Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits

ISBN-13: 9789811529511 / Angielski / Miękka / 2021 / 504 str.

N. Manikanda Boopathi

Spis treści

1.       Setting the Background

a)      Trends in Agricultural Product Demand: Functional Foods and Value Added Products

b)      Evolving New Crop Cultivars

                                             i.            Achievements

                                           ii.            Obstacles and Challenges

a)       Germplasm Exchange: International Laws and Governance

b)            Biotech Crops and Biosafety Issues

                                          iii.            Alternatives

                                         iv.            Scope of genetic mapping and Marker Assisted Selection

c) Need for this Book: What can be expected?

 

2.       Germplasm Characterization: Utilizing the Underexploited Resources

a)      Types of Germplasm: Natural Vs Man-made (crop specific germplasm repository, mutagenized population), Global Germplasm Resources

b)      Phenotyping for morphological and agronomic traits

i)         Conventional Methods of phenotyping: Biotic and Abiotic Stress Resistance, Yield and Quality Traits

ii)        Recent Developments in Phenomics and Way Forward

iii)      Case study in rice germplasm characterization for drought resistance: Formation of fundamental requirements

iv)     Traits useful for characterization

c)       Allele mining

d)      Genetic diversity and Clustering

i)         Software

ii)        Principle behind the genetic diversity analysis

iii)      Principle of measuring goodness-of-fit of a classification

e)      Genetic Diversity analysis using molecular markers

f)       DNA Barcoding and its utilization of germplasm exploitation

g)      Polymorphic Information Content and its importance

h)      Diversity and Phylogenetic Tree: Importance in Mapping Population Development

i)        Parental selection

 

3.       Mapping Population Development

a)      Mapping population and its importance in genetic mapping

b)      Selfing and Crossing techniques in crop plants

c)       F₂ progenies

d)      F₂ derived F₃ (F_2:3) populations

e)      F₂ inter-matting or immortalized F₂ populations

f)       DH lines

g)      BC progenies

h)      RILs

i)        NILs, Exotic libraries and advanced backcross populations

j)        Chromosomal Segment Substitution Lines

k)      Backcross Inbred Lines

l)        Advanced Inter-cross Lines

m)    Recurrent Selection Backcross Population

n)      Interconnected Mapping Populations

o)      Four-way cross population

p)      Multi-cross populations/Multiparent Advanced Generation Inter-cross (MAGIC) Populations

q)      Nested association mapping populations

r)       Mapping Populations for Cross-Pollinated Species

s)       Mapping Populations for autopolyploids

t)       Natural populations

u)      Chromosome specific genetic stocks for linkage mapping

v)      Combining Markers and Populations

w)    Characterization of Mapping Populations

x)      Choice of Mapping Populations

y)      Challenges in mapping population development and solutions

z)       Subset of Population for Bulk Segregant Analysis

aa)   Characterization of Mapping Populations: Size, Segregation Ratios and other properties that determines success of QTL mapping and MAS

bb)  Selection of Mapping Populations:

i) Comparisons

ii) Things to be remembered

 

4.       Genotyping

a)      Markers and its importance

b)      Morphological markers

c)       Biochemical markers or Isozymes

d)      Molecular markers

e)      Genome structure and organization

f)       Classification of Molecular Markers: Classical and Updated Types

g)      Hybridization Based Markers

i) RFLP

ii) Diversity Array Technology (DArT)

iii) Single Feature Polymorphism

iv) Other types of Microarray Based Molecular Markers

h)     Arbitrarily primed PCR-based markers

i) RAPD

ii) AP-PCR and DAF

iii) AFLP

i)      Sequence specific PCR based markers

i) Microsatellite based marker technique

ii) SNP (Novel Methods to Detect, Genotyping Procedures, Utility in Genetic Mapping and MAS)

iii) SFP

iv) SCAR

v) CAPS and dCAPS

vi) RAMP

vii) SRAP

viii) TRAP

ix) Start Codon-Targeted Polymorphism

x) CAAT Box-Derived Polymorphism

xi) Conserved DNA-Derived Polymorphism

xii) Conserved Region Amplification Polymorphism

xiii) Intron-Targeting Polymorphism

j)      Single strand conformation polymorphism

k)     Transposable elements (TE) based molecular markers

l)      Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ) Marker

m)   Restriction site associated DNA (RAD) markers

n)     RNA-based molecular markers

o)    Way Forward in development of new kind of molecular markers: Recent Developments in Sequence Based Molecular Markers

p)    Role of ‘omics’ in Molecular marker development (refer chapter 11)

q)    Selection of Marker Technology

r)      Marker Genotyping and Scoring

s)     Polymorphic Information Content: Practicing with molecular markers

t)      Analyzing the genotype score: Chi-square test

u)     Χ² test to analyze the segregation ratio using the program ANTMAP

5.       Linkage Map Construction

a)      Introduction to Genome Maps: Linkage, cytogenetic and physical maps

b)      Basics of linkage mapping: Mendelian rations, meiosis, crossing over and partial linkage

c)       Mapping function and Genetic Distance Calculation: Methods and Procedures

d)      Mapping of genetic markers: genetic consideration, general procedure and validation

e)      Testing of linkage: LOD scores, Threshold, Comparison and Confirmation

f)       Fine Tuning the Linkage: Grouping, ordering and spacing

g)      Methods to Detect and Avoid Sources of Error

h)      Chromosomal assignment

i)        Allopolyploidy and autopolyploidy

j)        Bridging linkage maps to develop unified linkage maps

k)      High-Resolution Mapping

l)        Mapping of Major Genes: Strategies, Methods and Procedures

m)    Selective Genotyping and Mapping: Basics and Procedure

n)      Merging Linkage Maps to Cytogenetic Maps and Physical Maps: Genetic Considerations

o)      Software for Linkage Mapping:

i) List of Linkage Mapping Software and Basic Understanding

ii) Considerations for Selection of Best Software

 

6.       Phenotyping

a)      Phenomics

                                             i.            Advances in Phenomics

                                           ii.            Applications in QTL mapping

b)      Phenotyping vs. QTL mapping

c)       Need for precise phenotyping

d)      Phenotyping for biotic stress

                                             i.            Explaining the concept with a Case study

e)      Phenotyping for abiotic stress

                                             i.            Explaining the concept with a Case study

f)       Heritability of phenotypes

g)      Statistical analysis of phenotypic data

                                             i.            Simple Statistics

                                           ii.            Heritability Estimation

                                          iii.            Correlation Analysis

 

7.       QTL Identification

a)      QTL: a prelude

b)      Single marker analysis: Principle, Methods and Procedure

c)       Interval mapping: Principle, Methods and Procedure

d)      Multiple QTLs: Principle, Methods and Procedure

e)      Composite interval mapping: Principle, Methods and Procedure

f)       QTL mapping software:

i) List of QTL Mapping Software and Basic Understanding

ii) Considerations for Selection of Best Software

g)      Multiple trait mapping

h)      Testing for linked vs. pleiotropic QTLs

i)        Multiple interval mapping or multiple QTL mapping

j)        Statistical significance

k)      Permutation testing

l)        Bootstrapping

m)    Permutation vs. bootstrapping and other methods

n)      QTL x QTL interaction: impact of epistasis

o)      QTL x Environment interaction

p)      Congruence of QTLs: across the environments and across the genetic backgrounds is the key in MAS

q)      Meta-QTL analysis

r)       Concluding remarks on QTL methods

s)       Alternatives in classical QTL mapping: Understanding and Practicing Different Strategies

t)       Bulked segregant analysis and selective genotyping: Basics, genetic considerations and Procedures

u)      Genomics assisted breeding: Basics, genetic considerations and Procedures

v)      Array mapping: Basics, genetic considerations and Procedures

w)    Association mapping: Basics, genetic considerations and Procedures

x)      Nested association mapping: Basics, genetic considerations and Procedures

y)      EcoTILLING: Basics, genetic considerations and Procedures

z)       Challenges and Troubleshooting in QTL mapping

aa)   Way forward to incorporate into regular crop breeding program

 

8.       Fine Mapping

a)      Need for fine mapping or high resolution mapping

b)      Types of markers suitable for fine mapping

                                                         i.            Marker Type Conversion

c)       Physical mapping and its role in fine mapping

d)      Comparative mapping

e)      Genetical genomics or eQTL mapping

f)       Map based cloning

                                             i.            Explaining with case studies

g)      Validation of QTL

h)      Testing the markers in related germplasm accessions

 

9.       Marker Assisted Selections

a)      Prelude

b)      Why should we use MAS?

c)       What prevents the use of MAS?

d)      Prerequisites for an efficient marker assisted program

e)      Procedure for generalized MAS program for selection from breeding lines / populations

f)       Marker assisted back cross breeding: Principles and Procedures

g)      Gene pyramiding or stacking: Principles and Procedures

h)      Accelerated methods of gene pyramiding: Principles and Procedures

i)        Marker assisted recurrent selection: Principles and Procedures

j)        AB-QTL: Principles and Procedures

k)      Mapping-as-you-go: Principles and Procedures

l)        Application of MAS in germplasm storage, evaluation and use

m)    Resources for MAS on the web

 

10.   Success Stories in MAS

a)      MAS in Major Crop: Tomato

b)      MAS in Major Crop: Maize

c)       MAS in Major Crop: Wheat

d)      MAS in Major Crop: Rice

e)      MAS in Major Crop: Cotton

f)       MAS in Major Crop: Soybean

g)      Varieties released through MAS

h)      Hybrids released through MAS

i)        MAS in multinational companies

j)        Contrasting stories

k)      Conclusions and future prospects

 

11.   Towards genetically improved crop plants: Roles of ‘Omics and MAS

a)      Molecular breeding platforms

                                             i.            Comparisons of Techniques in molecular, biochemical and physiological studies and its integration into MAS

b)      Prelude on Molecular techniques

c)       Expression profiling

d)      cDNA library construction

e)      Differential display and representational difference analysis

f)       Subtractive hybridization

g)      Microarray

h)      Nucleic acid sequencing

i)        Serial analysis of gene expression (SAGE)

j)        cDNA-AFLP

k)      RFLP coupled domain directed differential display (RC4D)

l)        Gene tagging by insertional mutagenesis

m)    Post transcriptional gene silencing

n)      microRNAs

o)      Biochemical techniques

p)      Proteomics

q)      Genomics assisted breeding

r)       Functional markers

s)       Comparative genomics

t)       Identification of novel molecular networks and construction of new metabolic pathway

u)      Bioinformatics and MAS

 

 

12.   Forthcoming Perspectives in MAS

a)      MAS in orphan crops

b)      MAS in Horticultural Crops:

                                             i.            Vegetables,

                                           ii.            Fruit Crops,

                                          iii.            Medicinal and Aromatic Crops

                                         iv.            Landscaping Plants

c)       MAS in developing countries

d)      Perspectives of MAS in Commercial Breeding Program

e)      Community efforts and their implications in MAS

f)       Field and laboratory infrastructure improvement

g)      Genetic Mapping and MAS: Lessons learnt and concluding remarks

 

O autorze

Dr. N. Manikanda Boopathi is currently working as a Professor (Biotechnology) at the Department of Plant Biotechnology, CPMB&B, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. He completed his Master’s and Doctoral  studies in Plant Biotechnology at TNAU and subsequently trained at the International Rice Research Institute, the Philippines. He has taught more than 25 courses for undergraduate and graduate students and offered invited lectures and demonstrations at several institutions both in India and abroad. His scientific works have been honored with several awards. He has extensive experience in QTL mapping and marker assisted selection in rice, cotton, mungbean and tomato. He has successfully completed several national and international research projects and is currently engaged in nationwide and worldwide network projects that address the problems of biotic and abiotic stress. His publications and other details can be found at https://sites.google.com/a/tnau.ac.in/drnmb/home. 

Blurb

The first edition of this book, Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits, was widely appreciated as the first of its kind on this topic and has been listed as a reference work in several agricultural universities’ curricula. A great deal has happened over the last five years, making it high time to incorporate recent developments in genetic mapping and report on novel strategies in marker assisted selection in crop plants as a second edition. 

This book addresses a range of topics, including: new marker types and their genotyping methods based on high-throughput technologies, advances in genomics and their role in new marker development, improvements in genetic mapping strategies and software updates, developments in phenomics and their applications in QTL mapping, and how to incorporate these developments and advances in marker assisted selection in crop plants. Similar to the first edition, each technique and method is explained using a step-by-step method, allowing the book to serve as a self-study guide for scholars whose work involves the genetic improvement of crop plants for any trait of interest, particularly for biotic and abiotic stress resistance.

In addition, the book offers a valuable guide for undergraduate and graduate students at agricultural universities and institutes that are interested and/or involved in the genetic improvement of crop plants using modern tools. In addition, the bibliography includes a list of suggested works for pursuing further research on the topics covered.