Genetic diversity in <Emphasis Type="Italic">in vitro</Emphasis>-conserved germplasm of <Emphasis Type="Italic">Curcuma</Emphasis> L. as revealed by RAPD markers

A set of 30 accessions of five Curcuma species-C. latifolia, C. malabarica, C. manga and C. raktakanta and 13 morphotypes (identified on the basis of morphological markers) of C. longa conserved in the In Vitro Genebank at National Bureau of Plant Genetic Resources, New Delhi, were subjected to RAPD analysis. Of the 200 RAPD primers screened, 21 polymorphic primers were selected for further study. Mean genetic similarities based on Jaccard’s similarity coefficient ranged from 0.18 to 0.86 in accessions of cultivated species, i.e., C. longa and from 0.25 to 0.86 in wild species. The dendrogram derived from the RAPD data corroborated the morphological classification of the morphotypes. The efficiency of individual RAPD primers was also compared; primers OPC-20, OPO-06, OPC-01 and OPL-03 were adjudged highly informative in discriminating the germplasm of Curcuma.     

Plant regeneration in <Emphasis Type="Italic">Curcuma</Emphasis> species and assessment of genetic stability of regenerated plants

An efficient plant regeneration protocol was developed from rhizomes of two Curcuma species C. longa and C. amada. Response was highly dependent on the season, with above 69 % of culture developing adventitious shoots during spring. Greatest regeneration and multiplication was observed in modified Murashige and Skoog (MS) medium supplemented with 13.31 μM benzyladenine and 2.68 μM α-naphthalene acetic acid (NAA) in C. longa or 2.46 μM indolebutyric acid in C. amada. Effect of sugars and agar at different concentrations were also studied and 2 % maltose and 0.7 % agar were found optimum for shoot multiplication and regeneration. Most plantlets developed roots simultaneously but others formed roots when subcultured in ½ MS medium supplemented with 2.68 μM NAA. Plants were successfully hardened in greenhouse with 80 % survival. The genetic purity of micropropagated plantlets was analyzed using RAPD and protein profiles.     

RAPD based genetic relationships between populations of three chemotypes of Cunila galioides Benth.

Cunila galioides, a popular aromatic and medicinal plant of South Brazil, is one of the 12 South American species of the genus Cunila. With a center of distribution on the highlands of South Brazil, C. galioides has been separated in three chemotypes, characterized by high concentrations of citral, ocimene and menthene, respectively. Twenty populations collected at Rio Grande do Sul and Santa Catarina States, were analyzed by RAPD using 20 arbitrary primers that generated 239 scorable bands. Genetic distances were calculated using Jaccard's coefficient. Cluster analysis was carried out using the Single Linkage method. The analysis with RAPD markers revealed wide variation within C. galioides that reflected a high level of diversity within this species. Cluster and canonical discriminating analysis indicated that the populations of the citral and menthene chemotypes are more closely related to each other, and the populations of the ocimene chemotype represent a different genetic pool.     

Genetic diversity and population structure in the Brazilian Cattleya labiata (Orchidaceae) using RAPD and ISSR markers

Brazilian orchids are currently threatened with extinction due to habitat loss and, because of their high ornamental value, intense collecting pressure. Genetic diversity can play a key role in the survival of endangered orchid species. Here we provide the first data on genetic diversity and structure of wild populations in the genus Cattleya, in particular C.?labiata, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. We studied 130 individuals, 117 belonging to Cattleya?labiata and 13 from 10 other species in the same genus. Data generated from 12 ISSR and 12 RAPD primers were used to determine genetic variability via a model-based Bayesian procedure (Structure) and molecular variance analysis. In addition, Shannon index, genetic diversity and Jaccard coefficients were also estimated. The marker data indicated that C. labiata has a high level of polymorphism, and five reconstructed populations were identified by Structure. The unweighted pair group method with arithmetic mean dendrogram did not group the samples by origin, which was also confirmed by Bayesian analysis, demonstrating the complex genetic structure of C.?labiata. Other Cattleya species showed no relationship with any C.?labiata sample. This genetic characterization of Cattleya from northeast Brazil contributes to knowledge of the genetic structure of the species and can be used to define strategies for conservation and breeding programmes.     

Genetic Relationship of <Emphasis Type="Italic">Curcuma</Emphasis> Species from Northeast India Using PCR-Based Markers

Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD), 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic fragments. ISSR confirmed maximum polymorphism of 98.55% whereas RAPD and AFLP showed 93.22 and 97.27%, respectively. Marker index and polymorphic information content varied in the range of 8.64–48.1, 19.75–48.14, and 25–28 and 0.17–0.48, 0.19–0.48, and 0.25–0.29 for RAPD, ISSR, and AFLP markers, respectively. The average value of number of observed alleles, number of effective alleles, mean Nei’s gene diversity, and Shannon’s information index were 1.93–1.98, 1.37–1.62, 0.23–0.36, and 0.38–0.50, respectively, for three DNA markers used. Dendrograms based on three molecular data using unweighted pair group method with arithmetic mean (UPGMA) was congruent and classified the Curcuma species into two major clusters. Cophenetic correlation coefficient between dendrogram and original similarity matrix were significant for RAPD (r = 0.96), ISSR (r = 0.94), and AFLP (r = 0.97). Clustering was further supported by principle coordinate analysis. High genetic polymorphism documented is significant for conservation and further improvement of Curcuma species.     

Analysis of Genetic Diversity of Persea bombycina “Som” Using RAPD-Based Molecular Markers

The utility of RAPD markers in assessing genetic diversity and phenetic relationships in Persea bombycina, a major tree species for golden silk (muga) production, was investigated using 48 genotypes from northeast India. Thirteen RAPD primer combinations generated 93 bands. On average, seven RAPD fragments were amplified per reaction. In a UPGMA phenetic dendrogram based on Jaccard’s coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity. The grouping in the phenogram was highly consistent, as indicated by high values of cophenetic correlation and high bootstrap values at the key nodes. The accessions were scattered on a plot derived from principal correspondence analysis. The study concluded that the high level of genetic diversity in the P. bombycina accessions may be attributed to the species’ outcrossing nature. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis.     

Chemotaxonomic studies on rhizome extract compositions of twenty Curcuma species from South India

The chemical composition of volatile methanolic rhizome extracts of twenty Curcuma species was studied and the components were identified using gas chromatography–mass spectrometry (GC-MS) method. The major components identified in the majority of the species were beta-caryophyllene epoxide, camphor, retinal and alloaromadendrene oxide. Based on the presence of major chemical components, cluster analysis was performed for all the Curcuma species studied. All the twenty species were grouped based on the presence or absence of a particular compound and a dendrogram was constructed, which grouped the 20 species into eight clusters. By conventional morphological methods, the identification of Curcuma up to species level is difficult; hence the chemical composition of the rhizome methanolic extracts can be used as an important tool for species identification and chemotaxonomic study.     

Genetic diversity and genetic relationships in Hyacinthaceae in India using RAPD and SRAP markers

Genetic diversity and relationship among three genera namely Drimia, Dipcadi and Ledebouria of Hyacinthaceae in India was studied using RAPD and SRAP markers. Twenty one RAPD primers and nine SRAP were used for analyzing 41 accessions. RAPD gave an average 12.6 markers per primer, while SRAP generated 10.1 markers per primer pair. The family emerged very diverged with high polymorphism. The study resolved the three genera into monophyletic groups corresponding to three subfamilies; Urginoideae, Hyacinthoideae and Ornithogaloideae. Drimia wightii emerged a very distinct species and species specific markers were obtained with both marker systems. AMOVA analysis also revealed the genera to be quite well diverged. The two markers showed high correlation (r = 0.932) in Mantel matrix crresspondance test. The combined data also showed a very good correlation with the respective markers individually.     

Divergence of genomic DNA in species of the subgenus Camptochironomus (Diptera, Chironomidae) differing in their cytogenetic similarity levels

The variation and divergence of genomic DNA in four species of the subgenus Camptochironomus (C. tentans, C. dilutus, C. pallidivittatus, and C. setivalva) differing in the level of their cytological similarity were analyzed using the RAPD (Randomly Amplified Polymorphic DNA) method. A high level of variation in the RAPD markers was found in the species studied. Genetic distances (GD) were assessed between natural C. tentans populations, between different species of the camptochironomus sibling species group (C. tentans, C. dilutus, and C. pallidivittatus), and between these species and C. setivalva which is outside this sibling species group. The GD values obtained characterize the levels of genomic differentiation among natural populations (GD = 0.248), among sibling species (GD = 0.635), and between incipient species (GD = 0.784) of the subgenus Camptochironomus. The degree of genomic DNA divergence between sibling and incipient species in the subgenus Camptochironomus was found to be lower than that in the genus Chironomus. The rate of genomic DNA divergence appears to be lower than the rate of chromosomal divergence in species of the subgenus Camptochironomus.     

Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

Jacaranda decurrens (Bignoniaceae) is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2%) polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA) using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA) and Pearson''s correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006) between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.     

Molecular Characterization of <Emphasis Type="Italic">Cyclamen</Emphasis> Species Collected from Different Parts of Turkey by RAPD and SRAP Markers

The genus Cyclamen (family Myrsinaceae) contains about 20 species, most of which occur in the Mediterranean region. Turkey has critically important Cyclamen genetic resources. Molecular characterization of plant materials collected from different regions of Turkey in which Cyclamen species grow naturally, namely Adana, Antalya, Ayd?n, Mu?la, ?zmir, Denizli, Kahramanmara?, Osmaniye, Eski?ehir, Trabzon, and Rize provinces, was performed using RAPD and SRAP markers. DNA was successfully amplified by 30 RAPD primers and 14 SRAP primer pairs. Among the 470 bands generated by the RAPD primers, 467 were polymorphic. The number of bands detected by a single primer set ranged from 11 to 22 (average of 15.6). The percentage polymorphism was 99.3 % based on the RAPD data. In the SRAP analysis, a total of 216 bands were generated, showing 100 % polymorphism. The number of bands detected by a single primer set ranged from 9 to 22 (average of 15.4). All data were scored and UPGMA dendrograms were constructed with similar results in both marker systems, i.e., different species from nine provinces of Turkey were separated from each other in the dendrograms with the same species being clustered together.     

Assessment of genetic diversity in Colletotrichum falcatum Went accessions based on RAPD and ISSR markers

Sugarcane is susceptible to red rot disease caused by phytopathogenic fungus Colletotrichum falcatum Went which ultimately affect the economy of farmers as well as sugar based industry. One of the various ways to control this devastating disease is to develop disease resistance sugarcane cultivar and this requires the complete understanding of genetic makeup of pathogen. Although South Gujarat is well known sugarcane cultivating area, less published data can be found about PCR-based genetic diversity in prevalent C. falcatum accessions. So, present investigation aims at finding molecular variation among the ten accessions of C. falcatum using RAPD and ISSR molecular markers. A total of 35 RAPD and 39 ISSR primers were screened across 10 C. falcatum accessions, of which 15 RAPD and 21 ISSR primers have showed consistent amplification. Statistics related to genetic variation were estimated using NTSYS-PC by means of Dice’s coefficient. The results revealed 80.6% and 68.07% polymorphism and similarity coefficient ranged from 0.43 to 0.91 and 0.73 to 0.93 in RPAD and ISSR analysis respectively. The dendrogram generated using RAPD, ISSR and combined RAPD-ISSR grouped accessions into different clusters which reveal considerable level molecular variation among the C. falcatum accessions. It is also evident from PCA plots that accessions are rather dispersed with tested marker systems indicating good genetic base. So, in nut shell, we found considerable genetic variation and relatedness within C. falcatum accessions collected from different areas of south Gujarat, India using RAPD and ISSR markers.     

Biochemical and Molecular Characterization of Some Centaurea Species Growing in the Eastern Anatolia Region of Turkey

Random amplified polymorphic DNA (RAPD) and fatty acid (FAME) profiles were used to examine phenotypic and genetic relationships among 16 Centaurea species growing wild in the eastern Anatolia region of Turkey. Thirteen decamer primers were used to examine polymorphism. According to the RAPD results, 99 amplicons in the size range of 50–1000 bp were produced from 13 primers in 16 Centaurea species. Genetically four distinct groups were determined among the species of Centaurea, which represents high genetic variation. In the 16 species, 14 fatty acids were determined according to FAME results. Both FAME and RAPD results showed that C. virgata is genetically different from other species. The differences in the composition of fatty acids among Centaurea species suggest that fatty acid profiles could be used to differentiate among some of these species. Results of this study show that RAPD and FAME analyses are consistent.     

CAAT box- derived polymorphism (CBDP): a novel promoter -targeted molecular marker for plants

The availability of a simple, reproducible and cost-effective molecular marker is a prerequisite for plant genetic analysis. We have developed a novel promoter-targeted marker, CAAT box- derived polymorphism (CBDP) using the nucleotide sequence of CAAT box of plant promoters. CBDP, like random amplified polymorphic DNA (RAPD), uses single primer in polymerase chain reaction (PCR) for generating markers. However unlike RAPD, the CBDP primers are 18 nucleotides long and consist of a central CCAAT nucleotides core flanked by the filler sequence towards the 5′ end and di- or trinucleotides towards the 3′ end. In this study, a small set of 25 CBDP primer was designed and initially tested in a representative set of eight cultivars of jute for generation of polymorphic markers. Further, to achieve high reproducibility, a touchdown PCR was employed with an annealing temperature of 50ºC. All the CBDP primers generated polymorphic markers in jute cultivars, and an UPGMA dendrogram based on Jaccard’s similarity grouped them into two clusters represented by Corchorus capsularis and C. olitorius, respectively. Interestingly, such grouping of jute cultivars was consistent with genetic relationships established earlier for these cultivars using other DNA markers. Moreover, these CBDP primers also generated polymorphic markers in representative sets of cotton (Gossypium species) and linseed (Linum usitatissimum ) cultivars. Given the high success rate of CBDP primers in generating markers in the tested species and advantages like ease in marker development and assay with reproducible profiles, they could potentially be exploited in other species as well for assessing genetic diversity, cultivar identification, construction of linkage map and marker- assisted selection.     

Pollen morphology of Chinese Curcuma L. and Boesenbergia Kuntz (Zingiberaceae): Taxonomic implications

In order to find new non-molecular evidence to support the phylogenetic and taxonomic position, pollen grains of 20 populations of 16 species of Chinese Curcuma L. and Boesenbergia Kuntz (Zingiberaceae) were investigated under SEM and TEM. The pollen grains are spherical and ovoid, nonaperturate. The pollen wall is composed of a very thin exine and a thick intine. The exine is psilate or echinate. The intine consists of two layers, i.e., a thick, channeled layer (exintine) and an inner homogenous layer (endintine). The results reveal morphological congruence between the pollen grains of species of Curcuma, which according to DNA sequence data appears to be a polyphyletic genus. However the uniform pollen morphology in Curcuma provides no evidence to divide this genus into separate taxonomic entities. Our results on pollen morphology also do not provide any additional evidence to either unite or segregate Boesenbergia albomaculata and Curcumorpha longiflora in the same genus and demonstrate that more taxonomic data on the genus Boesenbergia and its relatives are needed before a final decision can be made.     

Genetic characterization of two hill stream fish species Barilius bendelisis (Ham.1807) and Barilius barna (Ham.1822) using RAPD markers

Genetic structure of four wild populations of two hill stream fishes Barilius bendelisis (Ham.1807) and B. barna (Ham. 1822) from Uttarakhand, India, was studied using RAPD markers. Eight selective primers provided distinct and consistent RAPD profiles in both the species, producing a total of 47 and 35 scorable bands in B. bendelisis and B. barna respectively. The bands in the range 666–4,830?bp were scored for consistent results. The RAPD profiles generated by all the eight primers revealed varying degrees of polymorphism (25.00–50.00?%). The average genetic diversity (h) was estimated as 0.1661 and 0.1606 among the four populations of B. bendelisis and B. barna respectively.     

Ribosomal FISH mapping reveals hybridity in phytoestrogen producing Curcuma species from Thailand

Species in the genus Curcuma (Zingiberaceae) that are cultivated widely in Thailand for their phytoestrogen-producing rhizomes are called wan-chak-motluk. Five cultivars belonging to Curcuma comosa (cultivars with 2n?=?42 and 63) and Curcuma elata (2n?=?63) were examined using the molecular cytogenetic method of fluorescence in situ hybridisation (FISH) in order to identify genetic relationships among these cultivars based on chromosomal maps of the 18S?C25S ribosomal loci. The results revealed hybrid features in this Curcuma species group and a significant similarity among wan-chak-motluk cultivars. The main features included: (1) the presence of the single largest ribosomal site, assigned the Cc1 marker site, in the somatic 2n complement of all cultivars, and (2) the odd numbers of ribosomal sites in the complements, most often in sets of three. We therefore propose that the cultivar with 2n?=?42 (C. comosa) is a homoploid hybrid species comprised of two different ancestral genomes and has a diploid status with the basic chromosome number x?=?21. The cultivars with 2n?=?63 (C. comosa and C. elata) are most probably triploids arising within the 2n?=?42 diploid species/cultivars via a meiotic modification, rather than from hybridisation between diploid and tetraploid plants. The knowledge about genetic and genomic relationships among wan-chak-motluk cultivars will be important in the research projects that aim to explore and promote new plant materials for cultivation.     

Molecular discrimination of six species of Bagrid catfishes from Indus river system using randomly amplified polymorphic DNA markers

Bagrid catfishes constitute a very important group of fishes having immense commercial importance in south-east countries. The phylogenetic relationships and genome specificity among six species of Bagrid catfishes (Mystus bleekeri, M. cavasius, M. vittatus, M. tengara, M. aor and M. seenghala) were investigated using RAPD markers as discriminating characters for the first time. 511 RAPD fragments were generated using ten decamer primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 92 and 2,863 bp, which were assigned to 155 RAPD loci. Clearly resolved and repeatable bands were scored for their presence or absence in a binary matrix. Different RAPD profiles were observed for all the six Mystus species. In the present study three group diagnostic, eleven group exclusive and 18 species-specific markers were generated. Thus six Mystus species can be successfully differentiated on the basis of these 18 species-specific RAPD markers. UPGMA dendrogram constructed on the basis of genetic distance formed two distinct clusters, M. seenghala and M. aor form one separate cluster from other four species i.e., M. tengara, M. cavasius, M. bleekeri and M. vittatus. The inferences drawn from the above study clearly showed their genetic distinctness from the other four Mystus species and supported their inclusion into a separate genus, Sperata.     

Clonal structure of natural populations of Cryptomeria japonica growing at different positions on slopes,detected using RAPD markers

Cryptomeria japonica D. Don (Japanese cedar), an economically important timber species endemic to Japan, is dominant on ridges and upper slopes in cool-temperate natural forests of Kyoto Prefecture. Recruitment of sexual progeny in the area near the Japan Sea is extremely rare, and propagation occurs predominantly through clonal growth by layering. The development pattern that occurs with layering and the resulting complexity of the population structure make it difficult to identify distinct clones, even by excavation. Therefore, we used the randomly amplified polymorphic DNA (RAPD) technique to examine the clonal structure of upper- and lower-slope plots established in two C. japonica populations in Kyoto Prefecture. A total of 263 plants sampled from four plots were analyzed using 10 arbitrarily chosen decamer primers, which produced 50 highly reproducible RAPD bands. There was a different clonal structure in upper- and lower-slope plots. Lower-slope plots were made up of a small number of genets with many ramets, while upper-slope plots were made up of a large number of genets with a few ramets. Clonal diversity measured using PD, Simpson’s D, and Fager’s E was higher in the upper-slope plots. These results show that natural C. japonica populations maintain relatively high clonal variation, compared with other clonal plant species, and that repeated seedling recruitment occurred more frequently in upper-slope plots than in lower-slope plots.     

ISSR and RAPD Markers Assessed Genetic Variation of Aerides maculosum — an Epiphytic Orchid from Goa, India

Aerides maculosum Lindl is one of the most important orchids valued for its beautiful inflorescence/flowers. The present study aimed to understand the level of genetic variation among the populations of A. maculosum using RAPD and ISSR markers. Among the 35 primers tested, 13 RAPD and 6 ISSR primers were selected for the analysis. Total of 101 RAPD and 40 ISSR fragments were generated. High level of polymorphism was recorded in RAPD (90.45%) compared to ISSR (72.85 %). Nei’s average genetic identity values for different populations of A. maculosum- ranged from 0.465 to 0.762 (RAPD), while for ISSR it ranged from 0.475 to 0.975. The present study provides important insights about genetic variation in A. masculosum and may facilitates the conservation and management of this species.