markers and their role

DNA Markers in Plant
Breeding
Presented by- Miss. Habde Sonali
Vijay
Reg. No 014/047
Genetics and Plant breeding M. Sc. 2nd year

WHAT IS A MARKER ???
Marker: an object used to indicate a position,
place, or presence of a particular object
 A bookmark.
A milestone.
 A tombstone.

Any property of individual showing heritable variations is
referred to as a character.
Morphological
Cytological
Biochemical
DNA markers
The character which can be easily identified are referred
as marker character.

Morphological Markers
• Phenotypic markers
• Naked eye marker
This are related to shape, size, colour and
morphological parameters.
Used in varietal identification.
Hulled Naked Black White

Proteins Markers
•Biochemical markers are related to
variations in protein and amino acid
banding pattern. Gel electrophoresis
studies are used for identification of
biochemical markers.
Isozymes:
A species of enzyme that exists
into two or more structural forms
which are easily identified by
their activities

DNA MARKERS
 Genetic markers represent genetic differences between individual
organisms or species.
 Generally, they do not represent the target genes themselves but act
as‘signs’ or ‘ﬂags’.
 Genetic markers that are located in close proximity to genes
(i.e.tightly linked) may be referred to as gene ‘tags’.
 Such markers themselves do not affect the phenotype of the trait of
interest because they are located only near or ‘linked’ to
genes controlling the trait.
 All genetic markers occupy speciﬁc genomic positions within
chromosomes (like genes) called ‘loci’ (singular ‘locus’).
Simply speaking, DNA marker is a small region of DNA
sequence showing polymorphism (base deletion, insertion and
substitution) between different individuals

ADVANTAGES OF MOLECULAR MARKERS
OVER MORPHOLOGICAL MARKERS
This are neutral sites.
Located in non coding site.
Do not affect the trait of interest.
Numerous and abundantly available.
Not get affected by environment or morphological
stage of plant.

Polymorphism
-Parent 1 : one band
-Parent 2 : a smaller band
-Offspring 1 : heterozygote = both bands
-Offspring 2 : homozygote parent 1
Polymorphism
Parent 1 : one band
-Parent 2 : no band
-Offspring 1 : homozygote parent 1
-Offspring 2 : ????
P 2P 1 O 2O 1
Gel configuration
Co-dominant marker
P 2
Gel configuration
P 1 O 1 O 2
Dominant marker

• Polymorphic
• Co-dominant inheritance
• Occurs and recurrent occurence throughout
the genome
• Variable and Reproducible
• Easy, fast and cheap to detect
• Selectivity neutral to environment
• High resolution with large number of samples
• Associated with specific locus
• Possible data exchange among different lab
• Cost and time effective
Ideal marker system

DNA markers may be broadly divided into
three classes based on the method of their
detection:
(1) Hybridization based
(2) Polymerase chain reaction based
(3) DNA sequence-based

HYBRIDIZATION BASED MARKERS
In hybridization based markers, DNA profiles are
visualized by hybridizing the restriction endonuclease
digested DNA fragment, to a labelled probe, which is
a DNA fragment of known sequence.
e.g. Restriction fragment length polymorphism
(RFLP).

Denaturation
Elevated temperature
Known DNA sequence
Restriction Fragment
Length Polymorphism
DNA/DNA Hybridization

The technique is based on restriction enzymes that reveal a
pattern difference between DNA fragment sizes in individual
organisms
Difference at a few nucleotides possibly due to point mutation,
insertion/deletion, translocation, inversion, and duplication lead to
change in DNA sequences at the restriction sites can result in the
gain, loss, or relocation of a restriction site.
RFLPs can be applied in diversity and phylogenetic studies.
It is widely used in gene mapping studies because of their
high genomic abundance, ample availability of different
restriction enzymes and random distribution throughout
the genome

3
6
2
61 2 43 5
4
5
1
MFG
RFLP Polymorphisms interpretation

• Advantages
– Reproducible
– Co-dominant
– Simple
– Robust
– Reliable
– Transferable across
population.
– Easily scored
– No need of sequence
information
• Disadvantages
– Time consuming
– Expensive
– Use of radioactive
probes
– Large quantity DNA
required
– Limited
polymorphism

PCR BASED MARKERS
Using PCR and/or molecular hybridization followed by
electrophoresis (e.g. PAGE – polyacrylamide gel
electrophoresis, AGE – agarose gel electrophoresis, CE
– capillary electrophoresis), the variation in DNA
samples or polymorphism for a specific region of DNA
sequence can be identified based on the product
features, such as Band size and Mobility.

Polymerase Chain Reaction
Powerful technique for amplifying DNA
Amplified DNA are then separated
by gel electrophoresis

RANDOMLY AMPLIFIED POLYMORPHIC DNA
 These are DNA fragments amplified by the PCR using short synthetic
primers (generally 10 bp) of random sequence.
 Oligonucleotides serve as both forward- and reverse-primers.
 Amplified fragments separated by agarose gel electrophoresis
 Polymorphisms can be detected after ethidium bromide staining as
the presence or absence of bands of particular sizes
 Polymorphisms are of primer annealing sites or length differences in
the amplified sequence between primer annealing sites
Application
RAPDs ranging from studies at the individual level (e.g.
genetic identity) to studies involving closely related species and
gene mapping studies to fill gaps not covered by other markers

RAPD MARKERS
DNA markers which developed by amplifying random
sequence of specific markers through the used of random
primers.

RAPD Polymorphisms among landraces of sorghum
M
Sequences of 10-
mer
RAPD primers
Name Sequence
OP A08 5’ –GTGACGTAGG- 3’
OP A15 5’ –TTCCGAACCC- 3’
OP A 17 5’ –GACCGCTTGT- 3’
OP A19 5’ –CAAACGTCGG- 3’
OP D02 5’ –GGACCCAACC- 3’
RAPD gel configuration

Advantages Disadvantages
-Less time consuming -Low reproducibility
-simple, quick, easy a nd efficient assay -Incapable to detect allelic
-Low quantity of DNA required -difference heterozygote
-Provide dominant marker -unsuitable for transfer
band and comparison
-High genomic abundance -uninterpretation of profile
-Random distribution throughout genome
-No need of blotting or hybridization
-No need of sequence data information
-Automate procedure
-Detect high level of polymorphism
-RAPD product of interest can be converted into SCAR, SNP

AMPLIFIED FRAGMENT LENGTH
POLIMORPHISM
This technique combines the power of RFLP with PCR-based technology by
ligating primer recognition sequences (adaptors) to the restricted DNA.
The key feature of AFLP is its capacity for “genome representation” and the
simultaneous screening of representative DNA regions distributed randomly
throughout the genome. AFLPs are DNA fragments (80-500 bp) obtained from
digestion with restriction enzymes, followed by ligation of oligonucleotide
adapters to the digestion products and selective amplification by the PC
AFLP is based on the selective PCR amplification of restriction fragments
from a total double-digest of genomic DNA under high stringency conditions,
i.e., the combination of polymorphism at restriction sites and hybridization of
arbitrary primers. Because of this AFLP is also called selective restriction
fragment amplification (SRFA).

AFLPs can be applied in studies
- Genetic identity
- Fingerprinting
- Biodiversity studies
- Analysis of germplasm collections
- Identification of clones and cultivars
- Phylogenetic studies of closely
related species.
- Genotyping of individuals
-Construction of genetic DNA marker maps
-Construction of Physical maps
- Transcript profiling
High genomic abundance and generally random distribution
throughout the genome make AFLPs a widely valued technology for
gene mapping studies.

Advantages-
• High multipex ratio and genotyping throughput.
• Reproducible across lab
• Small quantity of DNA is required
• No need of sequencing or probe collection
Disadvantages-
• High quality of DNA is required for restriction enzyme
digestion
• polymorphic info content is low
• Marker development is complicated and not cost efficient
for locus specific markers.

SIMPLE SEQUENCE REPEATS
• SSRs, also called microsatellites,
• Short tandem repeats (STRs)
• Sequence-tagged microsatellite sites (STMS)
• PCR-based markers.
• Tandem repeats of short nucleotide motifs (2-6 bp/nucleotides long).
• Widely distributed in plant and animal genome
 SSR markers are characterized by their hyper-variability,
reproducibility, co-dominant nature, locus-specificity, and
random genome-wide distribution in most case.
• There are over 35,000 SSR markers developed and mapped onto
all 20 linkage groups in soybean
Since the 1990s SSR markers have been extensively used in
constructing genetic linkage maps, QTL mapping, marker-assisted
selection and germplasm analysis in plants.

SSR (Simple sequence repeat)
DNA markers which developed by amplifying microsatellite
in the genome:
Sequence Primer
ACTGTCGACACACACACACACGCTAGCT (AC)7
TGACAGCTGTGTGTGTGTGTGCGATCGA
ACTGTCGACACACACACACACACGCTAGCT (AC)8
TGACAGCTGTGTGTGTGTGTGTGCGATCGA
ACTGTCGACACACACACACACACACACGCTAGCT (AC)10
TGACAGCTGTGTGTGTGTGTGTGTGTGCGATCGA
ACTGTCGACACACACACACACACACACACACGCTAGCT (AC)12
TGACAGCTGTGTGTGTGTGTGTGTGTGTGTGCGATCGA

AATCCGGACTAGCTTCTTCTTCTTCTTCTTTAGCGAATTAGGP1
AAGGTTATTTCTTCTTCTTCTTCTTCTTCTTCTTAGGCTAGGCGP2
P1 P2
SSR polymorphisms
Gel configuration

Advantages
• Readily analyzed by PCR
• Easily detected by PAGE OR AGE
• Multiplexed
• High throughput genotyping
• Can be automated
• Need very small quantity of DNA
Disadvantages
• Need nucleotide information for primer designing
• Labour intensive marker development process
• High start up cost for automated detection

CLEAVED AMPLIFIED POLYMORPHIC
SEQUENCE
Cleaved Amplified Polymorphic Sequence (CAPS): CAPS are DNA
fragments amplified by PCR using specific 20-25 bp primers,
followed by digestion of the PCR products with a restriction enzyme.
Subsequently, length polymorphisms resulting from variation in the
occurrence of restriction sites are identified by gel electrophoresis of
the digested products.
CAPS are also referred as PCR-Restriction Fragment Length
Polymorphism (PCR-RFLP) and predominantly applied in gene mapping
studies.
These markers are co-dominant in nature.

SEQUENCE CHARACTERIZED AMPLIFIED
REGIONS
This technique was introduced by Michelmore et al (1991) and Martin et al
(1991).
It overcome the limitations of RAPDs.
In this, the RAPD fragments that are linked to a gene of interest are
cloned.
 Based on the terminal sequences, longer primers (20-mers) are designed.
More specific amplification of a particular locus.
The presence or absence of the band indicates variation in sequences.
The SCAR markers are dominant markers.
Applications of SCARs are in gene mapping studies, marker
assisted selection (Paran and Michelmore 1993), and comparative
mapping or homology studies among related species,

INTER SIMPLE SEQUENCE REPEAT
Inter Simple Sequence Repeats (ISSR): Amplification of DNA segments
present in between two identical microsatellite repeat regions oriented in
opposite directions.
It uses microsatellites as primers in a single primer PCR reaction
Target multiple genomic loci to amplify mainly ISSR of different sizes.
ISSR analysis can be applied in studies involving genetic identity,
parentage, clone and strain identification, and taxonomic studies of
closely related species as well as in gene mapping studies
The technique is simple, quick, and the use of radioactivity is not essential
Advantages
• Randomly distributed throughout
genome
• High polymorphism
Disadvantage
• Possibility of nonhomology of
similar-sized fragment.
• Have reproducibility problem

EXPRESSED SEQUENCE TAGS
Once cDNA representing an expressed gene is isolated, scientists can
sequence nucleotides from either the 5' or 3' end to create 5' expressed
sequence tags (5' ESTs) and 3' ESTs, respectively.
A 5' EST is obtained from the portion of a transcript (exons) that usually
codes for a protein.
ESTs are also used for designing probes for DNA microarrays to
determine the gene expression, construction of high-density genetic
linkage maps and physical maps.
It is more popular in identifying new and active genes

SEQUENCE TAGGED SITES
Sequence Tagged Site (STS): STS, a short, unique sequence was first
developed by Olsen et al., (1989) as DNA landmarks in the physical
mapping of the human genome, and later adopted in plants.
STS markers are codominant, highly reproducible, suitable for high
throughput, automation, and technically simple to use.
Two or more clones containing the same STS must over lap and the
overlap must include STS. Any clone can be sequenced and used as STS
provided that it contains a unique sequence.

DNA SEQUENCE BASED MARKERS
SNP MARKERS
 An SNP is a single nucleotide base difference between two DNA
sequences or individuals.
 SNPs can be categorized according to nucleotide substitutions either as
transitions (C/T or G/A) or transversions (C/G, A/T, C/A or T/G).
 In practice, single base variants in cDNA (mRNA) are considered to be
SNPs as are single base insertions and deletions (indels) in the genome.
 SNPs provide the ultimate/simplest form of molecular markers as a single
nucleotide base is the smallest unit of inheritance, and thus they can provide
maximum markers.
 Microsatellites represent tandem repeats but their repeat motifs are shorter
(1-6 bp). If nucleotide sequences in the flanking regions of the microsatellite
are known, specific primers (generally 20-25 bp) can be designed to amplify
the microsatellite by PCR.

SNPs
(Single Nucleotide Polymorphisms)
Any two unrelated individuals differ by one base pair every 1,000 or
So, referred to as SNPs.
Many SNPs have no effect on cell function and therefore can be used
as molecular markers.
Hybridization using fluorescent dyes
SNPs on a DNA strand
DNA markers which their polymorphism can be determined by single
nucleotide difference

They can be used for population genetics studies and gene
mapping, ranging from the individual level (e.g. clone and
strain identification) to that of closely related species.
Advantages-
• High level of polymorphism so are more informative
Disadvantages-
• High development cost
• Mutation result in null allele formation result in error in
genotyping scoring

APPLICATIONS OF MOLECULAR MARKERS IN
PLANT BREEDING
Phylogeny study, Varietal distinction and cultivar
registration
Germplasm evaluation and characterisation
Gene Tagging, Genome mapping, Linkage analysis
Marker Assisted Breeding

CONSTRUCTION OF GENETIC LINKAGE MAPS
Genetic linkage map graphically represents the arrangement of the
innumerable loci, which include morphological and isozyme as well as
DNA markers, along the chromosome. The distance between these loci is
expressed in centimorgans (cM) which represents the recombination rates
between the loci (1 cM 5 1% recombination).
Development of a source of probes and identification of polymorphic
probes.
 Segregation analysis
Statistical analysis
The very first genome map in plants was reported in maize (Gardiner et al.
1993), followed by rice (McCouch et al. 1988), Arabidopsis (Nam et al. 1989),
etc., using RFLP markers. Maps for several other crops like potato, barley,
banana, and members of Brassicaceae have been constructed (Winter and
Kahl 1995). Microsatellite markers, especially STMS markers, have been found
to be extremely useful in genome mapping.

LINKAGE MAP IN VARIOUS CROPS
The very first genome map in plants was reported in maize (Gardiner et
al. 1993),
followed by rice (McCouch et al. 1988),
Arabidopsis (Nam et al. 1989), etc., using RFLP markers.
Maps for several other crops like potato, barley, banana, and members
of Brassicaceae have been constructed (Winter and Kahl 1995).
Microsatellite markers, especially STMS markers, have been found to
be extremely useful in genome mapping.
STMS markers are used as potential diagnostic markers for important
traits in plant breeding programs
RAPDs have also played important role in saturation of the genetic
linkage maps and gene tagging.

TAGGING ECONOMICALLY IMPORTANT GENES
A direct application of genetic linkage
maps has been in tagging genes of
economic importance with molecular
markers.
The detection of linkages between
markers and the gene can be performed
using various statistical methods which
include analysis of variance models.
Software packages are available to
compute and analyze such data
Wheat
Hessian fly H23, H24
Leaf rust Lr9, Lr24
Powdery mildew Pm1,Pm2,
Pm3, Pm4
Rice
Bacterial leaf blight Xa-1,
Xa-3, Xa-4, xa-5, Xa-10,
Xa21
Blast Pi-2(t), Pi-4(t), Pi-5(t),
Pi-7(t), Pi-10(t), Pi(t)
Tomato
Fusarium wil I1, I2 t
Brassica spp
White rust ACA1

MAP BASED CLONING
It refers to the isolation of a gene corresponding to a target trait using
molecular maps. Map-based cloning consists of four major steps:
i. Development of a high-resolution molecular linkage maps in the region of
interest.
ii. Physical mapping of the region of interest by yeast artificial chromosome
(YAC) or bacterial artificial chromosome (BAC) contigs.
iii. Identification of appropriate YAC or BAC clones for isolating putative
clones harbouring the gene of interest.
iv. Verification through transformation that the target gene is isolated.
Martin et al (1992) was the first to clone a disease resistance gene Pto in
tomato using map-based cloning.
Map-based cloning or positional cloning also known as reverse genetics, is
a strategy in which knowledge of chromosomal gene location is required.

PREPARATION OF SATURATED LINKAGE
MAPS
Saturated linkage maps are a pre-requisite for gene tagging, marker
assisted selection and map based gene cloning.
Saturated linkage maps have been developed in several crop plants
like maize, rice, tomato, wheat, potato, barley, cotton, Brassica etc.
In rice centromere positions in all the 12 linkage groups have been
defined.
The markers used for developing saturated maps include RFLPs,
RAPDs, SSRs, AFLPs, SNPs, DArT and a combination of these.

COMPARITIVE MAPPING ANALYSIS
 This is the most useful application of linkage map analysis.
 To compare genome of distant related or cross compatible taxa.
 By using common set of DNA hybridizing probe mapping of 1 taxa.
to predict linkage relationship of another taxa.
Uses
To predict genome organization and evolution of species under
study
Synteny features has been exploited in following studied species
Tomato and potato
Tomato and Pepper
 Wheat, rice , maize
 Mungbean and cowpea etc
Apart from mapping and tagging of genes,
an important utility of RFLP markers has
been observed in detecting gene
introgression in a backcross breeding and
synteny mapping among closely related
species

MAS IN PLANT BREEDING
Marker assisted selection is the breeding strategy in which selection is
based on molecular marker closely linked to gene of interest rather than
gene itself.
It refers to the use of DNA markers that are tightly-linked to target loci as a
substitute for or to assist phenotypic screening.
Indirect Selection for a primary trait(trait of economic importance) via direct
selection for a secondary trait(marker), which is independent of growth
stage, environment and GxE interaction
DNA markers in combination with PCR have enabled MAS to become a
practical breeding method.
Marker assisted selection offers a unique opportunity to circumvent many
traditional problems associated with phenotypic selection for traits of
interest.

Prerequisites for an efficient marker-assisted breeding program
1.Appropriate marker system and reliable markers.
2.Quick DNA extraction and high throughput marker
detection.
3.Genetic maps
4.Knowledge of marker-trait association
5.Quick and efficient data processing and
management

QTL MAPPING
Agronomically important traits such as yield, quality, maturity, and
resistance to several biotic and abiotic stresses are controlled by a
relatively large number of loci, each of which makes a small positive or
negative contribution to the final phenotypic value of the trait.
Such loci are termed “quantitative trait loci” (QTLs)
Are called Polygenic Traits
Principle- DNA marker is linked to a QTL controlling the phenotype of
interest
Types-1. Single marker
analysis
2.Simple Interval
mapping
3. Composite Interval
mapping
 Marker-assisted selection increases
the efficiency and flexibility of a
breeding program by selecting for
genotypes linked to target genes or
quantitative trait loci (QTL).

MARKER-ASSISTED BACKCROSSING
MABC aims to transfer one or a few genes/QTLs of interest from one
genetic source (serving as the donor parent and maybe inferior
agronomically) into a superior cultivar or elite breeding line (serving as
the recurrent parent) to improve the targeted trait.
MABC is based on the alleles of markers associated with or linked to
gene(s)/QTL(s) of interest instead of phenotypic performance of
target trait.
Recovery of recurrent parent
genome is given by the formula:
1-(1/2)m+1
m is number of generation
of selfing or backcrossing
MABC Application in rice, wheat,
barley, cotton, soybean, common bean
and pea have reported.

FOREGROUND AND BACKGROUND SELECTION
In foreground selection, the selection is made only for the marker allele(s) of
donor parent at the target locus to maintain the target locus in heterozygous state
until the final backcrossing is completed.
The effectiveness of foreground selection depends on
-The number of genes/loci involved in the selection
-The marker-gene/QTL association
-Linkage distance and the undesirable linkage to the target gene/QTL.
In background selection, the selection is made for the marker alleles of
recurrent parent in all genomic regions of desirable traits except the target
locus, or selection against the undesirable genome of donor parent.
The effectiveness of background selection depends on
-No. of markers,
-more genotyping
-larger population
Elimination of gene from donar parent

MARKER ASSISTED GENE PYRAMIDING
Marker-assisted gene pyramiding (MAGP) is one of the most important
applications of DNA markers to plant breeding. Gene pyramiding has been
proposed and applied to enhance resistance to disease and insects by
selecting for two or more than two genes at a time.
Pyramiding of multiple genes/QTLs may be achieved through different
approaches: multiple-parent crossing or complex crossing, backcrossing, and
recurrent selection.
Desirable 3-4 genes from different lines be integrated by convergent
backcrossing or stepwise backcrossing.
For more no. of genes complex or multiple crossing or recurrent selection
may be preffered.
Marker-assisted complex or convergent crossing (MACC) can be undertaken
to pyramid multiple genes/QTLs.

MARKER-ASSISTED RECURRENT SELECTION
Recurrent selection is widely regarded as an effective strategy for the
improvement of polygenic traits
The effectiveness and efficiency of selection are not so satisfactory as -
phenotypic selection is highly dependent upon environments
-genotypic selection takes a longer time (2-3 crop seasons at least for one
cycle of selection).
Markerassisted recurrent selection (MARS) is a scheme which allows
performing genotypic selection and intercrossing in the same crop season for
one cycle of selection
So it enhance the efficiency of recurrent selection and accelerate the
progress of the procedure
For complex traits such as grain yield, biotic and abiotic resistance,
MARS has been proposed for “forward breeding” of native genes and
pyramiding multiple QTLs

GERMPLASM CHARACTERISATION
“core” collection thus represents most of the diversity in the germplasm
collection and allows one to extrapolate conclusions to the entire
collection.
DNA markers have been used extensively in fingerprinting genotypes
“Band-map” is a convenient graphical method to describe the DNA
fingerprints of individuals.
Band map graphs are formulated on the basis of band frequency and
band number.
A “core” collection thus represents most of the diversity in the
germplasm collection and allows one to extrapolate conclusions to the
entire collection.

DNA FINGERPRINTING
DNA fingerprinting has found extensive applications in determination of
seed purity, in resolution of uncertainities in parentage, for legal protection of
improved varieties, and in genetic diagnostics
The repetitive and arbitrary DNA markers are of choice in genotyping of
cultivars. Microsatellites like (CT)10, (GAA)5, (AAGG)4, (AAT)6,
(GATA)4, (CAC)5 (Gupta et al. 1994), and minisatellites (Ramakrishna et
al. 1995) have been employed in DNA fingerprinting for the detection of
genetic variation, cultivar identification, and genotyping.
Quantification of genetic diversity, characterization of accessions in plant
germplasm collections, and taxonomic studies.
Unequivocally diverse materials like rice, wheat, grapevine, soybean, are
genotyped by Microsatellite markers.

DIVERSITY ANALYSIS OF EXOTIC GERMPLASM
The exotic germplasm for breeding is selected on the basis of certain
characteristic features such as (a) the exotic germplasm must
possess a significant number of unique DNA polymorphisms
(throughout the genome) relative to the modern-day cultivars and
(b) each exotic germplasm has to be genetically dissimilar (on the
basis of DNA profiling
Pakniyat et al. 1997 used AFLP for studying variation in wild
barley with reference to salt tolerance and associated ecogeography
and a number of reports are coming up each day for different
systems.
Similarly, ISSR markers are used for diversity analysis of pine, rice,
and also in wheat (Blair et al. 1999).

RFLPs have been used in evolutionary studies for
deducing the relationship between the hexaploid
genome of bread wheat and its ancestors (Gill et al.
1991).
A number of transposon elements like tos1-1, tos2-1,
and tos3-1 retrotransposons have been used to detect
the genetic differences between different species of
rice and even between ecotypes of cultivated rice,
wherein they were found to distinguish between the
cultivars of Asian and African rice, O. sativa and O.
Glaberrima (Fukuchi et al. 1993).

 Retro-element Wis-2 detect genomic variation in wheat and
related grass spp.
 STS markers specific to chloroplast or mitochondrial DNA
have been useful in providing seed- and pollen-specific
markers.
Specific markers like STMS (sequence-tagged
microsatellite markers), ALPs (Amplicon length
polymorphisms), or STS markers have proved to be
extremely valuable in the analysis of gene pool variation of
crops during the process of cultivar development and
classification of germplasm
Now the trend is shifting toward use of EST to study
evolution of functional gene of target or goal.

Collard, B.C.Y., M.Z.Z. Jahufer, JB Brouwer, and E.C.K. Pang. 2005.
An introduction to markers, quantitative trait loci (QTL) mapping
and marker-assisted selection for crop improvement: the basic concepts
Euphytica 142: 169-196.
Blair MW, Panaud O, McCouch SR. 1999. Inter-simple sequence repeats
(ISSR) amplification for analysis of microsatellite motif frequency and
fingerprinting in rice (Oryza sativa L.). Theor. Appl. Genet. 98: 780-792
Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S. 1993. Map
in maize using an immortalized F2 population. Genetics 134: 917-930
Fukuchi A, Kikuchi F, Hirochika H. 1993. DNA fingerprinting of cultivated
rice with rice retrotransposon probes. Jpn. J. Genet. 68: 195-20
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The most wonderful mystery of life may well be the
means by which it created so much diversity from so
little physical matter.’
-E. O. Wilson, The Diversity of Life

markers and their role

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