فصلنامه ژنتیک نوین
سال هفدهم شماره 2 (پیاپی 69، تابستان 1401)

Wheat is the main food of near 40 percent of the world's population. Due to the growing population of the world and global climate changes, increasing the yield performance of field crops is one of the most important challenges facing plant breeders. Leaf rust is one of the most important fungal diseases that dramatically reduces wheat production. In general, the management of fungal diseases depends mostly on several factors such as tracing virulent pathogens, genetic and pathological diversity in the pathogen population, production of resistant cultivars, and development of resistance genes in different epidemiological regions. Due to the complexity and time-consuming stages for improving resistant wheat cultivars to a specific disease by traditional methods, the employment of molecular marker-assisted selection as one of the powerful tools in increasing the efficiency, accuracy, and speed of breeding programs for disease resistance is of particular importance. Using molecular markers, breeders will be able to produce improved cultivars containing resistance genes against various diseases, including leaf rust (Lr genes), with greater speed and accuracy. In this study, our attempt is centered on discussing the most important loci controlling resistance to wheat leaf rust disease and corresponding molecular markers associated with identified Lr genes.

Newcastle disease (ND) is a well-known and major viral disease of poultry industry all over the world. Viral matrix (M) protein is a structural protein linking the viral envelope with the virus core that plays an important role in pathogenesis. It plays a crucial role in virus assembly and interact with the ribonucleoprotein (RNP) complex as well as with the viral membrane. Due to the role of matrix protein, this study was performed to complete previous studies to identify a Newcastle disease virus (NDV) isolate naming CH/RT40/IR/2011 which is prevalent in commercial broiler flocks in Khorasan Razavi province. The full M protein gene of the RT40 was amplified using specific primers and then cloned into a PTZ57R/T cloning vector. The cloning vector product was sequenced from both directions and data analyses were performed using CLC Main Workbench 5.5. The phylogenetic tree was constructed with the maximum likelihood method in MEGA 6. Nucleotide sequencing of M protein gene (nt: 1241), phylogenetic tree and analysis of genetic distances between genotypes showed that RT40 was similar to Iranian (MF417546) and Iraqi (MT370499, MT370497) NDVs subgenotype VII.1.1. Investigation of amino acid sequence of the nuclear localization signals (247KKGKKVTFDKIEEKIRR263) and other matrix gene protein regions revealed that this virus was very similar to very virulent NDVs. These results completed the prat of information required for full characterization of RT40 as well as for introduction of a native NDV strain.

Soil salinity is one of the most agricultural problems that reduces the growth and yield of crops. Although, barley is the most salinity- tolerant plant among cereals but its seedling stage is the most sensitive developmental stage to salinity stress. Thereby to study the effect of salinity stress at seedling stage on biochemical traits including thiobarbituric acid reactive material (TBARM), catalase activity, and proline values, a factorial based on randomized complete design with four replications was conducted. The experimental factors included two levels of salinity (EC= 0 and 22 ds/m-1) and two barley genotypes (sensitive (Fajr) and tolerant (Afzal)). ANOVA results showed a significate effect for interaction between salinity and genotype (p<0.01) on all traits. Under salinity stress, thiobarbituric acid reactive material (TBARM), catalase activity, and proline values were increased in root and shoot of both genotypes at seedling stage. The higher value of proline and catalase activity, lower level of TBARM were observed in tolerant genotype (Afzal). Therefore, it seems that tolerant genotype copes with the oxidative and osmotic stresses induced by salinity through the increment of antioxidant activity and compatible solutes, respectively. Moreover, relative expression of three genes (NHX3, CAT1 and TIP2;3) in root and shoot were investigated under salinity stress at seedling stage. Expression pattern of NHX3, CAT1 and TIP2;3 genes in tolerant genotype under salinity stress revealed that they play roles in the salinity tolerance of barley. Thereby, aforementioned genes could be used as promising candidate genes for genetic tolerance to salinity stress in crops.

Cancer is one of the leading causes of death in the world. In most cases, it can be treated if the disease is detected earlier. One way to diagnose cancer is to use microarray data, which, unlike imaging, does not contain harmful rays to humans. Microarrays have many genes that complicate and take time to analyse, so selecting useful genes is one of the key steps in diagnosing the disease. The proposed method in this paper has two main phases, the first of which is the selection of effective genes. In the next phase, the disease is diagnosed from the selected genes by the first phase. In the past, many algorithms such as Ridge have been proposed for this purpose, which according to the results of experiments, the accuracy of the method proposed in this paper is superior to them. In this paper, leukaemia and colon cancer datasets are used as input and evaluation of the proposed method. The precision of the proposed method for locating genes and diagnosing leukaemia and colorectal cancer is 97.62% and 92.31%, respectively. The results obtained from this method compared to other existing methods in terms of precision in the leukaemia dataset 2.39% and in the colorectal cancer dataset 5.62% improved; It is also easier to access and less expensive than biological experiments.

Low temperature stress is a kind of abiotic stress directly affecting growth and productivity of important agricultural products including wheat, worldwide. The purpose of the present study was to investigate the relationship between developmental regulation with low temperature tolerance, hydrogen peroxide (H2O2) accumulation and the expression of antioxidant enzymes genes in different phenological development stages in lines (RIL) of crosses between Pishtaz and Norstar wheat. Winter- and facultative-habit genotypes in the second period of low temperature acclimation, coinciding with the saturation range of the vernalization requirement, reached their maximum of low temperature tolerance, followed by a decrease in low temperature tolerance at the reproductive phase in third period of low temperature acclimation. Spring genotypes had very limited low temperature tolerance. Relative expression of TaVRT-1 gene in spring genotypes showed high and constitutively expression during low temperature acclimation periods. However, the relative expression of this gene in winter- and facultative-habit genotypes is expressed only after vernalization saturation. The relative expression of antioxidant enzymes genes were higher in winter- and facultative-habit genotypes than spring- habit genotypes, and reached its maximum in the second period of low temperature acclimation. Along with the increasing of relative expression of TaVRT-1 gene and decreasing antioxidant enzymes genes in the third period of cold acclimation, the accumulation of H2O2 reached maximum. Our results suggested that winter- and facultative-habit genotypes decreased the expression of TaVRT-1 gene and subsequently increased the length of the vegetative phase and the relative expression of antioxidant enzymes genes. Such reactions prevented the oxidative damage induced by low temperature stress and promoted more tolerant of low temperature.

Satureja genus, from the Lamiaceae family, is a medicinal plant that is widely distributed in the southern regions of Iran. Different species of this plant have many medicinal properties such as antioxidant properties and medical applications. However, lack of molecular markers, especially microsatellite markers, has severely limited the development of Satureja genetic researches. Therefore, in this study, 271907 and 225534 transcripts were obtained with average lengths of 1079 and 1018 bp and N50 values equal to 1802 and 1740 for S. khuzistanica and S. rechengeri, respectively. The assembly process of short reads of transcriptome sequences of S. khuzistanica and S. rechengeri was used to identify microsatellite markers. In the present study, 44624 and 34546 SSR loci were identified in S. khuzistanica and S. rechengeri, respectively. Among these markers, dinucleotide repeat motifs were the most abundant, followed by mononucleotide and trinucleotide. In S. khuzistanica and S. rechengeri, the results of blast of transcripts containing SSR showed that 72.27% and 75.32% of the transcripts had at least one record in the non-redundant protein database, respectively. Functional annotation was performed through the search for homology and gene ontology (GO). In total, 14792 (33.4%) transcripts with SSR markers for S. khuzistanica and 12480 (36.12%) transcripts with SSR markers for S. rechengeri were classified into three groups of GO. Gene ontology analysis reported that most of the assembled transcripts are related to the Molecular Function (MF) group. 45% of the total transcripts containing microsatellites were allocated to 401 pathways, in which the biosynthesis of secondary metabolites was identified as the second pathway with the maximum number of members after the metabolic pathways. This is the first report about the identification of microsatellite markers from the transcriptome sequence of Satureja and this information could be an effective source for breeding programs of this medicinal plant.

Capoeta is one of the most important genera of the Cyprinidae because of its diversity and range of distribution with at least 36 valid species in the Middle East. Most species of this genus are morphologically similar to each other, and mixed or intermediate populations of them can be seen in many places. It is difficult for researchers to identify them. Although relatively extensive studies have been performed on members of this genus, the main purpose of these studies was to investigate a complex or description of members of this genus. In this regard, Capoeta Cytb gene sequences were extracted from the NCBI. After modifying and aligning the sequences, the best evolutionary model for the dataset was selected by ModelFinder and the phylogenetic tree was drawn with IQTREE. According to the results, the presence of 19 valid species of this genus, belong to three main clades of Iran-Anatolia, Aralo-Caspian and Mesopotamia, was confirmed. Also, the presence of C. razii were confirmed in the Tigris Basin and C. birunii regards as C. coadi synonym. In addition, presence of C. sevangi in Iran was not confirmed.

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.

Basil (Ocimum basilicum L.) is a medicinal and aromatic plant, which is used in traditional Iranian medicine. Monoterpenes, sesquiterpenes and phenylpropanoids make up the bulk of the essential oil of basil. A significant part of terpenoids is composed of the volatile monoterpene compound linalool, which is very important in the plant's tolerance mechanism against various environmental stresses due to its defensive effects. Linalool synthase (Lins), as a key enzyme of terpenoids biosynthesis pathway, converts the main precursor of monoterpenes into final compound linalool. In current research, to explore the formation and transcriptional control exerted on this pathway, relative expression profile of key gene in the biosynthesis pathway of linalool (ObLins) were evaluated in the three cultivars of O. basilicum under control (100% FC) and the three levels of drought stress (W1: 75% FC, W2: 50% FC and W3: 25% FC) using quantitative real-time PCR. In order to regulate the expression pattern of ObLins gene under drought stress, isolation, characterization and functional analysis of pObLins promoter were performed. The results show that in the promoter of this gene, regulatory elements responsive to drought stress including MBS, MYB-site, WRKY710S, W-Box, CCAAT-Box, DRE2 and CBFHV and the binding site of transcription factors influencing gene transcription of linalool synthase is present under drought stress. Transient expression of the GUS gene under pObLins promoter control in Nicotiana tabacum leaves showed that this promoter with the presence of core elements was able to direct the basal expression of this gene. Due to the presence of cis-regulatory elements responding to biotic and abiotic stresses in the ObLins gene promoter, it is expected that this promoter will be able to express the ObLins gene in response to environmental stresses by regulating its transcription rate.

Drought stress is one of the most important abiotic stresses that limits crop production in the world. Identification of superior crop genotypes is the first step of breeding programs, while molecular markers reduce the time needed for breeding projects. Sugar beet is one of the most important crops that plays a key role in providing food in the world. In this research, 20 sugar beet hybrids were used to study diversity with 10 SSR primers and 9 RAPD primers to determine the relationship between this diversity and drought tolerance. Genetic variability indices in sugar beet showed that the highest PIC (Polymorphism Information Content) in the SSR and RAPD were related to BQ583448 marker (76%) and J marker (44%). Cluster analysis based on molecular data was performed using Jaccard's similarity coefficient and UPGMA method. Cluster analysis of STI and molecular markers showed that SSR markers BQ583448 and FDSB502 and RAPD markers: J and A caused segregation of susceptible and drought tolerant genotypes. Assessment of genetic variation in drought tolerance with SSR marker was almost useful and can be used in drought tolerance improvement programs.

The objective of the present study is to investigate the response of halophyte Aeluropus littoralis to salinity stress. This experiment was conducted in three levels of treatments containing control (without salt), 200 and 400 mM NaCl with three replications for each.  The changes were measured at 6 and 24 h after applying salt treatment. The results showed that the soluble sugar content increased with increasing time and NaCl concentration, So thatو This increase was observed at both treatment after 24h and only at 400 mm after 6h salt stress. Also, The proline content also increased significantly in the both concentrations at the 24 h compared to the 6 h after salt stress. On the other hand, protein content  at 6 h and 200 mM concentration was no significant different, but there was a significant decrease in protein content at 400 Mm treatment at the same time. in contrast, the protein content was significantly decreased both concentrations at 24 h. The results of relative gene expression analysis showed that PYL gene expression was strongly affected by salinity stress and showed a significant decreasing trend (p <0.05). So that, the rate of this reduction at 6 hours is much higher than at 24 hours. ABF gene expression generally showed an increasing trend, which increased significantly in both treatments at 24 h. Therefore, it can be stated that soluble sugars and proline as adaptive compounds in response to salinity stress in Aeluropus littoralis plant and abscisic acid signaling pathway are strongly affected by salinity stress

Tomato yellow leaf curl viral disease (TYLCV) is one of the main limiting factors that has caused great damage to tomato crop in tropical and subtropical regions of the world. Several genes have been identified from various sources that cause plant resistance to TYLCV virus disease and have been integrated into tomato crop genotypes. Pyramiding of these genes can lead to Stable resistance and, in addition, Causes resistance to several strains of the virus. The results of this study showed that viral infection increases the level of phenol and flavonoid compounds as well as antioxidant enzymes in the host plant, while lines containing the Ty-2 and TY-1/3 genes They had lower synthesis and expression of non-enzymatic antioxidant compounds (phenol and flavonoids) and antioxidant enzymes (catalase, peroxidase, guaiacol peroxidase and polyphenol oxidase). Also, in the study of TYLCV virus genome concentration using quantitative polymerase chain reaction technique, it was observed that the lines containing two Ty-2 and TY-1/3 compared to control plants had the lowest rate of the virus genome. This matter indicates the low rate of virus replication in the host plant. According to the observations of this study, by combining different TY genes, a desirable level of resistance in desirable but sensitive tomato lines against TYLCV virus can be achieved.