Molecular characterization of turnip mosaic potyvirus (TuMV) infecting radish (Raphanus sativus L.)

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dc.contributor.advisorBhardwaj, S. V.
dc.contributor.authorParmar, Nehanjali
dc.date.accessioned2017-06-03T11:18:22Z
dc.date.available2017-06-03T11:18:22Z
dc.date.issued2012
dc.description.abstractRadish (Raphanus sativusL.) is an edible root crop of family Brassicaceaewhich is grown worldwide especially in Asia. Turnip mosaic potyvirus(TuMV; genus: Potyvirus, family: Potyviridae) is considered as one of the most important viruses in the world that infect field-grown vegetables and displays a large natural as well as experimental host range. TuMV was found to be prevalent in different regions of India. In all, nineisolates were collected on the basis of symptoms from areas comprising Himachal Pradesh (Mandi, Solan, Shimla and Kinnaur), Chandigarh, Punjab (Ludhiana), Haryana (Karnal), New Delhi (West Patel Nagar) and Rajasthan (Bharatpur). During serological detection, ELISA tests were conducted. All seven isolates except from New Delhi and Rajasthan reacted positively with monoclonal antibodies against TuMV. These studies were further confirmed through RT-PCR using specific primers for coat protein (CP) gene as a molecular detection procedure. A cDNA of approximately 1000 bp was amplified from all the seven TuMV Indian isolates. The RTPCR products were subsequently cloned and sequenced. The sequenced product of all the seven TuMV Indian isolates (IND1-IND7) was approximately 986 bp whichcomprised of 54 bp of the 3´ end of nuclear inclusion b (NIb) gene, the whole CP gene and 65 bp of the 3´ untranslated (UTR) region. CP gene of all the seven Indian isolates of TuMV was 867 bp long, encoding 288 amino acid residues which were submitted to NCBI. Accession numbers JQ246074 to JQ246080 and AFE55681to AFE55687 were assigned to seven TuMV Indian isolates IND1 to IND7 CP gene nucleotide and amino acid sequences, respectively. Conserved motif DAG (Asp-Ala-Gly) and NAG (Asn-Ala-Gly), which has beenreported to be important for potyvirustransmission by aphids, were found at positions 6-8 and 56-58 aa residues, respectively in the seven TuMV Indian isolates CP gene sequences. Another conserved motif, GDD (Gly-Asp-Asp) which has been identified as a hallmark of RNA dependent RNA polymerase was observed at 158-160 aa position in all the seven CP gene sequences of Indian isolates of TuMV. Percent homology of CP gene of seven Indian isolates among themselves and with other TuMV isolates retrieved from NCBI database was within the range of 87-99% and 92-100% at nucleotide and amino acid level, respectively. Phylogenetic analysis based upon nucleotide and amino acid sequences using UPGMA, NJ, MP and ME methods inferred classification of seven TuMV Indian isolates, tentatively into basalBR group, due to its occurrence nearest to those isolates of TuMV which have been earlier classified to this group. Conserved domain for TuMV CP gene was observed at 51-287aa position in all the seven test Indian isolates. Computational predictions for various restriction enzymes were also carried out. Alpha helixconsensus secondary structure was predicted and found to dominate in all the seven protein sequences of CP gene of Indian isolates of TuMV.en_US
dc.identifier.urihttp://krishikosh.egranth.ac.in/handle/1/5810017177
dc.language.isoenen_US
dc.publisherYSPUen_US
dc.subBiotechnology
dc.subjectTurnip, Mosaic potyvirus, Radishen_US
dc.these.typePh.D
dc.titleMolecular characterization of turnip mosaic potyvirus (TuMV) infecting radish (Raphanus sativus L.)en_US
dc.typeThesisen_US
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