Akhtar J. Khan

A divergent isolate of Tomato yellow leaf curl virus from Oman with an associated DNAβ satellite: an evolutionary link between Asian and the Middle Eastern virus–satellite complexes

Tomato is cultivated in the coastal region of Al-Batinah, in the Sultanate of Oman, during the winter season, to meet the high demand for fresh produce in the domestic market. In order to identify the causal agent of a widespread disease associated with infestations of the whitefly Bemisia tabaci (Genn.) leaves were collected from tomato plants showing symptoms characteristic of the disease in Al-Batinah during 2004 and 2005. Total nucleic acids were isolated from the tomato leaves and used as the template for Φ29 DNA polymerase amplification of begomoviral circular DNA. Putative full unit length begomoviral DNA multimers were digested with Nco I and cloned into the plasmid vector pGEM7Zf+. The complete nucleotide (nt) sequence was determined as 2,765 bases, indicative of a monopartite begomoviral genome. A comparison of the genome sequence for the seven field isolates examined, indicated that they shared 99% nt identity. The virus from Oman was most closely related to TYLCV-IR at 91% nt identity, a monopartite begomoviral species described previously from Iran. Based on the guidelines of the ICTV the Oman isolate has been designated TYLCV-Om and is considered an isolate of TYLCV-IR. A satellite DNA (satDNA β), was amplified by polymerase chain reaction using degenerate primers and cloned, and the DNA sequence was determined. Analysis of the complete nt sequence of 1,371 bases indicated that the satDNA shared 88.5% similarity with its closest relatives, which are DNAβ molecules from tomato in Pakistan. This is the first report of a satDNA β associated with the TYLCV species. The TYLCV-Om and associated satDNA, thus represent a begomovirus-complex at the Asian-Middle East crossroads that quiet uniquely share geographical and genetic hallmarks of both.

Viscoelastic properties of pectin-co-solute mixtures at iso-free-volume states.

Small-deformation oscillatory measurements were performed on pectin-sucrose-glucose syrup systems at a total level of solids of 81%, with the polysaccharide content being fixed at levels of industrial use (1%). The experimental temperature range was between 50 and - 50 degrees C. Analysis of the temperature dependence of viscoelastic processes by the equation of Williams, Landel, and Ferry provides values of fractional free volume for the temperatures covering the glass transition region. The shift factors used in the conversion of mechanical spectra into master curves were normalised at suitably different temperatures so that their temperature dependence becomes coincident. The treatment implies an iso-free-volume state and relates to changes in the monomeric friction coefficient with increasing levels of intermolecular interactions in the mixture. A free-volume related glass transition temperature was defined and manipulated markedly by introducing pectin of variable degrees of esterification to the sucrose-glucose syrup system.

Complete Nucleotide Sequence of Watermelon Chlorotic Stunt Virus Originating from Oman

Watermelon chlorotic stunt virus (WmCSV) is a bipartite begomovirus (genus Begomovirus, family Geminiviridae) that causes economic losses to cucurbits, particularly watermelon, across the Middle East and North Africa. Recently squash (Cucurbita moschata) grown in an experimental field in Oman was found to display symptoms such as leaf curling, yellowing and stunting, typical of a begomovirus infection. Sequence analysis of the virus isolated from squash showed 97.6–99.9% nucleotide sequence identity to previously described WmCSV isolates for the DNA A component and 93–98% identity for the DNA B component. Agrobacterium-mediated inoculation to Nicotiana benthamiana resulted in the development of symptoms fifteen days post inoculation. This is the first bipartite begomovirus identified in Oman. Overall the Oman isolate showed the highest levels of sequence identity to a WmCSV isolate originating from Iran, which was confirmed by phylogenetic analysis. This suggests that WmCSV present in Oman has been introduced from Iran. The significance of this finding is discussed.

Oman: a case for a sink of begomoviruses of geographically diverse origins

Oman is a trading nation and intensive agriculture is only a recent phenomenon. Exotic geminiviruses have recently emerged as a constraint to horticultural crops, and can be traced to trade and human migration. Greater phytosanitary precautions need to be implemented to limit future problems and prevent their outward spread.

Molecular Characterization of the 16S rRNA Gene of Phytoplasmas Detected in Two Leafhopper Species Associated with Alfalfa Plants Infected with Witches' Broom in Oman

Two leafhopper species, Austroagallia avicula and Empoasca sp., were consistently found in alfalfa fields infected with witches’ broom phytoplasma (OmanAlfWB) in the Al-Batinah, Dakhliya, North and South Sharqiya, Muscat, and Al-Bureimi regions of the Sultanate of Oman. Phytoplasmas from both leafhoppers were detected by specific polymerase chain reaction (PCR) amplification of the 16S rRNA gene and the spacer region in direct PCR using P1/P7 primer pairs. Comparative RFLP profiles of the amplified rRNA gene and the spacer region from leafhopper phytoplasmas and from 20 phytoplasma controls yielded patterns referable to phytoplasmas belonging to the peanut witches’ broom group (16SrII group). In particular, extensive RFLP analyses with the endonucleases HpaII, Tru9I, Tsp509I, and RsaI indicated that the phytoplasmas in A. avicula and Empoasca sp. were identical but showed some differences from OmanAlfWB; however, RFLP patterns obtained with TaqI showed the OmanAlfWB and the phytoplasmas from the two leafhoppers to be identical. Direct PCR products amplified from phytoplasma leafhopper DNA using the P1/P7 primer pair were cloned and sequenced yielding 1758 bp and 1755 bp products from A. avicula and Empoasca sp. respectively; the homology of these sequences with OmanAlfWB and papaya yellow crinkle phytoplasmas was more than 98%. A phylogenetic tree based on the 16S rRNA gene and spacer region sequences from 44 phytoplasmas revealed that the phytoplasmas from the leafhoppers clustered with OmanAlfWB, papaya yellow crinkle, and gerbera phyllody phytoplasmas, all belonging to 16SrII group, but were distinct from lime witches’ broom phytoplasma, the most commonly found phytoplasma in the Sultanate of Oman.

Introduction of East African cassava mosaic Zanzibar virus to Oman harks back to ''Zanzibar, the capital of Oman''

Cassava mosaic disease (CMD) is the most devastating disease of the subsistence crop cassava (Manihot esculenta) across Africa and the Indian subcontinent. The disease is caused by viruses of the genus Begomovirus (family Geminiviridae)—seven species have been identified so far. The Sultanate of Oman is unusual among countries in Arabia in growing cassava on a small scale for local consumption. During a recent survey in A’Seeb wilayat of Muscat governorate, Oman, cassava plants were identified with symptoms typical of CMD. A begomovirus, East African cassava mosaic Zanzibar virus (EACMZV), was isolated from symptomatic plants. This virus was previously only known to occur in Zanzibar and Kenya. During the 19th Century, Zanzibar was governed by Oman and was so important that the Sultan of Oman moved his capital there from Muscat. After a period of colonial rule, the governing Arab elite was overthrown, following independence in the 1960s, and many expatriate Omanis returned to their homeland. Having gained a liking for the local Zanzibar cuisine, it appears that returning Omanis did not wish to do without dishes made from one particular favorite, cassava. Consequently, they carried planting material back to Oman for cultivation in their kitchen gardens. The evidence suggests that this material harbored EACMZV. Recently, Oman has been shown to be a nexus for geminiviruses and their associated satellites from diverse geographic origins. With their propensity to recombine, a major mechanism for evolution of geminiviruses, and the fact that Oman (and several other Arabian countries) is a major hub for trade and travel by air and sea, the possibility of onward spread is worrying.

Engineering crops for resistance to geminiviruses

Abstract Geminiviruses are a large family of single-stranded DNA viruses that cause significant losses in economically important crops worldwide. The majority of these diseases are caused by geminiviruses that are whitefly-transmitted and are placed in the genus Begomovirus. They often exist in disease complexes and undergo high levels of recombination and mutation, allowing them to adapt rapidly to new hosts and new environments. Thus, an effective resistance strategy must be general in character and able to target multiple viruses. Several protein-based and RNA-based transgenic resistance approaches have been exploited and remarkable progress has been made in this direction. Though most of these approaches have been tested only in model plants, they provide a basis of resistance mechanisms and can be adopted in crop plants. This chapter covers the genetic engineering approaches based on pathogen-derived resistance (PDR) and some recent alternatives to PDR, including the use of DNA-binding proteins, peptide aptamers, GroEL homologs, and geminivirus-inducible toxic proteins. These alternatives are collectively placed under the umbrella of non-pathogen-derived resistance (NPDR). The drawbacks of some of these approaches and possible strategies to overcome these problems are also discussed.

Evaluation of indigenous Omani legumes for their nutritional quality, phytochemical composition and antioxidant properties

Four indigenous Omani legumes (faba bean, cowpeas, chickpeas and lentils), collected from three different regions of Oman, were evaluated for their proximate composition, phytochemical contents and antioxidant properties. The proximate composition varied significantly. Regional variability however, did not affect the proximate composition, except crude protein content of cowpea and chickpea. The average values for moisture, protein, fat, fibre and ash ranged from 8.5% to 9.6%, 22.5% to 23.9%, 1.1% to 1.8%, 4.5% to 7.6% and 3.1 to 3.5% respectively. Both variety and regional variability affected the phytochemical contents. The average total phenol contents, tannins, and flavonoids ranged from 15.1 to 131.8 mg GAE/100 g, 13.2 to 100.8 mg CAE/100 g and 1.7 to 19.9 mg CAE/100g respectively, whereas the oxalates and saponins contents ranged from 56.1 to 197.8 and 2,699.1 to 3,598.1 mg/100 g respectively. A significant correlation was observed between the total phenol contents and the reducing power of legumes.

A Study on Germination Rate, Dry Matter Weight and Amylase Activity of Medicago sativa L. (alfalfa) under Induced NaCl Stress

Different Omani alfalfa cultivars were exposed to NaCl concentration in the range of 4, 6, 8 and 10 dSmO¾1 to measure germination, vegetative growth and amylase activity. The results showed moderate tolerance of alfalfa against salt stress. Alfalfa genotypes A215 and A29 appeared to be more tolerant than all other 8 genotypes. Dry matter stress index (DSMI) were calculated which varied from 0.2 to 1.2 with a high index value for 8 dSmO¾1 than the other NaCl dilutions. The amylase activity was found to be directly proportional to the salt stress. Thus the results showed that alfalfa is moderately tolerant to salinity especially A29 and A215 genotypes, which can be recommended for cultivation in semi arid regions.