Bayesian analysis of direct and maternal effects for birthweight in Iranian buffaloes using Gibbs sampling

2016 ◽  
Vol 56 (5) ◽  
pp. 859 ◽  
Author(s):  
Navid Ghavi Hossein-Zadeh
Keyword(s):  
Animal Model ◽  
Gibbs Sampling ◽  
Maternal Effects ◽  
Threshold Model ◽  
Genetic Selection ◽  
Genetic Effects ◽  
Phenotypic Variance ◽  
Environmental Variance ◽  
Selection Decisions ◽  
Estimate Variance

Calving records from April 1994 to March 2010 comprising 8570 calving events from the first three parities of 734 buffalo herds of Iran were analysed using a linear animal model to estimate variance components and heritability for birthweight. A linear animal model including direct and maternal genetic effects with covariance between them and maternal permanent environmental effect was implemented by Gibbs sampling methodology. A single Gibbs sampling chain with 500 000 rounds was generated by the Threshold Model program. Posterior means of direct and maternal heritabilities and repeatability for birthweight were 0.21, 0.15 and 0.23, respectively. Estimate of correlation between direct and maternal genetic effects for birthweight was –0.71. Also, the ratio of permanent environmental variance to phenotypic variance was 0.02. Along with the direct genetic effects, the contribution of maternal effects to the phenotypic variance of birthweight may provide producers with information to optimally use the reported estimates when making selection decisions. The results of this study indicated that exploitable genetic variation observed for birthweight could be considered in designing future selection programs for Iranian buffaloes and improvement in birthweight could be attained by genetic selection.

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

2017 ◽  
Vol 57 (2) ◽  
pp. 216 ◽  
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.

scholarly journals A Comparison of Twin Birthweight Data From Australia, the Netherlands, the United States, Japan, and South Korea: Are Genetic and Environmental Variations in Birthweight Similar in Caucasians and East Asians?

2005 ◽  
Vol 8 (6) ◽  
pp. 638-648 ◽  
Author(s):  
Yoon-Mi Hur ◽  
Michelle Luciano ◽  
Nicholas G. Martin ◽  
Dorret I. Boomsma ◽  
William G. Iacono ◽  
...  
Keyword(s):  
United States ◽  
The Netherlands ◽  
South Korea ◽  
Maternal Effects ◽  
The United States ◽  
Phenotypic Variance ◽  
Physical And Mental Health ◽  
East Asians ◽  
Environmental Variance ◽  
Males And Females

AbstractBirthweight has implications for physical and mental health in later life. Using data from Caucasian twins collected in Australia, the Netherlands and the United States, and from East Asian twins collected in Japan and South Korea, we compared the total phenotypic, genetic and environmental variances of birthweight between Caucasians and East Asians. Model-fitting analyses yielded four major findings. First, for both males and females, the total phenotypic variances of birthweight were about 45% larger in Caucasians than in East Asians. The larger phenotypic variances were mainly attributable to a greater shared environmental variance of birth- weight in Caucasians (ranging from 62% to 67% of variance) than Asians (48% to 53%). Second, the genetic variance of birthweight was equal in Caucasians and East Asians for both males and females, explaining a maximum of 17% of variance. Third, small variations in total phenotypic variances of birthweight within Caucasians and within East Asians were mainly due to differences in nonshared environmental variances. We speculate that maternal effects (both genetic and environmental) explain the large shared environmental variance in birthweight and may account for the differences in phenotypic variance in birthweight between Caucasians and East Asians. Recent molecular findings and specific environmental factors that are subsumed by maternal effects are discussed.

scholarly journals Genetic parameters for direct and maternal effects on growth traits of sheep

2012 ◽  
Vol 55 (6) ◽  
pp. 603-611 ◽  
Author(s):  
F. Ghafouri-Kesbi ◽  
H. Baneh
Keyword(s):  
Maternal Effects ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Selection Criterion ◽  
Information Criterion ◽  
Phenotypic Variance ◽  
Environmental Variance ◽  
Daily Gain

Abstract. The aim of the present study was to estimate (co)variance components and corresponding genetic parameters for birth weight (BW), weaning weight (WW), 6-month weight (W6), 9-month weight (W9), average daily gain from birth to weaning (WWDG), average daily gain from weaning to 6 months (W6DG) and average daily gain from 6 months to 9 months (W9DG) for a nucleus flock of Iranian Makooei sheep. Genetic parameters were estimated by REML procedure fitting six animal models including various combinations of maternal effects. The Akaike information criterion (AIC) was used to determine the most appropriate model. Estimates of direct heritability (h2) ranged from 0.13 (W6DG) to 0.32 (BW). Maternal effects were found to be important in the growth performance of the Makooei sheep, indicating the necessity of including maternal effects in the model to obtain accurate estimates of direct heritability. Estimates of maternal heritability (m2) ranged from 0.05 (W6) to 0.16 (WWDG) and the estimates of proportion of maternal permanent environmental variance to phenotypic variance (c2) were in the range between 0.05 (BW) and 0.10 (W6). Direct additive genetic correlations were positive in all cases and ranged from 0.00 (BW/W9DG) to 0.99 (WW/WWDG). Phenotypic correlations showed a broad range from −0.27 (WW/W9DG) to 0.99 (WW/WWDG). Estimates of genetic parameters showed that genetic improvement through selection programs is possible. WW would be a suitable selection criterion since it has acceptable direct heritability and relatively high genetic correlation with other traits.

scholarly journals Religious Attendance Moderates the Environmental Effect on Prosocial Behavior in Nigerian Adolescents

2019 ◽  
Vol 22 (1) ◽  
pp. 42-47 ◽  
Author(s):  
Yoon-Mi Hur ◽  
Hoe-Uk Jeong ◽  
Frances Ajose ◽  
Ariel Knafo-Noam
Keyword(s):  
Prosocial Behavior ◽  
Environmental Influences ◽  
Model Fitting ◽  
Interaction Model ◽  
Genetic Effects ◽  
Religious Attendance ◽  
Phenotypic Correlation ◽  
Phenotypic Variance ◽  
Environmental Variance ◽  
Frequent Attenders

AbstractThere is a growing body of literature linking religious attendance to prosocial behavior (PB). The main purposes of the present study were to estimate genetic and environmental influences on the frequency of religious attendance (FRA) and to explore whether and how FRA moderates genetic and/or environmental influences on PB. As part of the Nigerian Twin and Sibling Study, 2860 (280 monozygotic male, 417 monozygotic female, 544 dizygotic male, 699 dizygotic female, and 920 opposite-sex dizygotic) twins (mean age = 14.2 years; SD = 1.7 years; age range = 12–18 years) completed a questionnaire regarding FRA and a PB scale. Similar to the findings from western twin samples, FRA showed substantial shared environmental influences of 74% (95% CI = 69%, 78%), with absence of genetic effects. The phenotypic correlation between FRA and PB was modest but positive and significant (r = .12; p < .01), suggesting that PB is higher among more frequent attenders than among less frequent attenders. The results of gene–environment (G × E) interaction model-fitting analysis revealed that FRA changed individual environmental experiences rather than genetic effects on PB such that while genetic variance was stable, non-shared environmental variance declined, leading the total phenotypic variance of PB to decrease with increasing levels of religious attendance.

scholarly journals Selection for feed efficiency using the social effects animal model in growing Duroc pigs: evaluation by simulation

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
William Herrera-Cáceres ◽  
Juan Pablo Sánchez
Keyword(s):  
Animal Model ◽  
Direct Reduction ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Genetic Effects ◽  
Social Effects ◽  
High Rate ◽  
Phenotypic Variance ◽  
Feed Conversion ◽  
The Social

Abstract Background Traits recorded on animals that are raised in groups can be analysed with the social effects animal model (SAM). For multiple traits, this model specifies the genetic correlation structure more completely than the animal model (AM). Our hypothesis was that by using the SAM for genetic evaluation of average daily gain (ADG) and backfat thickness (BF), a high rate of improvement in feed conversion ratio (FCR) might be achieved, since unfavourable genetic correlations between ADG and BF reported in a Duroc pig line could be partially avoided. We estimated genetic and non-genetic correlations between BF, ADG and FCR on 1144 pigs using Bayesian methods considering the SAM; and responses to selection indexes that combine estimates of indirect (IGE) and direct (DGE) genetic effects for ADG and BF by stochastic simulation. Results Estimates of the ratio of the variance of DGE to the phenotypic variance were 0.31, 0.39 and 0.25 and those of the total genetic variance to the phenotypic variance were 0.63, 0.74 and 0.93 for ADG, BF and FCR, respectively. In spite of this, when the SAM was used to generate data and for the genetic evaluations, the average economic response was worse than that obtained when BV predictions from the AM were considered. The achieved economic response was due to a direct reduction in BF and not to an improvement in FCR. Conclusions Our results show that although social genetic effects play an important role in the traits studied, their proper consideration in pig breeding programs to improve FCR indirectly is still difficult. The correlations between IGE and DGE that could help to overcome the unfavourable genetic correlations between DGE did not reach sufficiently high magnitudes; also, the genetic parameters estimates from the SAM have large errors. These two factors penalize the average response under the SAM compared to the AM.

Genetic and maternal effects on juvenile survival and fitness-related traits in three populations of Atlantic salmon

2015 ◽  
Vol 72 (5) ◽  
pp. 751-758 ◽  
Author(s):  
Aimee Lee S. Houde ◽  
Craig A. Black ◽  
Chris C. Wilson ◽  
Trevor E. Pitcher ◽  
Bryan D. Neff
Keyword(s):  
Atlantic Salmon ◽  
Maternal Effects ◽  
Environmental Effects ◽  
Genetic Architecture ◽  
Life Stage ◽  
Random Mating ◽  
Genetic Effects ◽  
Phenotypic Variance ◽  
Offspring Performance ◽  
Additive Genetic Effects

Although studies addressing natural selection have primarily focused on additive genetic effects because of their direct relationship with responses to selection, nonadditive genetic and maternal effects can also significantly influence phenotypes. We partitioned the phenotypic variance of survival and fitness-related traits in juvenile Atlantic salmon (Salmo salar) from three allopatric populations (LaHave, Sebago, and Saint-Jean) into additive genetic, nonadditive genetic, and maternal environmental effects using a full-factorial breeding design. We also modelled the potential increase in offspring performance if nonrandom mating (e.g., mate choice) is considered instead of random mating. The three populations exhibited significant differences in trait values as well as the genetic architecture of the traits. Nevertheless, nonadditive genetic and maternal environmental effects tended to be larger than the additive genetic effects. There was also a shift from maternal environmental to genetic effects during development in two of the populations. That is, maternal environmental effects were larger at early (egg and alevin) life stages, whereas nonadditive effects were larger at the later (fry) life stage. The amount of additive genetic effects was small, suggesting the traits will respond slowly to selection. We discuss how different maternal environmental effects across years may influence the genetic architecture of offspring traits.

Egg weight and reproduction traits in laying hens: estimation of direct and maternal genetic effects using Bayesian approach via Gibbs sampling

2000 ◽  
Vol 70 (1) ◽  
pp. 9-16 ◽  
Author(s):  
A. Sewalem ◽  
K. Johansson
Keyword(s):  
Gibbs Sampling ◽  
Maternal Effects ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Genetic Effects ◽  
Egg Weight ◽  
Zygote Development ◽  
Reproduction Traits ◽  
Female Reproductive Traits ◽  
Weight Trait

AbstractFertility, generally considered as a trait of the two parents, is perhaps best defined as the interaction between the male and female gametes in the production of a viable zygote. Although zygote development and hatchability are traits of the embryo influenced by maternal effects, in most previous studies they have been considered to be female reproductive traits. The aim of this work was to study the influence of sire on fertility and hatchability traits and to estimate the (co)variance components of direct and maternal genetic effects under a Bayesian setting via Gibbs sampling. We measured the fertility of 6396 eggs and the hatchability of 5393 embryos on an individual basis. In addition, egg weight from 42 to 63 weeks of age (EW63) was recorded on an individual egg basis. The sire accounted for a significant amount of the variation infertility and hatchability. For direct heritability, the marginal posterior mean, for fertility and hatchability were almost equal (0·24). The maternal heritabilities for fertility and hatchability were 0·20 and 0·18, respectively. The direct heritability value for the egg weight trait was high. The direct-direct genetic correlation between egg weight and hatchability was negative and significant. The genetic correlations between the direct effect of the egg weight trait and maternal effects for fertility and hatchability were low, with variable signs, and were not significant. On the other hand, significant negative genetic correlations between direct and maternal effects of fertility and hatchability were obtained (the posterior means were –0·56 for FE and –0·55 for HC).

scholarly journals Model comparisons and genetic parameter estimates of growth and the Kleiber ratio in Shal sheep

2013 ◽  
Vol 56 (1) ◽  
pp. 264-275 ◽  
Author(s):  
H. Mohammadi ◽  
M. M. Shahrebabak ◽  
H. M. Shahrebabak ◽  
A. Bahrami ◽  
M. Dorostkar
Keyword(s):  
Maternal Effects ◽  
Growth Traits ◽  
Genetic Parameter ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Genetic Effects ◽  
Parameter Estimates ◽  
Phenotypic Variance ◽  
Kleiber Ratio ◽  
Lamb Growth

Abstract. Genetic and phenotypic parameters were estimated for lamb growth traits for the Shal sheep using an animal model. Data on lamb growth performance were extracted from available performance records at the Shal sheep Station in Qazvin, Iran. Studied traits were body weights of lambs at birth (BW), at 3 months of age as weaning weight (WW), 6 months weight (6MW), 9 months weight (9MW), yearling weight (YW), average daily gain from birth to weaning (ADG) and Kleiber ratio from birth to weaning (KR). Significant random effects for each trait were determined by fitting additive direct genetic effects, additive maternal effects, covariance between additive direct and additive maternal effects, maternal permanent environmental and maternal temporary environmental (common litter) effects under twelve animal models. Univariate analyses were carried out under the most appropriate model, determined by AIC test. Direct heritability estimates for BW, WW, ADG, KR, 6MW, 9MW and YW were 0.13, 0.19, 0.18, 0.05, 0.16, 0.18 and 0.19, respectively. Maternal additive genetic effects were fitted only for BW and WW; corresponding estimates of 0.12 and 0.10 obtained for maternal heritability of BW and WW, respectively. Maternal permanent environmental effects have low contribution in expression of KR and lead to estimates of 0.06 and 0.06 for maternal permanent environmental variance as a proportion of phenotypic variance (c2) of these traits, respectively. All pre-weaning traits, except KR, were affected by litter effects. The magnitude of ratio of common litter variance to phenotypic variance (l2) was 0.05, 0.12 and 0.14 for BW, WW and ADG, respectively. Direct genetic correlations were positive and ranged from 0.09 for KR-YW to 0.80 for WW-ADG; phenotypic ones ranged from 0.18 for KR-YW to 0.87 for WW-ADG.

scholarly journals The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults

Metabolites ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 6
Author(s):  
Eun Pyo Hong ◽  
Seong Gu Heo ◽  
Ji Wan Park
Keyword(s):  
Type 2 Diabetes ◽  
Cardiovascular Disease ◽  
Risk Prediction ◽  
Linear Mixed Model ◽  
Threshold Model ◽  
Snp Markers ◽  
Polygenic Risk Score ◽  
Phenotypic Variance ◽  
Prediction Approach

Personalized risk prediction for diabetic cardiovascular disease (DCVD) is at the core of precision medicine in type 2 diabetes (T2D). We first identified three marker sets consisting of 15, 47, and 231 tagging single nucleotide polymorphisms (tSNPs) associated with DCVD using a linear mixed model in 2378 T2D patients obtained from four population-based Korean cohorts. Using the genetic variants with even modest effects on phenotypic variance, we observed improved risk stratification accuracy beyond traditional risk factors (AUC, 0.63 to 0.97). With a cutoff point of 0.21, the discrete genetic liability threshold model consisting of 231 SNPs (GLT231) correctly classified 87.7% of 2378 T2D patients as high or low risk of DCVD. For the same set of SNP markers, the GLT and polygenic risk score (PRS) models showed similar predictive performance, and we observed consistency between the GLT and PRS models in that the model based on a larger number of SNP markers showed much-improved predictability. In silico gene expression analysis, additional information was provided on the functional role of the genes identified in this study. In particular, HDAC4, CDKN2B, CELSR2, and MRAS appear to be major hubs in the functional gene network for DCVD. The proposed risk prediction approach based on the liability threshold model may help identify T2D patients at high CVD risk in East Asian populations with further external validations.

130 Utilization of Nutrack to Assess Variance Components and Heritability of Activity Traits

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 17-17
Author(s):  
Lexi M Ostrand ◽  
Melanie D Trenhaile-Grannemann ◽  
Garrett See ◽  
Ty B Schmidt ◽  
Eric Psota ◽  
...  
Keyword(s):  
Animal Model ◽  
Mixed Models ◽  
Variance Components ◽  
Average Speed ◽  
Genetic Variances ◽  
Sow Longevity ◽  
Selection Decisions ◽  
Recorded Data ◽  
Residual Variances ◽  
And Behavior

Abstract Overall activity and behavior are integral components of sows remaining productive in the herd. This investigation studied overall activity of group housed replacement gilts and the heritability of various activity traits. Beginning around 20 wk of age, video recorded data of approximately 75 gilts/group for a total of 2,378 gilts over 32 groups was collected for 7 consecutive d using the NUtrack System, which tracks distance travelled (m), avg speed (m/s), angle rotated (degrees), and time standing (s), sitting (s), eating (s), and laying (s). The recorded phenotypes were standardized to the distribution observed within a pen for each group. The final values used for analysis were the average daily standardized values. Data were analyzed using mixed models (RStudio V 1.2.5033) including effects of sire, dam, dam’s sire and dam, dam’s grandsire and granddam, farrowing group, barn, pen, and on-test date. Sire had an effect on every activity trait P &lt; 0.001), and dam had an effect on average speed (P &lt; 0.001). The dam’s sire had an effect on all activity traits (P &lt; 0.001) and the dam’s grandsire had an effect on average speed (P &lt; 0.001). Heritabilities and variance components of activity traits were estimated in ASReml 4 using an animal model with a two-generation pedigree. Genetic variances are 0.17 +/- 0.029, 0.19 +/- 0.034, and 0.11 +/- 0.024, residual variances are 0.37 +/- 0.023, 0.41 +/- 0.027, and 0.41 +/- 0.022, phenotypic variances are 0.54 +/- 0.018, 0.60 +/- 0.020, and 0.52 +/- 0.016, and heritabilities are 0.32 +/- 0.048, 0.32 +/- 0.049, and 0.21 +/- 0.044 for average speed, distance, and lie respectively. NUtrack offers potential to aid in selection decisions. Given the results presented herein, continued investigation into these activity traits and their association with sow longevity is warranted.

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