Molecular Plant Breeding 2016, Vol.7, No.9, 1-16
http:// mpb.biopublisher.ca
3
fungus and 4 fold higher of genetic recombination
have been found in
D. melanogaster
on stressful
heterogenous SFS as compared to mild- moist NFS
(Nevo, 1997).
2 Genomic Diversity Analysis by RAPD
Analysis
Study and investigation of variations in genes can be
helpful in understanding various phenomena at
molecular level (Hibbett, 1992). Random amplified
polymorphic DNA analysis can be helpful in
identifying genomic modifications among organisms
of even same species due to high variability of
markers (Sunnucks, 2000; Nawaz et al., 2013).
Increased numbers of genetic characters lead towards
studying the diversity of fungal species (Ellstrand
and Roose, 1987). There are two types of basic
markers, PCR and non-PCR based, which are easy to
use with reliability, precision of analysis, statistical
influence and confidence of revealing polymorphism
in genes and genomes (Agerwal et al., 2008).
Molecular markers which are PCR based are
excellent tools for defining relationships in fungi at
genetic level (Welsh and McClelland, 1990; Duran et
al., 2009). The significance of PCR-based marker
methods is due to that it is rapid and needs small
amount of genomic DNA (Jacobson and Hedren,
2007). Random amplified polymorphic DNA analysis
first applied on genomic diversity analysis was based
on the use of oligonucleotide primers and genomic
DNA (Williams et al., 1990). Genomic variations of
different fungal species can be studied by using
RAPD markers (Crowhurst et al., 1991). Random
amplified polymorphic DNA technique involved the
availability of priming site on whole genome for a
single primer in inverted position and closes enough
to allow PCR amplification (Whitekus et al., 1994).
The short primers optimized for RAPD analysis have
become genomic markers which can be used for
quantitative assessment of genomic similarities of
strains from same or different species of organisms
(Leung et al., 1992).
In addition to RAPD several other marker systems
are being applied for exploration of biodiversity
including RFLP, SSR and AFLP (William and Clair,
1993; karp et al., 1997). According to Nesbitt et al.,
(1995) RAPD markers can be used in paternity
analysis, taxonomic-based identification and genetic
diversity (Van de Ven and McNicol, 1995). Random
Amplified Polymorphic DNA analysis is being used
for generating genomic maps (Tulsieram et al., 1992)
and in detecting loci of interest for studying
molecular biodiversity in fungi (Plomion et al.,
1996). Random Amplified Polymorphic DNA
markers are cheap and utilize little amount of
genomic DNA for analysis (Soares et al., 2008).
Random Amplified Polymorphic DNA markers
analysis is more reliable in terms of reproducibility
and provides high resolution of genotype
distribution in natural populations (Brahmane et al.,
2008). Therefore, RAPD has been a very popular
molecular technique to generate genus-specific,
species specific or strain-specific diagnostic DNA
fragments or fingerprints, identifying genes linked
to traits of interest; undertaking genetic diversity
studies and gene mapping for development of
diagnostic and identification of living organisms
(Bazzicalupo and Fani, 1996; Abad et al., 1998;
Ransom et al.,
1998).
Random Amplified
Polymorphic DNA is also being used in population
genetics studies like genetic diversity, divergence
within and among populations based on assumption
of Hardy-weinberg equilibrium (Brown and
Epifanio, 2003). It detects the genetic variations in
the genome of an organism in terms of sequence
variation at the priming regions (Magalhães et al.,
2007). Similarities in banding profiles among
strains (i.e. the number and sizes, but not the
intensity of amplified bands) can be calculated and
used to infer strain relationships (Dutra et al., 2008).
Random Amplified Polymorphic DNA technique
can also be applied to estimate the populations, for
which no particular molecular markers have been
established, thus facilitating the screening process
of genetic variability (Lacerda and Wrobel, 2001).
Due to nucleotide sequence differences either by
insertions or deletions in the fragment size between
two primer sites, length differences occur that may
lead to polymorphism which is related to genomic
diversity (Agerwal et al., 2008).
Shah et al., (2006) differentiated the
A. niger
genome
by using RAPD and the 0.7 kb fragment amplified
was used to further differentiate from other strains of
A. niger
(ATCC 16880). Genetic relationship among
