American Journal of Plant Sciences, 2015, 6, 2426-2438
Published Online September 2015 in SciRes.
How to cite this paper: Avendaño, R., Díaz, E.G., Valdez-Melara, M., Solano, N.C., Villalob os, A.M., Cascante, F.A., Bena-
vides, B.W. and So lís -Ramos, L.Y. (2015) Genetic Diversity Analysis of Jatropha Species from Costa Rica Using AFLP Markers.
American Journal of Plant Sciences, 6, 2426-2438.
Genetic Diversity Analysis of Jatropha
Species from Costa Rica Using AFLP Markers
Roberto Avendaño1, Elmer García Díaz2, Marta Valdez-Melara2, Nefertiti Chaves Solano1,
Aníbal Mora Villalobos1, Francisco Aguilar Cascante1, Bruce Williamson Benavides2,
Laura Y. Solís-Ramos2*
1Center for Biotechnological Innovations (CENIBiot), CeNAT-CONARE, San José, Costa Rica
2School of Biology, University of Costa Rica, San José, Costa Rica
Email: *laura.solisramos@uc
Received 4 August 2015; accepted 25 September 2015; published 28 September 2015
Copyright © 2015 by authors and Scientific Research Publishing Inc.
This work is licensed under the Creative Commons Attribution International License (CC BY).
The genetic diversity from species of the genus Jatropha collected from Costa Rica was analyzed by
AFLP (amplified fragments length polymorphism). The study consisted of 114 accessions from 15
populations of 4 different species: J. curcas, J. c ostaricensis, J. gossypifolia and J. stevensii. These
were collected from different locations in Costa Rica. Three different primers were used, resulting
in 428 loci, and they were classified in three categories: unique and double bands (UBD), rare
bands (RB) and shared bands (SB). The UBD were excluded for a total of 339 polymorphic loci
used for the UPGMA dendrogram and principal component analysis (PCA). The species that ob-
tained the highest average of polymorphic loci was J. curcas, which obtained the highest percen-
tage of polymorphic loci (80.24%), followed by J. gossypifolia (79.35%), J. costaricensis (78.76%),
and finally J. stevensii (40.71%). The average for the polymorphic loci was of 69.76%. Thus, the
phylogeny of the Jatropha species in Costa Rica was elucidated, showing J. curcas more related to J.
stevensii and this one with J. costaricensis, and J. gossypifolia as the most distant member of the
genus. For the best of our knowledge this is the first report of a genetic analysis of J. costaricensis
and J. stevensii. The obtained molecular evidence showed high levels of polymorphisms in the
present study compared with reports from Africa, India, and China. The molecular diversity esti-
mated in our analysis, together with agronomical or morphological data, can be very useful for
plant breeding programs, given the importance of Jatropha species in oil production. Interestingly,
Central American Jatropha material can be used to increase the genetic base of J. curcas popula-
tions localized in Asia and Africa, where reduced genetic diversity has been reported.
Jatropha spp., AFLP, Molecular Markers, Polymorphism, Genetic Diversity
*Corresponding a uthor.
R. Avendaño et al.
1. Introduction
The genus Jatropha is morphologically diverse with 1 60 - 175 old and new w orld woody species comprising of
trees, shrubs, rhizomatous subshrubs, tuberous perennial herbs, geophytes, and facultative annuals, which are
distributed chiefly in the tropical and sub-tropical regions of America, Africa and India [1]. J. costaricensis is
described from Guanacaste, Costa Rica [2], J. stevensii is described from collections in Dept. Boaco in Nicara-
gua [3], and J. gossypifolia L. is a major weed in Australia [4]. Jatropha stevensii represents yet another exten-
sion of the Mexican xerophytic element into Central America, and the second record for Jatropha subg. curcas
[3]. Easy adaptation to different kinds of marginal lands, drought endurance, avoidance by animals, and its short
time interval to give first yield make th is plant species more attractive for cultivation [5]. The species can g row
even in areas with extreme climate and soil conditions which could not be inhabited by most of the agricultural-
ly important plant species that circumvent the food versus fuel resentment [6].
Assessment of genetic diversity using molecular markers is crucial for the efficient management and conser-
vation of plant genetic resources in gene banks [7]. There are very few studies on the genetic diversity of J.
curcas that involve a variety of populations and molecular marker technologies [7]-[13]. Two common features
of the majority of these stud ies are the inclusion of only a narrow selection of genetic materials, typically w ithin
one or a few countries [7]-[9] [12] [14], and the fact that they have generally revealed low genetic diversity
within countries [10] [15]-[18].
Most of the research was focused on J. curcas originating from India, and it showed low genetic diversity [8]
[9] [14] [15] [19]. Ranade et al. [15] characterized 22 accessions from six regions using RAPD and amplifica-
tion of minisatellite DNA (DAMD) profiles and separated the wild and non-wild accessions; they observed a
low level of variation among accessions within a g roup [15]. The analysis of the genetic diversity among 28 ac-
cessions using RAPD and amplified fragment length polymorphism (AFLP) revealed low genetic diversity in J.
curcas [19], and similar results have been reported by Basha and Sujatha [9] and Tatikond a et al. [8]. In another
research done in India, Sudheer et al. [14 ], using microsatellite marker s, also concluded a genetic d isequilibriu m
of J. cu rca s. The n arrow genetic base of J. c ur ca s in India has been attributed to the small number of introduced
plants an d the ir veget a t i ve propaga t ion [7].
For Chinese samples of J. curcas, 58 accessions were assessed in a study based on simple sequence repeat
(SSR) and AFLP analysis, it demonstrated low levels of variation [7]. Ther efore, the genetic diversity of J. cur-
cas in China may only represent part of the Indian population [7].
In this way, it is likely that there is a greater genetic diversity in J. curcas individuals from the center of origin;
however, with the exception of research using germplasm from Guatemala [20] and Mexico [10] [13] [16], rela-
tively less work has appeared from its center of origin, as well as Africa and other regions of the tropics where it
occurs extensively. Although genetic diversity of J. curcas in its native Central America is still unknown, it is
suggested that germplasm for genetic improvement programs should be introduced from its native range rather
than from other introduced populations [7]. Therefore, a collaborative global Jatropha genetic diversity evalua-
tion effort is immediately needed for a better use of this valuable spe c ies in breeding pr og r a ms.
The present study surveys the molecular diversity in four wild species of Jatropha from Cos ta Rica: J. costa-
ricensis, J. curcas, J. gossypifolia and J. stevensii, by using amplified fragment length polymorphism analysis
(AFLP). AFLP is a rich information marker system due to its ability to generate a large number of polymorphic/
informative loci simultaneously in a single lane with a single-primer combination, as compared to RAPDs,
RFLPs and microsatellites [8]. With AFLP, which does not require any prior DNA sequence information, the
main disadvantage of SSR markers is that they need to be isolated again from most species being examined for
the first time, and the development of the s e markers is both time consuming and expensive [8].
2. Materials and Methods
2.1. Plant Materials
Samples of leaves of Jatropha spp. were collected from Diriá and Santa Rosa National Parks, off road and
commercial availability, fo r a total of 114 samples (Table 1).
2.2. AFLP Analysis
The genomic DNA of Jatropha sp. samples were extracted using the NucleoSpin Plant II commercial system
R. Avendaño et al.
Table 1. Details of the Jatropha spp. accessions used for the AFLP analysis collected in Costa Rica.
Species N. of individuals N. of populations Site
J. costaricensis
7 1 Península Santa Elena, Area Conservación Guanacaste, La Cruz.
Cantera La Marbolita.
4 1 Península Santa Elena, Area Conservación Guanacaste, La Cruz.
22 1 Cerro La Flor, Playas del Coco, Carrillo, Guanacaste.
J. curcas
3 1 Tárcoles, Puntarenas.
16 1 Fila cenizosa, Parque Nacional Diriá, Santa Cruz, Guanacaste.
12 1 Parque Nacional Diriá, Santa Cruz, Guanacaste.
J. gossypifolia 42
4 Liberia, Guanacaste.
1 Nicoya, Guanacaste.
1 La Cruz, Guanacaste.
1 Carrillo, Guanacaste.
1 Palmares, Alajuela.
J. stevensii 8 1 Parque Nacional Santa Rosa, La Cruz, Guanacaste.
Total 114 15
(Macherey-Nagel). AFLP plant mapping kit, with ligation and pre-selective amplification core mix modules,
(Life Technologies, USA) was used for AFLP fingerprinting according to the manufacturer’s instructions. The
restriction-ligation reactions were performed using genomic DNA, with EcoRI and MseI enzymes, EcoRI and
MseI adaptors and T4 ligase at room temperature overnight. The restriction-ligation product was diluted 1:2.
The DNA prepared by restriction-ligation was pre-amplified using EcoRI-A and MseI-C primers. The pre-am-
plified product was diluted 1:20 with sterile deionized water. The diluted pre-amplification products were am-
plified using selective f luorescent dye-labeled EcoRI primers with the following combination: E-AGC/M-CTA,
E-ACT/M-CTA and E-AGG/M-CTA [8] [19]. Data collection of selective amplification products was carried
out on a 3130xl genetic analyzer (Applied Biosystems, USA). The polymorphic loci were classified in 3 catego-
ries: unique and double bands (UBD), rare bands (RB) (present in less than 10% accessions) and shared loci
2.3. Data Analysis
The genetic diversity analysis (principal coordinates, AMOVA, banding pattern) were in GenAlEx with binary
database of AFLP, both for species and for populations. The phylogenetic tree was made in the Infotstat soft-
ware using the Jaccard index. The genetic distance matrix resulting from GenAlEx analysis was used in the
SigmaPlot 12.0 software to generate 3D graphic. The GenAlEx program was used to obtain allele frequencies,
heterozygosity estimated, values of “p” and “q” to calculate the statistics ( PI C, EMR, MI, RP, DI) of the p rimers.
Equations were programmed in excel and were run with data.
AFLP scoring was conducted using GeneMapper v4.1 with default parameter settings (Applied Biosystems,
USA). Sample fingerprints were individually scored and statistically analyzed, assuming fragment size as a lo-
cus, they were considered as biallelic (present = 1, absent = 0) and made the binary matrix. Phylogenetic tree
according to Jaccard and band pattern analysis were constructed using the binary matrix. The genetic distance
was calculated as proposed by Huff et al. [21]:
Dn n
= −
Equation (1), Here,
= number of shared character states, n = total number of binary characters. When
calculated across multiple loci for a given pair of samples, this is equivalent to the total of state differences
among the two DNA profiles. The genetic distance matrix was subject of principal coordinates and AMOVA
analysis using GenAlEx v6.5.1. Analysis of molecular variance (AMOVA) procedure follows the methods of
Peakall and Smouse [22]:
R. Avendaño et al.
( )
Equation (2), Whe re ,
= among-population variable , and
= within-populat i on variable.
Genotyping data obtained from the AFLP primer combinations was used for assessing the discriminatory
power of AFLP primer combinations by evaluating three parameters [23]: 1) polymorphism information content
(PIC), 2) marker index (MI), and 3) resolving po wer (RP).
The PIC value for each AFLP primer combination was calculated as proposed by Roldan-Ruiz et al. [24]:
( )
ffΦ= −
(3 )
Equation (3), where PICi is the polymorphism information content of marker i, fi the frequency of the marker
fragments, which were present and 1 fi the frequency of marker fragments, which were absent. PIC was aver-
aged over the fragments for each primer combination. The marker index was calculated as given in Varshney et
al. [25]:
Equation (4), w here EMR: The effective multiplex ratio (E) is defin ed as the product of the total number of
loci/fragments per primer (n) and the fraction of polymorphic loci/fragments (β) (E = n * β).
Resolving power of each primer was calculated according to Prevost and Wilkinson [26]:
RP b
(5 )
Equation (5), where
represents fragment informativeness. The
can be represented into a 0 - 1 scale by
the following formula:
( )
12 0.5
Equation (6), whe re p is the proportion of the 48 accessions containing the fragment.
Diversity values were calculated for each locus as proposed by Russell et al. [27]:
1DI Pi= −
Equation (7),
is the phenotypic frequency for each AFLPs-primer combination.
3. Results
3.1. AFLP Profiling and Marker Polymorphism
A total of 3 combinations of AFLP primers were used in the study to generate AFLP profiles over 114 acces-
sions of Jatropha species collected in the province of Guanacaste, Costa Rica. In the analysis of the AFLP pro-
file, only the loci with high resolution were considered. A total of 428 loci were generated and distributed ho-
mogeneously within 3 primer combinations (Table 2). The polymorphic loci were classified in 3 categories:
unique and double bands (UBD), rare bands (RB), and shared loci (SB) (Table 3). The first consist of loci
present in one or two samples by specific primer combinations. The UBD loci were excluded and, for further
analysis, a total of 339 loci (TL) were used (Table 3). By this analysis, J. curcas obtained the highest percentage
of polymorphic loci (80.24%), followed by J. gossypifolia (79.35%), J. costaricensis (78.76%), and finally J.
stevensii (40.71%). The average for the polymorphic loci was of 69.76%.
3.2. Discriminatory Power of AFLP Primer Combination
3.2.1. Polymorphism Information Content (PIC)
The PIC value for polymorphic fragments oscillated between 0.245 and 0.269, with an average of 0.257 per
primer combination. With the purpose of distinguishing different primer combinations, the PIC value for all the
generated fragments by primer combination were averaged to obtain an average PIC value, corresponding to
each primer combination. The highest PIC value was observed for the E-ACT/M-CTA primer combination and
the lowest for the E-AGG/M-CTA primer (Table 2).
R. Avendaño et al.
Table 2. Marker attributes for AFLP combinations used.
Primer combinations PICa EMRb MIc RPd DIe
E-ACT/M-CTA 0.269 112 30.99 26.50 0.911
E-AGG/M-CTA 0.245 110 26.96 21.81 0.943
E-AGC/M-CTA 0.256 116 29.72 23.47 0.944
Average 0.257 113 29.22 23.93 0.933
aPolymorph i sm information content (PIC); bEffective multiplex ratio (EMR); cMarker index (MI). d Resolving power (RP); eDiversity Index (DI)
Table 3. Number of polymorphic bands in relation to primer combinations. TB = T otal bands. P B = Polymorphic Bands.
MB = Monomorphic Ban ds. UBD = Unique a nd Double Ban ds. RB = Rare Bands < 10% from samples. SB = Shared Ba nds >
70% from samples.
Primer combinations TB PB MB % Polymorphism UBD RB SB
EcoRI-ACT X MseI-CTA 146 146 1 99.34 33 76 4
EcoRI-AGG X MseI-CTA 138 138 0 100 28 75 2
EcoRI-AGC X MseI-CTA 144 144 0 100 28 76 0
3.2.2. Marker Index (MI)
The MI value had a range between 26.96 and 30.99 with an average of 29.22 per primer combination. The high-
est MI value (30.99) was observed for the E-ACT/M-CTA primer and the lowest MI value (26.96) for the
E-AGG/M-CTA primer (Table 2).
3.2.3. Resolving Power (RP)
The RP is a characteristic for each primer combination that indicates the discriminatory potential of the primer
combination. The RP range was 21.81 to 26.50 with an average of 23.93 per primer combination. The highest
value (26.50) was shown for the E-ACT/M-CTA primer and the lowest for the E-AGG/M-CTA primer (Table
3.2.4. Diversity Index (DI)
The diversity index value for 339 polymorphic loci ranged between 0.911 and 0.944 with an average of 0.933
per AFLPs-primer combinations. Highest value (0.944) was scored with the primer pair for E-AGG/M-CTA and
the lowest value (0.911) for the primer pair E-ACT/M-CTA (Table 2).
3.3. Genetic Relationships of Jatropha Populations
The results of the principal component analysis (PC) showed that samples grouped by species in four groups
(Figure 1). By doing the same analysis by species, the distribution was confirmed and the variation increased,
explained by 100% (Figure 2) . The cluster analysis shows that the species J. cur cas and J. stevensii are gen eti-
cally close, and at the same time, these were close with J. costaricensis. Consequently, J. gossypifolia is the far-
thest compared to the others (Figure 3).
Analyzing the total band patterns by species, J. curcas presented the highest band quantity (273), followed by
J. gossypifolia (271), then J. costaricensis (268), and finally J. stevensii (145). From the 281 bands of J. costa-
ricensis, 242 have a frequency equal or higher than 5%, resulting in the species with the highest quantity. Fur-
thermore, J. curc as with 238 bands, then J. gossypifolia with 214 bands, and J. stevensii with 145 bands. J. cos-
taricensis was the species with the highest quantity of private bands (24), then J. gossypifolia (13 bands), J.
curcas (5 bands), and J. ste vensii (none) (data not showed). In relation with the average of the expected hetero-
zygosity, J. curcas obtained the highest value (0.177), then J. costaricensis (0.161), J. gossypifolia (0.160), and
finally J. stevensii (0.124) (Figure 4). The AMOVA analysis of the different species of Jatropha showed that
genetic differences exist both between and within species (n = 114, PhiPT = 0.471, P < 0.01) (Figure 5). Sub-
sequently, an analysis for genetic difference was performed for the J. costaricensis and J. curcas species. For J.
costaricensis , I and II populations showed no genetic difference between them (n = 11, PhiPT = 0.01, valor P =
0.40), but toge ther t hey prese nted di ffere nces with popul at ion III (n = 33, Phi PT = 0.47, value P < 0.01) (Figure 6).
R. Avendaño et al.
Figure 1. Genetic relations of 4 species of Jatropha base d on the principal component analysis (PCA). Percentage of varia-
tion explained by the 2 axis: 53.82%.
Figure 2. Principal coordinates per species. J. curc as n = 31, J. costarricenses n = 33, J. gossypifolia n = 42, J. stevensii n =
8. Percentage of variation explained by the 3 axis = 100%.
R. Avendaño et al.
Figure 3. Phylogenetic tree for 4 species of Jatropha based in Jaccard coefficient similarity. cophenetic
correlation = 99. J. curcas n = 31, J. costarricens es n = 33, J. gossypifolia n = 42, J. stevensii n = 8.
Figure 4. Banding pattern between species of Jatropha.
Figure 5. Percentage of molecular variation between and within J. curcas, J. gossypifolia, J. costaricen-
sis and J. ste vensii. Pops: populations.
R. Avendaño et al.
Figure 6. Principal coordinates between the different populations of J. costaricensis. Percentage of variation explained by
the 2 axis = 63.69%. I = Península Santa Elena, Area Conservación Guanacaste, La Cruz, Guanacaste. Cantera La Marbolita.
II = Penísula Santa Elena, Àrea de Conservación Guancaste, La Cruz, Guanacaste. Nearness of river Potrero Grande. Sam-
ples marked with an asterisk. III = Cerro La Flor, Playas del Coco, Carrillo, Guanacaste.
Unlike J. costaricensis , the 3 populations of J curcas are genetically different from each other (n = 31, PhiPT
= 0.39, P < 0.01). Populations I and III had the greatest genetic difference in the study (n = 15 PhiPT = 0.54, P <
0.01). Although the populations II and III overlap in a region according to the principal coordinate analysis
(Figu re 7 ), th ese po pulatio n s were g eneticall y d if feren t (n = 28, PhiPT = 0.38, P value < 0.01). Similarly for the
populations I and II, although th e ir genetic difference is lower (n = 19, PhiPT = 0.24, P < 0.01).
4. Discussion
4.1. AFLP Profiling and Marker Polymorphism
It has been shown that the amplified fragment length polymorphism analysis (AFLP) is an efficient method for
the molecular characterization and phylogenetic relation studies among the Jatropha species [14] [17] [19]. In
this study, the level of polymorphism based on AFLP with 3 primer combinations was high and sufficient to dis-
tinguish the four species of Jatropha (J. costaricensis, J. curcas, J. gossypifolia and J. stevensii) collected in
Costa Rica. This result agrees with other studies where AFLP technique allowed to estimate the genetic rela-
tionships of germplasm (J. curcas) and to detect a high level of polymorphism [13]. Unique, rare, shared, and
double fragments detected by the 3 primer combination were identified. The primer combination named
E-ACT/M-CTA was found to be more effective to detect a higher number of unique fragments and a good
number of rare fragments. Therefore, these primer combinations are useful for the detection of informative
fragments in the Jatropha germplasm. The availability of rare fragments present in different accessions, together
with the genetic dissimilarity data, may be useful for the improvement of species through conventional methods
as molecular improvement trials, like marker assisted selection (MAS) and the occurrence of shared fragments
in accession. It is very useful to understand the relations and similarities between accessions [8].
4.2. Discriminatory Power of AFLP Primer Combination
A number of markers attributes like PIC, MI and RP have been used in different studies to evaluate the informa-
R. Avendaño et al.
Figure 7. Principal coordinates between the different populations of J. curcas. Percentage of variation explained by the two
axis = 58.78%. I = non toxic commercial variety. II = Fila cenizosa, Parque Nacional Diriá, Santa Cruz, Guanacaste. III =
Parque Nacional Diriá, Santa Cruz, Guanacaste.
tive or discriminatory po wer in the pr imer combination in gen etic d ivers ity stud ies [8 ]. In this s tudy, the 3 AFLP
primer combinations showed an average PIC of 0.257. The maximum PIC value for bi-allelic markers as AFLP
can be expected of 0.264. Based on the PIC value, the E-ACT/M-CTA primer combination is the recommended
for the analysis of Ja tropha germplasm in our study. The MI parameter confirmed in our study that the
E-ACT/M-CTA combination is recommended to use it in the analysis of germplasm, which showed a value of
30.99. In this study, an MI value was obtained in the range of 26.96 - 30 (29.22 average) and a PIC value in the
range of 0. 245 - 0.269 (0.257 average), which are comparable to other studies. The primer combination used in
our study showed RP values be t we e n 21.81 - 26.50 (23.93 average).
4.3. Genetic Relationships of Jatropha Pop ulations
Also, it is important to optimize the design of the genetic improvement program to select genotypes and develop
new populations [27]. In plant species, the genetic diversity tends to be higher near the geographical origin,
which has been demonstrated in studies of J. curcas showing high genetic diversity in samples collected in
Mexico (Veracruz, Puebla, Chiapas, Quintana Roo) [13] [16] [28]-[30]. This supports the hypothesis, based on
morphological data and the natural distribution, indicating the Mesoamerican region (Mexico and Central
America) as the possible center of origin of J. curcas [28]-[31]; although th e average of the genetic diver sity is
limited, compared to the reported by other taxa from other endemic species.
Apart from J. curcas, the genetic diversity from other species of the genus considered native from Central
America is still unknown. Therefore our research is pioneer in the study of the genetic diversity of 4 species of
the genus Jatropha in the natural distribution area (Central America), and mainly of J. costaricensis. For the
best of our knowledge this is the first report of a genetic analysis of J. costaricensis and J. stevensii. In the 114
accessions analyzed, high levels of polymorphisms were obtained compared with the reported from studies with
materials from Africa, India and, China [13] [14] [17] [30] [32]. This pronounced genetic diversity indicates
higher probabilities to improve the species by interspecific crossing, which has been successfully documented
R. Avendaño et al.
previously (J. curcas × J. integerrima) [11] [19] [33]. The interspecific hybridization reveals the possibility of
obtaini ng hybrids of J. curcas with other species of Jatropha [11].
Both PCA and UPGMA dendrogram divided the IV population in principal groups, coinciding by species.
The dendogram shows high genetic similarity (Jaccard’s similarity coefficient) between J. curcas and J. steven-
sii, and these two with J. costa r ic ensis, and farthest with J. gossyp ifolia. This suggests that J. curcas with J. ste-
vensii and J. costaricensis could have a common ancestor and more distant J. gossypifolia. This is consistent
with the reports that point J. curcas, J. integerrima, J. glandulifera, and J . gossypifolia as native from America,
and that they have been introduced to tropical countries in Africa and South East Asia (Indian, Indonesia, Ma-
laysia and China) [30] [31] [34] [35].
However, our results differ from those found by Popluechai et al. [32 ], which report J. gossypifolia and J. in-
tegérrima closer to J. curcas. Also the same AFLP phylogram obtained by Sudheer et al. [19] showed a major
cluster conformed by 5 species of Jatropha (J. curcas, J. glandulifera, J. gossypifolia, J. integerrima, and J.
tanjorensis) and a minor cluster with J. multifida and J. podagrica, distributed in India. Basha and Sujatha [11],
by combined data of RAPD and ISSR markers, grouped J. curcas with J. gossypifolia determining them as close
relatives and as natural hybrid J. tanjorensis.
In another study using RAPD markers, all accessions of J. curcas were grouped in one group; a second group
was formed of 6 species: J. ramanadensis, J. gossypiifolia, J. podagrica, J. tanjorensis J. villosa and J. in-
tegérrima, and finally a separate group of J. glandulifera [36]. J. curcas is considered the ancestral primitive
species due to its morphological distinctive characteristics, where other species evolved from J. curcas and an-
cestral forms [37].
In our study, the principal component analysis (PCA) with only the accessions from J. curcas showed the
formation of III principal groups, suggesting a broad genetic base from the germplasm. This germplasm base
shows genotypes that could have few and probably unique genetic changes. This agrees with Pecina-Quintero et
al. [13], where several accessions of J. curcas collected in three agro-climate regions of Chiapas, Mexico,
showed high diversity. This shows nonrandom mating between groups and/or regions of accessions of J. curcas,
which makes the selection of representative co llections difficult. According to Pecina-Quintero et al. [13], these
changes can be the result of the evolution of J. curcas to different environments or adaptation to different habi-
tats, contrary to the study by He et al. [16], where AFLP analysis r eported low genetic diversity from materials
from Madagascar, Tanzania, and Surinam. Also, from four combinations of fluorescent primers, the genetic
variation was characterized by 63 populations of J. curc as from 10 countries in Asia, Africa, and Mexico result-
ing in low genetic diversity between populations [17]. Nevertheless, the analyzed Mexican populations showed
high values of genetic variation [16] [17]. In general, it has been demonstrating low genetic variation between
accessions of J. cu rc as in Africa and Asia, and the reasons are no t clearly defined [32 ]. However, Subramanyam
et al. [24] reported high genetic diversity of J. curcas collected in 10 different eco-climate regions in India but
by using RAPD markers. The variation of the genetic diversity within species is commonly related with the
geographic range, reproduction mode, mating system, seed dispersal, and fertility [38].
Taking into account the local and global results [13] [16] [17] [32], we suggest that the high genetic variation
detected between and within the populations of Jatropha curcas could be explained because of America being
considered the range for the natural distribution of the species [31]. Th e introduction of this germplasm could be
used to broaden the genetic base of Jatropha in countries like Africa and Asia (mainly in China and India),
where the genetic diversity has been reported as low (35% - 50%), partly attributed to reduced genetic flow be-
tween populations, favored by the limited seed dispersal which occurs by gravity and anthropogenic dispersal
(clonal reproduction) [10] [17] [32] [39]. It is agreed by several authors to use the germplasm from the range of
natural distribution (Central America and Mexico) in genetic breeding programs for the species (mainly J. cur-
cas) to broaden the genetic base [10] [17] [18] [32] [39], instead of germplasm from the same origins or intro-
ductions [7]. Knowledge of the genetic diversity of wild species Jatropha from Costa Rica will be useful for
breeding programs and for the development of improved varieties. Understanding the genetic diversity, in-
ter-relatedness, and d ifferentiatio n of wild and introduced subpopulations of the species is a critical step towards
selection and breeding of superior genotypes [17].
Conduct studies to determine whether the differentiation between populations of J. costarricensis is due to
stochastic factors such as relief or wind direction, or if the distance between populations prevents pollen reach
the nearest population, or flowering patterns differ between populations, or if there is an anthropomorphic factor,
or the poll inators can’t reac h ne ighboring popula t ions.
R. Avendaño et al.
The number of samples obtained was due to factors such as difficult access to collection sites, the fact that the
species is deciduous and scarcity of individuals in some species. It was not possible to analyze microsatellites
because the genome of some of the species under study is unknown.
5. Conclusion
The AFLP primer combination AFLP E-ACT/M-CTA can be used in an efficient way for the differentiation of
the four species, as it resulted in the highest number of polymorphic markers, which were specific for the spe-
cies and population s of J. c u rc a s and J. costaricensis. The identification of private bands per species can be used
for screening samples of Jatropha spp. from unknown origin when comparing the unknown sample with the
panel of private bands. The genetic analysis that elucidates the phylogeny of the Jatropha ssp. species states that
J. curcas is more related to J. stevensii, those two with J. costar icensis, and J. gossypifolia as the farthest mem-
ber of the genus. The populations of J. curcas are different between them. The identification collection and the
maintenance of such genetically diverse wild germplasm from Costa Rica are of great importance in economic
improvement of this species and for the selection of promising lines. Also the populations with very little or no
human intervention may contribute more substantially towards the germplasm heterogeneity of Jatropha costa-
ricensis for traits such as adaptability and oil yield.
This work was supported by the Vicerrectoría de Investigación of the University of Costa Rica and the National
Center for Biotechnological Innovations—CENIBiot, through the p roject No. 111-B2-503 and CB-D1-2010 re-
spectively. To Mario Fernández, Kimberly Valverde, Alexis Briceño, Jorge Gómez Laurito+, Rafael Acuña,
Joaquín Ruiz and Marcela Peña for their cooperation with the co llecting of materials. Max Chavarría, Che mistry
School, Universidad de Costa Rica and Research Center for Natural Products (CIPRONA), for the comments on
the manuscript.
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