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Genus Medicago belonged to family Fabaceae is one of the most important forage legumes. Annual species of this genus are indigenous to Mediterranean region and used for prevention of soil erosion, green manure and forage. In this research, genetic variability and classification of 14 annual medicago truncatula genotypes using ISSR markers was done. 9 out of 15 ISSR primers which possessed suitable polymorphism and amplification were used for fingerprinting of studied genotypes. Totally, 71 bands were amplified via ISSR primers which 11 bands were monomorphic and 60 bands were polymorphic across genotypes. Based on Jaccard similarity coefficient, minimum similarity (0.25) was seen between TN8.3 (Tunisia) and TN6.18 (Tunisia) and maximum similarity (0.82) was seen between TN8.3 (Tunisia) and SA28064 (Cyprus). Population structure analysis using STRUCTURE software subdivided them into 9 subpopulation. In this study, maximum admixture was occurred in TN1.21 (Tunisia), A10 (Australia), F83005-5 (France), SA22322 (Syria), A20 (Australia), and DZA315-16 (Algeria) genotypes. Results revealed that annual self-pollinated M. truncatula had noticeable genetic variation which Is accurately detectable using ISSR molecular markers

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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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The flowering and fructification period of the Chilean strawberry (Fragaria chiloensis (L.) Duch.) is restricted to approximately 2 mo, which seriously limits the commercial development of the species. The objective of the current investigation was to identify Inter Simple Sequence Repeat (ISSR) polymorphisms associated with flowering duration in accessions of F. chiloensis. The flowering duration data related to 41 accessions obtained over 3 years were analyzed, and a set of 40 ISSR primers tested. Two clusters were obtained through the Partitioning Around Medoids algorithm, with 23 vs. 18 accessions, and 64.1 vs. 95.6 days of flowering, respectively. Flowering duration, between the two groups, was significantly different. The years also revealed a significant effect, on flowering duration, between the two groups. Ten of the ISSR primers tested revealed reproducible and consistent banding patterns, displaying a total of 106 putative loci, of which 79 were polymorphic. Three ISSR loci (811₇₇₉, 844₆₇₀, 841₉₈₀) were identified owing to their significant contribution to the differentiation among the accessions. Similarly, three ISSR loci (811₆₀₀, 812₁₁₈₀, 841₉₈₀) exhibited a significant correlation with the flowering duration variation. Locus 841₉₈₀, which presented the highest level of correlation with flowering duration, was isolated, cloned and sequenced, but it showed only a low level of homology with the relevant sequences published in the GenBank database. The identified loci showing high correlation with the flowering time could help build Quantitative Trait Loci (QTL) maps for selection and improvement programs in the Fragaria sp. genus or other related species.

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Macrophomina phaseolina is an important soil-borne pathogen causing charcoal rot in many important crop plants including sesame, in Iran. A total of 60 isolates of M. phaseolina were collected from the main sesame producing regions in ten provinces of Iran. The genetic diversity among M. phaseolina populations was estimated using Inter-Simple Sequence Repeat (ISSR), focusing particularly on geographic differentiation. Five ISSR primers generated 105 discernible DNA bands, of which 85 (77.11%) were polymorphic. The greatest value of variability (PPB: 60.00%; H: 0.185; I: 0.284) was estimated for Fars population, whereas the least variability (PPB: 9.52%; H: 0.042; I: 0.060) was estimated for Kerman population. Total gene diversity exhibited high levels of variability (H_T = 0.186). Analysis of molecular variance indicated a large proportion of genetic variability within populations.

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 Genetic diversity in cluster bean (Cyamopsis tetragonoloba L.; Fabaceae) genotypes was studied using Inter-Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) to derive conclusions about diversity analysis in groups of accessions of a germplasm. The two methods, individually as well as cumulatively revealed the range of diversity in profiles among 104 genotypes collected from different geographical regions of India. A simulated clustering of the collected plant genotypes was divided into defined affinity groups using Structure program and the cluster analysis of molecular markers data revealed six broad sub-clusters. These results were validated with a Principal Coordinate analysis. The combined data was more informative than either of the individual method data. The diversity range was found to be wide and the presence of six broad clusters suggests the existence of many genetic lineages that can constitute useful starting points for the use of germplasm diversity in the selection and improvement of the cluster bean crop.

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Witches' broom disease of lime caused by 'Candidatus Phytoplasma aurantifolia' is considered as one of the most destructive disease of Mexican lime in southern Iran, Oman, and the United Arab Emirates. The causative phytoplasma is vectored by a leafhopper, Hishimonus phycitis (Distant, 1908). Six ISSR markers and mitochondorial Cytochrome c Oxidase I (COI) gene were used to unveil genetic variation of the leafhopper populations from thirteen different regions of Iran. Analysis of ISSR markers revealed that Forg (Fars) and Qale'e Qazi (Hormozgan) significantly diverged from the other populations. However, the COI sequences were highly conserved among all populations and resided all the populations in a single clade. Mantel test exhibited no correlation between genetic and geographical distances. Our results demonstrated genetic differentiations among the H. phycitis populations, which might have been induced by ecological or geographical isolation and may affect the vectoring capability of this insect.
 

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Artemisia annua L. is an important medicinal plant used as an original source of artemisinin for treating malaria. Although there is a wide distribution of A. annua in Hyrcanian Areas (Mazandaran, Guilan, and Golestan Provinces in N Iran), no considerable effort has been made for diversity assessment. In this study, morphological, phytochemical, and molecular characterization of A. annua accessions in this area were assessed using 4 quantitative characteristics (height, fresh weight, dry weight, and trichome density), artemisinin content, and 15 ISSR primers. Using these traits, a high level of morphological, phytochemical and molecular diversity was revealed among A. annua accessions in the provinces (populations) of Hyrcanian Areas. At inter-population level, the highest value of artemisinin was observed in Mazandaran Province. Moreover, significant correlation between artemisinin content and trichome density was observed that could be useful for indirect selection of artemisinin yield in different accessions of A. annua. In addition, fifteen ISSR primers generated a total number of 222 amplified bands, consisting of 177 and 45 polymorphic and monomorphic loci across the 60 accessions, respectively. These results indicate that ISSR-PCR is a reliable tool for fingerprinting A. annua at the intra-population level. Our results altogether are valid contributions for gene bank management and Artemisia annua breeding programs.

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Ziziphora clinopodioides Lam., a medicinal plant of Lamiaceae family, is a widespread species all over Iran. In this investigation, the genetic diversity of 10 ecotypes of Ziziphora clinopodioides was evaluated using morphological, phytochemical, and molecular markers. ISSR and iPBS markers were applied for the molecular analysis. The average of polymorphic bands per primer in the iPBS and ISSR markers were 4.4 and 6.68, with the average polymorphism of 79.49 and 92.03%, respectively. The ecotypes of Evard and Sorkhgarive had the highest values of the important breeding traits, including the shortest internode, the highest ratio of leaf to vegetative body weight, the highest essential oil yield, and the total phenol content. The results showed that ecotypes had a wide variation in terms of all studied markers. Principal Coordinate Analysis (PCoA) confirmed the results of molecular clustering of ecotypes, but phytochemical and morphological data did not have alignment with that. Also, there was no correspondence among the geographical locations of habitats and the phytochemical, morphological, and molecular markers data.

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Mutagenesis has been one of the effective methods for creating genetic diversity and plant mutants can be significant bio-resources for crop breeding and functional genomics studies. The genetic and phenotypic diversity of 95 selected mutants from 17 mutant populations, obtained from an EMS mutagenized rice Hashemi variety, were phenotypically and molecularly assessed in M₃ generation. Phenotypic variation of these mutants showed that grain yield components varied among the selected mutants compared to the control plants. In parallel, genetic diversity assessed by 13 Inter-Simple Sequence Repeats )ISSR) primers showed that the number of amplified fragments per primer varied from 4 (pr1-7) to 11 (ISSR-7, ISSR-11). In general, 13 primers amplified 99 fragments, 50 of which were polymorphic (52.92%). The genetic variation created by ISSR markers within 17 populations varied from 11.11% in HM9 (Hashemi Mutant Line number 9) to 45.45% in HM2. The average molecular polymorphism value was 0.27. In the total genetic variance, 95% of differences were attributed to within-population diversity, and 5% were related to among-populations. The Unweighted Pair-Group Method with Arithmetic mean (UPGMA) trees illustrating ISSR diversity classified the rice mutant population into seven groups, which were further supported by model-based STRUCTURE analysis. In general, the studied mutant genotypes revealed desirable genetic characteristics in populations 13 and 17, with em₃h204 and em₃h280 genotypes being the most divergent. 

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Association analysis using phenotypic information and molecular markers may provide valuable information for molecular breeding and marker-assisted selection. The objectives of this study were to determine markers associated with sugar parameters and important agronomic traits of watermelon and to estimate the level of genetic diversity. Ninety-six watermelon lines were genotyped by combining SSR (Simple Sequence Repeat), ISSR (Inter-Simple Sequence Repeat) and iPBS (Inter-Priming Binding Sites) marker data. These genotypes were also assessed for population structure, Linkage Disequilibrium (LD), and Association Mapping (AM) of sugar parameters and other important agronomic traits. In the analysis, 583 markers had LD values to a certain degree. A general linear model was developed using only the Q matrix showing the population structure in association mapping, a complex linear model using a kinship matrix, and a complex linear model using both the Q and K matrix linear models. The regression model explanation rates for the 26 characters varied from 11.3 to 81.3%. The highest rates of regression model explanation were measured for fruit firmness (81.3%) and fruit height (78.2%). It might be possible to determine the genes associated with these studied characteristics, to contribute to future genetic and breeding studies, and to be used in Marker-Assisted Selection (MAS) studies.