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The dry bubble disease, caused by Lecanicillium fungicola, is an important fungal disease of white button mushroom in Iranian mushroom production farms. Twenty-three isolates of the pathogen collected in Iran and identified as L. fungicola var. fungicola, were compared for genetic polymorphism, diversity in growth rate and virulence. Ten Universal Rice Primers (URP) were used to evaluate the genetic diversity of L. fungicola var. fungicola. URP analysis showed that the genetic diversity of Iranian isolates was low (average 10 % over the 10 primers used) and that they were almost clonal. Relative correlations between geographical origins of isolates and molecular grouping were observed but there was no correlation between mycelial growth rate, virulence assays and URP patterns. Significant differences were observed between isolates based on mycelial growth rate and virulence assays. The high level of genetic homogeneity is attributed to the effect of fungicides used for control of the mushroom diseases which might have imposed a significant selection pressure on the fungal populations.  

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Beet western yellows virus (BWYV), a species of the genus Polerovirus in the family Luteoviridae, is an agriculturally important virus infecting over 150 plant species in 23 dicotyledonous families worldwide. A survey of BWYV in canola fields in Golestan and Tehran provinces of Iran using indirect triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) indicated 8.3 % infection. The presence of BWYV was confirmed by amplification of the coat protein (CP) gene of the virus via running a reverse transcription-polymerase chain reaction (RT-PCR) on total RNA extracted from ELISA positive leaf tissues. DNA sequences of the BWYV coat protein (CP) gene of seven Iranian isolates were determined and compared at the nucleotide (nt) and amino acid (aa) levels with those of twelve BWYV isolates from different countries deposited in GenBank. Sequence analysis data showed that the identity of BWYV-CP at nt and aa levels among the Iranian isolates were 93.4 % to 100 % and 93.2 % to 100 %, respectively. The maximum similarity of isolates at nt and aa levels were 97.2 and 96.6 %, which occurred among two Iranian isolates (Ir 8 and Ir 100) and four isolates from France (L39967 and X13063) and England (L39973 and L39970). The recombination analysis among the nineteen isolates including seven Iranian isolates revealed that there was no distinct intra-specific recombination event among BWYV isolates. This is the first report of sequencing and analyzing of the BWYV CP gene of Iranian BWYV isolates.

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The citrus leafminer, Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae) is a major invasive pest of citrus in Tunisia. In order to help the implementation of an efficient integrated management strategy, it was essential to assess the genetic diversity and population structure of the pest. For this purpose, random-amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was applied, using eight oligo-nucleotide primers, to reveal genetic variability among eight populations of P. citrella, originating from the north, center and south of Tunisia. A total of 66 RAPD markers and 33 phenotypes were generated. Inter-population polymorphism was revealed, using the percentage of polymorphic markers (62.12 %), mean number of phenotypes generated per primer (4.125) and mean genetic distance (0.199). Hierarchical analysis, using the UPGMA method, indicated that the genetic variability was influenced by the regional distribution. This pattern of population clustering was supported by Principal Coordinate Analysis (PCO). Yet, a weak correlation (0.69) was revealed between genetic and geographic distances, suggesting that climatic contrariety between the north and south of Tunisia plays a major role in the differentiation of P. citrella, leading to a restriction of gene flow between populations. Results obtained in this work show clear genetic differences, which should be considered in the development of control strategies.  

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Plants infected by arbuscular mycorrhizal fungi can tolerate and recover more rapidly from different biotic and abiotic stresses such as soil water deficits than uninfected plants. Thereby study of the dominant mycorrhiza species in the fields under drought stresses is very useful for increasing crop productivity in these conditions and promising for biological fertilizer production in the future. The objective of this research was to study the variations in morphological and molecular diversity of arbuscular mycorrhizal fungi (AMF) and identification of dominant AMF in wheat and barley fields of some arid and semi arid regions of Iran. For this purpose, about 66 samples containing root and rhizospher soils of wheat and barley plants were collected from some arid and semi arid regions of Iran (Isfahan, Tehran, Ghazvin, Arak, Tabriz). After trap culture of observed mycorrhiza in the samples, they were identified using morphological and molecular techniques. The ITS-rDNA of AMF in root DNA extracts of wheat and barley amplified with the primer pair LSU-Glom1/SSU-Glom1 as specific primer for AMF and ITS4/ITS5 as general primers in the first and second reactions of PCR (nested PCR), respectively. Aliquots of the positive second PCR products were cloned. Positive colonies were digested with Taq1. The restriction fragment length polymorphism (RFLP) patterns of digested samples were compared and 1-3 representatives of each pattern at each cloning reaction were sequenced. Morphological and molecular diversity of AMF showed that more than 90% AMF observed in the regions belong to genus Glomus which coordinates with morphological studies and followed by G. intraradices. Also these studies confirmed presence of following species in some regions: G. fasciculatum, G. geosporum, G. sinosum, G. constrictum, G. macrocarpum and Glomus sp. and Acaulospora (Acaulospora sp.). It is important to note that the species G. etunicatu and G. dimorphicum were not detected in the morphological studies and Glomus mosseae was the most dominant AMF species in the all studied regions.

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Genetic diversity relationships of 50 isolates of Cytospora schulzeri on apple from different parts of the Semirom region were analyzed using 15 polymerase chain reaction (PCR) based markers, 7 random amplified polymorphic DNAs (RAPDs) and 8 Microsatellite primed polymerase chain reaction (MP-PCR). Using 7 selected RAPD primers 113 bands were generated, of which 81 bands were polymorphic (71.7%), with an average of 11.57 polymorphic fragments per primer, and with 8 selected MP-PCR primers 107 amplified bands were observed with 78 polymorphic bands (72.3%), with an average of 9.75 polymorphic fragments per primer. In RAPD marker, number of polymorphic bands varied from 8 (241) to 15 (230, 238, OPA13) with an average of 11.57 per primer and which varied in size from 200 to 3750 bp. Percentage of polymorphism ranged from 64% (203 and 232) to a maximum of 83% (238). In MP-PCR marker, number of polymorphic bands varied from 6 (CAG) to 12 (GTG and ATG) with an average of 9.75 per primer and which varied in size from 200 to 3500 bp. Percentage of polymorphism ranged from 54% (CAG) to a maximum of 81% (ACTG). By combining markers, a total of 220 bands were detected, of which 159 bands (72%) were polymorphic and produced on an average 10.6 polymorphic bands per primer. The results showed that both markers were suitable for the detection of genetic polymorphism among apple C. schulzeri isolates. Estimated genetic relationship using similarity co-efficient (Jaccard’s) values between different pair of accessions varied from 0.54 to 0.89 in RAPD, 0.62 to 0.89 in MP-PCR and 0.62 to 0.87 with combined markers based similarities. High cophenetic correlation between the similarity matrix and corresponding dendrogram was obtained by RAPD + MP-PCR marker (r = 0.81). Cluster analysis of the data using UPGMA based on Jaccard´s similarity coefficient, divided the isolates into six groups, showing a high genetic diversity among populations of C. schulzeri.

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Ninety one monoconidial Bipolaris isolates were obtained from lesions on different parts of rice in different locations of Mazandaran province during the summer of 2009. Bipolaris species were identified using morphological features such as color and shape of colony and color and size of conidia and conidiophores. The isolates were separated into two species; 85 (93.4%) isolates belonged to Bipolaris oryzae and the remaining 6 (6.6%) isolates to Bipolaris cynodontis. Therefore B. oryzae is regarded as the major cause of rice brown spot disease in Mazandaran province. In order to analyze genetic diversity among B. oryzae isolates, 71 isolates were subjected to fingerprinting analysis by rep-PCR using BOX and REP primers. In cluster analysis, 15 clonal lineages and 54 haplotypes were identified. The largest clonal lineage contained with 36 haplotypes was the most common lineage. These results also indicate a relatively high level of genetic diversity among B. oryzae isolates. Also, pathogenicity test of a few B. oryzae isolates (12 isolates) was conducted under greenhouse condition and showed that those isolates were pathogenic to rice seedlings of cv. Tarom. All isolates produced some leaf spots 24 h after inoculation.

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The genetic structure, diversity and population kinship of four strains of ornamental barb, Puntius tetrazona, viz. tiger, green, albino and rose barb, was studied through microsatellite markers.  Genomic DNA was extracted from dorsal fin tissue of 160 individuals (40 per strain) using kit and its protocol from Denazist Co.  PCR amplification was performed using four pairs of microsatellite primers (Sm17, Sm25, Ma106 and Ma109). PCR products were electrophoresed on 8% acrylamide gel and stained with silver nitrate. The results showed that all loci were polymorphic. A total of 21 alleles for four markers in four strains was found. The mean number of alleles per locus at the population level was 5.25, and the number of alleles per polymorphic locus varied between 3 and 6. Average number of the observed alleles in tiger, green, albino and rose barb strains were 3.25, 3.25, 4 and 3.25, respectively. The observed and expected heterozygosity averages were 0.24 and 0.49, respectively. Most cases significantly deviated from Hardy-Weinberg equilibrium (p≤0.01). The analyses of molecular variance showed high genetic diversity (97%) within populations. The F_st value was 0.03 which indicates the low genetic differentiation between populations. UPGMA cluster analysis based on Nei genetic distance showed two different populations inhabiting the regions. Therefore, the microsatellite markers used in this study were found suitable for the different strains, and the degree of diversity was very low between strains, indicating a high degree of kinship.

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This study was designed to investigate the genetic diversity and relationships between yield and related traits in oily sunflower lines. 152 sunflower lines collected from different parts of the world were investigated at completely randomized design with nine replications on Urmia University in 1391 under pot conditions. 14 agro-morphological traits including plant height, stem diameter, number of leaves, leaf length, leaf width, petiole length, head diameter, 100 seed weight, head dry weight, , seed yield per plant, number of days from planting to flowering, and number of days from planting to maturity, dehulled kernel to whole kernel and harvest index were measured. Analysis of variance revealed significant differences among genotypes for all studied traits. Among the traits, the highest coefficient of phenotypic variation was observed for seed yield per plant (56.30), harvest index (44.4) and head dry weight (35.44). The results of correlation analysis showed that there is significant and positive correlation between seed yield per plant with most of the studied traits. Results of sequential path analysis revealed that the variables such as number of leaves, dehulled kernel to whole kernel, head diameter, and plant height were arranged as the first-order variables. Cluster analysis subdivided the genotypes into 4 groups. The maximum distance were observed between the genotype from groups 3 and 4 (28.30).

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The thermophilic fungus Mycothermus thermophilus is one of the most important thermophilic fungi in mushroom composting process. Thirty nine isolates of M. thermophilus were collected from nine provinces of Iran and were identified as M. thermophilus based on morphological features and ITS regions. The studied isolates significantly increased the growth of Agaricus bisporus hyphae compared to control when used in vitro situation. Also the colony morphology of the mushroom changed when it grew on the colony of M. thermophilus. While the studied thermophilic isolates were morphologically different, no diversity was observed in terms of Random Amplified Polymorphic DNA (RAPD) finger-printing. The genetically clonal population of M. thermophilus collected from Iranian mushroom composting farms was attributed to lack of sexual reproduction, similar raw materials used in compost formulations, compost temperature, and concentration of ammonia during pasteurization as selection pressures.

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The aim of this study was to identify different population broodstocks of Litopenaeus vannamei and effect of inbreeding and cross-inbreeding on genetic characteristics and inbreeding coefficient of offspring in the next generation. According to origin of broodstocks kept in hatcheries of Bushehr province in the first generation, different populations were identified through microsatellite method from Hybrid, High health and Molokai stocks then, in the next generations genetic characteristics of offspring from their inbreeding and cross-inbreeding were examined. The results showed that the amount of genetic diversity in Molokai and High Health stocks (0.46±0.09 and 0.50±0.07) was more than hybrid stock (0.38±0.06). The inbreeding coefficients of Molokai, High Health and hybrid stocks were 0.14, 0.31 and 0.41, respectively. Due to the low genetic distance between the hybrid and Molokai stocks, after mixing them together Molokai and High Health populations were introduced as the first generation broodstock. In the second generation, despite the high genetic diversity in the offspring of Molokai×High Health (0.47±0.12) and High Health×Molokai (0.39±0.08) than the offspring of Molokai×Molokai (0.19±0.04) and High Health× High Health (0.11±0.03), these values were reduced compared to the first generation. The lowest and highest inbreeding coefficients were related to the offspring of Molokai×High Health (0.268 ±0.18) and Molokai× Molokai (0.853±0.145), respectively. According to the results, it can be said that the lack of knowledge about the genetic characteristics of broodstocks and mating between individual relationships (full and half sib) can reduce genetic characteristics and genetic depression due to increased inbreeding coefficients in next generations.

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This study was conducted to assess genetic diversity among the 32 tall fescue half-sib families using a randomized complete block design (RCBD) experiment in the four replicates. Based on analysis of variance, significant differences were observed among studied genotypes at the probability of 1% for plant height, canopy diameter, days to heading, days to pollination, crown diameter, fresh forage yield, dry forage yield, number of stem and seed yield in first harvest and in canopy diameter, crown diameter, fresh forage yield and dry forage yield in second harvest. Based on the results of mean comparisons, highest dry forage yield in the first harvest was obtained in genotype 32 by 758.5 grams. Principal component analysis by considering eigenvalues greater than one, caused to introduction of three components which determined 80.5% of the variation among the samples. In cluster analysis, the greatest of distinction between the groups was achieved with three clusters, and by cutting the dendrogram genotypes in three groups. According to the results, the third cluster was superior to other two clusters in terms of most traits. The genotypes of third cluster, according to the value of this cluster in terms of forage yield and seed yield will be of particular importance in breeding programs. In the breeding of cross-pollinated forage crops, success in selection depends on creating diversity by genetic recombination and achievement of heterosis. Due to the distance between groups 1 and 3, probably the most successful crosses will be achieved among genotypes of these two groups.

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The fungus Ustilago maydis causes common smut disease in corn. Under favorable conditions, it can cause severe damage to corn. In this study, the genetic structure of U. maydis populations in Iran from the most corn-growing regions of seven provinces, including Ardebil, Fars, Isfahan, Kerman, Kermanshah, Khuzestan, and Qazvin, was evaluated using rep-PCR with primers; BOX, ERIC, and REP. Rep-PCR reactions with 109 isolates of U. maydis produced seven distinct clusters consistent with their geographical origin with few exceptions. The results of AMOVA revealed significant genetic differences within and between pathogen populations. The Euclidean similarity coefficient and the UPGMA algorithm indicate five distant clusters based on the disease severity index. The mean comparison of the disease severity index grouped target isolates into 18 clades using the Tukey test. Our findings showed that the pathogenicity assay-based grouping was not consistent with those of the geographical origin of the isolates nor their genetic similarity.

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The applicability of RAPDs, AFLPs, and SSRs to examine genetic relationships in 36 populations of Triticum boeoticum from West of Iran was investigated. A total of 224 (135 polymorphic), 979 (429 polymorphic) and 246 (145 polymorphic) bands/alleles were detected using 14 RAPD primers, 17 AFLP primer combinations and 17 well distributed, mapped SSR markers, respectively. The polymorphic information content (PIC) value was high for SSRs (0.81) but low for RAPDs (0.45) and AFLPs (0.56) reflecting the hypervariability of the first system. AFLPs carried the highest Marker Index (MI) value (14.19), reflecting the high multiplexity ratio of this system. The correlation coefficients of similarity were statistically significant for all the three marker systems employed. UPGMA cluster plots separated the 36 populations into three major groups based on their RAPD fragment similarities, and into two major groups based on their AFLP, SSR and RAPD+AFLP+SSR genotypic similarities. These different marker systems should provide different levels of information, important in the management of germplasm resources. A good level of genetic diversity observed in the populations of Kermanshah and Lorestan Provinces shows that T. boeoticum invades a wide range of agroecosystems in the West of Iran.

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Rye is one of Iran's most important crops, known as Secale, belonging to the Poaceae. In this research, genetic diversity of 39 families of rye populations from different regions of Iran, the USA, and the Soviet :union: was evaluated with the ISSR marker. The results showed that 8 ISSR initiators produced 48 bands which included 18 polymorphic bands (37.5% polymorphism). The mean of polymorphic information content (PIC) and marker index value (MI) for ISSR primers was 0.15 and 7.2 respectively. The highest PIC (3.0) was related to primer 5+6 and the highest MI (0.96) reached for primer 1+6. After observing polymerase chain reaction products on an agarose gel and scoring DNA bands, the analysis was performed with NTSYS software. The cluster analysis dendrogram of UPGMA and Jaccard's similarity coefficient divided the rye populations into 9 groups, the results were compiled with grouping by principal component analysis. The results of analysis of Molecular Variance indicated an in-species variation more than inter-species variation. The mean Nei genetic variation (h) was 350 and the mean of Shannon index (I) in rye species was 523, which indicates a relatively good variety within species. The results showed that the ISSR marker was a useful tool in determining genetic variation of inter and intra specific of rye.

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Enzyme electrophoresis was used to measure genetic variation within, and divergence among, three generations of recently bred synthetic alfalfa generations (Syn1, Syn2, and Syn3) originating from a polycross of 12 selected parents and several cultivars. Three isozyme loci, exhibiting tetrasomic inheritance in 10-day seedlings, were detected from five enzymatic systems analyzed by polyacrylamide slab gel electrophoresis for about 100 individuals of each alfalfa population. Very high levels of heterozygosity (ranging from 0.521 to 0.699) were observed within alfalfa populations, using polymorphic loci. The reduction in heterozygosity was about 5% from Syn1 to Syn2 and from Syn2 to Syn3. The last open pollinated generation was found to be in W-H equilibrium as well as Gharayonja, a native ecotype under examination, using c2-test. Application of Wright's Fstatistics revealed that the estimated overall inbreeding coefficient, (FIT), of 9.4% was mainly related to inbreeding or double reduction in alfalfa (FIS= 8.61%) rather than random genetic drift or population differentiation (FST= 1.6%). Therefore, due to very large intra-population diversity, the breeding program of the synthetic alfalfa did not generate a large variety differentiation. However, the use of seedling allozymic loci can be applied successfully for estimation of the population genetic parameters.

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In this study, the genetic diversity of 10 different accessions of Andrographis paniculata was investigated using protein and SRAP markers. In the vegetative stage, protein and DNA were extracted from the leaves. The results of protein profile indicated a total of 20 bands with 64.15% polymorphism. To evaluate genetic diversity at the DNA level, 6 SRAP primers were used and a total of 583 scalable bands were observed.  A total of 549 bands had polymorphism with an average of 91.5 for the studied primers. The highest polymorphism (99.12%) and the lowest polymorphism (84.21%) were observed in E1/M1 E2/M2 primers, respectively. Cluster analysis produced four main clusters. Genetic diversity indices were calculated for all gene loci, including the average genetic diversity of Nei’s (0.27) and the mean of Shannon’s index with a value of 0.41. High level of population differentiation (Gst = 0.79) and good level of gene flow (Nm = 1.3) were estimated between the grouped populations. Molecular analysis of variance showed that intra-population variance (58%) was higher than inter-population variance (42%). Overall, the results of study showed a high genetic diversity in both protein electrophoresis pattern and in polymorphic bands separated using SRAP markers with emphasis on the greater efficiency of SRAP markers than protein markers, which can be selected in parents with genetic distance. It is widely used to produce dispersing and mapping populations in hybridization programs and to breed or improve desirable traits, as well as to protect and manage the germplasm of this plant.

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Comparative assessment of genetic diversity of 122 durum wheat genotypes (Triticum turgidum L. var. durum) was performed using 73 SSAP polymorphic fragments, 123 AFLP polymorphic loci and 104 SSR alleles. SSAP and AFLP data showed a clear demarcation between the cultivars and landraces and SSR data classified cultivars and landraces according to their origin. Furthermore, the estimated genetic diversity of Iranian landraces was higher compared to the foreign entries and a loss of genetic diversity was observed from landraces to cultivars. This study determined that differences in genetic relationships revealed by SSAP, AFLP and SSR distances could not be attributed solely to differences in the level of polymorphism detected by each marker system. The molecular evidence of genetic diversity decrease of the durum wheat gene pool further strengthens the strategic relevance of undertaking appropriate genetic conservation measures for food security.