قربانعلی نعمت زاده

Arthrospira platensis (Spirulina) is a valuable photosynthesizing prokaryote with numerous industrial and food applications. Fatty acid desaturase enzymes (FADs) are responsible for the production of monounsaturated and polyunsaturated fatty acids. In the present study, the genome of A. platensis C1 was investigated using bioinformatics methods in order to identify ApFAD genes family. A total of 8 ApFAD genes were identified in Spirulina genome and classified into Omega, Sphingolipid, CrtR_beta-carotene-hydroxylase and Acyl-CoA groups. Four conserved histidine motifs that are essential for binding to the di-iron structures and catalytic activities were identified. Investigation of post-translational modifications of ApFAD proteins revealed a wide range of glycosylation and phosphorylation changes. Evaluation of FAD gene promoter regions revealed different types of cis-regulatory elements responsive to phytohormones and stress conditions, especially in Omega (ApFAD-6) and Acyl-lipid (ApFAD-3) desaturases. Also, protein-protein interaction networks showed the relations between ApFADs and genes involved in dealing with stresses through the biosynthetic process of secondary metabolites and electron transfer. Analysis of RNA-seq data of orthologous genes in Arabidopsis showed the potential of Omega and Acyl-lipid genes, such as ApFAD-3, ApFAD-6 and ApFAD-7, in response to various environmental stresses. In general, the results of this study can contribute to a more complete understanding of the function of FAD genes in Spirulina and lay the basis for the transgenic study of these genes with the aim of increasing the content of unsaturated fatty acids, improving the nutritional value of oils, as well as promoting the stress tolerance of plants.

Cyanobacteria improve soil fertility and organic product productivity by synthesizing growth-promoting substances, phosphate solubilization, and biological nitrogen fixation. We investigated the effect of eight various cyanobacterial strains on the germination-stage development of three different rice varieties namely Fajr, Roshan, and Tarem. The ammonium transporter (AMT) gene family was studied because ammonium is the most favored form of nitrogen that flooded rice can absorb. The majority of the experimental parameters were considerably impacted by cyanobacteria. In contrast to the qualitative cultivar Tarem Hashemi, germination characteristics were considerably enhanced when eight cyanobacteria strains were co-cultivated with two high-yielding cultivars, Roshan and Fajr. The amounts of nitrate and ammonium were highest in strain 7, with concentrations of 0.08 μg/ml and 0.010 μg/ml, respectively, out of the eight strains tested for nitrogen excretion. In silico analysis discovered 12 gene loci and 15 OsAMT isoforms in the rice genome. Examining the OsAMT gene family members in protein domain-specific databases revealed that all of the examined genes (excluding OsAMT3;4) include an ammonium-transporting protein domain. Three groups of OsAMTs were identified based on their gene structures and evolutionary relationships; each group shared common motif patterns and exon/intron order. The identification of active and inactive OsAMT genes in bioinformatic analysis could bring new insights into functional genomics studies of the rice ammonium transporter gene family, particularly in co-cultivation with cyanobacteria.

Heat shock protein of 90 kDa or HSP90 plays an important dynamic role in regulating biotic and abiotic stresses through multiple functional mechanisms. The present study aimed to perform a comprehensive analysis of the HSP90 gene family in soybean. In total, 20 HSP90 genes from soybean were identified and showed unequal distribution on the 13 chromosomes. The evolutionary tree divided these genes into three main groups based on their subcellular localization. In Group I, nearly all of the HSP90 genes are distributed in the nucleus or cytoplasm. In Group II, the HSP90s were mostly classified in the endoplasmic reticulum. HSP90 genes were exclusively found in the mitochondria or chloroplast in Group III. Phylogenetic relationships have shown that genes in similar subgroups have the same exon-intron structure and number of introns. Glyma14g219700, Glyma17g258700, and Glyma07G207600 were identified as hub proteins based on their high degrees of interaction. In addition, Glyma02g302500, Glyma08g332900, Glyma14g219700, Glyma17g258700, and Glyma18g074100 genes displayed high expression levels in all of the tissues at different developmental stages. These findings provide a complete overview of the GmHSP90 gene family classification and evolution, which can help to identify the functional properties of the HSP90 genes in soybean growth and development.

Necrotic enteritis (NE) is an economically important disease, caused by Clostridium perfringens type G strains, and is one of the major targets of antibiotics used in poultry feed.

This study aimed to genotypically characterize virulent strains of C. perfringens isolated from healthy and diseased birds in Iran.

Eleven isolates were derived from necrotic enteritis cases, and 27 were from healthy chickens. Isolations were performed using blood agar. To assess whether zmp is generally associated with avian NE, 38 C. perfringens isolates were screened using PCR and western blotting. The involvement of these toxins as virulence factors was investigated using cytotoxicity assays.

All isolates carried the phospholipase c (plc) gene regardless of their origin and virulence. The zinc metallopeptidase (zmp) gene was found in the isolates collected from birds affected by necrotic enteritis. Furthermore, Necrotic enteritis like B (NetB) was only found in 36.36% of the isolates derived from necrotic enteritis-infected birds. Western blot analysis further confirmed the expression of Alpha toxin, NetB, and Zmp in different isolates. Incubation of Leghorn Male Hepatoma (LMH) cells with crude C. perfringens toxins indicated that the supernatants of all bacterial strains were toxic toward LMH cells at different dilutions. In addition, crude toxins of the Cp28 strain expressing Alpha toxin, Zmp, and NetB showed an approximately 50% cytotoxic dose (CD50) at a 1:34 dilution. Strain Cp119.2, which produces both ZMP and the Alpha toxin, and strain Cp48, which only produces the Alpha toxin, showed CD50 at 1:23 and 1:4 dilutions, respectively.

It seems that both NetB and Zmp play major roles in the cytotoxicity and pathogenicity of this organism.

Salinity stress is one of the most important limitations of rice cultivation worldwide. On the other hand, the use of physical and chemical mutagens can be very important not only to the development and combination of new genes or alleles with agricultural importance but also to introduce genotypes more adaptable and stable to adverse weather and soil conditions. For this reason, with the development and progress of rice varieties that are tolerant and adapted to salinity, it is possible to increase the sustainable production of this stable food. Therefore, the present study was conducted with the aim of investigating the response of the tenth generation (M10) of rice mutants to salinity stress in the reproductive stage using agronomic and biochemical characteristics.

In this research, 13 mutant lines of Seng-e-Tarem, Hashemi and Khazar cultivars using gamma ray irradiation from Cobalt 60 which have been previously identified as tolerant lines in molecular studies were used along with the tolerant cultivars of Nonabukra and Deylamani and sensitive cultivars of IR29 and Sepidrood. The genotypes were exposed to three levels of salinity (0, 4 and 8 dS/m) from the source of sodium chloride. A factorial experiment based a randomized complete block design (RCBD) and a factorial split based a RCBD with three replicates were used to evaluate agronomic traits along with yield and biochemical traits, respectively. The measured parameters were tillers number (TN), the number of filled (NFG) and unfilled grains (NUG), 1000 grains weight (TGW), plant height (PH), Days to 50% of flowering (DTF) and the paddy yield (PY), and for the biochemical traits, the activity of catalase (CAT) and superoxide dismutase (SOD), protein (PN), proline (PR) and malondialdehyde (MDA) contents and electrolyte leakage (EL) percentage.

The results of the variance analysis showed that the effect of salinity and genotype and their interactions were significant for all the measured traits. A wide range of genetic diversity was observed among the genotypes for the agronomic and biochemical traits. Among the traits, PY was identified as the best and the most indicative trait to classify the tolerant genotype under salt stress conditions. Among the investigated mutants at different levels of salinity, the highest PY was recorded in MP6, MP10 and Deylamani genotypes, respectively. PY value in MP10 mutant at the salinity level of 8 dS/m was closed to Deylamani variety (tolerant check). With the increase of salinity from zero to 8 dS/m, the measured traits adversely affected. The cluster analysis diagram of studied genotypes based on agronomic traits and PY at a salinity level of 4 dS/m classified the genotypes into three separate groups. The genotypes MP2, MP3, MP4, MP9, and MP10 were grouped in the second group, in which Deylamani cultivar was also present as a tolerant check. The cluster analysis diagram of agronomic traits and PY at the salinity stress level of 8 dS/m divided the genotypes into four different groups. In the third group, two genotypes of MP9 and MP10 were included with Tarem Deylamani variety (tolerant check). The correlation coefficient between agronomic traits in 8 dS/m of salt conditions showed that PY had a positive and significant correlation with PH (r=0.51), the NFG (r=0.88) and TGW (r=0.63). Also, there is a negative correlation between DTF with PH (r=-0.70) and NFG (r=-0.62) and a positive and significant correlation with TN (r=0.60). Biplot analysis divided the studied lines into four groups based on agronomic traits at a salinity level of 4 dS/m. The first group includes six mutant lines as very sensitive group, the second group includes two mutant lines as sensitive group, the third group with three genotypes including lines MP9, MP10 and Tarem Deylamani variety (tolerant check) as tolerant group and the fourth group with six genotypes included lines MP11, MP12, MP13 and Nonabukra variety (international tolerant check) as well as Sepidrood and IR29 varieties as high salt tolerant group. Also, biplot analysis based on agronomic traits at a salinity level of 8 dS/m divided the studied lines into four groups. The first group consisted three mutant lines as very sensitive group, the second group included six lines as sensitive group, the third group involved five genotypes including MP11 and MP13 lines and Nonabukra varieties (tolerant check), Sepidrood and IR29 as the tolerant group and the fourth group with three genotypes included MP9 and MP10 lines and Tarem Deylamani variety (native tolerant check) as high salt tolerant group. For biochemical traits at 8 dS/m of salt stress, the highest amount of SOD was recorded in Deylamani cultivar (tolerant check), PN for MP2 mutant, PR for MP3 mutant, and the lowest amount of EL and MDA was recorded for MP2 and MP10 mutants, respectively.

In general, PY of MP10 mutant line in salt stress conditions was closed to Deylamani as a native salt tolerant cultivar, therefore could be introduced as a superior line for further research in saline conditions.

Soybean seed contains about 20% oil and 40% protein and is considered as a strategic oilseed plant. Identification of the relationship between morphological traits and seed yield and improving the traits that have strong associtation with seed yield can increase the efficiency of the soybean breeding programs for seed yield improvement.

To determine the suitable indirect selection index for seed yield in soybean, the important morphological traits were evaluated in 10 soybean cultivars in randomized complete block design with three replications and multivariate statistical methods in research farm of Sari University of Agriculture Sciences and Natural Resources, Sari, Iran, in two growing seasons (2020 and 2021).

The results showed that there was significant differences between soybean cultivars for the morphological traits which indicates considerable variation among Iranian soybean cultivars. The results also showed that cv. Telar with the highest number of branches, number of pods plant-1, number of seeds pod-1 and pods weight plant-1 had the highest seed yield (5400 kg.ha-1) in the 2020 and cv. Katol with the tallest plant height, the highest number of branches, pods weight plant-1 and the 100-seed weight had the highest seed yield in 2020 and 2021 (5200 and 7688 kg.ha-1, respectively). The results of multivariate analysis showed that among the studied traits, pods weight plant-1 and plant height directly, the number of pods plant-1 with a direct effect on the pods weight plant-1 and also the 100 seed weight with a direct effect on plant height had highly positive effects on seed yield in soybean. Furthermore, the number of pods plant-1 showed negative relationship with 100 seed weight. Moreover, the results of cluster analysis showed that cv. Telar and cv. Parto were distinguished from other cultivars for short plant height and high number of pods plant-1, cv. Katol for tall plant height and high 100-seed weight and cv. Tapur for high number of seeds pod-1.

Since pods weight plant-1, plant height, number of pods plant-1 and 100 seed weight showed high positive direct effects on seed yield, therefore, cv. Prato and cv. Telar with the highest number of pods plant-1 and cv. Katol with the tallest plant height and the highest 100 seed weight can be considered for seed yield improvement in soybean breeding programs.

One of the main priorities of using heterosis for development of hybrid rice is to identify the suitable fertility restorer lines. Therefore, to identify suitable fertility restorer lines and evaluate rice hybrids, 36 F1 hybrids developed from crossing of two cytoplasmic male sterile lines, JelodarA and NedaA, together with 13 lines from local cultivars and four foreign fertility restorer lines as paternal lines as well as JelodarA and NedaA, as second crop, using randomized complete block design in three replications in the research farm of Tabaristan Genetics and Agricultural Biotechnology Research Institute, Sari, Iran, in 2019 and 2020. Mean comparison of morphological traits of F1 hybrids showed that the highest fertility and grain yield belonged to H28, H27, H33, H30 and H29 hybrids, which was mainly due to high fertile tiller number, 1000-grain weight and high panicle fertility. Using SSR molecular markers including RM 171, RM 490 and RM 3148 associated with the fertility restorer genes Rf3 and Rf4 for selection of superior hybrids revealed that RM 3148 marker could identify superior hybrids resulted from crossing of paternal lines IR68078-15-2-1-2-2-R, IR65622-151-1-2-2-2R and IR86403-5-5-2-1-1-1-1-1R with male sterile JelodarA which had similar band as fertility control restorer line and H27, H29 and H33 hybrids. These hybrids had both bands i.e. heterozygous, and based on this marker they carry Rf4rf4 alleles. RM 171 marker also showed the likely presence of Rf4 gene in IR 68078-15-2-1-2-2-R and IR 65622-151-1-2-2-2-R lines and hybrids developed from them. The F1 hybrids had both alleles in heterozygous from Rf4rf4. The results of this experiment showed that IR65622-151-1-2-2-2R was the suitable fertility restorer line for NedaA cytoplasmic male sterile, and IR68078-15-2-1-2-2-R and IR86403-5-5-2-1-1-1-1-1R were suitable fertility restorer lines for JelodarA cytoplasmic male sterile. These fertility restorer lines and cytoplasmic male sterile genotypes can be used in hybrid rice development programs.

NAC (NAM, ATAF1/2, and CUC2) proteins are the plant-specific transcription factors (TFs) that play roles in diverse developmental processes and stress responses. In the present study, a total of 68 NAC genes were identified in Aeluropus littoralis, a salt secreting halophytic grass, belongs to family Poaceae. By analysis of cis regulatory elements of AlNAC genes promoter, many cis-acting regulatory elements related to growth and development, phytohormone and stresses defense were found in the promoter of AlNAC genes. These hormone-responsive elements, include P-box, TCA element, CGTCA-motif and TGACG-motif, TGA-element, ERE and ABRE, which were associated with gibberellic acid, salicylic acid, jasmonic acid, Auxin, ethylene and abscisic acid response, respectively. For stress responsive elements, TC-rich repeats, ARE, MBS, LTR; and W box, can be noted which are related to defense and stress, anaerobic induction, drought inducibility, low-temperature inducibility, and wound stress, respectively. The different types of cis regulatory elements in the promoter of AlNAC genes and the variability in transcription factors associated with these regulatory elements indicates the important role of these genes in plant development and defense against stress. By analyzing AlNAC32 candidate gene expression using RT-qPCR it was revealed that AlNAC32 was up-regulated under salt, drought and ABA phytohormone stresses in leaf, stem and root tissues, implying its role in multiple abiotic stresses tolerance. These findings provided valuable information for further research on the functions and applications of AlNACs in A. littoralis growth and adaptation to stress.

Cyanobacteria are the oldest oxygenic photoautotrophs on earth with a wide ecological distribution. They increase soil productivity by affecting its physicochemical properties. Increasing the application of chemical fertilizers is harmful. Therefore, it has become necessary to look for alternative renewable resources to meet at least a part of the demand for crops. In this study, aimed at increasing the efficiency of cyanobacterial biofertilizer, the effects of nitrogen, phosphorus and potassium elements in the form of urea, superphosphate and potassium chloride fertilizers were evaluated on nitrogen fixation activity measured by gas chromatography, nifH gene expression and the growth of cyanobacterium Aliinistoc sp. In general, the growth and nitrogen fixation activity of the sample decreased as the concentration of nitrogen and phosphorus sources increased. The most effect of nitrogen source was on nitrogenase activity, and at the end of the experimental period compared to the beginning (before treatment), the amount of nitrogenase activity decreased 50 and 100% in the presence of 10 and 100 mg/L urea, respectively. Phosphorus had a significant effect on the growth of the sample, and at the highest concentration of superphosphate (500 mg/L), growth declined about 80%. On the other hand, potassium especially at the lowest concentration (125 mg/L), significantly increased growth by about 20% and doubled nitrogenase activity. In addition, the evaluation of nifH gene expression confirmed the pattern of nitrogenase activity. In general, the results of this study indicate that the dosage of elements used in combination with cyanobacterial biofertilizers should be considered.

Rice is a good source of energy and has the highest protein efficiency among plant proteins. However, its protein content is relatively low compared to other cereals. Seed storage protein in rice classified into four groups: albumin and globulin in aleurone layer, and prolamine and glutelin in endosperm. Therefore, during the bleaching process of rice grains, albumin proteins and part of globulin are removed by its bran. Since the protein content of the grain and its amount will be directly related to its nutritional quality and due to the importance of rice grain in diet, seed storage proteins quality in a quantitative and qualitative breeding population of rice such as two new mutant cultivars, Roshan and Shahriar, with their parents (Nemat and Amol3 respectively) as well as qualitative varieties, Sang-tarom, along with two different varieties of brown and black rice was studied.

Qualitative properties of grain proteins were evaluated based on their solubility as well as the seed storage proteins For albumin, globulin, prolamine and glutelin proteins. Quantification of stored proteins was performed by Bradford reagent and quantification of their subunits by densitometric analysis.

The results showed that there is a significant difference for the amount of seed storage proteins of different rice genotypes. So that Sang-tarom and Roshan cultivars had the highest amount of albumin protein (19.53 and 22.40 mg/g respectively). This was while the brown grain variety with the lowest amount of albumin and globulin protein and the highest amount of glutelin and prolamine proteins has the highest amount of total protein (1640.43 mg/g). Evaluation of the banding pattern of stored storage proteins also showed that this banding pattern was the same in different genotypes except in Roshan (60 kDa) and Shahriar (13 kDa) mutant cultivars. Densitometric analysis of protein subunits also showed that the highest amount of glutelin subunits was present in Sang-tarom cultivar and the lowest in Shahriar cultivar and brown grain variety. Also, the highest amount of prolamine subunits was observed in Sang-tarom cultivar and brown grain variety and the lowest in Shahriar cultivar. As Shahriar cultivar was able to have the highest amount of glutelin to prolamine protein.

Although the profiles of seed storage proteins in different varieties of rice are the same, but this pattern is different in the two cultivars of mutant Roshan and Shahriyar. So that, the absent of the 60kDa subunit of proglutelin and the 13kDa subunit of prolamine can be used as protein markers in both Roshan and Shahriar, respectively. Our study demonstrated that although there is a significant relationship between protein subunits and the amount of stored proteins, but there was no significant relationship between stored proteins with different quantitative and qualitative rice cultivars. Therefore it seems that improving the seed storage protein quality will probably not limit the improvement of new rice cultivars with desirable quantitative and qualitative characteristics.

The CBL-CIPK signaling network, which decodes calcium signals triggered by environmental stresses, is one of the most crucial signal transduction systems in plants. Proteins bound to calcium ions serve as sensor molecules, receiving cellular calcium ion signals and transmitting messages to the downstream gene cascade. Because of its tolerance to abiotic stresses, especially salinity stress, and its relationship to cereals, many researchers are interested in the molecular mechanisms of the halophyte grass Aeluropus littoralis. The in-silico discovery of the AlCIPK gene family and their expression profile in responses to salinity stress were considered in this analysis due to this plant's genome sequence's availability.

Using local TblastN program, the CIPK protein sequences of Arabidopsis thaliana gene families were blasted against A. littoralis genomic sequences. BlastP was used to verify all sequences after redundant sequences were removed. The detected proteins were analyzed in various protein domain databases such as Pfam, PROSITE, and InterProScan to identify, annotate, and interpret domain structures. In all of AlCIPK, the SALAD approach was used to perform similarity clustering based on motifs patterns. The exon and intron arrangement were determined by comparing the predicted CDS against AlCIPK genomic sequences in the gene structure display server (GSDS). Expasy-Prosite was used to determine the domain structure. A signal-dependent software based on SignalP 5.0 was used to identify signal peptides in proteins. Exploring the expression pattern of AtCIPK genes at various growth and developmental stages using Genevestigator (https://www.genevestigator.com/gv/plant.jsp) and the EFP browser (http://bar.utoronto.ca/). Transcriptome research was used to examine the expression patterns of AlCIPK genes in leaf and root tissues under salinity stress and recovery conditions.

Based on sequence homology with Arabidopsis genes, 20 CIPK genes were discovered in the A. littoralis genome. The Arabidopsis AtCIPK homologous proteins were used to name the Aeluropus CIPK genes. According to subcellular localization analysis, these proteins are active in a specific cellular compartment. The phylogenetic tree of 20 AlCIPK, 26 AtCIPK, and 33 OsCIPK showed that these 79 CIPKs are closely related. Exon/intron structure analysis was used to separate all AlCIPK into intron-poor and intron-rich classes. The expression of 25 AtCBL gene family members in 68 samples under salinity stress was compared using Genevestigator tools, which revealed that all 25 genes tested in different developmental/ environmental stages, including control and stress, had different expression patterns. A tissue-specific expression pattern was discovered after analyzing these AtCBL genes' expression pattern in both root and shoot tissues. In salinity stress and recovery conditions, the expression profile pattern of AlCIPK genes in leaf and root tissues was distinct. The distinct expression profiles of the AlCIPK gene family confirmed their functional and structural convergence.

Systematic study of members of this gene family revealed that CIPKs in Halophyte grass, i.e., A. littoralis, share main CIPK family characteristics with other monocotyledonous and dicotyledonous plants, which are likely important factors in this species' adaptation and stress tolerance. The lack of homologous AtCIPK24 genes in the Aeluropus genome is a key finding in this study, suggesting that the CBL-CIPK gene network in this plant has a distinct regulatory function, necessitating further studies. Future studies using the RT-qPCR method to examine the expression of AlCBL and AlCIPK gene family genes under different abiotic stresses could aid in understanding the mechanism of SOS-related gene expression regulation. This study's findings reveal the functional characteristics of the calcium gene family and provide essential information for future research on their functional roles.

Although plant breeding has been able to increase rice yield, the quality of cooking and eating quality is still one of the most important economic factors in rice production. In order to better understand the genetic relationships between quantitative and qualitative properties, the most important agronomic traits, physicochemical properties and storage protein characteristics in two new mutant cultivars of rice, their parents and ancestors were evaluated. The results of agronomic traits showed that two mutant cultivars Roshan and Shahriar, have the highest yield (8500 and 8000 kg/ha respectively) accompanied by desirable agronomic characteristics such as lodging resistance, early maturity period, high number of tillers and more panicle length. Evaluation of qualitative properties also showed that these two new mutant cultivars characterized by good cooking and eating properties. As Roshan, show moderate amylose content (AC) and both of them were in terms of gelatinization temperature (GT) and gel consistency (GC) similar to Sangetarom, a quality cultivar. Also, Roshan cultivar, like Sangetarom, was differentiated by the recessive allele of BADH2 gene for fragrance. On the other hand, Shahriar cultivar also showed a significant decrease for prolamin protein. In general, the results show that there is no significant relationship between agronomic characteristics and yield with grain biochemical properties, such as cooking and eating quality, fragrance and storage protein content. These results promise that by identifying and pyramiding desirable alleles, especially alleles involved in starch synthesis, fragrance and prolamin protein can be obtained rice cultivars with higher qualitative properties.

Yield of hybrid cultivars is 20 to 30% higher than conventional cultivars. On the other hand, the most important challenge for hybrid breeders, especially in Iran, is the selection of parental genotypes that have fertility restorer genes and ultimately lead to heterosis.

The present study was performed by evaluating the morphological traits of 19 rice genotypes and the linked of three SSR molecular primers related to Rf3 and Rf4 genes. These genotypes were planted in 2019 in the research farm of Genetics and Agricultural Biotechnology Institute of Tabarestan in a randomized complete block design with three replications. Quantitative and agronomic traits, especially paddy yield, were evaluated. DNA extraction was performed by CTAP method with modification from leaf samples. Three SSR markers linked with two major RF3 genes including RM490 and RM 3148 markers and RF4 gene linked with RM171 marker were used to identify fertility restorer genes in rice.

The results of comparing the mean of rice genotypes showed that P15-6 genotype with 118.33 was the earliest and all foreign genotypes with a maturity of 150 days were the latest. The highest yield of genotypes (above 700 g / m2) is related to Neda genotypes, IR 86403-5-5-2-1-1-1-1-1-1R, P15-6, P12-5-3-3-2- 2-1, P12-5-3-3-2-1-1 and P8-7-2-1-4-2-1-1, which due to the number of fertile tiller, the number of fertile panicle, 1000-seed weight and panicle fertility has been high. In the results of cluster analysis, parental cultivars were divided into three groups: in the first group (medium yield, long cluster length, high number of full seeds, and long grain length) the Jelodar cultivar, in the second group (maximum cluster fertility, 1000-seed weight and high paddy yield) Neda cultivar along with four other lines and all foreign cultivars are in the third group (late, short grain length and high grain density). Principal component analysis divided the studied traits into four main components with eigenvalues ​​above one, which in total explained 82.61% of the data changes, which these four components are more valuable and express the relationship between the traits. In total, the band pattern of three markers showed that IR 68078-15-2-1-2-2-R, IR65622-151-1-2-2-2-R and NSIC RC434 genotypes had fertility restorer genes.

Summary of all 3 SSR markers showed that genotypes P9-7-1-1-1, P11-6-2-1-1-1, P14-1 and P15-2 with two markers RM3148, RM490, have Rf3 gene and haven’t Rf4 genes and the reason that some genotypes have been identified as Rf gene with RM3148 marker but not detected with RM490 marker may be due to crossover between the desired gene and marker, so genotypes with fertility restorer gene are fertility restorer lines and can be used in hybrid rice program.

The calcineurin B-like protein (CBL) is an essential calcium sensor that plays a crucial role in plant growth, development and stress responses. The identification of a cis-acting element in the promoter region of the CBL gene family in three plants, including Oryza sativa (OsCBL), Arabidopsis thaliana (AtCBL), and Arabidopsis littoralis (AtCBL), was investigated because of their importance and involvement in signal transduction under abiotic and biological stresses. Sub-cellular localization of 10 AtCBL, 10 OsCBL and six AlCBL genes showed that AtCBL4, AtCBL10, AlCBL4.2, AlCBL4.3 and AlCBL10 proteins were located in the plasma membrane. 26 CBLs were identified and grouped into two major groups based on their orthologous relatedness in the phylogenetic tree. According to a comparative analysis of the gene structure of the CBLs gene family, about 66 percent of AlCBL genes, 60 percent of AtCBL genes, and 80 percent of OsCBL genes had eight exons and seven introns. Cis-regulatory elements were identified and grouped into eight distinct classes. The ABRE, ARE, GC motif, MBS, DRE, STRE, and LTR motifs were essential stress-related elements. Different regulatory mechanisms in the promoter region of AtCBLs are responsible for their distinct expression patterns, which are regulated by numerous tissue-specific and stress-specific cis-elements. The functional analysis of AlCBL4.2 (which contains six as-1 motifs) will provide useful information about this gene's regulatory processes due to its tissue-specific and enhancer feature of as-1 motif.

MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target NAC genes. In the present study, 68 putative NAC domain-encoding genes (NACs) were identified in Aeluropus littoralis, a halophyte plant of family Poaceae. Among the AlNAC genes identified, 4 were predicted putative targets for regulation by miR164. The high conservation of miR164 recognition sites in AlNAC genes indicates the essential role of target sites in the normal function of these genes as transcription factors. Expression profile of AlNAC1L.1 candidate gene in response to salt and drought stresses and ABA phytohormone in leaf, stem and root tissues was analyzed by RT-qPCR. The results showed that AlNAC1L.1 gene down-regulated in all tissues at 6 hours after applying stresses. Among the treatments, 600 mM NaCl treatment reduced AlNAC1L.1 expression in leaf, stem and root tissues to about -217, -26 and -9 folds, respectively. Therefore, the AlNAC1L.1 which is ortholog of known Oryza miR164-targeted NAC gene OMTN6, may play negative regulatory role in response to salt, drought and ABA treatments. These results indicated that function of some NAC proteins might be conserved among species. Collectively, these findings provided a useful resource for further analysis of the interactions between NAC genes and their intricate regulation by miR164 in response to abiotic stresses.

Calcium-dependent protein kinase (CPK), as a member of Ser/Thr kinases superfamily, plays a vital role in responding and adapting to biotic and abiotic stresses. The halophyte plant, Aeluropus littoralis, has been considered an attractive model to improve genetic resources of crops and plant stress genomic research. In order to identify the A. littoralis CPK gene family, the whole genome sequences were used to analyze the phylogenetic relationships, exon/intron structure, protein motif/domain organization and the prediction of protein-protein interaction networks. Fourteen AlCPK genes were identified in A. littoralis that were homologous to nine Arabidopsis thaliana CPK genes. The protein domain analysis of AlCPK showed that all studied genes belong to the CPK family due to having several EF-hand (except for AlCPK29.2, which does not have an EF-hand domain) and Kinase domains. AlCPK29.2 protein had the lowest molecular weight and aliphatic index, the highest instability index and gravy among the studied proteins. Gene structure analysis showed that most of AlCPKs (69.8%) have more than seven exons. Besides, AlCPK8 protein was predicted with two N-myristoylation and two palmitoylation motifs, while CPK34.1 protein lacked N-myristoylation, and palmitoylation motif and AlCPK5.1 protein had three palmitoylation motifs. Transcriptome analysis of 34 members of the AtCPK gene family in five abiotic stresses showed that AtCPK genes had diverse expression at different treatments, which could be evidence for AtCPK tissue/ stress-specific expression. The ABF4 gene was identified as one of the components of ABA signaling in AlCPK protein-protein interactions. The findings of this research can be used to classify the roles and pathways of the stress response by studying AlCIPK gene expression under different abiotic stresses.

The question of the origin of life on earth has been one of the most fundamental questions of ontology throughout human history, and has been generally debated between experimental scientists and religious scholars. Therefore, the main purpose of this paper is to examine the viewpoints of the Quranic exegetes and experimental scientists on the emergence of life on earth. In this regard, after examining the literal and technical meanings of some relevant terms such as life, experimental science and scientific exegesis, the viewpoints of the Muslim exegetes on the origin of life on earth were analyzed. Thereafter, some of the most famous theories and hypotheses of experimental scientists on this subject were discussed and analyzed. The research methodology used in this article is the descriptive-analytical method; whereby the collected data were presented and analyzed based on logical and textual evidences. The library research method was used for data collection. The findings indicate that the Quran did not explicitly discuss the origin of life on earth, but provided detailed reports about the creation and the origin of human beings. Also, many of the theories/hypotheses proposed by the ancient and contemporary experimental scientists on the origin and origin of life on earth are inconsistent with the Quranic accounts.

The question of the origin of life on Earth is one of the fundamental but controversial subjects hotly disputed among the scientists and the religious circles. Therefore, the purpose of this research was to examine the qur’ānic and experimental scientific perspectives on the issue of the origin of life on Earth. In this paper, after examining the literal meanings and the technical usages of relevant terms, the relationship between the Qur’ān and experimental science is examined. The qur’ānic verses (including the Qur’ān 21:30 and 24:45) and the interpretations of the Muslim qur’ānic exegetes have been discussed. Thereafter, some prominent scientific theories/hypotheses such as the special creation, aquatic origin, spontaneous generation, eternity of life, evolution, and RNA and DNA worlds are discussed and critically reviewed. The descriptive-analytical research method was used in this study, is and the findings showed that the Qur’ān discusses the origin of life on the Earth mysteriously and it does not offer a single, unified theory regarding it. Likewise, the majority of the theories/hypotheses proposed by the ancient and contemporary scientists on the origin of life on Earth are not in conformity with the qur’ānic report.

Although the opening of the silique is a valuable mechanism for the distribution of seeds in nature, it is also a significant problem in oilseed rape cultivation. Seed shedding from siliques at and after maturity is commonly referred to as pod shatter, and it reduces the grain yield of oilseed rape (Brassica napus). This factor, also called dehiscence, can cause losses of up to 50% of potential grain yield if harvesting is delayed and in adverse weather conditions. As a general consideration, canola is susceptible to shattering, and there is little genetic diversity associated with silique shattering tolerance in its commercial lines hence, increasing shatter tolerance is an important breeding objective.

In the present study, eleven parents were used to generate 55 hybrids. The experiment was carried out as a complete randomized block design with three replications at the seed and plant improvement institute. Silique Shattering Tolerance Index (SSTI) using Random Impact Test (RIT) and other related traits were measured during 2018. Griffing's model I of method II was used for the analysis of variance and the estimation of genetic parameters. Correlation coefficients for the studied traits and other calculations were performed using the SPSS software and Excel program.

Analysis of variance of genotypes showed high genetic diversity for the studied traits. Similarly, the general and specific combining ability variances were significant for most traits such as grain yield and the silique shattering tolerance index. This indicates the contribution of additive and non-additive effects in the genetic control of these traits. The general heritability of the studied traits was observed in the range of 78.81% to 93.87%. Correlation coefficients of traits showed a positive and significant correlation between silique shattering tolerance index with grain yield and oil content. Moreover, Zarfam and ES Artist with a good performance and silique shattering tolerance index are considered the best general combiners. Okapi×Zarfam, Nafis×ES Artist, Ahmadi×Nafis, Ahmadi×ES Neptune, Zarfam×ES Neptune, Nafis×ES Natalie, and Nima×ES Natalie are recommended as the best specific combinations for mechanized oilseed rape harvest and improvement of the shattering tolerance trait.

Low specific heritability of grain yield can be due to the more outstanding contribution of non-additive effects than additive effects. Various research studied variable estimation for general and specific combining ability and other parameters due to the difference in genetic materials and different weather conditions.

Calcineurin B-like proteins (CBLs), which act as a secondary messenger molecule in the subfamily of the calcium sensor gene family, play a key role in regulating physiological processes, plant growth and development. In order to identification and comparison of proteins involving in calcium signaling in two model of halophyte and glycophyte plants, in silico analysis of the CBL gene family were done in Aeluropus littoralis and Arabidopsis thaliana. Based on sequence homology and orthological relationships with Arabidopsis genes, 6 genes identified in Aeluropus were classified into three protein groups: AlCBL4, AlCBL2 and AlCBL10. Multiple sequence allignment of the CBL gene family in Aeluropus littoralis confirmed the presence of four EF-hand domains in all genes, which provide a structure for calcium ion binding. The high similarity of the physicochemical properties of most Aeluropus proteins to Arabidopsis as well as the strong orthological relationship with each other may indicate the preservation of the function of these genes in the evolutionary process. Analysis of AtCBLs expression patterns in different organs/ abiotic stresses showed that these genes have unique expression profiles due to functional and structural convergent. Different expression profiles of AlCBLs in Aeluropus transcriptome would be an evidence for the functional divergent of these genes. The results obtained from this study can provide valuable information about the properties of this gene family and their functional roles in tolerating to abiotic stresses for future studies.

Downy mildew is one of the most important diseases of cucumber plants reducing production in the world. Despite the availability of some fungicides to control the disease, demands for new and reliable natural products has been increased. In this study, the effects of salicylic acid (SA) and Azelaic acid (AZA) on some biochemical properties and expression of defense genes in cucumber plants were studied. Gene expression analysis indicated that expression of both β-1,3- glucanase and chitinase genes were increased after inoculation with Pseudoperonospora cubensis, but this increase was much higher for chitinase gene in SA-treated plants and for β-1,3- glucanase in AZA-treated plants. Also, chlorophyll a, b and total flavonoids contents in AZA and SA-treated plants were higher compared to control 6 hours after inoculation with pathogen. Total phenolic content was also increased in SA and AZA treated plants compared to the control 6 and 72 hours after treatment, respectively. These findings indicate that pretreatment of cucumber plants with SA and AZA prompts faster defense responses and increases the efficiency of the defense system against downy mildew.

This research was carried out to investigate the relationship between agronomic traits and yield using 132 spring wheat genotypes in alpha-lattice design with two replications at the Agricultural Research Station of Gonbad-e-Kavos. Variance analysis showed that genotypes were significantly different for all traits. The grain yield had very high correlation with the biomass, grain filling duration, seed filling rate, 1000-seed weight, spike weight, Grain weight per spike, days to heading and days to maturity at 1% of probability level. Grain yield was considered as a dependent trait. Biomass, 1000-grain weight and spike length, number and weight were entered into the regression model, respectively. The results showed that in breeding programs with the aim of increasing grain yield, selection should be based on biomass, 1000-grain weight, number and weight of spikes and days to heading. The cluster analysis was performed using the traits introduced into the regression model and traits with high correlation with the performance. Results of cluster analysis showed that genotypes 10, 12, 16, 20, 22, 25, 31, 38, 53, 54, 67, 70, 72, 87, 96, 97, 98, 112 and 123 were in group 4. Genotypes in group 4 were superior to other groups in terms of grain yield, 1000-grain weight, spike weight, grain weight per spike, days to heading and seed filling rate. It is suggested that the genotypes in group 4 should be tested in several years and locations and the best genotype(s) should be introduced.

Soybeans are considered as a main source of oil and protein production in the world. On the other hand, soybean seeds are one of the most important sources of protein that is directly or indirectly (in the livestock industry) in the human diet due to its favorable and inexpensive proteins. In this study some of agronomic characteristics (such as: plant height, number of branches, number of pods, seed weight, seed yield and day to maturity) and also seed storage protein quality properties (such as: soluble protein content, protease inhibitors contents and lectin protein) in six mutant lines and nine cultivars were studied. The results demonstrated that the 032-240-D-P1 and 032-240-D-P4 mutant lines have a high grain yield potential in addition to desirable agronomic traits. In terms of qualitative properties of grain proteins, Nekador and Caspian cultivars had the highest protein and the highest of albumin and globulin storage proteins, respectively. Also, the evaluation of anti-nutritional factors also revealed that all the mutant lines and Arian cultivar had the lowest protease inhibitors (PIA) and lectin (HAU) protein, which could be considered as promising genotypes for the soybean breeding programs. Results from this study suggested that the 032-240-D-P4 mutant line by high seed yield and the lowest of anti-nutritional factors could be studied as a new variety.

Hypericum perforatum is a medicinal plant which Hypericin, Hyperforin and phenolic compounds are its active secondary metabolites. Hairy root induction by Agrobacterium rhizogenes in this plant is difficult and has low efficiency. In the present study two inoculation methods, immersion in bacterial suspension and direct injection of A. rhizogenes has been compared. For this purpose, the best conditions for H. perforatum hairy root induction including A. rhizogenes strains (A4, LBA9402, NCPPB2656), plant explants (Stem, Apical bud, leaves), co-cultivation media (MS, ½MS, B5, and ½B5) and Acetosyringone (AS) concentration (0 and 100 µM) were specified and used for comparative analysis. It was found that strain A4, Stem explants, ½MS co-cultivation medium without AS constitute the best conditions for hairy root induction of H. perforatum. Transgenic nature of the potential hairy roots was confirmed using PCR and specific rolB and rolC genes primers. The results showed that the efficiency of applying direct injection method is four times higher than immersion in bacterial suspension in H. perforatum hairy root induction. In general, the results indicate that direct injection can be the method of choice to successful hairy root induction in H. perforatum.

Antibacterial, antifungal and antioxidant activity of methanolic extracts of Colocynth (Citrullus colocynthis) seeds, Camelthorn  (Alhagi maurorum) fruit and Chinaberry (Melia azedarach) leaves on eight bacteria and three fungi, which usually cause damage to agricultural products examined in this research.

Antimicrobial activity of selected plants in six concentrations on 11 microorganisms including, three gram-positive bacteria vs. Bacillus subtilis, Staphylococcus aureus, and Rathayibacter toxicus, and five gram-negative bacteria vs. Escherichia coli, Pseudomonas aeruginosa, Pseudomonas syringae subsp. syringae, Pseudomonas viridiflava, and Xanthomonas campestris pv. campestris, as well as three fungi vs. Pyricularia oryzae, Fusarium oxysporum and Botrytis cinerea was measured using the disk diffusion method. Also, the antioxidant activity of the extracts of these  plants was evaluated by measuring the enzymes of catalase and guaiacol peroxidase and evaluating the ability to trap DPPH radicals. In addition, the amount of total phenols and flavonoids in these plants extracts were measured.

Methanolic extract of Colocynth seeds had the highest antibacterial activity, the highest activity of catalase and guaiacol peroxidase enzymes and the highest percentage of DPPH radical inhibition. Methanolic extracts of these plants had no effect on fungal colony growth.

Methanolic extract of Colocynth seeds can be considered as potential sources of bactericides in agriculture.