Genetic evaluation of lamb performance in Outaouais Arcott and Suffolk sheep, their crosses and Canadian Arcott- or Hampshire-sired three-breed crosses

A crossbreeding study was used to assess the growth performance of the Outaouais Arcott and Suffolk breeds, their two breed crosses and specific three-breed crosses sired by either Canadian Arcott or Hampshire rams. In a sheep flock maintained under a semi-confinement management system, Suffolk lambs, weighing 3.8 kg at birth, were not significantly heavier than Canadian Arcott- or Hampshire-sired crossbred lambs. Lambs of the Outaouais breed were 26% lighter (P < 0.05) than those of the Suffolk breed, and their two breed crosses had birth weights between the two parental purebreds. The relative ranks among the breeds and their crosses had not changed by 42 d of age with lamb weights ranging from 10.6 to 12.6 kg. By 120 d of age the Canadian Arcott- and Hampshire-sired lambs weighed approximately 28–29 kg and were not significantly different in weight from the Outaouais and Suffolk breeds and their two breed crosses. Additive and maternal genetic effects m the Suffolk breed were significantly greater than in the Outaouais breed for birth weight by 12.9 and 12.6% respectively. By 42 d, no difference was detected between breeds for direct genetic effect. However, the maternal effect favoured the Suffolk breed by 15.8% (P < 0.05). By 120 d, the direct genetic effect was significantly greater in the Outaouais breed by 9.8%, but maternal genetic effects continued to favour the Suffolk breed by 12.5% (P < 0.05). Heterosis effects were generally small (< 3.1%) and not significant for lamb weights. The terminal sire breeds showed no significant difference between Canadian- and Hampshire-sired lamb weights. Generally, results obtained for two analyses (least squares model and multi-trait animal model) of the same data set were consistent. However, the animal model would be preferable when estimating parameters and breeding values from an unbalanced data set with unequal subclass frequencies. Key words: Lambs, weight, genetic effects, heterosis, animal model

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Prediction of genetic merit for growth rate in pigs using animal models with indirect genetic effects and genomic information

Genetics Selection Evolution ◽

10.1186/s12711-020-00578-y ◽

2020 ◽

Vol 52 (1) ◽

Cited By ~ 1

Author(s):

Bjarke G. Poulsen ◽

Birgitte Ask ◽

Hanne M. Nielsen ◽

Tage Ostersen ◽

Ole F. Christensen

Keyword(s):

Growth Rate ◽

Animal Model ◽

Genetic Effect ◽

Predictive Performance ◽

Genetic Effects ◽

Relationship Matrix ◽

Genomic Information ◽

Indirect Genetic Effects ◽

Group Members ◽

Direct Genetic Effect

Abstract Background Several studies have found that the growth rate of a pig is influenced by the genetics of the group members (indirect genetic effects). Accounting for these indirect genetic effects in a selection program may increase genetic progress for growth rate. However, indirect genetic effects are small and difficult to predict accurately. Genomic information may increase the ability to predict indirect genetic effects. Thus, the objective of this study was to test whether including indirect genetic effects in the animal model increases the predictive performance when genetic effects are predicted with genomic relationships. In total, 11,255 pigs were phenotyped for average daily gain between 30 and 94 kg, and 10,995 of these pigs were genotyped. Two relationship matrices were used: a numerator relationship matrix ($${\mathbf{A}}$$ A ) and a combined pedigree and genomic relationship matrix ($${\mathbf{H}}$$ H ); and two different animal models were used: an animal model with only direct genetic effects and an animal model with both direct and indirect genetic effects. The predictive performance of the models was defined as the Pearson correlation between corrected phenotypes and predicted genetic levels. The predicted genetic level of a pig was either its direct genetic effect or the sum of its direct genetic effect and the indirect genetic effects of its group members (total genetic effect). Results The highest predictive performance was achieved when total genetic effects were predicted with genomic information (21.2 vs. 14.7%). In general, the predictive performance was greater for total genetic effects than for direct genetic effects (0.1 to 0.5% greater; not statistically significant). Both types of genetic effects had greater predictive performance when they were predicted with $${\mathbf{H}}$$ H rather than $${\mathbf{A}}$$ A (5.9 to 6.3%). The difference between predictive performances of total genetic effects and direct genetic effects was smaller when $${\mathbf{H}}$$ H was used rather than $${\mathbf{A}}$$ A . Conclusions This study provides evidence that: (1) corrected phenotypes are better predicted with total genetic effects than with direct genetic effects only; (2) both direct genetic effects and indirect genetic effects are better predicted with $${\mathbf{H}}$$ H than $${\mathbf{A}}$$ A ; (3) using $${\mathbf{H}}$$ H rather than $${\mathbf{A}}$$ A primarily improves the predictive performance of direct genetic effects.

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A note on heritability estimates for growth traits in male and female Romanov sheep

Animal Science ◽

10.1017/s0003356100006966 ◽

1993 ◽

Vol 57 (2) ◽

pp. 326-328 ◽

Cited By ~ 1

Author(s):

G. A. María ◽

K. G. Boldman ◽

L. D. van Vleck

Keyword(s):

Animal Model ◽

Birth Weight ◽

Maximum Likelihood ◽

Random Effects ◽

Fixed Effects ◽

Growth Traits ◽

Genetic Effect ◽

Male And Female ◽

Males And Females ◽

Direct Genetic Effect

A total of 1855 records were analysed using restricted maximum likelihood (REML) techniques to estimate heritabilities separately for males and females lambs on birth weight (BW), weaning weight (WW), 90-day weight (W90) and average daily gains birth to weaning (Cl) and weaning to 90 days (C2). An animal model including fixed effects of year × season, parity, litter size and rearing type; and random effects of direct genetic effect (h2D) and residual was applied. Estimates ofh2Dfor BWwere 048 (males) and 0·50 (females); for WW 0·35 (males) and 0·22 (females); for W90 0·21 (males) and 0·31 (females); for Cl 0·20 (males) and 0·25 (females); and for C2 0·18 (males) and 0·29 (females).

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Genetic parameters for calving difficulty using complex genetic models in five beef breeds in Australia

Animal Production Science ◽

10.1071/an14571 ◽

2016 ◽

Vol 56 (5) ◽

pp. 927 ◽

Cited By ~ 5

Author(s):

M. G. Jeyaruban ◽

D. J. Johnston ◽

B. Tier ◽

H.-U. Graser

Keyword(s):

Genetic Parameters ◽

Linear Models ◽

Random Effect ◽

Genetic Correlations ◽

Genetic Effect ◽

Genetic Effects ◽

Gestation Length ◽

Calving Ease ◽

Direct Genetic Effect ◽

Calving Difficulty

Data on Angus (ANG), Charolais (CHA), Hereford (HER), Limousin (LIM) and Simmental (SIM) cattle were used to estimate genetic parameters for calving difficulty (CD), birthweight (BWT) and gestation length (GL) using threshold-linear models and to examine the effect of inclusion of random effect of sire × herd interaction (SxH) in the models. For models without SxH, estimated heritabilities for direct genetic effect of CD were 0.24 (±0.02), 0.22 (±0.04), 0.31 (±0.02), 0.22 (±0.04) and 0.17 (±0.01) for ANG, CHA, HER, LIM and SIM, respectively, whereas maternal heritabilities ranged from 0.13 to 0.20. Estimated heritabilities for direct genetic effect of BWT were 0.38 (±0.01), 0.37 (±0.03), 0.46 (±0.01), 0.35 (±0.02) and 0.36 (±0.01) for ANG, CHR, HER, LIM and SIM, respectively, whereas maternal heritabilities ranged from 0.08 to 0.11. Estimated heritabilities for direct genetic effect of GL were 0.59 (±0.02), 0.42 (±0.04), 0.50 (±0.03), 0.45 (±0.04) and 0.42 (±0.03) for ANG, CHR, HER, LIM and SIM, respectively, whereas maternal heritabilities ranged from 0.03 to 0.09. Genetic correlations between direct genetic effects of CD with BWT were highly positive and with GL were moderately positive for all five breeds. Estimated genetic correlations between direct genetic effects and maternal genetic effects (rdm) ranged across the five breeds from –0.40 (±0.05) to –0.16 (±0.02), –0.41 (±0.03) to –0.27 (±0.08) and –0.47 (±0.10) to –0.06 (±0.12) for BWT, GL and CD, respectively. Fitting SxH interaction as additional random effect significantly increased the log-likelihood for analyses of BWT, GL and CD of all breeds, except for GL of CHA. The estimated heritabilities were less than or equal to the estimates obtained with models omitting SxH. The rdm increased (i.e. became less negative) for BWT, GL and CD of all five breeds. However, the increase for GL was not substantially high in comparison to the increase observed for BWT and CD. Genetic parameters obtained for BWT, GL and CD, by fitting SxH as an additional random effect, are more appropriate to use in the genetic evaluation of calving ease in BREEDPLAN.

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Estimates of genetic parameters and genetic trends for production and reproduction traits in Iranian buffaloes (Bubalus bubalis)

Animal Production Science ◽

10.1071/an15370 ◽

2017 ◽

Vol 57 (2) ◽

pp. 216 ◽

Cited By ~ 7

Author(s):

Navid Ghavi Hossein-Zadeh

Keyword(s):

Animal Model ◽

Gibbs Sampling ◽

Genetic Selection ◽

Genetic Effect ◽

Reproductive Traits ◽

Bubalus Bubalis ◽

Reproduction Traits ◽

Estimate Variance ◽

Direct Genetic Effect ◽

Genetic Trends

Calving and milk production records from April 1992 to March 2012 comprising 5353 records of age at first calving (AFC), 2972 records of 305-days milk yield (MY) and 2349 records of interval between first and second calving (CI) from the first lactation buffaloes within 785 herds of Iran were analysed using a linear animal model to estimate variance components and heritability for these traits. A linear animal model including direct genetic effect was implemented by Gibbs sampling methodology. A single Gibbs sampling chain with 300 000 rounds was generated by the TM program. Genetic trends were obtained by regressing yearly mean estimates of breeding values on birth year. Posterior mean estimates of direct heritabilities for MY, AFC and CI were 0.46 ± 0.21, 0.20 ± 0.06 and 0.21 ± 0.14, respectively. The posterior means of direct genetic correlation between MY-AFC, MY-CI and AFC-CI were –0.31, 0.01 and –0.17, respectively. Estimates of direct genetic trends for MY, AFC and CI were negative and significant, and their corresponding values were –1.50 ± 0.05 (P < 0.0001), –0.04 ± 0.001 (P < 0.0001) and –0.02 ± 0.005 (P < 0.001), respectively. Medium to high direct heritability estimates for productive and reproductive traits would be due to higher additive genetic variances for these traits and implied that applicable genetic variations observed for productive and reproductive traits could be applied in designing future genetic selection plans for Iranian buffaloes.

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Genetic association between cows’ stayability to three years of age and juvenile growth traits in Canadian Angus herds

Canadian Journal of Animal Science ◽

10.4141/a03-128 ◽

2005 ◽

Vol 85 (2) ◽

pp. 139-143 ◽

Cited By ~ 3

Author(s):

D. P. Rasali ◽

G. H. Crow ◽

J. N. B. Shrestha ◽

A. D. Kennedy ◽

A. Brûlé-Babel

Keyword(s):

Fixed Effects ◽

Growth Traits ◽

Genetic Correlations ◽

Genetic Effect ◽

Genetic Effects ◽

Birth Season ◽

Angus Cattle ◽

Body Weights ◽

Direct Genetic Effect ◽

Maternal Heritability

Bivariate linear animal models were fit using MTDFREML programs for the analysis of cows’ stayability to 3 yr (STAY3, n = 1, 703) as a binary scored trait paired with body weights at birth (BW, n = 6,116), 205-d weaning (WW, n = 5,360,) and 1 yr of age (YW, n = 5250) in Angus cattle. For STAY3, the model included a fixed effect due to herd ×year of cow’s birth along with a random direct genetic effect. For each of BW, WW and YW, the model included fixed effects due to herd ×birth year, birth season, birth type, calf’s sex and the age of dam (as linear and quadratic covariates), while the random effects were direct and maternal genetic effects and permanent maternal environmental effects. Survival analysis revealed that the risk of cows, 10 yr or less in age, being culled from five Canadian Angus herds was highest between 2 and 3 yr of age. The direct heritability (h2) estimates for BW, WW and YW were 0.54, 0.73 and 0.47, respectively, and corresponding maternal heritability estimates were 0.14, 0.33 and 0.13, respectively. Furthermore, the direct h2 estimate for STAY3 from three bivariate analyses was 0.23–0.24. Estimates of direct-maternal genetic correlations of BW, WW and YW were -0.18, -0.70 and -0.39, respectively. The direct genetic correlations of STAY3 with BW, WW and YW were -0.15 to -0.09 indicating that selection for growth would have less detrimental influence on the stayability trait of cows. The correlations of direct genetic effects of STAY3 with maternal genetic effects of BW, WW and YW were between 0.20 and 0.25, indicating their favorable relationships as correlated traits. Key words: Stayability, growth traits, heritability, genetic correlations, beef cattle

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Estimation of genetic parameters for melanoma in the Old Kladruber horse

Czech Journal of Animal Science ◽

10.17221/5134-cjas ◽

2012 ◽

Vol 57 (No. 2) ◽

pp. 75-82 ◽

Cited By ~ 4

Author(s):

L. Vostrý ◽

B. Hofmanová ◽

H. Vostrá Vydrová ◽

J. Přibyl ◽

I. Majzlík

Keyword(s):

Animal Model ◽

Genetic Variation ◽

Correlation Coefficient ◽

Fixed Effects ◽

Genetic Parameters ◽

Rank Correlation ◽

Genetic Effect ◽

Pedigree Information ◽

Direct Genetic Effect ◽

Estimation Of Genetic Parameters

The aim of this study was to assess the prevalence of melanoma to investigate a possible genetic variation of this trait in the Old Kladruber horse. A total of 564 grey varieties of the Old Kladruber horse, 238 males and 326 females, with five generations of ancestors (n = 1245 animals) were analysed. Melanoma status was recorded for different stages. Three different analyses were conducted: a linear animal model (LM) with melanoma classified into five categories, threshold animal model (TM) with melanoma classified into five categories and threshold animal model (TMb) with melanoma classified into two categories (0 = absence, 1 = presence). All models included the fixed effects of year of evaluation, age, line, sex, greying level, random direct genetic effect, and the effect of animal’s permanent environment. Heritability for melanoma occurrence was estimated for LM – 0.09, for TM – 0.27, and for TMb – 0.11. The coefficient of repeatability was estimated for LM – 0.77, for TM – 0.90, and for TMb – 0.99. The values of the Pearson’s correlation coefficient and Spearmen’s rank correlation coefficient among breeding values estimated by LM, TM, and TMb models were from 0.82 to 0.88 and from 0.83 to 0.90, respectively, for data with pedigree information and from 0.77 to 0.84 and 0.77 to 0.88, respectively, for a subset of animals with measurements. Results suggest that additive genetic variation of melanoma occurrence in the Old Kladruber horse seems large enough to be exploited in a specific breeding programme.  

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Is the Genotype-Phenotype Map Modular?: A Statistical Approach Using Mouse Quantitative Trait Loci Data

Genetics ◽

10.1093/genetics/156.1.305 ◽

2000 ◽

Vol 156 (1) ◽

pp. 305-311 ◽

Cited By ~ 2

Author(s):

Jason G Mezey ◽

James M Cheverud ◽

Günter P Wagner

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Statistical Approach ◽

Genetic Effects ◽

Statistical Distribution ◽

Data Set ◽

Alveolar Region ◽

Phenotypic Characters ◽

Statistical Support ◽

Complex Characters

Abstract Various theories about the evolution of complex characters make predictions about the statistical distribution of genetic effects on phenotypic characters, also called the genotype-phenotype map. With the advent of QTL technology, data about these distributions are becoming available. In this article, we propose simple tests for the prediction that functionally integrated characters have a modular genotype-phenotype map. The test is applied to QTL data on the mouse mandible. The results provide statistical support for the notion that the ascending ramus region of the mandible is modularized. A data set comprising the effects of QTL on a more extensive portion of the phenotype is required to determine if the alveolar region of the mandible is also modularized.

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Ownership Variation in Violated Regulations and National Care Standards: Evidence From Social Care Providers

Nonprofit and Voluntary Sector Quarterly ◽

10.1177/08997640211001448 ◽

2021 ◽

pp. 089976402110014

Author(s):

Anders M. Bach-Mortensen ◽

Ani Movsisyan

Keyword(s):

Social Care ◽

Negative Binomial ◽

Third Sector ◽

Care Providers ◽

Data Set ◽

Logistic Regression Models ◽

For Profit ◽

Care Services ◽

Significant Difference ◽

Research Gap

Social care services are increasingly provisioned in quasi-markets in which for-profit, public, and third sector providers compete for contracts. Existing research has investigated the implications of this development by analyzing ownership variation in latent outcomes such as quality, but little is known about whether ownership predicts variation in more concrete outcomes, such as violation types. To address this research gap, we coded publicly available inspection reports of social care providers regulated by the Care Inspectorate in Scotland and created a novel data set enabling analysis of ownership variation in violations of (a) regulations, and (b) national care standards over an entire inspection year ( n = 4,178). Using negative binomial and logistic regression models, we find that for-profit providers are more likely to violate non-enforceable outcomes (national care standards) relative to other ownership types. We did not identify a statistically significant difference between for-profit and third sector providers with regard to enforceable outcomes (regulations).

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Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽

10.1186/s12864-021-07792-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Akio Onogi ◽

Toshio Watanabe ◽

Atsushi Ogino ◽

Kazuhito Kurogi ◽

Kenji Togashi

Keyword(s):

Population Size ◽

Genomic Prediction ◽

Variance Components ◽

Variance Component ◽

Predictive Accuracy ◽

Genetic Effect ◽

Genetic Effects ◽

Additive Effects ◽

Additive Variance ◽

Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

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Adverse reactions of targeted therapy in cancer patients: a retrospective study of hospital medical data in China

BMC Cancer ◽

10.1186/s12885-021-07946-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ruofei Du ◽

Xin Wang ◽

Lixia Ma ◽

Leon M. Larcher ◽

Han Tang ◽

...

Keyword(s):

Targeted Therapy ◽

Cancer Patients ◽

Adverse Reactions ◽

Cox Regression ◽

Target Therapy ◽

Skin Damage ◽

Data Set ◽

Patients With Cancer ◽

Number Of Patients ◽

Significant Difference

Abstract Background The adverse reactions (ADRs) of targeted therapy were closely associated with treatment response, clinical outcome, quality of life (QoL) of patients with cancer. However, few studies presented the correlation between ADRs of targeted therapy and treatment effects among cancer patients. This study was to explore the characteristics of ADRs with targeted therapy and the prognosis of cancer patients based on the clinical data. Methods A retrospective secondary data analysis was conducted within an ADR data set including 2703 patients with targeted therapy from three Henan medical centers of China between January 2018 and December 2019. The significance was evaluated with chi-square test between groups with or without ADRs. Univariate and multivariate logistic regression with backward stepwise method were applied to assess the difference of pathological characteristics in patients with cancer. Using the univariate Cox regression method, the actuarial probability of overall survival was performed to compare the clinical outcomes between these two groups. Results A total of 485 patients were enrolled in this study. Of all patients, 61.0% (n = 296) occurred ADRs including skin damage, fatigue, mucosal damage, hypertension and gastrointestinal discomfort as the top 5 complications during the target therapy. And 62.1% of ADRs were mild to moderate, more than half of the ADRs occurred within one month, 68.6% ADRs lasted more than one month. Older patients (P = 0.022) and patients with lower education level (P = 0.036), more than 2 comorbidities (P = 0.021), longer medication time (P = 0.022), drug combination (P = 0.033) and intravenous administration (P = 0.019) were more likely to have ADRs. Those with ADRs were more likely to stop taking (P = 0.000), change (P = 0.000), adjust (P = 0.000), or not take the medicine on time (P = 0.000). The number of patients with recurrence (P = 0.000) and metastasis (P = 0.006) were statistically significant difference between ADRs and non-ADRs group. And the patients were significantly poor prognosis in ADRs groups compared with non-ADRs group. Conclusion The high incidence of ADRs would affect the treatment and prognosis of patients with cancer. We should pay more attention to these ADRs and develop effective management strategies.

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