One of the main objectives of plant breeding is defining the relationship between genotype and phenotype. Nowadays, molecular markers provide powerful tools to evaluate this relationship for plant breeders. In this study, genetic diversity of 112 rice lines was evaluated by 20 pairs of SSR markers which linked to drought tolerant alleles. Totally, 77 polymorphic alleles with mean of 3.85 alleles per primer pairs were amplified. The minimum number of alleles was belonged to RM28199 and RM212 markers with 2 alleles, and the maximum number of alleles was belonged to RM72 marker with 6 alleles. The range of PIC for the examined markers was 0.30 to 0.72 and the mean of PIC was 0.58. The maximum amount of PIC was belonged to RM85 and RM20A markers and the minimum of PIC was belonged to RM28099 marker. Considering the gene diversity coeficient, RM28099 and RM 85 markers had minimum (0.33) and maximum (0.76) diversity, respectively. The stepwise regression analysis of the microsatellite data and morphologic traits identified 62 and 54 informative alleles for the evaluated traits in flooding and drought conditions, respectivly. Cluster analysis based on molecular data divided the genotypes into 7 groups. Considering the appropriate distribution of amplified DNA by the studied markers in this study, markers that have high separation power and high association with important agronomic traits in drought stress condition (if further experiments confirmed them), could be employed in plant breeding programs of drought stress.‌

Chrysanthemum (Chrysanthemum morifolium) is one of the most important ornamental plants which plays a significant role in the development of gardening industry in the world. The knowledge of genetic diversity is one of the prerequisite criteria for Chrysanthemum breeding with important economic goals. Molecular markers have a significant share in elucidation of inter and intra species genetic diversity. To this end, genetic diversity of a number of Iranian cultivars was molecularly investigated by sequencing a part of rDNA, using ITS4 and ITS5 primers. Genetic distance between Chrysanthemum cultivars ranged from 0.05 to 10.15, demonstrating the power of ITS region in revealing the genetic diversity among cultivars of morifolium, suggesting Iranian cultivars have been genetically improved from morifolium species. Genetic diversity assessment of Iranian Chrysanthemum cultivars demonstrated that presumably inter, intra species or even inter population hybridization may have been involved in creating enormous genetic diversity among Chrysanthemum cultivars.

Melon is an important crop cultivated in moderate climate regions of the world. One of the most important diseases of this plant is vascular wilt caused by Fusarium oxysporum f.sp. melonis (Fom). Infection of farm by this pathogen can result in huge damage around the world. Development of resistant varieties is the most effective method for disease control. Four races of 0, 1, 2 and 1,2 have been reported for this pathogen and 1 is more versatile and dangerous races especially in the north half of Iran. Garmak, as an important variety in Isfahan province, is susceptible to race 1. Single dominant gene of Fom-2 induces resistance against race 0 and 1. In this research, the resistance gene was transferred from Isabelle into Garmak using SNP marker assisted back-crossing. The screening of plants in BC₁, BC₂, and BC₃ generations was carried out using artificial inoculation. This gene was sequenced partially in parental genotypes and resistant and susceptible alleles were discriminated. In order to verify the resistant plants survived after artificial inoculation in BC₃, plants were genotyped using the SNP marker and HRM method. This method distinctly separated three genotypes (RR, Rr and rr) from each other.  The resistance of most plants was verified by molecular method. However, among resistant genotypes identified by artificial inoculation method, there were some susceptible plants identified by molecular method, indicating the more confidence of molecular method in genotyping of plants. With selfing of BC₃ resistant plants and selection of homozygote resistant plants, it is possible to develop resistant Garmak variety.

Plant Breeding has utilized a wide range of techniques and methods to improve the quality and quantity of plants. The molecular markers are the tools that have provided a new perspective for plant breeding advancements. This article has reviewed the various advantages and uses of molecular markers and the utilization of the high potential of natural polymorphisms within communities, combined with the abilities of conventional plant breeding methods. The marker attributes are not subject to environmental influence and their high frequency of these markers in their number, high structural diversity are as part of their benefits in identifying identities, determining the genetic diversity of species and studying relationship between populations. They may aid in discovering more information about protecting and maintaining genetic stock collections, identifying varieties, determining genes with chromosomal location and the number of genes controlling traits. Genome sequencing, the preparation of physical and genetic maps, genomic fingerprinting of plants are some of the other applications of this tool in plant breeding. The high efficiency of selection with the help of markers in selection of genotypes has been emphasized as the parent of crosses and selection with the help of a marker in breeding programs and genomic selection. New technologies offers new opportunities to shape genetic variation in the improvement of specific plant breeding programs. Nowadays development of next-generation sequencing technology, genome sequencing and high throughput approaches for markers have facilitated EST-derived simple sequence repeat (EST-SSR) marker development as well as single nucleotide polymorphism (SNP) marker. These markers can be successfully employed in accelerating research and plant breeding programs.

In the present study, in order to evaluate the drought tolerance indices and their relationship with ISSR markers, 12 rapeseed genotypes were studied using a factorial experiment based on completely randomized block design under the three irrigation treatments (control and irrigation after drainage of 60 and 85% moisture content) in the greenhouse of Mohaghegh Ardabili University, Iran. Drought tolerance genotypes were evaluated by quantitative indices including MP, GMP, SSI, STI and TOL. Cultivars in all five of indices at two levels of stress exhibited significant differences. Regarding the results of the mean comparison at both levels of stress, SLMO46 was identified as the most resistant cultivar with the highest amount of MP and STI, and Karun was the most sensitive one with the highest amount of SSI index. According to the results of factor analysis, in the first level of stress, Sarigol32 and Karun were sensitive, and in the second level of stress, Talaye and Sarigol32 were sensitive as well. SLMO46 was known to be resistant to stress in both levels of stress. Phenotypic correlation of grain yield under stress and non-stress conditions was investigated in two levels of stress with 5 drought indices. In first level of stress condition, grain yield had a positive and significant correlation with mean productivity, geometric mean of productivity and stress tolerance index. In the second level of stress condition, the same correlation was observed with the difference that there was no significant correlation between drought tolerance and tolerance indices. Canonical correlation analysis was performed between drought indices and molecular markers. Five ISSR primers (5, 9, 11, 14 and 19) with the highest polymorphic percentages were used for calculation using the first factor coefficients. ISSR-PCR was used to identify some of the molecular markers associated with drought tolerance indices. A total of 106 clear and score-able loci were amplified by 18 ISSR primers, of which 60 bands (56.6%) were polymorphic. Finally, according to the results, these markers can be used in rapeseed breeding programs for drought tolerance.

In order to analyze the genetic components of agronomic traits among 116 F9 recombinant lines derived from crosses of Ahlamitarom × Sepidroud rice cultivars, an experiment was conducted as a randomized complete block design in research farm of Gonbad Kavous University of Agriculture with three replications in 2016 and 2017. Genetic linkage map provided with 80 SSR markers, 28 iPBS Markers (79 polymorphic alleles), 7 IRAP markers (17 polymorphic alleles) and 26 ISSR markers (70 polymorphic alleles), which covered 1275.4 cM of the rice genome. QTL analysis was performed by Composite Interval Mapping. In two years, 15 QTLs detected for the studied traits. The additive effected varied from 6.725 g for grain weight up to -85.626 g for grain weight. Also, R² for the detected QTLs explained from 11.3% to 20% of the total variation. The highest R² was related to grain weight in the first year of experiment. Among the detected QTLs, qGWs on chromosome 1, were found to be stable and large effector QTLs for rice (Oryza sativa L.) grain weight, and can be used in marker-assisted breeding and selection programs after validation.

In this study, variation of beta-glucan content was assessed in 20 barley line and cultivars based on complete block design with three replications. Genetic diversity of these genotypes was also evaluated using ISSR markers. Beta-glucan extracted by an enzymatic method. Significant differences were found at the level of 1% among barley genotypes for beta-glucan content. The beta glucan content was variable from 7.21 to 12.48 and, the Yosef, E94B3 and E94B17 genotypes hold the highest content of the beta-glucan. ISSR primers with average polymorphism of 66.79%, genetic diversity of 0.25 and Shannon index of 0.37 were determined as efficient markers for studying genetic diversity. The barley lines and cultivars were assigned in two distinct groups according to their genetic pedigree. On the basis of non-parametric Kruskal-Wallis, Spearman correlation, and stepwise regression analysis, nine informative primers were detected explaining highest seed’s beta-glucan content variations ranging from 24.3 to 42.4 percent. The ISSR6 (700), the combination of ISSR1+ISSR4 (1400) and IS2+ ISSR2 (1400) primers were the most informative primers for the beta-glucan content. The informative markers provide possible functional and efficient marker based selection method and, screening the barley germplasms for the highest beta-glucan content.

Estimation of genetic diversity and evaluation of plant germplasm is the most important step in collection and management of plant genetic resources. Also, comparison of different DNA-based genetic markers in diversity evaluation and then advising the most efficient markers is very important. In order to investigate genetic variation among Persian oak (Quercus brantii Lindi.) populations of Lorestan province (Iran), 20 genotypes were collected from different geographical and climatic regions. After DNA extraction, polymerase chain reactions (PCR) were used for study of polymorphism using three markers including ISJ, ISSR and SCoT. Genotyping was performed using the polymorphic bands obtained from all three markers separately, and also by combining the data of three markers. PCR results of the primers showed 91 polymorphic bands with an average of 71% per locus. The ISSR marker with 44 bands had the most polymorphic bands. Genotypes were discriminated by ISJ, ISSR and SCoT markers in 5, 6 and 5 groups, respectively, and using the combined data of three markers, genotypes were classified in 5 groups (each group included more than one genotype) and 3 group (each group included one genotype).  The results showed that the obtained clustering by different markers were nearly consistent with clustering of genotypes based on the climatic origin of genotypes. The most similarity between the groupings was between ISJ and ISSR markers with 89%. Overall, the results indicated the usefulness of markers used to estimate genetic distances between different oak communities.

In order to identify QTLs controlling agronomically traits, landrace Tarom and rice Tarom mutant were crossed. SSR, ISSR, iPBS and IRAP markers were amplified in 250 F₂ individuals to prepare the linkage map. Number of tillers, 100 grain weight, number of filled grains, number of unfilled grains, plant height, panicle length, number of branches, stem diameter, grain length, grain width, grain shape, straw weight, days to maturity, flag leaf length and flag leaf width were measured for 250 individuals. The linkage map covered 970.9 cM of rice genome. The distance between two adjacent markers was calculated to be 12.77 cM. Based on the results, a total of 13 QTLs were identified for the evaluated traits. For all studied traits, alleles transferred from the parents to the QTLs detected increased grain yield. Most QTLs were detected for days to flowering. Three QTLs were located on chromosomes 10 and 4 (two QTLs) for days to flowering. qLDF-4a and qLDF-4b had a negative additive effect and the parent alleles of the mutant landrace Tarom reduced the number of days to flowering. These QTLs explained 11.6% of the phenotypic variance. Since the population under study was derived from a cross between landrace and mutant Tarom cultivars and the resulting population varied only in the mutated genes; so, the QTLs detected in this study were more accurate in location and expression levels, and after validation of them, they could be recommended for marker assistant selection breeding programs.

Cultivar identification in micro-propagated date palm seedlings is laborious so that application of molecular markers to facilitate and acceleration of the procedure seems inevitable. Given the need for control the originality of micro- propagated date palm seedlings, the aim of this study was evaluation of SSR markers usability to cultivar identification in micro-propagated date palm seedlings. Original samples of Green Ghanami, Red Ghanami, Gantar, Deiry, Ostaemran, Barhi, Medjool, Zahedi and Piarum cultivars were used control. Taking into account the rigidity of leaves and subsequently high consumption of liquid nitrogen to powder leaves, an efficient method for powdering of leaves using Tissue Lyser II instrument was optimized. Eight SSR primer pairs were used for polymerase chain reaction. The Results showed that by using these molecular markers and reliable controls, determination of micro- propagated date palm cultivars is feasible. Clustering of cultivars showed that all of them were differentiated using five SSR primer pairs including mPdCIR025, mPdCIR057, mPdCIR070, PDAG1003 and DP175. Also, barcoding of scored band illustrated that c1 allele (230 to 240 bp) for Piarum cultivar and d3 allele (220 to 230 bp) for Medjool cultivar were exclusive. Totally to make the results referable, cultivar identification diagram was drawn up.