This slideshow covers the topic on types of markers and their applications in the field of agriculture.

1. MASTER’S SEMINAR ON
APPLICATIONS OF
MOLECULAR MARKERS IN
PLANT BREEDING
GP-591(1+0)
SPEAKER:-
SHUBHAM YADU
MSc.(Ag.) Previous
DEPARTMENT OF GENETICS AND PLANT
BREEDING
J

2. CONTENTS:
 WHAT IS A MARKER?
 TYPES OF MARKERS?
 WHAT IS A MOLECULAR MARKER?
 APPLICATIONS OF MOLECULAR MARKERS IN
PLANT BREEDING ….

3. What isa Marker?
•
Marker isan allelic difference or variation at a given locusin the DNAthat can
beobservedat morphological,biochemical ormolecularlevel.
Molecularmarkerare basedonnaturallyoccurringchanges orpolymorphismin
DNAsequence(deletion, substitution, addition,tandemrepeat orduplication)
All molecular markers occupy specific genomic positions within the
chromosomek/as ‘loci’
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5. They can visually distinguish qualities like seed structure,flower color,
growth habit and other important agronomic traits.
MMORPHOLOGICAL MARKERS
DISADVANTAGES :- UNSTABLE ,LIMITED NUMBER AND LESS
POLYMORPHISM

6. Biochemical Markers
• Biochemical markers, or isozymes, are multi-molecular
forms of enzymes which are coded by various genes, but
have the same functions.
Disadvantages: limited in number, less polymorphismand
affected by 8p/7l/a20n19ttissues and different plantBB-gr2owthstages.

7. DNA/Molecular Markers
• The DNA-based markers represent variation in
genomic DNA sequences of different
individuals.
• They are based on naturally occurring
polymorphism in DNA sequence i.e., base pair
addition, deletion, substitution.
• They are detected as differential mobility of
fragments in a gel, hybridization with an array or
PCR amplification, or as DNA sequence
differences.
• They are used to ‘flag’ the position of a
particular gene or the inheritance of a
particular character.

9. DNA/Molecular Markers
A. Onthe basisof ability to discriminatebetween same
ordifferent species
1. Co-dominant:discriminatebetween homoand
heterozygotes
2. Dominant: which do not discriminate
between homoand heterozygotes
Theycanbevisualized by:
a. Gelelectrophoresis
b. Ethidium bromideor silver staining
c. Radioactiveorcolorimetric probes

10. Comparisonbetween co-dominant &
dominant markers
P1 P2 F1 P1 P2 F1
AA aa Aa BB bb Bb

12. APerfectMolecularMarker
Polymorphic Co-dominant
Reproducible Robust
Costeffective Easytouse
Highthroughput Closelylinkedto the trait of interest
Marker
Trait Marker

13. Other markers:
 Cleaved Amplified Polymorphic
Sequence
(CAPS/PCR-RFLP)
Inter Simple Sequence
Repeat Other markers:
 Cleaved Amplified Polymorphic
Sequence
(CAPS/PCR-RFLP)
 Inter Simple Sequence Repeat
(ISSR)
 Single-strand conformation Polymorphism
(SSCP) (ISSR)

14. 1.Marker Assisted Selection (MAS)
• Marker assisted selection (MAS) is indirect selection for a
gene /QTL based on molecular markers closely linked to the
gene /QTL
• A tool that can help plant breeders to select more efficiently
for desirable crop traits
• Molecular markers can also be used for negative selection
for elimination of undesirable genes, from segregating
population

17. ADVANTAGES OF MAS:

18. Limitations of MAS:
MAS is a costly method
 It requires well equipped laboratory
MAS requires well trained manpower for handling of sophisticated
equipments
The detection of various linked DNA markers (AFLP, RFLP, RAPD,
SSR, SNP etc.) is a difficult, laborious and time consuming task.
 health hazards

19. Quantitative Trait Loci
The loci controlling quantitative traits are called
quantitative trait loci or QTL. Term first coined by
Gelderman in 1975.
It isthe region of the genome that
isassociated with an effect on a
quantitative trait.
It can be a single gene or cluster of linked genes that
affect the trait.
2.QTL:

21. Summary of QTL analysis
Recombinant Inbred Lines
(RILs,F2,F3,Doubled Haploid Lines)
Genotype with
molecular markers
Analyse trait data for each
line
Link trait data with marker data
- Mapping software
Parent 1 Parent 2
Trait QTL mapped at bottom of
small chromosome
QTL
Create a
Linkage
map with
molecularm
arkers

22. 3.Confirmation of Hybridity
• Heterozygosity of F1 can be
detected

23. 4.LinkageMapping
• For linkage mapping we want mapping population which is
immortal, universal, homozygous (true breeding type) and
doesnot fluctuate
BC1F2,F2,DH,F2:F3,RILs,NILs•

24. Linkage
Map

25. • Initially, evolutionary studies were totally
dependent on the geographical and
morphological changes among the
organisms.
• Advancements in the techniques of
molecular biology offer extended
information about the phylogeny and
evolution, molecular markers are being
used on a large scale nowadays.
5.Phylogenetic and evolutionary studies

26. • This research was carried out to study the genetic diversity
among the 50 aromatic rice accessions using the 32 simple
sequence repeat (SSR) markers.
• The objectives of this research were to quantify the genetic
divergence of aromatic rice accessions using SSR markers and
to identify the potential accessions for introgression into the
existing rice breeding program.

27. 27

28. • The dendrogram based on UPGMA and Nei’s genetic
distance classified the 53 rice accessions into 10
clusters.
• Analysis of molecular variance (AMOVA) revealed that
89% of the total variation observed in this germplasm
came from within the populations, while 11% of the
variation emanated among the populations.
• Using all these criteria and indices, seven accessions
(Acc9993, Acc6288, Acc6893, Acc7580, Acc6009,
Acc9956, and Acc11816) from three populations have
been identified and selected for further evaluation
before introgression into the existing breeding program
and for future aromatic rice varietal development.

29. 6.Heterosis Breeding
• Leeetal (1989) in cornsuggestedthat RFLPanalysisprovides an
alternative to field testing
Sincethen several attempts were madeto correlate
heterosiswith variability at molecularlevel
Melchinger etal (1991) analyzed 32 maizeinbred linesfor
heterosis
Stuberet al (1992) mappedQTLscontributing to heterosisin the
crossbetween elite maizeinbred lines B73andMo17
Xio et al (1995) mapped QTLs for heterosis in one of the
highest yielding indica x japonica hybrids and proposed
domianceasthe major causeof heterosisin rice.
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30. 7.Gene Pyramiding:
• Gene Pyramiding is the process of combining several genes
together into a single genotype
• Widely used for combining multiple disease
resistance genes for specific races of a pathogen.
• Pyramiding is extremely difficult to achieve using
conventional methods.
• Consider phenotyping a single plant for multiple forms of
seedling resistance-almost impossible
Important to develop durable disease resistance against
different races

31. 33
Gene Pyramiding
Process of combining several genes usually from 2 different parents, together into a
single genotype
Breeding plan
P1 × P2
F1
Gene A +B
MAS
Select F2 plants that have
Gene A and GeneB
Genotypes
P1 :AAbb × P2 : aaBB
F1 :AaBb
F2 AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb Aabb AaBb Aabb
aB AaBB AaBb aaBB aaBb
Ab AaBb Aabb aaBb aabb
(Hittalmani & Liu et al., 2000)

32. 8.Assessment of genetic diversity
Genetic diversity is the first hand
information.
Excellent tool for accessing genetic
diversity.
Direct utility in breeding programme.
Genetic diversity using molecular
markers has been studied.

33. 9.Sex identification
In plant kingdom dioecy (4% of angiosperm)
Development of male/ female specific markers
Early identification of male & female plants
Efficiency in improving of dioecious vegetables (Ivy gourd, Pointed
gourd , Spine gourd, Asparagus etc.)
Codominant STS markers enabling the differentiation of XY
from YY males in asparagus were developed by Reamon Buttner and
Jung (2002).
BAC-derived diagnostic markers for sex determination in
asparagus by Jamsri & co worker (2003)

34. 3.DNA finger printing for varietal
Identification and ascertaining variability in germplasm.
• Useful for characterization of accessions in plants.
F1 Chilli hybrids was determined using two molecular techniques RAPD
and ISSR.
Genome sequenced crops
Cucumber - 367mb
Potato - 844mb
Chinese cabbage - 283.8mb
Tomato - 900mb
Melon -450mb
Watermelon - 375mb
10.DNA fingerprinting for varietal
identification

35. The main uses of DNA Markers in Plant breeding and crop improvement is
Assessment of purity/Testing of Hybrid, Mapping major genes , Mapping male fertile
genes ,Mapping diseases resistance genes , Diversity Analysis , Mapping of QTL ,
Gene Pyramiding , Map based cloning of genes , Marker Assisted Selection , Marker
assisted backcross breeding , Phylogeny and evolution With the highly advanced
molecular genetic techniques, we are still not achieving our goals due to inaccurate
phenotyping. There is a need to make the molecular marker technology more precise,
productive and cost effective in order to investigate the underlying biology of various
traits of interest.
CONCLUSION