Genotype-by-Environment Interaction and Stability Analysis | p. 1 |
Genotype-by-Environment Interaction | p. 3 |
Heredity and Environment | p. 3 |
Qualitative Traits | p. 4 |
Quantitative Traits | p. 4 |
Genotype-by-Environment Interaction | p. 5 |
Implications of GEI in Crop Breeding | p. 7 |
The Breeding Phase | p. 7 |
Environmental (E), Genetic (G), and GE Interaction Contributions | p. 7 |
Additional Breeding Programs | p. 8 |
Genetic Gain Reduction | p. 8 |
Increased Field Evaluation Cost | p. 8 |
Early- and Advanced-Performance Testing | p. 8 |
The Performance Evaluation Phase | p. 8 |
Problem in Identifying Superior Cultivars | p. 8 |
Increased Cost of Variety Testing | p. 9 |
Causes of Genotype-by-Environment Interaction | p. 9 |
Stability Analyses in Plant Breeding and Performance Trials | p. 11 |
Stability Concepts and Statistics | p. 11 |
Static vs. Dynamic Concept | p. 11 |
Stability Statistics | p. 12 |
Simultaneous Selection for Yield and Stability | p. 14 |
Contributions of Environmental Variables to Stability | p. 14 |
Stability Variance for Unbalanced Data | p. 15 |
Dealing with Genotype-by-Environment Interaction | p. 16 |
Correct Genetic Cause(s) of GE Interaction | p. 17 |
Characterize Genotypes and Environments | p. 17 |
QTL-by-Environment Interaction | p. 17 |
Breeding for Stability/Reliability of Performance | p. 18 |
Early Multi-Environment Testing | p. 18 |
Resource Allocation | p. 19 |
GGE Biplot: Genotype + GE Interaction | p. 19 |
GGE Biplot and Multi-Environment Trial Data Analysis | p. 21 |
Theory of Biplot | p. 23 |
The Concept of Biplot | p. 23 |
Matrix Multiplication | p. 23 |
Presenting the Matrix Multiplication Process in a Biplot | p. 24 |
The Inner-Product Property of a Biplot | p. 26 |
Visualizing the Biplot | p. 29 |
Visual Comparison of the Row Elements within a Single Column | p. 29 |
Visual Comparison of the Column Elements within a Single Row | p. 29 |
Visual Comparison of Two Row Factors for Each of the Columns | p. 30 |
Visual Comparison of Two Column Factors for Each of the Rows | p. 30 |
Visual Identification of the Largest Column Factor within a Row | p. 32 |
Visual Identification of the Largest Row Factor within a Column | p. 32 |
Relationships among Columns and among Rows | p. 34 |
Relationships among Columns | p. 34 |
Relationships among Rows | p. 35 |
Biplot Analysis of Two-Way Data | p. 36 |
Introduction to GGE Biplot | p. 39 |
The Concept of GGE and GGE Biplot | p. 39 |
The Basic Model for a GGE Biplot | p. 41 |
Methods of Singular Value Partitioning | p. 42 |
Genotype-Focused Scaling | p. 42 |
Environment-Focused Scaling | p. 44 |
Symmetric Scaling | p. 44 |
Equal-Space Scaling | p. 44 |
Merits of Different Scaling Methods | p. 47 |
An Alternative Model for GGE Biplot | p. 49 |
Three Types of Data Transformation | p. 56 |
Generating a GGE Biplot Using Conventional Methods | p. 57 |
Biplot Analysis of Multi-Environment Trial Data | p. 63 |
Objectives of Multi-Environment Trial Data Analysis | p. 63 |
Simple Comparisons Using GGE Biplot | p. 65 |
Performance of Different Cultivars in a Given Environment | p. 65 |
Relative Adaptation of a Given Cultivar in Different Environments | p. 67 |
Comparison of Two Cultivars | p. 67 |
Mega-Environment Investigation | p. 73 |
"Which-Won-Where" Pattern of an MET Dataset | p. 73 |
Mega-Environment Investigation | p. 77 |
Cultivar Evaluation for a Given Mega-Environment | p. 83 |
Cultivar Evaluation Based on Mean Performance and Stability | p. 83 |
The Average Environment Coordinate | p. 85 |
How Important is Stability? | p. 88 |
Evaluation of Test Environments | p. 89 |
Interrelationships among Environments | p. 89 |
Discriminating Ability of the Test Environments | p. 91 |
Environment Ranking Based on Both Discriminating Ability and Representativeness | p. 91 |
Environments for Positive and Negative Selection | p. 92 |
Comparison with the AMMI Biplot | p. 93 |
Interpreting Genotype-by-Environment Interaction | p. 94 |
The General Idea | p. 94 |
Causes of GE Interaction Represented by PC1 | p. 96 |
Causes of GE Interaction Represented by PC2 | p. 98 |
Some Comments on the Approach | p. 98 |
GGE Biplot Software and Applications to Other Types of Two-Way Data | p. 101 |
GGE Biplot Software--The Solution for GGE Biplot Analyses | p. 103 |
The Need for GGE Biplot Software | p. 103 |
The Terminology of Entries and Testers | p. 104 |
Preparing Data File for GGEbiplot | p. 104 |
The Observation Data Format | p. 104 |
The Matrix Data Format | p. 106 |
Organization of GGEbiplot Software | p. 107 |
File | p. 110 |
View | p. 111 |
Visualization | p. 111 |
Find QTL | p. 113 |
Format | p. 113 |
Models | p. 114 |
Data Manipulation | p. 114 |
Biplots | p. 115 |
Scaling (Singular Value Partitioning) | p. 115 |
Accessories | p. 116 |
Help | p. 117 |
Log File | p. 117 |
Functions for a Genotype-by-Environment Dataset | p. 117 |
Functions for a Genotype-by-Trait Dataset | p. 118 |
Functions for a QTL-Mapping Dataset | p. 118 |
Functions for a Diallel-Cross Dataset | p. 119 |
Functions for a Genotype-by-Strain Dataset | p. 119 |
Application of GGEbiplot to Other Types of Two-Way Data | p. 119 |
GGEbiplot Continues to Evolve | p. 119 |
Interactive Stepwise Regression | p. 120 |
Interactive QQE Biplot | p. 120 |
Three-Way Data Input and Visualization | p. 120 |
Interactive Statistics | p. 120 |
Cultivar Evaluation Based on Multiple Traits | p. 121 |
Why Multiple Traits? | p. 121 |
Cultivar Evaluation Based on Multiple Traits | p. 122 |
Which is Good at What | p. 122 |
Which is Bad at What | p. 122 |
Comparison between Two Cultivars | p. 127 |
Interrelationship among Traits | p. 127 |
The Triangle of Grain Yield, Loaf Volume, and Flour Extraction | p. 127 |
Cultivar Evaluation Based on Individual Traits | p. 127 |
Cultivar Evaluation Based on Two Traits | p. 135 |
Identifying Traits for Indirect Selection for Loaf Volume | p. 135 |
Identification of Redundant Traits | p. 142 |
Comparing Cultivars as Packages of Traits | p. 142 |
Comparing New Genotypes with the Standard Cultivar | p. 144 |
What is Good with the Standard Cultivar? | p. 144 |
Traits for Indirect Selection for Cookie-Making Quality | p. 144 |
Investigation of Different Selection Strategies | p. 150 |
Systems Understanding of Crop Improvement | p. 150 |
Systems Understanding, Independent Culling, and the Breeder's Eye | p. 150 |
Enlarging the System Capacity by Reinforcing Factors outside the System | p. 158 |
Three-Mode Principal Component Analysis and Visualization | p. 158 |
QTL Identification Using GGEbiplot | p. 159 |
Why Biplot? | p. 159 |
Data Source and Model | p. 160 |
The Data | p. 160 |
The Model | p. 160 |
Grouping of Linked Markers | p. 160 |
Gene Mapping Using Biplot | p. 162 |
QTL Identification via GGEbiplot | p. 175 |
Strategy for QTL Identification | p. 175 |
QTL Mapping of Selected Traits | p. 175 |
Yield | p. 175 |
Heading Date | p. 177 |
Maturity | p. 182 |
Plant Height | p. 182 |
Lodging | p. 182 |
Test Weight | p. 182 |
Kernel Weight | p. 182 |
Interconnectedness among Traits and Pleiotropic Effects of a Given Locus | p. 182 |
Understanding DH Lines through the Biplot Pattern | p. 192 |
Visualizing Marker and Trait Values of the DH Lines | p. 192 |
Marker Nearest to the QTL | p. 192 |
Estimating Missing Values Based on the Biplot Pattern | p. 198 |
QTL and GE Interaction | p. 202 |
Biplot Analysis of Diallel Data | p. 207 |
Model for Biplot Analysis of Diallel Data | p. 207 |
General Combining Ability of Parents | p. 208 |
Specific Combining Ability of Parents | p. 210 |
Heterotic Groups | p. 210 |
The Best Testers for Assessing General Combining Ability of Parents | p. 210 |
The Best Crosses | p. 215 |
Hypothesis on the Genetic Constitution of Parents | p. 215 |
Targeting a Large Dataset | p. 217 |
Shrinking the Dataset by Removing Similar Parents | p. 221 |
The Best Crosses | p. 221 |
GCA and SCA | p. 221 |
Best Tester | p. 221 |
Heterotic Groups | p. 221 |
Genetic Constitutions of Parents with Regard to PSB Resistance | p. 221 |
Advantages and Disadvantages of the Biplot Approach | p. 225 |
Biplot Analysis of Host Genotype-by-Pathogen Strain Interactions | p. 229 |
Vertical vs. Horizontal Resistance | p. 229 |
Genotype-by-Strain Interaction for Barley Net Blotch | p. 230 |
Model for Studying Genotype-by-Strain Interaction | p. 230 |
Biplots with Barley Lines as Entries | p. 231 |
Biplots with Net Blotch Isolates as Entries | p. 233 |
Genotype-by-Strain Interaction for Wheat Fusarium Head Blight | p. 239 |
Biplot Analysis to Detect Synergism between Genotypes of Different Species | p. 247 |
Genotype-by-Strain Interaction for Nitrogen-Fixation | p. 247 |
Biplot with Frankia Strains as Entries | p. 248 |
Biplot with Casuarina Species as Entries | p. 248 |
Wheat-Maize Interaction for Wheat Haploid Embryo Formation | p. 251 |
Biplot with Maize Genotypes as Entries | p. 251 |
Biplot with Wheat Genotypes as Entries | p. 251 |
References | p. 255 |
Index | p. 263 |
Table of Contents provided by Syndetics. All Rights Reserved. |