فصلنامه ژنتیک نوین
سال هفدهم شماره 3 (پیاپی 70، پاییز 1401)

The genetic resources of domestic chickens include a wide range of breeds and populations which vary greatly in body size, skin color, body weight, egg, and meat production. In the current study, to study phylogenetic relationships, genetic diversity, and inbreeding, whole-genome sequencing data of 54 chickens of a common ancestor (Red Junglefowl), native ecotypes, and commercial lines were applied. An average of 98 million short reads were processed using bioinformatics software and single-nucleotide polymorphisms (SNP) were called. The genetic structure of the populations was studied using Admixture, SNPhylo software and SNPRelate package. Plink software was used to perform quality control and to calculate inbreeding. Genetic diversity in the populations was estimated using VCFtools software. The results showed that the lowest genetic distance with the common ancestor was related to Lari ecotype and the highest and lowest common SNP with Red Junglefowl was related to Arian broiler line and Leghorn laying line, respectively. Inbreeding in commercial lines (Arian and Leghorn) was more than native ecotypes. Compared to the common ancestor, higher genetic diversity was observed in native ecotypes (Lari, Khazak and Marandi, respectively) than in commercial lines. Our results indicated the importance of using markers across the genome to increase awareness of potentially harmful homozygosity and to prevent the loss of genetic diversity of native ecotypes. Genetic diversity in native ecotypes can only be maintained through organized breeding programs.

Metabolic acclimation to cold stress plays an important role in the survival, growth and yield of crops. Proline, as an osmolyte may take part in counteracting cold-induced oxidative stress in chickpea. In this experiment, content of hydrogen peroxide (H2O2), putrescine (Put), proline, activity of diamine oxidase (DAO) and relative expression of diamine oxidase (DAO) gene in cold-tolerant (Sel96th11439) and cold-sensitive (ILC533) chickpea (Cicer arietinum L.) genotypes under cold stress (4 °C) as a factorial experiment in a Completely Randomized Design were studied. In tolerant genotype, H2O2 content after a significant increase on the first day of cold stress decreased significantly on the sixth day of cold stress compared to control condition (up to 4.7%), while its accumulation was observed in sensitive genotype (up to 50%). These results indicated a relative acclimation to cold stress in tolerant genotype. Under cold stress, GABA and Put contents in tolerant genotype were higher compared to sensitive genotype (up to 1.47- and 3.2-fold, respectively). Under cold stress, increasing GABA content in tolerant genotype was accompanied with an increase in DAO activity and relative expression of DAO gene as biosynthetic pathway of this metabolite (up to 1.87- and 1.72-fold, respectively). The maximum activity of this route was observed in tolerant genotype on the sixth day of cold stress. Under cold stress, accumulation of proline in tolerant genotype led to reduce cell damage (H2O2 results) and improved cold tolerance. These indices were useful in assessment of chickpea genotypes under cold stress and breeding programs.

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is a leading cause of cancer-related death worldwide. Many studies confirm that the interaction between microRNAs and mRNAs plays an important role in the incipience and progression of HCC. Accordingly, to better appreciate the miRNA-mRNA interaction, gene expression data from liver tissue (GSE39791) was analyzed. Finally, six up-regulated and 62 down-regulated genes were identified using the LIMMA package in R. After that, significant mRNAs were analyzed by the miRNet database based on liver tissue; significant interactions of 56 microRNAs were found that targeted mRNAs, miRNA-mRNA network was visualized by Cytoscape software. Pathways analysis and biological processes of significant mRNAs with clusterProfiler and Goplot packages showed that the retinol metabolism, drug metabolism and chemical carcinogens pathways were the most significantly affected in HCC. But, the detoxification of inorganic compounds, retinol metabolism and terpenoid metabolism were the most meaningful in biological processes. Examination of signalling pathways revealed that the metabolic pathway is a critical biomarker in both of these two types of gastrointestinal cancer, which may serve a role in the pathogenesis. Examination of signaling pathways revealed that, the metabolic pathway as a critical biomarker in both of these two types of gastrointestinal cancer, which may serve a role in the pathogenesis. In summary, the present survey provided evidence that could support the prognosis of liver tumors in the future.

Black cumin is one of the most important native medicinal plants of Iran, which the seeds of this plant are used in the diet and have no side effects for human. Previous studies have shown the medicinal effect of this plant in various fields, but so far, no study has been done on the anti-cancer effect of the seeds of this plant. In this study, the anti-cancer effect of cumin seed extract on MCF-7 breast cancer cells was investigated. Firstly, the analysis of important pathways and genes affected by phytochemical inhibitors in the treatment of cancer was identified by text-mining. After extracting cumin seeds, the viability of MCF-7 cells treated with different concentrations of the extract were investigated using the Neutral Red method. Then flowcytometry technique was used to evaluate the effect of the extract on the apoptotic process. Finally, the expression of several important genes obtained from text-mining analysis was evaluated using real-time PCR. The effect of the extract on cell viability was dependent on the concentration. Black cumin seed extract at a dose of 160 μg/ml reduced cell viability by 50% in MCF-7 cells. Treated with black cumin extract, the genes obtained from text-mining analysis showed a change that could have a positive effect on cancer treatment. The present study showed for the first time that black cumin seed extract can induce apoptosis in MCF-7 cancer cells.

Black or stem rust disease with fungal agent Puccinia graminis f. sp. tritici is one of the most important and destructive wheat diseases in the world, and also,in Iran. Production of resistant cultivars (use of genetic resistance) by identifying sources of resistance, transfer of their resistance genes and pyramidization of effective resistance genes in desirable wheat genotypes (Commercial cultivars and lines under introduction which are susceptible to disease but high in yield), is the most effective method of sustainable control of this disease. Previous results of seedling stage evaluation of wheat line S-83-4 were acceptable as a resistance reaction to many stem rust pathogens in the country (2014-2016). In order to study the inheritance and type of action of genes controlling resistance components including infection type and latent period in line S-83-4, this line was crossed with sensitive cultivar Avocet'S ' and base generations F1, F2 , BC1 and BC2 were produced in farm conditions. Seedlings of parents and generations were inoculated by the high virulent race TTTTF (Boroujerd region) in greenhouse and compared based on a randomized complete block design in three replications. Weight analysis of variance showed a significant difference between generations in terms of measured resistance components (infection type and latent period). The average degree of dominance was higher than one for both traits, indicating over-dominance genetic control. Epistasis interaction effects of additive × additive and dominance × dominance were significant for the both traits. For both measured traits, broad-sense heritability was estimated as moderate, while narrow-sense heritability was low indicating meaningful effct of dominance in controlling of the both studied traits. To improve the studied traits, it is ideal to apply the selection in advanced separating generations (after reaching relative purity) resulting from crossing with S-83-4 line. According to the results of segregating genes estimates, more than one gene is involved in the genetic control of the measured resistance components. According to the results of race determination, by molecular analysis of six effective resistance genes/loci of stem rust (Sr22, Sr24, Sr25, Sr26, Sr31 and Sr39) by the respective specific markers in line S-83-4, the presence of Sr31 resistance gene, confirmed.

MicroRNAs (miRNA) are small (22 nucleotide) non-coding RNA molecules that post-transcriptionally regulate gene expression. Previous research has shown that miRNA plays an essential role in plant tolerance to adverse environmental conditions. In our study, we focused on the miR164 family in rice (Oryza sativa), an important food crop. We used a bioinformatics approach to analyze the sequences of all osa-miR164 of the miR164 family of rice, evaluate the expression profile of osa-miR164 under different stress conditions, predict cis-regulatory elements at the promoters of osa-miR164 genes, and simultaneously predict the miR164-targeted genes and their expressions. The results showed that the mature osa-miR164 sequences are highly conserved, but the precursor sequences are highly variable. The variation in the precursor sequences of osa-miR164 genes resulted in different expressions under stress conditions. In addition, different cis-regulatory elements in the promoter sequences of osa-miR164 genes could explain the different expression patterns of osa-miR164 genes. Some possible osa-miR164 target genes were discovered and their expression were studied under different stress conditions. Overall, the results of this study provided a valuable resource for further identification and evaluation of the interaction between osa-miR164 family target genes in response to abiotic stress.

The yarrow (Achillea spp. L) is one of the most important medicinal plants in the treatment of diseases and food industry. However, there are still limited reports on the genetic diversity and genetic relationships of yarrow species in the country. Therefore, the recent study was performed in order to (1) evaluate the genetic diversity between and within species of some Achillea species in Sanandaj and heir suburbs using SSR molecular markers and (2) to evaluate the efficiency and potential of microsatellite markers (SSR) in the separation and differentiation of the studied species and accessions of yarrow genus. Genetic diversity was assessed in 28 yarrow accessions belonging to seven vehicle species using 16 pairs of SSR markers. Genomic DNA was extracted by CTAB method from fresh and soft leaves of two to three week plantlets obtained from accessions seed culture as bulk. The products of PCR amplification were seperated by 2.5% metaphor agarose gel electrophoresis and photographed with a document gel apparatus. The PopGene, GenAlEx 6.2, DARwin 5, PASTv3.18 softwares were used to calculate genetic parameters, molecular variance analysis, similarity matrix, cluster analysis and principal component analysis (PCA). Twelve pairs of SSR primers set identified 56 alleles among yarrow species. The average percentage of polymorphs and the number of polymorphic alleles were 82.56% and 3.92, respectively. The average of polymorphic information content (PIC) was 0.324. Based on molecular analysis of variance, 64% of the available variance was intra-species and 36% was inter-species. The mean of total similarity coefficients between species and between populations were 0.76 and 0.588, respectively. Cluster analysis separated the populations to a high extent (82%) and also put up the studied species into three separate groups. The results of principal coordinate analysis (PCA) were comparable with the results of cluster analysis and similarity matrix and confirmed them to a large extent. Generally, the studied accessions of yarrow showed a relatively high genetic diversity, so that the highest amount belonged to intra-species diversity. The SSR marker had high efficiency and potential in detecting genetic diversity, separation and differentiation of yarrow populations and species. Therefore, these markers will help identify elite genotypes for domestication and breeding programs of these plants.

The genus of Aegilops is one of the most important wild relatives of wheat, and different species of this genus have a wide distribution in Middle East and West Asia. Knowledge about the genetic diversity of Aegilops species provides useful information which can be exploited for breeding programs of wheat. In this study, genetic diversity of 60 Agilops accessions from three different species were investigated using three different DNA markers. CBDP, SCoT and ISSR primers amplified 130, 135 and 152 polymorphic fragments respectively. The average of polymorphism information content (PIC) for CBDP, SCoT and ISSR primers were 0.37, 0.34 and 0.39 respectively indicated the efficiency and usefulness of the used primers. The neighbor-joining (NJ) based clustering using marker data, classified all 60 accessions into three main groups and the investigated accessions were clustered based on the genetic structure. The results of analysis of molecular variance based on CBDP, ISSR and SCoT data showed that the variance among populations covered 66%, 45% and 42% of total variation respectively. Besides, among all three species, Ae. triuncialis showed the maximum number of private allels indicating its unique genetic background. Our results revealed high levels of genetic diversity within all three species, showing high potential of studied germplasm for using in breeding programs. Further, our findings indicated that all three marker systems were useful techniques for evaluation of genetic diversity, however, CBDP and SCoT markers which are generated from the functional regions of the genomes, would be more useful for evaluation of genetic diversity than random or semi random PCR based markers.

In a breeding program, knowledge on the effect of genes plays a key role in designing breeding programs and realizing effective selection. In this study, the breeding value for 17 traits in maize was estimated by using SNP markers data via Best linear unbiased prediction (BLUP) method. Among the studied genotypes; genotype 25*/89 in terms of date to emergence of male flowers, genotype P13L2 in terms of chlorophyll content had the highest breeding values. Genotype S2/QPM/SUKMA (Indonesia) in terms of plant dry weight, leaf length, plant height and genotype R59 (Paternal) in terms of first cob emergence date and genotype 1264/1 in terms of second cob emergence date had the highest breeding values, respectively. Genotype Kahia P16L4 showed positive and high breeding value in terms of grain weight per plant. P11L7 for cob number, P9L6 for cob length, P10L5 for leaf width, leaf area index, diameter of beginning part of cob, middle diameter of cob, cob weight and plant height had the highest breeding values. Considering the total breeding values of the studied traits, genotypes such as P10L5, P16L6 Kahia, P10L7, P10L9 had the highest rank. The estimated narrow sense heritability for the studied traits was in the range of 0.22 to 0.94. Genotypes with the highest breeding value have the highest ability to transfer their traits to offspring. Therefore, they can be used as a desirable parent to modify these traits in crop breeding programs.

Medicinal plants are the source of more than 25% of all drugs consumed in the world, which play a special role in the supply of anti-cancer drugs. One of the more important of these drugs is Taxol. The natural source of this valuable substance is the species of Yew (Taxus baccata). Taxol production takes place in a complex enzymatic pathway that is influenced by a variety of factors, so the aim of this study was to identify the effect of methyl jasmonate on altering the expression of the Taxadiene synthase (ts) gene and Taxol production in Yew. In the following research, plant samples were treated with methyl jasmonate in different concentrations of 0, 100, 250 and 500 μM for two different hours of 48 and 72, during which time they were stored samples in phytotron. Then, ts gene expression was measured by Real Time PCR approach. In addition, the amount of Taxol production was evaluated by HPLC technique and the obtained data was analyzed. The results showed that at 72 hours, expression of ts gene at a concentration of 250 μM was 1.13 times higher than the control plant and the lowest gene expression with less than 5% of the control plant was related to 250 μM treatment in 48 hours. Chromatography analysis showed that the highest amount of Taxol produced in the treated plant with a concentration of 500 μM methyl jasmonate and at time of 72 hours was 0.307 mg/g dry weight. Also, treatment of 250 μM methyl jasmonate with 72 hours and production of 0.08 mg Taxol was the lowest. Pearson correlation test showed that there is no clear relationship between gene expression and Taxol production. This is due to the complex effects of methyl jasmonate on gene expression and Taxol production at different time. Despite many efforts to identify the biosynthetic pathway of Taxol, a clear and accurate imagine of it still is not available. Therefore, it is important to study the important genes involved in this biosynthetic pathway.

In this study, geneti diversity of 28 genotyped of rapeseed using 7 markers ISSR, 3 indicates Retrotransposons and 22 combined markers were evaluated. The results of cluster analysis and molecular evaluation UPGMA with method by criteria simple matching coefficient using data from primer ISSR, Retrotransposons and hybrid primer ISSR and Retrotransposons 28 genotypes studied in 3 groups, the groups were: 14, 9 and 5 genotypes are among the groups, the first group is the largest group, but the morphological traits of 28 genotypes by UPGMA and Euclidean distance criteria were divided into 4 groups. Grouping results of cluster analysis by linear discriminant analysis using Fisher's 100 percent for molecular.