Browsing by Author "Shafeeq Rahman"

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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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    Characterization of Annur and Bedakam Ecotypes of Coconut from Kerala State, India, Using Microsatellite Markers
    (2014-02) Rajesh, M.K.; Samsudeen, K.; Rejusha, P.; Manjula, C.; Shafeeq Rahman; Anitha Karun
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    Characterization of gibberellin 2-oxidase isoforms in coconut (Cocos nucifera L.)
    (2015-12) Shafeeq Rahman; Gangaraj, K.P.; Amal Vasu; Anitha Karun; Rajesh, M.K.
    Gibberellins (GAs) are plant hormones that are essential for many developmental processes in plants, including seed germination, stem elongation, leaf expansion, trichome development, pollen maturation and the induction of flowering. Gibberellin 2-oxidase (GA2-ox) regulates plant growth by inactivating endogenous bioactive GAs through 2β-hydroxylation. There is no information about GA2-ox encoding genes or their functions in coconut. In this study, we have identified 10 transcripts encoding different isoforms of GA2-ox from coconut leaf transcriptome data. Sequence comparison and phylogenetic analysis revealed that these 10 transcripts represented different types of GA2-ox. The secondary structure, three dimensional structure and active sites of these 10 isoforms were predicted. Docking studies of different active GAs with these isoforms was also carried out.
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    Characterization of Kuttiyadi ecotype of coconut (Cocos nucifera L.) using morphological and microsatellite markers
    (2014-12) Manjula, C.; Samsudeen, K.; Shafeeq Rahman; Rajesh, M.K.
    West Coast Tall (WCT) is the most popular coconut cultivar grown by the farmers in Kerala, which occupies over 95 per cent of the area under coconut. The long history of coconut cultivation throughout Kerala state has resulted in the development of many ecotypes of WCT. The present work compares the similarity/diversity of the morphological and molecular characteristics of the Kuttiyadi ecotype growing in the hilly, midland region of Kozhikode District, Kerala with those of the WCT cultivar of the coastal region of Kasaragod District, Kerala, using vegetative, reproductive and fruit component characters and microsatellite markers. Geographically, these two locations show a wide range of variation for soil and climactic factors. The vegetative, reproductive and fruit component characteristics and microsatellite markers showed wide variations between selected WCT palms from Kasaragod and Kuttiyadi. The similarity index based on Dice’s coefficient, obtained after pair-wise comparison of Kuttiyadi and WCT samples with 15 SSR markers, revealed that the percentage similarity varied from the coefficient range 0.20 to 0.97 between the WCT and Kuttiyadi palms. UPGMA clustering clearly distinguished the two populations with WCT and Kuttiyadi forming separate clusters. STRUCTURE analysis was also carried out, which also showed that the two populations studied were distinct
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    Development of EST‑SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.)
    (2020) Preeti P; Shafeeq Rahman; Naganeeswaran, S.; Sabana, A.A.; Gangaraj, K.P.; Jerard, B.A; Niral, V.; Rajesh, M.K.
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    Estimation of out-crossing rate in West Coast Tall cultivar in coconut using microsatellite markers
    (2012-11) Rajesh, M.K.; Rijith, J.; Shafeeq Rahman; Ramya, K.; Sajini, K.K.; Anitha Karun
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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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    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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    Morphological and molecular characterization of Kuttiyadi ecotype of coconut (Cocos nucifera L.)
    (2012-11) Manjula, C.; Samsudeen, K.; Shafeeq Rahman; Rajesh, M.K.
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    Scope of novel and rare bulbiferous coconut palms (Cocos nucifera L.)
    (2013) Jerard, B.A.; Rajesh, M.K.; Elain, S.A.; Sajini, K.K.; Shafeeq Rahman; Fayas, T.P.; Anitha Karun
    A naturally occurring, rare bulbiferous coconut palm was identified at the Central Plantation Crops Research Institute, Regional Station, Vittal in Karnataka State, India, among West Coast Tall population. The palm produces only bulbil shoots in leaf axils in place of normal inflorescence. The identified palm happened to be twins in which one member was more vigorous than the other, but both of them produced only bulbil shoots instead of floral parts. Morphological and molecular studies on these palms revealed the main palm and their bulbil progenies are genetically uniform. The genetic uniformity of the twin mother palms and their bulbil progenies was confirmed through microsatellite analysis using 10 polymorphic SSR primer pairs specific to coconut and has been well demonstrated to differentiate coconut cultivars. The primary and secondary bulbil shoots were found to be capable of growing into independent plants making it possible to use them as propagules to develop a homogeneous clonal population hitherto unavailable in coconut. The bulbils showed axillary growth in 6–12th leaf axil which further again develop as secondary bulbils indicating the complete vegetative state of the palm. Comparison of shoot apices of a normal seedling with bulbil shoot revealed variation in cell growth pattern. Conservation of bulbiferous palms as a unique genetic resource needs to be taken up to utilize these rare sources for future breeding programmes, provided their seed-fertility can be restored.