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Kofoid and White) Chitwood in Tomato MOLECULAR CHARACTERIZATION AND ALLELOPATHIC MANAGEMENT OF Meloidogyne incognita (KOFOID AND WHITE) CHITWOOD IN TOMATO BY ISHRAT NAZ A dissertation submitted to The University of Agriculture, Peshawar in partial fulfillment of the requirement for the Degree of DOCTOR OF PHILOSOPHY IN AGRICULTURE (PLANT PATHOLOGY) DEPARTMENT OF PLANT PATHOLOGY FACULTY OF CROP PROTECTION SCIENCES THE UNIVERSITY OF AGRICULTURE, PESHAWAR, KHYBER PAKHTUNKHWA, PAKISTAN FEBRUARY, 2013 MOLECULAR CHARACTERIZATION AND ALLELOPATHIC MANAGEMENT OF Meloidogyne incognita (KOFOID AND WHITE) CHITWOOD IN TOMATO BY ISHRAT NAZ A dissertation submitted to The University of Agriculture, Peshawar in partial fulfillment of the requirement for the Degree of DOCTOR OF PHILOSOPHY IN AGRICULTURE (PLANT PATHOLOGY) Approved by: ____________________________ Chairman Supervisory Committee Prof. Dr. Saifullah ____________________________ Co-Supervisor Prof. Dr. M. Rafiullah Khan (Director Phytopharmaceutical & Nutraceutical Research Laboratory (PNRL), University of Peshawar ____________________________ Member Prof. Dr. Musharaf Ahmad ____________________________ Member Prof. Dr. Iftikhar Hussain Khalil ____________________________ Chairman & Convener Board of Studies Prof. Dr. Saifullah ____________________________ Dean, Faculty of Crop Protection Sciences Prof. Dr. Mian Inayatullah ____________________________ Director Advanced Studies and Research Prof. Dr. Farhatullah DEPARTMENT OF PLANT PATHOLOGY FACULTY OF CROP PROTECTION SCIENCES THE UNIVERSITY OF AGRICULTURE, PESHAWAR, KHYBER PAKHTUNKHWA, PAKISTAN FEBRUARY, 2013 MOLECULAR CHARACTERIZATION AND ALLELOPATHIC MANAGEMENT OF Meloidogyne incognita (KOFOID AND WHITE) CHITWOOD IN TOMATO By ISHRAT NAZ THESIS APPROVED BY: EXTERNAL EXAMINER: _______________________ MOLECULAR CHARACTERIZATION AND ALLELOPATHIC MANAGEMENT OF Meloidogyne incognita (KOFOID AND WHITE) CHITWOOD IN TOMATO BY ISHRAT NAZ THESIS APPROVED BY: EXTERNAL EXAMINER: _______________________ ACKNOWLEDGEMENTS Allah Almighty bestowed upon me the capability to complete this task and I express my absolute gratitude to Him. I take pride in acknowledging my assiduous and humble supervisor Prof. Dr. Saifullah, Chairman Department of Plant Pathology, The University of Agriculture, Peshawar, for his cooperation, valuable suggestions, constructive criticism and providing me all facilities during the course of this research work. I express my thanks to Dr. Musharaf Ahmad, Department of Plant Pathology, The University of Agriculture, Peshawar for technically reviewing the manuscript and for agreeing to be on my advisory committee. I am highly grateful to my affectionate co-supervisor, Prof. Dr. M. Rafiullah Khan, Director Phytopharmaceutical and Neutraceutical Research Laboratory (PNRL), Institute of Chemical Sciences, University of Peshawar for providing me all the lab facilities, technical and scholarly guidance and helpful discussions during my three years period at the PNRL. I highly acknowledge the contribution of my co-supervisor and his team particularly in the NMR spectroscopy and structure elucidation of phytochemical compounds. I am pleased to acknowledge my foreign supervisor, Dr. Vivian Carol Blok, Principle Investigator in Plant Pathology and Nematology, Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Scotland, UK, for providing me all the lab facilities, technical guidance and for treating me like her own family member during my six months stay at her institute. I am grateful to Dr. Juan. E. Palomares-Rius for providing me help and support in molecular work, sequencing and Dr. Jim for his valuable suggestions in statistical analysis. My heartiest thanks are extended to Dr. Sean Conner and Dr. Alexander at the JHI for helpful discussions and conduction of GC/MS analysis. I am highly indebted to the Higher Education Commission (HEC) of Pakistan, for financial support through indigenous (5000 PhD) fellowship program and for a visit to the James Hutton Institute under the International Research Support Initiative program (IRSIP) for six months. I am thankful to Mr. Sardar Ali, Assistant Professor, Department of Agriculture, Haripur University who stood as my PhD scholarship guarantor to the HEC. I am thankful to my parents, brothers, sisters and all those who assisted me in any way in the completion of this study. ISHRAT NAZ i MOLECULAR CHARACTERIZATION AND ALLELOPATHIC MANAGEMENT OF Meloidogyne incognita (KOFOID AND WHITE) CHITWOOD IN TOMATO Ishrat Naz and Saifullah Department of Plant Pathology, Faculty of Crop Protection Sciences, The University of Agriculture, Peshawar, Pakistan February, 2013 ABSTARCT Root knot nematodes (Meloidogyne spp.) are important obligate parasites attacking many vegetables, fruits and ornamentals worldwide. Nematode populations from thirty commercial production fields of tomato of Malakand division in the Khyber Pakhtunkhwa province of Pakistan showed wide variations within and among species using the perineal pattern morphology and molecular tools. Three species viz., Meloidogyne incognita, Meloidogyne javanica and Meolidogyne areanaria were found either alone or co-infesting tomato roots (80.3%) and soil (87.3%). Disease was prevalent 100% with an average of 52.0% in the study area. More than one root knot nematode species were found together in the same plant roots; however, Meloidogyne javanica, occurred with the highest frequency (70.33%). A comprehensive molecular characterization of root knot nematode (RKN) populations belonging to ten localities of the Khyber Pakhtunkhwa province was carried out at the James Hutton Institute (JHI), Scotland, UK, employing the ribosomal DNA (rDNA) primers (D2A/D3B and 194/195) and species-specific SCAR primers i.e. Finc/Rinc (M. incognita), Fjav/Rjav (M. javanica) and Far/Rar (M. arenaria). Regardless of the species, the D2-D3 of 28S of rDNA gene and ITS2 region between 5S and 18S rDNA genes amplified the expected bands of approximately 750 bp and 720 bp, respectively common to all the populations tested. The SCAR primers generated species-specific bands of 1200, 670 and 420 bp in M. incognita, M. javanica and M. arenaria, respectively. Meloidogyne spp., were discriminated using mtDNA as an additional genetic marker. The C2F3/1108 primer pair amplified the COII/lrRNA region of mtDNA and produced a 1.7 Kb size band common to all the three species of RKNs except Meloidogyne chitwoodi (520 bp), Meloidogyne fallax (520 bp) and Meloidogyne enterolobii (750 bp), employed as negative control. Restriction digestion of the mtDNA-PCR product (1.7 Kb) with different 4-bp (Hinf 1, Taq 1, Mbo1, Alu 1) and 6-bp (Eco R1) restriction enzymes, amplified characteristic diagnostic patterns in each Meloidogyne spp., except the Taq1 enzyme which did not cleave the mtDNA-PCR product. The Hinf I generated three-banded diagnostic fragments (1700, 1300 and 400 bp) in M. incognita. The Mbo1 (viz., 1700, 1300, 1000, 720 and 520 bp) and Eco R1 (1700, 1200 and 520 bp) generated a five and three banded- pattern in all RKN populations respectively, whereas the Alu 1 enzyme produced frequent cuts in the mitochondrial genomes of all the three tested species. Genetic diversity among and within Meloidogyne species and populations were determined using the randomly amplified polymorphic (RAPD) DNA method. Three RAPD primers SC 10-30, OPG-13 and OPG-19 grouped the three mitotic species (Meloidogyne incognita, M. javanica, M. arenaria), in distinct separate cluster than the other species (M. chitwoodi, M. fallax, M. hapla and M. enterolobii) utilized as positive control. Meloidogyne javanica and M. arenaria were grouped more closely (50 %) than M. incognita (42.8 %). DNA sequencing ii of the 28S rDNA gene fragment of selected eight nematode genotypes (T1, W2, M3, J3, F2, J4, R2 and H1) belonging to three species (M. javanica, M. incognita, M. arenaria) representing the Khyber Pakhtunkhwa province were deposited to the Genbank with accession numbers (JQ317912-19). The intra-specific variability ranged from 3 nucleotides (0.4% differences) (between J3 and T1) to 27 nucleotides (4.2 % differences) (between W2, M3 and J3) for M. javanica (636 bp alignment). Sequence analysis of D2- D3 expansion segment of 28S rDNA did not discriminate the three closely related Meloidogyne spp. Juveniles and eggs of M. incognita were challenged in a series of in vitro experiments to plant extracts and pure compounds from a medicinal herb and annual weed, Fumaria parviflora Lam. The roots and stem crude extracts of the above plant showed the highest hatch inhibition (74.42 and 64.33%) and juvenile mortality (78.83 and 64.33%) against M. incognita at 12.5 mg mL-1. In in vitro experiments, the n-hexane extracts of the roots and stems showed the highest hatch inhibition (100%) and J2s mortality (100%). Hatch inhibition and J2s mortality were directly related to exposure time. The area under cumulative percentage hatch inhibition (AUCPHI) and mortality (AUCPM) were both augmented with increase in concentration. Silica gel column chromatography of the n- hexane and methanol fractions afforded eleven (F1 to F11) and seven (FM2.1 to FM2.7) sub-fractions, respectively. The F3 (98.77 %), F4 (90.25%) and FM2.1 (99.75%) exhibited the highest hatch inhibition at a concentration of 400 µg mL.-1 The J2s mortality for F3, F11, F4 and FM2.1 were 95.00, 88.25, 86.0 and 100%, respectively. The phytochemical screening of F. parviflora revealed the presence of seven classes of bioactive compounds (viz., alkaloids, flavonoids, glycosides, tannins,
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