فصلنامه ژنتیک نوین
سال پانزدهم شماره 2 (پیاپی 61، تابستان 1399)

Sequence-specific nucleases (SSNs) has been proposed as a powerful tool for basic and applied plant biology researches and seems to be an effective method for resolving current issues in agriculture. Here, we describe the principle and application of available genome editing tools, including meganucleases (MN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat-associated CRISPR/Cas9 system. Among these; CRISPR/Cas9 is the most recently characterized and rapidly developed genome editing technology, and has been successfully utilized in a wide variety of organisms. This review specifically illustrates the power of CRISPR/Cas9 as a tool for plant genome engineering and describes the strengths and weaknesses of the CRISPR/Cas9 technology compared to two well-established genome editing tools, ZFNs and TALENs.

Quince (Cydonia oblonga Mill.) is considered as a self-compatible species, but some levels of self-incompatibility also have been reported in its cultivars and genotypes. Therefore in this research allelic diversity, isolation and deposition of alleles has been considered in some indigenous quince cultivars and genotypes of Iran. The primes were designed according to the C1 to C5 conserved regions of apple and pear species. 55 genotypes, cultivars and related species of quince were evaluated and amplification of this locus demonstrated various band lengths between 500 to 1100 bp with 13 various sizes. After partial sequencing, these bands primarily were coded as Sq1 to Sq13, but the frequency of two putative alleles, Sq13 and Sq4 where higher than other respectively with 17.7 and 14.4%. Sequencing of the first self-incompatibility allele (S1) in KM1 genotype or cultivar Torsh Esfahan revealed the highest homology of this allele with S6 of apple species Malus domestica Borkh. and Ss (S111) of pear species Pyrus communis L., respectively, with 94 and 93 of nucleotide similarity.

Ursolic acid is a natural compound of tryptophan pentacyclic which is found in flowers and fruits, as well as in some medicinal plants such as mint, basil, savory. In this study, the effect of ursolic acid on C2C12 cells and satellite cells (SC) which are isolated from native day-old chicks was investigated. First, the cells were cultured using the pre-plating method. Then, to determine the appropriate dose of ursolic acid, the MTT technique was used. Also, qRT-PCR technique was used to investigate the expression of genes involved in the proliferation and differentiation of satellite cells. Data were analyzed using SPSS software, the independent t-student test was used for mean comparison between the treated and control groups.  Microscopic images and the results of the flow cytometry technique using PAX7 antibodies confirmed the nature of satellite cells. Also, the results have been illustrated  that ursolic acid at a concentration of 0.00025 mg / ml significantly increased the expression of genes involved in the proliferation and differentiation of satellite cells, including PAX7, MyoD and Myogenin (p <0.05). Ursolic acid appears to increase muscle hypertrophy in native chickens through increasing the expression of the PAX7, Myogenin and MyoD genes. As a result, ursolic acid can be suggested as a suitable material for improving the growth in native chickens.

Phylogenetic relationships of Bromus pectinatus complex and its intersectional hybrid origin were studied using nrDNA ITS and ETS and, plastid matK datasets. A total of 37 taxa representing three outgroups (Hordeum marinum, Triticum turgidum, Littledalea alaica) and 34 taxa of Bromus species were included in phylogenetic analyses. Phylogenetic interspecies relationships were constructed by Bayesian and likelihood analysis. On the basis of the present study, sects. Genea and Bromus were not monophyletic. The plastid and nuclear ribosomal data indicated incongruency related to sects. Bromus and Genea due to the position of B. gedrosianus and B. pulchellus (B. pectinatus complex) as well B. oxyodon and B. sewerzowii, supporting intersectional hybrid origins for these species. Molecular trees didn’t support the hybrid origin of B. pectinatus complex from B. japonicus because of their placement in separated clades. Plastid data were confirmed relationship between B. sterilis and B. tectorum with B. pectinatus complex.

Tortrix viridana L., commonly known as green oak leaf roller, is a major harmful herbivorous pest for oak forests that cause severe yield loss via almost complete defoliation during the pest outbreak in spring. In spite of importance of controlling this pest , little is known about the population structure and DNA-based genetic diversity of this pest in Iran. In this study, genetic structure and diversity of 105 genotypes representing 16 populations of Tortrix viridana from North-Zagros forests was studied using inter simple sequence repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers. Ten ISSR primers amplified a total of 127 bands of which 121 were polymorphic. Also, eight RAPD primers produced a total of 105 fragments with 105 polymorphic bands. Estimated coefficient of inter-population genetic differentiation (ΦST) based on ISSR and RAPD primers were 0.26 and 0.18 respectively. Molecular analysis of variance (AMOVA) showed that most of the total revealed genetic diversity distributed within populations than between populations for both marker systems. The gene flow estimate (Nm) among populations was 0.461 (ISSR) and 0.527 (RAPD), suggesting restricted gene flow, the poulations are not genetically distinct. These findings could provide important information on the population genetic diversity of this destructive pest, which can be suitable in designing effective strategies for integrative management of this pest in Zagros forests.

Drought is one of the most important abiotic stresses in agriculture, which limit crops production. Drought tolerance is a complicated trait that is controlled by polygenes, which is expresses the difficulty of breeding of drought tolerance. Variety of strategies has been used to improve this trait in crops, including traditional selection methods and genetic engineering. In this case, irradiation is an appropriate approach for improving the level of genetic variation in a short time. Many studies show that the expression of most genes in environmentally variable conditions is based on the combination control of several transcription factors and their binding to the elements in the promoter. Therefore sequencing of one of the genes involved in the degradation of proteins (26Sp7) using genome sequencing, sequencing of promoter using NEW PLACE and plantCARE software, And the expression pattern 26Sp7 in mutant line T-65-58-8 (semi-drought tolerant) derived from Tabasi (drought-sensitive) radiated with gamma rays in seedling stage during drought stress by QRT-PCR were studid. The expression of the 26Sp7 in Tabasi and mutant showed an increase in all stress treatments. So, in the mutant line, it has peaked in 3 hours after start of stress. On the other hand, in Tabasi, with the onset of drought stress, the expression of this gene increased, until it reached maximum in 48 hours after stress. The expression in the Tabasi showed an increase in gene expression in all stress treatments, which in turn probably indicates the destruction of proteins in drought stress treatments, which also verified the sensitivity of this variety. on the other hand, the promoter sequences of this gene indicate regulatory elements during drought stress such as dehydration responsive elements (DRE) and the binding site of MYB and MYC proteins and abcisic acid responsive elements (ABRE) and responded to light (GT) and gene transcription regulator elements such as the TATA box and the CAAT box. Thus, the increased expression of this gene during drought stress may be attributed to the binding sites of transcription factors that cause this gene expression during drought.

Bean is one of the protein-rich legumes that can cause collar rot and severe loss of yield due to Sclerotium rolfsii. Bean cultivation in Guilan is mainly devoted to spring and summer cultivation date of some kind of dwarf local beans with red and red veins on the seeds. The 30 selected local beans in Guilan, with the most pathogenic strain of S. rolfsii, were subjected to artificial infection in the greenhouse. Disease Severity Index (DSI) and morphological traits associated with the reaction to the fungus were measured. Eight linked SCAR markers with resistance to bean fungal disease were also used for additional evaluation. Expression changes of the three defense genes including of chitinase (Chiti), chalcone isomeras (ChI), and phenylalanine ammonia lyase (PAL) were analyzed using Real -time PCR in selected lines from each of the resistant, tolerant and sensitive groups, with intervals. They were evaluated at 2, 4 and 6 days after artificial infection with S. rolfsii fungus. Statistical analysis and screening of genotypes using greenhouse data and SCAR markers led to the separation of genotypes and the identification of one resistant, 21 tolerant and semi-susceptible and 8 fully sensitive genotypes. The results showed that the Chiti gene had a similar trend with a gradual increase in expression over the time in resistant and tolerant lines, although the rate of expression in resistant was higher than tolerances. Although the expression of ChI and PAL genes was increasing in resistant genotypes, the expression changes over the time were not the same as the Chiti gene trend. Therefore, the Chiti gene may be a major factor in the resistance of S. rolfsii fungi to local beans in Guilan.

The Yaghoot grape of Sistan is the earliest grape cultivar in Iran and its product is harvested at the end of May. The early ripening in grape is a desirable trait, because the product will be harvested before starting the warm and dry 120-day winds so it can escape the Sistan heat season. In this study, the expression pattern of two genes, Chalcone Synthase and ABA-8′ Hydroxylase, as transcription factors involved in the early ripening process of Yaghooti grape cultivar were investigated during different developmental stages. The leaf samples related to early ripening cultivars Red and White Yaghooti and late cultivars Fakhri and Cheshm-e-gavi and Sangi intermediate cultivar  as control treatment were studied during two development stages of grape clusters (filling and ripening the berries) using Real-time PCR method. The results of the expression changes of the studied genes showed a meaningful expression pattern in early cultivars compared by late cultivars during differnet developmental stages in grape clusters. The findings indicated that the ABA-8′ Hydroxylase gene was a transcription factor involved in the early ripening of the Sistan Yaghooti grape cultivar, and the Chalcone Synthase gene are playing an important role in ripening and changing the color of the berries.

Cynara cardunculus L is a diploid herbaceous plant and perennial. Artichoke sugar is a fructan that has the least effect on blood sugar and is very useful for diabetics in this regard. The aim of this study was to isolate, identify, and evaluate the relative expression of the fructan 1-exhohydrolase gene (FEH1) gene in the artichoke plant. In order to identify and evaluate the molecular evolution of FEH1 gene, DNA was extracted from leaf samples of artichoke and after amplification was sequenced by PCR technique. Also in order to investigate the effects of salinity, silver nanoparticles of green synthesis and salicylic acid on the change of relative expression of FEH1 gene, an experiment was performed as a factorial in a completely randomized design in a greenhouse. The relative expression pattern of this gene was measured by Real Time PCR. The results of analysis and analysis of nucleotide sequences of the FEH1 gene showed that the highest frequency belonged to Guanin (31.56) and the lowest frequency belonged to Tymien base(12.4). The results of the Neutrality test also showed a directional choice on this gene during evolution. A phylogenetic study of the FEH-1 gene sequence and its comparison with other similar sequences in different plants proved that the similarity between the studied sequences was high(more 90%) and the plants were slightly different from each other in terms of genetic distance. The results of comparing the mean interactions of salicylic acid and salinity concentrations showed that the application of 12  ds m-1of salinity alone significantly increased the expression of FEH1 gene at the probability level of one percent. The use of salicylic acid in combination with salinity moderated the effects of salinity and also reduced FEH1 gene expression. Also, the results of comparing the average interaction of salicylic acid and nano silver concentrations showed that in the treatment of 200 and 400 mM salicylic acid with 40 mM nano silver at the probability level 1% expression of FEH1 gene in artichoke plant increased significantly. Clearly, it was found that both in terms of expression and expression intensity of FEH1 gene, there is a high potential to focus on increasing soluble sugars and ultimately increase plant tolerance to salinity stress in artichoke .

Edible oils are one of the essential commodities in the food basket of the people. Maintaining oil oxidative stability to extend shelf life and enhance the quality and nutritional value of the product is particularly important. This is achieved by increasing the content of natural antioxidants such as tocopherols as additives or by modifying their content and composition in oilseed plant through metabolic engineering of key enzymes or transcription factors involved in tocopherol biosynthesis. The present study aimed to identify transcription factors corresponding to conserved motifs in the promoter regions of VTE4 and its orthologous genes as a limiting bottleneck in tocopherol biosynthesis using bioinformatics tools. The results showed that the transcription factors mainly belonged to hemodomain-like (24.4%), bZIP (17.1%), SANT / MYB (14.6%), K-box (12.2%), MADS-box (12.2%) and MYB (12.2%) families. Furthermore, functional analysis of transcription factors indicated a significant interaction between response to abiotic stresses, hormone signaling pathways, especially abscisic acid and gibberellic acid, and the tocopherol biosynthesis pathway. On the other hand, the prominent role of light stimuli, in particular, red and infrared light, and light signaling pathway components was observed in the induction of expression of VTE4’s transcription factors.