dam age at parity (1 to 7+ years), and birth and rearing type (born as single, twin, or triplet and more, and reared as single or multiple), and a random effect of contemporary group. Linear covariates of slaughter age or carcass weight were included in the carcass trait models, while a scanning weight covariate was used for ultrasound trait models. Male lambs were found to be significantly heavier during growth, had greater HCW and PRICE, and lower FATGR and CONF than female lambs. As expected, terminal breeds (HA, SU, CD) tended to have greater growth, greater HCW and PRICE, and lower FATGR than maternal (DP, RI, RV, PO) breeds. This information could be utilized by Canadian sheep producers to manage their flocks to maximize the revenue of lambs marketed through price grid classification systems.

scholarly journals Genomic prediction and QTL mapping of root system architecture and above-ground agronomic traits in rice (Oryza sativa L.) with a multi-trait index and Bayesian networks

2021 ◽  
Author(s):  
Santosh Sharma ◽  
Shannon R M Pinson ◽  
David R Gealy ◽  
Jeremy D Edwards
Keyword(s):  
Oryza Sativa ◽  
Root System ◽  
System Architecture ◽  
Genomic Prediction ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Root System Architecture ◽  
Root Tips ◽  
Phenotypic Data ◽  
Genomic Predictions

Abstract Root system architecture (RSA) is a crucial factor in resource acquisition and plant productivity. Roots are difficult to phenotype in the field, thus new tools for predicting phenotype from genotype are particularly valuable for plant breeders aiming to improve RSA. This study identifies quantitative trait loci (QTLs) for RSA and agronomic traits in a rice (Oryza sativa) recombinant inbred line (RIL) population derived from parents with contrasting RSA traits (PI312777 x Katy). The lines were phenotyped for agronomic traits in the field, and separately grown as seedlings on agar plates which were imaged to extract RSA trait measurements. QTLs were discovered from conventional linkage analysis and from a machine learning approach using a Bayesian network (BN) consisting of genome-wide SNP data and phenotypic data. The genomic prediction abilities (GPAs) of multi-QTL models and the BN analysis were compared with the several standard genomic prediction methods. We found GPAs were improved using multi-trait (BN) compared to single trait genomic prediction in traits with low to moderate heritability. Two groups of individuals were selected based on genomic predictions and a modified rank sum index (GSRI) indicating their divergence across multiple RSA traits. Selections made on genomic predictions did result in differences between the group means for numerous RSA. The ranking accuracy across RSA traits among the individual selected RILs ranged from 0.14 for root volume to 0.59 for lateral root tips. We conclude that the multi-trait genomic prediction model using BN can in some cases improve the GPA of RSA and agronomic traits, and the GSRI approach is useful to simultaneously select for a desired set of RSA traits in a segregating population.

scholarly journals 304 Transgenerational influence of prenatal stress on temperament, birth weight, and weaning weight of Brahman calves

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 3-3
Author(s):  
Brittni P Littlejohn ◽  
David G Riley ◽  
Don A Neuendorff ◽  
Charles R Long ◽  
Thomas H Welsh ◽  
...  
Keyword(s):  
Birth Weight ◽  
Prenatal Stress ◽  
Fixed Effects ◽  
Linear Models ◽  
Random Effect ◽  
Mixed Linear Models ◽  
Birth Season ◽  
Weaning Weight ◽  
Exit Velocity ◽  
Transportation Stress

Abstract The objective was to evaluate the transgenerational influence of prenatal transportation stress (PNS) on temperament, birth weight, and weaning weight in Brahman calves. Dams were derived from multiparous cows that were transported for 2 h at 60, 80, 100, 120, and 140 d of gestation (n = 48) or maintained as Controls (n = 48). Heifers born to Transported or Control cows were followed through maturity and their calves (n = 79; 35 calves born to Control dams and 44 to PNS dams) studied across multiple years. Calf birth and weaning weights were recorded. Calf temperament at weaning was evaluated utilizing pen score (PS; 1=calm and 5=excitable), exit velocity (EV; m/sec), and temperament score (TS; (PS+EV)/2). Data were analyzed using mixed linear models. Fixed effects included dam treatment, calf sex, and birth season nested within birth year (season nested within year was identified as an efficient parameterization). Calf sire was a random effect. Birth weight was not affected by dam treatment, calf sex, or season nested within year (P > 0.1). Weaning weight was greater in males than females (P < 0.01). Weaning weight was affected by season nested within year (P < 0.01). DOA at weaning was a covariate for weaning weight (0.74±0.09 kg; P < 0.01), but not PS, EV, or TS (P < 0.1). Weaning weight was not affected by dam treatment (P > 0.1). TS was affected by season nested within year (P = 0.04) but not dam treatment or calf sex (P > 0.1). EV was not affected by dam treatment, calf sex, or season nested within year (P > 0.1). PS was affected by season nested within year (P < 0.01) but not calf sex (P > 0.1). Calves born to PNS dams had greater (P = 0.02) PS than calves born to Controls (3.17±0.20 and 2.58±0.22, respectively). There was a transgenerational influence of PNS on temperament but not birth or weaning weight.

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 PSIII-8 Impact of SYNOVEX® ONE GRASS implantation during suckling on pre-weaning calf growth performance

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 239-239
Author(s):  
Shane Newton ◽  
Payton Dahmer ◽  
Larry Corah ◽  
Keith Harmoney ◽  
John Jaeger ◽  
...  
Keyword(s):  
Growth Performance ◽  
Random Effect ◽  
Cost Effective ◽  
Recent Decade ◽  
Estradiol Benzoate ◽  
Beef Steers ◽  
Weaning Weight ◽  
Trenbolone Acetate ◽  
Calf Growth ◽  
Randomized Design

Abstract Historic data supports the use of pre-weaning implants to maximize beef calf weaning weight, but their use has declined over the recent decade. A total of 96 beef steers (initially 85.2 kg BW and > 45 d of age) were used in a 168-d study to evaluate the effects of Synovex C® implantation during suckling on pre-weaning calf growth performance. At initial processing, calves were individually weighed and allotted in a completely randomized design to one of two treatments: 1) not implanted (control) or 2) implanted with 150 mg of trenbolone acetate and 21 mg of estradiol benzoate (SYNOVEX® ONE GRASS, Zoetis, Kalamazoo, MI). All calves were weighed on d 0 (implantation), 83, 126 and 168 (weaning), with ADG calculated for each period. Data were analyzed using the GLIMMIX procedure of SAS (v9.4, Cary, NC). There were 48 replicates per treatment, with grazing location as a random effect. While there were no detected differences in BW during the initial phases (P > 0.10), implanted calves tended to have greater (P = 0.100) greater weaning weight than non-implanted calves (279 vs. 265 kg, respectively). Calves implanted with SYNOVEX® ONE GRASS had 0.8, 0.12, and 0.16 kg/d greater (P < 0.05) ADG than those that were not implanted in all three phases. This resulted in an average of 0.10 kg/d greater (P = 0.002) ADG in implanted calves overall compared to the control. In conclusion, this research showed significant increases in suckling calf ADG in implanted calves compared to their non-implanted counterparts, which led to a tendency for 14-kg greater weaning weights. Additional research is warranted to consider the post-weaning growth and impact of re-implanting, but this data reinforces previous literature that suckling calf implantation continues to be cost effective for cow-calf producers.

scholarly journals Basics of Statistics for Clinical Research in Hand Surgery

2018 ◽  
Vol 46 (02) ◽  
pp. 150-171 ◽  
Author(s):  
Roberto Rosales ◽  
Isam Atroshi
Keyword(s):  
Clinical Research ◽  
Linear Models ◽  
Surgical Intervention ◽  
Statistical Tests ◽  
Hand Surgery ◽  
Descriptive Statistics ◽  
Data Matrix ◽  
P Value ◽  
Real Value ◽  
Tunnel Syndrome

AbstractStatistics, the science of numerical evaluation, helps in determining the real value of a hand surgical intervention. Clinical research in hand surgery cannot improve without considering the application of the most appropriate statistical procedures. The purpose of the present paper is to approach the basics of data analysis using a database of carpal tunnel syndrome (CTS) to understand the data matrix, the generation of variables, the descriptive statistics, the most appropriate statistical tests based on how data were collected, the parameter estimation (inference statistics) with p-value or confidence interval, and, finally, the important concept of generalized linear models (GLMs) or regression analysis.

scholarly journals MCKAT, a multi-dimensional copy number variant kernel association test

2021 ◽  
Author(s):  
Nastaran Maus Esfahani ◽  
Daniel Catchpoole ◽  
Javed Khan ◽  
Paul J. Kennedy
Keyword(s):  
Copy Number ◽  
Kernel Method ◽  
Random Effect ◽  
Random Effect Model ◽  
Score Test ◽  
Copy Number Variant ◽  
Association Test ◽  
P Value ◽  
Single Pair ◽  
Related Trait

AbstractBackgroundCopy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia.Consequently, the interest in studying a possible association of CNVs to specific disease traits is growing. However, due to the specific multi-dimensional characteristics of the CNVs, methods for testing the association between CNVs and the disease-related traits are still underdeveloped. We propose a novel multi-dimensional CNV kernel association test (MCKAT) in this paper. We aim to find significant associations between CNVs and disease-related traits using kernel-based methods.ResultsWe address the multi-dimensionality in CNV characteristics. We first design a single pair CNV kernel, which contains three sub-kernels to summarize the similarity between two CNVs considering all CNV characteristics. Then, aggregate single pair CNV kernel to the whole chromosome CNV kernel, which summarizes the similarity between CNVs in two or more chromosomes. Finally, the association between the CNVs and disease-related traits is evaluated by comparing the similarity in the trait with kernel-based similarity using a score test in a random effect model. We apply MCKAT on genome-wide CNV datasets to examine the association between CNVs and disease-related traits, which demonstrates the potential usefulness the proposed method has for the CNV association tests. We compare the performance of MCKAT with CKAT, a uni-dimensional kernel method. Based on the results, MCKAT indicates stronger evidence, smaller p-value, in detecting significant associations between CNVs and disease-related traits in both rare and common CNV datasets.ConclusionA multi-dimensional copy number variant kernel association test can detect significantly associated CNVs with any disease-related trait. MCKAT can help biologists detect significantly associated CNVs with any disease-related trait across a patient group instead of examining the CNVs case by case in each subject.

scholarly journals Comparative efficacy between ketamine, memantine, riluzole and d-cycloserine in patients diagnosed with drug resistant depression: a meta-analysis

2019 ◽  
Vol 8 (6) ◽  
pp. 1132
Author(s):  
Nishita H. Darji ◽  
Devang A. Rana ◽  
Supriya D. Malhotra
Keyword(s):  
Rating Scale ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Fixed Effect ◽  
P Value ◽  
Drug Resistant ◽  
Effect Model ◽  
Resistant Depression ◽  
Glutamate Modulators

Background: Glutamate modulators are having immense potential and are newer entities for treating drug resistant depression. The objectives were to generate statistical evidence on basis of existing data of ketamine, memantine, riluzole and d-cycloserine in resistant depression.Methods: A total of 14 RCTs following PRISMA guidelines and matching inclusion and exclusion criteria were collected of ketamine (5), memantine (3), riluzole (2) and d-cycloserine (4) vs placebo in drug resistant depression. Only RCTs with primary diagnosis of drug resistant depression (Previously on two standard antidepressant therapy) were included. Studies with treatment response rate, 50% reduction in total score of the depression rating scale-Montgomery-Åsberg Depression Rating Scale or the Hamilton Depression Rating Scale or Beck Depression Inventory was chosen as clinical outcome measure. RevMan 5.3 software was used for the analysis.Results: In ketamine group using random effect model SMD was 2.122 (95% CI 0.659-3.584). P-value was statistically significant (random effect p <0.005 and in fixed effect <0.001). In memantine group, using random effect model -0.963 was SMD and (95% CI -1.958-0.0324). P-value was <0.001, significant in fixed effect. In riluzole group, SMD was -0.564 with (95% CI -3.927-2.799) in random effect. P-value was 0.741. In d-cycloserine group SMD was 0.316 with (95% CI -1.252-1.885) in random effect. P-value was 0.690.Conclusions: Ketamine showed best efficacy followed by memantine. Riluzole and DCS as such have no efficacy although its acts by same glutamate pathway. More molecular based research is required in use of glutamate modulators in resistant depression.

Sign in / Sign up

Export Citation Format

Share Document