Browsing by Author "Rachana, K.E."

Now showing 1 - 18 of 18
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    Amplification and sequencing of partial–length disease resistant gene homologues coding NBS LRR-type proteins in coconut
    (2012-11) Rachana, K.E.; Naganeeswaran, S.; Rajesh, M.K.
    Pseudomonas spp. and compared with other gene predicting tools. This tool can be used for the functional annotation of the microbial genome data providing insights into genome evolution and identifying different strains containing LTTR genes.
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    Biology, damage potential and molecular identification of Conogethes punctiferalis Guenee in cocoa (Theobroma cacao Linn.)
    (2013-12) Alagar, M.; Rachana, K.E.; Keshava Bhat, S.; Shafeeq Rahman; Rajesh, M.K.
    Conogethes punctiferalis is an important polyphagous pest attacking many economically important crops. Recently, C. punctiferalis has been found to be an emerging pest in cocoa and was found to feed and bore into cocoa pods. The larvae feed on the rind of cocoa cherelles/pods, later bore into pods, feed the internal contents of the pods, the granular faecal pellets are seen outside the pods. When pods/cherelles touch each other, it is easy for the larvae to damage more than one pod/cherelle. Pods damaged by Conogethes are exposed to secondary infection by pathogens that lead to pod rot. The larvae sometimes feed on flower buds and flowers cushions. The damaged flower cushions may dry and shed prematurely. The damage of C. punctiferalis on cocoa is observed from December and peak incidence is noticed during March to May. On an average 2 per cent damage was recorded in the Central Plantation Crops Research Institute, Regional Station, Vittal. In order to develop a DNA-based molecular identification system for this species, primers were designed based on two nuclear genes viz., ribosomal protein S5 (RPS5) gene and carbamoyl phosphate synthetase/aspartate transcarbamylase/dihydroorotase (CAD). PCR-amenable DNA was isolated from C. puntiferalis larva. The designed primers amplified single bands of expected sizes using genomic DNA as template. The amplicons were purified, cloned and sequenced and sequence analysis revealed close homology to the gene of interest from related moths.
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    Comparative transcriptome profiling of healthy and diseased Chowghat Green Dwarf coconut palms from root (wilt) disease hot spots
    (2018) Rajesh, M.K.; Rachana, K.E.; Kulkarni, K.; Sahu, B.B.; Thomas, R.J.; Anitha Karun
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    Computational prediction and characterization of miRNA from coconut leaf transcriptome
    (2015) Naganeeswaran, S.; Fayas, T.P.; Rachana, K.E.; Rajesh, M.K.
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    Development of a RAPD-derived SCAR marker associated with tall-type palm trait in coconut
    (2013) Rajesh, M.K.; Jerard, B.A.; Preethi, P.; Regi Jacob Thomas; Fayas, T.P.; Rachana, K.E.; Anitha Karun
    Coconut palms are classified into two major types, viz. talls and dwarfs, based on plant stature. The selection of coconut seedlings in the nursery, presently relying solely on morphological markers, often results in selection of out-crossed seedlings. Hence, identification of molecular markers for distinguishing tall/dwarf character at an early stage of growth assumes importance. In the present investigation, a RAPD marker for tall-type palm trait was identified using a pooled DNA approach. Screening of tall and dwarf palm bulked DNA with 200 decamer primers revealed a primer OPA09, producing a unique band of around 260 bp exclusively in tall accessions. The primer was used for screening and validation in individual tall and dwarf coconut accessions representing different geographic regions. The band was present in all the tall accessions, but absent in the dwarfs. Furthermore, sequence characterized amplified region (SCAR) primers were designed from the unique RAPD amplicon. The primers produced a specific 260-bp amplicon in tall accessions, but not in dwarf accessions. The SCAR marker was utilized in assessing the purity of hybrid seedlings of D×T (Dwarf×Tall) cross. The results pave the way for ensuring genuineness/quality of hybrid seedlings of coconut.
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    Differentiation of Phytophthora species associated with plantation crops using PCR and high-resolution melting curve analysis
    (2018) Prathibha, V.H.; Vinayaka Hegde; Sharadraj, K.M; Rajesh, M.K; Rachana, K.E.; Chowdappa, P
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    Estimation of out-crossing rates in populations of West Coast Tall cultivar of coconut using microsatellite markers
    (2014-12) Rajesh, M.K.; Rijith, J.; Shafeeq Rahman; Preethi, P.; Rachana, K.E.; Sajini, K.K.; Anitha Karun
    Understanding of mating system of a plant species has fundamental importance for formulation of genetic conservation strategies and breeding programmes. The pattern of gene flow, via pollen, has a profound influence on the genetic structure within a population. Various genetic parameters, obtained from molecular marker studies, can be used to assess estimates of mating system. The aim of this study was to estimate the rate of outcrossing in West Coast Tall (WCT) cultivar of coconut, which is predominant in India, using microsatellite simple sequence repeats (SSR). Two WCT mother palms and their 88 progenies, collected as embryos for five months, were screened using 15 highly polymorphic microsatellite primers. The mating parameters were estimated using mixed mating model (MLTR software) and the extents of similarity between the mother palms and their progenies were analyzed using the NTSYS software. The percentage similarity between the mother palm and its progenies, as deduced using microsatellite data, ranged from 55 to 74 per cent. The progenies were also analyzed using a RAPD primer capable of distinguishing Tall and Dwarf palms. All the progenies were found to possess the Tall-type marker indicating that the pollen was derived from Tall palms in all the cases. The results revealed the WCT cultivar to be pre-dominantly out-crossing and indicated that proper sampling and indicated that proper sampling and breeding strategies are required to sustain the high genetic diversity found.
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    Genetic variation in coconut black headed caterpillar (Opisina arenosella Walker) population in India
    (2016) N. B. V. Chalapathi Rao; Sabana. A.A.; Rachana, K.E.; Rajesh, M.K.
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    Identification of expressed resistance gene analog sequences in coconut leaf transcriptome and their evolutionary analysis
    (2015) Rajesh, M.K.; Rachana, K.E.; Naganeeswaran Sudalaimuthu Asari; Shafeeq Rahman; Regi J. Thomas; Shareefa, M.; Merin Babu; Anitha Karun
    Coconut, an important crop of the tropics and subtropics, is susceptible to a variety of diseases and enhancing disease resistance has been the major goal of coconut breeding programs all over the world. Information on the presence and distribution of disease resistance (R) genes, which play a primary role in the detection of pathogens and the initiation of specific plant defenses, is scarce in coconut. In this study, RNA-Seq was used to generate the transcriptome of leaf samples of coconut root (wilt) disease-resistant cultivar Chowghat Green Dwarf. Comprehensive bioinformatics analysis identified 243 resistance gene analog (RGA) sequences, comprising 6 classes of RGAs. Domain and conserved motif predictions of clusters were performed to analyze the architectural diversity. Phylogenetic analysis of deduced amino acid sequences revealed that coconut NBS-LRR type RGAs were classified into distinct groups based on the presence of TIR or CC motifs in the N-terminal regions. Furthermore, qRT-PCR analysis validated the expression of randomly selected NBS-LRR type RGAs. The results of this study provide a sequence resource for development of RGA-tagged markers in coconut, which would aid mapping of disease-resistant candidate genes. In addition, we hope that this study will provide a genomic framework for isolation of additional RGAs in coconut via comparative genomics and also contribute to the deciphering of mode of evolution of RGAs in Arecaceae.
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    Maintenance of embryogenic potential of calli derived from embryonic shoot of West Coast Tall cv. of coconut (Cocos nucifera L.)
    (2015) Bhavyashree, U.; Lakshmi Jayaraj, K.; Rachana, K.E.; Muralikrishna, K.S; Sajini, K.K.; Rajesh, M.K; Anitha Karun
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    Maintenance of embryogenic potential of calli derived from embryonic shoot of West Coast Tall cv. of coconut(Cocos nucifera L.)
    (2015-08) Rachana, K.E.; Muralikrishna, K.S.; Sajini, K.K.; Rajesh, M.K.; Anitha Karun
    Maintenance of embryogenic potential of calli is important as the totipotency is often lost in a short time in vitro. This caters to the need for year round availability of somatic embryos in a regenerable state. In the present study, 14 media combinations, with either 2,4-D or picloram as auxin source, were tested for maintaining embryogenic calli obtained from embryonic shoot explants of coconut. Irrespective of type and concentration of auxins, callusing was observed in all the media combinations. However, high dose of 2,4-D (above 74.6 μM) in the initial medium resulted in intense browning and lesser percentage of callusing. Embryogenic nature of calli could be maintained to a maximum of 21 weeks in medium supplemented with 2,4-D (74.6 μM) and subsequent culturing into higher concentration of 2,4-D (90.4 μM). Gene expression studies carried out using qRT-PCR revealed that genes such as ECP, GST, LEAFY and WUS were highly expressed in long term embryogenic calli (21 week old) and genes such as SERK, GLP, WRKY and PKL in initial embryogenic calli (21 days old). The study concludes that coconut plumular calli could be maintained for longer periods without compromising on the embryogenic potential of the calli.
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    Molecular Identification of Entomopathogenic Nematode Isolate and its Virulence to White Grub, Leucopholis burmeisteri (Coleoptera: Scarabaeidae)
    (2016) Rajkumar; Rachana, K.E.; Rajesh, M.K.; sabana, A.A.; Nagaraja, N.R; Shahin, S.; Subaharan, K.
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
    Production and supply of quality planting material is significant to coconut cultivation but is one of the major constraints in coconut productivity. Rapid multiplication of coconut through in vitro techniques, therefore, is of paramount importance. Although somatic embryogenesis in coconut is a promising technique that will allow for the mass production of high quality palms, coconut is highly recalcitrant to in vitro culture. In order to overcome the bottlenecks in coconut somatic embryogenesis and to develop a repeatable protocol, it is imperative to understand, identify, and characterize molecular events involved in coconut somatic embryogenesis pathway. Transcriptome analysis (RNA-Seq) of coconut embryogenic calli, derived from plumular explants of West Coast Tall cultivar, was undertaken on an Illumina HiSeq 2000 platform. After de novo transcriptome assembly and functional annotation, we have obtained 40,367 transcripts which showed significant BLASTx matches with similarity greater than 40 % and E value of ≤10−5. Fourteen genes known to be involved in somatic embryogenesis were identified. Quantitative real-time PCR (qRT-PCR) analyses of these 14 genes were carried in six developmental stages. The result showed that CLV was upregulated in the initial stage of callogenesis. Transcripts GLP, GST, PKL, WUS, and WRKY were expressed more in somatic embryo stage. The expression of SERK, MAPK, AP2, SAUR, ECP, AGP, LEA, and ANTwere higher in the embryogenic callus stage compared to initial culture and somatic embryo stages. This study provides the first insights into the gene expression patterns during somatic embryogenesis in coconut.
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    Potential of start codon targeted (SCoT) markers for assessment of genetic diversity of arecanut (Areca catechu L.)
    (2016-09) Rajesh, M.K.; sabana, A.A.; Rachana, K.E.; Ananda, K.S.; Anitha Karun