Basic_QTL_Marker-assisted_Selection_Sourabh.ppt

This presentation provides an introduction to quantitative trait loci (QTL) analysis and marker-assisted selection (MAS) in plant breeding. The presentation begins by explaining the type of quantitative traits. The process of QTL analysis, including the use of molecular genetic markers and statistical methods, is discussed. Practical examples demonstrating the power of MAS are provided, such as its use in improving crop traits in plant breeding programs. Overall, this presentation offers a comprehensive overview of these important genomics-based approaches that are transforming modern agriculture.

1. Sourabh Kumar
Department of Genetics and Plant Breeding
Chaudhary Charan Singh University, Meerut
Marker Assisted Selection

2. Crop Improvement Strategies

3. Molecularbreedingusesmolecularmarkerdatato
enhancebreedingactivities,improveselection
efficiency,andoptimizebreedingprogramplanning
andexecution.
Molecular breeding

4. Continuous Traits
MeristicTraits
Categorical TraitsOrdinal traits
Binary Traits
Quantitative
Traits ?

6. QTL ?
Agene/setofgenesorgenomicregions
associatedwiththeexpressionofa
quantitativetrait;referredtoas
QuantitativeTraitLocus(QTL).
Different type of QTLs:-
Main effect QTLs
Small effect QTLs
E-QTLs
e-QTLs
m-QTL
p-QTLs etc.

8. 1. Mapping Population
2. Genotypic data
3. Phenotypic data
4. Marker Linkage Map
5. Appropriate software packages
Pre-requisites for QTL Analysis

9. Mapping Population

10. Genotypic data

11. Marker Linkage Map

13. •Quantitativetraitlocus(QTL)analysis:astatisticalmethodlinkstwotypesof
information—phenotypicdata(traitmeasurements)andgenotypicdata(usually
molecularmarkers)—inanattempttoexplainthegeneticbasisofvariationin
complextraits(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

15. Bulk Segregant Analysis

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. M
1 A
m
1 a
M
2
m
2
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)

19. Introduction to MAS
Markerassistedselectionormarkeraided
selection(MAS)isanindirectselection
processwhereatraitofinterestis
selected based on a marker
(morphological,biochemicalorDNA
based)linkedtoatraitofinterest(e.g.
productivity,biotic/abioticstressor
quality),ratherthanonthetraititself.
ThistermfirstusedbyBeckmannand
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 mustbe polymorphic
1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8
RM84 RM296
P
1P
2
P
1P
2
Not polymorphic Polymorphic!

23. Bacterial blight
Blast
BPHHopper 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
F
1
RPX
BC
1F
1
Target trait
Yield
Quality
Stress resistance
Donor
Parent
Recurrent
Parent

27. F
2
P
2
F
1
P
1 x
large populations consisting of
thousands of plants
ResistantSusceptible
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

35. Pusa
Basmati 1

36. P
1 x F
1
P
1 x P
2
CONVENTIONAL BACKCROSSING
BC1
VISUAL SELECTION OF BC1 PLANTS THAT
MOST CLOSELY RESEMBLE RECURRENT
PARENT
BC2
MARKER-ASSISTED BACKCROSSING
P
1 x F
1
P
1 x P
2
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–ageneforimprovingqualityofproteininmaize
Anaturalspontaneousmaizemutantwithsoftandopaquegrain
wasfoundinamaizefieldsinUSAduringthe1920swhichwas
laternamedasopaque2(o2)maizebySingleton.

38. o2 utilization in breeding programmes
Resulted
Soft endosperm
Damaged kernels
Susceptibility to
pests and fungal
diseases
Inferiorfoodprocessing
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
actualreports 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 notbe 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