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The knowledge about genetic diversity in the wild relatives of wheat provides useful information for breeding programs and gene pool management. In the present study, the genetic diversity among some of the cultivated wheat accessions and wild relatives belonging to T. aestivum, T. durum, T. urartu, Ae. tauschii and Ae. speltoides species was evaluated using 15 CBDP primers. A total of 141 bands amplified, which all of them were polymorphic. The average of polymorphic information content (PIC = 0.48) and resolving power (Rp = 10.67) revealed high efficiency of these markers to further genetic diversity assay. Furthermore, the average percentage polymorphic loci (PPL), number of observed (Na) and effective (Ne) alleles, Shannon’s information index (I), and gene diversity (H) are 72.48%, 1.44, 1.64, 0.38 and 0.26, respectively. These were coincided in essence with the analysis of molecular variance (AMOVA) results, indicating that 63 and 37% of genetic variation were found within different species, respectively. Genetic relationships inferred from a nighbour-joining dendrogram clustered accessions into main three groups. This grouping pattern was matched with the groups obtained by principal coordinate analysis (PCoA), revealing all accessions grouped based on their genomic constitution. Taken together, our results suggest CBDP markers will be useful for genetic diversity and phylogenetic studies in the domesticated and wild relatives of wheat. Hence, the use of this technique in other breeding programs such as, QTL mapping and construction of linkage maps are recommended.

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Phytohormones and PGRs are influencing factors in the production of secondary metabolites. Papaverace family includes valuable alkaloids with commercial importance and Papaver bracteatum belongs to this family. Benzylisoquinoline alkaloids are a diverse group of more than 2500 specified natural compounds with medicinal effect which are found in 5 plant families including Papaveraceae. In vitro plant cell culture is a promising source for high rate secondary metabolites production. In this study, the effect of methyl jasmonate (MJ) and phloroglucinol (PG) in three different concentration, 0, 100 and 200 uM and mg/L, individually and in combination together, on the stimulation of thebaine and sanguinarine production in Papaver bracteatum cell suspension cultures was studied. Both elicitors significantly increased yields of thebaine and sanguinarine production compared to the control. Thebaine production 48 hours after elicitation with concentration of 200uM MJ and 100mg/L PG was about 68.63-fold and sanguinarine production at the same period with concentration of 200uM MJ and 200mg/L PG increased about 107.71-fold more than control. It seem that increases can due to synergic effects of used elicitors in this suspension cell culture. Adding MJ and PG, each one lonely, also increased yields of thebaine and sanguinarine. The results of this study showed that the use of PGRs can motivate biosynthetic cycle of the production and accumulation of morphinan alkaloids in plants and levels of this alkaloids can be eleveted comparing to control plants.

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Genetic variation was investigated for the number of 15 Agropyron cristatum accessions using the 15 ISSR primers, among them 12 primers were scored. The ISSR primers produced the number of 71 bands. The polymorphism has been observed for the number of 66 bands. The primers of IS₁ and UBC₈₅₇ presented the highest number of bands, i. e. eight bands; while the IS₇ and UBC₈₆₉ showed the lowest number which is only three bands. The primer of UBC₈₄₄ were showed the lowest polymorphism percentage (83.33%) and IS₂, IS₆, IS₇, UBC₈₄₈, UBC₈₆₅, UBC₈₆₈ and UBC₈₆₉ had the highest polymorphism percentage (100%). The polymorphism percentage average was 94.15%. The average of bands was 5.92 in each primer for 15 genotypes and the average of polymorphic bands was 5.50. IS₆, UBC₈₆₅ and UBC₈₆₉ could determinate genetic distance of genotypes better than other primers. The genotypes of G4 with G2 had the most similarity and G1 with G8 had the lowest similarity. The results of UPGMA cluster analysis based on Jacard's similarity coefficient were classified the genotypes in three groups, which confirmed by principal coordinate analysis and molecular variance analysis. The genetic diversity of the populations was matched based on the studied marker with their geographic distribution, and the populations of Gorgan and Isfahan were similar, which, on the other hand, showed greater distance with Karaj populations.

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Aegilops genus is the main genetic source of variation for wheat breeders due to its breeding potential such as tolerance to both abiotic and biotic stresses. The main objective of this study were to evaluate the genetic diversity in 91 Aegilops accessions belonging to Ae. cylindrica and Ae. crassa using microsatellite (SSR) markers. A total of 49 fragments were amplified using 25 tested primers in which 48 products were polymorphic. The average values of polymorphic information content (PIC) and gene diversity (H), resolving power (Rp) and marker index (MI) were 0.26, 0.34, 1.29 and 0.51, respectively. The results of molecular variance analysis (AMOVA) showed the highest portion of genetic variance referred to inter-species compared to intra-species. Based on genetic variation parameters, the highest values of variation parameters were recorded in Ae. crassa than Ae. cylindrica accessions. Cluster analysis based on Jaccard’s coefficients and neighbor-joining algorithm grouped all investigated accessions into two main clusters, so that all accessions were clearly separated from each other. The result of principal coordinate analysis (PCoA) revealed that the first two components accounted for 64.98% of the total molecular variation. The PCoA-based biplot grouped all investigated accessions into two main groups. The result of population structure showed that all investigated accessions were recognized into five subpopulations, and F_ST index among them varied between 0.52 and 0.76 with an average of 0.76. In conclusion, these results indicated high genetic variation in Aegilops genus collection and could be used in Wheat improvement programs and other genetic studies like QTL and association mapping are recommended.

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Triticum and Aegilops genera are the main gene pool of bread wheat due to their breeding potential such as tolerance to various abiotic and biotic stresses. The main objective of this study was to evaluate the genetic diversity in 95 landraces and wild relative accessions belonging to T. aestivum and Ae. tauschii using microsatellite (SSR) markers. A total of 49 polymorphic fragments were amplified using 25 tested primers. The average values of number of alleles, polymorphic information content (PIC) and gene diversity (H) were 1.96, 0.32 and 0.41, respectively. The results of molecular variance analysis (AMOVA) showed the highest portion of genetic variance referred to within species compared to between them. According to genetic variation parameters, the highest values of variation parameters were estimated for Ae. tauschii than T. aestivum accessions. Cluster analysis based on Jaccard’s coefficients and neighbor-joining algorithm grouped all investigated accessions into two main clusters, so that some of accessions from each species were placed in the same sub-cluster. The result of principal coordinate analysis (PCoA) revealed that the first two components accounted for 50.38% of the total molecular variation. The biplot rendered based on the first two components was accordance with the grouping pattern obtained from cluster analysis. The population structure analysis grouped all investigated individuals into four main subpopulations so that the average of F_ST index among them was 0.50. In general, our results revealed a high level of genetic diversity within T. aestivum and Ae. tauschii species as well as the used markers were capable well to present of this diversity.

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In the present study, genetic diversity and population structure in the 80 Iranian Aegilops accessions were investigated using CBDP markers (CAAT-box derived polymorphism) markers. Twelve CBDP primers amplified a total of 94 fragments, which out all of them were polymorphic. The mean values of polymorphic information content (PIC), resolving power (Rp) and marker index (MI) indicated that the used primers could exploited for further assessing relationships among investigated genotypes and population structure analysis. The results of molecular analysis of variance (AMOVA) showed that the genetic variation between populations is more than variation within them. Based on genetic variation parameters, the highest number of observed alleles (Na), number of effective alleles (Ne), gene diversity (He), Shannon’s information index (I) and percentage of polymorphic loci (PPL) were found in Ae. triuncialis species. Cluster analysis and population structure grouped all investigated genotypes into three main clusters, so that the grouping patterns were consistence with their genomic constitutions. In conclusion, our results revealed the high rate of genetic diversity in Iranian Aegilops accessions. Due to high adaptation of wild relatives to their habitats, hence they can be used as a valuable gene source for wheat breeding programs.

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Evaluation of genetic diversity in a gene pool contributes to the effective conservation of genetic resources and truncates the breeding programs time. Genetic diversity plays a very important role in reducing genetic vulnerability during breeding process. In the present study, genetic diversity of 96 durum wheat genotypes were evaluated using 12 SCoT primers. Our results revealed that the SCoT primers generated 76 polymorphic bands, with an average of 5.42 fragments per primer. The values of marker index (MI) and polymorphism information content (PIC) indicated that SCoT markers were efficient for detection of genetic diversity in durum wheat germplasm. The average of PIC and MI values for the SCoTmarkers were 0.46 and 2.51, respectively. According to Shannon’s index (I), Nei’s genetic diversity (He), the observed (Na) and effective (Ne) number of alleles, the ICARDA population showed a higher level of genetic diversity than the CIMMYT population. Neighbor-joining clustering method was used to generate a dendrogram and a large number of genotypes were classified in different groups, based on their origins. The result of the principal coordinate analysis (PCoA) was in good agreement with those obtained
from the neighbor-joining clustering. These results revealed a desirable genetic diversity among the investigated lines and confirmed that the SCoT technique is a suitable tool for studying genetic diversity in durum wheat germplasm.

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In this study,the genetic diversity and population structure of 90 Ferula assa foetida L. genotypes were evaluated using 13 ISSR primers. The results indicated that ISSR primers reproduced a total of 186 polymorphic bands with an average of 14.38 bands per primer. The mean values of marker index (MI) and  the polymorphic information content (PIC) for ISSR primers were 4.98  and 0.37, respectively, and showed that ISSR primers were highly efficient in ­the identification of genetic diversity in Ferula populations. In comparison between the studied populations, the population of Kerman includes 33 genotypes based on the values of the number of effective alleles (Ne), heterozygous values (H), Shannon index (I), and the total number of alleles (Na) observed was more diverse. The­ ­analysis of molecular variance  (AMOVA) results showed that 8% of the total changes are related to  between population diversity, while 92% of the changes are justified by within population diversity. In other words, ISSR primers showed significant genetic diversity between and within wild relatives. Cluster analysis and population structure divided all evaluated genotypes into 5 main categories, respectively. According to the results obtained from this analysis, the value of K=5 was in the optimal range. These results illustrate that there is a relatively high genetic diversity in the Ferulas  population  and ISSR markers are beneficial tools for studying genetic diversity in this germplasm.
 
 

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Genetic uniformity is one of the most important prerequisites in micropropagation of plant species. In the present study, the genetic fidelity of 28 plantlets of damask rose(Rosa damascena ) derived from three different media treatments supplemented with various concentrations of Plant Growth regulators(PGRs) was assessed by SCoT and ISSR markers. solid MS medium was used for the establishment stage of explants and regenerated shoots  were subcultured in VS medium supplemented with three different combinations of PGRs. For rooting, the plantlets were subcultured on MS medium supplemented with IAA and IBA and the rooted plants were transferred and acclimated in the greenhouse. Genomic DNA of in vitro raised clones was extracted from young leaf tissues. 20 SCoT and 20 ISSR primers were used to evaluate of the genetic fidelity of in vitro propagated plantlets. Out of 40 primers screened, only 14 SCoT and 11 ISSR primers produced clear and scorable bands. 25 SCoT and ISSR primers amplified 139 loci, of which only 35 bands were polymorphic. The average number of polymorphic bands per primer were 1.5 and 1.3 for SCoT and ISSR markers respectively. Based on the estimated genetic parameters and results of data analysis, in general, a low variability was detected among the tissue culture-raised plantlets. Particularly, the plantlets derived from the media II and III shower a lower variability than those derived from the media I; hence, the media II and III can be successfully employed for the commercial multiplication of damask rose without much risk of genetic instability.  

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Various species of genus Trigonella are important from medical and food aspects.
Assessment of genetic diversity is an important principal for plant breeding, providing an opportunity to identify the novel genetic characters and new genes for breeders. In the current work, 90 fenugreek ecotypes were evaluated for genetic diversity using several start codon targeted polymorphism (SCoT) and universal rice primer (URP) markers. Ten SCoT and 10 URP primers amplified a total of 100 and 109 fragments, respectively, which out all fragments were polymorphic. The mean values of polymorphic information content (PIC) for both marker systems was 0.34. However, the highest means values for MI and Rp parameters were estimated for URP compared with SCoT markers. The results of the molecular analysis of variance (AMOVA) based on SCoT, URP, and SCoT+URP data showed that the genetic variation within populations is more than between them. Based on genetic variation parameters, the highest number of observed alleles (Na), Shannon’s information index (I), Nei’s genetic diversity (H) and the percentage of polymorphic loci (PPL) were found in T. foenum-graecum and T. monantha species. Cluster analysis based on each marker and pooled data clustered all investigated samples into three main clusters. Furthermore, our results indicated that the grouping pattern obtained by pooled data is in accordance to taxonomic structure of species. In conclusion, our results revealed the high rate of genetic diversity within fenugreek ecotypes. Hence, this germplasm can be used as a valuable gene source for breeding programs.

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Among cereals, barley (Hordeum vulgre L.) is the most salt-tolerant crop‚ and is grown in a wide range of climatic conditions. Identification and expression analysis of genes involved in stress tolerance is considered one of the effective approaches to improve plant tolerance to salinity. In the present study, effects of salinity stress were investigated on the expression of SOS1, NHX1, and HvHKT3 genes in barley seedling plants. Based on results, the 200 mM NaCl treatment increased the expression of studied genes by 12.87, 2.19, and 2.54% compared with the control treatment. Furthermore, there is a significant difference among the tested genotypes in terms of all studied genes. Means comparison revealed that G3 (D10*2/4/Productive/3/Roho//Alger/Ceres362-1-1) showed the higher relative expressions for SOS1, NHX1, and HvHKT3 genes compared with another genotype and the check genotype (cv. Mehr). Hence, it seems that this genotype has considerable potential to use in breeding programs to improve salinity tolerance in barley due to its salinity tolerance. In conclusion, our results indicated the role of antiporters genes in barley in response to salinity stress.
 

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The genus of Aegilops is one of the most important wild relatives of wheat, and different species of this genus have a wide distribution in Middle East and West Asia. Knowledge about the genetic diversity of Aegilops species provides useful information which can be exploited for breeding programs of wheat. In this study, genetic diversity of 60 Agilops accessions from three different species were investigated using three different DNA markers. CBDP, SCoT and ISSR primers amplified 130, 135 and 152 polymorphic fragments respectively. The average of polymorphism information content (PIC) for CBDP, SCoT and ISSR primers were 0.37, 0.34 and 0.39 respectively indicated the efficiency and usefulness of the used primers. The neighbor-joining (NJ) based clustering using marker data, classified all 60 accessions into three main groups and the investigated accessions were clustered based on the genetic structure. The results of analysis of molecular variance based on CBDP, ISSR and SCoT data showed that the variance among populations covered 66%, 45% and 42% of total variation respectively. Besides, among all three species, Ae. triuncialis showed the maximum number of private allels indicating its unique genetic background. Our results revealed high levels of genetic diversity within all three species, showing high potential of studied germplasm for using in breeding programs. Further, our findings indicated that all three marker systems were useful techniques for evaluation of genetic diversity, however, CBDP and SCoT markers which are generated from the functional regions of the genomes, would be more useful for evaluation of genetic diversity than random or semi random PCR based markers.
 

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Genetic diversity identification is an important step for plant breeding procedure. Triticum urartu as the A-genome donor of wheat, is a valuable source for wheat breeding due to its rich allelic diversity for important traits such as agronomic characteristics, protein quality and biotic stress tolerance. In this study, the genetic diversity and population structure of 85 T.urartu accessions collected from different geographic regions of Iran were investigated using ISSR markers. 16 ISSR primers generated 164 fragments which all were polymorphic. The average of polymorphism information content (PIC) and marker index (MI) were 0.44 and 4.53 respectively, revealed a high resolving power of ISSR primers. The dendrogram generated using the NJ algorithm based on Jaccard’s dissimilarity coefficient, classified all 85 accessions into two main groups which was confirmed by Structure analysis. Analysis of molecular variance (AMOVA) showed a higher distribution of genetic diversity within populations (96%), than between them (4%) and according to the diversity indexes including number of effective alleles (Ne), Shannon’s index(I) and Nei’s gene diversity (He), there were an equal variation within seven investigated populations. The results showed a high amount of genetic variation among tested accessions, which provide further insights into conservation and future utilization of wild wheat resources. Besides, these results confirmed the efficiency of ISSR markers as reliable technique in estimating the genetic diversity and fingerprinting.

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Fenugreek (Trigonella foenum-graecum L.) as an important aromatic and medicinal plant is a rich source of the Diosgenin and Trigonelline. Genetic diversity analysis using reliable methods provides useful information for the crop breeding programs and conservation of genetic resource. In the present study, 40 Fenugreek genotypes were evaluated for genotypic diversity using two gene-targeted markers. Seven SCoT and ten CBDP primers amplified 78 and 93 fragments in which 65 and 78 were polymorphic, respectively. The average of polymorphism information content (PIC) for SCoT and CBDP Primers were 0.37 and 0.29 respectively, that showed a higher resolving power of SCoTs than CBDPs. The dendrogram generated using the UPGMA algorithm based on Dice distance coefficient, classified all 40 investigated samples into four main groups. Furthermore, these results were confirmed by principal coordinate analysis (PCoA). Analysis of molecular variance (AMOVA) showed a higher distribution of genetic diversity within populations (66%), than between them (34%). Among all five investigated populations, the highest values of diversity indexes such as number of effective alleles (1.54), Shannon’s index (0.46) and Nei’s gene diversity (0.31) were estimated for population IV indicating the higher variation within this population than others. These results showed a high amounts of genetic variation among tested genotypes, which can be used in breeding programs. Moreover, the results revealed that these two gene-targeted markers are suitable and reliable techniques for DNA fingerprinting and genetic diversity investigations.