ArticlePDF Available

Genetic diversity and conservation of common bean (Phaseolus vulgaris L., Fabaceae) landraces in Nilgiris

  • Government Arts College, Udhagamandalam,Tamil Nadu,INDIA.

Abstract and Figures

Genetic diversity was studied among 20 common bean (Phaseolus vulgaris L.) landraces collected from different traditional farming villages of Nilgiris District, Tamil Nadu, India, with Random Amplified Polymorphic DNA (RAPD) markers. Evaluation of genetic diversity is essential for conservation, management and to trace the hybrids. Thirteen RAPD primers were selected from an initial screening with 72 primers. The PCR product revealed 102 bands, out of which 63 were found to be polymorphic (63.5%). Jaccard's pair-wise similarity coefficient (0.50 to 0.95) indicating an intra-specific genetic variation prevails in landraces of common bean in the Nilgiris biosphere reserve. No two accessions had a similarity of one or a distance of zero, showing that there were no duplicate entries. A dendrogram of the relationship of accessions constructed based on Jaccard's coefficients of 102 RAPD markers using the average distance method (UPGMA), separated the accessions into two major clusters, A and B, with Mesoamerican and Andean gene pools respectively. Principal coordinate analysis of the same dataset revealed similar results as those of the dendrogram, with the first two components accounting for 61.8% of the total variation. Among the 20 landraces, seven were Mesoamerican origin, 11 Andean origin, and two were possible recombinants between the two gene pools. A correlation was observed between RAPD dendrogram clustering and seed weight. The common bean population of the Nilgiris is highly diverse and the Nilgiris can be considered as a secondary centre of genetic diversity of common bean. A better knowledge of genetic aspects of common bean will help in genetic improvement and conservation programmes for its endangered landraces in the Nilgiris.
Content may be subject to copyright.
*For correspondence. (e-mail:
Genetic diversity and conservation of common
bean (Phaseolus vulgaris L., Fabaceae)
landraces in Nilgiris
Franklin Charles Jose
*, M. M. Sudheer Mohammed
, George Thomas
George Varghese
, N. Selvaraj
and M. Dorai
Department of Plant Biology and Biotechnology, Government Arts College, Stone House Hill P.O., Udhagamandalam 643 002, India
Department of Plant Biology and Biotechnology, Government Arts College (Autonomous), Coimbatore 641 018, India
Department of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695 014, India
Horticultural Research Station, Tamil Nadu Agricultural University, Centenary Rose Park, Udhagamandalam 643 001, India
Genetic diversity was studied among 20 common bean
(Phaseolus vulgaris L.) landraces collected from dif-
ferent traditional farming villages of Nilgiris District,
Tamil Nadu, India, with Random Amplified Polymor-
phic DNA (RAPD) markers. Evaluation of genetic di-
versity is essential for conservation, management and
to trace the hybrids. Thirteen RAPD primers were sele-
cted from an initial screening with 72 primers. The
PCR product revealed 102 bands, out of which 63
were found to be polymorphic (63.5%). Jaccard’s
pair-wise similarity coefficient (0.50 to 0.95) indicating
an intra-specific genetic variation prevails in landraces
of common bean in the Nilgiris biosphere reserve. No
two accessions had a similarity of one or a distance of
zero, showing that there were no duplicate entries. A
dendrogram of the relationship of accessions con-
structed based on Jaccard’s coefficients of 102 RAPD
markers using the average distance method (UPGMA),
separated the accessions into two major clusters, A
and B, with Mesoamerican and Andean gene pools
respectively. Principal coordinate analysis of the same
dataset revealed similar results as those of the dendro-
gram, with the first two components accounting for
61.8% of the total variation. Among the 20 landraces,
seven were Mesoamerican origin, 11 Andean origin, and
two were possible recombinants between the two gene
pools. A correlation was observed between RAPD
dendrogram clustering and seed weight. The common
bean population of the Nilgiris is highly diverse and
the Nilgiris can be considered as a secondary centre of
genetic diversity of common bean. A better knowledge
of genetic aspects of common bean will help in genetic
improvement and conservation programmes for its
endangered landraces in the Nilgiris.
Keywords: Genetic variation, germplasm conservation,
multivariate analysis, Phaseolus vulgaris, RAPD markers.
HE common bean (Phaseolus vulgaris L.) was intro-
duced from the Americas into the Nilgiris approximately
400 years ago. It is the most important legume worldwide
for direct human consumption and has the broadest range
of genetic resources
. The Blue Mountains or Nilgiri hills
in Tamil Nadu, India, lies between 11°12N and 11°43N,
76°14E and 77°1E. The region is a veritable paradise
because of the rich and diversified geographical condi-
tions, flora and fauna which have played a pioneering
role in the introduction and cultivation of plants since
colonial times
. This region is highly species-rich and is
considered one of the 25 biodiversity hotspots of the
The importance of common bean landraces in Nilgiris
agriculture cannot be neglected. Most of these varieties
are resistant to anthracnose, bean common mosaic virus
and rust, can be grown even if there is scarcity of water.
Most of the landraces are tall plants, and produce pods in
long periods than the short duration commercial cultivars.
The seeds of these landraces are used as sowing material
by the traditional small-scale farmers, who are conserving
these landraces for centuries. The immense genetic diver-
sity of landraces of crops is the most directly useful and
economically valuable part of biodiversity. Unlike high-
yielding varieties, the landraces maintained by farmers
are endowed with tremendous genetic variability, as they
are not subjected to subtle selection over a long period.
Because of the limitations of morphological and bio-
chemical markers, efforts are being directed to use mole-
cular markers for characterizing germplasm diversity.
Molecular markers have demonstrated a potential to
detect genetic diversity and to aid in the management of
plant genetic resources
. In contrast to morphological
traits, molecular markers can reveal differences among
genotypes at the DNA level, providing a more direct,
reliable and efficient tool for germplasm characterization,
conservation and management. Several types of mole-
cular markers are available today, including those based
on restriction fragment length polymorphism (RFLP)
random amplified polymorphic DNA (RAPD)
, ampli-
fied fragment length polymorphism (AFLP)
and simple-
sequence repeats (SSRs)
In the present study, we have used RAPD method of
DNA fingerprinting, which is widely used in conservation
biology because of quick results, cost-effectiveness and
reproducibility. The PCR-based RAPD approach using
arbitrary primers requires only nanogram quantities of
template DNA, no radioactive probes, and is relatively
simple compared to other techniques
. RAPD is a useful
predictive tool to identify areas of maximum diversity
and may be used to estimate levels of genetic variability
in natural populations. Morphological, biochemical and
molecular analyses have been suggested for the evaluation
of genetic diversity in common bean from America
, Central Himalaya
, Italy
and China
So far, no systematic studies have been conducted to
assess the morphological and genetic variation in the
Nilgiris common bean landraces, because of unavailabi-
lity in outside markets. Tribal agricultural farmers mainly
use these beans to prepare traditional food items for their
own use. The genetic discrimination of an individual is an
important step in investigating the population biology of
any species and a major contribution that conservation
geneticists can make for evaluating population viability.
On the basis of the above, the present study was under-
taken to investigate genetic diversity and origin of P. vul-
garis L. landraces cultivated by tribal agricultural farmers
in the Nilgiris.
Materials and methods
Sample collection
The present study included 20 landraces of common bean
collected from different villages of the Nilgiris. The vil-
lages from where the seeds were collected, its common
name, phesolin type, growth habit, 100 seed weight and
altitude of the region above mean sea level were recorded
(Table 1). Two landraces (LR2 and LR9) were obtained
from the Regional Horticultural Research Station (RHRS)
of Tamil Nadu Agricultural University (TNAU). The
genotypes were selected for genetic analysis after thor-
ough morphological evaluation in the farmer’s field, ac-
cording to the IBPGR descriptor list for P. vulgaris
Plant height, seed coat colour and seed weight (expressed
in g/100 seeds) were used as the primary indicators of
morphological variation because of the marked difference
in these characters between different landraces. Twenty-
five seeds from each landrace were collected and germi-
nated under laboratory conditions. The healthy, young
leaves collected from these samples were used for RAPD
DNA isolation and primer screening
DNA was extracted from young, tender leaves collected
separately from each individual and stored at –70°C in
sealed polythene bags. Genomic DNA was isolated from
100 mg of the tender leaf tissues using Gen Elute Plant
Genomic DNA Purification Kit (Sigma) following the
manufacturer’s instructions. About 2 μl of genomic DNA
isolated from 100 mg of leaf tissue was subjected to elec-
trophoresis on a 0.8% agarose gel containing 500 ng/μl of
ethidium bromide. After electrophoresis, the gel was
viewed over a UV transilluminator and the quality and
quantity of DNA was assessed using undigested λ DNA
as control. Only extracts without RNA smears on agarose
gel and with UV-light absorption ratios (A260/A280)
between 1.8 and 2.0 were used. The genomic DNA was
diluted to 4 ng/μl and stored at 4°C as working solution,
while the stock DNA (undiluted) was stored at –20°C in
aliquots. Initial screening was done with 72 primers
(Operon Technologies Inc., CA, USA) using DNA from
five randomly selected landraces. PCR–RAPD analysis
was repeated at least twice and only primers producing
strong and reproducible bands were used in the final
analysis of all the 20 landraces.
Polymerase chain reaction
Polymerase chain reaction (PCR) was carried out in a
20 μl reaction volume containing 28 ng of genomic DNA,
1 unit of Taq DNA polymerase (Bangalore Genei), 4 μl
primer, 0.2 mM dNTPs, 10 mM Tris-HCl (pH 9.0),
1.5 mM MgCl
and 50 mM KCl. Amplification was car-
ried out in a thermocycler (Eppendorf) with an initial
strand separation at 94°C for 4 min, followed by 40
cycles of 1 min at 94°C, 1 min at 37°C and 1.5 min at
72°C. After 40 cycles, there was a final extension step of
5 min at 72°C. Amplification products were resolved on
1.2% agarose gels in 1% TAE buffer at 70 V. The gels
were photographed using a gel documentation system
(SynGene). Size of the amplified products was compared
to λ DNA/EcoRI double-digest marker (Bangalore Genei).
Data analysis
Each amplified RAPD marker was treated as a unit char-
acter and was scored as present (1) or absent (0) for each
sample. Ambiguous bands that could not be clearly dis-
tinguished were not scored. The percentage of polymor-
phism was calculated as the proportion of polymorphic
bands over the total number of bands. The 1/0 matrix was
prepared for all fragments scored and the data were used
to generate genetic similarity (GS) based on Jaccard’s
coefficient of similarity as follows: GS(ij) = a/(a + b + c),
where GS(ij) is the measure of genetic similarity between
individuals i and j, a is the number of polymorphic bands
that are shared by i and j, b is the number of bands pre-
sent in i and absent in j, and c is the number of bands pre-
sent in j and absent in i. Jaccard’s coefficients were used
to construct a dendrogram using UPGMA. The Jaccard’s
Table 1. Phaseolus vulgaris L. landraces in the Nilgiris
Village/place Altitude Growth habit Seed weight
Accession no. Market class of collection m amsl (I, III, IV) (g/100 seeds)
LR1 Cranberry Nanjanadu 2376 I 39.9
LR2 Black turtle RHRS, TNAU*
2376 I 16.5
LR3 Cranberry big Adigaratti 2261 I 53.0
LR4 Pale brown kidney Tumanatti 1920 I 36.7
LR5 White kidney Nanjanadu 2376 I 32.8
LR6 Red kidney Ozahatti 2261 I 46.0
LR7 Black bean Nanjanadu 2376 IV 32.3
LR8 Great northern Ebanad 1930 III 34.3
LR9 White eyed bean RHRS, TNAU*
2376 IV 23.7
LR10 Greenish striped kidney Nundala 2180 IV 67.2
LR11 Ash bean Nanjanadu 2376 IV 66.9
LR12 Large pinto Tuneri 2066 IV 66.0
LR13 Pinto bean Muttinadu 2200 IV 66.1
LR14 Pink bean Sholur 2277 IV 31.8
LR15 Black striped Wellington 2041 IV 68.2
LR16 White round Bikkatti 2532 IV 69.4
LR17 Dark brown Nanjanadu 2376 I 30.8
LR18 Brown kidney Kokkal 2270 IV 63.5
LR19 Dark brown Ebanad 2060 IV 36.6
LR20 Small kidney Muttinadu 2200 III 23.5
*Regional Horticultural Research Station, Tamil Nadu Agricultural University, Udhagamandalam.
similarity matrix was then used as the basis for ordination
by principal coordinates analysis (PCoA), which was
performed to show the distribution of the genotypes in a
scatter plot using the Multivariate Statistical Package
version 3 software.
DNA fingerprinting
DNA extracted from 20 common bean landraces was
examined for the PCR–RAPD patterns. Out of the 72
primers screened, 13 were selected based on robustness
of amplification, reproducibility, scorability of banding
patterns and were used for diversity analysis in all land-
races. The 13 selected decamer oligonucleotide primers
(Table 2) generated 102 amplification products, out of
which 63 bands (63.5%) were polymorphic. The number
of bands per primer ranged from 4 (OPE19) to 13 (OPJ9),
with an average of 7.8 bands per primer. The range of
polymorphic bands per primer was 3 (OPA1, OPA4 and
OPF16) to 7 (OPE6, OPJ9 and OPJ16), with a mean of
4.8 polymeric bands per primer (Table 2). The represen-
tative RAPD patterns generated by primers OPE6, OPA4
and OPE19 for 20 landraces are given in Figure 1. These
three primers are efficient in discriminating landraces
into Andean and Mesoamerican races.
Genetic similarity, cluster analysis and PCoA
The pair-wise Jaccard’s coefficients genetic similarity
matrix was prepared based on RAPD data. The genetic
similarity coefficients among the common bean landraces
varied from 0.50 (between varieties LR3 and LR9) to
0.95 (between varieties LR1 and LR16; Table 3). Cluster
analysis was performed on RAPD data using UPGMA,
which showed overall genetic relationships among the
landraces of common bean (Figure 2). PCoA was carried
out in order to determine the genetic relationships among
the landraces. The landraces were plotted on principal
coordinates 1 and 2, accounting for 53.0 and 8.8% of the
variation respectively, and together explaining 61.8% of
the total variation (Figure 3). UPGMA clustering and
PCoA of RAPD data indicated that the landraces of P.
vulgaris population comprise two major groups, clusters
M and A (Figure 2). The similarity coefficients ranged
from 0.50 to 0.95, indicating that the two clusters did not
show 100% similarity.
Mesoamerican, Andean and hybrid gene pools
Cluster ‘M’ comprised of seven landraces (LR2, LR7,
LR8, LR9, LR14, LR19 and LR20) which are of Meso-
american origin. Cluster ‘A’ comprised of 11 landraces
(LR1, LR16, LR12, LR13, LR18, LR3, LR11, LR10, LR4,
LR15 and LR6) which are of Andean origin. Cluster ‘H’
consists of two landraces (LR5 and LR17) which are hy-
brids. Maximum similarities were observed between LR8
and LR9, with a similarity value of 0.89. LR20 and LR19
formed a separate cluster within cluster M, with a similar-
ity value of 0.81. LR2 formed an operational taxonomic
unit in cluster M. The highest similarity (0.95) was ob-
served among LR1, LR16, LR12 and LR13. Cluster analy-
sis and PCoA of the similarity indices (Figures 2 and 3)
Table 2. Primers with their sequences used for RAPD analysis of Phaseolus vulgaris L. landraces in the Nilgiris. Total
number of bands, polymorphic bands, and percentage of polymorphism yielded by each primer are also listed
No. of Percentage of
Primer code Primer sequence (5 3) Total no. of bands polymorphic bands polymorphism
Total 102 63 63.5
Mean per primer 7.8 4.8
Figure 1. RAPD profile of 20 landraces of Phaseolus vulgaris L. pro-
duced using the random decamer primers OPE6, OPA4 and OPE19. M,
100 bp DNA ladder. Lane numbers correspond to the landtraces LR1 to
LR20 given in Table 1.
support the above results. In the RAPD dendrogram (Fig-
ure 2) two landraces, LR5 and LR17, formed a separate
group in the Andean gene pool, very closely associated
with the Mesoamerican gene pool. This may be a natural
hybrid gene pool between two major gene pools
. In
PCoA, the hybrid landraces (LR5 and LR17) formed a
distinct group different from the Mesoamerican and An-
dean gene pools (Figure 3).
RAPD clustering and seed weight
A correlation was observed between seed weight, RAPD
clustering and PCoA of RAPD data. The average 100
seed weight of Mesoamerican landraces ranged from 16.5
to 36.6 g and that of the Andean gene pool ranged from
36.7 to 69.4 g. Therefore, there was a fine separation of
the major gene pools with regard to seed weight, without
any overlapping between them. The hybrid gene pool
comprising two landraces, LR5 and LR17, with 100 seed
weight (32.8 and 30.8 g respectively) and phaseolin types
(‘S’ and ‘T’ respectively) was dwarf plants with kidney-
shaped seeds. Similarly, LR2, the landrace with the low-
est seed weight formed a distinct taxonomical unit in the
Mesoamerican group. Thus, a correlation was observed
between RAPD clustering and seed weight in common
bean landraces. This indicates that RAPD markers are
well suited to determine the genetic diversity and differ-
entiation present in common bean landraces in the
The present study addresses the utility of RAPD markers
in revealing genetic relationships at the molecular level
among landraces of common bean in the Nilgiris. Sources
of polymorphism in the RAPD assay may be due to base
change within the priming site sequence, deletions of
Table 3. Similarity matrix for Jaccard’s coefficients for 20 landraces (LR1-20) of Phaseolus vulgaris based on 102 bands obtained with 13 RAPD primers
LR1 LR2 LR3 LR4 LR5 LR6 LR7 LR8 LR9 LR10 LR11 LR12 LR13 LR14 LR15 LR16 LR17 LR18 LR19 LR20
LR1 1.00
LR2 0.55 1.00
LR3 0.89 0.56 1.00
LR4 0.90 0.56 0.84 1.00
LR5 0.71 0.70 0.68 0.70 1.00
LR6 0.90 0.58 0.89 0.88 0.73 1.00
LR7 0.53 0.81 0.54 0.53 0.65 0.53 1.00
LR8 0.54 0.80 0.56 0.53 0.64 0.52 0.90 1.00
LR9 0.53 0.83 0.50 0.52 0.63 0.53 0.88 0.91 1.00
LR10 0.84 0.57 0.90 0.84 0.71 0.89 0.56 0.55 0.53 1.00
LR11 0.88 0.57 0.91 0.83 0.69 0.88 0.55 0.58 0.53 0.89 1.00
LR12 0.87 0.58 0.86 0.82 0.65 0.90 0.54 0.52 0.52 0.86 0.86 1.00
LR13 0.92 0.56 0.89 0.87 0.69 0.93 0.54 0.54 0.53 0.89 0.88 0.95 1.00
LR14 0.58 0.82 0.55 0.57 0.67 0.57 0.85 0.88 0.89 0.57 0.59 0.55 0.57 1.00
LR15 0.84 0.57 0.83 0.77 0.64 0.86 0.51 0.52 0.53 0.80 0.84 0.88 0.84 0.55 1.00
LR16 0.95 0.53 0.91 0.87 0.68 0.90 0.52 0.55 0.51 0.86 0.88 0.87 0.92 0.55 0.84 1.00
LR17 0.76 0.68 0.73 0.73 0.79 0.74 0.66 0.68 0.66 0.71 0.74 0.68 0.70 0.68 0.67 0.74 1.00
LR18 0.89 0.56 0.86 0.82 0.68 0.87 0.57 0.58 0.58 0.85 0.85 0.86 0.91 0.58 0.83 0.89 0.75 1.00
LR19 0.60 0.79 0.57 0.59 0.72 0.58 0.77 0.82 0.81 0.56 0.60 0.54 0.55 0.80 0.56 0.57 0.75 0.59 1.00
LR20 0.54 0.80 0.54 0.52 0.65 0.53 0.78 0.79 0.80 0.53 0.54 0.52 0.51 0.77 0.53 0.55 0.68 0.55 0.82 1.00
priming site, insertions that render priming sites too dis-
tant to support amplification, and deletions or insertions
that change the size of the DNA fragments which act to
prevent its amplification
. RAPD markers were able to
distinguish groups within both the Andean and Meso-
american gene pools
. The polymorphism revealed by
RAPD has been problematic due to their dominance. As
heterozygotes are not normally detectable, the results are
not readily usable for computing Hardy–Weinberg equi-
librium or Nei’s standard genetic distance
. Therefore in
this study RAPD polymorphisms were analysed with a
phonetic distance measure (Jaccard’s coefficient) from
which a dendrogram was constructed (Figure 2), provid-
ing an indication of the diversity present within the land-
races of common bean.
Mesoamerican group
This group is represented by 35% of the total population,
with seven landraces (LR2, LR7, LR8, LR9, LR14, LR19
and LR20) in cluster M (Figure 2). In this group, one
dwarf (LR2), two tall non-woody (LR20 and LR8) and
four tall woody types (LR19, LR14, LR9 and LR7) were
described. The average weight of 100 seeds ranged from
16.5 to 36.6 g. As suggested by Evans
, the Meso-
american gene pool has both small (<25 g per 100 seed
weight) and medium (25–40 g per 100 seed weight)
seeds. The lowest seed weight (16.5 g per 100 seeds) was
observed in LR2. Zizumbo-Villarreal et al.
reported that
the average weedy seed weight ranged from 19 to
21 g/100 seeds and that of wild seeds ranged from 4 to
7 g/100 seeds. Moreover, this variety is less common in
cultivation and least preferred by farmers due to its small
black seeds. In the dendrogram cluster (Figure 2), this
formed an operational taxonomic unit very distant from
other Mesoamerican races, probably due to its unique
agro-morphological characteristics and the presence of
Figure 2. Genetic similarity dendrogram based on 102 RAPD mark-
ers in 20 common bean landtraces (LR1–LR20). M, Mesoamerican; H,
Hybrid; A, Andean.
some rare alleles. Such RAPD cluster with only one
accession in common bean landraces is common
DNA analysis with RAPD markers confirmed the exi-
stence of these three races among the climbing beans of
Mesoamerican origin in Guatemala and neighbouring
As evident from the dendrogram (Figure 2), the Meso-
american landraces in the Nilgiris are highly diverse with
a similarity coefficient lower compared to their Andean
counterpart. It has been calculated that more than 60% of
the world production derives from domesticates of Meso-
american origin
. Nevertheless, in the Nilgiris it repre-
sents only 35% of the total population and is used as both
snap and dry beans. One reason might be the preference
of farmers for the large-seeded Andean beans, at least for
dry beans, over the small-seeded Mesoamerican beans.
As a result, the distribution and use of Mesoamerican
beans are less in the Nilgiris compared to the Andean
races. Moreover, in recent years breeding activities have
focused on only a few highly priced, large-seeded market
classes that could have contributed to a reduction in ge-
netic diversity within the small-seeded, less desirable cul-
tivars. Regarding the landraces of common bean in the
Nilgiris, it is not true that farmers always select varieties
with big seeds; instead, they select plants for their special
requirements. For example, LR20 is small-seeded and
widely grown for its unique uses in certain recipes and
good market value. In spite of these hurdles, the Meso-
american germplasm in the Nilgiris is genetically more
diverse than the Andean race, which is evident from the
distribution of its landraces in the RAPD dendrogram
(Figure 2).
Andean group
This group consists of landraces in cluster B. This cluster
is constituted by 11 landraces (55% of the total), out of
which four are dwarf and seven are tall (Figure 2 and
Table 1). In this cluster, two dwarf varieties (LR5 and
LR17) formed a sub-cluster with a similarity value of
0.79 (Figure 2) and are considered to be hybrids between
the Mesoamerican and Andean gene pools. The Andean
race is characterized by large seeds, >40 g/100 seed
and T type phaseolin
. The average 100 seed
weight in Andean race ranged from 36.7 to 69.4 g (Table
1). The T type phaseolin was significantly correlated with
higher seed weight, increased overall seed protein and an
increase in the percentage of phaseolin compared to S
type phaseolin observed in Italian landraces
. A correla-
tion between plant height and seed weight in the Nilgiris
Andean gene pool was evident. The four dwarf plants had
seed weight <60.0 g, while all the tall landraces had
>60.0 g (Table 1).
In the Nilgiris, the majority of common bean under
cultivation was from the Andean gene pool. The same
Figure 3. Principal coordinate analysis of 20 landraces of common bean (LR1–LR20) based on Jaccard’s similarity coefficients.
phenomenon was noticed in other common bean-growing
regions such as China
, Italy
and Argentina
. The high
preference for Andean landraces may be due to some de-
sirable traits such as taste, growth habit, seed size and
colour. In the Nilgiris, LR4 is the major snap bean and
LR11 is the most preferred and highly priced dry bean.
This tall bean with ash coloured seed is widely cultivated
in almost all the villages. Tribal farmers prepare a special
dish out of these beans during special functions and festi-
vals. However, RAPD analysis revealed that this landrace
is closely associated with LR3 (Figure 2), a small-seeded
dwarf plant commonly used as dry beans.
The genetic diversity of the Andean race is a matter of
controversy. Many researchers are of the opinion that in
spite of vast diversity in plant and grain morphology,
generally Andean landraces of common bean proved to
have a very narrow genetic base. Beebe et al.
revealed a
narrow genetic base for the Andean race based on AFLP
analysis and the need for widening the genetic basis of
cultivated Andean landraces was suggested
. Our
findings in the Nilgiri beans throw light upon the fact that
the Andean races are genetically less diverse than the
Mesoamerican gene landraces (Figures 1–3). However,
the hybrid gene pool (LR5 and LR17) contributes signifi-
cantly to the genetic diversity of the Andean beans. Con-
trary to these findings, in a study in Argentina
, very
high diversity in four complex primitive races of Andean
beans was observed. In China, one of the secondary cen-
tres of common bean diversity, Xiaoyan et al.
that the level of diversity for Chinese landraces of
Andean origin was higher than that of Chinese landraces
of Mesoamerican origin due to the presence of more
infrequent alleles.
In this context, broadening the genetic base of the
Andean landraces must be considered. Previous studies
revealed that the Andean cultivars are more difficult to
. The introgression of additional genetic diver-
sity into the Andean domesticated gene pool may acquire
added importance in the light of genetic bottlenecks
induced by domestication in common bean
. One solu-
tion to this problem is the use of natural inter-gene pool
hybrids (LR5 and LR17) for breeding purposes.
Inter-gene pool hybrids
Landraces that possess phaseolin typical of one gene pool
and many morphological and allozyme traits of the other
gene pool are classified as inter-gene pool recombi-
. Two accessions, LR5 and LR17, formed a sepa-
rate group in PCoA (Figure 3). Both have 100 seed
weight 32.8 g and 30.8 g respectively, a characteristic
feature of the Mesoamerican race. The lack of correlation
between phaseolin type and RAPD data in these two
landraces might be due to a genetic recombination
between the Andean and the Mesoamerican gene pools. It
represents inter-gene pool introgression that occurred
naturally and selected by farmers in the Nilgiris. The
occurrence of recombinants in the Mesoamerican gene
pool was revealed
and an introgression of genes from
the Andean race was observed in Mexican landraces
when analysed with AFLP markers
. Rodino et al.
observed inter-gene pool recombinants in a core collec-
tion of common bean landraces from the Iberian penin-
sula, and evaluated them using morphological, agronomic
and biochemical markers. Xiaoyan et al.
Mesoamerican introgression in Chinese common bean
landraces when assessed with SSR markers.
Common bean is generally considered an autogamous
species, but out-crossing rates as high as 60–70% have
been observed
. Francisco et al.
reported exceptionally
high rates of out-crossing in some common bean cultivars
in California. In addition, it seems that even the lowest
rates of out-crossing reported are sufficient to generate
broad variability over hundreds or thousands of years
The inter-gene pool hybrids in the Nilgiris could have
been the result of a high frequency of pollinating insects
such as honeybees, short distances between plants and co-
cultivation of landraces from different gene pools
. Cul-
tivation of a mixture of Andean and Middle American
beans in close proximity in home gardens combined with
occasional out-crossing may have further facilitated
introgression between the two gene pools. On the other
hand, the genetic variation observed in these landraces
might have resulted during the long cultivation history of
the species (500 years), as an adaptation to the local agro-
climatic conditions. Once these adaptive variations are
fixed in the genotypes, subsequently they could have
been passed onto the next generation. In the end, these
could have resulted in locally adapted genotypes.
We cannot neglect the significance of this hybrid gene
pool in common bean improvement in the Nilgiris. The
genetically narrow Andean races can improve by crossing
with Mesoamerican germplasm. Nevertheless, such crosses
often produce poor progeny due to hybrid weakness
In this context, one alternative is to use landraces that
display the introgression of Mesoamerican genes, such as
those forming a sub-cluster in the Andean gene pool
(Figures 2 and 3). These inter-gene pool recombinants
may be of interest to breeders and geneticists because
they could constitute bridging germplasm that may aid in
the transfer of useful genes between the two gene pools.
Thus, these accessions may merit further studies. These
two landraces are dwarf, with small seeds most preferred
by farmers for their white seeds and snap beans respec-
tively. Therefore, the Nilgiris’ common bean germplasm
is more complex and contains additional diversity that
remains to be explored for genetic and breeding purposes.
RAPD and seed weight
Our study shows a correlation between RAPD clustering
and 100 seed weight (Table 1 and Figure 2). The landraces
varied in terms of seed size from a high of 69.4 g per 100
seed to a low of 16.5 g per 100 seed. A correlation bet-
ween RAPD banding pattern and seed size was observed
in Italian common bean landraces
. However, no correla-
tion was observed between RAPD branching pattern and
morphological data for landraces of common bean col-
lected from Central Himalaya
. In our study, with regard
to seed weight, no overlapping was observed between the
gene pools. Similarly, the small-seeded intergene pool
hybrids (LR5 and LR17) with seed weight 32.8 g per 100
seed and 30.8 g per 100 seed formed a sub-cluster in the
large-seeded Andean genepool. Duarte et al.
found a
close association between phenology and genetic analysis,
and suggested the loci that control molecular and morpho-
logical characteristics are closely associated.
These results indicate that the level of genetic variation
has not eroded since the introduction of the common bean
from the American centres of domestication into the
Nilgiris. The level of polymorphism observed in the pre-
sent study was moderately high, indicating a wide and
diverse genetic base for the common bean landraces in
the Nilgiris. The 63.5% RAPD polymorphic bands and
67% average genetic differentiation coefficient suggest
that the P. vulgaris landraces maintain a higher intra-
specific genetic diversity in the Nilgiris. There exist clear-
cut signs of introgression between the two gene pools as
indicated by the hybrids, which merit further investiga-
tion. The occurrence of both the gene pools in the Nilgiris
is highly significant for further breeding strategies like
interracial hybridization and production of ideal geno-
types of common bean. Such inter-gene pool and inter-
racial crosses will also facilitate broadening the genetic
base of cultivars and maximizing gains from selection for
plant type, adaptation, yield and resistance to high and
low temperature. The predominance of large-seeded
Andean germplasm in the Nilgiris is due to the preference
given by farmers and consumers over the small and
medium seeded Mesoamerican varieties. The present-day
common bean germplasm in the Nilgiris might be the last
remains of a vast introduction during colonial times.
Moreover, the common bean landraces in the Nilgiris
face serious threat of extinction with the introduction of
short-duration commercial cultivars. A study of molecu-
lar profiles to obtain DNA fingerprints in order to estab-
lish the molecular identity of common bean in the
Nilgiris for documenting the germplasm seems a worth-
while endeavour. Such DNA fingerprinting pattern would
also help monitor genetic stability in the common bean.
Our understanding of the genetic diversity of the P. vul-
garis population can contribute valuable guidelines for
conservation strategies and should therefore be an essen-
tial part of proper conservation management.
1. Singh, S. P., Improvement of small-seeded race Mesoamerican
cultivars. In Common Bean Improvement in the Twenty-First Cen-
tury (ed. Singh, S. P.), Kluwer, Dordrecht, 1999, pp. 225–274.
2. Hastings, K. B., The relationship between the Indian Botanic Gar-
den, Howrah and the Royal Botanic Gardens, Kew. Econ. Bot.
Bull. Bot. Surv. India, 1988, 28, 1–12.
3. Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G.
A. B. and Kent, J., Biodiversity hotspots for conservation priori-
ties. Nature, 2000, 403, 853–858.
4. Virk, P. S., Newbury, H. J., Jackson, M. T. and Ford-Lloyd, B. V.,
Are mapped or anonymous markers more useful for assessing
genetic diversity? Theor. Appl. Genet., 2000, 100, 607–613.
5. Song, Z. P., Xu, X., Wang, B., Chen, J. K. and Lu, B. R., Genetic
diversity in the northernmost Oryza rufipogon populations estimated
by SSR markers. Theor. Appl. Genet., 2003, 107, 1492–1499.
6. Botstein, D., White, R. L., Skolnick, M. and Davis, R. W., Construc-
tion of a genetic linkage map in man using restriction fragment length
polymorphism. Am. J. Hum. Genet., 1980, 32, 314–331.
7. Welsh, J. and McClelland, M., Fingerprinting genomes using PCR
with arbitrary primers. Nucleic Acids Res., 1990, 18, 7213–7218.
8. Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and
Tingey, S. V., DNA polymorphism amplified by arbitrary primers
as useful genetic markers. Nucleic Acids Res., 1990, 18, 6531–
9. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T. and
Hornes, M., AFLP: a new technique for DNA fingerprinting.
Nucleic Acids Res., 1995, 23, 4407–4414.
10. Tautz, D., Hypervariability of simple sequences as a general
source for polymorphic DNA markers. Nucleic Acids Res., 1989,
17, 6463–6471.
11. Williams, J. G. K., Hanafey, M. K., Rafalski, J. A. and Tingey,
S. V., Genetic analysis using random amplified polymorphic DNA
markers. Methods Enzymol., 1993, 218, 704–740.
12. Singh, S. P., Nodari, R. and Gepts, P., Genetic diversity in culti-
vated common bean: I. Allozymes. Crop Sci., 1991, 31, 19–23.
13. Singh, S. P., Gutierrez, J. A., Molina, A., Urrea, C. and Gepts, P.,
Genetic diversity in cultivated common bean: II. Marker-based
analysis of morphological and agronomic traits. Crop Sci., 1991,
31, 23–29.
14. Haley, S. D., Miklas, P. N., Afanador, L. and Kelly, J. D., Random
amplified polymorphic DNA (RAPD) marker variability between
and within gene pools of common bean. J. Am. Soc. Hortic. Sci.,
1994, 119, 122–125.
15. Beebe, S., Skroch, P. W., Tohme, J., Duque, M. C., Pedraza, F.
and Nienhuis, J., Structure of genetic diversity among common
bean landraces of Middle American origin based on correspon-
dence analysis of RAPD. Crop Sci., 2000, 40, 264–273.
16. Metais, I. C., Aubry, B., Hamon, R. J. and Peltier, V., Description
and analysis of genetic diversity between commercial bean lines
(Phaseolus vulgaris L.). Theor. Appl. Genet., 2000, 101, 1207–
17. Escribano, M. R., Santalla, M., Casquero, P. A. and de Ron, A.
M., Patterns of genetic diversity in landraces of common bean
(Phaseolus vulgaris L.) from Galicia. Plant Breed., 2006, 117,
18. Manoj, T., Singh, N. K., Meenal, R. and Narendra, K., RAPD
markers in the analysis of genetic diversity among common bean
germplasm from Central Himalaya. Genet. Res. Crop Evol., 2005,
52, 315–324.
19. Lioi, L., Piergiovanni, A. R., Pignone, D., Puglisi, S., Santantonio,
M. and Sonnante, G., Genetic diversity of some surviving on-farm
Italian common bean (Phaseolus vulgaris L.) landraces. Plant
Breed., 2005, 124, 576–581.
20. Xiaoyan, Z., Matthew, W. B. and Shumin, W., Genetic diversity
of Chinese common bean (Phaseolus vulgaris L.) landraces
assessed with simple sequence repeat markers. Theor. Appl.
Genet., 2008, 117, 629–640.
21. IBPGR, Descriptor list for Phaseolus vulgaris L. International
Board for Plant Genetic Resources, Rome, 1982.
22. Rodino, A. P., Santalla, M., Gonzalez, A. V., Ron, A. M. De and
Singh, S. P., Novel genetic variation in common bean from the
Iberian Peninsula. Crop Sci., 2006, 46, 2540–2546.
23. Rosales-Serna, R., Hernandez-Delgado, S., Gonzalez-Paz, M.,
Acosta-Gallegos, J. A. and Mayek-Perez, N., Genetic relationships
and diversity revealed by AFLP markers in Mexican common
bean bred cultivars. Crop Sci., 2005, 45, 1951–1957.
24. Lynch, M. and Milligan, B. G., Analysis of population genetic
structure with RAPD markers. Mol. Ecol., 1994, 3, 91–99.
25. Evans, A. M., Plant architecture and physiological efficiency in
the field bean. In Potentials of Field Bean and other Food Leg-
umes in Latin America (ed. Wall, D.), CIAT, Cali, Colombia,
1973, pp. 279–284.
26. Evans, A. M., Structure, variation, evolution, and classification in
Phaseolus. In Advances in Legume Science (eds Summerfield, R.
J. and Bunting, A. H.), Royal Botanic Gardens, Kew, UK, 1980,
pp. 337–347.
27. Zizumbo-Villarreal, D., Colunga-Garcia-Marin, P., Payro de la
Cruz, E., Delgado-Valerio, P. and Gepts, P., Population structure
and evolutionary dynamics of wild–weedy–domesticated com-
plexes of common bean in a Mesoamerican region. Crop Sci.,
2005, 45, 1073–1083.
28. Gepts, P., Osborn, T. C., Rashka, K. and Bliss, F. A., Phaseolin
protein variability in wild forms and landraces of the common
bean (Phaseolus vulgaris): evidence for multiple centers of
domestication. Econ. Bot., 1986, 40, 451–468.
29. Ilaria, M., Alessandra, B., Maurizio, M., Pietro, C. and Giovenni,
D., Characterization of some Italian common bean (Phaseolus
vulgaris L.) landraces by RAPD, semi-random and ISSR mole-
cular markers. Genet. Res. Crop Evol., 2007, 54, 175–188.
30. Ron, A. M., De, Menéndez, M. C. and Santalla, M., Variation in
primitive landraces of common bean (Phaseolus vulgaris L.) from
Argentina. Genet. Res. Crop Evol., 2004, 51, 883–894.
31. Beebe, S., Rengifo, J., Gaitan, E., Duque, M. C. and Tohme, J.,
Diversity and origin of Andean landraces of common bean. Crop
Sci., 2001, 41, 854–862.
32. Sonnante, G., Stocklom, T., Nodari, R. O., Becerra Velasquez, V.
L. and Gepts, P., Evolution of genetic diversity during the domes-
tication of common bean (Phaseolus vulgaris L.). Theor. Appl.
Genet., 1994, 89, 629–635.
33. Beebe, S., Toro, O., Gonzalez, A. V., Chacon, M. I. and Debouck,
D. G., Wild–weed–crop complexes of common bean (Phaseolus
vulgaris L., Fabaceae) in the Andes of Peru and Colombia, and
their implications for conservation and breeding. Genet. Res. Crop
Evol., 1997, 44, 73–91.
34. White, J., Kornegay, J., Castillo, J., Molano, C. H., Cajiao, C. and
Tejada, G., Effect of growth habit on yield of large-seeded bush
cultivars of common bean. Field Crops Res., 1992, 29, 151–161.
35. Rodino, A. P., Santalla, M., Ron, A. M. De and Singh, S. P., A
core collection of common bean from the Iberian peninsula.
Euphytica, 2003, 131, 165–175.
36. Wells, W. C., Isom, W. H. and Waines, J. G., Outcrossing rates of
six common bean lines. Crop Sci., 1988, 28, 177–178.
37. Ibarra-Perez, F. J., Ehdaie, B. and Wainess, G. J., Estimation of
out-crossing rate in common bean.
Crop Sci., 1997, 37, 60–65.
38. Gepts, P. and Bliss, F. A., F1 hybrid weakness in the common
bean: differential geographic origin suggests two gene pools in
cultivated bean germplasm. J. Hered., 1985, 76, 447–450.
39. Singh, S. P., Selection for seed yield in Middle American versus
Andean × Middle American interracial common bean populations.
Plant Breed., 1995, 114, 269–271.
40. Duarte, J. M., Santos, J. B. and Melo, L. C., Genetic divergence
among common bean cultivars from different races based on
RAPD markers. Genet. Mol. Biol., 1999, 22, 419–426.
ACKNOWLEDGEMENTS. We are grateful to Paul Gepts, Roberto
Bollini, Steve Beebe and Cesar Ocampo for their valuable suggestions,
the traditional ‘Badaga’ farmers of Nilgiri District who are conserving
and cultivating this germplasm for many centuries, and Dr M. Radha-
krishna Pillai, Director, RGCB, Thiruvananthapuram, for providing
necessary facilities to carry out RAPD analysis. This study was made
possible through a grant from the South Eastern Regional Office
(SERO), of the University Grants Commission, Hyderabad, in the form
of Minor Research Project to F.C.J. We thank the reviewers for their
in-depth review and valuable comments to improve this manuscript.
Received 10 December 2008; revised accepted 1 June 2009
... A correlation between plant height and total seed mass was evident in the current study, where taller landraces had heavier seeds per plant (>12 g) whereas shorter ones had lighter seeds (<12 g) (Tables 2 and 3). The current findings were similar to those of P. vulgaris landraces in Nilgiris, where four dwarf plants had seed mass <60.0 g, whereas tall landraces had >60.0 g (Jose et al. 2009). This suggests that the taller landraces D-50M50LB-Cl, D-50P50C-Cl, E-100YG-Cl, E-25YG-Cu, E-50M50LB-Cu, E-50B50C-Cl and E-50DB50C-Cl from KwaZulu-Natal are potential candidates for future large-scale farming and breeding towards vigorous growth and high seed yield. ...
... Isolate clustering was possibly due to its earliest flowering and pod formation as well as its production of the shortest and narrowest seeds (Table 3), whereas its association with others was based on their common origin (Table 1). Apparently, landraces with black seeds form an operational taxonomic unit relatively distant from other landraces, probably due to their unique agromorphological characteristics (Jose et al. 2009). ...
... The clustering of landraces with varying yellowishgreen seeds (E-100YG-Cl, E-50YG-Cl and E-25YG-Cu), and with 50% maroon, 50% light-brown seeds (E-50M50LB-Cu) from the Eshowe area in Group I of a biplot and Cluster II of a dendrogram (including D-50P50C-Cl, E-50B50C-Cl and E-50DB50C-Cl) could have resulted from their similarity in seed coat colour and the common area of origin. Similar findings were recorded among P. vulgaris accessions in Zimbabwe (Musango et al. 2016), Nilgiris (Jose et al. 2009) and Turkey (Yeken et al. 2018). These landraces were probably also associated because they had the tallest plants with thicker stems, highest chlorophyll content, numerous branches, broader leaves, longer pods, numerous pods and seeds and also heavier seeds compared with other landraces (Table 2 and 3). ...
Full-text available
Ndlangamandla VV, Ntuli NR. 2019. Variation on growth and yield traits among selected Phaseolus vulgaris landraces in KwaZulu-Natal, South Africa. Biodiversitas 20: 1597-1605. Phaseolus vulgaris L. (common bean) of American origin is grown worldwide for edible leaves, immature pods and dry seeds. This is the first comprehensive study conducted on variation among P. vulgaris landraces in South Africa. This study aimed to characterize variability in morpho-agronomic traits of P. vulgaris landraces. Twenty landraces were planted in a randomized complete block design with three replications. Variations in germination percentage as well as in stem, leaf, pod and seed traits were determined. Significant variations were recorded in all vegetative and reproductive traits except germination percentage and seed thickness. Vegetative traits correlated positively with each other, whereas reproductive traits correlated positively with both traits. Positive association of almost all traits with first and second components in a principal component analysis and biplot indicated them as potential discriminatory traits for landraces. The biplot and dendrogram associated landraces mainly according to their seed colour as well as growth and yield traits. This study revealed the potential vegetative and reproductive traits that can be used to select vigorously growing and high-yielding P. vulgaris landraces for future large-scale farming and breeding in South Africa. These traits could potentially result in desired plants with big stems, many branches, and numerous and broad leaves with high chlorophyll content, which will yield many, long and wide pods as well as many and heavy seeds. The taller landraces (D-50M50LB from KwaZulu-Natal show good potential for future large-scale farming and breeding for vigorous growth as well as high pod and seed yield.
... servation strategies and should therefore be an essential part of proper conservation management [8]. ...
... .8. While the highest number of allele was observed as 29 in the BM160 locus, BM175 locus by 25 alleles, BM156 locus by19 ...
Full-text available
Common bean (Phaseolus vulgaris L.), besides being an agricultural product that can be consumed as fresh vegetable, is a significant legume widely being planted in both Turkey and world. Because of having different usage areas, it is being considered as a valuable plant for human nutrition, trade and in many respects. In this study, we aimed at genetically characterization of the local and registered common bean genotypes and population structure of genotype groups belong to these common bean genotypes in Turkey. For this purpose, total 102 common bean genotypes including 93 local genotypes from 8 provinces, 7 cultivars and 2 reference cultivars were analyzed by 13 fluorescent SSR markers. As the result of the study, it was determined that the total SSR allele number was 192 and the average allele number was 14.8. While it was found that there were no synonymous genotypes, the highest heterozygosity rate was determined in three loci. Factorial correspondence analysis partially demonstrated substructure among common bean genotype groups. Structure analysis showed the same results as the Nm values and the Fst values. In the study, it was observed that SSR markers could be easily used in the molecular studies of common bean germplasm. The obtained results will be able to be used at the conservation, utilization of local common bean genetic resources and at the marker assisted selection studyings.
... The banding pattern of the RAPD primers goes well with the results obtained by Karp et al., 1997;Dursun et al., 2010;Jose et al., 2009;Biswas et al., 2010;Szilagyi et al., 2011 while evaluating the genetic diversity in common bean. In maize and wheat nearly similar banding pattern has been observed by ( Liu et al., 1999;Sivolap et al., 1997) and ( Bernado et al., 1997) respectively, indicating that RAPD markers have been effectively used for elucidating the genetic relationships among various cultivars. ...
... Similarity coefficient matrix was used to generate a dendrogram of common bean genotypes based on UPGMA analysis ( Fig. 2). Jose et al., 2009, found that Jaccard's pair-wise similarity coefficient value of 0.5 to 0.95 indicated an intra-specific genetic variation prevalent in landraces of common bean. 14 common bean genotypes were divided into two distinct clusters i.e. ...
... Among common bean growing countries in Africa, Ethiopia is considered to grow many varieties of the crop (Tura et al. 2018). The immense genetic diversity of landraces of crops is the most directly useful and economically valuable part of biodiversity (Jose et al. 2014). Unlike high yielding varieties, the landraces maintained by farmers are endowed with tremendous genetic variability, as they are not subjected to subtle selection over a long period. ...
Full-text available
Common bean (Phaseolus vulgaris L.) is an important source of food and income. However, its on-farm diversity and conservation by smallholder farmers is not known in the east Hararghe Zone of eastern Ethiopia. Thus, field survey was conducted from November 2018 to February 2019 to assess the on-farm diversity, cropping system and the role of gender in production and management of common bean varieties. Common bean producing districts were selected purposively whereas sub-districts (kebeles) were selected randomly. Three kebeles from each of the two major agro-ecological zones, two key informants and twelve general informants from each kebele were selected to constitute a total of 84 informants. The selection of general informants was stratified based on gender and wealth status. Structured interview guide was used to interview general informants whereas semi-structured interview guide was used to interview key informants. Descriptive and inferential statistical analyses were conducted in R (version 3.5.2). Seven farmers’ varieties of common bean were identified and their diversity was higher in tepid, moist mid highlands (M3) whereas cropped area (ha) was significantly (p < 0.05) higher in tepid sub-humid highlands (SH3) agro-ecology. Most activities of common bean were undertaken by male adults. Insect pests were the prominent constraints of common bean production. Farmers’ varieties were used as food and feed, and soil fertility management. Therefore, their on-farm and ex situ conservation, maintenance of endangered varieties, and shortage of cropping land due to chat plantation need special concern to promote their cultivation.
... This result concurs with findings by Shivachi et al. (2012) and Wang et al. (2007) who reported mean amplifications of 3.5 and 3.6 alleles per primer. In similar studies, on common beans involving microsatellites, Arunga et al. (2015), Jose et al. (2009) and Maras et al. (2008) reported mean amplifications of 2.17, 7.8 and 7.1 alleles per primer, respectively. Polymorphism information content is a closely related diversity measure (Botstein et al., 1980). ...
Full-text available
Lablab purpureus is a multipurpose legume mainly grown by subsistence farmers for pulse, forage and vegetable. Despite these diverse uses that can be combined successfully under various agronomic conditions, the bean has not been extensively exploited. Dolichos production in Kenya is constrained by low yielding varieties, pests, poor growing techniques and varieties with non-preferred taste and flavor. A study to characterize six newly bred Lablab genotypes (G2, B1, M5, LG1, W7 and G2), was initiated at the University of Eldoret using morphological and molecular markers. Morphological traits (qualitative and quantitative) were characterized using the descriptors of genus Lablab. Molecular characterization was done at the KEPHIS- Muguga laboratory, using ten SSR markers that are specific for Dolichos. Results from morphological characterization demonstrated a high variation for both qualitative and quantitative traits evaluated. Most of the quantitative traits were highly significant at 99.999% or (P≤ 0.001), except for number of racemes per plant and number of seeds per pod which were significant at 99.99% or (P≤ 0.01) and 99.95% or (P≤ 0.05), respectively. Microsatellite analysis produced six polymorphic primers mapping an average of 3.17 alleles per locus. The combination of morphological and DNA-based markers takes advantage of the best features of both marker types which can be beneficial in selection of best Lablab genotypes and in the process integrates the application of molecular markers to legume breeding.
... Using RAPDs and SRRs, mean amplifications of 5.69 and 3.6 alleles per primer, respectively were reported in lablab bean previously (Rai et al., 2010;Wang et al., 2007). Similar studies also found mean amplifications of over 7.0 alleles per primer in Phaseolus vulgaris (Jose et al., 2009;Maras et al., 2008) and 12.2 alleles per primer in soybean (Wang et al., 2006) which were much higher than that of ours. ...
Full-text available
Cite this article Haque, M.S., Islam, M.T., Saha, N.R., Hannan, M.A., Islam, M.M. 2020. Evaluation of morpho-molecular diversity and pod borer resistance in country bean. Journal of Bangladesh Agricultural University, 18(1): 25-33. ABSTRACT Country bean is a nutritious vegetable with commercial importance. Pod borer is a major pest of country beans in Bangladesh. Assessment of genetic variation among germplasm is a prerequisite for improvement of any crop. The present study was conducted to evaluate the yield potential, pod borer resistance and genetic diversity of 20 country bean varieties. At first, a field experiment was conducted with twenty cultivars to evaluate yield contributing characters and pod borer resistance. The data revealed that the variety Kaloputi showed the highest yield (2111.09 g) of pods plant-1. This variety (Kaloputi) had the highest number of pods plant-1 (271), lowest percentage (3.08%) of infestation, highest number (1086.0) of seeds plant-1 and highest dry seed yield over the other varieties. The variety BARI seem 5 showed the least performance in most of the parameters. Another experiment was conducted to find the genetic diversity among the 20 cultivars using SSR markers. The cluster analysis showed that the genotypes were divided into four groups. The cluster 1 was composed of seven BARI released varieties, cluster 2 was composed of two modern (IPSA seem 2 and BARI seem 8) and three local varieties (Khisamoti, Rifa and Goalgada), cluster 3 was constructed by six local and one modern variety (BARI seem 9) and Cluster 4 consisted of only cultivar Mostofa. The wide variations in phenotypic and genotypic level and pod borer resistance observed among the genotypes can be potentially used for future improvement of country bean.
... Bean cultivars Nebraska, Gomi and Goru are grouped together in the first subcluster, while bean cultivars Polysta, Ferrary, Mv309, Giza-9, Sonate, Argus, Xera and Amel grouped together in the second subcluster. The obtained results are in harmony agreement with those obtained by (El-Fiky and Wafaa, 2002;Monaj et al.,2005 andFranklin et al., 2009 ...
Full-text available
Abstract The present work was conducted to evaluate RAPD-PCR and AFLP (amplified fragment length polymorphism) marker systems for their ability to detect genetic diversity within and among some common bean (Phaseolus vulgaris) cultivars and tepary bean (Phaseolus acutifolius) lines and to compare the efficiency of these two marker types in the classification of accessions according to the gene pool of beans. The polymorphic fragments were obtained on the basis of 12 differentiating primers using the RAPD method and 4 differentiating primer combinations using the AFLP method. The 12 RAPD primers produced 119 polymorphic bands, while AFLP primer combinations produced 165 polymorphic bands. RAPD data analysis showed that the genetic similarity among thirteen Phaseolus accessions ranged from 44.6 to 93.8% while the AFLPs generated data show that the highest genetic similarity value was 86.7% and the lowest value was 27.7% with an average of 57.2%. The dendrogram generated with hierarchical UPGMA (unweighted pair group method with arithmetic mean) cluster analysis of the Jaccard’s similarity coefficient matrices revealed two major clusters, which were identified.
Full-text available
A prime role in matters of agrobiodiversity is held by landraces, which serve as a repository gene pool able to meet sustainable development goals and to face the ongoing challenges of climate change. However, many landraces are currently endangered due to environmental and socio-economic changes. Thus, effective characterization activities and conservation strategies should be undertaken to prevent their genetic and cultural erosion. In the current study, the morphological, genetic, and biochemical analyses were integrated with stress response-related studies to characterize the diversity of seven Italian autochthonous common bean landraces. The results showed that the morphological descriptors and the neutral molecular markers represent powerful tools to identify and distinguish diversity among landrace populations, but they cannot correlate with the stress tolerance pattern of genetically similar populations. The study also supported the use of proline as a biochemical marker to screen the most salt-sensitive bean landraces. Thus, to fully elucidate the future dynamics of agrobiodiversity and to establish the basis for safeguarding them while promoting their utilization, a multi-level approach should always be included in any local and national program for the characterization/conservation/use of genetic resources. This study should represent the basis for further joint research that effectively contributes to set/achieve Italian priorities towards sustainability in the framework of emerging environmental, societal, and economic challenges.
Full-text available
Cassia species is extensively used in herbal medicines, because it contains a set of chemically important compounds. In the present study, the genetic variability in five Cassia species from different locations of Tirunelveli District of Tamilnadu assessed through Random Amplified Polymorphic DNA (RAPD) markers. The species of Cassia were screened with eight primers of which five were found to be the most informative. These primers produced multiple band profiles with a number of amplified DNA fragments varying from 6 to 10. A total of thirty five polymorphic bands were observed. The genetic distance between the population ranged from 0.1214 to 1.7221 and the genetic identity ranged from 0.4857 to 0.8857. The overall observed and effective number of alleles is about 1.6571 and 1.4901 respectively. The percentage of polymorphic loci is 65.71. Nei overall genetic diversity is 0.2743.
Full-text available
The genetic relationships among 95 bean genotypes collected from different districts of Lake-Van Basin were determined by both phenotypic and molecular markers. In the phenotypic method, 71 morphological traits were examined and those with high correlations were excluded from the evaluation; then 61 measurements or observations of bean genotypes were employed. In the molecular method, 219 polymorphic ISSR markers obtained from 28 primers and 76 polymorphic RAPD markers obtained from 10 primers were employed. The genetic relationships among the bean genotypes were studied by examining dendrogram resulted from Euclidean distance obtained from phenotypic data and Euclidean distance and Jaccard’s coefficient obtained from molecular data. In the phenotypic characterization, the genotypes were originated 69.5 % to South America (Andean) and 30.5 % to Central America (Mesoamerican), and there were high genetic diversity among the genotypes. In the evaluation of combined phenotypic and molecular data, it was observed that the genotypes originated from Andean and Mesoamerican; dwarf and climbing genotypes; genotypes with white, other one-colored, and mottled seeds were clustered separately.
Full-text available
The objective of this study was to evaluate the degree of RAPD marker variability between and within commercially productive market classes representative of the Andean and Middle American gene pools of common bean (Phaseolus vulgaris L.). Six sets of near-isogenic lines were screened with oligonucleotide primers in the polymerase chain reaction-based RAPD assay. Simultaneous analyses with at least three sets of lines enabled us to score RAPD markers between the two major gene pools, races within the same gene pool, and different genotypes of the same race (within race). A “three-tiered” pattern of polymorphism was observed: between gene pools> between races> within races. The overall level of polymorphism between the Andean and Middle American gene pools was 83.4%. The overall level of polymorphism between races within the same gene pool was similar for Andean races (60.4%) and Middle American races (61.7%). The level of polymorphism between related commercial navy bean lines was 39.2% and between related commercial snap bean lines was 53.6 %. The inherent simplicity and efficiency of RAPD analyses, coupled with the number of polymorphisms detectable between related commercial genotypes, should facilitate the construction of RAPD-based genetic linkage maps in the context of populations representative of most bean breeding programs.
Full-text available
M13 DNA fingerprinting was used to determine evolutionary changes that occurred in Latin American germ plasm and USA cultivars of commonbean (Phaseolus vulgaris L.) during domestication. Linkage mapping experiments showed that M13-related sequences in the common-bean genome were either located at the distal ends of linkage groups or that they were unlinked to each other or to any previously mapped markers. Levels of polymorphism observed by hybridization with M13 (1 probe-enzyme combination) were comparable to those observed by hybridization with single-copy random PstI genomic probes (36 enzyme-probe combinations) but were higher than those observed for isozymes (10 loci). Results indicated that the wild ancestor had diverged into two taxa, one distributed in Middle America (Mexico, Central America, and Colombia) and the other in the Andes (Peru and Argentina); they also suggested separate domestications in the two areas leading to two cultivated gene pools. Domestication in both areas led to pronounced reductions in diversity in cultivated descendants in Middle America and the Andes. The marked lack of polymorphism within commercial classes of USA cultivars suggests that the dispersal of cultivars from the centers of origin and subsequent breeding of improved cultivars led to high levels of genetic uniformity. To our knowledge, this is the first crop for which this reduction in diversity has been documented with a single type of marker in lineages that span the evolution between wild ancestor and advanced cultivars.
Full-text available
into the domesticated populations or predominant gene flow from morphological and physiological characters related to domesticated to wild populations. The wild population in closest prox- imity to the crop within its complex was more similar to the domesti- the so-called domestication syndrome, including seed cated and weedy populations of its complex than to the rest of the dispersal (pod suture fibers, pod wall fibers), growth wild populations, suggesting displacement of the wild genetic diversity habit (determinacy, twining, number of nodes on the by gene flow from the domesticated population within its complex. main stem, number of pods, internode length), pod The high values of differentiation among wild, weedy, and domesti- length and seed weight, number of days to flowering, cated populations within each complex suggest high autogamy or photoperiodsensitivity,harvestindex,andseedpigmen- genetic drift. However, the values of gene flow among populations tation (Gepts and Debouck 1991; Koinange et al., 1996). within the complexes were close to one, theoretically sufficient to Geneticcompatibilitybetweenwildanddomesticated counteract genetic drift and/or autogamy. We therefore assume that populations leads to wild-weedy-domesticated hybrid human selection is the most important evolutionary mechanism for complexes in sites with sympatric distribution by intro- maintaining the high wild-domesticated differentiation by negative farmer selection of cultivated plants with morphological characters gression of genes fromwild populations to domesticated that suggest introgression. Farmers may influence the magnitude and ones or vice versa. Weedy populations are defined here characteristics of gene flow among populations within each complex as wild populations growing in crop fields that were not by the management of the distance between the crops and the wild planted by farmers. Because they may be the result populations, the diversity within the landraces sown, and the tolerance of this introgression, they usually show morphological and harvesting of weedy populations. The high geographic differentia- traits reminiscent of one or the other parent, such as tion of the wild populations, together with the local differences in larger seeds than the wild parent or seed color or color human selection practices and agronomic management, could have patterns similar to those observed in wild beans. These generated multiple evolutionary lineages after domestication. Domes- hybrid complexes constitute a valuable source of genes ticated populations within complexes were between two and four to the farmer or to the plant breeder (Debouck and times more diverse than the local commercial variety and four and
Full-text available
Landraces and bean (Phaseolus vulgaris L.) cultivars grown in Mexico are diverse, as are consumer preferences and agroecological production environments. Mexican common bean cultivars were analyzed using amplified fragment length polymorphism (AFLP) fingerprinting to examine the genetic relationships within and among races, based on the genotyping of 112 bred cultivars developed in Mexico. Molecular analysis of dry bean germplasm will be useful to corroborate previous cultivar characterizations and establish the genetic basis of improved germplasm, to facilitate the use of that diversity, and to implement the use of markers in selection. Germplasm included 111 cultivars belonging to Mesoamerica (25), Jalisco (39), Durango (28), and Nueva Granada (19) races, which are commonly cultivated throughout the bean-producing areas of Mexico. A Mexican P. coccineus species cultivar (Blanco Tlaxcala) was also included for comparison. Broad genetic diversity was found within bean races, and diversity values between races were similar. Most of the Nueva Granada germplasm was clearly different from that of all other races, whereas the P. coccineus cultivar was distinct from all P. vulgaris cultivars. A dendrogram based on the AFLP analysis did not clearly match with that made on the basis of racial classification. This mismatch was probably due to genetic recombination between Andean (Nueva Granada) and Mesoamerican (Jalisco, Durango, and Mesoamerica) gene pools. Utilization (if contrasting parents for specific crosses has also contributed to broadening the genetic basis of common bean.
Full-text available
Landraces of common bean (Phaseolus vulgaris L.) pertaining to the Andean gene pool are remarkably diverse in plant and grain morphology and agroecological adaptation. The objectives of this study were to determine the genetic structure of a large sample of Andean landraces, and to establish a correspondence between Andean landraces and wild bean populations that might have served as the source of domesticated bean. A total of 182 landraces representing the three recognized races of Andean bean and including many popping bean types were analyzed using amplified fragment length polymorphism (AFLP) technology with multiple correspondence analysis (MCA) and unweighted pair group method with arithmetic mean (UPGMA). Twenty-nine wild bean accessions representing the diversity of wild bean in South America and Middle America were also included. Two sets of primers were used to generate 189 polymorphic AFLP. The graph of the results of MCA indicated that most landrace accessions formed a single undifferentiated group, and analysis by UPGMA combined with bootstrapping confirmed this. A small number of outliers presented bands that suggested introgression from Mesoamerican beans. Among wild bean populations from South America, those from Bolivia graphed in closest proximity to the cultivated bean, suggesting that Bolivia might have been an important primary domestication site. The narrow genetic base of Andean beans emphasizes the need to broaden the genetic base of the Andean gene pool.
Full-text available
To assess genetic and environmental variation for outcrossing in common bean (Phaseolus vulgaris L.), a bulk of nine purple-hypocotyled (dominant), black-seeded, common bean lines (pollen parents) and six green-hypocotyled (recessive), white-seeded, common bean lines (seed parents) representing Mexican germplasm were used to estimate outcrossing rate. The experiment was conducted at Irvine and Riverside, CA, in mid-May and mid-July of 1989 and 1991. Outcrossing estimates were based on the proportion of purple- hypocotyled progeny from green-hypocotyled parents. Approximately 1400 single-plant families were progeny tested in which 120 278 seedlings were scored for the presence of anthocyanin in the hypocotyl. Of these, 113 246 were classified as selfed progeny and 7031 as hybrid progeny, giving rise to a weighted mean outcrossing rate of 6.9%. Entire progenies from each maternal line were grown and scored, and the minimum and maximum rates of outcrossing observed ranged between 0.0 and 78.0%. Mean outcrossing rate for the six white-seeded lines ranged from 4.41 to 10.16%. However, differences in outcrossing rate among these lines were not significant, nor were differences between dates of planting, locations, or years. The combined analysis of variance showed significant location x planting date x line interaction and year x location X line interaction, indicating that environmental factors had a strong effect on rate of outcrossing in the lines examined.
Among all Phaseolus beans of American origin, the small-seeded common bean (P. vulgaris L.) cultivars occupy by far the largest hectarage in the world (>6 million ha) and have the longest history of genetic improvement. A brief description of these beans, their major market classes, production regions, and production problems will be given in this chapter. This will be followed by the history of how beans have been improved, the genetic progress which has been achieved, current difficulties and challenges, breeding objectives and strategies, and future prospects.