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Open Access
QTL mapping for yield traits in vegetable cowpea
(Centre for Plant Biotechnology and Molecular Biology, College of Horticulture, Vellanikkara, 2017) Ashwin Varghese, V; KAU; Deepu, Mathew
Cowpea [Vigna unguiculata (L.) Walp.] is one of the most cultivated pulse crops in the semi-arid tropics of Asia, Africa, Southern Europe, and other parts of the world. It is used for both vegetable and fodder purpose. In India, kharif crop of vegetable cowpea is cultivated in an estimated area of 0.5 million hectares in states like Kerala, Karnataka, Tamil Nadu and Madhya Pradesh. Studies aimed at increased yield among crops were always challenged by the quantitative nature of traits. These quantitative traits are generally governed by multiple genes present in regions of the genome called quantitative trait loci (QTL). With the advent of molecular markers it is possible to localize the QTL with the help of linked markers, a process now widely known as QTL mapping. QTL mapping depicts the relative positioning of different markers on the chromosomes and their linkage to a specific trait. In cowpea, even though there has been few mapping efforts for traits such as resistance to Thrips tabaci and Frankliniella schultzei, flowering time, pod length and seed weight, an elaborate QTL map for yield and related traits is missing. Hence, the study “QTL mapping for yield traits in vegetable cowpea” was undertaken with the objective of mapping the SSR markers and identifying the quantitative trait loci for yield components in the genome of vegetable cowpea at the Centre for Plant Biotechnology and Molecular Biology (CPBMB), College of Horticulture, during February 2016 to June 2017. F3 plants maintained at CPBMB, derived from the cross of Sharika which is a pole type, long poded, high yielding but anthracnose and cowpea mosaic virus susceptible cultivar with Kanakamony which is a semi-trailing, medium-long poded, low yielding, anthracnose immune and cow pea mosaic virus resistant cultivar, were used to raise the F4 mapping population. Morphological observation for traits pod length, individual pod weight (IPW), pod number, days taken for first flowering (DTFF), total dry pod yield (TDPY), grains per pod, branch number, root length, plant height, plant weight, and response to anthracnose and cowpea mosaic virus diseases were recorded. High quality DNA was isolated from the parents and mapping population using the protocol standardized in this study. One hundred SSR primer pairs reported in cowpea were screened among the parental DNA for polymorphism. Thirty polymorphic primer sets were carried forward to genotype the F4 mapping population. The morphological and genotypic data were used to construct a linkage map using software ICIMapping. Two linkage groups, one having eight SSR markers distributed across 637 cM and another one having five SSR markers distributed across 271 cM were obtained. Two approaches, Single Marker Analysis (SMA) and Inclusive Composite Interval Mapping (ICIM) otherwise called Additive Linkage Mapping were followed for QTL mapping. LOD value threshold of 3.0 was used to determine the significance of QTL and linked markers. Multiple QTL hotspots were observed for different traits under study. An anchored marker, CLM0083 has been identified which was significantly linked to traits individual pod weight and total dry pod yield. The region between 25 cM to 125 cM on linkage group 1 had QTL hotspots harboring genes governing traits DTFF, TDPY, root length, plant length and plant height. This entire region was bracketed by two markers, CLM0244 at 24.25 cM and CLM0177 at 126.86 cM with an anchored marker CLM0008. This marker combination could be potentially used in marker assisted selection for the traits DTFF, TDPY, root length, plant length and plant height. Fine mapping of the QTL for these traits with large number of markers would provide more insights into the genes and hot spots involved in the yield contributing traits in cowpea.
Open Access
Development of an in vitro regeneration system and validation of genetic stability in phalaenopsis hybrid winter spot with molecular marker
(Centre for Plant Biotechnology and Molecular Biology, College of Horticulture, Vellanikkara, 2016) Asha Amal, Raj; KAU; Lissamma, Joseph
Phalaenopsis “Moth Orchids” are among the most beautiful flowers in the world. This genus has economic value for pot plant and cut flower production and is distributed throughout Southeast Asia. Most popular method of propagation for orchid is through in vitro propagation, as it produces large number of clones in relatively short duration. Despite its potential to produce numerous plants from a single leaf segment, it is liable to unpredictable mutations or somaclonal variation during the process of multiplication. Variation can arise due to many reasons such as type of media, plant growth regulators and its concentration, type of explants and number of subculture cycles. The percentage of the variation can range from 0-100% depending on varieties with an average of 10% among Phalaenopsis (Tokuhara and Mii, 1993). So the present investigation on “Development of an in vitro regeneration system and validation of genetic stability in Phalaenopsis hybrid Winter Spot with molecular marker” was taken up at the Center for Plant Biotechology and Molecular Biology, College of Horticulture from 2013-2016. Flowering mother plants of Phalaenopsis hybrid Winter Spot were used as explant source. Among the explants namely inflorescence node, transverse thin cell layer of leaf and root segments used for tissue culture study in this orchid, inflorescence node was the best with respect to culture response. The best surface sterilization treatment for leaf explants identified was treatment 0.1% bavistin + prill 2 drops (30 min) and 0.1 per cent HgCl 2 ( 8 min) which give maximum per cent of culture survival and minimum contamination rate. The best surface sterilization treatment for inflorescence node identified was treatment with 0.1% bavistin + 2 drops prill (30 min) , one minute dip in 70 per cent ethanol and 0.1% HgCl 2 (7 min).From different basal media (full MS and 1⁄2 MS) tried, response was observed only in the medium of Full MS for inflorescence node. Among the different growth regulators tried, MS medium supplemented with BA and TDZ was found to give good shoot regeneration from inflorescence node explants. MS +2mgl -1 TDZ recorded highest percentage (80%) of culture establishment, followed by MS + 4.5 mgl -1 of BA (55%) per cent of sprouting. Among the explants tried, only inflorescence node responded with sprouting. Root segment remained as such without any change, whereas leaf explants remained green up to 2 weeks, thereafter started drying in all the growth regulators combination. For induction of multiple shoot, MS medium supplemented with 4.5 mgl -1 BA resulted in the highest average number of multiple shoot (4.15). Elongation and rooting was observed in MS medium supplemented with BA 4.5mgl-1 +IAA 1mgl -1 with 80 % rooting. Root initials were observed 50 days after inoculation. The potting media, charcoal, brick pieces and sphagnum moss in the ratio of 1:1:1 was found ideal for hardening of Phalaenopsis hybrid winter spot with 100% survival. Genetic stability studies using RAPD marker were carried out with the mother plants along with three regenerants each. Six primers were selected based on DNA amplification pattern. In RAPD assay, M1 mother plant recorded the highest average polymorphism of 19.7% and M3 mother plant recorded the least average polymorphism of 8.18%. Using NTSYS software, the similarity coefficients for first, second and third plant between M1 mother plant, M2 mother plant and M3 mother plant and corresponding regenerants were 0.91, 0.92 and 0.93 respectively. In fourth plant, the similarity coefficient exhibited 100% similarity between mother plant, the first clone C1 and third clone C3. The established micropropagation protocol can be used with suitable modification for large scale production of other Phalaenopsis varieties.
Open Access
Evaluation of miRNA prediction tools and in silico analysis of micro and long non coding RNAs in sweet potato
(Department of Plant Biotechnology, College of Agriculture, Vellayani, 2018) Aswathy, M B; KAU; Sreekumar, J
The study entitled “Evaluation of miRNA prediction tools and in silico analysis of micro and long non coding RNAs in sweet potato (Ipomoea batatas L.)” was conducted at the ICAR-CTCRI, Sreekariyam. The objectives of the study is to compare different miRNA and target prediction tools and in silico analysis of the miRNAs and lncRNAs in sweet potato. The plant miRNA identification tools: NOVOMIR and miRPlant and miRNA-target prediction tools: psRNATarget and miRanda were compared. NOVOMIR and psRNATarget were found to be a better tool in miRNA identification and target prediction. MicroRNAs (miRNA) are 18-22nt small, endogenous non coding RNA that has prominent role in many biological processes. In the present study, we report the computational prediction of miRNAs and targets from expressed sequence tags (ESTs) of sweet potato. We predicted 13 novel potential miRNAs and 81 potential target genes and functionally characterized by BLASTX and BLAST2GO. The predicted target genes were credited with their role in signalling cascades, metabolism, and defence and stress responses. Another candidate that has more importance in the genome regulation is lncRNAs. lncRNAs are greater than 200 nucleotide length ncRNA candidate that holds functions at RNA level itself. RNAplonc is a plant long non coding RNA identification tool which uses 16 feature selection methods to predict long non coding RNA molecules. The present study which predicts 9215 lncRNAs and 8665 protein coding genes by RNAplonc in sweet potato for the first time using available ESTs sequences. Since there is a lack of lncRNA functional annotation tool, the functional analysis of predicted lncRNAs is quiet difficult. From the predicted miRNAs and lncRNAs two miRNAs and two lncRNAs were randomly selected for experimental validation by real time quantitative PCR using three different sweet potato varieties Sree Kanaka, ST13 and Khanjakad available at ICAR-CTCRI and compared the target gene’s expression in each variety. Validation results prove that both the miRNAs and lncRNAs shows their importance in crop improvement.
Open Access
Molecular characterization of katte mosaic virus of cardamom ( Elettaria cardmomum Manton )
(Centre for Plant Biotechnology and Molecular Biology, College of Horticulture,Vellanikkara, 2016) Abida, P S; KAU; Manglam Arya
Cardamom ( Elettaria cardamomum Maton) considered as “Queen of Spices” belongs to the family Zingiberaceae. Due to its aroma, cardamom is one among the most expensive spices in the world. Cardamom is infected by several fungal, bacterial and viral diseases. Katte or Cardamom mosaic disease is the most destructive viral disease affecting cardamom plantations worldwide. The disease is caused by Katte mosaic virus or Cardamom mosaic virus (CdMV) and spreads through infected suckers or through aphid Pentalonia nigronervosa Coq. The loss in yield due to katte disease ranges from 38 to 69 per cent and when infection occurs at early stage, the loss is complete. Management of katte disease totally depends on the use of disease free planting materials. As the infected plant often remains symptomless, identification and diagnosis of the virus becomes difficult at early stages. The present study was undertaken to develop serological and PCR based methods for identification and characterization of CdMV of cardamom. The infected and healthy samples were collected from four locations of Idukki and two locations of Wayanad districts of Kerala. The viral protein was isolated and purified from infected samples and SDS-PAGE analysis of purified protein from infected plants revealed the presence of 37 kDa band of viral coat protein. The purified protein from the infected plants was further used as antigen for the production of polyclonal antibody against CdMV in 6-9 month old rabbit. The rabbit was immunized with 5 mg of purified protein. The blood sample from the immunized rabbit was collected and the antibody was purified. The ODD (Ouchterlony Double Diffusion) assay was performed to standardize the titre of the antibody and results had shown that antigen-antibody complex was formed in 1:10, 1:100 and 1:150 dilutions of primary antibody. The indirect ELISA was carried out with 1:10, 1:100 and 1:150 dilutions of primary antibody and 1:200 dilution of secondary antibody. It was found that virus was easily detected in the crude extract of infected leaves with 1:100 dilution of primary antibody. Indirect ELISA was also performed for investigating the serological relationship of Katte mosaic virus with other viruses. The result of indirect ELISA revealed that the crude sap of infected cardamom leaves cross reacted with the antibody specific for Banana Bract Mosaic Virus (BBrMV) which also belongs to same potyvirus group. For the detection of CdMV through RT-PCR, the total RNA was isolated from the infected and healthy plants using Trizol and converted to cDNA. A total of 11 primers were designed for the amplification of coat protein gene of the virus using Primer 3 software. The primers designed were used for synthesis of second strand of cDNA and presence of virus was detected. Out of 11 primers, 8 primers were able to amplify the coat protein gene of the virus in infected plants. The band size of 250, 650, 750 and 950 base pairs were observed in infected plant but not in healthy plant samples. The viral amplicons of 250, 950, 750, 650 base pairs were generated with primers CP-2, CP-9, CP-10 and CP-11 respectively. These amplicons were further eluted, reamplified and sequenced. The nucleotide sequence annotated using bioinformatics tools BLASTn and BLASTx. The result of BLASTn showed 90 to 100 per cent nucleotide sequence similarity with CdMV whereas; the result of BLASTx revealed that the sequence had 55-100 per cent similarity with the coat protein of CdMV. The phylogenetic analysis was performed using 950 bp products generated with CP-9 primer. The phylogenetic tree was developed using MEGA.7 software by utilizing neibhourhood joining method. The result of phylogenetic analysis revealed that the isolates of Ambalavayal, Meppadi and Myladumpara are closely related and also related to isolates of Irettyar and Paravalam whereas, Pampadumpara isolate showed more variation to the above isolates. The methods developed in the present study are useful in detecting the Katte mosaic virus or Cardamom mosaic virus in the infected leaf samples of cardamom. The method will be useful in virus indexing, quarantine management in germplasm exchange, germplasm management, supply of disease free planting materials to the farmers and also for selecting the resistant line or cultivar for large scale production or incorporation in breeding programme for crop improvement.
Open Access
Molecular characterization of candidate gene for pungency in Capsicum spp.
(Centre for Plant Biotechnology and Molecular Biology, College of Horticulture,Vellanikkara, 2016) Anju Viswanath, KAU; Deepu Mathew
Chilli, also known as “Wonder spice”, has been cultivated since 3000 BC. Out of the 21 identified species of chilli, C. annuum, C. chinense, C. frutescens, C. baccatum and C. pubescens are the domesticated species. It is a major vegetable cum spice crop which can impart pungency, colour and aroma to the human foods. Pungency is one of the most important and peculiar character of all the species belonging to the genus Capsicum. Capsaicinoids are the alkaloid compounds which are responsible for pungency in chilli. Because of the nutraceutical properties possessed by these capsaicinoids, it has much importance in manufacturing several drugs. Though so many studies are conducted to understand the genetic mechanisms behind pungency, the gene action responsible for its production is still an enigma. This experiment was undertaken with the objective to assess the molecular mechanisms behind different levels of pungency in different species of Capsicum. The investigations were carried out in ten chilli genotypes namely, Ujwala, Anugraha, Byadagi Dabbi, Byadagi Kaddi, paprika Kt-Pl-19 and bell peppers Arka Gaurav and Arka Mohini (C. annuum), Vellayani Thejus (C. chinense) and White Khandari, Vellayani Samrudhi (C. frutescence). Among the genotypes Anugraha, Ujwala, Vellayani Thejus, Vellayani Samrudhi and White Kandari are pungent lines and Kt-Pl-19, Byadagi Dabbi, Byadagi Kaddi, Arka Mohini and Arka Gaurav are non-pungent lines. Good quality genomic DNA has been extracted from all the genotypes with an absorbance ratio ranging from 1.79 - 1.85 and concentration more than 1000 ng/μl. The DNA was screened with five pungency specific SCAR (Sequence Characterized Amplified Region) primers. Among the five SCAR primers used, three were specific for Pun1 locus (MAP1F/R, Pun1 1 fwd1/rev, Pun1 3 fwd/rev1) and two were specific for CS (Capsaicinoid synthetase) gene (CSF1/R2, BF7/R9). Pun1 and CS are the loci responsible for the synthesis of putative acyl- transferase and capsaicin synthase enzymes leading to the synthesis of capsaicinoids. The results revealed that MAP1F/R is the most significant primer which gave distinct amplifications in both pungent lines and non-pungent lines. A 15 bp deletion was clearly identified in the non-pungent lines compared to the pungent lines. This resultii revealed that the 15 bp deletion in the non-pungent lines is the reason for the absence of pungeny in them. The other two primers Pun1 1 fwd1/rev, Pun1 3 fwd/rev1 gave amplification only for pungent lines in C. annuum and C. frutescence respectively since Pun1 1 and Pun1 3 are the mutant alleles of Pun1 locus present in the respective species. The capsaicin, which is a capsaicinoid compound contributing about 69 per cent of pungency, is produced with the help of the capsaicin synthase enzyme produced from the CS gene. The primers specific for the CS gene have amplified only in the pungent lines. This result revealed that the nucleotide change in the primer binding region is the reason for the absence of pungency in them. The amplicon sequences of CS gene was subjected to insilico analysis such as BLASTn and Clustal Omega, which identified that the CS gene whose location was not yet confirmed also resides within the Pun1 locus. The insilico analysis has also proven that the 15 bp deletion identified in the non-pungent lines were located at the ORF3 in the Pun1 locus. This deletion in the coding region significantly affects the capsaicinoid formation for the pungency. Irrespective of the species, the deletions occurring in the coding regions of the Pun1 locus and CS gene, are the reasons for the variation of pungency levels in chillies. All the five primers attempted were promising and can be utilized to distinguish the pungent and non-pungent lines even in the seedling stage and hence in marker assisted selection (MAS). Identification of the location of CS gene inside the Pun1 locus is the most striking finding of this study. From this it can be infered that Pun1 locus, which is in the chromosome 2 of chilli is the major deciding locus for the production of capsaicinoids.
Open Access
Comparative evaluation of tools for gene regulatory network prediction and network reconstructioon using genomic data
(Department of Plant Biotechnology, College of Agriculture, Vellayani, 2018) Reshma Bhasker, T; KAU; Sreekumar, J
Developing regulatory network of genes controlling traits which are of importance economically and commercially are gaining much significance in present times. GRN’s provide an insight into the transcriptional mechanisms that regulate the robust and stochastic gene expression and their relationship with the phenotypic variability that can be utilized for better crop improvement strategies. The former approaches for Gene Regulatory Network construction mainly rely on using gene expression data as input, but the time consumption and high cost of expression analysis paved way for developing new methodologies that make GRN prediction easier. The integration of genomic information along with gene expression data, could make the process of Gene Regulatory Network (GRN) construction more reliable than using expression data alone as input source. Using this approach, we have tried to develop the regulatory network of genes controlling immunity in cassava with special context to Bacterial blight resistance. Initially the immunity related genes in cassava were identified by protein domain search and analysis using HMMER. Cassava specific genes were further filtered for high competency, mapped and annotated to determine its biological role and function. A set of 1919 immunity related genes in cassava were identified, out of which 22 of them were specifically conferring virus resistance, 727 of them were screened for bacterial blight resistance by microarray data integration and a network was created using they predicted interactions identified from 324 genes using STRING. The networks obtained was visualized using Cytoscape and cross validated with simulated dataset generated from SynTReN. The generated network if immunity related genes in cassava could give more insight into the defence mechanism in cassava that can help in adapting better crop improvement and management strategies. A comparison of various approaches used for GRN prediction like probabilistic method, mutual information-based method, correlation-based approaches etc was also done and various tool like ARACNE, WGCNA etc were evaluated. Networks with different sizes, 50, 100 and 150 was generated and the network parameters like clustering coefficient, network density etc were compared. Clustering coefficient does not seem to vary with increase in network size but network heterogeneity and density were observed to increase. The statistical analysis of the performance of different methods resulted into a conclusion that the mutual information based approaches are better tools for Gene Regulatory Network construction than the other methods and it performed with a specificity of 75.7% and a sensitivity of 79.4%.
Open Access
Assessment of antiinflammatory and antioxidant properties of chlorophytum laxum R.Br.
(Department of Plant Biotechnology, College of Agriculture, Vellayani, 2018) Arundhathy, G B; KAU; Suja, S R
The thesis entitled ‘Assessment of antiinflammatory and antioxidant properties of Chlorophytum laxum R. Br.’ was carried out in the Ethnomedicine and Ethnopharmacology Division of Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram during the academic year 2017-2018. The objective of the study was to scientifically evaluate antiinflammatory and antioxidant properties of an ethnomedicinal plant Chlorophytum laxum R. Br. (Neeruvatti). Chlorophytum laxum R. Br. (Neeruvatti), herbaceous plant of family Liliaceae is one of the important medicinal plant seen in grasslands. The tubers of Chlorophytum laxum R. Br. were collected from the hills of Western Ghats and maintained at JNTBGRI to conduct the pharmacological studies. Extraction procedures were carried to prepare the drugs of different doses for the study. Acute oral toxicity studies in mice and antiinflammatory studies in rats, were done as pharmacological analysis. The preliminary phytochemical investigation, tubers of Chlorophytum laxum has shown the presence of secondary metabolites like carbohydrates, phenols, alkaloids, proteins, steroids, tannin, saponins and glycosides that may be responsible for its medicinal properties. The content of total phenols in the ethanolic extract of Chlorophytum laxum expressed as gallic acid equivalents per gram of dry extract is 5.12 mg GA/g of extract. Toxicity studies of tuber extract were investigated in Swiss albino mice for 14 days by the administration of 4 doses 5, 50, 300 and 2000 mg/kg body weight and no symptoms of toxicity were seen in the animals even up to the highest dose. In detailed pharmacological studies, antiinflammatory potential of tuber extract was investigated in vivo by carrageenan induced paw oedema and formalin induced paw oedema and in vitro by HRBC membrane stabilization assay. The extract were administered at doses of 50, 150 and 450 mg/kg body weight orally in adult wistar rats and the maximum percentage inhibition of paw oedema in the right hind limb was shown by ECL 450 mg/kg in both the methods. ECL at higher concentration protect significantly the hypotonicity induced haemolysis of HRBC by in vitro antiinflammatory analysis. The antioxidant effect of ethanolic extract of C. laxum showed IC50 of 36.62 μg/mL in hydroxyl radical scavenging, 68.91 μg/mL in nitric oxide radical scavenging and 135.67 μg/mL in antilipid peroxidation assay. Total antioxidant capacity of ethanolic extract of tubers of C. laxum was found to be 90.04 μg AAE/g of dry extract. The antioxidant potential of C. laxum was compared with a standard and the results obtained gives the significant effect and almost equal effect. The results of current study will help to develop a monograph of the drug for reference. These results substantiate the traditional claim of the plant for its medicinal use.
Open Access
Development of infectious clones of cassava mosaic virus and their validation
(Department of Plant Biotechnology, College of Agriculture, Vellayani, 2018) Vishnu Narayanan; KAU; Makeshkumar, T
The study entitled “Development of infectious clones of cassava mosaic virus and their validation” was conducted at the ICAR- Central Tuber Crop Research Institute (ICAR-CTCRI), Sreekariyam, Thiruvananthapuram during 2017- 2018. The major objectives of the study were cloning and characterisation of SLCMV/ICMV infected leaf samples, construction of infectious clones of SLCMV/ICMV and agroinoculation of Nicotiana benthaminana with the partial dimers constructed in order to check the infectiousness of the viral clones. The whole genome amplification of SLCMV/ICMV DNA samples were done and cloned in pUC19 vectors to obtain pSLCMV A7 (2746 bp), pSLCMV B2 (2738 bp) and pICMV A5 (2739 bp) full length clones. The sequence of pSLCMV A7 showed maximum similarity of 99 % with ‘SLCMV-[TVM1]’ sequence in NCBI blast. While the sequence of pSLCMV B2 showed maximum similarity of 99 % with ‘SLCMV-[Ker20]’ sequence in NCBI blast. The sequence of pICMV A5 showed maximum similarity of 95 % with ‘ICMV-[Mah]’ sequence in NCBI blast. In order to develop infectious clones, partial dimers were constructed for SLCMV DNA-A and SLCMV DNA-B and cloned in binary vector pPZP201. These infectious clones were successfully transformed into wild type A. tumefaciens, Ach5 strain by triparental method. Then agroinoculation of N. benthamiana with the constructed partial dimers was found to be successful. After 14 days post inoculation, plants infected with DNA-A + DNA-B partial dimers showed severe symptoms like leaf curling, stunting. The plants infected with partial dimer of DNA-A alone showed mild symptoms like upward leaf curling which confirmed its monopartite lineage. While those plants agroinoculated with partial dimer of DNA-B alone did not show any symptoms. These efficient infectious clones of cassava mosaic virus and their subsequent inoculation technique would provide a major advancement to the resistance development in cassava.
Open Access
Characterization of selected curcuma species germplasm using morphological and molecular markers
(Department of Plant Biotechnology, College of Agriculture, Vellayani, 2018) Bimal Thomas; KAU; Asha, K I
Curcuma L., a perennial rhizomatous herb, is gaining global importance as a source of starch besides its medicinal property and use as a spice. Characterization of germplasm is very essential in crop plants and it is the basis for selection of accessions for use in crop improvement programmes. This research work was an attempt to characterize the fifteen selected accessions in eight species of Curcuma collected from different parts of India and maintained in the field gene bank of ICAR-CTCRI using morphological and molecular markers. Two accessions in each of C. amada, C. angustifolia, C. aromatica, C. decipiens, C. malabarica, C. raktakanta, C. zedoaria and one of C. longa were selected. These 15 accessions were morphologically characterized using 13 qualitative and 15 quantitative traits and a wide variability was observed. Dendrogram based on the morphological characters grouped the genotypes into four clusters. PCC analysis revealed that the accessions of the same species have shown more than 83% similarity except C. angustifolia. C. raktakanta accessions have shown a highest intra-specific similarity of 94%. C. decipiens accessions were found to be the highly variable from the most commonly exploited species C. longa while C. aromatica has shown highest similarity. PCA showed that the characters such as leaf midrib colour, rhizome flesh colour, leaf texture and aroma of rhizome have contributed mostly to the variability. Molecular characterization was done using 10 ISSR and 7 SSR markers. The total percentage polymorphism obtained by ISSR characterization was 94.31 while it was 91.11 percentage in the SSRs. C. angustifolia-1 was found to be highly variable from C. angustifolia-2 suggested the occurrence of intraspecific variability. The intra-specific similarity among C. raktakanta accessions were found to be highest than all other accession pairs. Clustering based on ISSR markers grouped the genotypes into five clusters while SSRs into six clusters. Mantel’s test showed a positive correlation between the morphological and molecular data. The results of the present study indicated that the morphological as well as the molecular tools were found to be very effective in the characterization of germplasm of Curcuma species for the developement of core collections and for further use in the crop improvement programmes.

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