Payame Noor UniversityCrop Biotechnology2252-078314120241022Study of promising Iranian pomegranate (Punica granatum L.) genotypes based on morphological and pomological characteristicsStudy of promising Iranian pomegranate (Punica granatum L.) genotypes based on morphological and pomological characteristics1141121010.30473/cb.2024.71803.1974FAMaryamFarsiDepartment of Plant Breeding, Yazd Branch, Islamic Azad University, Yazd, Iran.MehrshadZinolabediniDepartment of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.MansoorKalantarDepartment of Plant Breeding, Yazd Branch, Islamic Azad University, Yazd, IranMohammad RezaVazifeshenasYazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Yazd, IranReyhanehAsgarpour., Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, IranJournal Article20240717Pomegranate is a valuable fruit tree that exhibits favorable genetic diversity in Iran. The investigation of genetic diversity is the basis of plant breeding and is of particular importance. For this purpose, 38 morphological and pomological traits of 30 pomegranate genotypes were evaluated over two consecutive years. The results indicated that the genotypes displayed a high diversity in the studied traits, with the exception of the presence of anthocyanin in the branch of this year, aril color, fruit size, fruitful flower size, and intermediate cut of the leaf. The physiological disorder of fruit skin sensitivity to bursting had a positive correlation with fruit skin sensitivity to sunburn, but it showed a negative relationship with fruit skin thickness and tree mean yield. A positive correlation was observed between fruit size and fruitful flower size, and between fruitful flower percentage and flower position. The results of the principle component analysis revealed that the characteristics of fruit skin sensitivity to bursting, tree mean yield, fruit skin thickness, flower position, and fruit shape were the most key traits in determining the diversity between the studied genotypes. Based on the results of cluster analysis, the genotypes were divided into three groups, and the first group included genotypes with the lowest fruit skin sensitivity to bursting and sunburn. Among the cultivars studied, Rabab Malas Fars, Garch-shahvar, Shahvar-ghasrdasht, and Malas-Yazdi could be considered superior and desirable cultivars due to their low sensitivity to bursting and sunburn, as well as their high fruit number and tree yieldPomegranate is a valuable fruit tree that exhibits favorable genetic diversity in Iran. The investigation of genetic diversity is the basis of plant breeding and is of particular importance. For this purpose, 38 morphological and pomological traits of 30 pomegranate genotypes were evaluated over two consecutive years. The results indicated that the genotypes displayed a high diversity in the studied traits, with the exception of the presence of anthocyanin in the branch of this year, aril color, fruit size, fruitful flower size, and intermediate cut of the leaf. The physiological disorder of fruit skin sensitivity to bursting had a positive correlation with fruit skin sensitivity to sunburn, but it showed a negative relationship with fruit skin thickness and tree mean yield. A positive correlation was observed between fruit size and fruitful flower size, and between fruitful flower percentage and flower position. The results of the principle component analysis revealed that the characteristics of fruit skin sensitivity to bursting, tree mean yield, fruit skin thickness, flower position, and fruit shape were the most key traits in determining the diversity between the studied genotypes. Based on the results of cluster analysis, the genotypes were divided into three groups, and the first group included genotypes with the lowest fruit skin sensitivity to bursting and sunburn. Among the cultivars studied, Rabab Malas Fars, Garch-shahvar, Shahvar-ghasrdasht, and Malas-Yazdi could be considered superior and desirable cultivars due to their low sensitivity to bursting and sunburn, as well as their high fruit number and tree yieldhttps://cropbiotech.journals.pnu.ac.ir/article_11210_c95ef734da87c4dd06ec247e4c1c19ec.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022The effect of 24-epibrasinolide (24-EBL)on physiological and biochemical pathways of lettuce (Lactuca Sativa L.) under drought stress conditionsThe effect of 24-epibrasinolide (24-EBL)on physiological and biochemical pathways of lettuce (Lactuca Sativa L.) under drought stress conditions15281121310.30473/cb.2024.70956.1964FAZeinabChaghakaboodiDepartment of Plant Production Engineering and Genetics, Campus of Agriculture and Natural Resources, Faculty of agriculture, Razi University. Kermanshah, Iran.Seyed HasanMousaviGreenhouse and Controlled Environments Research Center, Department of Post Harvest Physiology and Technology, Horicultural Sceinces Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran.MahdiKakaeiFaculty of Engineering, Department of
Agricultural Sciences, Payame Noor
University, Tehran, Iran.Journal Article20240406Brassinosteroids are steroid hormones that are essential for the growth and development of plants and play a significant role in plant responses to stress. This study delves into examining how 24-epibrassinolide influences seedling indices, physiological and biochemical traits in specific lettuce genotypes under drought stress. The factorial experiment was conducted using a completely randomized statistical design with four replicates at the research laboratory of plant physiology, Faculty of Agriculture, Agriculture and Natural Resources Campus, Razi University, Kermanshah, Iran in 2023. The experiment included two selected lettuce genotypes, namely Icy and Romance, as the first factor. The second factor comprised seed pretreatment at four levels of priming with 24-epibrassinolide (0, 50, 100, and 150 μM), while the third factor consisted of drought stress at four levels (0%, 10%, 20%, and 30%) induced by mannitol. The assessed traits encompassed germination rate, root length, stem length, Relative Water Content (RWC), total sugar content, total phenol content, and flavonoid content. Comparative analysis of average traits revealed that the levels of biochemical traits, specifically total sugar (0.480 mg/l), phenol (460.83 mg/l), and flavonoid (1.047 μg/l), escalated with higher levels of drought stress. Principal component analysis indicated that the first two components elucidated 64% of the variations. The findings suggest that priming with 150μM of 24-epibrassinolide hormone is advisable to attain the highest seedling indices in lettuce. According to the results obtained in this research, the Roman line is introduced as the best line in drought stress conditions.Brassinosteroids are steroid hormones that are essential for the growth and development of plants and play a significant role in plant responses to stress. This study delves into examining how 24-epibrassinolide influences seedling indices, physiological and biochemical traits in specific lettuce genotypes under drought stress. The factorial experiment was conducted using a completely randomized statistical design with four replicates at the research laboratory of plant physiology, Faculty of Agriculture, Agriculture and Natural Resources Campus, Razi University, Kermanshah, Iran in 2023. The experiment included two selected lettuce genotypes, namely Icy and Romance, as the first factor. The second factor comprised seed pretreatment at four levels of priming with 24-epibrassinolide (0, 50, 100, and 150 μM), while the third factor consisted of drought stress at four levels (0%, 10%, 20%, and 30%) induced by mannitol. The assessed traits encompassed germination rate, root length, stem length, Relative Water Content (RWC), total sugar content, total phenol content, and flavonoid content. Comparative analysis of average traits revealed that the levels of biochemical traits, specifically total sugar (0.480 mg/l), phenol (460.83 mg/l), and flavonoid (1.047 μg/l), escalated with higher levels of drought stress. Principal component analysis indicated that the first two components elucidated 64% of the variations. The findings suggest that priming with 150μM of 24-epibrassinolide hormone is advisable to attain the highest seedling indices in lettuce. According to the results obtained in this research, the Roman line is introduced as the best line in drought stress conditions.https://cropbiotech.journals.pnu.ac.ir/article_11213_28ad3e630d5e75c1852ed7d6fe843642.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022Identification of functional pathways and key genes effective in response to nitrogen deficiency stress in riceIdentification of functional pathways and key genes effective in response to nitrogen deficiency stress in rice29431121210.30473/cb.2024.71521.1971FAShayanKazemi-LifshagerdM.Sc. student Genetics and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.AtefehSabouriDepartment of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.ZahraPezeshkianDepartment of Animal Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran-
-BioGenTAC Inc., Technology incubator of Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, IranMohammad MehdiSohaniFull Professor Biotechnology, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.Journal Article20240607Rice, as the primary food source for a large portion of the global population, holds significant strategic importance worldwide. Variations in the availability of elements such as nitrogen can greatly impact rice production. Nitrogen is crucial for rice growth, development, and performance by influencing various physiological and biochemical processes in plant cells. Considering the importance of the role of nitrogen, the aim of this research was to identify key genes, study biological pathways, and analyze important protein-protein interactions in rice under nitrogen deficiency stress. In this regard microarray expression data sets were extracted from the NCBI database, and differentially expressed genes between control and stress conditions were identified. Using DAVID online tools, the molecular functions, pathways, and biological processes related to these genes were investigated. Cytoscape software was used to construct a gene network, and ten key genes were identified. The study revealed that signaling pathways and amino acid production are prominently activated in the initial hours of nitrogen stress. Under nitrogen deficiency, the expression of genes involved in iron ion transport and amino acid biosynthesis significantly increases. The synthesis of iron ion transporters is crucial for photosynthesis in plant leaves, contributing to the balance and stability of photosynthetic products and leading to changes in the plant's morphological characteristics and performance. It is expected that these key genes can be used in breeding programs to deal with nitrogen deficiency stress.Rice, as the primary food source for a large portion of the global population, holds significant strategic importance worldwide. Variations in the availability of elements such as nitrogen can greatly impact rice production. Nitrogen is crucial for rice growth, development, and performance by influencing various physiological and biochemical processes in plant cells. Considering the importance of the role of nitrogen, the aim of this research was to identify key genes, study biological pathways, and analyze important protein-protein interactions in rice under nitrogen deficiency stress. In this regard microarray expression data sets were extracted from the NCBI database, and differentially expressed genes between control and stress conditions were identified. Using DAVID online tools, the molecular functions, pathways, and biological processes related to these genes were investigated. Cytoscape software was used to construct a gene network, and ten key genes were identified. The study revealed that signaling pathways and amino acid production are prominently activated in the initial hours of nitrogen stress. Under nitrogen deficiency, the expression of genes involved in iron ion transport and amino acid biosynthesis significantly increases. The synthesis of iron ion transporters is crucial for photosynthesis in plant leaves, contributing to the balance and stability of photosynthetic products and leading to changes in the plant's morphological characteristics and performance. It is expected that these key genes can be used in breeding programs to deal with nitrogen deficiency stress.https://cropbiotech.journals.pnu.ac.ir/article_11212_57310a5ecaa4e5393b160a5e569615ec.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022The growth promoting effect of native cyanobacterial strains on rice germination, as well as a In silico analysis of ammonium transporter (OsAMT) gene familyThe growth promoting effect of native cyanobacterial strains on rice germination, as well as a In silico analysis of ammonium transporter (OsAMT) gene family45651114610.30473/cb.2024.70775.1961FAAliakbarBabajanpour BoraPh.D. Student in Genetic and Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Iran.0009-0007-0349-157XGholamaliRanjbarDepartment of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
3. Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan
(GABIT), Sari ASeyyed HamidrezaHashemi-petroudiDepartment of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)0000-0002-0870-1691GhorbanaliNematzadehSari Agricultural Sciences and Natural Resources University, University of the Philippines Los BanosHamidNajafi ZariniAssociate Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.Journal Article20240310Cyanobacteria 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.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.https://cropbiotech.journals.pnu.ac.ir/article_11146_167a4a312ee6403916cb3a35fd4b95ca.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022Gene and regulatory network modeling of transcriptomic patterns in defense priming of rapeseed against Sclerotinia sclerotiorum infectionGene and regulatory network modeling of transcriptomic patterns in defense priming of rapeseed against Sclerotinia sclerotiorum infection67861131110.30473/cb.2024.71791.1973FAHengamehTaheriAssistant Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, IranMohamad HamedGhodoum Parizi Pour2. Associate Prof, Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran.Journal Article20240715Sclerotinia stem rot (SSR), caused by the soil-borne fungus Sclerotinia sclerotiorum, adversely impacts seed quality in rapeseed (Brassica napus) causing a 10-20% reduction in crop yield. The biological control agent Pseudomonas chlororaphis PA23 can protect rapeseed from the deleterious effects of the hemibiotrophic fungus S. sclerotiorum by inducing systemic resistance. However, little is known about the molecular mechanisms underlying defense priming and its regulatory processes. In this study, we amid to identify the protein-protein interaction (PPI) networks, with a particular focus on potential hub genes, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and regulatory network analysis including hub genes promoter analysis and miRNA prediction in canola plants pre-treated by PA23 in the presence of S. sclerotiorum using transcriptome data. Using the computational algorithms of the CytoHubba plugin in the Cytoscape platform, nodes with the highest interactions within the gene network were identified as hub genes, which are mainly involved in the maintenance and retrieval of metabolic pathways and photosynthetic activities, controlling cellular oxidation/reduction (redox) status, biosynthesis of aromatic amino acids and plant hormones, activation of MAPK-mediated defense signals, regulation of sulfur assimilation and cysteine biosynthesis. Using clustering analysis based on the IPCA algorithm in the Cytocluster plugin, functional modules effective in defense priming against SSR infection were identified. These modules were primarily involved in the biosynthesis of aromatic amino acids and the production of defensive metabolites in the shikimate pathway. The promoter analysis of 5′UTR region of hub genes identified various cis-regulatory elements (CREs), such as auxin signaling-responsive motifs involved in regulating defense responses against S. sclerotiorum infection. Prediction of miRNAs targeting hub genes, using the web-based psRNATarget program, revealed that miRNAs belonging to the families miR172, miR395, miR6028, miR6029, miR6032, miR6035, miR166, miR156, miR396 and miR824 play key roles as regulatory elements in the gene expression network of hub genes. These findings can aid in establishing biological control systems for plant disease management and protection of agricultural systems, as well as in advancing the fundamental mechanisms for developing disease-tolerant varieties.Sclerotinia stem rot (SSR), caused by the soil-borne fungus Sclerotinia sclerotiorum, adversely impacts seed quality in rapeseed (Brassica napus) causing a 10-20% reduction in crop yield. The biological control agent Pseudomonas chlororaphis PA23 can protect rapeseed from the deleterious effects of the hemibiotrophic fungus S. sclerotiorum by inducing systemic resistance. However, little is known about the molecular mechanisms underlying defense priming and its regulatory processes. In this study, we amid to identify the protein-protein interaction (PPI) networks, with a particular focus on potential hub genes, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and regulatory network analysis including hub genes promoter analysis and miRNA prediction in canola plants pre-treated by PA23 in the presence of S. sclerotiorum using transcriptome data. Using the computational algorithms of the CytoHubba plugin in the Cytoscape platform, nodes with the highest interactions within the gene network were identified as hub genes, which are mainly involved in the maintenance and retrieval of metabolic pathways and photosynthetic activities, controlling cellular oxidation/reduction (redox) status, biosynthesis of aromatic amino acids and plant hormones, activation of MAPK-mediated defense signals, regulation of sulfur assimilation and cysteine biosynthesis. Using clustering analysis based on the IPCA algorithm in the Cytocluster plugin, functional modules effective in defense priming against SSR infection were identified. These modules were primarily involved in the biosynthesis of aromatic amino acids and the production of defensive metabolites in the shikimate pathway. The promoter analysis of 5′UTR region of hub genes identified various cis-regulatory elements (CREs), such as auxin signaling-responsive motifs involved in regulating defense responses against S. sclerotiorum infection. Prediction of miRNAs targeting hub genes, using the web-based psRNATarget program, revealed that miRNAs belonging to the families miR172, miR395, miR6028, miR6029, miR6032, miR6035, miR166, miR156, miR396 and miR824 play key roles as regulatory elements in the gene expression network of hub genes. These findings can aid in establishing biological control systems for plant disease management and protection of agricultural systems, as well as in advancing the fundamental mechanisms for developing disease-tolerant varieties.https://cropbiotech.journals.pnu.ac.ir/article_11311_3b0f7ad7f8e2aba1d8c2dcc263a49f56.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022Identification of FAD family genes in the genome of Spirulina (Arthrospira platensis) microalgae and investigation of cellular functions in response to abiotic stressesIdentification of FAD family genes in the genome of Spirulina (Arthrospira platensis) microalgae and investigation of cellular functions in response to abiotic stresses871061121110.30473/cb.2024.70853.1963FASaharFarajiDepartment of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, IranGhorbanaliNematzadehProfessor, Genetics and Agricultural Biotechnology Institute of Tabarestan, Sari Agricultural Sciences and Natural Resources University, Sari, IranSeyed KamalKazemitabarAssociated Professor, Department of Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, IranAliPakdin-PariziCitrus and medicinal plants department, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, IranJournal Article20240316Arthrospira 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.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.https://cropbiotech.journals.pnu.ac.ir/article_11211_8a2af899721c89802cdaff805eae9333.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022Algae-based biofertilizers: applications and challengesAlgae-based biofertilizers: applications and challenges1071211121410.30473/cb.2024.71040.1965FAMajidAziziAgricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.0000-0003-3629-3055SaeedSoheilivandAgricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.Journal Article20240416The global algae market was valued at USD 19.8 Billion in the year 2021 and it is expected to reach USD 36 Billion in 2028 by Compound Annual Growth Rate (CAGR) of 10.5%. Eukaryotic green algae and Gram-negative prokaryotic cyanobacteria are widely used in pharmaceutical, food, cosmetic, aquaculture, poultry and biofuel industries. Algae are also used in agriculture based on sustainable development by facilitating increased access to nutrients, maintaining organic carbon and soil fertility, increasing plant growth and crop yield, and stimulating soil microbial activity. Heterocyte-forming cyanobacteria, which have acclimated to diverse environmental conditions, represent a unique subset of photosynthetic prokaryotes capable of nitrogen fixation via the nitrogenase enzyme system. In addition, green algae and cyanobacteria by producing metabolites such as growth hormones, polysaccharides and antimicrobial compounds play an important role in their colonization in the phyllosphere and rhizosphere of plants and the proliferation of microbial and eukaryotic communities in the soil. Currently, the development of the consortium of cyanobacteria with bacteria or fungi or microalgae and biofilms based on them has expanded the scope of using algae. This review focuses on the application of algae in the production of crops and the protection and management of natural resources, the challenges of using algae and their commercial aspects in agriculture.The global algae market was valued at USD 19.8 Billion in the year 2021 and it is expected to reach USD 36 Billion in 2028 by Compound Annual Growth Rate (CAGR) of 10.5%. Eukaryotic green algae and Gram-negative prokaryotic cyanobacteria are widely used in pharmaceutical, food, cosmetic, aquaculture, poultry and biofuel industries. Algae are also used in agriculture based on sustainable development by facilitating increased access to nutrients, maintaining organic carbon and soil fertility, increasing plant growth and crop yield, and stimulating soil microbial activity. Heterocyte-forming cyanobacteria, which have acclimated to diverse environmental conditions, represent a unique subset of photosynthetic prokaryotes capable of nitrogen fixation via the nitrogenase enzyme system. In addition, green algae and cyanobacteria by producing metabolites such as growth hormones, polysaccharides and antimicrobial compounds play an important role in their colonization in the phyllosphere and rhizosphere of plants and the proliferation of microbial and eukaryotic communities in the soil. Currently, the development of the consortium of cyanobacteria with bacteria or fungi or microalgae and biofilms based on them has expanded the scope of using algae. This review focuses on the application of algae in the production of crops and the protection and management of natural resources, the challenges of using algae and their commercial aspects in agriculture.https://cropbiotech.journals.pnu.ac.ir/article_11214_b857b63152ad4d92fb13992564a85c6e.pdfPayame Noor UniversityCrop Biotechnology2252-078314120241022Comparative analysis of secondary metabolite clusters synteny in eleven Oryza species and three related speciesComparative analysis of secondary metabolite clusters synteny in eleven Oryza species and three related species1231341130910.30473/cb.2024.70435.1953FASahandSasaniDepartment of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, IranSajadRashidi MonfaredDepartment of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.DanialKahrizi1. Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.MasoumehKhanahmadiAcademic Center for Education, Culture & Research (ACECR), Kermanshah, IranJournal Article20240130The rice (Oryza sativa) is part of the Poacea family and is one of the most important crops in the world. In this project, the presence of synteny in the clusters involved in the biosynthesis of secondary metabolites is known in the rice plant with 11 different species of Oryza and 3 related species. Genome sequences of all studied species were received from the NCBI database, and then the genes involved in the biosynthesis of secondary metabolites, which were located in the specific clusters were retrieved from the planti smash database. All genes were selected to align against 13 other species to identify sequences which similar to rice gene clusters using blastn tools. To map the genes of each species with the genome of the same species, gmap software was used. In the last step, gene blocks with synteny were identified using MCScanX software. According to the results, the existence of synteny in the clusters was proven in O. rufipogom, O. punctata and O. sativa indica species. After identifying the common regulatory factors of gene clusters, it is possible to regulate the expression of all gene clusters simultaneously to produce more content for the final products. On the other hand, due to the Co-inheritance of the genes located in each cluster, it could be possible to transfer desirable gene clusters by producing substitution lines that carry that gene cluster.The rice (Oryza sativa) is part of the Poacea family and is one of the most important crops in the world. In this project, the presence of synteny in the clusters involved in the biosynthesis of secondary metabolites is known in the rice plant with 11 different species of Oryza and 3 related species. Genome sequences of all studied species were received from the NCBI database, and then the genes involved in the biosynthesis of secondary metabolites, which were located in the specific clusters were retrieved from the planti smash database. All genes were selected to align against 13 other species to identify sequences which similar to rice gene clusters using blastn tools. To map the genes of each species with the genome of the same species, gmap software was used. In the last step, gene blocks with synteny were identified using MCScanX software. According to the results, the existence of synteny in the clusters was proven in O. rufipogom, O. punctata and O. sativa indica species. After identifying the common regulatory factors of gene clusters, it is possible to regulate the expression of all gene clusters simultaneously to produce more content for the final products. On the other hand, due to the Co-inheritance of the genes located in each cluster, it could be possible to transfer desirable gene clusters by producing substitution lines that carry that gene cluster.https://cropbiotech.journals.pnu.ac.ir/article_11309_83e9991a12a12a730200ed98c5264587.pdf