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3. Morphological Characterization and Assessment of Genetic Variability of Tylenchulus semipenetrans Populations from Southern Iran

Author

Rumiani Mohammad, Zouhar Miloslav, Karegar Akbar, Hamzehzarghani Habiballah, Tahmasebi Ahmad, and Rashidifard Milad

Subjects
citrus nematodes, coi, d2-d3 of 28s rdna, haplotype, its rdna, morphometric, sequencing, Biology (General), QH301-705.5
Abstract

Molecular data should be combined with morphological data to enhance the reliability of phylogenetic and diagnostic studies on nematodes. In this study, the citrus nematode Tylenchulus semipenetrans collected from citrus orchards in different localities in Fars province, southern Iran, was characterized using the partial sequencing of ITS rDNA, D2-D3 of 28S rDNA and COI mtDNA genes. We also morphometrically characterized the second-stage juveniles (J2) and male specimens. The results showed that T. semipenetrans is a genetically homogeneous species, and only minor nucleotide differences were detected among the populations. Phylogenetic studies demonstrated that most Iranian populations were grouped together, and there were no differences among the populations. However, sequence alignment of ITS, D2-D3 of 28S rDNA and COI mtDNA revealed 17, 24, and 16 single nucleotide variations (SNVs) and 11, 12, and 11 single-nucleotide polymorphisms (SNPs), respectively. The results of the morphometric analysis showed slight morphometric differences among and within the populations of T. semipenetrans. The morphometric differences among citrus nematode populations and the haplotype topology of the populations did not correlate with their geographical origin and host type. The constructed phylogenetic trees showed a close relationship between Tylenchulus and Trophotylenchulus. In addition, the phylogenetic relationships showed that T. musicola is the closest taxon to T. semipenetrans. The results of this study provide a better understanding of the diversity of T. semipenetrans populations and may shed light on the genetic variation of citrus nematode.

Published
2024
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17. Morphological Characterization and Assessment of Genetic Variability of Tylenchulus semipenetransPopulations from Southern Iran

Author

Rumiani, Mohammad, Zouhar, Miloslav, Karegar, Akbar, Hamzehzarghani, Habiballah, Tahmasebi, Ahmad, and Rashidifard, Milad

Abstract

Molecular data should be combined with morphological data to enhance the reliability of phylogenetic and diagnostic studies on nematodes. In this study, the citrus nematode Tylenchulus semipenetranscollected from citrus orchards in different localities in Fars province, southern Iran, was characterized using the partial sequencing of ITS rDNA, D2-D3 of 28S rDNA and COI mtDNA genes. We also morphometrically characterized the second-stage juveniles (J2) and male specimens. The results showed that T. semipenetransis a genetically homogeneous species, and only minor nucleotide differences were detected among the populations. Phylogenetic studies demonstrated that most Iranian populations were grouped together, and there were no differences among the populations. However, sequence alignment of ITS, D2-D3 of 28S rDNA and COI mtDNA revealed 17, 24, and 16 single nucleotide variations (SNVs) and 11, 12, and 11 single-nucleotide polymorphisms (SNPs), respectively. The results of the morphometric analysis showed slight morphometric differences among and within the populations of T. semipenetrans. The morphometric differences among citrus nematode populations and the haplotype topology of the populations did not correlate with their geographical origin and host type. The constructed phylogenetic trees showed a close relationship between Tylenchulusand Trophotylenchulus. In addition, the phylogenetic relationships showed that T. musicolais the closest taxon to T. semipenetrans.The results of this study provide a better understanding of the diversity of T. semipenetranspopulations and may shed light on the genetic variation of citrus nematode.

Published
2024
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19. Potato-infecting Ralstonia solanacearum strains in Iran expand knowledge on the global diversity of brown rot ecotype of the pathogen

Author

Sedighian, Nasim, Taghavi, S. Mohsen, Hamzehzarghani, Habiballah, van der Wolf, Jan M., Wicker, Emmanuel, Osdaghi, Ebrahim, Sedighian, Nasim, Taghavi, S. Mohsen, Hamzehzarghani, Habiballah, van der Wolf, Jan M., Wicker, Emmanuel, and Osdaghi, Ebrahim

Abstract

Bacterial wilt and brown rot disease caused by Ralstonia solanacearum species complex (RSSC) is one of the major constraints of potato (Solanum tuberosum) production around the globe. During 2017 to 2018, an extensive field survey was conducted in six potato-growing provinces of Iran to monitor the status of bacterial wilt disease. Pathogenicity and host range assays using 59 bacterial strains isolated in Iran showed that they were pathogenic on eggplant, red nightshade, pepper, potato and tomato, while nonpathogenic on common bean, cowpea, cucumber, sunflower, zinnia and zucchini. PCR-based diagnosis revealed that the strains belong to the phylotype IIB/sequevar 1 (IIB/I) lineage of the RSSC. Furthermore, a five-gene multilocus sequence analysis and typing (egl, fliC, gyrB, mutS, and rplB) confirmed the phylogenetically near-homogeneous nature of the strains within IIB/I lineage. Four sequence types were identified among 58 IIB/1 strains isolated in Iran. Phylogenetically near-homogeneous nature of the strains in Iran raise questions about the mode of inoculum entry of the bacterial wilt pathogen into the country (one-time introduction versus multiple introductions), while the geographic origin of the Iranian R. solanacearum strains remains undetermined. Furthermore, sequence typing showed that there were shared alleles (haplotypes) and sequence types among the strains isolated in geographically distant areas in Iran, suggesting intranational transmission of the pathogen in the country.

Published
2020

22. Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Khojasteh, Moein, Taghavi, S. Mohsen, Khodaygan, Pejman, Hamzehzarghani, Habiballah, Chen, Gongyou, Bragard, Claude, Koebnik, Ralf, Osdaghi, Ebrahim, UCL - SST/ELI/ELIM - Applied Microbiology, Khojasteh, Moein, Taghavi, S. Mohsen, Khodaygan, Pejman, Hamzehzarghani, Habiballah, Chen, Gongyou, Bragard, Claude, Koebnik, Ralf, and Osdaghi, Ebrahim

Abstract

This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas tran

Published
2019

23. Numerical Taxonomy Helps Identification of Merliniidae and Telotylenchidae (Nematoda: Tylenchoidea) from Iran

Author

GHADERI, REZA, HAMZEHZARGHANI, HABIBALLAH, and KAREGAR, AKBAR

Subjects
principal component analysis, Pratylenchoides, correlation, Amplimerlinius, hierarchical cluster analysis
Abstract

Numerical taxonomy was used for identification and grouping of the genera, species, and populations in the families Merliniidae and Telotylenchidae. The variability of each of 44 morphometric characters was evaluated by calculation of the coefficient of variability (CV) and the ratio of extremes (max/min) in the range of 1,020 measured females. Also correlation and regression analyses were made between characters to find potential collinearities. Hierarchical cluster analysis (HCA) was used for (i) grouping 21 genera in the superfamily Dolichodoroidea based on literature data coded for states of 18 diagnostic characters, and (ii) for grouping Iranian populations belonging to selected genera. Furthermore, STEPDISC analysis was used for (i) grouping 11 genera of Merliniidae and Telotylenchidae based on the measurements of 35 characters from 1,007 Iranian female specimens, and (ii) grouping measured females of eight species of Amplimerlinius and Pratylenchoides. The multivariate data analysis approach showed robust enough to summarize relationship between morphometric characters and group genera, species, and populations of the nematodes and in particular help to identify the genera and species of Amplimerlinius and Pratylenchoides.

Published
2017

24. Çeşitli azot ve ekim oranları altında kanola-örtü bitkisi-yabancı ot sisteminin verim kaybının modellenmesi

Author

Hamzehzarghani, Habiballah, Kazemeini, Seyed-Abdolreza, and Edalat, Mohsen

Subjects
Verim komponentleri, Yield components, Nitrogen, Tahmin, Azot, Modeling, Yield loss, Kanola, Modelleme, Canola, Prediction, Verim kaybı
Abstract

Possible use of cereal cover crops as a sustainable alternative weed control option in canola fields through optimizing cover crop and its density in canola-weed-cover cropping tripartite systems was modeled using a gamma density function with four parameters. The effect of competition between main crop (canola), cover crop (wheat or barley) and weeds on canola yield was studied in an experiment conducted in 2012/2013. Each cover crop was sown in four seeding rates: 0, 25, 50 and 75 percent under two nitrogen rates of 75 and 150 kg ha-1 . Weed suppression measured as canola relative yield was associated with the increase of seeding rate of cover crop according to a modified gamma density function. Parameters alpha, kappa, eta and lambda summarized the effect of N application on yield response under no cover crop conditions, measure of treatment effect on the curve amplitude, the plant density at which crop yield maximizes and the curve slope at the right tail which was an indication of the treatment effect on the rate of yield reduction beyond the seeding rate that maximized the crop yield, respectively. Model diagnostics and agreement analysis showed that the modified gamma density function described the functional response of the main crop to seeding rate of the cover crop equally well across a variety of treatment effects. Response curve analysis showed that in both levels of nitrogen, canola yield was more responsive to barley as cover crop when compared to winter wheat. Kanola arazilerinde yabancı otlar ile mücadelede tahılların örtü bitkisi olarak kullanımları ve kullanım yoğunluğu dört parametreli gama yoğunluk fonksiyonu kullanılarak modellenmiştir. 2012/2013 yıllarında ana bitki (kanola), örtü bitkisi (buğday veya arpa) ve yabancı otların birbiri ile yarışının kanola verimi üzerine etkisi çalışılmıştır. Her bitki dört farklı ekim sıklığı (% 0, 25, 50 ve 75) ve iki farklı (75 ve 150 kg ha-1 azot) ile ekilmiştir. Gama yoğunluk fonksiyonu ile kanolanın veriminin örtü bitkisinin ekim sıklığına bağlı olması durumundan yararlanılarak yabancı ot baskılanması hesaplanmıştır. Alfa, kappa, eta ve lambda parametreleri sırasıyla örtü bitkisi olmadığı durumda azotun verime etkisini, eğri üzerinde uygulamanın etkisini, ana ürün veriminin maksimum olduğu bitki yoğunluğunu ve uygulamanın verim kaybına etkisini gösteren eğriyi özetlemektedir. Modelleme sonucunda gama yoğunluk fonksiyonu ana bitkinin ekim sıklığına tepkisini tanımlayabilmiştir. Çalışma sonuçları, tüm azot seviyelerinde kanola veriminin arpaya buğdaydan daha fazla tepki gösterdiğini ortaya çıkarmıştır.

Published
2016

28. Spread and colonization pattern of ‘CandidatusPhytoplasma aurantifolia’ in lime plants [Citrus aurantifolia(Christm.) Swingle] as revealed by real-time PCR assay

Author

Mazraie, Mohsen, Izadpanah, Keramatollah, Hamzehzarghani, Habiballah, Salehi, Mohammad, and Faghihi, Mohammad

Abstract

Lime witches’-broom (WBDL) is a devastating disease of Mexican lime trees in southern Iran.‘CandidatusPhytoplasma aurantifolia’ is associated with the disease. Understanding the pattern of colonization and spread of ‘Ca. P. aurantifolia’ within lime trees is critical for its accurate detection during the latent period of the disease. In the present study, the distribution pattern of the WBDL phytoplasma in graft inoculated lime seedlings was investigated under greenhouse conditions and its seasonal variation of concentration in symptomless lime trees was evaluated in an infected orchard using qPCR assay. Repeated sampling from various tissues of graft-inoculated lime seedlings was carried out at various times post-inoculation. In the field, leaf samples were taken from symptomless trees in an infected orchard in March, August and December. Our results showed that after entrance into the lime seedlings, ‘Ca. P. aurantifolia’ moved downward into the roots as well as upward into the apical leaves. The concentration of phytoplasma in apical leaves showed an initial high followed by a decrease before establishment of infection and subsequent symptom appearance. The spread of the phytoplasma from root to the aerial parts was rather slow. Severe witches’ broom symptoms appeared on the grafted branches 10 months after grafting. At this time, the highest phytoplasma DNA concentration was found in descending order in stems and leaves of witches’ brooms, crown, various parts of the root, and stem bark and apical leaves of the symptomless branches. Results of the field experiment revealed that concentration of ‘Ca. P. aurantifolia’ cells in infected trees was highest in August compared to that in December and March. Our result would be useful for rapid detection of WBDL phytoplasma during the latent period of the disease.

Published
2019
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29. Chemical control of downy brome, littleseed canarygrass and green foxtail in rapeseed in southern ıran

Author

Valaie, Niusha, Kazemeini, Seyed Abdolreza, and Hamzehzarghani, Habiballah

Subjects
Green foxtail, Downy brome, Littleseed canarygrass, Herbicide, Canola, Adjuvant
Abstract

In order to investigate the effect of herbicide and choice of adjuvant on three grass weed species; downy brome (Bromus tectorum), littleseed canarygrass (Phalaris minor) and green foxtail (Setaria viridis); a greenhouse study was conducted in a factorial experiment laid out in randomized complete block design. Treatments included herbicide at five levels (propaquizafop, fluazifop-p-butyl, cycloxydim, sethoxydim and quizalofop-p-ethyl) each applied at two concentrations and either with/without adjuvant (volck or citoweet). The performance of herbicides and adjuvants was evaluated by rating the effect of treatment on an ordinal scale in each experimental unit at 10 and 20 days after planting (DAP). The results showed that herbicide efficiency rating distributions were significantly different between two times (10 and 20 DPA). Application of quizalofop-p-ethyl and propaquizafop were recorded as the best herbicide treatments in controlling the weeds used in this study 10DAP, however the difference between herbicides faded at 20 DAP. Also, no significant effect was found for concentration of herbicides and type of adjuvant. In addition, 30 days after herbicide application, maximum dry weight and leaf area of canola was recorded for cycloxydim, propaquizafop and quizalofop-pethyl, respectively whereas minimum dry weight and leaf area of canola was observed in pots sprayed with sethoxydim and fluazifop-p-butyl respectively.

Published
2012

36. Studies on the nematicidal activity of stinging nettle ( Urtica dioica ) on plant parasitic nematodes.

Author

Nasiri, Mostafa, Azizi, Kourosh, Hamzehzarghani, Habiballah, and Ghaderi, Reza

Subjects
NEMATOCIDES, STINGING nettle, PLANT nematodes, NEMATODE control, PLANT parasites, GREEN manure crops, NEMATODE populations
Abstract

The effect and the potential application of stinging nettle exudates in controlling plant nematodes were investigated. The effect of root exudates of the stinging nettle interplanted with tomato and bean and its potential application as green manure for reducing the population of plant nematodes were also investigated. The results showed that the counts of the nematodes in the base of stinging nettle were significantly lower than those in the 2 m radius from the plant. Comparison of mean counts of the nematodes showed a differential controlling effect of stinging nettle exudates on the nematodes. The counts of the nematodes in pots pre-sown with stinging nettle were reduced, while in pots planted with tomato plants the reductions were significantly lower. The application of stinging nettle as green manure in nematode-infected pots planted with tomato/bean caused significant reductions in the counts of the nematodes. [ABSTRACT FROM AUTHOR]

Published
2014
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37. Evaluation of different empirical models to estimate safflower yield loss from redroot pigweed ( Amaranthus retruflexus L.) under water stress conditions.

Author

Hamzehzarghani, Habiballah, Kazemeini, Seyed Abdolreza, and Edalat, Mohsen

Subjects
*EMPIRICAL research, *SAFFLOWER, *BLOODROOT, *GOOSEFOOTS, *PHYSIOLOGICAL stress, *IRRIGATION, *WEEDS
Abstract

To evaluate yield loss models in safflower–redroot pigweed systems, two field experiments were conducted during the 2007 and 2008 growing seasons. The relative yield loss of the crop was recorded in plots laid out in a split-plot design with three irrigation treatments as main plots [100, 75 and 50% FC (field capacity)] and five weed densities (0, 3, 6, 9 and 12 m−2) as subplots in three replicates. Among Cousens, Spitters, and Kropff & Lotz models, Spitters was the best predictor of yield loss and showed the lowest RMSE (0.001–0.002), high Adj-R 2 (0.824–0.929), highest precision (0.962–0.981) and accuracy (constant and systematic biases of 0.000–0.103 and 0.863–1.040, respectively), and random residuals plot. The Cousens, and Kropff & Lotz models showed relatively good fit, although they had higher RMSE values, larger constant and systematic biases, and nonrandom residual plots. The reliability of all models was influenced by irrigation treatment, with generally larger constant and systematic biases at 50% irrigation, causing yield loss under/overprediction under 100 and 50% irrigation, respectively. The parameters of the Spitters model correctly explained the biological function of water shortage on yield response; however, the parameters of other models failed to represent a biologically acceptable yield response function, particularly at 50% irrigation. [ABSTRACT FROM PUBLISHER]

Published
2012
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