فصلنامه ژنتیک نوین
سال هجدهم شماره 2 (پیاپی 73، تابستان 1402)

The Valerian plant (Valeriana officinalis) contains compounds that can be used to treat nerve disorders, epilepsy, and sleep disorders. Terpenes (sesquiterpenoids) are the major group of compounds in this plant, whose biosynthesis pathway is poorly understood. Due to the lack of genomic sequence, studies based on de novo transcriptome assembly are important to elucidate more genes of the terpenoid biosynthetic pathway in this valuable medicinal plant. To reconstruct de novo assembly of RNA-Seq data from previously published SRR data for V. officinalis, Trinity and rnaSPAdes were used in this study. The primary assemblies were then analyzed using additional tools, such as CAP3 and CD-HIT-EST, in an attempt to determine the most effective de novo assembly. Based on the results of quality assessment tools such as rnaQUST, SeqKit statistics, and BUSCO, the combination of CAP3 and CD-HIT tools successfully produced an optimal assembly for Trinity (T-CAP-CD). A total of 57.78% of T-CAP-CD assembly genes were annotated in three subgroups (BP, MF, CC) with the highly accurate plant-specific Hayai-Annotation Plants annotation tool. The reconstruction of the KEGG pathway revealed 30 ortholog genes in the terpenoid biosynthetic backbone pathway and 8 ortholog genes in the sesquiterpenoid biosynthesis pathway. By performing homology search of T-CAP-CD transcriptome against PlantTFDB v.5, the most frequent transcription factor families were identified as bHLH (9.5 %), NAC (7.3 %), and MYB (6.6 %), respectively.

The embryonic development program is the response of the mammalian organism during a critical period of development that qualitatively changes development. The study of genes is a way to improve the fetal development program and increase skeletal muscle meat production. In this research, the data were downloaded from the GEO database with the accession number GSE23563. The LIMMA package was used to control the quality of raw data and analyze the differentially expressed genes. Analysis of gene ontology and biological pathways was done using Enrichr online server. STRING software was used to find interactions between genes and Cytoscape software was used to further analyze interactions and display their network. The results showed that a total of 445 genes were differentially expressed between 70 and 120 days of pregnancy, and a total of 84 genes were differentially expressed between 120 and 135 days of pregnancy. Using Venn diagram software, 34 common genes were identified between these periods. The results of gene ontology and pathway showed that in the period of 70 to 120 days, regulation of cell population proliferation, muscle tissue development, myoblast differentiation, negative regulation of developmental growth, negative regulation of developmental process, positive regulation of cell development, regulation of fibroblast proliferation, Signaling pathways (PI3K-Akt, HIF-1, Rap1, PPAR, MAPK), ECM receptor interaction, insulin resistance and in the period of 120 to 135 days, regulation of cell differentiation, regulation of differentiation Muscle cells, positive regulation of cell differentiation, positive regulation of developmental process, regulation of cell population proliferation, negative regulation of growth, negative regulation of cell population proliferation, embryonic organ development, Signaling pathways (MAPK, p53), the important functional activities and pathways were related to the development of skeletal muscle during the pregnancy period of sheep. Hub genes ESR1, PTK7, TNFSF11, and CEBPB were identified among the common genes between the two time periods. These genes can be used in animal breeding to solve the problems of low birth weight animals, reducing meat production, diseases caused by low animal weight and increasing mortality at birth.

High sugar content in melon is one of the most important goals in breeding programs. To develop hybrid cultivars with favorable traits and high sugar content, the two wide cultivating cultivars of “Samsoori” and “Saveh” were crossed with a commercial hybrid of “Galia” and F5 families were produced with pedigree selection method. In this study 32 F5 families along with the parental genotypes were evaluated in a randomized complete block design in farm and yield, number of fruits per plant, days to harvest, fruit related traits and sugar content were measured. The results showed that except the number of fruits per plant, for other traits there were highly significant difference among families. SNP marker related to sugar content candidate gene (SlERF1) was genotyped in 41 random selected plants from F5 generation. The sequence of the reported SNP which associated with sugar content was verified by sequencing and showed polymorphism between parental genotypes. Sequencing data revealed that two genotypes of A1A1 and A2A2 among plants tested in F5 generation with no heterozygote genotype. The sugar content of A1A1 (12.7ºB) genotypes were highly significant from that of A2A2 (10.3ºB) genotypes. Therefore the efficiency of this SNP in SlERF1 candidate gene for selection of favorable lines was validated. This molecular marker can accelerate the breeding of sugar content in breeding programs in future. Also, the 15 plants with A1A1 genotypes can be crossed with each other to produce hybrid cultivars.

Species belonging to the Aegilops genus are one of the most important genetic resources of wheat. This germplasm due to its breeding potential usually is served in wheat breeding programs. In the present study, genetic diversity among 60 accessions belonging to Ae. crassa and Ae. cylindrica were investigated using start codon targeted polymorphism (SCoT) markers. The obtained banding pattern showed that in total 171 fragments were amplified across all investigated accessions, out of which 156 were polymorphic. The average values for polymorphism information content (PIC), resolving power (Rp), and marker index (MI) indices were estimated as 0.30, 16.27, and 3.18, respectively. The results of molecular analysis of variance (AMOVA) indicated that the most portion of genetic variation was belonged to within species than between them (79% vs. 21%). Based on the genetic variation parameters, Ae. crassa species showed greater levels of genetic variation compared with Ae. cylindrica species. The results of cluster analysis based on Jaccard’s similarity matrix grouped all investigated accessions into two main groups, so that the grouping pattern was in accordance with their genomic constitution. Moreover, the results of principal coordinate analysis (PCoA) confirmed the grouping pattern obtained by cluster analysis. In conclusion, our results revealed considerable efficiency of SCoT markers in grouping the studied germplasm; hence the use of this marker system could be recommended in other genetic studies.

Streptococcus pyogenes type a (GAS a) is a gram-positive bacterium and the most important group of streptococci. Streptococcal pharyngitis requires appropriate antibiotic treatment to prevent transmission and side effects at the same time as consumption and subsequent consequences. The aim of this study is bioinformatics investigation of active compounds of 16 medicinal species on tyrosine phosphatase enzyme (SP-PTP). This research was done using descriptive-analytical method. For this purpose, at first, 850 phytochemical compounds in 16 plant species including thyme, aloe vera, clove, cinnamon, barberry, eucalyptus, ginger, hyssop, sage, nettle, turmeric, fleawort, violet, oregano, licorice and mangrove were collected from articles and their chemical formulas were obtained from PubChem database. The desired protein was downloaded from the PDB server. After that, preparation of protein and natural compounds (ligand) were performed for molecular docking analysis by DS Visualizer, Chimera5 and AutoDockToolssoftwares. Then, the active site was detected using castp online server and PyMOL software, molecular docking of plant compounds and desired protein was done with Auto Dock Vina software. The results were analyzed by lig plot+ and Discovery Studio 2.1 softwares. After that, physicochemical properties of compounds were obtained from the Swiss ADME server and the toxicity class of compounds was determined based on Lipinski's rules using Toxtree software. Among the investigated compounds, 19 compounds including 5'-Methoxyhydnocarpin, Linalyl acetate, 1,3-diisopropylnaphthalene, Ellagic acid, Umbelliferone, Carnosol, Berberine, Berlambine, Tannin, Quercetin, Aesculetin, Apoatropine, Coumarin, e-Coumarin showed the highest rate of tyrosine phosphatase enzyme inhibition. The compound alpha-Bourbonene has low absorptivity with the advantage of low mutagenicity. Considering results of this research, it can be concluded that among the most important studied compounds, the Linalyl acetate compound in the fleawort with the highest interaction and having suitable characteristics such as low mutagenicity, high gastrointestinal absorption and following Lipinski's law can be considered as a suitable compound for inhibition of this bacteria.

Waterlogging is one of the abiotic stresses that reduce the growth and productivity of sugarcane. Sugarcane is relatively tolerant to waterlogging however the damage to this plant related to genotypes, environmental conditions, stage of development and the duration of stress. Due to the lack of sufficient information on the regulatory role of miRNAs and their target genes in the response of sugarcane to waterlogging stress, based on the results of studies in model and related plants such as sorghum, miR160 and miR393 and their target genes i.e. AEF17 and AFB2, their selection and expression were investigated using qRT-PCR method in two varieties CP48-103 and CP69-1062 under treatment of 7 and 14 days of waterlogging stress compared to control plants. The results of comparing the relative expression showed that miR160 and miR393 had an increased expression in both varieties under stress conditions, and their negative inhibition role in reducing the expression of the target genes, i.e. ARF17 and AFB2, was revealed. The role of negative regulation of miR160 and miR393 on ARF17 and AFB2 genes were more in 14 days stress, also this role was more prominent in CP69-1062 variety compared to CP48-103 variety.

Evaluation of molecular and morpho-physiological traits of wheat such as grain yield, grain yield component, growth index values and the expression of some genes in the pathway of drought tolerance, including TaNAC67 and TaMYB73 in the farm of Kurdkoi Agricultural Research Center by split plots with randomized complete blocks design in four replications in this reserach was studied. Drought treatment includes levels of -0.3 (field capacity as a control treatment), -2 and -4 were considered as a main factor and bread wheat cultivars (Baharan, Ehsan, Kalate and Marwarid) as a sub factors. Rain shield was used to control rainfall. Traits such as leaf area (LA), dry matter, crop growth rate (CGR) and relative growth rate (RGR) as well as spike length, thousand grain weight, plant height and grain yield were measured. To evaluation of TaNAC67 and TaMYB73 genes expression, RNA was extracted from the leaves and Real time PCR technique was used. The results showed that all investigated morphological traits decreased under the drought stress. Baharan cultivar had the highest grain yield in the control treatment, but by increasing stress, the largest decrease in grain yield occurred in this cultivar. In case of gene expression evaluation, Ehsan cultivar can be introduced as a cultivar with high drought tolerance. Analysis of variance showed that effect of stress, variety and interaction effect between stress and variety on plant height, spike length, thousand grain weight and grain yield were significant at the probability level of 1% but block effect was not significant for any of studied traits. Comparison of average for drought stress on plant height, spike length, thousand grain weight and grain yield of cultivars showed that these traits decreased by increasing drought stress intensity. Comparison of average for variety and interaction effect between stress and variety on plant height, spike length and thousand seed weight showed that the Ehsan variety had the highest amount of these traits and it has significant difference with the other three varieties. Comparing of average for cultivar and interaction effect between stress and variety on grain yield trait showed that Baharan cultivar had the highest value and it has significant difference with other cultivars. The results of leaf area and dry matter showed that the Baharan variety has the highest sensitivity to drought stress and this sensitivity was higher in the pollination stage than other stages. Relative growth rate results showed that decreases rate of this index in Kalate variety was lower than other varieties. The results of evaluating the growth rate of the crop under drought stress conditions showed that cultivars had different reactions. The results of TaMYB73 and TaNAC67 genes expression under drought stress conditions showed increase in expression for -2 than the control in all cultivars but with the increase of stress intensity from -2 to -4, different cultivars showed different expression levels for the expression of these genes. In the condition of drought stress -4, only cultivar Ehsan showed increase of gene expression for TaMYB73 compared to the control and stress -2 times, and it had a significant difference with other cultivars. Also, the highest expression of TaNAC67 gene in -4 stress conditions was for the kalate variety.

High-temperature stress is an environmental challenge limiting plant productivity and growth. Plants have evolved various mechanisms to respond to heat stress. In this study, to explore the molecular aspects and functional analysis of heat tolerance, the microarray data of the expression profile of heat stress in Arabidopsis seedlings were retrieved from the gene expression omnibus database (GEO) database with accession number GSE103398. After quality control and data normalization, the Limma package was used to assess the differentially expressed genes (DEGs). The 7780 heat responsive DEGs were identified with the criteria of p-value <0.01 and |log2Fold change| > 2 which were further analyzed by bioinformatics tools for gene ontology (GO) classification, KEGG pathways analysis, protein-protein interaction networks and potential hob genes. For the biological process (BP), the most enriched GO terms in heat stress responsive DEGs were related to the regulation of transcription, oxidation-reduction process and response to abscisic acid. Based on the KEGG enrichment metabolic pathway, plant hormone signal transduction, biosynthesis of secondary metabolites and glycerophospholipid metabolism pathways were found to be majorly affected under heat stress. Among the identified candidate–hub genes with high connectivity in modules, Auxin Response Factor 5/MONOPTROS (ARF5/MP), TIR1 (transport inhibitor response1) as auxin receptor, Arabidopsis Histidine Kinase 4 (AHK4)/ WOL(Wooden Leg) as cytokinin receptor, SDP1-LIKE (Sugar –dependent1 –like) involved in TAG degradation, 2-lysophosphatidic acid transferase 2/4 (LPAT2/4) involved in TAG biosynthesis and pyrroline-5-carboxylate synthetase1/2 (P5CS1/2) involved in proline biosynthesis were introduced as genes playing critical roles in responding to heat stress. Function analysis of the hob genes disclosed that the acclimatization responses to heat stress were mainly associated with control of root and shoot apical meristem activity, hypocotyl elongation, vascular tissues development, heat shock protein activation, changes in the membrane lipid composition and cellular redox homeostasis. Therefore, breeding strategies must be developed to enhance heat tolerance by manipulating the components involved in these pathways.

To investigate the expression pattern of genes encoding antioxidant enzymes under water deficit stress in spring bread wheat, a factorial experiment was conducted in a randomized complete block design in 2020. In this study, agronomic traits, enzyme-related traits, antioxidant activity as well as the amount of gene expression affected by irrigation and salicylic acid were measured. In this study, there was a significant difference between irrigation levels and salicylic acid in terms of the effect on all traits. There was a significant difference between interaction treatments in terms of the effect on all traits except spike length and 1000-kernel weight. Mean comparison of interaction treatments showed that foliar spraying of 1 mM salicylic acid under 100% plant water requirement treatment had the highest plant height (64.76 cm), number of tillers per plant (3.71), number of seeds per spike (21.2) Dry matter yield (15.14 g / plant) grain yield (10.68 g / plant), chlorophyll an (8.66 mg / g fresh weight), chlorophyll b (2.66 mg / g fresh weight), Carotenoids (4.13 mg / g wet weight). While the highest content of leaf proline (0.53 mg / g fresh weight), leaf phenol (Galic acid / 82 DW9 / 82), catalase activity (97.09 mMolH2O2 / min mg protein), ascorbate peroxidase (mMolH2O2) / min mg protein 03/120), superoxide dismutase (mMolH2O2 / min mg protein 89/330) was allocated to foliar application of 1 mg salicylic acid under 50% plant water requirement. In this study, water deficit stress and salicylic acid foliar application had a synergistic effect on increasing the activity of antioxidant enzymes. The highest expression of superoxide dismutase, polyphenol oxidase, and catalase genes was observed by foliar application of 1 and 2 mM salicylic acid, and the highest expression of ascorbate peroxidase gene was observed by 1 mM foliar application of salicylic acid under 50% plant water requirement treatment. Application of salicylic acid under irrigation 50 and 75% of plant water requirement increased the expression of antioxidant genes in comparison with salicylic acid control treatment in each plant water require treatments and under 100% plant water requirement.

RNA sequencing is currently a suitable choice for studying the transcriptome of non-model plants which by faster identification of gene networks and patterns of genes producing secondary metabolites, can be effective in increasing these compounds. In this study, in order to identify some genes involved in the construction of the terpenoid skeleton in the aerial branches (leaves and flowers) of the medicinal plant Lavandula angustifolia cv. Hidcote using RNA sequencing, with the high-throughput Iluumina HiSeq2500 technique. After controlling the quality of the reads using FastQC and Trimmomatic software, 306995557 reads with suitable quality were produced, which after de novo integration with the Evidentialgene program, resulted in the production of 262412 unigenes with an average length of 1181.07 and N50 equivalent to 1633 nucleotides. In order to identify unigenes related to the biosynthetic pathway of terpenoid skeleton, the sequence of unigenes was loaded in KASS database. A total of 17,777 unigenes were identified in 122 biological pathways, the "terpenoid skeleton" pathway with 88 unigenes was one of the most identified pathways among the 1,664 unigenes of the secondary metabolite biosynthesis pathway. In general, the results of the functional interpretation of the genes led to the identification of 27 genes in the biosynthesis pathway of the terpenoid skeleton, which included all the genes of the two main biosynthetic pathways of the terpenoid skeleton (mevalonic acid (MVA) pathway in cytosolic and methyl-erythritol-phosphate (MEP) pathway in plastid) from the beginning of the pathway to the production of isopentenyl diphosphate (IPP). The identification of the sequence of the genes of the biosynthetic pathways of the terpenoid skeleton and the functions related to it can become a basis for further research by advancing the goals of metabolite engineering of these genes.

Carum copticum is as an herbal medicine from the family Apiaceae with compounds such as thymol, cement, alpha-pinene, gametropin, betapinene, micron, and carvacrol in the treatment of angina, kidney stones, asthma, rheumatism, influenza that used as a strong disinfectant and boost digestion. In this study, expression of beta-amyrin acid synthase (beta-Amirinsanthase) under different treatments of silver nanoparticles (0, 30, 60, 90 ppm), chitosan (0, 100, 150, 200 ppm) and populations (Sistan and Pakistan) was investigated. Solubility was carried out in the quaternary stage at 48 hours and 72 hours. The results of analysis of variance showed that the application of chitosan eclipses and silver nanoparticles caused a change in the beta-amyrein gene expression pattern. The highest expression, 48 hours after treatment, was observed with just about 150 ppm of chitosan. By increasing chitosan concentration, a significant decrease occurred in the expression of the gene for 72 hours while treatment with 90 ppm of silver nanoparticles in 48 hour after treatment has the most gene expression. In the effects of chitosan (150ppm) and silver nanoparticles (90ppm) based on 48 hours after treatment was observed the most gene expression for both populations. Overall, the results of this study showed that chitosan and silver nanoparticle elicitors had a positive effect on beta-amyrein gene expression, but the highest expression was obtained in Pakistan population at 48 hours intervals.