Retrospective Evaluation of Parental Selection in Nursery Tests of Juglans regia L. Using a Mixed Model Analysis

Summary Results of early testing in Juglans regia performed over the period 1993-2002 are presented. A total of 37 progenies were evaluated for establishment, growth traits, and phenology at ages one and two during two or more sowing years in the nursery. Independent culling selection was applied on parental trees to the family-mean values using specific truncation points for establishment, diameter and total height. In addition, parental selection was performed on unbiased predictions (BLUPs) of parental breeding values using a multivariate mixed model analysis in order to account for the unbalanced nature of the entire data set. Genetic parameters (heritabilities, correlations) of juvenile traits were also estimated. Except for second year growth traits, the genetic control of most characters was quite high, with heritability estimates ranging from 0.51 (establishment) to 0.93 (flushing date). Growth performance and establishment did not bear a common genetic control according to non-significant genetic correlations, but a higher growth was typical of early flushing families. Changes in parental ranking for growth after comparison of familymean and BLUP-based estimates of parental performance were considerable. This observation, together with the larger proportion of culled progenies in the former method (about 70%), suggests a sizeable loss of genetic gain by using unadjusted parental means. It is concluded that current evaluation and selection schemes using family-mean values should be reconsidered by i) relaxing truncation points for selection on establishment and growth traits and ii) re-evaluating progeny test data using a mixed model framework to unveil valuable material otherwise neglected due to unaccounted environmental influence on family performance.

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Estimating inbreeding depression for growth and reproductive traits using pedigree and genomic methods in Argentinean Brangus cattle

Journal of Animal Science ◽

10.1093/jas/skab289 ◽

2021 ◽

Author(s):

Natalia S Forneris ◽

Carolina A Garcia-Baccino ◽

Rodolfo J C Cantet ◽

Zulma G Vitezica

Keyword(s):

Inbreeding Depression ◽

Mixed Model ◽

Growth Traits ◽

Reproductive Traits ◽

Single Step ◽

Multiple Trait ◽

Model Framework ◽

Data Set ◽

Inbreeding Coefficients ◽

Genomic Inbreeding

Abstract Inbreeding depression reduces mean phenotypic value of important traits in livestock populations. The goal of this work was to estimate the level of inbreeding and inbreeding depression for growth and reproductive traits in Argentinean Brangus cattle, in order to obtain a diagnosis and monitor breed management. Data comprised 359,257 (from which 1,990 were genotyped for 40,678 SNP) animals with phenotypic records for at least one of three growth traits: birth weight (BW), weaning weight (WW) and finishing weight (FW). For scrotal circumference (SC), 52,399 phenotypic records (of which 256 had genotype) were available. There were 530,938 animals in pedigree. Three methods to estimate inbreeding coefficients were used. Pedigree-based inbreeding coefficients were estimated accounting for missing parents. Inbreeding coefficients combining genotyped and nongenotyped animal information were also computed from matrix H of the single-step approach. Genomic inbreeding coefficients were estimated using homozygous segments obtained from a Hidden Markov model (HMM) approach. Inbreeding depression was estimated from the regression of the phenotype on inbreeding coefficients in a multiple-trait mixed model framework, either for the whole data set or the data set of genotyped animals. All traits were unfavorably affected by inbreeding depression. A 10% increase in pedigree-based or combined inbreeding would result in a reduction of 0.34 - 0.39 kg in BW, of 2.77 - 3.28 kg in WW and 0.23 cm in SC. For FW a 10% increase in pedigree-based, genomic or combined inbreeding would result in a decrease of 8.05 - 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped data set.

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Conventional and Mixed Model Approach to Estimate Heterosis of the Growth Traits in Boer Goat’s Crossbred Offspring Populations

Caraka Tani Journal of Sustainable Agriculture ◽

10.20961/carakatani.v34i1.27620 ◽

2019 ◽

Vol 34 (1) ◽

pp. 55

Author(s):

Nuzul Widyas ◽

Sigit Prastowo ◽

Tristianto Nugroho ◽

Adi Ratriyanto

Keyword(s):

Conventional Method ◽

Mixed Model ◽

Growth Traits ◽

Average Daily Gain ◽

Random Effect ◽

Model Analysis ◽

Parameters Estimation ◽

Mixed Model Analysis ◽

Mixed Model Approach ◽

Model Approach

Heterosis is often utilized as a success indicator in a crossbreeding program. It is defined as the deviation of the crossbred means relative to their parental breeds. Heterosis mechanism is highly dependent on the genetic factors and thus, we incorporated genetic information in its estimation. The objective of this article was to compare heterosis estimated with conventional and mixed model approaches. In total, phenotypes of 3804 individuals were recorded. Data were obtained from a crossbreeding experiment involving Boer bucks and Jawarandu does. Observed traits were birth weight, weaning weight and average daily gain. Conventional and mixed model methods were used to estimate the heterosis. The heterosis values (%) between B×B vs B×J, estimated with conventional method were -11.38, -10.51 and -10.39; with mixed model were -6.23, -9.27 and -9.68 for BW, WW and ADG respectively. Heterosis values in B×(B×J) relative to B×B, estimated with conventional method were -6.16, -10.35 and -11.69; whereas with mixed model were -8.01, -10.82 and -9.14 for BW, WW and ADG respectively. Conventional method tends to underestimate the means phenotype with lower standard errors compared to mixed model analysis results in all traits. Conventional method also introduces biased heterosis estimates compared to the mixed model. Conventional method ignores any potential effects in the estimation procedures; whereas mixed model approach incorporates all the systematic and random effect including family relationship information. Thus, mixed model produced more reliable results in genetic parameters estimation. We recommend employing mixed model analysis in estimating heterosis.

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Mixed model analysis of variance, assuming equal variance and equal covariances

PsycEXTRA Dataset ◽

10.1037/e537552008-001 ◽

1957 ◽

Cited By ~ 1

Author(s):

M. B. Danford ◽

Harry M. Hughes

Keyword(s):

Analysis Of Variance ◽

Mixed Model ◽

Model Analysis ◽

Mixed Model Analysis ◽

Equal Variance

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Classical and Bayesian mixed model analysis of microarray data for detecting gene expression and DNA differences

10.31274/etd-180810-559 ◽

2009 ◽

Author(s):

Cumhur Yusuf Demirkale

Keyword(s):

Gene Expression ◽

Microarray Data ◽

Mixed Model ◽

Model Analysis ◽

Mixed Model Analysis

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Mixed Model Analysis in Longitudinal Studies

Applied Mixed Model Analysis ◽

10.1017/9781108635660.010 ◽

2019 ◽

pp. 131-150

Keyword(s):

Longitudinal Studies ◽

Mixed Model ◽

Model Analysis ◽

Mixed Model Analysis

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Efficient Bayesian mixed-model analysis increases association power in large cohorts

Nature Genetics ◽

10.1038/ng.3190 ◽

2015 ◽

Vol 47 (3) ◽

pp. 284-290 ◽

Cited By ~ 573

Author(s):

Po-Ru Loh ◽

George Tucker ◽

Brendan K Bulik-Sullivan ◽

Bjarni J Vilhjálmsson ◽

Hilary K Finucane ◽

...

Keyword(s):

Mixed Model ◽

Model Analysis ◽

Mixed Model Analysis

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Size-related boldness is not altered by stomach flushing in a terrestrial salamander

Amphibia-Reptilia ◽

10.1163/15685381-bja10054 ◽

2021 ◽

pp. 1-6

Author(s):

Sebastiano Salvidio ◽

Andrea Costa ◽

Fabrizio Oneto

Keyword(s):

Body Condition ◽

Mixed Model ◽

Linear Mixed Model ◽

Animal Personality ◽

Model Analysis ◽

Mixed Model Analysis ◽

Linear Mixed Model Analysis ◽

Before And After ◽

Trophic Strategy ◽

The Relationship

Abstract Animal personality is a relatively neglected field in amphibian research. In this study we assessed the influence of stomach flushing, a non-lethal technique used in amphibian dietary studies, on the boldness behaviour of the cave salamander Speleomantes strinatii. The time of emergence from a shelter located in an unfamiliar environment (a proxy for individual boldness) was measured in 26 cave salamanders before and after stomach flushing, while 14 non-flushed salamanders were tested as controls. Boldness was a repeatable behaviour for salamanders and larger individuals emerged from their shelter more rapidly than smaller ones. Linear mixed model analysis showed that flushing, sex and body condition had no effect on this behaviour. These findings are promising in the framework of the study of salamander personality. In particular, our results will be useful when exploring the relationship between individual trophic strategy and boldness, aggression or exploration behaviours in terrestrial salamanders.

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