DSpace Repository :: Browsing by Author "Manimekalai, R."

Browsing by Author "Manimekalai, R."

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Analysis of expressed sequence tags (ESTs) from cocoa (Theobroma cacao L) upon infection with Phytophthora megakarya
(2012) Naganeeswaran, S.; Elain Apshara, S.; Manimekalai, R.
Phytophthora megakarya, the causative agent of cacao black pod disease in West African countries causes an extensive loss of yield. In this study we have analyzed 4 libraries of ESTs derived from Phytophthora megakarya infected cocoa leaf and pod tissues. Totally 6379 redundant sequences were retrieved from ESTtik database and EST processing was performed using seqclean tool. Clustering and assembling using CAP3 generated 3333 non-redundant (907 contigs and 2426 singletons) sequences. The primary sequence analysis of 3333 non-redundant sequences showed that the GC percentage was 42.7 and the sequence length ranged from 101 – 2576 nucleotides. Further, functional analysis (Blast, Interproscan, Gene ontology and KEGG search) were executed and 1230 orthologous genes were annotated. Totally 272 enzymes corresponding to 114 metabolic pathways were identified. Functional annotation revealed that most of the sequences are related to molecular function, stress response and biological processes. The annotated enzymes are aldehyde dehydrogenase (E.C: 1.2.1.3), catalase (E.C: 1.11.1.6), acetyl-CoA C-acetyltransferase (E.C: 2.3.1.9), threonine ammonia-lyase (E.C: 4.3.1.19), acetolactate synthase (E.C: 2.2.1.6), O-methyltransferase (E.C: 2.1.1.68) which play an important role in amino acid biosynthesis and phenyl propanoid biosynthesis. All this information was stored in MySQL database management system to be used in future for reconstruction of biotic stress response pathway in cocoa.
Analysis of genetic diversity and population genetic structure in coconut (Cocos nucifera L) using RAPD, ISSR and SSr markers
(2004) Manimekalai, R.
Analysis of segregating populations of West Coast Tall variety of coconut using microsatellite markers
(2006) Manimekalai, R.; Rubavathi, V.B.; Thomas Regi, J.; Nair, R.V.; Rajesh, M.K.
In vitro antagonistic studies with native Trichoderma spp viz., T.viride, T.harzianum & T.hamatum and a bacterial strain of Pseudomonas fluorescens revealed that the mycelial growth of the coconut pathogens viz., Ganoderma applanatum and G.lucidum (basal stem rot pathogens) and Thielaviopsis paradoxa (stem bleeding pathogen) was highly inhibited by T.viride (more then 80%). Pseudomonas fluorescens completely inhibited the growth of both the species of Ganoderma, whereas only 33% inhibition was observed in the growth of T.paradoxa. All the three species ofTrichoderma were found to be very effective in producing specific volatile met.abolites against T.paradoxa. The volatile metabolites of P.fluorescens completely inhibited G.applanatum and Glucidum but non-volatile metabolites were not effective. Application of 50 g of talc formulation of Trichoderma viride or T.harzianum or T.hamatum with combination of5 kg neem cake/palm/year in basins around the palm was found to be effective in the management ofbasal stem rot disease and smearing oftalc powder paste ofTrichoderma viride or T.harzianum or T.hamatum reduced bleeding patches due to stem bleeding disease. Developed a common biointensive "10M package against basal stem rot and stem bleeding diseases.
Assessment of the genetic diversity of Indian coconut accessions and their relationship to other cultivars, using microsatellite markers
(No. 145 Plant Genetic Resources Newsletter, 2006) Devakumar, K.; Jayadev, K.; Rajesh, M.K.; Chandrasekhar, A.; Manimekalai, R.; Kumaran, P.M.; Parthasarathy, V.A.
Coconut cultivation in the Indian subcontinent over many centuries has given rise to diverse cultivar types, identi- fied based on discernible morphological traits, geographical locations and farmers’ choice. The Indian coconut germplasm base has also been enriched through introductions from other major coconut growing regions of the world. This study assessed the genetic diversity in a range of coconut accessions, and their relationship to other major coconut cultivars, using microsatellite markers. Microsatellite assay was used for 23 Indian accessions (15 Talls and 6 Dwarfs) and for 21 exotic accessions (18 Talls and 6 Dwarfs). A total of 48 alleles were detected in the Indian accessions by using 8 microsatellite primers (average 6 alleles per locus). More alleles were detected in the Indian accessions than in the exotics, indicating the presence of a wide allelic spectrum in the Indian accessions. Mean gene diversity ranged from 0.00 for ‘Chowghat Green Dwarf’ to 0.59 for ‘Lakshadweep Ordinary Tall’, with an overall mean of 0.32. The within-population variation was slightly higher (53%) than the betweenpopulation variation (47%), suggesting recent local adaptation and subsequent divergence among Indian cultivars. An UPGMA dendrogram separated the Indian accessions into two groups, one clustering with South-east Asian cultivars, which are introgressed types, and another clustering with African and Sri Lankan cultivars. The results are discussed in terms of diversity of Indian coconut accessions and relationships to other major coconut cultivars.
Biotechnology and Genomics in Palms
(2013) Manimekalai, R.; Rajesh, M.K.; Manju, K.P.
Bulk Line Analysis in Coconut (Cocos nucifera L.) for Inferring Relationship between Talls, Dwarfs and Niu Leka Dwarf Forms
(2010) Manimekalai, R.; Nagarajan, P.
Coconut is an important an oil crop of India. Coconut (Cocos nucifera L.) is botanically classified in to two major groups based on its stature as Tall palms and as Dwarf palms. The Talls can also be referred to as var. Typica (Nav) and the Dwarfs as var. Nana (Griff). Further, intermediate forms of coconut referred to as Aurantiaca are also available. The technique Bulk Line analysis is employed for the identification of tall / dwarf bulk specific RAPD marker. Thirty random primers were used to amplify the DNA bulks of talls, dwarfs and intermediate coconut types. Out of 30 primers 22 primers showed polymorphism between the DNA bulks. The primers OPM 02, OPM 06, OPC 13 produced specific markers. Out of 40 polymorphic markers five markers were common to tall bulk and dwarf bulk; on the other hand 29 markers were common between the tall bulk and Niu Leka Dwarf. To reveal the overall relationship between the bulked samples presence or absence of RAPD marker data were analysed with the NTSYS software. Jaccard’s similarity coefficient was highest between talls and Niu Leka Dwarf. The resultant dendrogram showed clustering of talls and Niu Leka types together whereas, dwarf types were separated out.
Cocoa and Oil palm putative gene database
(2011) Manimekalai, R.; Rakesh, V.H.; Anoop, S.; George V. Thomas
Oil palm and cocoa are important plantation crops and require bioinformatics tools to hasten the research output and aid in crop improvement programmes. The current work was undertaken to assign putative function to available Expressed Sequence Tags (ESTs) of oil palm and cocoa. Annotated ESTs of cocoa and oil palm were developed into searchable database. ESTs of oil palm and cocoa were first retrieved from dbEST. FASTA formatted EST sequences were converted into contigs by running in CAP3. The contigs sequences were run in BLAST tool and their putative functions were predicted based on homology. A database of annotated ESTs was developed using MySQL and PHP programs. In this database, ESTs of cocoa and oil palm, BLAST results and gene information were stored as different tables. The database homepage contains six menus namely Home, About database, Tool, Useful links, Site map and Contact us. The same page contains annotated gene information for cocoa and oil palm separately. For browsing the annotated ESTs of cocoa and oilpalm, separate text boxes are provided such as ESTs, blast results and gene information. The text box ESTs of oil palm has links to six different tables which stores information about six different tissues and cocoa contains seven different tables, which stores information about seven different tissues. The gene information contains the contig number, similarities found in each organism, accession number, structure accession number and gene function. The cocoa and oil palm putative gene database - COPGENE is hosted at CPCRI bioinformatics website (www.bioinfcpcri.org).
Cocoa EST database: Comprehensive database of Cocoa Expressed Sequence Tags (ESTs)
(2015) Naganeeswaran, S.; Elain Apshara, S.; Manimekalai, R.; Amal Vasu; Malhotra, S.K.
Coconut
(2017) Perera, L.; Manimekalai, R.; Sudarsono, S.; Maskromo, I.; lestari, P.
A database for coconut crop improvement
(2005) Velamoor Rajagopal; Manimekalai, R.; Krishnamurthy Devakumar; Rajesh; Anitha Karun; Niral, V.; Murali Gopal; Shamina Aziz; Marimuthu Gunasekaran; Mundappurathe Ramesh Kumar; Arumugan Chandrasekar
Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA.
Diverse Targets of Phytoplasma Effectors: From Plant Development to Defense Against Insects
(2011) Akiko Sugio; Allyson M. MacLean; Heather N. Kingdom; Victoria M. Grieve; Manimekalai, R.; Saskia A. Hogenhout
Phytoplasma research begins to bloom (75). Indeed, this review shows that substantial progress has been made with the identification of phytoplasma effectors that alter flower development, induce witches’ broom, affect leaf shape, and modify plant-insect interactions. Phytoplasmas have a unique life cycle among pathogens, as they invade organisms of two distinct kingdoms, namely plants (Plantae) and insects (Animalia), and replicate intracellularly in both. Phytoplasmas release effectors into host cells of plants and insects to target host molecules, and in plants these effectors unload from the phloem to access distal tissues and alter basic developmental processes. The effectors provide phytoplasmas with a fitness advantage by modulating their plant and insect hosts. We expect that further research on the functional characterization of phytoplasma effectors will generate new knowledge that is relevant to fundamental aspects of plant sciences and entomology, and for agriculture by improving yields of crops affected by phytoplasma diseases.
DNA polymorphism among coconut (Cocos nucifera L.) cultivars and reciprocal cross derivatives differing in drought tolerance
(2004-12) Manimekalai, R.; Nagarajan, P.; Bharathi, M.; Naresh Kumar, S.
Coconut seedlings of Laccadive Ordinary Tall (LCT). Gangabondam Green Dwarf (GBGD) and their reciprocal cross combinations were analysed by molecular markers viz. Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR). These seedlings were evaluated for water stress tolerance based on leaf water potential measured during stress and non- stress periods. Thc leaf water potential decreased during stress period. The differences among the individuals for leaf water poteniial during stress were not significant. The molecular markers revealed the genetic structure of the cultivars and derivatives clearly. In the dendrogram. individuals of GBGD and GBGD X LCT formed one cluster and LCT and LCT X GBGD formed another cluster. The individuals of LCT and LCT X GBGD showed variation among themselves and they were scattered in the principal co-ordinate plot. Even though the parents are same. the reciprocal cross derivatives behaved differently for leaf water potential and showed polymorphism at DNA level. When the dwarf palm was used as female parent, the F, s were similar to female parent in their banding pattern.
An Efficient Method of DNA Extraction from Theobroma Cacao and Cola Nitida Leaves
(2003) Anuradha Sane; Anuradha Upadhyay; Manimekalai, R.; Parthasarathy, V.A.
Evidence of 16SrXI group phytoplasma DNA in embryos of root wilt diseased coconut palms
(2013) Manimekalai, R.; Smita Nair; Soumya, V.P.
The root wilt disease (RWD) is a major phytoplasma disease of coconut palms in South India. Phytoplasma belonging to the 16SrXI group has been associated with the disease. In our earlier studies we detected phytoplasma from leaves, inflorescence and roots of symptomatic palms in the nested PCR. In this work we examined the embryo from diseased palms for the presence of phytoplasma through semi-nested PCR assay with primers 1F7/7R3 - 1F7/7R2 specific for phytoplasma 16S rRNAgene. Out of 270 embryos collected in four rounds of sampling from two different locations, positive amplification was obtained for 45 (16.67 %) embryos. Sequencing and blastn analysis confirmed the presence of coconut root wilt phytoplasma. To check the potential seed transmission of phytoplasma, mature nuts from diseased palms were germinated in poly bags under disease free conditions and seedlings were sampled for DNA isolation and nested PCR analysis. But phytoplasma DNA could not be detected in any of the seedlings raised in poly bags.
Genetic relationship and diversity in Indian coconut accessions based on RAPD markers
(2004) Anuradha Upadhyay; Jayadev, K.; Manimekalai, R.; Parthasarathy, V.A.
Randomly amplified polymorphic DNA (RAPD) markers were used to analyze genetic diversity and genetic relationship among coconut accessions. DNA from 81 palms representing 20 accessions, 15 Indian and 5 exotic, was used to amplify with 8 highly polymorphic primers. The 8 primers yielded 77 markers, with an average of 9.6 markers per primer. The within-accession genetic diversity ranged from 0.057 to 0.196. In general, tall accessions were more heterozygous as they had higher proportions of polymorphic bands and genetic diversity. The proportion of variation explained by within accession and between accession diversity was 0.58 and 0.42, respectively. Similarly exotic accessions exhibited more variation. Dwarfs from geographically distant regions did not cluster separately. Based on the similarity matrix, cluster and principal coordinate analysis was performed. A dendrogram of genetic relationship was obtained. The extent of genetic diversity and genetic relationship among accessions is discussed.
Genetic variation of selected progney lines of coconut(cocos nucifera.L) based on simple sequence repeat markers
(2005) Manimekalai, R.; Nagarajan, P.; Bharathi, M.; Karun, A.; Kumar, S.N.; Kumaran, P.M.
Identification of RAPD markers linked to sex determination in palmyrah (Borassus flabellifer L.)
(2007-10) Jiji George; Anitha Karun; Manimekalai, R.; Rajesh, M.K.; Remya, P.
Improved protocol for AFLP analysis as a base for tagging root (wilt) resistance genes in coconut
(2002) Rajesh, M.K.; Jayadev, K.; Chandrasekhar, A.; Anuradha Upadhyay; Devakumar, K.; Manimekalai, R.; Nair, R.V.; Parthasarathy, V.A.
The root (wilt) disease of coconut is endemic in Southern districts of Kerala and the adjoining areas of Tamilnadu causing enonnous loss of nuts. Integrated management practice is the only suggested method to reduce its effect to some extent while development of resistant varieties will offer permanent solution, for which concrete breeding efforts are required. Considering Ute long life cycle of coconut, selection of resistant varieties through conventional methods will be time consuming and laborious. Molecular markers offer numerous advantages over markers traditionally used in plant mapping and selective breeding. AFLP (Amplified Fragment Length Polymorphism) is a versatile DNA fingerprinting technique for marker assisted selection which combines universal applicability with high powers of discrimination and reproducibility. In this preliminary ttudy for tagging root(wh6 resistkce genesiicoconut, AFLP parameters, geirunning a& silver staining conditions were optimized. Also, primer pairs detecting variations between resistant and susceptible palms were selected.
Informative Inter Simple Sequence Repeat (ISSR) primers for genetic analysis of coconut (Cocos nucifera L.) germplasm
(2005) Manimekalai, R.
Inter Simple Sequence Repeat (ISSR) markers for identification of germplasm and diversity analysis in coconut (Cocos nucifera L.)
(2012) Manimekalai, R.
Inter Simple Sequence Repeat (ISSR) is a powerful molecular marker technique used for variety of purposes like genetic diversity analysis, phylogeny information, germplasm identification, gene tagging etc. In the present paper, 33 coconut (Cocos nucifera L.) germplasm representing different geographical regions have been fingerprinted with highly polymorphic ISSR markers. Ten polymorphic primers targeting the microsatellite regions were used to amplify the coconut germplasms. Ten primer produced 104 polymorphic markers with 87 percent polymorphism. Cluster analysis was carried out among 33 accessions by UPGMA using the software POPGENE ver.1.32. The dendrogram revealed five clusters. Based on the fingerprint data germplasm specific markers were identified using the primers UBC 810, UBC 915, UBC 823, UBC 824 and UBC 855 . The marker UBC 815was specific to Panama Tall (PNT) and Saint Vincent Tall (STVT). The marker 1673 UBC 854m was specific to Nuwehnug Tall (NWHT). ISSR markers were proved to be useful for generating fingerprints and for deriving genetic relationships in coconut.

Browsing by Author "Manimekalai, R."

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