SlideShare a Scribd company logo
Sourabh Kumar
Department of Genetics and Plant Breeding
Chaudhary Charan Singh University, Meerut
Marker Assisted Selection
Crop Improvement Strategies
Molecular breeding uses molecular marker data to
enhance breeding activities, improve selection
efficiency, and optimize breeding program planning
and execution.
Molecular breeding
Continuous Traits
Meristic Traits
Categorical Traits Ordinal traits
Binary Traits
Quantitative
Traits ?
QTL ?
A gene/set of genes or genomic regions
associated with the expression of a
quantitative trait ; referred to as
Quantitative Trait Locus(QTL).
Different type of QTLs:-
 Main effect QTLs
 Small effect QTLs
 E-QTLs
 e-QTLs
 m-QTL
 p-QTLs etc.
1. Mapping Population
2. Genotypic data
3. Phenotypic data
4. Marker Linkage Map
5. Appropriate software packages
Pre-requisites for QTL Analysis
Mapping Population
Genotypic data
Marker Linkage Map
• Quantitative trait locus (QTL) analysis: a statistical method links two types of
information—phenotypic data (trait measurements) and genotypic data (usually
molecular markers)—in an attempt to explain the genetic basis of variation in
complex traits (Falconer & Mackay, 1996; Kearsey, 1998; Lynch & Walsh, 1998).
Approaches for QTL Analysis:
1. Single Marker Analysis
2. Interval Mapping(IM):-
 Simple Interval Mapping (SIM)
 Composite Interval Mapping (CIM)-Including Inclusive IM
 Multiple Interval Mapping (MIM) etc.
QTLs Analysis & Its Approaches
Single Marker Analysis (SMA)
 Detect associations between molecular markers and
traits of interest
Four Methods:-
1. ‘t’ Test
2. Regression Analysis
3. ANOVA
4. Maximum Likelihood Approach
A
a
M
m
QTL Marker
Bulk Segregant Analysis
ADVANTAGES AND LIMITATIONS OF SMA
Advantages
• Simplest method of QTL detection.
• Use basic statistical software.
• Not need linkage map.
Disadvantages/Limitations
 Confounded QTL effects & position, no determine
 Statistical Power is low
 Epistasis interaction can not be determine
 So, many false positive
M1 A
m1 a
M2
m2
Simple Interval Mapping (SIM)
Composite Interval Mapping (CIM)
 Use most significant markers as Cofactors
 CIM: Refinement of SIM
 CIM: Combining interval mapping with multiple
regression approach
 Power of QTL detection is increased, reduction of
bias in the estimation of QTL position and effects.
Inclusive Composite Interval Mapping (ICIM)
Introduction to MAS
Marker assisted selection or marker aided
selection (MAS) is an indirect selection
process where a trait of interest is
selected based on a marker
(morphological, biochemical or DNA
based) linked to a trait of interest (e.g.
productivity, biotic/abiotic stress or
quality), rather than on the trait itself.
This term first used by Beckmann and
Soller (1983).
What is molecular marker ?
• Ideally markers should be <5 cM from a gene or QTL
Note: Using a pair of flanking markers can greatly improve
reliability but increases time and cost
Marker A
QTL
5 cM
RELIABILITY FOR
SELECTION
Using marker A only:
~95%
Marker A
QTL
Marker B
5 cM 5 cM
Using markers A and B:
~99.5%
Markers must be
tightly-linked to target loci!
Markers must be polymorphic
1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8
RM84 RM296
P1 P2
P1 P2
Not polymorphic Polymorphic!
Bacterial blight Blast
BPH
Hopper Burn
False Smut
Sheath Blight
 Drought
 Heat
 Submergence
 Salinity
 Nutrients deficiency
Major constraints: Biotic and abiotic Stresses
General Steps in MAS-
1.Selection of parents.
2.Development of Breeding Population.
3.Isolation of DNA.
4.Scoring of marker.
5.Correlation with Morphological traits.
(1) LEAF TISSUE
SAMPLING
(2) DNA EXTRACTION
(3) PCR
(4) GEL ELECTROPHORESIS
(5) MARKER ANALYSIS
Overview of
‘marker
genotyping’
Marker Assisted Backcross Breeding (MABB)
Foreground selection
Recombinant selection
Background selection
Phenotypic selection
X
F1 RP
X
BC1F1
 Target trait
 Yield
 Quality
 Stress resistance
Donor
Parent
Recurrent
Parent
F2
P2
F1
P1 x
large populations consisting of
thousands of plants
Resistant
Susceptible
MARKER-ASSISTED SELECTION (MAS)
MARKER-ASSISTED BREEDING
Method whereby phenotypic selection is based on DNA markers
Marker-assisted backcrossing
Selection
for target
gene or
QTL
1 2 3 4
Target
locus
1 2 3 4
1 2 3 4
BACKGROUND
SELECTION
TARGET LOCUS
SELECTION
FOREGROUND
SELECTION
BACKGROUND SELECTION
Accelerates the
recovery of the
recurrent parent
genome
Pusa
Basmati 1
P1 x F1
P1 x P2
CONVENTIONAL BACKCROSSING
BC1
VISUAL SELECTION OF BC1 PLANTS THAT
MOST CLOSELY RESEMBLE RECURRENT
PARENT
BC2
MARKER-ASSISTED BACKCROSSING
P1 x F1
P1 x P2
BC1
USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS
THAT HAVE MOST RP MARKERS AND SMALLEST %
OF DONOR GENOME
BC2
Discovered first high lysine mutant (1935) - o2
Reported second mutant for change in amino acid composition
(1935) - fl2
Discovery of QPM
 Opaque2 – a gene for improving quality of protein in maize
 A natural spontaneous maize mutant with soft and opaque grain
was found in a maize fields in USA during the 1920s which was
later named as opaque2 (o2) maize by Singleton.
o2 utilization in breeding programmes
Resulted
Soft endosperm
Damaged kernels
Susceptibility to
pests and fungal
diseases
Inferior food processing
Reduced yields
Early efforts and experiences in using o2 cultivars
pleiotropic effects of this gene
Application of MAS
1.It is useful in gene pyramiding for disease and insect
resistance.
2.Uses in backcrossing programme.
3.It is being used for transfer of male sterility into
cultivated genotypes from different sources.
4.MAS is being used for improvement of quality
characters in different crops such as for protein
quality in maize, etc…
Advantage of MAS
1. Accuracy,
2. Rapid Method,
3. Non-transgenic Product,
4. Identification of Recessive Alleles,
5. Early Detection of Traits,
6. Screening of Difficult Traits,
7. Highly Reproducible,
8. Small Sample for Testing, etc…
Achievements of MAS
1.Rice-a. (PB1 x JRBB55) Improved Pusa
Basmati 1, b. Improved Sambha
Mahsuri(BPT5204),
2.Maize - Improved QPM-9,
3.Pearlmillet - HHB67-2,
4.Wheat - Patwin, etc
Revolutionary Basmati Rice Varieties
Pusa Basmati 1
Improved Pusa Basmati 1
Current status of molecular breeding
• A literature review
indicates thousands of
QTL mapping/GWAS
studies but not many
actual reports of the
application of MAS in
breeding
• Why is this the case?
Some possible reasons to explain the low
impact of MAS in crop improvement
• Resources (equipment) not available
• Markers may not be cost-effective
• Accuracy of QTL mapping studies
• QTL effects may depend on genetic
background or be influenced by
environmental conditions
• Lack of marker polymorphism in breeding
material
• Poor integration of molecular genetics and
conventional breeding
Basic_QTL_Marker-assisted_Selection_Sourabh.ppt

More Related Content

Similar to Basic_QTL_Marker-assisted_Selection_Sourabh.ppt

Marker assistant selection
Marker assistant selectionMarker assistant selection
Marker assistant selection
Pawan Nagar
 
MAS
MASMAS
Marker assisted selection
Marker assisted selectionMarker assisted selection
Marker assisted selection
DrSunil Bhakar
 
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
IRJET Journal
 
Marker assisted backcross breeding
Marker assisted backcross breedingMarker assisted backcross breeding
Marker assisted backcross breeding
Anilkumar C
 
Marker assisted selection( mas) and its application in plant breeding
Marker assisted selection( mas) and its application in plant breedingMarker assisted selection( mas) and its application in plant breeding
Marker assisted selection( mas) and its application in plant breeding
Hemantkumar Sonawane
 
Selection based on markers
Selection based on markersSelection based on markers
Selection based on markers
Tanuja M
 
Marker Assisted Selection
Marker Assisted SelectionMarker Assisted Selection
Marker Assisted Selection
Khushbu
 
markers in plant breeding.
markers in plant breeding.markers in plant breeding.
markers in plant breeding.
Alemu Abate
 
QTL mapping and analysis.pptx
QTL mapping and analysis.pptxQTL mapping and analysis.pptx
QTL mapping and analysis.pptx
SarathS586768
 
Marker assisted selection in plants
Marker assisted selection in plantsMarker assisted selection in plants
Marker assisted selection in plants
iqraakbar8
 
Omics for crop improvement (new)
Omics for crop improvement (new)Omics for crop improvement (new)
Omics for crop improvement (new)
Gokul Dhana
 
Biotechnological interventions for crop improvement in fruit crops.pptx
Biotechnological interventions for crop improvement in fruit crops.pptxBiotechnological interventions for crop improvement in fruit crops.pptx
Biotechnological interventions for crop improvement in fruit crops.pptx
Punjab Agricultural University, Ludhiana
 
Biotechnological interventions for fruit crops improvement
Biotechnological interventions for fruit crops improvementBiotechnological interventions for fruit crops improvement
Biotechnological interventions for fruit crops improvement
Punjab Agricultural University, Ludhiana
 
marker assisted selection
marker assisted selectionmarker assisted selection
marker assisted selection
Bhargava Bhanu Kadthala
 
Marker assisted selection (rice).pptx
Marker assisted selection (rice).pptxMarker assisted selection (rice).pptx
Marker assisted selection (rice).pptx
Elizabeth Philip
 
Ganesh gp 509
Ganesh gp 509Ganesh gp 509
Ganesh gp 509
9494458298
 
Application of molecular markers in Plant Breeding
Application of molecular markers in Plant BreedingApplication of molecular markers in Plant Breeding
Application of molecular markers in Plant Breeding
ShubhamYadu1
 
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
FOODCROPS
 
Marker Assisted Breeding in Maize
Marker Assisted Breeding in MaizeMarker Assisted Breeding in Maize
Marker Assisted Breeding in Maize
Nivethitha T
 

Similar to Basic_QTL_Marker-assisted_Selection_Sourabh.ppt (20)

Marker assistant selection
Marker assistant selectionMarker assistant selection
Marker assistant selection
 
MAS
MASMAS
MAS
 
Marker assisted selection
Marker assisted selectionMarker assisted selection
Marker assisted selection
 
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
IRJET- Analysis of Hybrid Purity in Watermelon using Microsatellite Marker in...
 
Marker assisted backcross breeding
Marker assisted backcross breedingMarker assisted backcross breeding
Marker assisted backcross breeding
 
Marker assisted selection( mas) and its application in plant breeding
Marker assisted selection( mas) and its application in plant breedingMarker assisted selection( mas) and its application in plant breeding
Marker assisted selection( mas) and its application in plant breeding
 
Selection based on markers
Selection based on markersSelection based on markers
Selection based on markers
 
Marker Assisted Selection
Marker Assisted SelectionMarker Assisted Selection
Marker Assisted Selection
 
markers in plant breeding.
markers in plant breeding.markers in plant breeding.
markers in plant breeding.
 
QTL mapping and analysis.pptx
QTL mapping and analysis.pptxQTL mapping and analysis.pptx
QTL mapping and analysis.pptx
 
Marker assisted selection in plants
Marker assisted selection in plantsMarker assisted selection in plants
Marker assisted selection in plants
 
Omics for crop improvement (new)
Omics for crop improvement (new)Omics for crop improvement (new)
Omics for crop improvement (new)
 
Biotechnological interventions for crop improvement in fruit crops.pptx
Biotechnological interventions for crop improvement in fruit crops.pptxBiotechnological interventions for crop improvement in fruit crops.pptx
Biotechnological interventions for crop improvement in fruit crops.pptx
 
Biotechnological interventions for fruit crops improvement
Biotechnological interventions for fruit crops improvementBiotechnological interventions for fruit crops improvement
Biotechnological interventions for fruit crops improvement
 
marker assisted selection
marker assisted selectionmarker assisted selection
marker assisted selection
 
Marker assisted selection (rice).pptx
Marker assisted selection (rice).pptxMarker assisted selection (rice).pptx
Marker assisted selection (rice).pptx
 
Ganesh gp 509
Ganesh gp 509Ganesh gp 509
Ganesh gp 509
 
Application of molecular markers in Plant Breeding
Application of molecular markers in Plant BreedingApplication of molecular markers in Plant Breeding
Application of molecular markers in Plant Breeding
 
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
Jiankang Wang. Principle of QTL mapping and inclusive composite interval mapp...
 
Marker Assisted Breeding in Maize
Marker Assisted Breeding in MaizeMarker Assisted Breeding in Maize
Marker Assisted Breeding in Maize
 

Recently uploaded

Your Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective UpskillingYour Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective Upskilling
Excellence Foundation for South Sudan
 
How to Setup Warehouse & Location in Odoo 17 Inventory
How to Setup Warehouse & Location in Odoo 17 InventoryHow to Setup Warehouse & Location in Odoo 17 Inventory
How to Setup Warehouse & Location in Odoo 17 Inventory
Celine George
 
Advanced Java[Extra Concepts, Not Difficult].docx
Advanced Java[Extra Concepts, Not Difficult].docxAdvanced Java[Extra Concepts, Not Difficult].docx
Advanced Java[Extra Concepts, Not Difficult].docx
adhitya5119
 
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
imrankhan141184
 
How to Create a More Engaging and Human Online Learning Experience
How to Create a More Engaging and Human Online Learning Experience How to Create a More Engaging and Human Online Learning Experience
How to Create a More Engaging and Human Online Learning Experience
Wahiba Chair Training & Consulting
 
Liberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdfLiberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdf
WaniBasim
 
How to deliver Powerpoint Presentations.pptx
How to deliver Powerpoint  Presentations.pptxHow to deliver Powerpoint  Presentations.pptx
How to deliver Powerpoint Presentations.pptx
HajraNaeem15
 
MARY JANE WILSON, A “BOA MÃE” .
MARY JANE WILSON, A “BOA MÃE”           .MARY JANE WILSON, A “BOA MÃE”           .
MARY JANE WILSON, A “BOA MÃE” .
Colégio Santa Teresinha
 
BBR 2024 Summer Sessions Interview Training
BBR  2024 Summer Sessions Interview TrainingBBR  2024 Summer Sessions Interview Training
BBR 2024 Summer Sessions Interview Training
Katrina Pritchard
 
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdfবাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
eBook.com.bd (প্রয়োজনীয় বাংলা বই)
 
Film vocab for eal 3 students: Australia the movie
Film vocab for eal 3 students: Australia the movieFilm vocab for eal 3 students: Australia the movie
Film vocab for eal 3 students: Australia the movie
Nicholas Montgomery
 
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
GeorgeMilliken2
 
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) CurriculumPhilippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
MJDuyan
 
spot a liar (Haiqa 146).pptx Technical writhing and presentation skills
spot a liar (Haiqa 146).pptx Technical writhing and presentation skillsspot a liar (Haiqa 146).pptx Technical writhing and presentation skills
spot a liar (Haiqa 146).pptx Technical writhing and presentation skills
haiqairshad
 
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
Nguyen Thanh Tu Collection
 
Gender and Mental Health - Counselling and Family Therapy Applications and In...
Gender and Mental Health - Counselling and Family Therapy Applications and In...Gender and Mental Health - Counselling and Family Therapy Applications and In...
Gender and Mental Health - Counselling and Family Therapy Applications and In...
PsychoTech Services
 
A Independência da América Espanhola LAPBOOK.pdf
A Independência da América Espanhola LAPBOOK.pdfA Independência da América Espanhola LAPBOOK.pdf
A Independência da América Espanhola LAPBOOK.pdf
Jean Carlos Nunes Paixão
 
Temple of Asclepius in Thrace. Excavation results
Temple of Asclepius in Thrace. Excavation resultsTemple of Asclepius in Thrace. Excavation results
Temple of Asclepius in Thrace. Excavation results
Krassimira Luka
 
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptxBeyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
EduSkills OECD
 
Main Java[All of the Base Concepts}.docx
Main Java[All of the Base Concepts}.docxMain Java[All of the Base Concepts}.docx
Main Java[All of the Base Concepts}.docx
adhitya5119
 

Recently uploaded (20)

Your Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective UpskillingYour Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective Upskilling
 
How to Setup Warehouse & Location in Odoo 17 Inventory
How to Setup Warehouse & Location in Odoo 17 InventoryHow to Setup Warehouse & Location in Odoo 17 Inventory
How to Setup Warehouse & Location in Odoo 17 Inventory
 
Advanced Java[Extra Concepts, Not Difficult].docx
Advanced Java[Extra Concepts, Not Difficult].docxAdvanced Java[Extra Concepts, Not Difficult].docx
Advanced Java[Extra Concepts, Not Difficult].docx
 
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
Traditional Musical Instruments of Arunachal Pradesh and Uttar Pradesh - RAYH...
 
How to Create a More Engaging and Human Online Learning Experience
How to Create a More Engaging and Human Online Learning Experience How to Create a More Engaging and Human Online Learning Experience
How to Create a More Engaging and Human Online Learning Experience
 
Liberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdfLiberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdf
 
How to deliver Powerpoint Presentations.pptx
How to deliver Powerpoint  Presentations.pptxHow to deliver Powerpoint  Presentations.pptx
How to deliver Powerpoint Presentations.pptx
 
MARY JANE WILSON, A “BOA MÃE” .
MARY JANE WILSON, A “BOA MÃE”           .MARY JANE WILSON, A “BOA MÃE”           .
MARY JANE WILSON, A “BOA MÃE” .
 
BBR 2024 Summer Sessions Interview Training
BBR  2024 Summer Sessions Interview TrainingBBR  2024 Summer Sessions Interview Training
BBR 2024 Summer Sessions Interview Training
 
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdfবাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
বাংলাদেশ অর্থনৈতিক সমীক্ষা (Economic Review) ২০২৪ UJS App.pdf
 
Film vocab for eal 3 students: Australia the movie
Film vocab for eal 3 students: Australia the movieFilm vocab for eal 3 students: Australia the movie
Film vocab for eal 3 students: Australia the movie
 
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
What is Digital Literacy? A guest blog from Andy McLaughlin, University of Ab...
 
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) CurriculumPhilippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
Philippine Edukasyong Pantahanan at Pangkabuhayan (EPP) Curriculum
 
spot a liar (Haiqa 146).pptx Technical writhing and presentation skills
spot a liar (Haiqa 146).pptx Technical writhing and presentation skillsspot a liar (Haiqa 146).pptx Technical writhing and presentation skills
spot a liar (Haiqa 146).pptx Technical writhing and presentation skills
 
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
 
Gender and Mental Health - Counselling and Family Therapy Applications and In...
Gender and Mental Health - Counselling and Family Therapy Applications and In...Gender and Mental Health - Counselling and Family Therapy Applications and In...
Gender and Mental Health - Counselling and Family Therapy Applications and In...
 
A Independência da América Espanhola LAPBOOK.pdf
A Independência da América Espanhola LAPBOOK.pdfA Independência da América Espanhola LAPBOOK.pdf
A Independência da América Espanhola LAPBOOK.pdf
 
Temple of Asclepius in Thrace. Excavation results
Temple of Asclepius in Thrace. Excavation resultsTemple of Asclepius in Thrace. Excavation results
Temple of Asclepius in Thrace. Excavation results
 
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptxBeyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptx
 
Main Java[All of the Base Concepts}.docx
Main Java[All of the Base Concepts}.docxMain Java[All of the Base Concepts}.docx
Main Java[All of the Base Concepts}.docx
 

Basic_QTL_Marker-assisted_Selection_Sourabh.ppt

  • 1. Sourabh Kumar Department of Genetics and Plant Breeding Chaudhary Charan Singh University, Meerut Marker Assisted Selection
  • 3. Molecular breeding uses molecular marker data to enhance breeding activities, improve selection efficiency, and optimize breeding program planning and execution. Molecular breeding
  • 4. Continuous Traits Meristic Traits Categorical Traits Ordinal traits Binary Traits Quantitative Traits ?
  • 5.
  • 6. QTL ? A gene/set of genes or genomic regions associated with the expression of a quantitative trait ; referred to as Quantitative Trait Locus(QTL). Different type of QTLs:-  Main effect QTLs  Small effect QTLs  E-QTLs  e-QTLs  m-QTL  p-QTLs etc.
  • 7.
  • 8. 1. Mapping Population 2. Genotypic data 3. Phenotypic data 4. Marker Linkage Map 5. Appropriate software packages Pre-requisites for QTL Analysis
  • 12.
  • 13. • Quantitative trait locus (QTL) analysis: a statistical method links two types of information—phenotypic data (trait measurements) and genotypic data (usually molecular markers)—in an attempt to explain the genetic basis of variation in complex traits (Falconer & Mackay, 1996; Kearsey, 1998; Lynch & Walsh, 1998). Approaches for QTL Analysis: 1. Single Marker Analysis 2. Interval Mapping(IM):-  Simple Interval Mapping (SIM)  Composite Interval Mapping (CIM)-Including Inclusive IM  Multiple Interval Mapping (MIM) etc. QTLs Analysis & Its Approaches
  • 14. Single Marker Analysis (SMA)  Detect associations between molecular markers and traits of interest Four Methods:- 1. ‘t’ Test 2. Regression Analysis 3. ANOVA 4. Maximum Likelihood Approach A a M m QTL Marker
  • 16. ADVANTAGES AND LIMITATIONS OF SMA Advantages • Simplest method of QTL detection. • Use basic statistical software. • Not need linkage map. Disadvantages/Limitations  Confounded QTL effects & position, no determine  Statistical Power is low  Epistasis interaction can not be determine  So, many false positive
  • 17. M1 A m1 a M2 m2 Simple Interval Mapping (SIM) Composite Interval Mapping (CIM)  Use most significant markers as Cofactors  CIM: Refinement of SIM  CIM: Combining interval mapping with multiple regression approach  Power of QTL detection is increased, reduction of bias in the estimation of QTL position and effects. Inclusive Composite Interval Mapping (ICIM)
  • 18.
  • 19. Introduction to MAS Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (morphological, biochemical or DNA based) linked to a trait of interest (e.g. productivity, biotic/abiotic stress or quality), rather than on the trait itself. This term first used by Beckmann and Soller (1983).
  • 20. What is molecular marker ?
  • 21. • Ideally markers should be <5 cM from a gene or QTL Note: Using a pair of flanking markers can greatly improve reliability but increases time and cost Marker A QTL 5 cM RELIABILITY FOR SELECTION Using marker A only: ~95% Marker A QTL Marker B 5 cM 5 cM Using markers A and B: ~99.5% Markers must be tightly-linked to target loci!
  • 22. Markers must be polymorphic 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 RM84 RM296 P1 P2 P1 P2 Not polymorphic Polymorphic!
  • 23. Bacterial blight Blast BPH Hopper Burn False Smut Sheath Blight  Drought  Heat  Submergence  Salinity  Nutrients deficiency Major constraints: Biotic and abiotic Stresses
  • 24. General Steps in MAS- 1.Selection of parents. 2.Development of Breeding Population. 3.Isolation of DNA. 4.Scoring of marker. 5.Correlation with Morphological traits.
  • 25. (1) LEAF TISSUE SAMPLING (2) DNA EXTRACTION (3) PCR (4) GEL ELECTROPHORESIS (5) MARKER ANALYSIS Overview of ‘marker genotyping’
  • 26. Marker Assisted Backcross Breeding (MABB) Foreground selection Recombinant selection Background selection Phenotypic selection X F1 RP X BC1F1  Target trait  Yield  Quality  Stress resistance Donor Parent Recurrent Parent
  • 27. F2 P2 F1 P1 x large populations consisting of thousands of plants Resistant Susceptible MARKER-ASSISTED SELECTION (MAS) MARKER-ASSISTED BREEDING Method whereby phenotypic selection is based on DNA markers
  • 28. Marker-assisted backcrossing Selection for target gene or QTL 1 2 3 4 Target locus 1 2 3 4 1 2 3 4 BACKGROUND SELECTION TARGET LOCUS SELECTION FOREGROUND SELECTION BACKGROUND SELECTION Accelerates the recovery of the recurrent parent genome
  • 29.
  • 30.
  • 31.
  • 32.
  • 33.
  • 34.
  • 36. P1 x F1 P1 x P2 CONVENTIONAL BACKCROSSING BC1 VISUAL SELECTION OF BC1 PLANTS THAT MOST CLOSELY RESEMBLE RECURRENT PARENT BC2 MARKER-ASSISTED BACKCROSSING P1 x F1 P1 x P2 BC1 USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS THAT HAVE MOST RP MARKERS AND SMALLEST % OF DONOR GENOME BC2
  • 37. Discovered first high lysine mutant (1935) - o2 Reported second mutant for change in amino acid composition (1935) - fl2 Discovery of QPM  Opaque2 – a gene for improving quality of protein in maize  A natural spontaneous maize mutant with soft and opaque grain was found in a maize fields in USA during the 1920s which was later named as opaque2 (o2) maize by Singleton.
  • 38. o2 utilization in breeding programmes Resulted Soft endosperm Damaged kernels Susceptibility to pests and fungal diseases Inferior food processing Reduced yields Early efforts and experiences in using o2 cultivars pleiotropic effects of this gene
  • 39. Application of MAS 1.It is useful in gene pyramiding for disease and insect resistance. 2.Uses in backcrossing programme. 3.It is being used for transfer of male sterility into cultivated genotypes from different sources. 4.MAS is being used for improvement of quality characters in different crops such as for protein quality in maize, etc…
  • 40. Advantage of MAS 1. Accuracy, 2. Rapid Method, 3. Non-transgenic Product, 4. Identification of Recessive Alleles, 5. Early Detection of Traits, 6. Screening of Difficult Traits, 7. Highly Reproducible, 8. Small Sample for Testing, etc…
  • 41. Achievements of MAS 1.Rice-a. (PB1 x JRBB55) Improved Pusa Basmati 1, b. Improved Sambha Mahsuri(BPT5204), 2.Maize - Improved QPM-9, 3.Pearlmillet - HHB67-2, 4.Wheat - Patwin, etc
  • 42. Revolutionary Basmati Rice Varieties Pusa Basmati 1 Improved Pusa Basmati 1
  • 43. Current status of molecular breeding • A literature review indicates thousands of QTL mapping/GWAS studies but not many actual reports of the application of MAS in breeding • Why is this the case?
  • 44. Some possible reasons to explain the low impact of MAS in crop improvement • Resources (equipment) not available • Markers may not be cost-effective • Accuracy of QTL mapping studies • QTL effects may depend on genetic background or be influenced by environmental conditions • Lack of marker polymorphism in breeding material • Poor integration of molecular genetics and conventional breeding