polymorphism

The study of genetic diversity with the help of molecular markers is the main precondition and an important step in the improvement of vegetable plants, including tomato and is the basis for the effective use of heterosis and the protection of genetic pools. Several studies have been conducted using molecular markers between different tomato lines, but there is little studies in Iran. Based on this, the present study intends to estimate the genetic distance between a numbers of tomato lines using ISSR molecular markers.

In the present study, 12 tomato lines were investigated using microsatellite primers (ISSR) at Sari University of Agricultural Sciences and Natural Resources. Polymerase chain reaction (PCR) was performed by ISSR primers and PCR products fractioned on 1.5% using agarose gel electrophoresis then the bands were analysed.

The primers used showed acceptable polymorphism (85.28) and suitable score able banding patterns. The highest and lowest polymorphism information content (PIC) with values of 0.40 and 0.22 were related to ISSR2 and ISSR10 primers, respectively. The ISSR2 primer was more efficient than other primers in identifying and classifying the studied lines. The degree of genetic similarity varied from 0.23 to 0.95 between the studied lines and lines Fanal and Harlekyn had the most similarity and lines CP with Bibor and after that SP with Bibor showed greatest genetic distances. Results of cluster analysis and evaluation of quantitative characterestics of studied lines showed that genotypes 4, 5, 6 and 8 placed in first group had better yield and earliness comparing other genotypes.   

Lines CP, SP and Bibor had a great genetic distance from each other and hybridization between CP and SP with Bibor as well as utilizing of selected genotypes in first group is recommended for next breeding programs in tomato. The ISSR2 primer has useful information in distinguishing the studied lines than other primers and its useful in breeding programs of tomato.

In the present study, 11 ISSR, 2 Retrotransposon and 15 Retrotransposon + ISSR composed markers (REMAP) were evaluated among 27 genotypes of Soybean. 130 polymorphic bands were produced from 28 primers. The maximum percentage of polymorphism were 77% for UBC808, 54% for TOS-2 and 70% in UBC808+TOS-1 marker. The mount of Nei′s, Shanon and PIC index for UBC808, UBC811, UBC825, HB-12, TOS-2, UBC807+TOS1 and UBC834+TOS-1 indicated that theses markers could be used to assessment of genetic variation. The result of cluster analysis using complete linkage algorithms clustered 27 studied genotype in 4 distinct groups with 4, 9, 9 and 5 genotype in respected group. Discriminant function analysis using the Fisher′s linear method showed that the complete linkage method separated the genotypes with 96/3 percent accuracy. Morphological characteristics of genotype were evaluated in a completely randomized design with factorial arrangements whit two factors, The first factor were salt stress treatments at 0 (check), 30, 60 and 90 mM NaCl and the second factors was genotypes. ANOVA showed significant differences among varieties and level of Treatment for all measured morphological traits, and in interaction of cultivar×stress for all traits except Shoot fresh weight, shoot dry weight, root dry weight and shoot's weight difference between wet and dry. The cluster analysis based on within group′s method clustered genotype at different salt stress treatment in 4 clusters, and the accuracy of cluster analysis revealed by discriminant analysis was 92/6%. The correlation between the two similarity matrices was not significant by Mantel test. Analysis using marker-assisted selection of bands that enhance salt tolerance traits mean they can be used to identify resistant soybean genotypes..

Saffron is a triploid and sterile plant having no or little genetic variation. Mutation induction is a way of increasing genetic diversity in vegetatively propagated plants. The first step in the mutation induction is to perform a radio-sensitivity test for determining the proper dose of gamma ray. Therefore, the aim of this study was to test the sensitivity of different doses of gamma ray in two conditions of cold and non-cold treatment of saffron corms. For this purpose, a factorial experiment with two factors including cold pre-treatment (cold and non-cold) and different doses of gamma ray (0, 5, 10, 15, 20 and 25 Gy) was conducted in a randomized complete block design with three replications. Growth and morphological characteristics such as plant height, number of leaves per plant, leaf dry weight, sprouting rate and percentage in the first year (MV1), and attributes related to daughter corms and flower yield, such as mean height of the stigma and dry weight of the stigma in the second year (MV2) were measured. The results of the study showed that the effect of cold treatment, radiation and their interaction was statistically significant, with the increase in gamma dose, most of the traits decreased significantly compared to the control. The radio-sensitivity test for the mean of plant height and sprouting rate and percentage, corm weight in two levels of pre-cold treatments showed that 50% survival was in the range of 15±2 Gray. According to the radio-sensitivity test, the number of leaves per plant was less susceptible to gamma rays. In order to study the genetic diversity of the gamma-irradiated saffron. The mutated samples of saffron were evaluated using RAPD and ISSR molecular markers. Cluster analysis was performed using the UPGMA method for both marker systems. The results showed that there was polymorphism between the control samples and radiated samples. In general, the results showed that the RAPD and ISSR markers could detect the polymorphic mutants and identify saffron mutants.

Take-all is one of the most important diseases of wheat in wet areas, causing significant damage in these areas, and there has not introduced any resistant varieties against this disease until now. Therefore, efforts to identify the resistance genes to this disease and developing resistant varieties or cultivars with lower susceptible in bread wheat have a great importance.In this research, in order to identify the markers related to resistance to a isolate of take-all (T-41), a population of F2 derived from crosses of susceptible genotypes (1546 and 164) with resistant genotype (1528) and bulk segregate analysis (BSA) where used. After planting the F2 population and parents in the greenhouse and artificial infection the plants with the fungus, the plant phenotype was determined according to the amount of contamination by scoring. After DNA extraction of parents and F2 population, two bulk of DNA was prepared from resistant and susceptible individuals based on disease scores. The bulks and parental DNAs where analyzed by RAPD, SCoT, ISSR and SSR primers and PCR reaction. Among the primers are used, only one ISSR primer produced a band of 400 bp in the resistant parent and bulk which was not found in the susceptible parent and bulk. Then, all individuals of bulks and F2 where genotyped for this marker and regression and chi-square analysis showed a significant relationship between this marker and the disease score. The regrsion of disease score on band 400bp (b = -0.709) indicates that this band is more abundant in low scores (resistant individuals). Also, the distribution of F2 individuals in one of the crosses confirmed the existence of the epistatic (9sensetive: 6 semi sensitive: 1resistance) relationship

Saffron is the most valuable spice in the world. It is genetically a monomorphic clone. However, differences in phenotype and quality have been reported. The most important agro-economically phenotypic variation is the appearance of flowers with more than three stigmas. The main objective of this study was to study the genetic variability of saffron clones with more than 3 stigmas using SSR and ISSR molecular markers. In this research, saffron clones with more than three stigmas were collected along with the corm and the root from Saffron fields of Qaen and Sarayan, South Khorassan province, then transferred as a whole to the Biotechnology Laboratory of the Faculty of Agriculture, the University of Birjand. The number of stigmas in each flower was counted. Genomic DNA was extracted according to the CTAB method from leaves of the flower with more than three stigmas. Flower with more than three stigmas was larger and had more petals than ordinary ones. The most frequent number of flowers with more than three stigmas was related to four and five stigmas with 38%. Six-spike samples with a frequency of 14% were observed. Among the collected samples, only one specimen with seven stigmas was observed. Of the 48 tested ISSR primers on the bulk of DNA, only 16 primers had amplified bands and selected. The results of agarose gel electrophoresis for ISSR primers amplified the bands ranged from 100 to 1000 bp. By examining the bands formed for ISSR primers, no significant polymorphism was observed between different clones of saffron. Therefore, based on this marker system, no sign of genetic diversity was observed between clones with different number of stigmas. Among the tested SSR markers, 10 primer pairs showed amplified band among the clones. The results of correlation analysis based on Spearman correlation coefficient showed that there was no statistically significant correlation between microsatellite marker alleles and number of stigmas.

In the recent years, false jagged-chickweed (Lepyrodiclis holosteoides) has become one of the most problematic broadleaf weeds in wheat and canola fields of temperate and cold regions of Iran. Due to the the importance of the time of emergence of seedlings in the success of weed competition in crop ecosystems and consequently, the use of effective weed management methods, a series of studies were conducted in the fields of Karaj and in the Weed Research Department of Iranian Institute of Plant Protection (Tehran) during 2013-2016 to determine the biological aspects of dormancy and germination of this invasive weed seeds. Results showed that there is polymorphism in seed dormancy of false jagged-chickweed. Dormancy of false jagged-chickweed seeds can be classified in the physiological category (which is related to the presence of chemical inhibitors inside the seed and the hormonal balance between Abscisic acid and Gibberellic acid). Also, seeds of false jagged-chickweed are very photo sensitive in the germination process. The results showed that first date of the emergence of false jagged-chickweed occurred in the second half of November and seed vigor of this weed reduced significantly by increasing of seeds longevity. Lepyrodiclis seedlings emerged in form of multiple flashes during autumn and winter, however more than 85 percent of total emerged seedlings appeared after receiving 552 GDD over the period of December 12th to January 12th.

Persian walnut (Juglans regia L.) belongs to the family of Juglandaceae and is one of the most important nut crops in Iran. Until recently, all of the fruitful walnut trees grown in Iran are seedling originated and thus, they exhibit a significant variation, especially in nut and kernel characteristics. Therefore, the identification of the promising genotypes based on the phenotypic traits is essential in breeding programs. The aims of the current work were to evaluate 119 Persian walnut trees in different western regions of Iran based on nut and kernel characteristics, and then to detect genetic relationships among desirable genotype using ISSR marker.
  In this research, 119 Persian walnut genotypes collected from different parts of the west of Iran were evaluated based on nut characteristics. Based on the primary evaluation, 30 superior genotypes that had desirable characters in nut and kernel properties, such as nut and kernel weight, kernel percentage, kernel removal from the nut, kernel plumpness, and kernel filled were selected and then, the genetic variation among them was evaluated using 10 ISSR primers.
  The preliminary evaluation of 119 walnut genotypes illustrated that most of the evaluated genotypes showed high variability for the measured traits related to nut and kernel. Among the nut and kernel characters, the kernel shriveling showed the highest coefficient of variation (114.02%), while the lowest CV was related to the nut diameter (8.68%). Among walnut genotypes, both nut and kernel weight varied from 7-19.8 g and 2.8-9.20 g, respectively. The genetic relationship among 30 promising genotypes with ten ISSR primers indicated a considerable level of variability. All of the ISSR primers were polymorphic and produced a total of 79 alleles among the 30 genotypes, which 77 alleles were polymorphic. The size of the amplified fragments ranged from 200 bp to 1700 bp. The number of the observed alleles for each locus ranged from 3 (HB10) to 13 (UBC-807), with an average of 7.7 alleles per locus. Polymorphic index content (PIC) was observed to be highest (0.82) in the UBC-807 locus, while the HB10 locus had the lowest value (0.51) with an average of 0.75 among ISSR locus. The Jaccard’s genetic similarity coefficient ranged from 0.31 to 0.85 among the genotypes. The cluster analysis performed based on ISSR data using UPGMA, divided the genotypes into seven major groups.
  Finally, the results of this study showed that there was high variability among walnut genotypes in terms of quantitative and qualitative characteristics of the nut and the kernel. In this study, the average nut and kernel weight among walnut genotypes varied. The difference in nut and kernel properties of germplasm under the same geographical conditions may be the result of genotypic factors. The results indicated that some genotypes (16, 4, 24, 26, 11, and 17) had desirable traits in the nut and kernel. Moreover, the Persian walnut is of most important horticultural crops grown in Iran. Therefore, these genotypes can be propagated according to the vegetative methods and used for commercial cultivation or utilized for traditional breeding and advanced biotechnology studies to achieve superior progenies.

Milk Thistle (Silybum marianum L.) is a plant from the Asteraceae family that has high therapeutic properties due to its secondary metabolites, such as silymarin. Considering the significant therapeutic effects of this plant and the necessity of its cultivation in Iran, evaluation of its genetic diversity is important for breeding purposes. In the present study, the genetic relationship of eight milk thistle accessions was studied using CDDP and SCoT markers. Based on the results of the molecular evaluation, a total of 62 detectable bands were obtained from seven selective SCoT primers, of which 53 polymorphic band (85.48%) were found, while from the seven CDDP primers, a total of 58 detectable bands were obtained, of which 50 bands were polymorphic (86.2%). The mean polymorphic information content index (PIC) obtained from CDDP and SCoT markers were 0.39 and 0.23, respectively. Both the CDDP and SCoT markers showed more variation between accessions than within accessions. The high level of genetic diversity observed in the studied accessions can be used in milk thistle breeding programs.

Identification and classification of genetic source are important in plant breeding and genetic diversity. In order to evaluate genetic diversity of 48 Facultative wheat genotypes belong to north of IRAN, an experiment was done using 10 ISSR primers in the genetic laboratory of Gonbad Kavous University. Out of 62 produced fragments, 41 fragments were polymorphic. The number of polymorphic bands were different from 2 to 8 for each primer. The maximum number of polymorphic bands were related to PRI – 10. PIC value were variable between 0.375 to 0.498 and Marker index were variable between 18.75 to 39.84. The maximum percent of polymorphism with 80% were belong to PRI-4 and PRI–10, and the minimum percent of polymorphism with %50 were belong to (PRI -2 PRI -4), (PRI -3 PRI -4) and PRI-5. (PRI-3 PRI-4) and PRI-5 showed maximum Shanon index with 0.666 and 0.502, respectively. The maximum and minimum Nei genetic variability were observed for (PRI-3 PRI-4), and PRI-5 as 0.336 and 0.474 respectively. Maximum (1.908) and minimum (1.584) number of effective alleles obtained for (PRI-3 㴒4), and PRI-5, respectively. The 48 genotypes were grouped in four groups by using Jacard Coefficient similarity in UPGMA cluster analysis. Cluster analysis showed that ISSR markers are reliable to manifest higher level polymorphism. It also showed that ISSR indicators is useful to evaluate genetic variability and breeding programs in wheat.

Iran is one of the important distribution centers of medicinal species, including plant saffron (Crocus sativus L.). The presence or absence of genetic diversity in common native and commercial cultivars of saffron of the country has always been one of the important questions for researchers of this filed. In the present study, varioussaffronsamplesfrom different regions of Iran, including seventeen cultivated samplesfrom North Khorasan, Khorasan Razavi, South Khorasan, Lorestan and Ilam, eight wild types (C. haussknechtii) from Lorestan, Kermanshah and Ilam and one wild type (C. cancellatuse) from Kermanshah were collected and then their genetic diversity was obtained using random amplified polymorphism DNA (RAPD) marker. A total number of 161 DNA bands were produced by eight primers with an average of 14.3 bands; the primer Oligo 340 produced the most number of bands. The polymorphism percentage mean was 73.77%. Cluster analysis using UPGMA method divided the samplesinto four groups. In this grouping, there was a minimum distance between saffron populations collected from Kermanshah and Ilam. In other words, these two populations had the maximum genetic similarity with each other. The maximum similarity was observed between the samplescollected from Saleh-Abad and Lomar in Ilam and the minimum similarity was observed between ecotypes collected from Bisotoon in Kermanshah and Torbat-jam in the Khorasan Razavi province. In most cases, samples of different species were divided into different groups such that it can be said that this Genus has a great diversity. Although there are some samples of wild species (C. haussknechtii) that were with saffron crop species in a group in which there exists many molecular Genetics similarities between these species that is indicative of a common genetic background.

Recogniting the genetic diversity and classification of inheritancepools is one of important activities in the field of breeding and maintaining genetic resources in plants. In order to assess the genetic diversity in 48 genotypes of soybean amplification of gene loci was performed by using 10 ISSR primers In Genetics and Plant Breeding laboratory, College of Agriculture andNatural Resources, University of gonbad Kavos.Among 68 amplifed fragment of caltivars were generated, 34 fragments were ploymorphic.The number of polymorphic bands per primer varied from 2 to 5 and the most of polymorphic bands was related to PRI-4. Pic values varied between 0.147 to 0.058 and the marker indexwasbetween 8.39 to 1.56, for primers. The highest and lowest percentage of polymorphic belonged to primer PRI-2 (66.66) and primer PRI-5 (28.57). Primer PRI-5 showed the maximum value of Shanon index (0.678) and primer PRI-1 had the lowest Shanon index with a value of 0.467. The greatest amount of genetic variation was observed in primer PRI-5 with value of 0.485 and the lowest genetic diversity in primer PRI-1 with value 0.3. The highest number of effective alleles obtained for primer PRI-5 with a value of 1.943 and a minimal number of effective allels for primer PRI-1 with a value of 1.479. Maximum level ofmarker index obtained forprimer PRI-6 with value of 8.39 which indicating a higher resolution of this primer than the otherand the lowest was observed in primer PRI-5 with a value of 1.65. Culaster analysis method UPGAM and jacards similarity coefficient grouped 48 genotypes in four separate groups.The result showed ISSR marker is amarker system for detecion of high levels of polymorphism and can be usedto investigation genetic diversity and breeding program in soybean.

Determining the level of genetic diversity and relationships among genotypes is necessary to identify the parents for different breeding purposes. In the present study, genetic diversityof 55 samples of wild barley germplasm, Hordeum spontaneum, collected from different regions of the world was evaluated using 14 microsatellite (SSR) markers. A total of 52 alleles were amplified with an average of 5.2 alleles per locus and average frequency of the major allele was 0.51. Polymorphic information content (PIC) ranged from 0.37 to 0.81 with an average of 0.629 and gene diversity or expected heterozygosity ranged from 0.38 to 0.82 with an average of 0.635. Results of the measured diversity parameters in the studied markers showed that Bmag007, EBmac0701 and Bmac134 were the most appropriate markers to separate genotypes. Cluster analysis based on SSR data and UPGMA method using simple matching similarity matrix assigned the genotypes into six groups. The genotypes belonging to each group were generally collected from a specific geographical region. In many cases, a mismatch between the genotypes and its geographical region was observed. Based on these results, the highest similarity was observed between Syria and Jordan genotypes and the samples from Kazakhstan had lowest similarity to the genotypes collected from these two countries. The result of this research showed that there is considerable genetic diversity in the studied wild barley samples which can be used to improve the cultivated barley after the identification of their useful genes.

Genetic diversity of 45 wheat varietions were studied using AFLP markers. From 11 primer combinations of PstI and Mse1for obtaining AFLP polymorphism, six primer combinations (P-CGA/M-CTA, P-ATG/M-CTG, P-ATG/M-CAT, P-AGT/M-CTA, P-AGT/M-CAG and P-ATG/M-CAG) produced polymorphic bands. Totally, 328 bands be produced that 207 bands (63.10%) were polymorphic, which showing high polymorphism among genotypes. PIC was variable between 0.39 in P-AGT/M-CAG and 0.44 in P-ATG/M-CT. According to Nei’s gene index and Shanon’s information index, the highest and the lowest genetic diversity within genotypes on the basis primer combinations were obtained in P-ATG/MM-CAT and P-CGA/M-CTA primer combinations. Cluster analysis based on furthest neighbors linkage and Nei's genetic distance categorized the genotypes into six clusters. The highest and lowest number of genotypes situated in sixth (41.86%) and fourth (4.65%) clusters, respectively. The similarity's range based on Dice similarity coefficient changed between 0.57-0.99. Arta and Ghods had the highest genetic similarity (0.99) and Azadi and Koohdasht owned the lowest genetic similarity.

Wheat (Triticum aestivum L.) is a member of the Poaceae family، an annual and self-pollinated crop which has three groups of 14، 28 and 42 chromosomes with genome formula AA، AABB، AABBDD that the chromosomes are located in three homeologous genomes A، B and D. Wheat has an extremely large genome of 16 × 109 base pairs with more than 80% repetitive DNA and an average of 810 mega base pairs in each chromosome with 10 µm length. Wheat is the most important crop in universe and in Iran، known as strategic and basic commodities. This crop plays an important role in both aspects of production and consumption with a lot of genotypes that requires efficient and accurate means of identifying their relationships and determining their genetic diversity levels. Present study aims to determine the genetic diversity and genetic distances of 91 doubled haploid lines of wheat and their parents using SSR markers and assess the ability of microsatellite markers for detecting polymorphisms based on the variants among their germplasm. Results showed that the number of alleles per locus ranged from 2 to 8 and the allelic value of polymorphism information content (PIC) ranged from 0. 12 for Xgwm46 to 0. 87 for Xgwm186 with an average of 0. 5. A total of 39 alleles were detected. Diversity and genetic relationships of the samples were analyzed using Nei and Li and UPGMA statistical methods and the studied lines were classified into three common groups.

Evaluation of the genetic potential of lettuce germplasm by classical methods or using molecular markers is crucial in breeding programs and introduction of new cultivars. Assessment of genetic diversity of Iranian lettuce genotypes collected from different provinces was conducted in laboratory at Seed and Plant Improvement Institute, Karaj. Forty two genotypes of Iranian lettuce with a foreign cultivar were evaluated using 17 RAPD primers. Primers produced total of 807 polymorphic bands. The highest number of polymorphic bands (78 bands) was produced by primer P9 and the lowest number (15 bands) by P6. The size of produced bands of primers varied from 280 to 3000 bp. Jaccard similarity coefficients was calculated for 43 genotypes, that varied from 0 to 0.324. The highest similarity was observed between genotypes no. 13 and 14 (0.324), no. 19 and 20 (0.314) and no. 7and 8 (0.300). Cluster analysis of molecular data, at the similarity level variation 0.25 clustered Iranian lettuces into four groups. Generally, the results of this experiment showed a high genetic diversity in Iranian lettuce genotypes and revealed that RAPD is a useful and effective technique for classification of Iranian lettuces.