scholarly journals Reconstruction of networks with direct and indirect genetic effects

2019 ◽  
Author(s):  
Willem Kruijer ◽  
Pariya Behrouzi ◽  
Daniela Bustos-Korts ◽  
María Xosé Rodríguez-Álvarez ◽  
Seyed Mahdi Mahmoudi ◽  
...  
Keyword(s):  
Causal Inference ◽  
Indirect Effects ◽  
Fixed Effects ◽  
Genetic Variance ◽  
Mixed Model ◽  
R Package ◽  
Genetic Effects ◽  
Phenotypic Trait ◽  
Individual Plant ◽  
Functional Relationships

ABSTRACTGenetic variance of a phenotypic trait can originate from direct genetic effects, or from indirect effects, i.e., through genetic effects on other traits, affecting the trait of interest. This distinction is often of great importance, for example when trying to improve crop yield and simultaneously controlling plant height. As suggested by Sewall Wright, assessing contributions of direct and indirect effects requires knowledge of (1) the presence or absence of direct genetic effects on each trait, and (2) the functional relationships between the traits. Because experimental validation of such relationships is often unfeasible, it is increasingly common to reconstruct them using causal inference methods. However, most of the current methods require all genetic variance to be explained by a small number of QTLs with fixed effects. Only few authors considered the ‘missing heritability’ case, where contributions of many undetectable QTLs are modelled with random effects. Usually, these are treated as nuisance terms, that need to be eliminated by taking residuals from a multi-trait mixed model (MTM). But fitting such MTM is challenging, and it is impossible to infer the presence of direct genetic effects. Here we propose an alternative strategy, where genetic effects are formally included in the graph. This has important advantages: (1) genetic effects can be directly incorporated in causal inference, implemented via our PCgen algorithm, which can analyze many more traits and (2) we can test the existence of direct genetic effects and improve the orientation of edges between traits. Finally, we show that reconstruction is much more accurate if individual plant or plot data are used, instead of genotypic means. We have implemented the PCgen-algorithm in the R-package pcgen.

scholarly journals Reconstruction of Networks with Direct and Indirect Genetic Effects

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 781-807 ◽  
Author(s):  
Willem Kruijer ◽  
Pariya Behrouzi ◽  
Daniela Bustos-Korts ◽  
María Xosé Rodríguez-Álvarez ◽  
Seyed Mahdi Mahmoudi ◽  
...  
Keyword(s):  
Causal Inference ◽  
Indirect Effects ◽  
Fixed Effects ◽  
Genetic Variance ◽  
Mixed Model ◽  
Control Plant ◽  
Genetic Effects ◽  
Phenotypic Trait ◽  
Individual Plant ◽  
Functional Relationships

Genetic variance of a phenotypic trait can originate from direct genetic effects, or from indirect effects, i.e., through genetic effects on other traits, affecting the trait of interest. This distinction is often of great importance, for example, when trying to improve crop yield and simultaneously control plant height. As suggested by Sewall Wright, assessing contributions of direct and indirect effects requires knowledge of (1) the presence or absence of direct genetic effects on each trait, and (2) the functional relationships between the traits. Because experimental validation of such relationships is often unfeasible, it is increasingly common to reconstruct them using causal inference methods. However, most current methods require all genetic variance to be explained by a small number of quantitative trait loci (QTL) with fixed effects. Only a few authors have considered the “missing heritability” case, where contributions of many undetectable QTL are modeled with random effects. Usually, these are treated as nuisance terms that need to be eliminated by taking residuals from a multi-trait mixed model (MTM). But fitting such an MTM is challenging, and it is impossible to infer the presence of direct genetic effects. Here, we propose an alternative strategy, where genetic effects are formally included in the graph. This has important advantages: (1) genetic effects can be directly incorporated in causal inference, implemented via our PCgen algorithm, which can analyze many more traits; and (2) we can test the existence of direct genetic effects, and improve the orientation of edges between traits. Finally, we show that reconstruction is much more accurate if individual plant or plot data are used, instead of genotypic means. We have implemented the PCgen-algorithm in the R-package pcgen.

scholarly journals Metabolic Adaptations to Dynamic Energy Requirements during Lactation and Pregnancy in Dairy Cows with Varying Proportions of Holstein and Simmental Breed

Proceedings ◽  
2020 ◽  
Vol 73 (1) ◽  
pp. 9
Author(s):  
Deise Aline Knob ◽  
André Thaler Neto ◽  
Helen Schweizer ◽  
Anna Weigand ◽  
Roberto Kappes ◽  
...  
Keyword(s):  
Energy Balance ◽  
Dairy Cows ◽  
Fixed Effects ◽  
Mixed Model ◽  
Negative Energy ◽  
Negative Energy Balance ◽  
Repeated Measure ◽  
Holstein Cows ◽  
Mixed Model Analysis ◽  
Genetic Groups

Depending on the breed or crossbreed line, cows have to cope with a more or less severe negative energy balance during the period of high milk yields in early lactation, which can be detected by beta-hydroxybutyrate (BHBA) and non-esterified fatty acids (NEFAs) in blood. Preventing cows from undergoing a severe negative energy balance by breeding and/or feeding measures is likely to be supported by the public and may help to improve the sustainability of milk production. The aim was to compare BHBA and NEFA concentrations in the blood of Holstein and Simmental cows and their crosses during the prepartum period until the end of lactation. In total, 164 cows formed five genetic groups according to their theoretic proportion of Holstein and Simmental genes as follows: Holstein (100% Holstein; n = 9), R1-Hol (51–99% Holstein; n = 30), F1 crossbreds (50% Holstein, 50% Simmental; n = 17), R1-Sim (1–49% Holstein; n = 81) and Simmental (100% Simmental; n = 27). NEFA and BHBA were evaluated once a week between April 2018 and August 2019. A mixed model analysis with fixed effects breed, week (relative to calving), the interaction of breed and week, parity, calving year, calving season, milking season, and the repeated measure effect on cows was used. Holstein cows had higher NEFAs (0.196 ± 0.013 mmol/L), and Simmental cows had the lowest NEFA concentrations (0.147 ± 0.008 mmol/L, p = 0.03). R1-Sim, F1 and R1-Hol cows had intermediate values (0.166 ± 0.005, 0.165 ± 0.010, 0.162 ± 0.008 mmol/L; respectively). The highest NEFA value was found in the first week after calving (0.49 ± 0.013 mmol/L). BHBA did not differ among genetic groups (p = 0.1007). There was, however, an interaction between the genetic group and week (p = 0.03). While Simmental, R1-Sim and F1 cows had the highest BHBA value, the second week after calving (0.92 ± 0.07 and 1.05 ± 0.04, and 1.10 ± 0.10 mmol/L, respectively), R1-Hol and Holstein cows showed the BHBA peak at the fourth week after calving (1.16 ± 0.07 and 1.36 ± 0.12 mmol/L, respectively). Unexpectedly, Holstein cows had a high BHBA peak again at week 34 after calving (1.68 ± 0.21 mmol/L). The genetic composition of the cows affects NEFA and BHBA. Simmental and R1-Sim cows mobilize fewer body reserves after calving. Therefore, dairy cows with higher degrees of Simmental origin might be more sustainable in comparison with Holstein genetics in the present study.

PSV-11 The effects of pelleting and extrusion on nutrient composition and protein quality measurements in a variety Canadian pulses

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 302-302
Author(s):  
Cara Cargo-Froom ◽  
Anna-Kate Shoveller ◽  
Daniel A Columbus ◽  
Chris Marinangeli ◽  
Elijah Kiarie ◽  
...  
Keyword(s):  
Protein Content ◽  
Faba Bean ◽  
Fixed Effects ◽  
Crude Protein ◽  
Mixed Model ◽  
Protein Quality ◽  
Positive Impact ◽  
Nutrient Composition ◽  
Crude Protein Content ◽  
Quality Measurements

Abstract Alternative forms of protein are an important focus in nutrition. This study sought to compare the effects of pelleting and extrusion on nutrient composition and protein quality measurements of Canadian pulses. Pulses used for the study included: 2 pea variety (Amarillo and dunn), lentils, chickpeas, and faba bean. Ingredients were ground through a 10/64” or a 2/64” screen to create a coarse and fine ground product, respectively. Both coarse and fine ground ingredients were pelleted at 60–65, 70–75, and 80–85 C0. Fine ground ingredients were extruded at three different temperatures (110, 130, 150 C0) and two moisture levels (18 and 22%). Samples were collected for all runs at the beginning, middle, and end of each run for both pelleted and extruded samples. Samples were analyzed for proximate analysis, amino acids including lysinoalanine, total and damaged starch, and total dietary fibre (including insoluble and soluble). Data were analyzed using a mixed model via proc glimmix in SAS, where ingredient, process, grind, temperature, and extrusion moisture were treated as fixed effects with different interactions selected based on model investigated. Crude protein content of whole pulses was highest in faba bean and lowest in the Amarillo pea, with faba bean protein content significantly higher than all other pulses, and lentil protein content significantly higher than Amarillo peas (P < 0.05). All pelleting temperatures, nested within grind, significantly increased crude protein content of all pulses compared to whole pulses (P < 0.05). All extrusion moistures significantly increased crude protein content of all pulses compared to whole pulses (P < 0.05) and moisture/temperature interactions were significantly higher for all pulses compared to whole pulses (P < 0.05). Amino acid comparisons produced similar significant results. This suggests that pelleting and extrusion processing can have a positive impact on protein content of pulses and protein quality measurements in pulses.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P < 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

Evaluation of genetic markers for litter size in Meishan synthetic and Large White pigs

1996 ◽  
Vol 1996 ◽  
pp. 18-18
Author(s):  
O.I. Southwood ◽  
S. Hoste ◽  
T.H. Short ◽  
A.J. Mileham ◽  
D. Cuthbert-Heavens
Keyword(s):  
Litter Size ◽  
Fixed Effects ◽  
Oestrogen Receptor ◽  
Mixed Model ◽  
Receptor Gene ◽  
Large White ◽  
Service Type ◽  
Sib Families ◽  
Natural Service ◽  
Size Data

A significant relationship between the oestrogen receptor gene (ESR) and litter size has been detected in USA populations of Large White and a synthetic comprising 50% Meishan (Rothschild et al., 1995). Animals carrying two copies of the favourable allele (B) had an extra pig born per litter than those that did not have the allele. This paper reports on results observed in a UK 50% Meishan synthetic and four UK Large White lines.Litter size data from 50% Meishan synthetic (L93) full-sib females where more than one ESR genotype was segregating. Data were analysed using a mixed model with full relationships and including the fixed effects of season of farrowing, parity, ESR genotype (AA, AB or BB) and service type (AI or natural service). Heritiability and permanent environmental effects for litter size were assumed as 0.09 and 0.11, repectively. A total of 27 full-sib families were represented and included 62 sows and 139 litter records. Hypothesis testing used the option in PEST under a mixed model (Groeneveld et al., 1991).

scholarly journals Goats Given Transdermal Flunixin Meglumine Displayed Less Pain Behavior After Castration

2020 ◽  
Author(s):  
Amanda Lee ◽  
Meggan Graves ◽  
Andrea Lear ◽  
Sherry Cox ◽  
Marc Caldwell ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Body Position ◽  
Random Effect ◽  
Pain Behavior ◽  
Bout Duration ◽  
Flunixin Meglumine ◽  
Meat Goats ◽  
Transdermal Application

AbstractPain management should be utilized with castration to reduce physiological and behavioral changes. Transdermal application of drugs require less animal management and fewer labor risks, which can occur with oral administration or injections. The objective was to determine the effects of transdermal flunixin meglumine on meat goats’ behavior post-castration. Male goats (N = 18; mean body weight ± standard deviation: 26.4 ± 1.6 kg) were housed individually in pens and randomly assigned to 1 of 3 treatments: (1) castrated, dosed with transdermal flunixin meglumine; (2) castrated, dosed with transdermal placebo; and (3) sham castrated, dosed with transdermal flunixin meglumine. Body position, rumination, and head- pressing were observed for 1 h ± 10 minutes twice daily on days −1, 0, 1, 2, and 5 around castration. Each goat was observed once every 5-minutes (scan samples) and reported as percentage of observations. Accelerometers were used to measure standing, lying, and laterality (total time, bouts, and bout duration). A linear mixed model was conducted using GLIMMIX. Fixed effects of treatment, day relative to castration, and treatment*day relative to castration and random effect of date and goat nested within treatment were included. Treatment 1 goats (32.7 ± 2.8%) and treatment 2 goats (32.5 ± 2.8%) ruminated less than treatment 3 goats (47.4 ± 2.8%, P = 0.0012). Head pressing was greater on day of castration in treatment 2 goats (P < 0.001). Standing bout duration was greatest in treatment 2 goats on day 1 post-castration (P < 0.001). Lying bout duration was greatest in treatment 2 goats on day 1 post-castration compared to treatment 1 and treatment 3 goats(P < 0.001). Transdermal flunixin meglumine improved goats’ fluidity of movement post-castration and decreased head pressing, indicating a mitigation of pain behavior.

scholarly journals The Impact of Misspecified Random Effect Distribution in a Weibull Regression Mixed Model

Stats ◽  
2018 ◽  
Vol 1 (1) ◽  
pp. 48-76
Author(s):  
Freddy Hernández ◽  
Viviana Giampaoli
Keyword(s):  
Weibull Distribution ◽  
Random Effects ◽  
Mixed Models ◽  
Fixed Effects ◽  
Mixed Model ◽  
Random Effect ◽  
Estimation Procedure ◽  
Weibull Regression ◽  
Two Parameters ◽  
The Impact

Mixed models are useful tools for analyzing clustered and longitudinal data. These models assume that random effects are normally distributed. However, this may be unrealistic or restrictive when representing information of the data. Several papers have been published to quantify the impacts of misspecification of the shape of the random effects in mixed models. Notably, these studies primarily concentrated their efforts on models with response variables that have normal, logistic and Poisson distributions, and the results were not conclusive. As such, we investigated the misspecification of the shape of the random effects in a Weibull regression mixed model with random intercepts in the two parameters of the Weibull distribution. Through an extensive simulation study considering six random effect distributions and assuming normality for the random effects in the estimation procedure, we found an impact of misspecification on the estimations of the fixed effects associated with the second parameter σ of the Weibull distribution. Additionally, the variance components of the model were also affected by the misspecification.

scholarly journals PSXI-32 Potential improvements in milk production of mid lactating Holstein cows through changes in the defoliation intensity on a mixed pasture

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 384-385
Author(s):  
Oliver Fast Hinz ◽  
Pablo Chilibroste ◽  
Gabriel Menegazzi ◽  
Matías Oborsky ◽  
Pablo Soca ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Festuca Arundinacea ◽  
Fixed Effects ◽  
Mixed Model ◽  
Body Condition Score ◽  
Random Effect ◽  
Milk Composition ◽  
Control Treatment ◽  
Condition Score

Abstract An experiment was performed to study the effect of two contrasting defoliation intensities of a fescue based pasture on milk production of 24 mid lactating multiparous cows. The animals were blocked according to parity, body weight (587 ± 42 kg), body condition score (2.77 ± 0.16) and calving date, and were randomly allocated to one of these two treatments: lax treatment (TL) 12 cm and control treatment (TC) 6 cm, with four replications. It was used a second-year pasture of Festuca arundinacea and Lotus corniculatus (2530 ± 180 kgDM/ha), divided into eight plots of 0.3 ha. Each plot was grazed by three cows during as many days as necessary until the defoliation height of each treatment was achieved. This would be determined by daily measures of the pasture height. Animals had one grazing session from 8:00 to 16:00 h. Both treatments received 7.5 kgDM of supplementation (17% Crude Protein; 2.81 Mcal/kgDM) in individual troughs. The cows were milked twice a day (05:00 and 17:00 h). Milk production was registered daily while milk composition was measured at the beginning and at the end of the experiment (samples from two consecutive milking). For milk yield results, a mixed model was used (Glimmix procedure, SAS 9.2, 2010) to analyse with treatment, day and their interaction as fixed effects and block as a random effect. While milk composition was analysed with only treatment as fixed effect. Milk yield was greater for TL than TC, while there was no difference in milk composition between treatments (Table 1). There is a significant effect of the day and an interaction between treatment and day (Figure 1), as difference was greater for TL to the end of the grazing period. This leads to the conclusion that it is possible to improve the milk production through less defoliation intensity.

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