Topics in Molecular Plant Breeding

Biotechnological Tools for Broadening Genetic Variation

Biotechnological Tools for Broadening Genetic Variation
Introduction
Application of Biotechnology Tools in Plant Breeding
GM Crops Worldwide
Biotechnology Crops Graph
New Variety Workflow
Relative Costs of Development
Gene Stacking
Stacked Gene Examples
Gene Stacking Technologies
New Biotechnological Tools for Plant Transformation
Genome Editing
Zinc-Finger Nucleases (ZNFs)
Application of ZNF Technology
TALENs
Fusion of TALEs
Application of TALENs
Artificial Chromosomes
Advantages of Artificial Chromosomes
RNAi
Transposon Mutant Collections
Trangenic Events
Various Silencing Processes
Tilling
Legal Considerations
Regulated Articles
GM Testing
Coexistence
Application of Markers for Parent Selection
Successful Hybridization
Usefulness Concept
Applying the Usefulness Concept
Reflection
References
References (2)
References (3)

Cluster Analysis, Association & QTL Mapping

Introduction
Objectives
Measures of Distance Among Genotypes
Barley Example
Similarity Measure
Distance Measures
Euclidean Distance
Principal Component Analysis
Conceptual Interpretation
Example Data
Discussion
Cluster Analyses
K-Means Clustering
Hierarchical Clustering
Linkage Disequilibrium
Linkage Disequilibrium - Definition
Deviation
Try This! Activity
Estimation of LD
Estimation of LD: Standardized D
Study Question 1
Sources of LD: Mutation
Sources of LD: Migration
Sources of LD: Drift/Sampling
Sources of LD: Mixing of sub-populations
Decay of LD
Affecting Parameters: Linkage
Affecting Parameters: Population Size
Affecting Parameters: Mating System
Further Thought
Marker-Phenotype Associations
Genome-Wide Association Studies
R-squared
Rapid LD Decay
Barley Example
Sources of LD
Data Analysis of GWAS
GWAS: Summary
Discussion
QTL Mapping
Population Types
F2 Populations
Backcross Populations
Recombinant Inbred Lines
Advanced Intercross Lines
Doubled Haploids
NAM Population
QTL Mapping Methods
Mapping Methods Summary
Single Marker Analysis
Single Marker Analysis (2)
Single Marker Analysis (3)
Simple Interval Mapping
Effects at Flanking Markers
Quantitative Trait Locus (QTL) Mapping
Regression Model
Backcross Regression Interval Model
Composite Interval Mapping
Multiple QTL Problem
Multiple QTL Solution
Multiple Interval Mapping (MIM)
Reflection
References
Cluster Analysis, Association & QTL Mapping

Comparative Mapping and Genomics

Introduction
Introduction to Structural Genomics
Overview
Genetic Maps
Physical Maps
Restriction Mapping
Physical Maps and Genome Sequencing
Comparative Mapping
Description
Colinearity and Synteny
Orthology Example
Micro-Colinearity Example
Orthology and Mapping
Grass Genome Map
Linear Comparative Map
Soybean and Arabidopsis Linkage
Web-Based Mapping Tools
Try This: NCBI MapViewer
Try This: NCBI MapViewer
Try This: NCBI MapViewer
Try This: NCBI MapViewer
Try This: NCBI MapViewer
Comparative Genomics
Description
Gene Prediction
Try This: Arabidopsis Analysis
Try This: Arabidopsis Analysis
Try This: Arabidopsis Analysis
Try This: Arabidopsis Analysis
Detecting Copy Number Variations
Comparative Genomic Hybridization
Gene Cloning
Analysis of Genome Evolution
Genome Evolution: Details
Domestication and Heterosis
Challenges: Large Genomes
Challenges: Transposable Content
Challenges: Map Assembly
Challenges: Map Assembly
Challenges: Map Assembly
Challenges: Map Assembly
Challenges: Map Assembly
Challenges: Repeated Sequences
Summary
Reflection
References (1)
References (2)
For Your Information
FYI: aCGH Applications
FYI: Cloning Approaches
Comparative Mapping and Genomics

Data Management and Quality Control

Introduction
Marker Data Pipelines
Marker Data Information
Equipment for Marker Data Development
Steps in Marker Data Production
Steps in Marker Data Production - Step 1
Steps 2 to 4
Step 5
Steps 6 and 7
Step 8
Steps 9 and 10
Causes of Errors in Marker Data Production
Errors in Marker Production
GMO Detection Methods
DNA-Associated Causes of Errors
PCR in GMO Testing
Sources of Error
GM Testing Plan
Operation Characteristic Curve
Laboratory Sources of Error
Lab Error Sources - Various Results and Reactions
Data Management and Quality Control
Parameters for GMO Detection
Steps in Genotyping Process
Status of Marker Technology in Breeding Companies
Reflection
References
References
Data Management and Quality Control
For Your Information
Steps in Marker Data Production
Contribution of Haploid Genomes
DNA Isolation and Quality
Amplification/Labelling
False Positive and Negative Results

Genome Construction

Genome Construction
Introduction
Introduction
Objectives
Recapitulation of the Concept of Genetic Gain
Definition
Commercialization Challenges
Crop Yield Progress
Global Food Demand Trends
Need for Advancement
Multi-Objective Optimization
Introduction
Pareto optimal solutions
Operations Research in Plant Breeding
Introduction
Step 1: Defining the Problem
Step 2: Developing a Model
Step 3: Designing a Suitable Algorithm
Step 4: Solving the Problem
Genome Construction vs. Genomic Selection
Reflection
References

Genomic Tools for Variety Registration and Protection

Introduction
Plant Variety Protection
Objectives
International Rules for Certified Seed Production
Effects of Concentration in Global Seed Security
Regulation and Policies
Rules and Standards
ISF Activities
ISF Rules Effecting Crop Varieties
ISF Rules and Usages Example
Setting Standards
Molecular Characterization
Main Considerations
Examples of Genomic Tools
Genomic Tools to Use in Maintenance Breeding
Maintenance Breeding
Example of Maintenance Breeding
Rapid Micro-Propagation
Current Global Status
Report on Top Four GM Crops
Approved GM Crops Table
GM Crop Statistics
Tracking Dispersal Routes
Coexistence Concept
Range of Coexistence Measures
Isolation Distances
Practical Limits of Detection
Production Chains
Additional Costs
Lawsuits for Patent Infringement
Past Lawsuit Examples
UPOV and Its Rules for Protection of New Varieties
International Union for the Protection of New Varieties of Plants
UPOV Rules for Variety Registration
Comparison of Principal Differences Among Patent Laws
The Fourth Provision
Exceptions to the UPOV Breeder's Right
DUS Testing and the Potential for Inclusion of Genomic Tools
DUS Testing is a Required Step
Example of DUS Testing Rules
Projections for Oilseed Supplies
Test Guidelines
Characteristics of Varieties
Questions About Testing Sites
Characteristics Table
Key Codes Table
Non-DNA Markers
Markers with Potential Use
Variety Identification Work
SSR Markers
Biochemical and Molecular Techniques
Molecular Characteristics and Calibration
Threshold Level Graphs
GAÏA Distance Method
Anonymous Markers
Summarizing Outcomes
Conclusions
Essentially Derived Varieties
Reflection
References (1)
References (2)
References (3)
Acknowledgements

Introduction to Bioinformatics

Introduction
Database Types
Objectives
Access and Use of Sequence Databases
About NCBI
Sign Up for NCBI
NCBI Training
Information Retrieval from NCBI
Searching NCBI by Keywords
Try This: Access and Use of Sequence Databases
Try This: Access and Use of Sequence Databases
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
Try This: Access and Use of Sequence DBs
NCBI BLAST
BLAST Interface
BLAST Features
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Try This: Using NCBI BLAST
Plant Species Sequence Databases
MaizeGDB
MaizeGDB: Tutorials
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Try This: Using MaizeGDB
Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Try This: Multiple Sequence Alignment
Finding Polymorphisms
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Try This: Using Clustal Omega
Developing Marker Assays
Summary
Reflection
Introduction to Bioinformatics

Marker Assisted Backcrossing

Marker Assisted Backcrossing
Introduction
General Considerations
The Goal of Backcrossing
Genotype Structures
Limitation of BC Method
Marker-Assisted Backcrossing
Examples of Marker-Assisted Backcrossing
3 Steps of MABC
Foreground Selection
Estimating Number of Individuals
Estimating Number of Genes
Trait Introgression
Probability Model
The Reliability of Selection
Use of Markers
Transgenic Traits
Background Selection
Objective of Background Selection
The Versatility of MABC
Example of Background Selection
Controlling Linkage Drag
Reducing BC Generations
Reducing Linkage Drag
Target Locus
Minimum Population Size
Target Genotype
MABC for Single Gene
Comparing Different BC Strategies
Recurrent Parent Genome
Detect the Level of RPG
Results Using Different Ratios
Three-Stage Selection
Attaining a Desired Q10 Percentile
Detecting a Desired RPG Level
Altering Size of Populations
Key Points
A Two-Generation Breeding Plan
Developing Improved Lines
Proposed Guidelines
MABC for several genes
Detecting a Desired Genotype
Identification of Genotypes
Reflection
References

Marker-Assisted Selection and Genomic Selection

Marker-Assisted Selection and Genomic Selection
Introduction
Objectives
Limitations in QTL Mapping
QTL Dependicies
Impact Graph
MAS Strategies
MAS Strategies - F2 Enrichment
Obtaining Marker Scores
Derivation of a Selection Index
Interpretation of the Marker Score
Marker-Assisted Recurrent Selection
MAS Strategies Comparison
Efficiency of MAS
Selection Index
Estimating Relative Efficiency of MAS
Comparison to Phenotypic Selection
Factors Affecting Efficiency
Examples of Application in Crop Breeding
Example 1
Example 2
Example 3
Reasons for Varying Successes of MAS
Alternative Approaches to MAS
Mapping As You Go (MAYG)
Breeding by Design
The Principle of Breeding by Design
Genomic Selection
Advantage of Using GS
GS Principles
Application of GS
Important Factors
Two Population Types
GS Methods
The Basic Model
Regression Models
Marker Difference
Simulation Studies
GS vs. MARS Comparison
Responses to Different Selections
MAS Compared to GS
Reflection
References (1)
References (2)

Marker Based Management of Plant Genetic Resources

Marker Based Management of Plant Genetic Resources
Introduction
Marker Application
Conserving and Mining Plant Genetic Resources (PGR)
Taxonomic Classification
Acquisition and Collection of Materials
Phylogenetic Analysis
Relationship Graph
Maintenance of Genetic Integrity of Genetic Resources
Core Collections
Size of Core Collection
Resynthesis of Allopolyploids
Exploitation of Secondary and Tertiary Gene Pools
Exploitation of Biodiversity
Exploitation of Secondary and Tertiary Genetic Resources
Molecular Analysis
Rice Breeding Options
Identification of Novel Genes and Alleles
Molecular Characterization
Utilization of Genetic Resources
Testing Identity of Conal Species During Multiplication Process
Grapevine
Oil Palm
Somaclonal Mutations
Miscanthus
Assigning Identity
Reflection
References

Markers and Sequencing

Objectives
Introduction
Genetic Variation
Principles of Sequencing
Principles of Sequencing - Introduction
Sequencing Efforts
Sanger's Dideoxy DNA-Sequencing Procedure
Sequenced Plant Species
Try This: Dideoxy Sequencing
Maxam & Gilbert Procedure
Try This: Maxam & Gilbert Sequencing
Next Generation Sequencing
Definition of Next Generation Sequencing
Pyrosequencing or 454 Sequencing
SOLiD
Illumina
SMRT Sequencing
Third-Generation Sequencing
Assembling Aspects of Nextgen
Sequence Alignment
General Bioinformatics Workflow
Third-Generation Sequencing
Suggested References
Genotyping by Sequencing
Genotyping by Sequencing - Description
Library Construction
Sequence Barcoding
Multiplexed Sequencing Process
Haplotype Maps
Data Imputation
Step 1
Step 2
Sliding Window Approach
Map Construction by NGS Sequencing
Bin Maps
Bin Map - Example
Tag SNPs
Study Question 1
DNA Markers
DNA Markers - Development
Molecular Markers
General Properties
RFLP
SSR
Try This: Activity
Try This: Activity
Try This: Activity
Try This: Activity
Try This: Activity
Try This: Activity
SSR - Strengths & Weaknesses
AFLP
SNP
SNP Explanation
SNP: TaqMan Assays
SNP: Sequenom MassArray System
Key Steps in Sequenom MassArray System
SNP: GoldenGate Assay
GoldenGate Assay
GoldenGate Assay
GoldenGate Assay
GoldenGate Assay
GoldenGate Assay
Indels
In Detail: Dye Swaps
Basic Marker Applications
Marker Applications - Genetic Fingerprinting
Try This! Genetic Fingerprinting
Genetic Fingerprinting by RFLP
Study Question 2
Genetic Fingerprinting Process
Gene Tagging
Study Question 3
Use of Linked Markers: Step 1
Use of Linked Markers: Step 2
Use of Linked Markers: Step 3
Markers and Selection
DNA Versus Non-DNA Markers
Groups of Non-DNA Markers
Visible Markers
Genetic Pathways from DNA to RNA
Microarray Technologies
Microarray Analysis
Microarray Analysis (2)
Microarray Analysis (3)
Microarray Analysis (4)
Protein-Based Markers
Isozymes
Metabolite-Based Biomarkers
Techniques for Profiling
Plant Phenomics
Discussion
Reflection
References
Markers and Sequencing
For Your Information
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Dideoxy Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing
FYI: Maxam & Gilbert Sequencing

Modern Tools for Line Development and Predicting Hybrid Performance

Overview
Introduction
Objectives
Breeding Schemes for Line Development
Doubled Haploids
Doubled Haploid - Definition
Methods of Producing Haploid Plants
Use of Inducers
Use of Inducers (Step 2)
Use of Inducers (Steps 3 and 4)
Inducer Effects
Application of DH Technology
Phenotypic Markers
Metabolite Markers
Doubled Haploids and Gene Pyramiding
Application Example
Challenges in Application
Other Concerns: Adapted Inducers
Other Concerns: Alternative Markers
Other Concerns: Toxicity
Genomic Tools for Hybrid Breeding
Description
Breeding Scheme
Associations
Molecular Basis of Heterosis
Changes in Gene Expression
Gene Expression Studies
Molecular Insight
Hemizygous Complementation
Genetic Similarity Analysis
Genomic Tools to Understand Heterosis
Predicting Hybrid Performance
DNA-Based Markers (1)
DNA-Based Markers (2)
Non-DNA Markers
Genetic Distance Formula
Euclidean Distance
Binary Distance
Correlation
Characterization of Heterosis
Interwoven Loop Design
Trait-Correlated Genes
Overrepresented GO Terms
Non-DNA vs. DNA-Based Markers
Reflection
References
Modern Tools for Line Development and Predicting Hybrid Performance

Modeling and Data Simulation

Introduction
Genetic Simulation Tools
Methods and Processes
QU-GENE
MBP
GREGOR, PLABSIM and GENEFLOW
COGENFITO
Summary of Programs and Functionality
Applying Computer Simulation
Computer Simulations
Example 1: Evaluating Plant Breeding Strategy
Findings
Example 2: Efficiency of Marker-Assisted Selection
Finding 1
Finding 2
How to Design a Simulation Experiment
New Breeding Methods
Assumptions of the Model
New Field Experiment Design
Simulate a Double Haploid Population
Possible Uses
Reflection
References (1)
Modeling and Data Simulation

Molecular Plant Breeding Concepts

Introduction
Objectives
Changes in Instrument Capacity
Developments in NGS
DNA Sequencing Costs
Traditional Plant Breeding
Genetic Structure of Variety Types
Genetic Variation Within a Variety
Breeding Categories
Seeds of Hybrid Varieties
Alternatives in Genetic Structure
Heterosis
Formation of Heterotic Groups
Basic Steps in Traditional Breeding
Integration of Molecular Genetics and Biotechnology with Plant Breeding
New Technology
Integration of Genomics
Application of Markers in Plant Breeding
Diagnostics in Plant Breeding
Diagnosis
Major Tasks
Classification of Diagnostic Methods
Using Molecular Techniques
Diagnostic Procedures
Perspectives
Use of Genomics and Biotechnology
Further Thought: Reflection
References
Acknowledgements