scholarly journals Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Genetics ◽  
2021 ◽  
Author(s):  
Marnin D Wolfe ◽  
Ariel W Chan ◽  
Peter Kulakow ◽  
Ismail Rabbi ◽  
Jean-Luc Jannink
Keyword(s):  
Mate Selection ◽  
Selection Criteria ◽  
Genetic Variance ◽  
Selection Index ◽  
Dominance Model ◽  
Genetic Covariance ◽  
Good Correspondence ◽  
Mean And Variance ◽  
Genetic Distribution ◽  
Selection Of

Abstract Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses were accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

scholarly journals Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

2021 ◽  
Author(s):  
Marnin D. Wolfe ◽  
Ariel W. Chan ◽  
Peter Kulakow ◽  
Ismail Rabbi ◽  
Jean--Luc Jannink
Keyword(s):  
Mate Selection ◽  
Genetic Variance ◽  
Cross Validation ◽  
Selection Index ◽  
Dominance Model ◽  
Genetic Covariance ◽  
Breeding Values ◽  
Root Crop ◽  
Genetic Variances ◽  
Truncation Selection

AbstractDiverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. We were able to predict all genetic variances and most covariances with non-zero accuracy. We also tested a directional dominance model and found significant inbreeding depression for most traits and a boost in total merit accuracy for root yield. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with excellent breeding values) and varieties (progeny with top performance).Author SummaryBreeders typically use truncation selection and invest significant resources evaluating progeny to find exceptional genotypes. We extended genetic variance and trait covariance prediction to include dominance and predicting the multivariate selection index variance. We enable mate selection based on potential to produce future parents (progeny with excellent breeding values) and/or varieties (progeny with top performance). Using cross-validation, we demonstrate that genetic variances and covariances can be predicted with non-zero accuracy in cassava, a staple tropical root crop.

scholarly journals Effects on phenotypic variability of directional selection arising through genetic differences in residual variability

2004 ◽  
Vol 83 (2) ◽  
pp. 121-132 ◽  
Author(s):  
WILLIAM G. HILL ◽  
XU-SHENG ZHANG
Keyword(s):  
Genetic Variance ◽  
Environmental Variability ◽  
Phenotypic Variability ◽  
Additive Genetic Variance ◽  
Directional Selection ◽  
Frequency Change ◽  
Phenotypic Variance ◽  
Additive Effects ◽  
Genetic Covariance ◽  
Mean And Variance

In standard models of quantitative traits, genotypes are assumed to differ in mean but not variance of the trait. Here we consider directional selection for a quantitative trait for which genotypes also confer differences in variability, viewed either as differences in residual phenotypic variance when individual loci are concerned or as differences in environmental variability when the whole genome is considered. At an individual locus with additive effects, the selective value of the increasing allele is given by ia/σ+½ixb/σ2, where i is the selection intensity, x is the standardized truncation point, σ2 is the phenotypic variance, and a/σ and b/σ2 are the standardized differences in mean and variance respectively between genotypes at the locus. Assuming additive effects on mean and variance across loci, the response to selection on phenotype in mean is iσAm2/σ+½ixcovAmv/σ2 and in variance is icovAmv/σ+½ixσ2Av/σ2, where σAm2 is the (usual) additive genetic variance of effects of genes on the mean, σ2Av is the corresponding additive genetic variance of their effects on the variance, and covAmv is the additive genetic covariance of their effects. Changes in variance also have to be corrected for any changes due to gene frequency change and for the Bulmer effect, and relevant formulae are given. It is shown that effects on variance are likely to be greatest when selection is intense and when selection is on individual phenotype or within family deviation rather than on family mean performance. The evidence for and implications of such variability in variance are discussed.

scholarly journals Analysis of Direct and Indirect Selection and Indices in Bread Wheat (Triticum aestivum L.) Segregating Progeny

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zine El Abidine Fellahi ◽  
Abderrahmane Hannachi ◽  
Hamenna Bouzerzour
Keyword(s):  
Bread Wheat ◽  
Yield Components ◽  
Selection Criteria ◽  
Flag Leaf ◽  
Selection Index ◽  
Triticum Aestivum L ◽  
Indirect Selection ◽  
Selection Methods ◽  
Simultaneous Selection ◽  
Selection Of

Three selection methods including direct and indirect selection along with selection index based on the phenotypic values of eleven traits of agronomic interest were assessed for their application in F4 bread wheat progenies. Significant genetic variation existed among parents and crosses for the traits measured. The following were the most efficient indices for simultaneous selection of superior lines for yield and its components: base index of Williams, followed by the sum of ranks index of Smith and Hazel. The selection-based index provided the highest grain yield gains as compared to the other selection criteria, except for flag leaf area, indicating that the direct and indirect monotrait selection were not appropriate in the situation analyzed in this work. PCA identified Ain Abid × Mahon-Demias, Ain Abid × Rmada, and Ain Abid × El-Wifak as the most promising populations. At 5% selection intensity, the top 30 lines selected were distinguished, in comparison with the standard check Hidhab, by significant improvements in yield and yield components.

The value of crossbreeding information in selection of poultry under a dominance model

1998 ◽  
Vol 66 (2) ◽  
pp. 519-528 ◽  
Author(s):  
P. Uimari ◽  
J. P. Gibson
Keyword(s):  
Genetic Variance ◽  
Pure Line ◽  
Dominance Model ◽  
Partial Dominance ◽  
Complete Dominance ◽  
Degree Of Dominance ◽  
Dominance Variation ◽  
Pure Lines ◽  
Selection Of ◽  
Better Than

AbstractA stochastic simulation was used to investigate the value of crossbreeding information in a two line crossbreeding system in poultry under different genetic scenarios. Populations consisted of 25 sires and 250 dams, which were mated to produce both purebred and crossbred progeny. The next generation parents were selected either based on purebred information (PLS) (sib means, and own performance for females) or additional crossbred sib means were included (CCPS). The trait under selection was controlled by 20 loci with varying degree of dominance. Pure lines differed in initial allele frequencies. If the trait was controlled by loci with partial dominance, little or no extra benefit was obtained from including crossbred information over the pure line information. Under complete dominance and overdominance CCPS outperformed PLS. As a practical rule, CCPS is better than PLS if the ratio between dominance variance and total genetic variance is around 0·3 or higher. In this case the most probable cause of the dominance variation is loci with full or overdominance.

scholarly journals Udder and Claw-Related Health Traits in Selection of Czech Holstein Cows

2019 ◽  
Vol 19 (3) ◽  
pp. 647-661
Author(s):  
Zuzana Krupová ◽  
Ludmila Zavadilová ◽  
Marie Wolfová ◽  
Emil Krupa ◽  
Eva Kašná ◽  
...  
Keyword(s):  
Selection Criteria ◽  
Selection Index ◽  
Genetic Selection ◽  
Selection Response ◽  
Clinical Mastitis ◽  
Holstein Cows ◽  
Breeding Objective ◽  
Economic Weights ◽  
The Impact ◽  
Selection Of

AbstractThe aim of the study was to investigate the impact of the implementation of new health traits into the breeding objective and selection criteria for Czech Holstein cows on the genetic selection response in the breeding objective traits. Incidence of overall claw diseases was included into the current breeding objective for cows (11 traits together). Three traits that indicated claw health (incidence of claw diseases overall and infectious and non-infectious claw diseases) and incidence of clinical mastitis were successively added to the current selection criteria in a cow selection index (a maximum of 19 traits). Selection responses in the breeding objective traits were estimated by applying the general principles of the selection index theory. The required genetic variances for the new traits, the economic weights for all breeding objective traits and the genetic correlations among the selection index traits were estimated within this study. The marginal economic weights, which were calculated for two-year-old cows by applying a bioeconomic model with implemented gene flow, were -193 and -168 € per case for clinical mastitis and overall claw disease incidence, respectively. Using the comprehensive selection index with 19 traits, the reduction in the incidence of both udder and claw diseases was calculated to be 0.004 cases per cow per year. At the same time, a more favourable genetic selection response was obtained for other functional traits, e.g., +0.020% for cow conception rate and +0.010 years for productive life of cow (which represented the profit of 67 € and 367 € per herd and per year, respectively) when compared to the current index. Based on this study, a direct selection of cows for claw and udder health is nowadays recommended to improve the health status of herds and economics in production systems.

SISTEM PENDUKUNG KEPUTUSAN PEMILIHAN GURU BERPRESTASI KOTA MEDAN MENERAPKAN METODE PREFERENCES SELECTION INDEX (STUDI KASUS : DINAS PENDIDIKAN KOTA MEDAN)

2018 ◽  
Vol 2 (1) ◽  
Author(s):  
Fajar Syahputra ◽  
Mesran Mesran ◽  
Ikhwan Lubis ◽  
Agus Perdana Windarto
Keyword(s):  
Decision Making ◽  
Decision Support ◽  
Decision Support System ◽  
Support System ◽  
Formal Education ◽  
Basic Education ◽  
Selection Index ◽  
Main Task ◽  
Selection Of

The teacher is a major milestone in the world of education, the ability and achievement of students cannot be separated from the role of a teacher in teaching and guiding students. Based on the Law of the Republic of Indonesia No. 14 of 2005 concerning Teachers and Lecturers, in Article 1 explained that teachers are professional educators with the main task of educating, teaching, guiding, directing, training, evaluating, and evaluating students in early childhood education through formal education, basic education and education medium. Whereas in Article 4 of the Act, it is explained that the position of teachers as professionals serves to enhance the dignity and role of teachers as learning agents to function to improve the quality of national education.Decision making is an election process, among various alternatives that aim to meet one or several targets. The decision-making system has 4 phases, namely intelligence, design, choice and implementation. These phases are the basis for decision making, which ends with a recommendation.The Preferences Selection Index (PSI) method is a rarely used decision support system method. This method is a method developed by stevanie and Bhatt (2010) to solve the Multi Criteria Decision Making (MCDM). With the right consideration, this method can be one of the tools to determine policies in decision-making systems, especially the selection of outstanding teachers. Determination of policies taken as a basis for decision making, must use criteria that can be defined clearly and objectively.Keywords: Decision Support System, PSI, Selection of Achieving Teachers

Selection of one-dimensional sedimentation: models for on-line use

1995 ◽  
Vol 31 (2) ◽  
pp. 193-204 ◽  
Author(s):  
Koen Grijspeerdt ◽  
Peter Vanrolleghem ◽  
Willy Verstraete
Keyword(s):  
Steady State ◽  
Selection Criteria ◽  
Data Sets ◽  
Concentration Profiles ◽  
A Posteriori ◽  
One Dimensional ◽  
On Line ◽  
Dynamic Concentration ◽  
Selection Of ◽  
Modelling Task

A comparative study of several recently proposed one-dimensional sedimentation models has been made. This has been achieved by fitting these models to steady-state and dynamic concentration profiles obtained in a down-scaled secondary decanter. The models were evaluated with several a posteriori model selection criteria. Since the purpose of the modelling task is to do on-line simulations, the calculation time was used as one of the selection criteria. Finally, the practical identifiability of the models for the available data sets was also investigated. It could be concluded that the model of Takács et al. (1991) gave the most reliable results.

scholarly journals Modeling, comparison and evaluation of one-DOF six-bar bioinspired jumping leg mechanisms

2021 ◽  
Vol 13 (2) ◽  
pp. 168781402199295
Author(s):  
Ziqiang Zhang ◽  
Qi Yang ◽  
Xingkun Liu ◽  
Chuanzhong Zhang ◽  
Jinnong Liao
Keyword(s):  
Center Of Mass ◽  
Principal Component ◽  
Analysis Method ◽  
Index Distribution ◽  
Inertial Moment ◽  
Structure Index ◽  
Mean And Variance ◽  
Research Objects ◽  
Leg Mechanisms ◽  
Selection Of

One degree-of-freedom (DOF) jumping leg has the advantages of simple control and high stiffness, and it has been widely used in bioinspired jumping robots. Compared with four-bar jumping leg, six-bar jumping leg mechanism can make the robot achieve more abundant motion rules. However, the differences among different configurations have not been analyzed, and the choice of configurations lacks basis. In this study, five Watt-type six-bar jumping leg mechanisms were selected as research objects according to the different selection of equivalent tibia, femur and trunk link, and a method for determining the dimension of the jumping leg was proposed based on the movement law of jumping leg of locust in take-off phase. On this basis, kinematics indices (sensitivity of take-off direction angle and trunk attitude angle), dynamics indices (velocity loss, acceleration fluctuation, and mean and variance of total inertial moment) and structure index (distribution of center of mass) were established, and the differences of different configurations were compared and analyzed in detail. Finally, according to the principal component analysis method, the optimal selection method for different configurations was proposed. This study provides a reference for the design of one DOF bioinspired mechanism.

scholarly journals A comparison of two methods for predicting changes in the distribution of gene frequency when selection is applied repeatedly to a finite population

1969 ◽  
Vol 13 (2) ◽  
pp. 117-126 ◽  
Author(s):  
Derek J. Pike
Keyword(s):  
Iterative Procedure ◽  
Gene Frequency ◽  
Finite Population ◽  
Transition Matrices ◽  
Single Cycle ◽  
Gene Frequencies ◽  
Mean And Variance ◽  
The Mean ◽  
The One ◽  
Selection Of

Robertson (1960) used probability transition matrices to estimate changes in gene frequency when sampling and selection are applied to a finite population. Curnow & Baker (1968) used Kojima's (1961) approximate formulae for the mean and variance of the change in gene frequency from a single cycle of selection applied to a finite population to develop an iterative procedure for studying the effects of repeated cycles of selection and regeneration. To do this they assumed a beta distribution for the unfixed gene frequencies at each generation.These two methods are discussed and a result used in Kojima's paper is proved. A number of sets of calculations are carried out using both methods and the results are compared to assess the accuracy of Curnow & Baker's method in relation to Robertson's approach.It is found that the one real fault in the Curnow-Baker method is its tendency to fix too high a proportion of the genes, particularly when the initial gene frequency is near to a fixation point. This fault is largely overcome when more individuals are selected. For selection of eight or more individuals the Curnow-Baker method is very accurate and appreciably faster than the transition matrix method.

Individual effects in variation analysis: Model, software, and research design

2013 ◽  
Vol 25 (1) ◽  
pp. 89-118 ◽  
Author(s):  
John C. Paolillo
Keyword(s):  
Research Design ◽  
Fixed Effects ◽  
Selection Criteria ◽  
Current Approach ◽  
Variation Analysis ◽  
Analysis Model ◽  
Individual Level ◽  
Mixed Effects Modeling ◽  
Variationist Sociolinguistics ◽  
Selection Of

AbstractIndividual-level variation is a recurrent issue in variationist sociolinguistics. One current approach recommends addressing this via mixed-effects modeling. This paper shows that a closely related model with fixed effects for individual speakers can be directly estimated using Goldvarb. The consequences of employing different approaches to speaker variation are explored by using different model selection criteria. We conclude by discussing the relation of the statistical model to the assumptions of the research design, pointing out that nonrandom selection of speakers potentially violates the assumptions of models with random effects for speaker, and suggesting that a model with fixed effects for speakers may be a better alternative in these cases.

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