Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Genetic Relationships of Pistacia Species and Cultivars by SCoT Markers Genetic Relationships of Pistacia Species and Cultivars by SCoT Markers 1 20 3510 10.22103/jab.2022.18817.1374 FA Mohsen Saadlou Parizi Ph.D. Student, Department of Production Engineering and Breeding Genetics, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran. Sodabeh Jahanbakhsh Godehkahriz Department of plant genetics and production engineering, Faculty of agriculture and natural resources, University of Mohaghegh Ardabili, Ardabil, Iran 0000-0002-8338-1069 Hosein Dashti Professor, Department of Genetics and Plant Production, Faculty of Agriculture, Valiasr University, Rafsanjan, Rafsanjan, Iran. email Roohallah Saberi Riseh Professor, Department of Plant Protection, Faculty of Agriculture, Valiasr University, Rafsanjan, Rafsanjan, Iran. Hojjat Hashemi Nasab Research Assistant Professor, Pistachio Research Center, Horticultural sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran Journal Article 2022 06 21 Objective Pistachio is one of the most important agricultural products and iran has the richest germplasm of pistachio in the world. The presence of this genetic resources will be an appropriate opportunity for use in breeding purposes. Knowledge of genetic relationships among pistachio genotypes has important role in it’s breeding programs. Molecular markers are one of the powerful tools for studying plant phylogenetic relationships. Start Codon Targeted (SCoT) technique is one of the molecular systems that used to assess the genetic relationship among different plant species and cultivars. This study was performed in order to evaluate the genetic relationships between a numbers of Pistacia species and cultivars using SCoT molecular markers and to assess the usefulness of this markers in differentiating this genus. Materials and methods Plant materials of this study are included 29 genotypes of domestic and wild species of genus Pistacia. A total of 25 SCoT primers were used to evaluate the genetic relationships. Genomic DNA were extracted from leaf samples using CTAB method with minor modifications. The quantity and quality of the extracted DNA were measured by spectrophotometer and agarose gel electrophoresis. Cluster analysis based on Jaccard’s similarity matrix and complete linkage algorithm and Principal coordinate analysis were performed using NTSYSpc 2.02e software. Results In total, 449 DNA fragments were amplified by primers out of which 433 bands (96/43%) were polymorphic. The average number of amplified fragments for each primer was 17.96 bands with a mean of 17.32 polymorphic bands per primer. A number of species-spicific marker were detected in some Genotypes. The average of polymorphism information content values varied from 0/18 to 0/38. Also, the values of marker indices ranged from 0/56 to 4/36. The range of similarity coefficients of genotypes varied between 25% to 68%. Cluster analysis divided Genotypes into two main cluster including vera (domestic) and wild species. Principal coordinate analysis separated vera cultivars and genotypes from wild species and confirmed the results of cluster analysis. Conclusions The results of this study demonstrated that SCoT molecular markers detected high polymorphism among pistachio species and cultivars and differentiated the studid genotypes. Therefore, SCoT Marker is a useful tool for studying phylogenetic relationships in genus Pistacia. Objective Pistachio is one of the most important agricultural products and iran has the richest germplasm of pistachio in the world. The presence of this genetic resources will be an appropriate opportunity for use in breeding purposes. Knowledge of genetic relationships among pistachio genotypes has important role in it’s breeding programs. Molecular markers are one of the powerful tools for studying plant phylogenetic relationships. Start Codon Targeted (SCoT) technique is one of the molecular systems that used to assess the genetic relationship among different plant species and cultivars. This study was performed in order to evaluate the genetic relationships between a numbers of Pistacia species and cultivars using SCoT molecular markers and to assess the usefulness of this markers in differentiating this genus. Materials and methods Plant materials of this study are included 29 genotypes of domestic and wild species of genus Pistacia. A total of 25 SCoT primers were used to evaluate the genetic relationships. Genomic DNA were extracted from leaf samples using CTAB method with minor modifications. The quantity and quality of the extracted DNA were measured by spectrophotometer and agarose gel electrophoresis. Cluster analysis based on Jaccard’s similarity matrix and complete linkage algorithm and Principal coordinate analysis were performed using NTSYSpc 2.02e software. Results In total, 449 DNA fragments were amplified by primers out of which 433 bands (96/43%) were polymorphic. The average number of amplified fragments for each primer was 17.96 bands with a mean of 17.32 polymorphic bands per primer. A number of species-spicific marker were detected in some Genotypes. The average of polymorphism information content values varied from 0/18 to 0/38. Also, the values of marker indices ranged from 0/56 to 4/36. The range of similarity coefficients of genotypes varied between 25% to 68%. Cluster analysis divided Genotypes into two main cluster including vera (domestic) and wild species. Principal coordinate analysis separated vera cultivars and genotypes from wild species and confirmed the results of cluster analysis. Conclusions The results of this study demonstrated that SCoT molecular markers detected high polymorphism among pistachio species and cultivars and differentiated the studid genotypes. Therefore, SCoT Marker is a useful tool for studying phylogenetic relationships in genus Pistacia.

https://jab.uk.ac.ir/article_3510_15e122e839dfdaa7ce969536f94aecf6.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 0621 03 23 Evaluation of the effect of carbon nanoparticles on the proliferation of calli of date palm (Majol cultivar) Evaluation of the effect of carbon nanoparticles on the proliferation of calli of date palm (Majol cultivar) 21 44 3511 10.22103/jab.2022.19357.1397 FA Sadaf Abedi MSC Student, Department of Plant Production, Faculty of Agricultural Sciences and Natural Resources, Gonbad Kavous University Leila Ahangar Assistant Professor, Department of Plant Production, Faculty of Agricultural Sciences and Natural Resources, Gonbad Kavous University 0000-0002-1158-9397 Reza Zarghami Faculty member of Agricultural Biotechnology Research Institute (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj Leila Maˈmani Faculty member of Agricultural Biotechnology Research Institute (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj Masome Naeemi Assistant Professor, Department of Plant Production, Faculty of Agricultural Sciences and Natural Resources, Gonbad Kavous University Journal Article Objective Nanotechnology, as a promising method for addressing sustainable agricultural issues, can increase propagation efficiency in palm tissue culture. This study aimed to prepare carbon nanoparticles and use the resulting nanocomposites to evaluate their efficiency in improving and increasing date callus formation. Materials and methods Three separate experiments were performed to propagate calluses consisting of meristematic microsamples of dates. In the first experiment, calli prepared in MS culture medium were transferred to four culture media with different hormonal treatments from NAA and 2iP, and in the second experiment, calli composed of meristematic date microsamples in MS culture medium were transferred to four culture media with separate treatments from NAA and BAP. Different hormones were transferred from NAA and BAP. In the third experiment, after determining the best hormonal treatments from the first and second experiments, carbon nanoparticles were synthesized from graphite, and calli composed of meristematic date microsomal samples were recreated in superior culture media with different concentrations of nanoparticles (0, 10, 20, 30, 40, 50 mg/L). Results Based on the results of the first experiment, treatments of 10 mg/L NAA + 30 mg/L 2ip and 0.1 mg/L NAA + 0.05 mg/L 2ip were selected as the best callus propagation treatments. In the second experiment, it was found that there was no statistically significant difference between the applied treatments of 10 mg/L NAA + 30 mg/L BAP and 10 mg/L NAA + 10 mg/L BAP with other treatments with different concentrations of BAP. The results of the third experiment showed that the use of 10 mg/L NAA + 30 mg/L BAP + 30 mg/L CNP can produce the most calluses. Conclusions Due to the positive effect of carbon nanoparticles on increasing the weight of commodities, treatment of 10 mg/L NAA + 30 mg/L BAP + 30 mg/L CNP becomes the most suitable option for calorific cultivar propagation. Objective Nanotechnology, as a promising method for addressing sustainable agricultural issues, can increase propagation efficiency in palm tissue culture. This study aimed to prepare carbon nanoparticles and use the resulting nanocomposites to evaluate their efficiency in improving and increasing date callus formation. Materials and methods Three separate experiments were performed to propagate calluses consisting of meristematic microsamples of dates. In the first experiment, calli prepared in MS culture medium were transferred to four culture media with different hormonal treatments from NAA and 2iP, and in the second experiment, calli composed of meristematic date microsamples in MS culture medium were transferred to four culture media with separate treatments from NAA and BAP. Different hormones were transferred from NAA and BAP. In the third experiment, after determining the best hormonal treatments from the first and second experiments, carbon nanoparticles were synthesized from graphite, and calli composed of meristematic date microsomal samples were recreated in superior culture media with different concentrations of nanoparticles (0, 10, 20, 30, 40, 50 mg/L). Results Based on the results of the first experiment, treatments of 10 mg/L NAA + 30 mg/L 2ip and 0.1 mg/L NAA + 0.05 mg/L 2ip were selected as the best callus propagation treatments. In the second experiment, it was found that there was no statistically significant difference between the applied treatments of 10 mg/L NAA + 30 mg/L BAP and 10 mg/L NAA + 10 mg/L BAP with other treatments with different concentrations of BAP. The results of the third experiment showed that the use of 10 mg/L NAA + 30 mg/L BAP + 30 mg/L CNP can produce the most calluses. Conclusions Due to the positive effect of carbon nanoparticles on increasing the weight of commodities, treatment of 10 mg/L NAA + 30 mg/L BAP + 30 mg/L CNP becomes the most suitable option for calorific cultivar propagation.

https://jab.uk.ac.ir/article_3511_9a85c12a21b76392747906fc7b2aff92.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 1401 10 01 Evaluation of genetic diversity of Estahban region fig genotypes based on morphological traits and SCoT molecular markers Evaluation of genetic diversity of Estahban region fig genotypes based on morphological traits and SCoT molecular markers 45 68 3512 10.22103/jab.2022.19157.1392 FA Elaheh Ranjbaran MSc Student, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran Mehdi Rahimi Associate Professor, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran 0000-0001-5625-3275 Maryam Abdolinasab Assistant Professor, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran. Hamid Zare Assistant Professor, Fig Research Station, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Estahban, Iran Mojtaba Kordrostami Assistant Professor, Department of Plant Breeding, Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran. Journal Article Objective Fig (Ficus carica) is a deciduous tree that is grown in arid and semi-arid regions. Figs, as an important crop, have undergone genetic erosion in recent decades due to living and non-living stresses. The aim of this study was to determine the genetic diversity of genotypes in Estahban using morphological traits and Start Codon Targeted (SCoT) molecular markers. Materials and methods In this study, 16 fig genotypes were evaluated in a completely randomized design with three replications based on their morphological traits. Also, their genomic DNA was extracted from leaves and the genotypic diversity of genotypes based on 10 SCoT primers was examined. Results Variance analysis showed a significant difference between traits, and cluster analysis based on morphological traits placed the genotypes in five groups. Eight primers amplified a total of 50 polymorphic bands, and SCoT12 and SCoT11 produced the most bands with 13 and 9 polymorphic bands, respectively. The polymorphic information content (PIC) for the SCoT primers varied between 0.3423 and 0.3791 with an average of 0.3595. Cluster analysis by UPGMA and Gower similarity criterion based on SCoT data, 16 fig genotypes were placed in four groups. The grouping based on the Bayesian method placed the genotypes in nine groups, although the genotypes were not differentiated and were a mixture of all nine groups. Conclusions The results indicate that the use of SCoT marker has a high advantage and plays an important role in the differentiation of fig genotypes. In general, it can be said that SCoT molecular markers and morphological traits have shown high diversity among genotypes. In general, the results obtained from this study indicate the existence of high genetic diversity in the germplasm of Estahban fig cultivars, which can be used in breeding programs by protecting this rich germplasm source. Objective Fig (Ficus carica) is a deciduous tree that is grown in arid and semi-arid regions. Figs, as an important crop, have undergone genetic erosion in recent decades due to living and non-living stresses. The aim of this study was to determine the genetic diversity of genotypes in Estahban using morphological traits and Start Codon Targeted (SCoT) molecular markers. Materials and methods In this study, 16 fig genotypes were evaluated in a completely randomized design with three replications based on their morphological traits. Also, their genomic DNA was extracted from leaves and the genotypic diversity of genotypes based on 10 SCoT primers was examined. Results Variance analysis showed a significant difference between traits, and cluster analysis based on morphological traits placed the genotypes in five groups. Eight primers amplified a total of 50 polymorphic bands, and SCoT12 and SCoT11 produced the most bands with 13 and 9 polymorphic bands, respectively. The polymorphic information content (PIC) for the SCoT primers varied between 0.3423 and 0.3791 with an average of 0.3595. Cluster analysis by UPGMA and Gower similarity criterion based on SCoT data, 16 fig genotypes were placed in four groups. The grouping based on the Bayesian method placed the genotypes in nine groups, although the genotypes were not differentiated and were a mixture of all nine groups. Conclusions The results indicate that the use of SCoT marker has a high advantage and plays an important role in the differentiation of fig genotypes. In general, it can be said that SCoT molecular markers and morphological traits have shown high diversity among genotypes. In general, the results obtained from this study indicate the existence of high genetic diversity in the germplasm of Estahban fig cultivars, which can be used in breeding programs by protecting this rich germplasm source.

https://jab.uk.ac.ir/article_3512_0dbb3fb9a5cd1d5f8a9075b5bb8070aa.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Identification of genes involved in ion transport under high salinity stress in rice seedlings Identification of genes involved in ion transport under high salinity stress in rice seedlings 69 84 3513 10.22103/jab.2022.19689.1409 FA Mojdeh Akbarzadeh Lelekami Ph.D. Student, Plant Breeding and Biotechnology Department, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran. Mohammad Hadi Pahlevani Associate Professor, Department, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran Khalil Zaynali Nezhad Assistant Professor, Plant Breeding and Biotechnology Department, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran. Keyvan Mahdavi Mashaki Assistant Professor, Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), Amol, Iran Andreas P.M. Weber Professor, Plant Biochemistry Department, Heinrich Heine University (HHU), Düsseldorf, Germany Dominik Brilhaus Assistant Professor, Plant Biochemistry Department, Heinrich Heine University (HHU), Düsseldorf, Germany. Journal Article 2022 08 19 Objective Rice is highly sensitive to salinity stress among crops. The sensitivity at seedling stage and reproductive phase causes damage to the essential processes of plant and ultimately reduces the yield. In saline environments, ion toxicity is increased by sodium uptake. Tolerant cultivars cope the salinity stress by low maintain of Na+/K+ in the photosynthetic organs. The entry and exclusion of ions in the plant cells is controlled by ion channels and transporters. Identifying and evaluating the expression pattern of genes encoding these transporters at different time points and organs was our objective. Materials and methods In present study, two rice genotypes of tolerant CSR28 and sensitive IR28 were used. The grown seedlings in hydroponic medium were exposed to 150 mM salinity treatment and the roots and shoots were collected after 6 and 54 h of the treatment. After RNA extraction, library construction and RNA-Seq analysis were performed and differential expressed gene identified. MapMan pathway analysis was used to identify the genes encoding ion transporters. Results The comparison of the two genotypes under specific salinity stress, identified 47 highly expressed genes encoding ion transporters which some of them showed genotype or organ-specific expression pattern. OsTPC1 and OsSOS3 genes, which are involved in the entry of Ca+ into cells and Ca+ receptors, respectively, had higher expression in the roots of the tolerant genotype than the susceptible genotype at 54 h time point. Considerably, high expression of the important genes such as OsSOS1 and OsNHX1 in the tolerant genotype indicated a low Na+ accumulation compared to the sensitive genotype. Other gene involved in ion homeostasis, such as OsHKT1, displayed more expression in the roots of the tolerant genotype at 54 h. Conclusions Generally, our findings revealed that the molecular mechanisms occurred in the roots under long-term salinity stress caused differences in salinity tolerance through various ion homeostasis. The results also indicated the role of the Ca+-related signaling pathway in the higher tolerance of CSR28. Specific expression patterns of some of the genes can be used as biomarker in the selection programs of salt-tolerant rice genotypes. Objective Rice is highly sensitive to salinity stress among crops. The sensitivity at seedling stage and reproductive phase causes damage to the essential processes of plant and ultimately reduces the yield. In saline environments, ion toxicity is increased by sodium uptake. Tolerant cultivars cope the salinity stress by low maintain of Na+/K+ in the photosynthetic organs. The entry and exclusion of ions in the plant cells is controlled by ion channels and transporters. Identifying and evaluating the expression pattern of genes encoding these transporters at different time points and organs was our objective. Materials and methods In present study, two rice genotypes of tolerant CSR28 and sensitive IR28 were used. The grown seedlings in hydroponic medium were exposed to 150 mM salinity treatment and the roots and shoots were collected after 6 and 54 h of the treatment. After RNA extraction, library construction and RNA-Seq analysis were performed and differential expressed gene identified. MapMan pathway analysis was used to identify the genes encoding ion transporters. Results The comparison of the two genotypes under specific salinity stress, identified 47 highly expressed genes encoding ion transporters which some of them showed genotype or organ-specific expression pattern. OsTPC1 and OsSOS3 genes, which are involved in the entry of Ca+ into cells and Ca+ receptors, respectively, had higher expression in the roots of the tolerant genotype than the susceptible genotype at 54 h time point. Considerably, high expression of the important genes such as OsSOS1 and OsNHX1 in the tolerant genotype indicated a low Na+ accumulation compared to the sensitive genotype. Other gene involved in ion homeostasis, such as OsHKT1, displayed more expression in the roots of the tolerant genotype at 54 h. Conclusions Generally, our findings revealed that the molecular mechanisms occurred in the roots under long-term salinity stress caused differences in salinity tolerance through various ion homeostasis. The results also indicated the role of the Ca+-related signaling pathway in the higher tolerance of CSR28. Specific expression patterns of some of the genes can be used as biomarker in the selection programs of salt-tolerant rice genotypes.

https://jab.uk.ac.ir/article_3513_0ffaca95e3e5242ba1097ad8a9a6e95d.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Implementation of association mapping for identification of ISSR markers linked with morphological characteristics of Ajowan (Trachyspermum copticum) Implementation of association mapping for identification of ISSR markers linked with morphological characteristics of Ajowan (Trachyspermum copticum) 85 102 3514 10.22103/jab.2022.19139.1402 FA Mahdieh Modareskia Ph.D. Student, Department of Horticulture, Faculty of Agriculture, Urmia University, Urmia, Iran. Reza Darvishzadeh Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran 0000-0001-5991-4411 Mohsen Modares Assistant Professor, Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, University of Advanced Technology, Kerman, Iran. 0000-0002-4884-2827 Hamid Hatami Maleki Associate Professor, Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran. Journal Article 2022 08 19 Objective Ajowan (Trachyspermum copticum) is a medicinal species that is very useful and is used to treat stomach problems and some other diseases. This study aimed to fingerprint Ajowan accessions collected from different geographical regions of Iran by using ISSR markers and identifying markers linked with agro-morphological traits through an association mapping approach. Materials and methods In this study, a number of 40 Ajowan genotypes related to 10 different populations from different regions of Iran were collected, and then their morphological characteristics were recorded in greenhouse conditions. Leaf samples were taken from each genotype and ISSR fingerprinting was done after DNA extraction. Results The results of descriptive statistics indicate the existence of genetic diversity in the germplasm of the studied Ajowan in terms of morphological characteristics and the highest and lowest coefficients of phenotypic variation were obtained for the number of seeds formed and the number of flowers per umbrella, respectively. Results of DNA fingerprinting using 12 ISSR primers lead to the amplification of 153 loci, 93 of which were polymorphic and the rest were monomorphic. Analysis of molecular variance depicted that 37% and 63% of total variation belonged to between and within populations. In this research private markers were detected for accessions collected from Hamedan and Rafsanjan. The study of population structure related to 40 Ajowan genotypes using ISSR data and STRUCTURE software placed them in two different subpopulations. Using an association mapping approach, significant positive markers for biological yield, shoot dry weight, harvest index, number of lateral branches, number of seeds formed, 100-seed weight, mean internode length, umbrella per flower, stem diameter, and single plant yield, number of umbrellas, number of leaves, number of flowers in an inflorescence and leaf length were identified. Conclusions In this research, the UBC807-2, UBC812-10, UBC818-8, UBC840-5, UBC848-4, UBC857-11, and UBC857-6 markers control more than one trait simultaneously and can thus be bred in breeding programs of Ajowan to a simultaneous selection of multiple traits. Objective Ajowan (Trachyspermum copticum) is a medicinal species that is very useful and is used to treat stomach problems and some other diseases. This study aimed to fingerprint Ajowan accessions collected from different geographical regions of Iran by using ISSR markers and identifying markers linked with agro-morphological traits through an association mapping approach. Materials and methods In this study, a number of 40 Ajowan genotypes related to 10 different populations from different regions of Iran were collected, and then their morphological characteristics were recorded in greenhouse conditions. Leaf samples were taken from each genotype and ISSR fingerprinting was done after DNA extraction. Results The results of descriptive statistics indicate the existence of genetic diversity in the germplasm of the studied Ajowan in terms of morphological characteristics and the highest and lowest coefficients of phenotypic variation were obtained for the number of seeds formed and the number of flowers per umbrella, respectively. Results of DNA fingerprinting using 12 ISSR primers lead to the amplification of 153 loci, 93 of which were polymorphic and the rest were monomorphic. Analysis of molecular variance depicted that 37% and 63% of total variation belonged to between and within populations. In this research private markers were detected for accessions collected from Hamedan and Rafsanjan. The study of population structure related to 40 Ajowan genotypes using ISSR data and STRUCTURE software placed them in two different subpopulations. Using an association mapping approach, significant positive markers for biological yield, shoot dry weight, harvest index, number of lateral branches, number of seeds formed, 100-seed weight, mean internode length, umbrella per flower, stem diameter, and single plant yield, number of umbrellas, number of leaves, number of flowers in an inflorescence and leaf length were identified. Conclusions In this research, the UBC807-2, UBC812-10, UBC818-8, UBC840-5, UBC848-4, UBC857-11, and UBC857-6 markers control more than one trait simultaneously and can thus be bred in breeding programs of Ajowan to a simultaneous selection of multiple traits.

https://jab.uk.ac.ir/article_3514_7288251b27c8f0e73f4d7f483b06a785.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Study of miRNAs involved in drought and salt stress stresses and ontology of target genes in Brassica species Study of miRNAs involved in drought and salt stress stresses and ontology of target genes in Brassica species 103 132 3515 10.22103/jab.2022.20206.1429 FA Neda Zolfaghari Khutbehsera MSc Student, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran. Mohammad Mohsenzadeh Golfazani Assistant Professor, Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran. Mohammad Mehdi Taghvaei Assistant Professor, Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran. Habibollah Samizadeh Lahiji Professor, Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran. 0000-0002-2278-9079 Journal Article 2022 08 23 Objective Abiotic stresses such as drought and salinity significantly affect plant growth and performance. Plants use strategies to adapt and tolerate drought and salt stress that may threaten their survival during their life cycle, one of which is miRNA-mediated post-transcriptional regulation. Materials and methods In the current research, miRNAs that showed significant expression during salt and drought stress were selected by checking the references to investigate this phenomenon in rapeseed plants. The phylogenetic tree was constructed to analyze and compare the evolutionary relationships and conservation of MicroRNA effective in drought and salinity stress in Brassica napus, Brassica rapa, and Brassica oleracea species. Target genes for selected miRNAs were identified using psRNATarget online software. Categorization and gene ontology of target genes and identification of biological pathways were accomplished; also, proteins were classified based on molecular function and biological processes. The Protein-protein interaction was analyzed to comprehensively interpret the relationships between the target genes. In the present study, 225 target genes for miRNAs were identified. Results After examining the protein interaction network, it was found that there were the most interactions between ribosomal, proteasome subunits and the ubiquitin-proteasome system. This result determined that drought and salinity stress leads to the activation of various biological systems and pathways and changes in gene expression along with the activation of the protein synthesis machine and alterations in protein content. By activating post-transcriptional gene regulation (PTGR) and post-translational modifications (PTMs), the plant regulates the abundance, activities, intracellular distribution, and transport of regulatory proteins involved in various growth processes as well as stress response. Conclusion The results of this study will lead to a broader perspective regarding stress and its effect on the pathways involved in cellular processes and will reveal the wide dimensions of the stress response. Objective Abiotic stresses such as drought and salinity significantly affect plant growth and performance. Plants use strategies to adapt and tolerate drought and salt stress that may threaten their survival during their life cycle, one of which is miRNA-mediated post-transcriptional regulation. Materials and methods In the current research, miRNAs that showed significant expression during salt and drought stress were selected by checking the references to investigate this phenomenon in rapeseed plants. The phylogenetic tree was constructed to analyze and compare the evolutionary relationships and conservation of MicroRNA effective in drought and salinity stress in Brassica napus, Brassica rapa, and Brassica oleracea species. Target genes for selected miRNAs were identified using psRNATarget online software. Categorization and gene ontology of target genes and identification of biological pathways were accomplished; also, proteins were classified based on molecular function and biological processes. The Protein-protein interaction was analyzed to comprehensively interpret the relationships between the target genes. In the present study, 225 target genes for miRNAs were identified. Results After examining the protein interaction network, it was found that there were the most interactions between ribosomal, proteasome subunits and the ubiquitin-proteasome system. This result determined that drought and salinity stress leads to the activation of various biological systems and pathways and changes in gene expression along with the activation of the protein synthesis machine and alterations in protein content. By activating post-transcriptional gene regulation (PTGR) and post-translational modifications (PTMs), the plant regulates the abundance, activities, intracellular distribution, and transport of regulatory proteins involved in various growth processes as well as stress response. Conclusion The results of this study will lead to a broader perspective regarding stress and its effect on the pathways involved in cellular processes and will reveal the wide dimensions of the stress response.

https://jab.uk.ac.ir/article_3515_5fef3eff51dc719c4a9f565a742d78f2.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 The application of genomic selection in improvement of molecular breeding programs in aquaculture The application of genomic selection in improvement of molecular breeding programs in aquaculture 133 156 3516 10.22103/jab.2022.20339.1436 FA Reza Pasandideh Assistant Professor, Iranian Shrimp Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bushehr, Iran. 0000-0003-3002-8605 Mohammadreza Mohammadabadi Professor, Animal Science Department, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran 0000-0002-1268-3043 Majid Pasandideh Assistant Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran. 0000-0001-5340-7072 Journal Article 2022 08 23 Objective Although aquaculture is the fastest sector in terms of animal protein production in the world, breeding programs in aquatic species have been delayed compared to livestock and plants. Breeding improvement programs in aquaculture are mainly based on using phenotypic and pedigree information in quantitative genetics. However, approaches based on genomic information such as marker assistant selection (MAS) and genomic selection (GS) have been used to improve economic traits in recent years. The present paper aimed to investigate the breeding principles in aquaculture from phenotypic selection to genomic selection, their advantages and limitations, and recent advances in different aquatic species. Results Genomic selection increases genetic gain in aquaculture through increasing accuracy of selection, decreasing generation interval, decreasing inbreeding rate, better control of genetic and environmental interactions, and selection of animals with less sensitivity to environmental variation. Especially, genomic selection is suitable for difficult-to-measure or low heritability traits such as disease resistance, feed intake, reproduction traits, and carcass quality. Reference population size, marker density, mating design, number and size of families, and a number of generations are effective factors in the accuracy of genomic selection in aquaculture. Continuous advances in cost-effective technologies for genotyping especially genotyping-by-sequencing (GBS) and bioinformatics will facilitate the faster application of genomic selection in aquaculture. Conclusions Although genomic selection has been used for about 20 aquatic species in recent years and has provided opportunities for the improvement of genetic gain. However, the advantages of this method should be evaluated in commercial and economic aquatic breeding programs. It is expected that genomic selection will be widely used in aquatic breeding in the future and pave the way for the sustainable development of this industry. Objective Although aquaculture is the fastest sector in terms of animal protein production in the world, breeding programs in aquatic species have been delayed compared to livestock and plants. Breeding improvement programs in aquaculture are mainly based on using phenotypic and pedigree information in quantitative genetics. However, approaches based on genomic information such as marker assistant selection (MAS) and genomic selection (GS) have been used to improve economic traits in recent years. The present paper aimed to investigate the breeding principles in aquaculture from phenotypic selection to genomic selection, their advantages and limitations, and recent advances in different aquatic species. Results Genomic selection increases genetic gain in aquaculture through increasing accuracy of selection, decreasing generation interval, decreasing inbreeding rate, better control of genetic and environmental interactions, and selection of animals with less sensitivity to environmental variation. Especially, genomic selection is suitable for difficult-to-measure or low heritability traits such as disease resistance, feed intake, reproduction traits, and carcass quality. Reference population size, marker density, mating design, number and size of families, and a number of generations are effective factors in the accuracy of genomic selection in aquaculture. Continuous advances in cost-effective technologies for genotyping especially genotyping-by-sequencing (GBS) and bioinformatics will facilitate the faster application of genomic selection in aquaculture. Conclusions Although genomic selection has been used for about 20 aquatic species in recent years and has provided opportunities for the improvement of genetic gain. However, the advantages of this method should be evaluated in commercial and economic aquatic breeding programs. It is expected that genomic selection will be widely used in aquatic breeding in the future and pave the way for the sustainable development of this industry.

https://jab.uk.ac.ir/article_3516_cf1cf43cba274ae7f413e864682b80f8.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Determination of population density of Aspergillus flavus and Aspergillus parasiticus in the last irrigation treatments before harvest in soil and fruits of pistachio trees Determination of population density of Aspergillus flavus and Aspergillus parasiticus in the last irrigation treatments before harvest in soil and fruits of pistachio trees 157 180 3517 10.22103/jab.2022.20091.1424 FA Amir Hossein Mohammadi Assistant Professor, Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran. 0000-0003-2842-0333 Naser Sedaghati Assistant Professor, Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran. 0000-0001-9374-3943 Masoumeh Haghdel Assistant Professor, Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran. 0000-0002-4323-9391 Seyd Javad Hosseinifard Assistant Professor, Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran. 0000-0002-9784-8141 Mehdi Mohammadi Moghadam Assistant Professor, Horticultural and Crop Sciences Research Department, Agricultural and Natural Resources Research and Education Center of Semnan Province (Shahrood), AREEO, Shahrood, Iran. Journal Article 2022 10 23 Objective Contamination of pistachio with Aspergillus and aflatoxin is one of the most important problems in the production and export of this valuable product. In this research, in addition to molecular identification of Aspergillus flavus and A. parasiticus and determination of the frequency of their toxigenic and atoxigenic isolates, the population of Aspergillus flavus clade was measured in soil, intact and cracked fruits of cv. Ohadi in 6 treatments of last irrigation before harvest (5, 10, 15, 20, 25 and 30 days). Materials and methods Isolation of Aspergillus flavus clade fungi from soil, intact and cracked fruits was done by serial dilution method on DRBC culture medium. Aspergillus flavus and A. parasiticus were identified by macromorphological and molecular (calmodulin primer) features and screening of toxigenic and atoxigenic isolates was performed using of coconut-agar medium (CAM) and thin layer chromatography (TLC). This experiment was carried out in a complete randomized block design with four replications during the years 2012 to 2014. Results Out of 233 collected isolates of Aspergillus flavus clade, 221 and 12 isolates belonged to Aspergillus flavus and A. parasiticus, respectively. Frequency of toxigenic isolates of A. flavus and A. parasiticus was 86.5, 87.5, 88.7% and 80, 75, 100% in cracked, intact fruits and soil, respectively. Based on the results of the combine analysis, the last irrigation treatments 30 and 25 days before harvest have the lowest and the last irrigation treatments 10 and 5 days before harvest have the highest population of Aspergillus flavus clade in the soil, intact and cracked fruits which showed significant difference with each other. Using of manure significantly increased the population of Aspergillus flavus clade, so that this increase in cracked, healthy fruits and soil in 2013 was 66, 83 and 114%, respectively. Conclusions The results of the present research showed that reduction of the interval between the last irrigation and the time of fruit harvesting (high moisture percentage of the surface soil of the orchard) and the using manure can increase the population of Aspergillus flavus clade in the soil, intact and cracked pistachio fruits. Increasing of the fungal population is accompanied by the frequency of toxigenic isolates of Aspergillus flavus and A. parasiticus. Adjusting the irrigation cycle, so that the last irrigation is 25 to 30 days before the fruit harvesting, can reduce the possibility of contamination of the pistachio kernels to Aspergillus and aflatoxin. Objective Contamination of pistachio with Aspergillus and aflatoxin is one of the most important problems in the production and export of this valuable product. In this research, in addition to molecular identification of Aspergillus flavus and A. parasiticus and determination of the frequency of their toxigenic and atoxigenic isolates, the population of Aspergillus flavus clade was measured in soil, intact and cracked fruits of cv. Ohadi in 6 treatments of last irrigation before harvest (5, 10, 15, 20, 25 and 30 days). Materials and methods Isolation of Aspergillus flavus clade fungi from soil, intact and cracked fruits was done by serial dilution method on DRBC culture medium. Aspergillus flavus and A. parasiticus were identified by macromorphological and molecular (calmodulin primer) features and screening of toxigenic and atoxigenic isolates was performed using of coconut-agar medium (CAM) and thin layer chromatography (TLC). This experiment was carried out in a complete randomized block design with four replications during the years 2012 to 2014. Results Out of 233 collected isolates of Aspergillus flavus clade, 221 and 12 isolates belonged to Aspergillus flavus and A. parasiticus, respectively. Frequency of toxigenic isolates of A. flavus and A. parasiticus was 86.5, 87.5, 88.7% and 80, 75, 100% in cracked, intact fruits and soil, respectively. Based on the results of the combine analysis, the last irrigation treatments 30 and 25 days before harvest have the lowest and the last irrigation treatments 10 and 5 days before harvest have the highest population of Aspergillus flavus clade in the soil, intact and cracked fruits which showed significant difference with each other. Using of manure significantly increased the population of Aspergillus flavus clade, so that this increase in cracked, healthy fruits and soil in 2013 was 66, 83 and 114%, respectively. Conclusions The results of the present research showed that reduction of the interval between the last irrigation and the time of fruit harvesting (high moisture percentage of the surface soil of the orchard) and the using manure can increase the population of Aspergillus flavus clade in the soil, intact and cracked pistachio fruits. Increasing of the fungal population is accompanied by the frequency of toxigenic isolates of Aspergillus flavus and A. parasiticus. Adjusting the irrigation cycle, so that the last irrigation is 25 to 30 days before the fruit harvesting, can reduce the possibility of contamination of the pistachio kernels to Aspergillus and aflatoxin.

https://jab.uk.ac.ir/article_3517_b5b0db7f3a77ca4fcf9eca57aa7181ca.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Investigating the effect of chitosan on gene expression, p5cs enzyme activity and proline content in rapeseed (Brassica napus L.) under salt stress Investigating the effect of chitosan on gene expression, p5cs enzyme activity and proline content in rapeseed (Brassica napus L.) under salt stress 181 200 3518 10.22103/jab.2022.18349.1348 FA Zohreh Khosravian MSc Student, Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran Monireh Ranjbar Assistant Professor, Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran. Ali Mohammad Ahadi Associate Professor, Department of Molecular Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran. Journal Article 2022 10 23 Objective Salinity is one of the most important stresses that reduce the yield of most plants. Plants use different mechanisms in response to environmental stresses. Chitosan and its oligomers are used in plants to resist abiotic stresses such as salinity. In this study, the effect of chitosan and salinity on gene expression and p5cs enzyme activity and proline content in rapeseed was investigated. Materials and methods For this purpose, rapeseed plants were treated with sodium chloride solution (0, 50, 100, and 150 mM) and chitosan (0, 5, and 10 mg/L). The experiment was performed as a factorial experiment with a completely randomized design in 3 replications. Treated plants were harvested to measure gene expression, p5cs enzyme activity, and proline content. Results With increasing salt concentration, the expression of the delta-1 proline-5 carboxylate synthetase (P5CS) gene, enzyme activity, and proline content increased. In the combined salinity of 100 mM with chitosan 10 mg/L, gene expression, activity, and proline content in rapeseed had the highest amount. The use of chitosan in the salt-containing medium compared to the salinity treatments in the same concentration, caused the P5CS gene to be expressed more, increased enzyme activity, and then more proline was synthesized. Therefore, there is a positive correlation between gene expression, enzyme activity, and the amount of proline produced. Conclusions According to the results, chitosan with a concentration of 10 mg / l in salinity treatment, by increasing gene expression and the activity of the enzyme delta-1-proline-5-carboxylate synthetase (P5CS), produced proline, which increases the plant's resistance to salinity stress. Objective Salinity is one of the most important stresses that reduce the yield of most plants. Plants use different mechanisms in response to environmental stresses. Chitosan and its oligomers are used in plants to resist abiotic stresses such as salinity. In this study, the effect of chitosan and salinity on gene expression and p5cs enzyme activity and proline content in rapeseed was investigated. Materials and methods For this purpose, rapeseed plants were treated with sodium chloride solution (0, 50, 100, and 150 mM) and chitosan (0, 5, and 10 mg/L). The experiment was performed as a factorial experiment with a completely randomized design in 3 replications. Treated plants were harvested to measure gene expression, p5cs enzyme activity, and proline content. Results With increasing salt concentration, the expression of the delta-1 proline-5 carboxylate synthetase (P5CS) gene, enzyme activity, and proline content increased. In the combined salinity of 100 mM with chitosan 10 mg/L, gene expression, activity, and proline content in rapeseed had the highest amount. The use of chitosan in the salt-containing medium compared to the salinity treatments in the same concentration, caused the P5CS gene to be expressed more, increased enzyme activity, and then more proline was synthesized. Therefore, there is a positive correlation between gene expression, enzyme activity, and the amount of proline produced. Conclusions According to the results, chitosan with a concentration of 10 mg / l in salinity treatment, by increasing gene expression and the activity of the enzyme delta-1-proline-5-carboxylate synthetase (P5CS), produced proline, which increases the plant's resistance to salinity stress.

https://jab.uk.ac.ir/article_3518_5401acfe633e6817b508b84d23686743.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Population structure identification of Turkmen and Darehshori horses using PCA, DAPC, and SPC methods Population structure identification of Turkmen and Darehshori horses using PCA, DAPC, and SPC methods 201 220 3519 10.22103/jab.2022.18795.1372 FA Ghazaleh Javanmard MSc Student, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. 0000-0001-5594-3004 Mohammad Moradi Shahrbabak Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. 0000-0002-5255-609X Hossein Moradi Shahrbabak Assistant Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. 0000-0002-6680-7662 Javad Rahmaninia Assistant Professor, Animal Sciences Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran. Mahdi Abbasi Firoozjaei MSc Student, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. Mohammad Bagher Zandi Assistant Professor, Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran. 0000-0001-9568-8933 Journal Article 2022 02 08 Objective Conservation of the genetic diversity of indigenous animals is very important. For the sustainable use of genetic resources, it is necessary to first study the genetic structure of populations. The main goals of this research were to identify the population structure of Turkmen and Darehshori horses using dense SNP markers and to compare the effectiveness of PCA, DAPC, and SPC methods in clustering these populations. Materials and methods For this purpose, 67 Turkmen and 39 Darehshori horses were genotyped using Illumina EquineSNP70 BeadChip. After applying quality control steps, five Turkmen horses and one Darehshori horse were removed. Then, the structure of populations was identified by three methods of principal component analysis (PCA), discriminant analysis of principal components (DAPC), and superparamagnetic clustering (SPC). These methods do not depend on previous assumptions and make it possible to analyze very large genome databases without prior knowledge of individual ancestry. These methods are also very fast and efficient. Results This study compared the efficiency of these three clustering methods in identifying population structures. All three methods were successful in separating the two breeds, and Turkmen and Darehshori breeds were grouped into separate genetic groups. The difference is that the DAPC method only separated the two main populations, but the PCA and SPC methods could identify several subpopulations in each breed. The results of this study showed that the SPC method for studying the population structure of indigenous breeds with unknown information can be more useful than other methods. Therefore, using this method, a suitable program can be designed to conserve and use genetic resources. Conclusions PCA, DAPC, and SPC methods were able to successfully identify the genetic structure of Turkmen and Darehshori breeds, and in general, it can be said that the information obtained from dense SNP markers can be a powerful tool for identifying the population structure of indigenous breeds. Objective Conservation of the genetic diversity of indigenous animals is very important. For the sustainable use of genetic resources, it is necessary to first study the genetic structure of populations. The main goals of this research were to identify the population structure of Turkmen and Darehshori horses using dense SNP markers and to compare the effectiveness of PCA, DAPC, and SPC methods in clustering these populations. Materials and methods For this purpose, 67 Turkmen and 39 Darehshori horses were genotyped using Illumina EquineSNP70 BeadChip. After applying quality control steps, five Turkmen horses and one Darehshori horse were removed. Then, the structure of populations was identified by three methods of principal component analysis (PCA), discriminant analysis of principal components (DAPC), and superparamagnetic clustering (SPC). These methods do not depend on previous assumptions and make it possible to analyze very large genome databases without prior knowledge of individual ancestry. These methods are also very fast and efficient. Results This study compared the efficiency of these three clustering methods in identifying population structures. All three methods were successful in separating the two breeds, and Turkmen and Darehshori breeds were grouped into separate genetic groups. The difference is that the DAPC method only separated the two main populations, but the PCA and SPC methods could identify several subpopulations in each breed. The results of this study showed that the SPC method for studying the population structure of indigenous breeds with unknown information can be more useful than other methods. Therefore, using this method, a suitable program can be designed to conserve and use genetic resources. Conclusions PCA, DAPC, and SPC methods were able to successfully identify the genetic structure of Turkmen and Darehshori breeds, and in general, it can be said that the information obtained from dense SNP markers can be a powerful tool for identifying the population structure of indigenous breeds.

https://jab.uk.ac.ir/article_3519_1fd7b875d3473501d1b771ebe934ca59.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Evaluation of Transcription Response to Drought Stress in Rice Using RNA-seq Meta-analysis Evaluation of Transcription Response to Drought Stress in Rice Using RNA-seq Meta-analysis 221 246 3520 10.22103/jab.2022.19691.1411 FA Shima Karami Ph.D. Student, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran. Behrouz Shiran Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran. 0000-0001-9997-4718 Rudabeh Ravash Assistant Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran. 0000-0001-7321-6337 Hossein Fallahi Assistant Professor, Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran. Arghavan Alisolitani Assistant Professor, University of California Riverside School of Medicine, Riverside, California, USA. Journal Article 2022 02 08 Objective Understanding the molecular mechanisms of response to stress such as drought can significantly improve the science of plant molecular breeding. Transcriptomic studies can make a large amount of information available to researchers. Integrating such data from different sources through advanced statistical methods such as meta-analysis provides a new opportunity to overcome biological complexity, identify differentially expressed genes (DEGs), and obtain more reliable results. The present study aimed to identify DEGs in response to drought stress using transcriptomic data through a meta-analysis of RNA-seq data. Materials and methods RNA-seq data were downloaded from the EMBL-EBI database and after preprocessing, high-quality reads were mapped on the rice reference genome with the STAR software. Differential expression genes were evaluated separately for each dataset using the edgeR package. The outputs were used for meta-analysis using the metaRNAseq package. Genes with different and significant expressions in response to drought stress were examined for functional enrichment, biological pathways, and protein interaction. Finally, hub genes were identified. Results According to the meta-analysis results, 6607 differential expression genes with average log2FC≥|1| And FDR≤0.05 were detected. 3313 and 3294 of them were regulated up and down, respectively, and 162 genes were not identified as DEG in individual analyzes and were identified only by meta-analysis, which shows the statistical power of this method in identifying new genes. The results of functional enrichment of DEGs indicate the induction of various metabolic pathways under stress including biosynthesis of secondary metabolites and amino acids, carbohydrate metabolism, and plant hormone signal transduction. Investigation of protein interaction and identification of hub genes also showed their role in stress response, oxidoreductase activity, and amino acid metabolism. Conclusions This study can increase our understanding of the molecular mechanisms of rice response to drought stress and be useful in identifying key and new genes, even as molecular markers to improve drought stress tolerance in rice breeding programs. Objective Understanding the molecular mechanisms of response to stress such as drought can significantly improve the science of plant molecular breeding. Transcriptomic studies can make a large amount of information available to researchers. Integrating such data from different sources through advanced statistical methods such as meta-analysis provides a new opportunity to overcome biological complexity, identify differentially expressed genes (DEGs), and obtain more reliable results. The present study aimed to identify DEGs in response to drought stress using transcriptomic data through a meta-analysis of RNA-seq data. Materials and methods RNA-seq data were downloaded from the EMBL-EBI database and after preprocessing, high-quality reads were mapped on the rice reference genome with the STAR software. Differential expression genes were evaluated separately for each dataset using the edgeR package. The outputs were used for meta-analysis using the metaRNAseq package. Genes with different and significant expressions in response to drought stress were examined for functional enrichment, biological pathways, and protein interaction. Finally, hub genes were identified. Results According to the meta-analysis results, 6607 differential expression genes with average log2FC≥|1| And FDR≤0.05 were detected. 3313 and 3294 of them were regulated up and down, respectively, and 162 genes were not identified as DEG in individual analyzes and were identified only by meta-analysis, which shows the statistical power of this method in identifying new genes. The results of functional enrichment of DEGs indicate the induction of various metabolic pathways under stress including biosynthesis of secondary metabolites and amino acids, carbohydrate metabolism, and plant hormone signal transduction. Investigation of protein interaction and identification of hub genes also showed their role in stress response, oxidoreductase activity, and amino acid metabolism. Conclusions This study can increase our understanding of the molecular mechanisms of rice response to drought stress and be useful in identifying key and new genes, even as molecular markers to improve drought stress tolerance in rice breeding programs.

https://jab.uk.ac.ir/article_3520_6c0958d82a830a02c0718147b1b565c1.pdf

Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 14 4 2022 12 22 Weighted gene co-expressed network analysis in barley and expression of hub genes involved at germination stage Weighted gene co-expressed network analysis in barley and expression of hub genes involved at germination stage 247 267 3521 10.22103/jab.2022.20183.1427 FA Zohreh Hajibarat Ph.D. Student, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. 0000-0001-5801-1886 Abbas Saidi Professor, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. 0000-0001-6721-5389 Mohammad Reza Ghaffari Assistant Professor, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran. Mehrshad Zeinolabedini Associated Professor, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran. Zahra Hajibarat Ph.D. Student, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran. Journal Article 2022 02 08 Objective Seed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules. Materials and methods Raw microarray data related to the germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h, and 71h after the germination stage. Then, weighted gene co-expression network analysis (WGCNA) was utilized for the detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression patterns after 9h, 18h, and 71h after the germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR. Results Most of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to a stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at the germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is a lack of information on the seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism of seed germination in barley. Conclusions The results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular-assisted selection and breeding of fast-germinating barley genotypes. Objective Seed germination is an important process that determines the beginning of the seed plant life cycle. However, the mechanism underlying seed germination in barley remains unclear. To understand the molecular mechanism of seed germination in barley, WGCNA analysis was used to detect the hub and responsive genes and to reveal the expression of the genes on seed germination. WGCNA is a valuable tool for studying the correlation between genes, identifying modules with high correlation, and identifying Hub genes in different modules. Materials and methods Raw microarray data related to the germination stage were obtained from the GEO microarray database for 0h, 3h, 9h, 18h, 33h, and 71h after the germination stage. Then, weighted gene co-expression network analysis (WGCNA) was utilized for the detection of co-expressed network genes. In the present study, a barley cultivar, Mahtab, was utilized to show expression patterns after 9h, 18h, and 71h after the germination stage. A total number of 4137 differentially expressed genes (DEG) were identified, with some genes showing higher expression in Mahtab and three genes verified by qRT-PCR. Results Most of these DEGs were involved in metabolic processes, cellular processes, glycolysis, and response to a stimulus. Hub gene in MEbrown was alpha/beta-Hydrolases superfamily protein, MEpurple was U-box domain-containing protein 4, and MEdarkgrey was B3 domain-containing transcription factor ABI3 which were positively correlated with germinated seeds. The results showed a microarray database and candidate genes for further study of barley at germination stages. In addition, DEGs were divided into three modules by WGCNA. In this study, gene modules associated with seed germination during barley seed germination were identified. Transcription factor and alpha/beta-hydrolase played an important role at the germination stage. Also, gene modules and hub genes at 9h, 18h, and 71h after germination were detected. As there is a lack of information on the seed germination requirements of barley, this research was conducted to study seed germination mechanisms as well as evaluation of hub genes to study molecular mechanism of seed germination in barley. Conclusions The results of the present study provide new insights into the molecular mechanism underlying barley seed germination. Based on the network analysis, transcription factors (TFs) and ubiquitin proteins were involved in germination. Most of the genes related to each module were related to proteins involved in carbohydrate metabolism, glycolysis, and protein degradation. Our gene expression results can serve as molecular markers in barley cultivars during seed germination. These findings can be suitable for molecular-assisted selection and breeding of fast-germinating barley genotypes.

https://jab.uk.ac.ir/article_3521_98afdcc1ebd85daa0f1749c5e56b9d8c.pdf