فصلنامه ژنتیک نوین
سال شانزدهم شماره 1 (پیاپی 64، بهار 1400)

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.

Gastritis is one of the most common diseases of human stomach. Most of the time, it is asymptomatic and if not treated, can cause atrophy in gastric tissue. Gastritis seems to be a consequence of Helicobacter pylori infection. H. pylori can induce DNA double strand breaks in DNA and activates the error-prone DNA repair pathways that result in accumulation of mutations and genomic instability which may mediate gastric carcinogenesis. In this study, we assessed expression of CHEK2, DCLRE1C and XRCC4 genes which are involved in cell cycle arrest and DNA double strand break repair systems happening with Gastritis. One hundred and eighty biopsy specimens were collected from patients who were referred for endoscopic examination. 60 samples including 30 cases (H. pylori positive Moderate chronic gastritis) and 30 controls (H. pylori negative Mild chronic gastritis) were selected for RNA extraction. Later cDNA was synthesized and Real-Time PCR was used to assess expression of CHEK2, DCLRE1C, XRCC4 and B2M genes. CHEK2, DCLRE1C and XRCC genes showed 5.88, 6.7 and 3.4 up-regulation respectively in comparison to the controls. Increasing level of CHEK2, DCLRE1C and XRCC4 genes might be related to activation of these genes after H. pylori infection.

Weeds are amongst the major constraints on crop production, which compete with crop plants for sunlight, water, nutrients, and space. Crops’ growth, development and yield are significantly affected by weeds. Glyphosate is one of the most important herbicides which is widely used around the world. Glyphosate inhibits the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme, which is a key enzyme in the biosynthesis pathway of aromatic amino acids. The goal of this study was transfer genes of plant origin in order to induce herbicide resistance in plants. The EPSPS gene from chickpea was cloned and two amino acid (Pro187Ala Thr183Ile) at key sites were substituted to make a glyphosate resistant enzyme. The expression of the EPSPS gene was investigated in the tobacco plant. The regeneration of EPSPS overexpressed leaves were examined in different concentrations of glyphosate (from 0 to 1 mM), the leaves regenerated in all glyphosate concentrations even at 1 mM. Moreover, the transgenic plants were sprayed with 1% glyphosate and they were survived and showed high level of tolerance. In conclusion, the edited EPSPS gene from chickpea is recommended as a suitable candidate gene for development of commercial transgenic crops.

Catharanthus roseus is an ornamental and evergreen plant, which is used in cancer treatment due to production of important alkaloids, Vinblastine and vincristin. C.  roseus is also of great importance for pharmaceutical industry. Vinblastine and vincristine in the terpenoid indole-alkaloid pathway (TIAs) synthesis in Low level. Difficulties with chemical synthetic production and low production level in plant lead to find practical solutions to increase the amount of these two economically important alkaloids. It seems plant growth regulators such as salicylic acid (SA) induce expression of major genes involved in vinblastine and vincristine production. In addition to increasing in the alkaloid content, especially vinblastine and vincristine, application of SA activates the plant defense system and under normal condition and in dealing with stresses, improve C.  roseus yeild. To this end, the relative expression of terpenoid indole alkaloids (TIAs) pathway genes in all three Indole, Terpenoid and Alkaloid pathways studied following foliar application of SA at a concentration of 0.01 mM by using qRT-PCR analysis. The results of this experiment showed that the mRNA transcript level of the first gene in the phenolic pathway reduced, although the down-regulation was not statistically significant. The transcript level of TIAs pathway genes were also increased after SA foliar application. The highest 4-O-acetyltransferase (Dat) gene transcription level observed at 24 and 48 h after treatment, suggesting Dat could be a primary responsive gene to SA treatment.

Salinity is considered as one of the abiotic stresses, which decreases the agricultural production of most crops around the world. Plants use different of adaptive mechanisms to counteract the deleterious effects of salinity as changes in gene expression patterns and the content of compatible osmolytes such as proline. This study was conducted to investigate the effects of salinity stress on expression of P5CS and PDH genes and proline content in canola. To do this, a factorial experiment with three replications was carried out in greenhouse of Agricultural Sciences and Natural Resources of Khuzestan University. Three different lines of doubled haploids (Tolerant, Semi- Tolerant and Sensitive) and two sampling times were considered as the first and second factors. The plant seedling were exposed to 150 mM NaCl as salinity stress at 4-leaf stage. Then, the sampling was performed at 6 and 24 hours after stress application. The results of P5CS gene expression showed that this gene was expressed more in the sensitive line after 6 hours from NaCl application, its expression decreased after 24 hours from starting of stress. On the other hand, the gene expression of P5CS increased sharply in the tolerated line after 24 hours of stress. Comparison of the relative mean of PDH gene expression showed that the sensitive line had a significant increase at both times (6 and 24 hours after stress), while a semi-tolerant line had a significant decrease in PDH expression. The content of proline was more in tolerant line than the others, but non-significant difference observed between the semi-tolerant and sensitive lines in terms of proline content. The results of this study indicated that the expression of PDH and P5CR genes depends on the intensity of plant tolerance and post stress times. With considering the more gene expression in P5CS and greater inhibition of PDH activity in tolerant line, more proline accumulation was occurred in tolerant genotype rather than sensitive one. Therefore, proline may be used as an indicator osmolality in the identification of salt stress tolerance in canola.

Cumin (Cuminum cyminum) from Apiaceae family is one of the important plants in traditional medicine because of its pharmaceutical properties. For the first time, we studied the meiotic behavior and seed pollen fertility under late-season drought stress condition (reproductive stage) and TiO2 nanoparticle treatment. To examine the different meiosis phases and determine meiotic aberration, premature flowers were collected from plants grown under drought stress and different levels of nanoparticles. Different aberration types, including stickiness, clumping, disorganized chromosome, anaphase bridge, delayed chromosome, leader chromosome, laggard chromosome, micronucleus, tripolar, syncyte and the nondisjunction of chromosomes were examined at all levels and different frequencies identified. Pollen fertility was evaluated with regard to its size. Pollen grains with natural size were considered as normal and potentially fertile. The highest reduction rate in fertility (13.33%) was observed in 0.03% nanoparticles with drought stress. The lowest fertility rate (0.69%) was observed in 0.015% nanoparticle with drought stress condition.

Central Nervous system provides body homeostasis and adaptation to environmental changes, thus deregulated nervous processes can accelerates aging. On the other hand, neurodegenerative disorders are age-dependent conditions. Since neurons are highly vulnerable to oxidative damage thus, the normal brain aging and neurodegenerative conditions share similar characteristics. Drosophila melanogaster is an excellent model organism to study brain aging and age-related neurodegenerative changes. It has been reported that human Tau over-expression in Drosophila brain leads to DNA oxidation and a wide spread chromatin relaxation leading to changes in expression level of specific target genes. In this study, in order to obtain a more accurate insight into the normal aging of the nervous system we quantified and compared expression levels of the same target genes in young flies (4 days old) and old flies (40 days old) of wild-type Oregon K Drosophila insects applying qRT-PCR technique. The results showed that a group of genes including Nvd, CG15115, Ir41a, CG15661 and Uif show decreased expression by getting aged, and CG40006, Dscam1, Ints3, and Gprk1 genes are up-regulated as the flies’ age is increased. The Snap25 gene expression did not change during aging. These results showed that as the age rises, the expression of the genes in the organisms of this living creature undergoes changes that are due to changes in the epigenetic patterns. But the observed changes are different than that of reported in tauopathy fly models. This pattern of changes in gene expression reflects reduction of metabolic and signaling activity and increased accumulation of damage in the cells, which ultimately leads to aging.

Phosphorus (P) is one of the most vital elements for all living organisms, which acts as a constituent of essential biomolecules and metabolic reactions. Plants to cope with phosphate (Pi) deficiency have developed different adaptive mechanisms, including induction of acid phosphatases genes, Pi transporters and release of organic acids in rhizosphere as well. Under conditions of phosphorus deficiency stress, maintaining cellular phosphorus homeostasis depends on the interactions between these components. In the present study, the relationship between gene expression pattern of three families of phosphate transporters PHT1, PHT2 and PHO1 in Arabidopsis thaliana in interaction with AtPAP26 as the dominant purple acid phosphatase among 29 identified PAPs in A. thaliana genome were studied under Pi-deficient and Pi-sufficient conditions (MS culture medium). For this purpose, three different genotypes including the wild type (Wt) plants Col-0 as the control, mutated homozygote plants with T-DNA fragment insertion (Mu26), and the homozygous overexpress plants (OE26) for AtPAP26 gene were used in all experiments. Our results showed a significant reduction in the expression level of PHT1, PHT2 and PHO1 genes, as well as the phosphatase activity in Mu26 plants compared to the Wt ones under -P condition. Under +P conditions, 58% and 42% incensement were observed in total and free phosphate content. In addition, the dry weight biomass increased 3- folds in the mutant plants compared to the wild type, respectively. On the other hand, the results showed the improvement of morphological and physiological characteristics in OE26 plants compared to Wt plants in both environmental conditions. Our result demonstrated that maintaining cellular phosphorus homeostasis in Arabidopsis plant requires the interaction of important phosphatases such as AtPAP26 with phosphate transporter in Pi stress conditions. These findings can be use in production of plants with the ability to absorb the minimum amount of phosphorus for plant growth under phosphorus stress.

Bread wheat is one of the most important cereals widely cultivated in the world. miRNAs are a type of small regulatory RNAs that have about 18-22 nucleotides long and can use as a novel breeding tool for plant genetic improvement. Because miRNAs are evolutionarily conserved between plant and animal kingdoms, the use of comparative genomics and computational methods to identify miRNAs is interesting. In this study, the goal was to identify potential new miRNAs in bread wheat by EST-based similarity search method. For this purpose, known plant miRNAs were used as reference against wheat ESTs and BLASTn was performed. Then, protein coding sequences were identified and deleted by BLASTx. The secondary structure was examined and then the candidate miRNAs were analyzed in the Rfam database. Finally, three new miRNAs were identified from this method, which were sequentially similar to the miRNAs known in Ae. tauschii. In order to confirm their presence in wheat and Agileops species containing D genome including tauschii, cylindrica and crossa, Real time PCR reaction was performed and finally confirmed the presence of myseq2 sequence in the shoots of studied plants. Identification of target genes of the confirmed miRNA revealed that most of them such as RGA, PIK and NB-ARC had an impact on resistance to various diseases and some of them played a role in resistance to abiotic stresses, such as drought and salt stress. The results showed that computational methods can be a suitable tool for predicting candidate miRNAs, which saves time and cost in identifying miRNAs.

Molecular markers have important role to improve yield of wheat through molecular plant breading. In this study, 13 SSR markers were applied to find marker trait association of 34 bread wheat and Chines Spring genotypes. The genotypes were cultivated in the field and 12 quantitative traits such as seed width, seed length, hundred-grain weight, spike length, No. seeds per spike, No. spikelet, flag leaf length, flag leaf width, days to anthesis, awn length, plant height, and peduncle length were recorded. In first, structure of population was studied by structure software. Marker trait association analysis with morphological data was done by tassel v.5 and General linear model (Glm). Structure study of population with ISSR data showed there were two subpopulations. The results from the SSR marker-trait association showed that Xgwm998-4B marker had significant association with seed length, 100-grain weight, seed width, no seeds per spike, plant height and peduncle length, Xgwm925-4B with seed width, no seeds per spike and days to anthesis, Xgwm910-4B with seed length, awn length and seed width, Xgwm891-4B with awn length and days to anthesis, Xgwm898-4B with seed width, days to anthesis and peduncle length, Xgwm710-4B with plant height, Xgwm888-4B with days to anthesis, Xgwm930-4B with peduncle length, Xgwm1084-4B with awn length, Xgwm295-7D with awn length, flag leaf length, days to anthesis and plant  height, Xgwm44-7D with 100-grain weight, days to anthesis, flag leaf length and flag leaf width, Xgwm885-7D with seed length, 100-grain weight and spikelet length. According to the results, the markers used in this study can be used for bread wheat molecular breeding.