Payame Noor UniversityCrop Biotechnology2252-078310320210522Bioinformatics analysis of calcium-dependent protein kinase (CPK) in Aeluropus littoralis L.Bioinformatics analysis of calcium-dependent protein kinase (CPK) in Aeluropus littoralis L.119791510.30473/cb.2021.58258.1834FAMozhdehArabM.Sc. Student in Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.HamidNajafi ZarriniAssociated Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.GhorbanaliNematzadehProfessor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)Seyyed HamidrezaHashemi-petroudiAssistant Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)0000-0002-0870-1691Journal Article20210110Calcium-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.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.https://cropbiotech.journals.pnu.ac.ir/article_7915_980eea68d6a375dcea8c4b819eee5416.pdfPayame Noor UniversityCrop Biotechnology2252-078310320210522Identification and classification of the WRKY transcription factors family in Japonica riceIdentification and classification of the WRKY transcription factors family in Japonica rice2134791910.30473/cb.2021.59060.1839FAParisaDaryaniDepartment of Plant Production and Genetics, University of Mohaghegh Ardabili, Ardabil, IranFatemehFarzaneh Piralger1. Department of Plant Production and Genetics, University of Mohaghegh Ardabili, Ardabil, IranNasserZareDepartment of Plant Production and Genetics, University of Mohaghegh Ardabili, Ardabil, IranZahra-SadatShobbarDepartment of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.RasoolAsghari ZakariaDepartment of Plant Production and Genetics, University of Mohaghegh Ardabili, Ardabil, IranJournal Article20210224WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in datasets for finding new members. An HMM profile of WRKY domain was also used to find WRKY gene family. Multiple sequence alignment was done using clustalW software, and phylogenetic trees were drawn using MEGA10 software based on a neighbour-joining method with a 1000 repeats bootstrap index. According to the results, 165 members of the WRKY gene family were found in rice, of which 63 were new members. Sequences were divided into three main groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 21 proteins with two WRKY conserved domains in group I, 53 proteins with one WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and 82 proteins with one WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. The chromosomal location of OsWRKYs was detected on the rice genome. The different groups were distributed on various chromosomes. The greatest number of OsWRKY genes (32 members) were located on chromosome 1. Following complementary research and identification of promising candidate genes involved in tolerance to each stress, they can be used to increase tolerance to the desired stresses and provide food security using genetic engineering or molecular breeding approaches.WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in datasets for finding new members. An HMM profile of WRKY domain was also used to find WRKY gene family. Multiple sequence alignment was done using clustalW software, and phylogenetic trees were drawn using MEGA10 software based on a neighbour-joining method with a 1000 repeats bootstrap index. According to the results, 165 members of the WRKY gene family were found in rice, of which 63 were new members. Sequences were divided into three main groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 21 proteins with two WRKY conserved domains in group I, 53 proteins with one WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and 82 proteins with one WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. The chromosomal location of OsWRKYs was detected on the rice genome. The different groups were distributed on various chromosomes. The greatest number of OsWRKY genes (32 members) were located on chromosome 1. Following complementary research and identification of promising candidate genes involved in tolerance to each stress, they can be used to increase tolerance to the desired stresses and provide food security using genetic engineering or molecular breeding approaches.https://cropbiotech.journals.pnu.ac.ir/article_7919_9e81bd91e4446583d3d62ca1c4ba75c8.pdfPayame Noor UniversityCrop Biotechnology2252-078310320210522Conventional and molecular breeding of sunflower (Helianthus annuus L.)Conventional and molecular breeding of sunflower (Helianthus annuus L.)3578792010.30473/cb.2021.58978.1838FAAlirezaNabipourAssistant Professor, Rice Research Institute of Iran, Mazandaran Branch, Agriculture Research, Education and Extension Organization, Amol, Iran.RezaDarvishzadehProfessor, Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.AhmadSarrafiProfessor, Laboratoire Ecologie Fonctionnelle, EcoLab, Dynabio, INP-ENSAT, 18 Chemin de Borde Rouge, BP 32607,
31326 Castanet-Tolosan, France.Journal Article20210305Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, tetraploid and hexaploid species, and common sunflower is a diploid species with a base chromosome number of x=17. Sunflower is grown mainly for its edible oil. Environmental stresses such as drought, salinity, unusual temperatures, heavy metal and UV radiation are serious threats to plant growth, metabolism and productivity. In recent years, astonishing advances in biotechnology, genetic engineering, and computer science have made breeding programs much faster, more accurate, and more efficient than ever before. New techniques, if properly incorporated into breeding programs, can dramatically increase the speed and accuracy of these programs and can reduce costs by an extraordinary amount. In this article, while briefly referring to conventional breeding methods, new methods and their application in sunflower breeding are discussed. In the last 10 years, the science of genomic has expanded the genetic information of quantitative traits, and marker assisted selection has become a practical tool.Oilseeds are undoubtedly one of the most strategic agricultural products; their production is of basic needs for food security in any society. Sunflower with the scientific name of Helianthus annuus L. is an annual, monoecy, dicotyledonous plant that belongs to composite family. This genus consists diploid, tetraploid and hexaploid species, and common sunflower is a diploid species with a base chromosome number of x=17. Sunflower is grown mainly for its edible oil. Environmental stresses such as drought, salinity, unusual temperatures, heavy metal and UV radiation are serious threats to plant growth, metabolism and productivity. In recent years, astonishing advances in biotechnology, genetic engineering, and computer science have made breeding programs much faster, more accurate, and more efficient than ever before. New techniques, if properly incorporated into breeding programs, can dramatically increase the speed and accuracy of these programs and can reduce costs by an extraordinary amount. In this article, while briefly referring to conventional breeding methods, new methods and their application in sunflower breeding are discussed. In the last 10 years, the science of genomic has expanded the genetic information of quantitative traits, and marker assisted selection has become a practical tool.https://cropbiotech.journals.pnu.ac.ir/article_7920_0acf6242b532b32dbcc6279490ad090b.pdfPayame Noor UniversityCrop Biotechnology2252-078310320210522Investigation of informative CBDP and SCoT markers for leaf rust, powdery mildew and septoria leaf blotch diseases in spring wheat genotypesInvestigation of informative CBDP and SCoT markers for leaf rust, powdery mildew and septoria leaf blotch diseases in spring wheat genotypes7996792110.30473/cb.2021.58562.1835FABehzadNaeimi NezamabadM.Sc. Student, Department of Plant Production, College of Agriculture and Natural Resources, University of Gonbad Kavous, Gonbad, Iran.FakhtakTalieiAssistant Professor, Department of Plant Production, College of Agriculture and Natural Resources, University of Gonbad Kavous, Gonbad, Iran.AbbasBiabaniAssistant Professor, Department of Plant Production, College of Agriculture and Natural Resources, University of Gonbad Kavous, Gonbad, Iran.HosseinSabouriAssociate Professor, Department of Plant Production, College of Agriculture and Natural Resources, University of Gonbad Kavous, Gonbad, Iran.MasumeKheirguDepartment of Horticulture and crop research, Golestan Kavous Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Gonbad Kavous, Iran.Journal Article20210113Fungal leaf diseases are the most destructive factors to wheat (Triticum aestivum L.) yield. Therefore, identification of resistance sources to important fungal diseases is a great importance to increase wheat yield. In order to identify informative CBDP and SCoT markers for leaf rust, powdery mildew and septoria leaf blotch disease, 63 wheat genotypes were planted through the augment design in agricultural research station of Araghimahaleh (Gorgan) during 2018-19. Clustering based on UPGMA, put the genotypes into 3 groups with 24, 17 and 22 individuals. Among the studied genotypes, genotypes No. 49 and 60 showed highest resistance to all three diseases. Association analysis showed that from 16 CBDP and SCoT primers, 99 bands produced in total, which 43 bands were polymorph. The maximum percent of polymorphism belonged to SCoT primers and the minimum polymorphism belonged to CBDP. SCoT11-2, CBDP 10-2 was shown significant correlation with all three diseases. SCoT21-3 was also significantly (PFungal leaf diseases are the most destructive factors to wheat (Triticum aestivum L.) yield. Therefore, identification of resistance sources to important fungal diseases is a great importance to increase wheat yield. In order to identify informative CBDP and SCoT markers for leaf rust, powdery mildew and septoria leaf blotch disease, 63 wheat genotypes were planted through the augment design in agricultural research station of Araghimahaleh (Gorgan) during 2018-19. Clustering based on UPGMA, put the genotypes into 3 groups with 24, 17 and 22 individuals. Among the studied genotypes, genotypes No. 49 and 60 showed highest resistance to all three diseases. Association analysis showed that from 16 CBDP and SCoT primers, 99 bands produced in total, which 43 bands were polymorph. The maximum percent of polymorphism belonged to SCoT primers and the minimum polymorphism belonged to CBDP. SCoT11-2, CBDP 10-2 was shown significant correlation with all three diseases. SCoT21-3 was also significantly (Phttps://cropbiotech.journals.pnu.ac.ir/article_7921_5822c7247a82d37820af119788baaf82.pdfPayame Noor UniversityCrop Biotechnology2252-078310320210522Investigation of the Effect of Sulforaphane Content of Brassica oleracea Extract on the Expression of NF-κB and STAT3 Genes Contributing Affecting the Inflammatory Response Pathway of Immune SystemInvestigation of the Effect of Sulforaphane Content of Brassica oleracea Extract on the Expression of NF-κB and STAT3 Genes Contributing Affecting the Inflammatory Response Pathway of Immune System97110806610.30473/cb.2021.57157.1830FAMahdiehShojaeeM.Sc., Department of Agricultural Biotechnology, Payame Noor University, Tehran, Iran.RaziehSarabadaniAssistant Professor, Department of Agricultural Biotechnology, Payame Noor University, Tehran, Iran.Journal Article20201211Inflammation is a natural response of the body’s immune system to disease, protecting the body in the form of a defensive mechanism. The immune system identifies the damaged body cells, stimuli, and pathogens to trigger the healing process – a mechanism that can engage the body with inflammation. In some cases, too long inflammation and excessive immune responses led to side effects and damages that dominate their benefits, leading to chronic inflammation and then engagement with different diseases. In the present research, effect of the broccoli sprouts extract on the expression of the NF-κB and STAT3 genes affecting the inflammatory response pathway of immune system was investigated. Results of gas chromatography – mass spectroscopy (GC-MS) and MTT assay confirmed the presence of the sulforaphane in the extract while rejecting their toxicity to cell lines. Moreover, the GAPDH and β-actin genes were used as internal control genes in the 1321N1 neural cell line, with the HFF cell line used as normal cell. The cells were treated with 2 mg of the extract for 3 days, during which time the changes in the immune system in terms of the genes expressions were monitored. The results showed that the sulforaphane attenuate the expressions of the NF-κB and STAT3 genes as two of the most important inflammatory mediating genes. It seems that the use of sulforaphane as active ingredient can effectively attenuate the cause of the disorders faced by the patients with immune system inflammation.Inflammation is a natural response of the body’s immune system to disease, protecting the body in the form of a defensive mechanism. The immune system identifies the damaged body cells, stimuli, and pathogens to trigger the healing process – a mechanism that can engage the body with inflammation. In some cases, too long inflammation and excessive immune responses led to side effects and damages that dominate their benefits, leading to chronic inflammation and then engagement with different diseases. In the present research, effect of the broccoli sprouts extract on the expression of the NF-κB and STAT3 genes affecting the inflammatory response pathway of immune system was investigated. Results of gas chromatography – mass spectroscopy (GC-MS) and MTT assay confirmed the presence of the sulforaphane in the extract while rejecting their toxicity to cell lines. Moreover, the GAPDH and β-actin genes were used as internal control genes in the 1321N1 neural cell line, with the HFF cell line used as normal cell. The cells were treated with 2 mg of the extract for 3 days, during which time the changes in the immune system in terms of the genes expressions were monitored. The results showed that the sulforaphane attenuate the expressions of the NF-κB and STAT3 genes as two of the most important inflammatory mediating genes. It seems that the use of sulforaphane as active ingredient can effectively attenuate the cause of the disorders faced by the patients with immune system inflammation.https://cropbiotech.journals.pnu.ac.ir/article_8066_41e03a943f0b8caf6d0e68d56aa060a4.pdfPayame Noor UniversityCrop Biotechnology2252-078310320210621Screening of Iranian potato germplasm for resistance to PVY and PVXScreening of Iranian potato germplasm for resistance to PVY and PVX111129806710.30473/cb.2021.58942.1837FAZahraHajibaratDepartment of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.AbbasSaidiDepartment of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.AhmadMosuapour GorjiDepartment of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.MehrshadZeinalabediniAgricultural Biotechnology Research Institute of Iran, Department of Systems and Synthetic Biology, Karaj, Iran. Agricultural Research, Education and Extension Organization (AREEO), Iran.Mohammad RezaGhaffari3. Agricultural Biotechnology Research Institute of Iran, Department of Systems and Synthetic Biology, Karaj, Iran. Agricultural Research, Education and Extension Organization (AREEO), Iran.RahimAhmadvandDepartment of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.Journal Article20210203Potato virus Y (PVY) and Potato virus X (PVX) are the most important potato-infecting agent causing yield loss and tuber quality reduction. In this study, an experiment was conducted in Karaj, Iran, to investigate the effects of mentioned viruses on the yield and resistance level of 33 potato genotypes. The experiment was performed based on randomized complete design in factorial format under two levels viruses with three replications. The results revealed that the viral infection had a significant impact on mean yield, seed yield (tuber size 35-55), ware yield (tuber size > 55 mm), and non-marketable yield (tuber size< 35). Based on cluster analysis for PVY, cluster VII was considered maximum resistant genotypes to PVY in terms mean absorption and yield, while cluster VI was identified susceptible genotypes in to PVY. According to cluster analysis of PVX virus, cluster I was considered highest resistant genotypes in terms mean absorption and yield and cluster III were maximum susceptible genotypes to PVX infection. Results of this study showed that genotype G23 with a mean-absorption of 0.01 and 0.032 for PVY and PVX, respectively, and mean yield of 4.1 kg/m2 was considered as a highly resistant genotype to both viruses. The concurrent selection of genotypes for high yield and resistant to both viruses (PVX and PVY) can facilitate potato breeding programs.Potato virus Y (PVY) and Potato virus X (PVX) are the most important potato-infecting agent causing yield loss and tuber quality reduction. In this study, an experiment was conducted in Karaj, Iran, to investigate the effects of mentioned viruses on the yield and resistance level of 33 potato genotypes. The experiment was performed based on randomized complete design in factorial format under two levels viruses with three replications. The results revealed that the viral infection had a significant impact on mean yield, seed yield (tuber size 35-55), ware yield (tuber size > 55 mm), and non-marketable yield (tuber size< 35). Based on cluster analysis for PVY, cluster VII was considered maximum resistant genotypes to PVY in terms mean absorption and yield, while cluster VI was identified susceptible genotypes in to PVY. According to cluster analysis of PVX virus, cluster I was considered highest resistant genotypes in terms mean absorption and yield and cluster III were maximum susceptible genotypes to PVX infection. Results of this study showed that genotype G23 with a mean-absorption of 0.01 and 0.032 for PVY and PVX, respectively, and mean yield of 4.1 kg/m2 was considered as a highly resistant genotype to both viruses. The concurrent selection of genotypes for high yield and resistant to both viruses (PVX and PVY) can facilitate potato breeding programs.https://cropbiotech.journals.pnu.ac.ir/article_8067_76d410e96448792996ce4e13e02e0a7c.pdf