Journal ArticleDOI
Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models
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TLDR
The conclusion is that statistical and physiological models can be fruitfully combined for the study of genotype × environment interaction.Abstract:
To study the performance of genotypes under different growing conditions, plant breeders evaluate their germplasm in multi-environment trials. These trials produce genotype × environment data. We present statistical models for the analysis of such data that differ in the extent to which additional genetic, physiological, and environmental information is incorporated into the model formulation. The simplest model in our exposition is the additive 2-way analysis of variance model, without genotype × environment interaction, and with parameters whose interpretation depends strongly on the set of included genotypes and environments. The most complicated model is a synthesis of a multiple quantitative trait locus (QTL) model and an eco-physiological model to describe a collection of genotypic response curves. Between those extremes, we discuss linear-bilinear models, whose parameters can only indirectly be related to genetic and physiological information, and factorial regression models that allow direct incorporation of explicit genetic, physiological, and environmental covariables on the levels of the genotypic and environmental factors. Factorial regression models are also very suitable for the modelling of QTL main effects and QTL × environment interaction. Our conclusion is that statistical and physiological models can be fruitfully combined for the study of genotype × environment interaction.read more
Citations
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Journal ArticleDOI
Phenotyping for drought tolerance of crops in the genomics era.
TL;DR: This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
Journal ArticleDOI
Models for navigating biological complexity in breeding improved crop plants
Graeme Hammer,Mark E. Cooper,François Tardieu,Stephen Welch,Bruce Walsh,Fred A. van Eeuwijk,Scott Chapman,Dean Podlich +7 more
TL;DR: Modelling approaches for complex traits at gene network, organ and whole plant levels provide a means to link phenotypic consequence to changes in genomic regions via stable associations with model coefficients.
Journal ArticleDOI
Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions
TL;DR: A newly developed ensemble method, soft rule fit, was used to improve this model and capture non-linear responses of QTL to stresses, enabling the modeling of quantitative trait loci by environment interaction (Q*E), on a genome-wide scale.
Journal ArticleDOI
Biplot Analysis of Genotype × Environment Interaction: Proceed with Caution
TL;DR: The need for use of confi dence regions for individual genotype and environment scores in biplots to make critical decisions on genotype selection or cultivar recommendation based on a statistical test is stressed.
Journal ArticleDOI
PAPER PRESENTED AT INTERNATIONAL WORKSHOP ON INCREASING WHEAT YIELD POTENTIAL, CIMMYT, OBREGON, MEXICO, 20–24 MARCH 2006 Understanding the physiological basis of yield potential in wheat
TL;DR: Significant attention is given to effects of weather on yield potential and recent advances in techniques for elucidating the physiological basis of genotype by year interactions, which appear to have been few attempts to validate physiological (or morphological) selection criteria for wheat yield potential in the last decade.
References
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Book
Genetics and Analysis of Quantitative Traits
Michael Lynch,Bruce Walsh +1 more
TL;DR: This book discusses the genetic Basis of Quantitative Variation, Properties of Distributions, Covariance, Regression, and Correlation, and Properties of Single Loci, and Sources of Genetic Variation for Multilocus Traits.
Journal ArticleDOI
The analysis of adaptation in a plant-breeding programme
K.W. Finlay,G.N. Wilkinson +1 more
TL;DR: Varieties from particular geographic regions of the world showed a similarity in type of adaptation, which provides a useful basis for plant introduction and breeding.
Journal ArticleDOI
A simple regression method for mapping quantitative trait loci in line crosses using flanking markers.
Chris Haley,Sara Knott +1 more
TL;DR: Methods for mapping QTL based on multiple regression which can be applied using any general statistical package are developed and it is shown that these regression methods produce very similar results to those obtained using maximum likelihood.
Book
Contemporary Statistical Models for the Plant and Soil Sciences
TL;DR: In this paper, the authors present a framework for estimating and testing t-tests in terms of statistical models by embedding Hypotheses Hypothesis and Significance Testing and Interpretation of the p-value classes of Statistical Models Data Structures.
Book
Introduction to graphical modelling
TL;DR: Graphical modelling is a form of multivariate analysis that uses graphs to represent models as mentioned in this paper, which enable concise representations of associational and casual relations between variables under study, and provide an introduction to graphical models whose emphasis is on its applications and on the practicalities rather than formal development.