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RAPD Marker-assisted Identification of Genetic Diversity among Mango

(Mangifera indica) Varieties in Mauritius

Article in International Journal of Agriculture and Biology · January 2011

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INTERNATIONAL JOURNAL OF AGRICULTURE & BIOLOGY
ISSN Print: 1560–8530; ISSN Online: 1814–9596
10–455/DYX/2011/13–2–167–173
http://www.fspublishers.org

Full Length Article

RAPD Marker-assisted Identification of Genetic Diversity

among Mango (Mangifera indica) Varieties in Mauritius
ANUSHA DEVI RAMESSUR AND V.M. RANGHOO-SANMUKHIYA1
Faculty of Agriculture, the University of Mauritius, Mauritius
1
Corresponding author’s e-mail: m.sanmukhiya@uom.ac.mu

ABSTRACT

Morphological and molecular techniques were used to evaluate the characteristics of 12 mango (Mangifera indica L.) varieties
cultivated in Mauritius and to compare their genetic relatedness. Genomic DNA was extracted from leaf samples and genetic
characterization was carried out using the RAPD technique making use of 30 decamer Operon primers. 77.1% polymorphism
was obtained with Operon primer OPD-2 being the least discriminatory in contrast to OPA-9 and OPL-14, which were most
polymorphic. An Un-weighted Pair Group Method with Arithmetic Mean dendogram of cophenetic ratio 0.9732 was
constructed with distance values of 0.222 to 0.667. Two major clusters consisting of a mixture of foreign and native mango
varieties were delimited with Overseer being the least related to the rest of the varieties. No clear distinction between the
landraces and exotic varieties was observed. Phenotypically similar José and Eugénie varieties were also genetically close.
The 3 ‘pickle’ varieties Dauphiné, Sabre and Blanc were within the same cluster. Considerable genetic variation was observed
between the studied mango varieties. The RAPD technique together with the analysis of morphological characters proved
useful for assessing the diversity existing between the mango varieties. In conclusion, the mango varieties used in this study
could be tapped in breeding programs aimed at cultivar improvement. © 2011 Friends Science Publishers

Key Words: Mango; Mangifera indica L; Mauritius; Genetic diversity; RAPD

INTRODUCTION collection, evaluation, characterization and documentation is

Mango (Mangifera indica L.), native to South-East
Asia, comprises 62 species about 16 of which have an
edible fruit. Mango was introduced in Mauritius two
centuries ago by the Dutch and has been in cultivation ever
since (Rouillard & Joseph, 1999). Prevailing favorable
climatic conditions allow the tropical fruit to thrive
particularly in the regions receiving 30 inches of rainfall
annually (France Du Pavillon, 1991). Flowering starts in
July over 5 months and mango yield peaks in summer
months notably from October to February.
Mango varieties of differing skin color, stone size,
sweetness and composition are available on the market,
some of which are native and others exotic ones introduced
from Australia, Israel, Reunion, America and Europe by the
Agricultural department in Mauritius to expand the local
‘genetic pool’ of the mango fruit (Seeruttun, 2001). An
important demand for mangoes exists in supermarkets and
hotels for certain varieties like José. Mango is not currently
exported but a market for export could be exploited for
delicious endemic varieties. These varieties represent
potential candidates for any future breeding work aimed at
producing high yielding, disease-resistant hybrids adapted to
the local microclimatic conditions. Genetic resources for
potential crop improvement are invaluable, hence their
important.
Traditionally, in Mauritius, mango varieties have been
differentiated based particularly on fruit characteristics like
size, shape and color, which being influenced by
environmental parameters, are unreliable. Molecular
markers, by virtue of their determinate number and
protection against environmental influence, can solve
problems posed by morphological markers. Identification of
genotype using molecular markers can help in identification
of trees for sale, minimizing the risk of mix-ups in orchards
(Struss et al., 2001) and different markers have been used to
study mango diversity namely Random Polymorphic DNA
(RAPD) markers and Amplified Fragment Length
Polymorphism (AFLP) and Inter Simple Sequence Repeat
(ISSR). RAPD was considered practical to use over the
other markers since the DNA purity required is lower, it is
less costly, does not require blotting and data can be
collected quickly (Welsh & McClelland, 1990; Williams et
al., 1990). Adato et al. (1995) used RFLP analysis based on
minisatellite probes and came to the conclusion that Indian
cultivars represented a varied group. Molecular markers are
co-dominant, specific and highly variable, rendering them
highly suitable to study diversity in supposedly related
populations or cultivars (Duval & Bunel, 2005).
Ravishankar et al. (2004) used dendogram analysis of

To cite this paper: Ramessur, A.D. and V.M. Ranghoo-Sanmukhiya, 2011. RAPD Marker-assisted identification of genetic diversity among mango
(Mangifera indica) varieties in Mauritius. Int. J. Agric. Biol., 13: 167–173
 RAMESSUR & RANGHOO-SANMUKHIYA / Int. J. Agric. Biol., Vol. 13, No. 2, 2011
RAPD and chloroplast DNA to group Indian cultivars into
two clusters based on embryo type and geographical origin.
In another study, Ravishankar et al. (2000) used RAPD
analysis on 18 Indian cultivars and came to the conclusion
that eastern, western and northern cultivars were genetically
close, while southern cultivars formed a different genetic
group. Recently, twenty-eight polymorphic microsatellite
loci for the mango genome were developed and described
(Duval & Bunel, 2005).
In Mauritius, Seeruttun (2001) carried out
morphological characterization of 16 important varieties on
the basis of fruit, skin colour, stone, pulp firmness and
sweetness. The current study adds to the previous one in
providing more insight into the morphology and genetic
diversity that exists among the mango varieties in the face of
growing interest in the potential of the mango production
sector. The aim of the study was to evaluate the genetic
relatedness between different mango varieties native and
exotic cultivated in Mauritius and to find the possible origin
of Mauritian mango varieties. Morphological data was
correlated with molecular data to validate their versatility to
be used for characterisation of these mango varieties.
MATERIALS AND METHODS
Plant material: The accessions used were both local and
exotic ones from America, Australia and Reunion as
follows: Dauphiné, Sabre, Blanc, Maison Rouge, Figette
and Overseer (local), Bowen (Australia), Irwin, Early Gold
(America), Jose, Eugenie and Christian (Réunion). Leaf
material (5 replicates of each variety) was collected in paper
bags from mango varieties at different accession sites from
the Ministry of Agroindustry and Fisheries (Mauritius)
namely Barkly, Plaisance experimental stations and Roches
Brunes Seed Production Center. The leaves were wrapped
in moist tissue paper and were refrigerated at -50°C when
not subjected to immediate use. All experiments were
carried out from August 2007 to March 2008 in the
molecular biology laboratory, Faculty of Agriculture, The
University of Mauritius.
Morphological characterization: Mature mango leaves
and ripe fruits of all 12 varieties were characterized based
on the International Plant Genetic Resources Institute
(IPGRI) descriptors for mango and the 1986 journal of the
Californian Rare fruit growers. The 9 leaf traits described
included base shape, apex shape, blade shape, margin,
colour at maturity, fragrance, pubescence, angle of
secondary veins to midrib and secondary vein curvature.
The 6 fruit traits described include skin colour, fruit form,
shoulder form, forms of the sinus and apex, beak form and
base form.
DNA isolation protocol and purification: Fresh leaf tissue
(0.5 g) was ground in liquid Nitrogen to form a thin powder,
which was transferred into 5 mL of freshly prepared,
preheated (60◦C) Cetyltrimethylammonium Bromide
(CTAB) buffer in a tube followed by addition of 0.2% (v/v)
168
β- mercaptoethanol and 2% (v/v) Polyvinylpyrrolidone
(PVP). The tube was incubated in a water bath held at 60◦C
for 45 min with intermittent swirling. 2/3 volume of
chloroform: isoamyl alcohol (24:1 v/v) was added to the
tube, which was tilted several times and centrifuged for 10
min at 2208 g. This extraction step was repeated twice. 2/3
volume of ice-cold isopropanol was added to the
supernatant and the tube was incubated at – 20°C overnight.
The tube was centrifuged for 30 min at 5652 g (40°C). The
supernatant was discarded and the DNA pellet was washed
with 70% ethanol followed by centrifugation for 2 min at
10000 rpm to resettle the pellet. The alcohol was poured off
and the DNA pellet was allowed to dry and thereafter it was
dissolved in 1 mL of TE buffer. The DNA was purified by
incubation with RNase followed by a phenol treatment.
RAPD reaction: RAPD reactions were carried out in a
DNA Thermocycler (MJ Research Inc. USA). Negative
controls comprised all PCR components excluding the
template. Each 25 µL reaction volume comprised 100 ng of
template DNA, 1X PCR Buffer (10 mM Tris Hcl pH 8.8; 50
mM KCl), 4 mM MgCl2, 0.2 mM dNTP, 0.5 µM of single
primer,1 U of Taq DNA polymerase. The thermal profile set
comprised a denaturation step of 5 min at 94°C, followed by
38 cycles of 30 s at 94°C, 30 s at 35°C, an extension at 72°C
for 2 min and a final extension at 72°C for 10 min. 30
Operon primers were used to screen for polymorphism.
PCR products were electrophoresed on 1.5% (w/v) agarose
gels using 0.5x TBE Buffer at 115 V and stained with
ethidium bromide (0.5 µg/mL) for visualization and
photographing under UV light.
RAPD profile analysis: The screened primers that gave
bands were used to amplify the DNA of all the 12 mango
varieties. Each genotype was characterized by its banding
pattern (Figs. 1-3), using the DNA hyperladder 2 (Bioline)
as basepair ladder. The RAPD markers as viewed from the
gels after electrophoresis and staining were converted into a
matrix of binary data, where the presence of the band
corresponded to value 1 and the absence to value 0. The
statistical software NTSYS-PC (Rohlf, 2005) and DARwin
5 software (Perrier & Jacquemoud-Collet, 1996) were used
to construct a UPGMA dendrogram using hierarchical
clustering. Using NTSYS software, a dissimilarity matrix
was calculated utilising Jaccard’s (1908) coefficient. The
matrix was converted to a dissimilarity matrix
corresponding to the complement
(dissimilarity=1−similarity). Cluster analysis based on the
dissimilarity matrix, was performed using un-weighted pair-
group method arithmetic averages (UPGMA) (Sneath &
Sokal, 1973) of the NTSYS–PC version 2.2 (Rohlf, 2005).
RESULT
Morphological characterization: A high degree of
similarity among varieties in some of the leaf traits e.g.,
curvature of secondary veins, angle of secondary veins
to midrib and leaf pubescence was observed (Table I).
 MOLECULAR STUDIES ON MANGO VARIETIES / Int. J. Agric. Biol., Vol. 13, No. 2, 2011

Table I: Morphological leaf traits of the different mango varieties

Dauphiné
Christian

Overseer
Eugénie

Maison

Barkly
Figette
Bowen

Rouge

Sabre

Blanc
Irwin

Early
Variety

Gold
José
1. Acute √ √ √ √ √ √ √ √ √
1. Leaf base shape 2.Obtuse √ √ √
1.Acute √ √ √ √ √ √
2. Leaf apex shape 2.Acuminate √ √ √ √ √ √
1.Lanceolate √ √ √
3. Leaf blade shape 2.Elliptic √ √ √ √ √ √
3.Oblong √ √ √
1.Wavy √ √ √ √ √ √ √ √ √ √
4. Leaf margin 2.Entire √ √
1.Dark green √ √ √ √ √ √ √
5. Colour of fully developed leaf 2.Green √ √ √ √ √
1.Mild √ √ √ √ √ √ √ √
6. Leaf fragrance 2.strong √ √ √ √
3.Absent
1.Absent √ √ √ √ √ √ √ √ √ √ √ √
2.Present
7. Leaf pubescence 2.Medium (45-60°) √ √ √ √ √ √ √ √ √ √ √ √
3.Narrow (45° )
8. Secondary vein curvature 1. Present √ √ √ √ √ √ √ √ √ √ √ √
2.Absent

Table II: Morphological fruit traits of the different mango varieties

Dauphiné
Christian

Overseer
Eugénie

Maison

Barkly
Figette
Bowen

Rouge

Sabre

Blanc
Irwin

Early
Gold
José

Variety

1. Green √
2. Yellow √ √ √ √ √
1.Skin colour 3. Orange √
4. Purple
5. Red √ √ √ √ √
1. Roundish √ √ √ √
2. Oval √ √ √
3. Cordate √
2. Fruit form 4. Peento
5. Oblong √
6. Ovate oblique √
7. Oblong reniform √
8. Ovate reniform √
1. Broadly rounded √ √ √
2.Rising then rounded √ √
3. Shoulder form 3.Ending in long curve √ √ √
4. Sloping √ √ √
5. Falling abruptly √
1.Sinus absent √ √ √ √ √
2.Slight sinus √ √
4.Forms of Sinus 3.Broadly rounded apex √
and apex 4.Broadly pointed apex √
5.Deep sinus √ √
6.Rounded apex √
1.Point absent √ √ √ √ √ √ √
2.Small point √
5. Form of the beak 3.Mammi form √
4.Curved beak √ √
5.Slightly prominent √
1.Flattened √
2.Slightly flattened √ √ √ √
6. Base form 3.Rounded √ √ √
4.Extended √
5.Obliquely flattened √ √
6.Necked √

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 RAMESSUR & RANGHOO-SANMUKHIYA / Int. J. Agric. Biol., Vol. 13, No. 2, 2011

Table III: RAPD markers used for the generation of Molecular characterization: The CTAB extraction
polymorphism in local and imported mango varieties protocol successfully yielded DNA (265-600 ng/µL) from
all the mango varieties with a A260/A280 ratio of 1.600–
Primer Primer sequence Number of Number of % 1.900. Out of 30 primers screened most polymorphism were
(5' - 3') markers polymorphic polymorphism
(Total) markers obtained using OPA-16, OPJ-13, OPL-14, OPD-02, OPW-
OPD-2 GGACCCAACC 6 0 0.0 04, OPD-10 and OPA-09 (Table III). Primer OPA-9 gave
OPD-10 TGTCTGGGTG 10 9 90.0 the greatest number of bands and together with OPL-14
OPL-14 GTGACAGGCT 9 9 100.0 were the most polymorphic and hence most discriminatory
OPJ-13 CCACACTACC 11 8 72.7
OPW-4 CAGAAGCGGA 13 7 53.8
between varieties in stark contrast to primer OPD-2, which
OPA-9 GGGTAACGCC 21 21 100.0 was not polymorphic at all (Table III).
Total 70 54 77.1 Two major clusters, A and B, could be delimited from
the UPGMA dendogram generated (Fig. 4). Cluster B
Fig. 1: RAPD reaction on the mango varieties following comprised Dauphiné, Sabre, Bowen and Blanc, while the
amplification using OPD-2 other encompassed Maison Rouge, Figette, Irwin, Early
Lanes 1,: Blanc , 2:Dauphiné , 3:Sabre ,4:Bowen , 5:José, 6: Eugénie,
Gold, Christian, Eugénie and José. In cluster B, Blanc
7:Maison Rouge, 8:Irwin, 9:Figette, 10: Early Gold, 11: Christian, 12:
Overseer, M: ladder, Ne :negative control clustered out separately. The Réunion varieties José and
Eugénie separated out as an independent clade in cluster A.
The other Mauritian varieties, Maison Rouge, Figette, Irwin,
Early Gold and Christian were found in another clade within
the same cluster A. Within this cluster, Early Gold was the
most different from the rest of the varieties of the group.
Dauphiné was particularly genetically very close to Sabre as
were Maison Rouge to Irwin and José to Eugénie. Local
varieties clustered with the American and Réunion ones in
cluster A and with the Australian one in cluster B. The local
variety Overseer was distantly related to the rest of the
mango varieties. Dissimilarity values ranged from 0.222 to
0.667; Dauphiné and Overseer were the two varieties with
most distantly related genotypes as inferred from the
dissimilarity matrix in contrast to the two closest varieties
Dauphiné and Sabre (Table IV). The dendogram had a high
goodness of fit and was robust as indicated by the
cophenetic ratio of 0.9732 and was hence reliable for the
Fig. 2: RAPD reaction on the mango varieties following analysis of the genetic relatedness among the varieties.
amplification using OPL-14
Lanes 1: negative control, 2: Blanc, 3: Dauphiné, 4: Sabre, 5: Bowen, 6:
José, 7: Eugénie, 8: Maison Rouge, 9: Irwin, 10: Figette, 11: Early Gold, DISCUSSION
12: Christian, 13: Overseer, M: Ladder
Each mango variety possesses a unique combination
of fruit and leaf traits setting it apart from the other varieties.
These sets of distinguishing morphological characteristics
constitute a basis for separating varieties. Certain characters
are uninformative for differentiating the varieties notably
‘curvature of secondary veins’, ‘angle of secondary vein to
midrib’ and ‘leaf pubescence’. Some leaf traits were similar
in the overwhelming majority of varieties e.g., the wavy leaf
margin, which were not useful in distinguishing varieties.
On average, the leaf traits between the varieties did not
show as much diversity as the fruit traits, suggesting the
superiority of the latter in easy differentiation of varieties.
These observations are congruent with the statement of
Singh (1960) statement that mango fruit characters form the
main basis for identification and classification of varieties of
In contrast, there appeared to be greater variation in the fruit which primary characters e.g., fruit and beak form are the
traits. Each fruit character (Table II) had a large number of most useful. Out of all the fruit traits, fruit form was
character states with many intermediate gradations between observed to be more variable among the varieties. A
extremes, while leaf character states were two to threefold. strikingly close phenotypic similarity between the varieties

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 MOLECULAR STUDIES ON MANGO VARIETIES / Int. J. Agric. Biol., Vol. 13, No. 2, 2011

Table IV: Dissimilarity matrix based on the proportion of shared RAPD fragments among different mango
varieties

Blanc Dauhiné Sabre Bowen José Eugénie Maison. Rouge Irwin Figette Early Gold Christian
Dauphiné 0.350
Sabre 0.350 0.222
Bowen 0.381 0.308 0.390
José 0.442 0.451 0.420 0.380
Eugénie 0.447 0.489 0.489 0.540 0.377
Maison Rouge 0.463 0.527 0.442 0.463 0.373 0.429
Irwin 0.527 0.481 0.481 0.500 0.407 0.436 0.222
Figette 0.420 0.490 0.490 0.537 0.441 0.444 0.291 0.327
Early Gold 0.447 0.386 0.422 0.447 0.436 0.440 0.429 0.377 0.444
Christian 0.370 0.447 0.378 0.500 0.400 0.431 0.333 0.340 0.314 0.333
Overseer 0.630 0.667 0.615 0.630 0.525 0.589 0.466 0.418 0.455 0.564 0.472

José and Eugénie with regard to fruit traits exists,
understandably giving rise to confusion in orchards. The
resemblance suggests that they may be closely related to
each other although it was found that few of the studied leaf
traits are shared between the two varieties.
Primers OPD-10, OPL-14 and OPA-9 were most
discriminatory in assessing genetic diversity between mango
varieties. The Réunion varieties José and Eugénie, which
were phenotypically similar in fruit traits clustered together
in the dendogram obtained following analysis of the RAPD
data, confirming similarity at genetic level as well. Primer
OPW-4 was most suitable in differentiating these two
varieties since many bands present in one variety were
absent in the other. These could hypothetically be associated
with the differential characteristics setting José apart from
Eugénie e.g., ‘acuminate leaf apex’ and ‘elliptic leaf blade’.
Local varieties Dauphiné and Sabre clustered together
although morphologically no such closeness was observed.
Similar disparities between molecular and morphological
data were made for Maison Rouge and Irwin. The use of
morphological traits was not always the best way to evaluate
genetic distance, since the degree of divergence between
genotypes at the phenotypic level was not necessarily
correlated with a similar degree of genetic difference.
Similar discrepancies between RAPD data and
morphologically based groupings were reported recently in
cashew (Damodaran et al., 2007). Maison Rouge and Irwin
shared a similar profile with most RAPD primers
particularly OPD-10, while on the other hand they could be
differentiated by OPL-14, OPJ-13, OPW-4 and OPA-9.
Interestingly, the three local varieties Dauphiné, Sabre and
Blanc, which are known to be less sweet with high fibre
content and hence suitable for pickling were within the same
cluster, indicating a close relationship between them. Most
probably their attributes that make them more suitable for
pickling than consumption as table fruits were inherited
from a common parent having its roots in Mauritius. With
OPD-10 for instance 80% of the markers were shared
among the three varieties. Dauphiné and Sabre could be
discriminated by OPA-9, which yielded a 600 and 650 bp
marker in Dauphiné and a 1200 bp one in Sabre.
Analysis of RAPD data showed that the mango
varieties did not cluster according to their country of origin.
One possible explanation regarding this association between
the supposedly distantly located genotypes could be
attributed to the unique and broad genetic base of the mango
species in general. Another could be that agro-climatic
conditions prevailing in the island could have triggered
adaptive changes in the introduced foreign varieties. This
possibility is acknowledged by Padmesh et al. (1998),
according to whom genotypes from different geographical
regions can be genetically similar to genotypes with similar
spatial relationships. Furthermore, compatibility between
the varieties being high, inter-varietal hybridization in
nature between the local and exotic varieties could have
given birth to new varieties. Karihaloo et al. (2003) reported
a high diversity within regions in India and confirmed that
this is not surprising given that mango is a cross-pollinated
plant and selecting superior strains according to taste among
naturally produced seedlings has given birth to the
commercial cultivars and the observed appreciable range of
variation (Mukherjee, 1950).
Mango was introduced two centuries back into
Mauritius and there are instances of typical local Mauritian
varieties being introduced in other countries like Jamaica
(Duval & Bunel, 2005). The local variety Overseer was
most distantly related to the rest of the varieties (local or
exotic). This is particularly evident from its distinct unique
shape thus sharing little similarity at genetic level with the
other varieties. Morphological traits like ‘leaf pubescence
absent’ and DNA bands e.g., the 1200 bp amplified by
OPD-10 were common to all the twelve varieties possibly
being ancestral in origin and characteristic of mango.
Originally, mangoes had no names associated with them and
monkeys were responsible for their propagation. They
hybridized, conserving their ancestral characteristics
(Rouillard & Joseph, 1999), which could explain their
similar genetic profile.
The study highlights the diversity of mango fruit forms
that exists in Mauritius, which has also been observed in
wild and cultivated Indian mango (Karihaloo et al., 2003).
Both molecular and morphological methods were effective
at portraying the variation. The dendogram clusters are not
in agreement with the geographical origin of the mango

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 RAMESSUR & RANGHOO-SANMUKHIYA / Int. J. Agric. Biol., Vol. 13, No. 2, 2011
Fig. 3: RAPD reaction on the mango varieties following
amplification using OPD-10
Lanes 1: Blanc, 2: Dauphiné, 3: Sabre, 4: Bowen, 5: José, 6: Eugénie, 7:
Maison Rouge, 8: Irwin, 9: Figette, 10: Early Gold, 11: Christian, 12:
Overseer, M: Ladder
Fig. 4: Dendogram generated using UPGMA cluster
analysis showing the relationships and diversity among
the twelve local and imported mango varieties- local
(L), Australian (Aus), American (Am) and from
Réunion (R)
cultivars. It is conceivable that, keeping in mind the
geographical proximity of Australia and Réunion to
Mauritius, foreign varieties could have originated from local
Mauritian varieties for instance, the Réunion variety
Christian and the landrace Figette - explaining the observed
relatedness. Similarly, Ravishankar et al. (2000) concluded
that cultivars in India might have arisen from germplasm in
172
a particular geographical area. There are documented cases
of an association of genotypes of different geographical
location as in the study on the genetic diversity of
Andrographis paniculata accessions from India, Thailand,
Malaysia and Indonesia, where Padmesh et al. (1998)
ascribed the observation to seed movement and gene flow.
Schnell et al. (1995) in their study of 25 accessions also
obtained a wide distribution of Indian cultivars in RAPD
based dendogram, which is indicating how cultivars may
vary in a specific region.
This study reports for the first time the genetic
diversity of mango varieties cultivated in Mauritius and will
pave the way for future studies aimed at better
understanding their genetic variation. These molecular
studies will help in identifying superior genotypes for
cultivar upgrading or for generating new cultivars. Better
understanding the distribution of genetic variation could
help in identifying superior genotypes for cultivar upgrading
or for use in generating new cultivars. These could give a
boost to the local mango ‘gene pool’ by bringing together
the greater adaptability of the landraces to the local agro-
climatic conditions and the commercial characters of value
from foreign varieties to give birth to appealing varieties
from the point of view of consumers and marketing to
capture the interest of export markets. Developing SCARS
(Sequence Characterized Amplified Region) primers based
on unique polymorphic bands obtained among varieties
could help in distinguishing morphologically similar
cultivars as in the case of José and Eugénie.
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(Received 31 August 2010; Accepted 24 September 2010)