Inclusion Of Maternal Effects Research Articles

Selecting an appropriate statistical model for estimating genetic parameters: A case study of pig maternal breeds in Czechia

A three-trait statistical model was designed for backfat thickness (BFT) and loin eye muscle depth (LMD) with accompanying variable average daily gain (ADG). Data from 82,507 Czech Large White and 37,556 Czech Landrace pigs were collected during on-farm performance testing from 2013 to 2022. Several animal models were tested with different combinations of effects and complexity. Model performance was evaluated by the linear regression (LR) method and predictivity. In Czech Large White, the preferred model comprised fixed effects of sex, birth year, herd, and ultrasound device, as well as random effects of herd-year-season (HYS), litter, and animal. In Czech Landrace, HYS was treated as fixed instead. The inclusion of maternal effects was not supported due to questionable impact on the main statistics. The selected model yielded mean absolute bias of 0.11 and 0.19, mean determination of 0.39 and 0.21, mean population accuracy of 0.36 and 0.31, and mean predictivity of 0.13 and 0.08 in Large White and Landrace, respectively. Heritability estimates were overall lower than those reported by other authors: 0.23, 0.10, and 0.10 in Large White and 0.26, 0.10, and 0.09 in Landrace for ADG, BFT, and LMD, respectively. Genetic correlations, on the other hand, reached relatively high values: 0.61, 0.61, and 0.66 in Large White and 0.71, 0.92, and 0.70 in Landrace for ADG-BFT, ADG-LMD, and BFT-LMD, respectively.

Dominance genetic and maternal effects for genetic evaluation of egg production traits in dual-purpose chickens

ABSTRACT1. A study was conducted to study direct dominance genetic and maternal effects on genetic evaluation of production traits in dual-purpose chickens. The data set consisted of records of body weight and egg production of 49 749 Mazandaran fowls from 19 consecutive generations. Based on combinations of different random effects, including direct additive and dominance genetic and maternal additive genetic and environmental effects, 8 different models were compared.2. Inclusion of a maternal genetic effect in the models noticeably improved goodness of fit for all traits. Direct dominance genetic effect did not have noticeable effects on goodness of fit but simultaneous inclusion of both direct dominance and maternal additive genetic effects improved fitting criteria and accuracies of genetic parameter estimates for hatching body weight and egg production traits.3. Estimates of heritability (h2) for body weights at hatch, 8 weeks and 12 weeks of age (BW0, BW8 and BW12, respectively), age at sexual maturity (ASM), average egg weights at 28–32 weeks of laying period (AEW), egg number (EN) and egg production intensity (EI) were 0.08, 0.21, 0.22, 0.22, 0.21, 0.09 and 0.10, respectively. For BW0, BW8, BW12, ASM, AEW, EN and EI, proportion of dominance genetic to total phenotypic variance (d2) were 0.06, 0.08, 0.01, 0.06, 0.06, 0.08 and 0.07 and maternal heritability estimates (m2) were 0.05, 0.04, 0.03, 0.13, 0.21, 0.07 and 0.03, respectively. Negligible coefficients of maternal environmental effect (c2) from 0.01 to 0.08 were estimated for all traits, other than BW0, which had an estimate of 0.30.4. Breeding values (BVs) estimated for body weights at early ages (BW0 and BW8) were considerably affected by components of the models, but almost similar BVs were estimated by different models for higher age body weight (BW12) and egg production traits (ASM, AEW, EN and EI). Generally, it could be concluded that inclusion of maternal effects (both genetic and environmental) and, to a lesser extent, direct dominance genetic effect would improve the accuracy of genetic evaluation for early age body weights in dual-purpose chickens.

Estimativas de parâmetros genéticos para características de crescimento de cordeiros mestiços Suffolk

Objetivou-se estimar os coeficientes de herdabilidade e correlação genética entre os pesos ao nascer (PN) e à desmama (PD) de cordeiros mestiços Suffolk, pertencentes a rebanho experimental. Assim, foram testados quatro modelos, os quais consideraram o efeito genético aditivo direto (Modelo 1), os efeitos genético direto e de ambiente permanente materno (Modelo 2), os efeitos aditivo direto, de ambiente permanente e genético materno (cov a,m=0) (Modelo 3), e no Modelo 4, além daqueles contemplados no Modelo 3, foi considerada cov a,m≠0. Após comparar os modelos por meio do teste de razão de verossimilhança (LRT), observou-se que o 3 foi o mais adequado, sendo que as estimativas de herdabilidade foram de baixa magnitude para PN e PD, iguais a 0,08±0,009 e 0,24±0,17, respectivamente, indicando pequena possibilidade de resposta à seleção direta. Da mesma maneira, o coeficiente de correlação genética entre estas características foi 0,43±0,39, resultado que implica pequena possibilidade de resposta correlacionada. A inclusão dos efeitos maternos é necessária para a estimação adequada de parâmetros genéticos para as características avaliadas.

Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

The crop seed is a complex organ that may be composed of the diploid embryo, the triploid endosperm and the diploid maternal tissues. According to the genetic features of seed characters, two genetic models for mapping quantitative trait loci (QTLs) of crop seed traits are proposed, with inclusion of maternal effects, embryo or endosperm effects of QTL, environmental effects and QTL-by-environment (QE) interactions. The mapping population can be generated either from double back-cross of immortalized F2 (IF2) to the two parents, from random-cross of IF2 or from selfing of IF2 population. Candidate marker intervals potentially harboring QTLs are first selected through one-dimensional scanning across the whole genome. The selected candidate marker intervals are then included in the model as cofactors to control background genetic effects on the putative QTL(s). Finally, a QTL full model is constructed and model selection is conducted to eliminate false positive QTLs. The genetic main effects of QTLs, QE interaction effects and the corresponding P-values are computed by Markov chain Monte Carlo algorithm for Gaussian mixed linear model via Gibbs sampling. Monte Carlo simulations were performed to investigate the reliability and efficiency of the proposed method. The simulation results showed that the proposed method had higher power to accurately detect simulated QTLs and properly estimated effect of these QTLs. To demonstrate the usefulness, the proposed method was used to identify the QTLs underlying fiber percentage in an upland cotton IF2 population. A computer software, QTLNetwork-Seed, was developed for QTL analysis of seed traits.

Estimates of (co)variance components for production and reproduction traits with different models in Fars native fowls

The estimates of direct and maternal genetic, in addition to maternal common environmental effects were considered for body weight at 1 day of age (BW1), body weight at 8 weeks of age (BW8), body weight at 12 weeks of age (BW12), egg weight at first day of laying (EW1), egg number (EN), mean egg weight at 28th, 30th, 32nd weeks (MEW), age at sexual maturity (ASM) and weight at sexual maturity (WSM) records on 44,390 Fars native fowls. Data were analysed with a series of 6 different single-trait animal models which included or excluded the maternal effects for all traits, using an AI-REML algorithm. For each trait, the most appropriate model was chosen based on likelihood ratio tests (LRT). Based on the most appropriate fitted models, direct heritability (h2) estimates ranged from 0.14 (BW1) to 0.64 (MEW). Both maternal genetic and common environmental effects were statistically significant for all of the studied traits except for EN. The estimates of maternal heritability (m2) ranged from 0.02 (MEW) to 0.32 (BW1), and the estimates of maternal common environmental variance as a proportion of phenotypic variance (c2) ranged from 0.02 (BW8, BW12, WSM, EW1 and MEW) to 0.25 (BW1) based on the fitted models. Correlation between direct and maternal additive genetic effects (ram) was significant for WSM, ASM, EW1 and MEW, and was negative for all of the studied traits. Overall, it was concluded that for more precise designing selection programs and increased efficiency of selection for production and reproduction traits of fowls, inclusion of maternal effects and direct genetic effect into the model is necessary.

Estimation of Genetic Parameters and Environmental Factors on Early Growth Traits for Lori Breed Sheep Using Single Trait Animal Model

The effects of different environmental factors and estimation of genetic parameters on early growth traits for Lori breed sheep including birth weight, weaning weight and body weight at 6 months of age using 19960 records from 35 herds of Lorestan Jahad Agriculture Organization were studied in the cities of Aleshtar, Khorramabad and Poldokhtar from 1995 to 2003. The effect of herd, sex of lambs, dam age and birth year on all traits and birth type had significant effect only on weaning weight. Different single trait animal models estimated the components of direct additive genetic variance, maternal genetic variance and maternal permanent environment variance through restricted maximum likelihood using environmental factors as a fixe effect and different random effects. The results showed that direct additive genetic effect had additionally significant effect on all traits moreover maternal additive genetic and maternal permanent environment effects. Results also revealed that the maternal permanent environment variance for all traits is higher than maternal genetic variance. Also the direct heritability for all traits was higher than maternal heritability. Estimation of the direct heritability from the birth to 6 months of age showed a reducing trend that could arise from high dependence of birth and weaning weight on maternal environment conditions as compared with the age conditions afterward. The genetic assessment of growth traits in Lori breed sheep without inclusion of maternal effect in animal model causes decreased selection accuracy and incorrect genetic assessment of the lambs.

Estudo genético-quantitativo de características de crescimento na raça Tabapuã

Estimaram-se os componentes de variância e covariância e as herdabilidades para os efeitos direto e materno, as correlações entre os efeitos direto e materno e a fração de ambiente permanente na variação total, utilizando-se o aplicativo MTDFREML, para os pesos ao nascer (PN), à desmama ajustado para 205 dias (P205), aos 365 (P365) e 550 (P550) dias de idade na raça Tabapuã, para avaliar o efeito materno e a associação dos efeitos direto e materno sobre características de crescimento. Os dados, provenientes do programa de controle ponderal da raça, foram registrados na fazenda Água Milagrosa, município de Tabapuã, São Paulo, no período de 1978 a 2002. As herdabilidades direta e materna foram: 0,32, 0,10; 0,20, 0,17; 0,21, 0,06 e 0,16; 0,03, para os pesos ao nascer, à desmama, aos 365 e 550 dias, respectivamente. As correlações entre os efeitos direto e materno para a mesma seqüência de pesos foram: -0,10; -0,20; -0,11 e -0,15. As frações do efeito de meio permanente na variância total foram: 1,41x10-6; 2,5x10-7; 2,4x10-7 e 4,0x10-6. Recomenda-se a inclusão do efeito materno nos esquemas de seleção de características de crescimento na raça Tabapuã.

Maternal effects on the genetic evaluation of Tabapuã beef cattle

The aim of this investigation was to study the influence of maternal effects on the genetic evaluation of sire production in Tabapuã beef cattle. Single and multiple trait analyses were done with adjusted animal weights at 120, 240 and 420 days of age. Antagonism was observed between additive direct and maternal genetic effects, with the maternal effect being higher until weaning. The inclusion of maternal effects in the models removed part of the additive variance only in single trait analyses and resulted in smaller means and standard deviations for the sire breeding values. The use of maternal effect associated with single or multiple traits may affect sire ranking. The contradictory results of the single and multiple trait analyses for additive direct and maternal effects indicate that caution is needed when considering recommendations about the importance of maternal effects in Tabapuã beef cattle.

Efficient design of crossbreeding experiments

The efficiencies of different experimental configurations for estimating additive (A) and heterotic (H) effects in purebred and crossbred populations derived from two parent breeds are examined. Allocation of resources over six groups is considered: the two parental breeds, the F1, the F2 and the backcrosses to the two parental breeds. Additive and heterotic effects are best estimated by allocating resources to the two parental groups and F1 in the proportions 35%, 35%, 30% and for many practical situations, an experiment involving numbers in the region 250-300 is reasonable. If it is not possible to include all three groups, other combinations involving a subset of them and some of the other three groups can be used to give estimates of A and H. However, even the best of these alternatives requires over twice the resources to give the same precision as the optimal design and, further, these estimates may be correlated. Relatively modest reallocation of resources to the F2 to estimate or test for an epistatic effect (E) leads to a minor reduction in the precision of estimates of A and H while giving reasonable precision for the estimate of E. The inclusion of maternal effects in the model greatly reduces the efficiency of estimation of A and H. Where one of the breeds is introduced through the sire line only, optimal allocation gives roughly equal replication to the pure lines and F1 but about 63% of allocation is placed in equal amounts on the two backcrosses produced through crossing F1 dams with pure sires of both breeds. The relevance of these results to the planning of livestock crossbreeding trials, particularly those involving a local and an exotic or imported breed, is discussed.