Progressive Research 8 (Special) : 223-231 (2013)

Society for Sci. Dev. in Agric. and Tech.

MOLECULAR MARKER ASSISTED SELECTION AND THEIR USE IN CROP

IMPROVEMENT
Jaydev Kumar1, S.P. Singh2, S.S. Gaurav3, S. Nath4, Lokendra Singh1, A.P. Singh5,
Arun Kumar4, Alankar Lamba1 and Shalendra Kumar1
1

Department of Genetics and Plant Breeding, C.S. Azad Univ. of Agric. and Tech., Kanpur 208 002 U.P.
Agriculture Research Station, Kalai, Aligarh (C.S. Azad Univ. of Agric. and Tech., Kanpur)
3
Department Biotechnology, Ch. Charan Singh Univeristy, Meerut-250004
4
Department of Genetics and Plant Breeding, N.D. Univ. of Agric. and Tech., Faizabad 224229
5
Indian Institute of Pulses Research, Kanpur 208 024 Uttar Pradesh
2

ABSTRACT
Molecular markers play an important role in improvement of field crops. Many morphological
markers generally corresponds the QTLs that can be seen visually. A range of reliable markers like
RFLP, RAPDs, AFLPS and SSRs etc. has been introduced to fulfill the demand of selection/
characterization in breeding programmes. The molecular markers (non morphological markers)
proved then importance having more merits over the morphological markers (conventional or
traditional markers). In the era of scientific progress, the old disciplines of quantitative genetics and
plant taxonomy have been reviewed by marker approach, which have immediate apply in supportive
research for advanced breeding programmes to achieved best yield for development of economic
condition of their country. Therefore, the successful application of DNA molecular markers as an
advanced technology for being genetic improvement in crops plant would base on close interaction
between plant breeders and technology, availability of skilled manpower and financial investors on
researches.
Key words:

Molecular markers, markers importance, PCR.

The theoretical advantages of using genetic markers

and potential value of genetic marker linkage map and
direct selection strategies in plant breeding were first
reported about eighty years old (Crouch and Ortiz
2004). Markers are characters whose pattern of
inheritance can be followed at the morphological (e.g.,
flower color) biochemical (e.g., protein and isozymes)
or molecular (DNA) levels. In other words, molecular
markers consist of special molecules, which represent
easily detectable differences among different strains of
a species. These markers can be based on proteins
e.g., isozyme, or DNA; the letter group of markers
consisted of a variety of markers and are extremely
adaptable. DNA marker technology has gradually
enhanced the efficiency of plant breeding programmes.
DNA based markers have responsible as versatile tools
and have occur their own position in various fields like
as taxonomy, plant breeding, genetic engineering etc.
(Joshi et al., 2011).
A number of companies have frequently using
markers to increase the potentiality in breeding
programmes from last two decades. Therefore, plant

geneticists consider MAS a useful way in plant

breeding programmes to makeup a successful plant
breeding strategies (Breren et al., 2010; Joshi et al.,
2011). Over the last few decades plant genomics has
been studied extensively about a revolution in this
area, and molecular markers are very useful for
genomic analysis (Joshi et al., 2011). In 1923, Sax
observed selection of minor genes of interest by
linkage with major genes, and could be scored more
easily. The more significant breakthrough in
agro-industries or biotechnology is coming from
research into the structure of genomes and the
genetics mechanism behind economically important
traits. The fast growth in genomic science is the way of
getting information on the identity, location, and
functional activities of genes affecting characters and
mapping single gene markers in many species of
higher plant species.
Based on diversity, different type of markers like
as morphological, phenological and agronomic
characteristics are available and these have
conventionally been used for estimating genetic

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Molecular market assisted selection and their use in crop improvement

variation. However, many traits are governed by

polygenic and influence by environmental conditions
and therefore, are difficult to evaluate with accuracy.
Molecular markers have been proven to be powerful
way in the assessment of genetic variation and in
elucidation of genetic relationship within and among
species (Chakravarthi and Naravaneni, 2006).
Molecular markers used for differentiation of
genotypes are abundant, but unlike morphological
traits, markers are not affected by environment (Staub
et al., 1997). Collecting DNA marker data to determine
whether phenotypic similar varieties are genetically
similar would therefore be of great interest in plant
breeding programme (Duzyaman, 2005). Molecular
markers are being used worldwide to tag specific
chromosome segments bearing the desired gene(s) to
be transferred (or incorporated) into breeding lines
(Crouch and Ortiz, 2004).
The use of molecular marker technique for
detecting differences in the DNA of individual plants has
many applications of value to crop improvement.
Markers can be used for dissecting polygenic traits into
their Mendelian components or QTLs and this
increasing understanding of the inheritance and gene
interaction for those traits markers selection
procedures (Hoisington et al., 2002).
The molecular marker are no longer looked upon a
single DNA fingerprinting markers in variability studies
but are being constantly modified to increase their
utility and to being automation in the processes of
genomic analysis. The discovery of polymeric chain
reaction (PCR) by Kary Mullis to extremely useful in all
experiments of molecular biology and genetic
engineering, which has open the way to development of
markers based gene tagging, mapping based cloning
of various important characteristics, synteny mapping,
variability analysis and market based selection of most
desirable lines/genotypes etc. The DNA markers offer
many more advantages over conventional phenotypic
markers as they provide.
In the early part of the 20th century, scientists
discovered that Mendelian factors of controlling
inheritance, which now call genes, were organized in
the linear form on cytogenetically defined structures
called chromosomes. The single genes adjoining within

define position are known as DNA markers. Molecular

markers are identifiable DNA sequence, present at
specific positions of the genome and correlated with
the inheritance of a character or associated a gene
(FAO, 2004). Thottappilly et al. (2002) observed to
markers as naturally occurring genetic polymorphism
and also which included protein and nucleic acid are
differ. Rapidly improvement of genomic research and
molecular biology has led to use of DNA markers in
plant improvement or plant breeding programme.
Markers are polymorphic (i.e. they must exist different
forms that the chromosome carrying the recessive
gene can be differentiated from the chromosome with
dominant gene means normal gene by the shape of
the marker it carries.). Molecular markers should not
be considered as normal genes while usually do not
have any biological effect. Based on markers,
polymorphism can be defined into three levels:
morphological, biochemical and molecular. The
development of DNA markers has irreversibly changed
the stream of plant genetics and breeding (Collard and
Mackill, 2006). According to Joshi et al., 2011, ideal
DNA markers should however pose the following
properties.
Highly polymorphism, which is the simultaneously
occur of a trait at the same population of two or
more discontinuous variants or genotypes,
Co-dominant inheritance: distinguishing form of
marker should be detected in a diploid organism
to allow discrimination of homo and heterozygote,
Frequent occurrence in a genome,
Easily available; fast and cheap to detect,
Highly reproducible and
Simple exchange of data between labs.
A molecular marker has all above defined
properties to achieve successful results. A wide range
of molecular markers are available which is detecting
polymorphism on DNA levels. These have been
classified into following categories with respect to
basic strategy and some major ones have been
described.
NON PCR BASED MOLECULAR MARKERS (like as
RFLP-restriction fragment length polymorphism)
This is the first worker technology to be used for

Kumar et al.,

225

detection of DNA based sequence polymorphism; was

RAPDs (Random Amplified Polymorphic DNA

developed in early 1980 (Farooq and Azam, 2002).

marker) use for detection of nucleotide sequence

This approach developed before the discovery of

polymorphism in DNA by use a single primer of arbitrary

PCR, so called non PCR based technique. The

nucleotide sequence (William et al., 1991).

RFLPs are easily inherited and are spontaneously

present in a Mendelian population, because the
majority of mutations altering in the form of nucleotides
are only recovered during evolution. The genetic
information is stored in the DNA base sequence found
on chromosome to inherited generation to generation
to create diversity within species. Plants are able to

Merits associated with RAPDs

In which use very small amount of DNA which
make possible to work the RFLPs. It is very fast
and highly efficient analysis having high density
genetic mapping as in many plant species such as
alfafa (Kiss et al., 1993).

but occasionally many causes like mutation changes

No involvement of radioactive assays (Kiss et al.,

1993).

in DNA operation (Joshi et al., 2011) to leads simple or

It has high reproducibility across labs.

large base pair alteration as a result of inversions,

Non-involvement of blotting or hybridization.

replicate their DNA with more accuracy and rapidly,

translocations, deletion, or transpositions to produce

loss of recognition site and rotate create to restriction
fragment in different lengths. Genomic restriction
fragment of different length between genotypes can be
detected by using of southern blots and by a suitable
probe. In this method, DNA is digested by the
restriction enzyme like EcoR1, which cut the DNA at
specific sequences, then electrophoreses, blotted on
a membrane and probed with a labeled clone. RFLPs
marker

is

provides

way

to

directly

follow

chromosome segments under recombination as they

follow Mendelian rules and greatly aid in the
construction of genetic maps. When an F1 plant
undergoes

meiosis

to

produce

gametes,

recombination takes place between chromosomes by

MODERATION OF RAPD
The polymorphism inheritance take place as
normal-mutant traits to create causes of lack of
information associated with markers which is
showed co-dominance.
Primers are very short; a mismatch of even a single
nucleotide can often prevent the primer from
annealing which result loss of band.
RAPDs are very sensitive to change the PCR
condition to create altering in amplified fragments.
Suffers from problems of repeatability in many
systems, especially when transferring between
populations or laboratories as is frequently
necessary with marker assisted selection
programme (Liu et al., 1994).

crossing over and this recombination is the basis of

markers, require DNADNA hybridization of probe

AFLP (AMPLIFIED
POLYMORPHISM)

DNA with sampled plant DNA.

It is based on PCR technique to using amplification for

PCR (POLYMERASE CHAIN REACTION) BASED

detection of primers from restriction of genomic DNA

APPROACHES

(Metthes et al., 1998). This technology allow to use of

PCR is also known as PEOPLES CHOICE

REACTION, come to replaced the technique of gene
cloning in molecular biology. This is an invitro method
of nucleic acid synthesis by which a particular
fragment of DNA can be specially replicated (Mullis
and Faloona, 1987). Based on PCR, molecular
markers are mainly included RAPDs, SSRs, AFLPs
and SNPs or their modifications.

simple DNA enzymatic cut on the short fragments (as

conventional genetic mapping and when use, RFLP

FRAGMENT

LENGTH

with RFLP analysis), but only small piece of fragments

can be studied following selective PCR amplification (Liu
et al., 1994). AFLP with RFLP is given more accuracy in
detection of diversity in their experimental results and
combines the especially of restriction analysis with PCR
amplification.

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Molecular market assisted selection and their use in crop improvement

approach. Generally, it is include (18-20 nucleotide

long) is depend on the sequences of two different
adjacent SSRs and correlated to introns, known to be
present in compound repeats.

Advantages :
More sensitive
Highly reproducible activity
It has universal applicable to detection of diversity.
Allow detection of restriction fragments in any
background with involvement of pooled DNA
samples and cloned DNA.
SIMPLE

SEQUENCE

REPEATS

OR

SHORT

TANDEM REPEATS OR MICRO SATELLITES

These are more usable and ideal markers for
distinguishing between and within a species gene
sequences in all eukaryotes (Farooq and Azam, 2002).
Simple sequence repeats are also known as
microsatellites. The term micro satellites were coined
by Litt and Lutty, 1989. The repeated sequence is often
simple, consisting of two, three or four nucleotides (di-,
tri-,and tetra nucleotide repeats respectively), and can
be repeated 3 to 100 times, with the longer loci
generally having more alleles due to the greater
potential for slippage. The variation in the number of
tandemly repeats units results in highly polymorphic
banding pattern (Farooq and Azam, 2002) which are
detected by PCR approach, using specific
transposable region primers where they are known.
Some other microsatellite based on the same principles
showed following.
RAMP (RANDOM AMPLIFIED MICROSATELLITE
POLYMORPHISM)
This is a microsatellite technique was termed random
amplified microsatellite polymorphism (Wu et al., 1994)
based on the randomly distribution of nucleotide
sequences flanking a simple sequence repeat. It shows
high degree of genetic polymorphism (Agarwal and
Srivastava, 2008). In this approach, use a radio labeled
primer carrying 51 anchors and 31 repeats which is
used to amplify genomic DNA in the presence or
absence of RAPD primers (Agarwal and Srivastava,
2008). The RAMP technique is representing
polymorphic product in respect to both dominant and co
dominant conditions and is detectable.
SAMPL

(SELECTIVE

AMPLIFICATION

OF

MICROSATELLITE POLYMORPHIC LOCI)

SAMPL marker is based on SSR modification of AFLP

OTHER MARKER SYSTEMS

The technique reveals allele size differences even of a
single base pair. A further advantage is the fact, that
microsatellite markers can easily be distributed
between labs by sharing primer sequences (Powell et
al., 1996; Nybom, 2004; Weising et al., 2005). For
reviews of microsatellite marker techniques see
Ellegren (2004), Gupta and Varshney (2000), Li et al.
(2002), for reviews of microsatellite marker
development see Mccouch et al., (1997), Zane et al.
(2002) and Weising et al., (2005).
MARKER ASSISTED SELECTION (MAS)
Collard and Mackill reported the basic merits of MAS
compared to traditional phenotypic selection in 2006,
which are :
Simpler compared to morphological breeding.
Selection may be carried out at initial selection
stage and single plants may be selected with high
reliability.
In this approach, linkages are sought between
DNA markers and agronomically important traits, such
as resistance to pathogens, insects and nematodes,
tolerance to biotic stresses, quality parameters and
magnitudes traits.
MAS have become promising and potent
techniques for integrating biotechnology with
conventional and traditional breeding. The essential
requirements for marker assisted selection in a plant
breeding programme are :
Markers are cosegregate with target traits.
Easy analysis based on PCR.
High reproducible
It should be economical to use and be user
friendly.
The utilization of molecular markers can be
obviously preventing loss of QTL. A QTL (Quantitative
Trait Locus) is a chromosomal region supposed to
contain a gene or genes that contribute to a
quantitative trait. In QTL mapping experiments the

Kumar et al.,

227

genetic basis of quantitative traits is dissected into their

single components. Many traits of agricultural
importance are quantitative, i.e. based on polygenes.
As environmental influences can have a considerable
effect on the expression of these traits, DNA markers
can have a great impact in breeding for such traits,
because selection for quantitative traits normally
requires large scale testing in various environments. In
this way it is possible to construct a genetic map,
showing the position of QTLs for a certain trait on the
different chromosomes. After this first step, QTL
analysis can be applied to plant breeding and
knowledge of QTL map locations is utilized for
selection of improved varieties. In addition,
agronomical important traits like as nutritional quality,
yield, flowering time and multiple resistance which
appear to follow complex, polygenic inheritance pattern
with easily analyzed by using molecular marker.
Evidence obtained from various crops indicate that
even such complicated traits appear to be determined
by only a few major or minor gene (s) reported by Frary
et al, 2000 and Thornsberry et al., 2001.

wheat and hence are highly useful marker for various

applications in wheat 15. Thus, these markers could be
used for selection of linked traits of agronomic
importance which would increase the efficiency and

APPLICATION OF MAS IN PLANT GENOMICS AND

The development of DNA markers for screening of

genotypes having resistance to diseases and pests in
jowar provided a great opportunities e.g., in breeding
new populations for striga prone climate (Crouch and
Ortiz, 2004). Five genomic regions correlated with
stable striga resistance from resistant line N13 have
been isolated across 10 fields trials in Mali and Kenya
and two randomly selected samples of a mapping
population included this resistance source, indicating

PLANT BREEDING FOR PLANT/CROP IMPROVEMENT

Molecular markers have been look upon as a tool for
large number of applications varies from position of
genes to carrying more desirable traits to use for
improvement of cultivars by help of molecular marker
assisted selection, called genome analysis which have
generated a vast amount of information and a number
of databases are being generated to preserve and
popularize it (Joshi et al, 2011). The molecular markers
helped in improvement of following crops to fulfill
varying breeding goals.
WHEAT
Motawei et al. (2007) used two types of molecular
markers, random amplified polymorphic DNA (RAPD)
and inter-simple sequence repeat (ISSR) to determine
the genetic diversity of 12 wheat lines and two wheat
cultivars (Yecora Rojo and West Bread). He was
observed that RAPD markers have shown to be
associated with various traits contributing to kernel
hardness in bread wheat. RAPD and ISSR markers
have proved to be the most polymorphic markers in

precision breeding.
At present, Heat stress due to increased
temperature is an important agricultural problem in
many areas of the world (Wahid et al., 2007). High
temperature during post-anthesis is a major problem of
wheat yield reduction in some regions in India as well
as in many wheat-growing regions of the world.
Mohamed et al., 2011 studied the inheritance pattern
of the grain filling rate as indicator for heat tolerant
genes and their study indicated that SSR markers,
combined with bulked segregant analysis, could be
used to identify molecular markers linked to the grain
filling rate as indicator for heat tolerance genes in
wheat and suggested that marker-assisted selection
with microsatellite primers might be useful for
developing to improved cultivars.
SORGHUM

that the QTL are biological realities.

MAIZE
Grain yield is one of the most important and
complicated traits for maize breeding programs, but its
evaluation and improvement are difficult and expensive
to assess due to its complex biology, environmental
interactions, and low heritability (Hallauer and Miranda
Filho, 1988). These characteristics have made grain
yield the primary trait of interest for QTL mapping
studies for marker-assisted selection (Tanksley, 1993
and Lee, 1995). Tropical maize germplasm have a
broad genetic base with greater variability than
temperate synthetic materials (Lanza et al., 1997), and
are exposed to a wide range of environmental stress,

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Molecular market assisted selection and their use in crop improvement

higher in the tropics than in temperate zones (Ribaut et

al., 1997). Analysis of QTL on tropical maize
germplams could identify novel genomic regions that
have not yet been defined by alleles with quantitative
effects. Restriction fragment length polymorphisms
(RFLP) have become the most widely used molecular
marker in the genetic analysis of quantitative traits in
maize (Coe et al., 1995). According to Knapp et al.,
(1990), the means across environments reduces the
standard error of the values of the evaluated traits,
increasing the precision and the power of mapping
QTLs. In maize, several studies reported that QTL
effects for grain yield, ear height and plant height are
largely independent of the environment, despite the
presence of significant genotype by environment
interaction (Stuber et al., 1992).
URDBEAN
Bhareti et al. (2012) worked to find out the genetic
diversity in Urd bean [(Vigna mungo (L.) Hepper]. They
studied 33 urdbean and one mungbean genotypes.
She observed the ISSR dendrogram was unable to
discriminate blackgram genotypes on the basis of their
inter-specific and intra-specific origin. All the genotypes
and checks exhibited more than 61% similarities and in
the most of the genotypes similarity ranges vary from
86-100%.
CHICKPEA
Many chickpea breeding programs are focused on
improving the genetic potential both to increase yield
and to provide protection against abiotic and biotic
stresses. Thus, three molecular markers, including
start codon targeted (SCoT) polymorphism, directed
amplification of minisatellite-region DNA polymerase
chain reaction (DAMD-PCR), and inter simple
sequence repeat (ISSR) markers, were compared in
terms of their in formativeness and efficiency for
analysis of genetic relationships among 38 accessions
of eight annual Cicer species (Amirmoradi et al., 2012)
and revealed diversity showed that Cicer reticulatum is
the closest wild species to the cultivated chickpea, and
this finding supports the hypothesis that C. reticulatum
is the most probable progenitor of the cultivated
species. C. bijugum, C. judaicum and C. pinnatifidum
were clustered together, and in other clusters C.
yamashitae and C. cuneatum were grouped close

together and suggested DAMD-PCR and SCoT

markers can be used as reliable techniques for
detecting levels of DNA polymorphism and genetic
relationship in Cicer (Amirmoradi et al., 2012). The
levels of genetic variation detected by these three types
of markers within and between Cicer species were
relatively higher against amount computed from RAPD
and AFLP markers (Sudupak et al. 2002; Nguyen et al.
2004).
PIGEON PEA
Pigeon pea is very usable and lead pulse crop in India
after chickpea. This crop is decline through many biotic
stress (Fusarium wilt, sterility mosaic virus,
Phytophthora blight and pod borer) and also
substantially reduce crop productivity of pigeon peas.
Resistance breeding to achieve both stability and
productivity are top priority in the genetic enhancement
of this pulse. Thus, DNA markers for pest and disease
resistance will also be of utmost importance. The
development of F1 hybrid cultivars of pigeon pea was
the first amongst the legume crops. For this reason, the
development of marker-assisted selection for new
sources of fertility restoration will also have high priority
in this crop (Crouch and Ortiz, 2004).
COWPEA
Cowpea is also a legumes crop grown in semi arid
tropics. Many biotic and abiotic factors are responsible
to reduction their yield potential. Thus in cowpea, the
use of markers for developing resistance to thrips,
bruchids, maruca, and pod borer is considered more
priority. In other terms, resistance genes are use as
marker for resistance to parasitic weed and drought are
considered a high priority interference reported by
Ntundu et al., 2004.
RAPESEED-MUSTARD
Genetic variability is of prime importance for the
improvement of many crop species including Brassica.
There is increasing number of reports where RAPDs
have been successfully used to estimate genetic
variability in Brassica (Demeke et al., 1992; Wang et
al., 2002; Dulson et al., 1998; Divaret et al., 1999). The
majority of the work utilizing molecular markers in
Brassica oilseed breeding has, to date, been based on
genetic mapping using various DNA marker systems,

Kumar et al.,

and in single segregating populations generated for

specific investigations of particular traits of interest.
Biotechnology and genetic engineering could be used
as a tool to help the conventional breeding for the
quality improvement of rapeseed and mustard. The
purpose of scientists at present study was to
characterize different B. juncea lines at molecular level
that could be utilized for selecting better parents and
subsequently provide a base for further strengthening
the Brassica breeding programme and they were seem
that PCR based assays like RAPDs can be used
effectively to estimate genetic variability in B. juncea
and also 15 B. juncea genotypes, genetically distinct
lines pointed out of the present study should be used in
future breeding programs for improving yield and
quality characteristics of Brassica (Khan et al., 2011).
SESAME
Sesame (Sesamum indicum L.) family Pedaliaceae, is
one of the most ancient oilseeds crop known to
mankind. Its has medicinal and pharmaceutical value
and is being used in many health care products.

229

Sesame seed contains 50-60% oil and 25% protein

with antioxidants lignans such as sesamolin, sesamin
and has been used as active ingredients in antiseptics,
bactericides, viricides, disinfectants, moth repellants,
anti-tubercular agents (Bedigian et al. 1985) and
considerable source of calcium, tryptophan,
methionine and many minerals (Johnson et al., 1979).
Genetic diversity of different materials can be studied
together by morphological traits, the geographical
origin and by using molecular marker techniques like
RFLPs, RAPDs or AFLPs. Recently, it has been
assumed that in plant breeding, diversity can be
reduced using biochemical molecular techniques. A
very high level of polymorphism has been observed
with the use of RAPD markers indicating a wide and
diverse genetic base of the sesame germplasm
analysed. Extremely wide distribution of sesame the
world over confirms the view of Hamrick and Godt
(1989) that geographic range is the best predictor of
level of variation as the endemic species h tavehe
lowest genetic diversity. Bhat et al. (1999) obtained a
comprehensive results from PCR amplifications with

Major classes of genetic markers (Crouch and Ortiz, 2004)

Morphological traits

Such as seed or flower color are seriously limited in number and their expression can be
differentially affected by the environment.

Proteins

Seed storage proteins, structural proteins and isozymes provide very cost effective markers
but their number may be limiting and their expression is not neutral.

Restriction fragment length

polymorphism (RFLP)

Requires hybridization of probe DNA with sampled plant DNA and although provides high
quality data has a severely restricted throughput potential.

Random amplified
polymorphic DNA (RAPD)

The first of a new generation of markers based on the polymerase chain reaction (PCR). This
technique uses arbitrary primers for initiating amplification of random pieces of the sampled
plant DNA. This technique requires no knowledge of the genome to be screened but suffers
from problems of inconsistency when transferred between populations and laboratories.

Simple sequence repeat

length polymorphism (SSR)

This technique provides high quality, highly consistent results but the markers are expensive
to develop as they require extensive sequence data from the species of interest. However,
once developed this type of marker is easily transferred between populations or laboratories
and is amenable to high throughput screening.

Amplified fragment length

polymorphism (AFLP)

In this approach the sample DNA is enzymatically cut up into small fragments (as with RFLP
analysis) but only a fraction of fragments are studied following selective PCR amplification.
Although this assay provides a great quantity of marker information, it is not particularly well
suited to high throughput marker assisted selection.

Expressed sequence tag

The development of EST markers is dependent on extensive sequence data of regions of the
genome that are expressed. However, once developed they provide high quality, highly
consistent results and because they are limited to expressed regions of the genome, markers
themselves are directly associated with functional genes. As with SSR markers, EST
markers are amenable to high throughput screening.

(EST)

Single nucleotide
polymorphism

The majority of differences between individuals are point mutations due to single nucleotide
polymorphisms. As such, there are a vast number of potential SNP markers in all species.
Massive amounts of sequence data are required to develop SNP markers, particularly as
many may be population specific. However, their great advantage lies in the potential to
screen them through simply yes/no tests that can be readily automated to facilitate
mega-throughput screening through the use of technologies such as micro arrays.

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Molecular market assisted selection and their use in crop improvement

the selected 24 random 10-mer primers were

statistically analysed. The value of Jaccards similarity
coefficients ranged from 0.19 to 0.89. The results
indicated the presence of high level of genetic diversity.
However, the extent of genetic diversity was greater in
the collections from Indian subcontinent as compared
to the exotics. Among the Indian accessions, the
collections from Rajasthan and North-eastern states
were highly diverse. The phonetic analysis grouped 48
out of 58 accessions in six clusters and the remaining
highly diverse accessions were placed outside these
close-knit clusters. The Bootstrap estimates obtained
by Wagner parsimony analysis were significant for
seven out of 49 nodes in the majority-rule consensus
tree (>95% occurrence).

REFERENCES
1.

2.

3.

4.

5.

6.

7.

8.

9.

Agarwal, M.; Shrivastava, N. and Padh, H. (2008).

Advances in Molecular marker techniques and their
applications in plant science. Plant cell rep, 27: 617613
Amirmoradi, B.; Talebi, R. and Karami, E. (2012).
Comparison of genetic variation and differentiation
among annual Cicer species using start codon targeted
(SCoT) polymorphism, DAMD-PCR, and ISSR
markers. Plant Syst.
Evol. DOI 10.1007/
00606-012-0669-6.
Bedigian, D.; Seigler, David, S.; Harlan and Jack, R.
(1985). Sesamin, sesamolin and the origin of sesame.
Biochemical Systematics and Ecology, 13(2): 133-139
Bhareti, P.; Singh, D.P. and Khulbe, R.K. (2012). Genetic
diversity in urdbean [(Vigna mungo (L.) Hepper]
revealed by ISSR markers. Journal of Food legumes,
25(2): 89-93.
Bhat, K.V.; Babrekar, P.P. and Lakhanpaul, S. (1999).
Study of genetic diversity in Indian and exotic sesame
(Sesamum indicum L.) germplasm using random
amplified polymorphic DNA (RAPD) markers.
Euphytica, 110: 21-33.
Bueren, E.; Backer, G.; Vriend, H. and Ostergard, H.
(2010). The role of Molecular markers and marker
assisted selection in breeding for organic agriculture.
Euphytica, 175(1): 51- 64.
Chakravarthi, B.K. and Naravaneni, R. (2006). SSR
marker based DNA fingerprinting and diversity study in
rice (Oryza sativa L.) African J. Biotech, 5 (9): 684-688
Collard, B.C.Y. and Mackill, D.J. (2008). Marker-Assisted
Selection: An Approach for Precision Plant Breeding in
the Twenty-First Century - Philosophical Transactions
of the Royal Society B: Biological Sciences 363:
557-572.
Crouch, J.H. and Ortiz, R. (2004). Applied genomics in

the improvement of crops grown in Africa. African

Journal of Biotechnology 3 (10): PP 489-496
10. Demeke, T.; Admas, R.P. and Chibbar, R. (1992).
Potential taxonomic use of random amplified
polymorphic DNA. RAPD. A case study in Brassica.
Theor. Appl. Genet. 84: 990-994.
11. Divaret, I.; Margale, E. and Thomas, G. (1999). RAPD
markers on seed bulks efficiently assess the genetic
diversity of a Brassica oleracea L. collection. Theor.
Appl. Genet. 98(6, 7): 1029-1035.
12. Dulson, J.; Kott, L.S. and Ripley, V.L. (1998). Efficacy of
bulked DNA samples for RAPD DNA fingerprinting of
genetically complex Brassica napus cultivars.
Euphytica, 102(1): 65-70.
13. Duzyaman, E. (2005). Phenotypic diversity within a
collection of distinct okra (Abelmoschus esculentus)
cultivars derived from Turkish landraces, Genet. Res.
And Crop Evol, 52: 1019-1030.
14. Ellegren, H. (2004). Microsatellites: simple sequences
with complex evolution. Nature Reviews Genetics, 5:
435-445.
15. FAO (2004). Scientific facts on genetically modified
crops.
16. Farooq S and Azam F. 2002. Molecular markers in plant
breeding 1: concepts and characterization. Pakistan
journal of biological sciences, 5 (10): 1135-1140.
17. Frary, A.; Clint, N.T.; Frary, A.; Grandillo, S.; Van der
Kannpe Knaap, E.; Cong, B.; Liu, J.; Meller, J.; Elber,
R.; Alpert, K.B. and Tanksely, S.D. (2000). A
quantitative trait locus key to the evolution of tomato
fruit size. Science, 289:85-88.
18. Gupta, P.K. and Varshney, R.K. (2000). The
Development and Use of Microsatellite Markers for
Genetic Analysis and Plant Breeding with Emphasis on
Bread Wheat. Euphytica, 113: 163-185.
19. Hamrick, J.L. and Godt, M.J.W. (1989). Allozyme
diversity in plants. In: A.H.D. Brown, M.T. Clegg, A.L.
Kahler & B.S. Wier (Eds), Plant Population, Genetics,
Breeding and Genetic Resources, pp. 318370.
20. Hoisington, D.; Bohorova, N.; Fennell, S.; Khairallah, M.;
Pellegrineschi, A. and Ribaut, J.M. (2002). The
application of biotechnology in wheat improvement and
production. Curtics, B.C. Rajaram S. and Gomez, H.
(eds). FAO, Rome.
21. Johnson, L.A.; Suleiman, T.M. and Lusas, E.W. (1979).
Sesame protein: a review and prospectus. Journal of
the American Oil Chemists Society, 56(3): 463-468.
22. Joshi, S.P.; Prabhakar, K.; Ranjekar, P.K. and Gupta,
V.S. (2011). Molecular markers in plant genome
analysis. http/www.ias.ac.in/currsci/jul25/articles 15.
htm. Pp 1-19
23. Khan, W.M.; Munir, I.; Farhatullah, A. M.; Iqbal, A.; Ali, I.;
Ahmad, D.; Ahmad, M.; Mian, A.; Bakht, J.; Inamullah
and Swati, Z.A. (2011). Assessment of genetic diversity
of Brassica juncea germplasm using randomly
amplified polymorphic DNA (RAPD) markers. African
Journal of Biotechnology, 10(19): 3654-3658.

Kumar et al.,
24. Kiss, G.B.; Osanandi, G.; Kalman, K.; Kalo, P. and Okesz,
L. (1993). Construction of a basic linkage map of alfalfa
using RFLP. RAPD, isozyme and morphological
markers. Mol. Gen Genet, 238: 129-137
25. Li, Y.C.; Korol, A.B.; Fahima, T.; Beiles, A. and Nevo, E.
(2002). Microsatellites: Genomic Distribution, Putative
Functions and Mutational Mechanisms: A Review.
Molecular Ecology, 11: 2453-2465.
26. Liu, C.J.; Witcombe, J.R.; Pittawy, T.S.; Nash, M.; Hash,
C.T.; Brusso, C.S. and Gale, M.D. (1994). An
RFLP-based genetic map of pearl millet (Pennisetum
glaucum). Theoretical and applied genetics, 8:
481-487.
27. Mccouch, S.R.; Chen, X.; Panaud, O.; Temnykh, S.; Xu,
Y.; Cho, Y.G.; Huang, N.; Ishii, T. and Blair, M. (1997).
Microsatellite Marker Development, Mapping and
Applications in Rice Genetics and Breeding. - Plant
Molecular Biology, 35: 89-99.
28. Mohamed, N.B.; Abdullah, A.A.; Elshafei1, A.A. and
Moustafa, K.A. (2011). Identification of new
microsatellite marker linked to the grain filling rate as
indicator for heat tolerance genes in F2 wheat
population. AJCS, 5(2):104-110.
29. Motawei, M.I.; Al-Doss, A.A. and Moustafa, K.A. (2007).
Genetic diversity among selected wheat lines differing
in heat tolerance using molecular markers. Journal of
Food Agriculture & Environment, 5 (1): 180-183. 2007.
30. Mullis, K.B. and Facoona, F.A. (1987). Specific synthesis
of DNA in vitro via a polymerase catalysed chain
reaction. Methods enzymological, 155: 335-350.
31. Nguyen, T.T.; Taylor, P.W.J.; Redden, R.J. and Ford, R.
(2004). Genetic diversity estimates in Cicer using AFLP
analysis. Plant Breed, 123: 173179.
32. Nybom, H. (2004). Comparison of Different Nuclear DNA
Markers for Estimating Intra-specific Genetic Diversity
in Plants. Molecular Ecology 13: 1143-1155.
33. Powell, W.; Morgante, M. and Andre, R. (1996). The
comparison of RFLP, RAPD, AFLP and SSR
(microsallite) markers for germplams analysis. Mol
Breed. 2: 225-238.

231

34. SAX, K. (1923). The association of size differences with

seed coat pattern and pigmentation in Phaseolus
vulgaris. Genetics, 8: 552-560.
35. Staub, J.C.; Serquen, F.C. and Mccreight, J.A. (1997).
Genetic diversity in cucumber (Cucumis sativus L.). An
evaluation of Indian germplasm. Genetic Res and Crop
Evolution, 44 (4): 315-326.
36. Sudupak, M.A.; Akkaya, M.S. and Kence, A. (2002).
Analysis of genetic relationships among perennial and
annual Cicer species growing in turkey using RAPD
markers. Theor Appl Genet. 105: 12201228.
37. Thornsberry, J.M.; Goodman, M.M.; Doebley, J.;
Kresovich, S.; Nielsen, D. and Bucker, E.S. (2001).
Dwarf polymorphisms Associate with variation in
flowering. Natural Genetics, 28: 286-289.
38. Thottappilly, G.; Magonouna, H.D. and Omitogun, O.G.
(2000). The use of DNA markers for rapid improvement
of crops in Africa. African Crop Science Journal, 8(1):
99-108.
39. Van der Maesen LJG. 1987. Origin, history and taxonomy
of chickpea. In: Saxena MC, Singh KB (eds), the
chickpea CAB Int Publ., UK, pp 1134.
40. Wahid, A.; Gelani, S.; Ashraf, M. and Foolad, M.R.
(2007). Heat tolerance in plants: An overview Envoi
and Exp Botany 61: 199223.
41. Weising, K.; Nybom, H.; Wolff, K. and Kahl, G. (2005).
DNA Fingerprinting in Plants - Principles, Methods, and
Applications. - Boca Raton (CRC Press).
42. William, M.N.V.; Pande, N.; Nair, S.; Mohan, M. and
Bennet, J. (1991). Restriction fragment length
polymorphism analysis of polymerase chain reaction
products amplified from mapped loci of rice (Oryza
sativa L.) genomic DNA. Theor. Appl. Genet., 82:
489-498.
43. Wu, K.S.; Jones, R.; Danneberger, L. and Scolnik, P.
(1994). Detection of microsatellite polymorphism
without cloning. Nucleic acids Res, 22: 3257-3258
44. Zane, L.; Bargelloni, L. and Patarnello, T. (2002).
Strategies for Microsatellite Isolation: A Review Molecular Ecology, 11: 1-16.