Shahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Mapping loci affecting live weight and body size in Lori-Bakhtiari sheep using paternal half-sib design and identification of biomarkers linked to growth rateMapping loci affecting live weight and body size in Lori-Bakhtiari sheep using paternal half-sib design and identification of biomarkers linked to growth rate115201110.22103/jab.2018.2011FAEbrahimAsadiAsistant Professor, Department of animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.RoyaHoriatGraduate M. Sc. degree, Department of animal Science, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.SaadolaahHooshmandProfessor, Department of Plant Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran.AliEsmaelizadehProfessor, Department of animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.0000-0003-0986-6639Journal Article20170703The aim of this study was to map loci affecting live weight and body size in Lori-Bakhtiari sheep and identification of biomarkers linked to growth rate in sheep. Quantitative trait loci (QTL) linkage analysis in a Lori-Bakhtiari sheep population was conducted using the regression-based interval mapping method. The mapping population consisted of 162 animals related to 5 paternal half families. Phenotypic data were measurements of birth weight (BW), weight at one month of age (W1), weaning weight (WW), weight at six months of age (W6), chest circumference (HG6), body length (BL6), wither height at six months of age (HT6), weight at nine months of age (W9) and yearling weight (W12). Five sires and their progeny were genotyped for microsatellite markers in a candidate region on sheep chromosome 1. Data were analyzed in two phases, individual family analysis and combined family’s analysis using a single-QTL model. Analysis based on individual families revealed QTL related to W1 (210.6 cM), near INRA011 marker segregating in the second family. In the third family, QTL affecting W1 and WW were identified at 252.6 and 223.6 cM, nearby MCM137 and LSCV105 markers, respectively. In addition, in the fourth family, a QTL underlying W1 was detected at 256.6 cM near LSCV105 marker. Combined analysis of all the families resulted to the identification of a QTL associated with W1 at position 254.6 cM relative to the centromere near the LSCV105 marker. There were two strong candidate genes close to the location of the detected QTL, the transferrin and PIT1 genes, thus these genes may account for the observed QTL effects for growth traits in Lori-Bakhtiari sheep.The aim of this study was to map loci affecting live weight and body size in Lori-Bakhtiari sheep and identification of biomarkers linked to growth rate in sheep. Quantitative trait loci (QTL) linkage analysis in a Lori-Bakhtiari sheep population was conducted using the regression-based interval mapping method. The mapping population consisted of 162 animals related to 5 paternal half families. Phenotypic data were measurements of birth weight (BW), weight at one month of age (W1), weaning weight (WW), weight at six months of age (W6), chest circumference (HG6), body length (BL6), wither height at six months of age (HT6), weight at nine months of age (W9) and yearling weight (W12). Five sires and their progeny were genotyped for microsatellite markers in a candidate region on sheep chromosome 1. Data were analyzed in two phases, individual family analysis and combined family’s analysis using a single-QTL model. Analysis based on individual families revealed QTL related to W1 (210.6 cM), near INRA011 marker segregating in the second family. In the third family, QTL affecting W1 and WW were identified at 252.6 and 223.6 cM, nearby MCM137 and LSCV105 markers, respectively. In addition, in the fourth family, a QTL underlying W1 was detected at 256.6 cM near LSCV105 marker. Combined analysis of all the families resulted to the identification of a QTL associated with W1 at position 254.6 cM relative to the centromere near the LSCV105 marker. There were two strong candidate genes close to the location of the detected QTL, the transferrin and PIT1 genes, thus these genes may account for the observed QTL effects for growth traits in Lori-Bakhtiari sheep.https://jab.uk.ac.ir/article_2011_c8758b517083196f05ac29810b924aca.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Genetic Diversity of Persian Crocodile Crocodylus Palustris Using Sequencing of D-Loop and Cyt b Regions of MitochondriaGenetic Diversity of Persian Crocodile Crocodylus Palustris Using Sequencing of D-Loop and Cyt b Regions of Mitochondria1738201210.22103/jab.2018.2012FAAhmadAfsharianPhD Student, Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.MohammadrezaNasiriProfessor, Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad. Mashhad, Iran.EsmaeilEbrahimiAssociate Professor, School of Molecular and Biomedical Science, The University of Adelaide, Australia.AliJavadmaneshAssistant Professor, Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.Journal Article20170811Identification of the genetic features of Persian mugger crocodile, the Gando, is crucial in management planning for conservation and preservation of this endangered species. Therefore, this study is aimed to investigate the genetic characteristics of Gando in Iran, based on population studies of the conserved and variable regions of the mitochondrial DNA. For this purpose, 12 samples of skin tissue and blood were collected from three regions of Chabahar city, south east of Iran. After DNA extraction, conserved and variable regions of the mitochondrial genome Cyt b and D-loop were amplified using PCR. The PCR products were sequenced and results were analyzed using bioinformatics software based on nucleotide data as well as protein codons. Results revealed that all samples had similar nucleotide sequences and no genetic variation was found among the samples. The closest species to Gando were Crocodylus palustris and then C. porosus. Comparison of sequences with other Crocodile species revealed the presence of 12 polymorphic loci among 1156 loci studied and also 5 haplogroups were introduced. As we didn’t find any nucleotide diversity among studied samples, therefore, to increase the genetic diversity of the Gando, it is essential to include specific conservational plans for this endangered species.Identification of the genetic features of Persian mugger crocodile, the Gando, is crucial in management planning for conservation and preservation of this endangered species. Therefore, this study is aimed to investigate the genetic characteristics of Gando in Iran, based on population studies of the conserved and variable regions of the mitochondrial DNA. For this purpose, 12 samples of skin tissue and blood were collected from three regions of Chabahar city, south east of Iran. After DNA extraction, conserved and variable regions of the mitochondrial genome Cyt b and D-loop were amplified using PCR. The PCR products were sequenced and results were analyzed using bioinformatics software based on nucleotide data as well as protein codons. Results revealed that all samples had similar nucleotide sequences and no genetic variation was found among the samples. The closest species to Gando were Crocodylus palustris and then C. porosus. Comparison of sequences with other Crocodile species revealed the presence of 12 polymorphic loci among 1156 loci studied and also 5 haplogroups were introduced. As we didn’t find any nucleotide diversity among studied samples, therefore, to increase the genetic diversity of the Gando, it is essential to include specific conservational plans for this endangered species.https://jab.uk.ac.ir/article_2012_253614bbac999b38b5b60cae531c4969.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Effect of cadmium stress on gene expression and enzyme activity of glutathione reductase of milk thistle (Silybum marianum)Effect of cadmium stress on gene expression and enzyme activity of glutathione reductase of milk thistle (Silybum marianum)3950201310.22103/jab.2018.2013FASorayaPourtabriziDept. Agronomy and Plant Breeding College of Agriculture, Shahid Bahonar University, Kerman, IranShahramPourseyediDept. Agronomy and Plant Breeding College of Agriculture, Shahid Bahonar University, Kerman, Iran.RoholahAbdeshahiDept. Agronomy and Plant Breeding, College of Agriculture, Shahid Bahonar University, Kerman, Iran.NaziNaderneghadDept. Biology, Faculty of Science, Shahid Bahonar University, Kerman, Iran.Journal Article20170509Cadmium (Cd) is a one of the heavy metals that causes oxidative stress in plants and Plants equipped with a scavenging ROS system to protect against this stress. In this study, changes of expression profile and enzyme activity of glutathione reductase (GR) were analyzed in milk thistle (Silybum marianum) seedlings in response to cadmium chloride concentrations (0, 300, 600 and 900 μM) using completely randomized design with two and five replications, respectively. Results of semi quantitative RT- PCR showed that gene expression of GR in stress plants leaves was significantly different from control plants. The lowest and highest gene expression was in control and 900 μM concentration of cadmium chloride, respectively. It could be concluded that glutathione reductase enzyme plays important role in enzymatic antioxidant defense system in response to cadmium toxicity in Silybum marianum.Cadmium (Cd) is a one of the heavy metals that causes oxidative stress in plants and Plants equipped with a scavenging ROS system to protect against this stress. In this study, changes of expression profile and enzyme activity of glutathione reductase (GR) were analyzed in milk thistle (Silybum marianum) seedlings in response to cadmium chloride concentrations (0, 300, 600 and 900 μM) using completely randomized design with two and five replications, respectively. Results of semi quantitative RT- PCR showed that gene expression of GR in stress plants leaves was significantly different from control plants. The lowest and highest gene expression was in control and 900 μM concentration of cadmium chloride, respectively. It could be concluded that glutathione reductase enzyme plays important role in enzymatic antioxidant defense system in response to cadmium toxicity in Silybum marianum.https://jab.uk.ac.ir/article_2013_8038da89e49ac5eabb489cfc6cea9fc1.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220The proteomic analysis of leaf in Rapeseed (Brassica napus L) under salt stressThe proteomic analysis of leaf in Rapeseed (Brassica napus L) under salt stress6451201410.22103/jab.2018.2014FANimaDolatabadi1 Ph.D. Student, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.MahmoodToorchi2 Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.MostafaValizadehProfessor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, IranAliBandehhaghAssociate professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.Journal Article20170403Salinity is one of the most important problems in arid and semi-arid areas that causes serious decrement in agricultural productions. Rapeseed is a superior oilseed due to the high quality of oil, large amounts of polyunsaturated fatty acids and oil yield. To deal with abiotic stress conditions, plants synthesize some essential metabolites, special structural proteins or metabolic enzymes pathways to overcome the stress. To identify the molecular mechanisms of salt responsiveness in rapeseed, proteome changes of Option500 a salt-sensitive genotype under salt stress was studied. An increase in proline and the Na<sup>+</sup> of leaf and a reduction in shoot dry weight, plant height, K<sup>+</sup> and K<sup>+</sup>/Na<sup>+</sup> were observed under salt stress (0, 150, 300 mM). Over 110 protein spots were identified by two-dimensional electrophoresis (2-DE) gels. 44 spots showed significant expression changes based on induction factor, which 7 spots were recognized significantly at 5% probability level. 1 and 6 spots were up and down-regulated, respectively. By using LC-MS/MS mass spectrometry analysis proteins that involved in energy production and photosynthesis were identified. Role of these proteins to salt stress response will be discussed.Salinity is one of the most important problems in arid and semi-arid areas that causes serious decrement in agricultural productions. Rapeseed is a superior oilseed due to the high quality of oil, large amounts of polyunsaturated fatty acids and oil yield. To deal with abiotic stress conditions, plants synthesize some essential metabolites, special structural proteins or metabolic enzymes pathways to overcome the stress. To identify the molecular mechanisms of salt responsiveness in rapeseed, proteome changes of Option500 a salt-sensitive genotype under salt stress was studied. An increase in proline and the Na<sup>+</sup> of leaf and a reduction in shoot dry weight, plant height, K<sup>+</sup> and K<sup>+</sup>/Na<sup>+</sup> were observed under salt stress (0, 150, 300 mM). Over 110 protein spots were identified by two-dimensional electrophoresis (2-DE) gels. 44 spots showed significant expression changes based on induction factor, which 7 spots were recognized significantly at 5% probability level. 1 and 6 spots were up and down-regulated, respectively. By using LC-MS/MS mass spectrometry analysis proteins that involved in energy production and photosynthesis were identified. Role of these proteins to salt stress response will be discussed.https://jab.uk.ac.ir/article_2014_cee8d6b7ce52554fd70354e37bbf44a2.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Promoter Analysis of S-Like RNase gene in Transgenic RicePromoter Analysis of S-Like RNase gene in Transgenic Rice6580201510.22103/jab.2018.2015FARudabehRavashAssistant Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekod, Iran.0000-0001-7321-6337BehroozShiranPlant Breeding and Biotechnology Department, Faculty of Agriculture, Shahrekord University, Shahrekord, IranEsmailEbrahimiProfessor, Plant Breeding and Biotechnology Department, Faculty of Agriculture, Shiraz University,
Shiraz, IranSadolaahHooshmandProfessor, Plant Breeding and Biotechnology Department, Faculty of Agriculture, Shahrekord University, Shahrekord, IranRudyDolferusProfessor, CSIRO Plant Industry, Canberra-AustraliaJournal Article20161227RNases participate in vital cellular functions such as DNA replication, transcription, splicing, and control of translation. S-like ribonucleases (S-like RNases) are homologous to S-ribonucleases (S-RNases), but are not involved in self-incompatibility in plants. In dicotyledonous plants, S-like RNase<em>s</em> play an important role in phosphate recycling during senescence and are induced by inorganic phosphate-starvation and in response to defense and mechanical wounding. Potensial effects of RNases in drought response might refer to intraction of several different functions. In this study, the promoter of S-Like RNase gene was inserted upstream of β-glucuronidase gene (GUS), <em>Agrobacterium tumefaciens</em>, transformed by electroporation with these constructs were used for co-culture for plant transformation. Histochemical staining method on root, Leaf and anther tissue of rice were done for measering promoter activity. Based on these results, we report tissue speciefic activity of S-Like RNase promoter in the anther of rice. Results indicate the high activity of S-Like RNase promoter in the anther tissue of rice however Expression level in the leaf was low and in the root was negligible. These results is confirmed by previeos studies using q-PCR that indicated high expression of S-Like RNase gene at the anther in comparison with other tissues.RNases participate in vital cellular functions such as DNA replication, transcription, splicing, and control of translation. S-like ribonucleases (S-like RNases) are homologous to S-ribonucleases (S-RNases), but are not involved in self-incompatibility in plants. In dicotyledonous plants, S-like RNase<em>s</em> play an important role in phosphate recycling during senescence and are induced by inorganic phosphate-starvation and in response to defense and mechanical wounding. Potensial effects of RNases in drought response might refer to intraction of several different functions. In this study, the promoter of S-Like RNase gene was inserted upstream of β-glucuronidase gene (GUS), <em>Agrobacterium tumefaciens</em>, transformed by electroporation with these constructs were used for co-culture for plant transformation. Histochemical staining method on root, Leaf and anther tissue of rice were done for measering promoter activity. Based on these results, we report tissue speciefic activity of S-Like RNase promoter in the anther of rice. Results indicate the high activity of S-Like RNase promoter in the anther tissue of rice however Expression level in the leaf was low and in the root was negligible. These results is confirmed by previeos studies using q-PCR that indicated high expression of S-Like RNase gene at the anther in comparison with other tissues.https://jab.uk.ac.ir/article_2015_65d2ea03425887a717c435081cfc5dbb.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Study of the effect of codon optimization on Anti-VEGF nanobody expressionStudy of the effect of codon optimization on Anti-VEGF nanobody expression81100201610.22103/jab.2018.2016FAMozhganSoleymanizadehPh.D. Student of Agriculture Biotechnology, Agriculture Faculty, Ferdowsi University of Mashhad, Mashhad, Iran.AbdolrezaBagheriProfessor of Department of Biotechnology and Plant Breeding, Agriculture Faculty, Ferdowsi University of Mashhad, Mashhad, Iran.MokhtarJalaiAssociate Professor of Department of Biotechnology, Agriculture Faculty, Tarbiat Modares University, Tehran, Iran.AlirezaSeyfiAssistant Professor of Department of Biotechnology and Plant Breeding, Agriculture Faculty, Ferdowsi University of Mashhad, Mashhad, Iran.MahdiBehdaniAssociate Professor of Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.FatemehKazemiAssistant Professor of Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.Journal Article20171206Plants can be exploited for the production of various recombinant proteins as valuable bioreactors <em>because of many reasons</em><em>.</em><em> </em>The use of plant viral vectors for the transient expression offers as a useful strategy for the large-scale production of proteins with pharmaceutical importance, such as antibodies within a very short time period. Today, cancer is the second cause of death in human society. Compelling evidence suggests that vascular endothelial growth factor (VEGF), due to its essential role in angiogenesis, is a critical target for cancer treatment. In This study, Anti-VEGF (Nb42) nanobody different fragments were transiently expressed under the control of a viral strong promoter in cucurbit plant using ZYMV-based viral vector. These fragments included natural nanobody sequence (Nb42I) and optimized nanobody sequence (Nb42II) for expression in plant. After inoculation of plants, the presence of transcripts of the Nb42 gene fragments in cucurbit inoculated plants was detected by using RT-PCR. Also, the recombinant protein expression was confirmed by Dot blotting, SDS-PAGE, Western blotting and ELISA. Based on the ELISA results, the expression level of Nb42I and Nb42II nanobody fragments was 2 and 6.8 μg/g of leaf tissue respectively. Taken together, recombinant Nb42 nanobody could be efficiently expressed in cucurbit plant and ZYMV-based expression system would be an appropriate platform for production of recombinant proteins in cucurbit plantsPlants can be exploited for the production of various recombinant proteins as valuable bioreactors <em>because of many reasons</em><em>.</em><em> </em>The use of plant viral vectors for the transient expression offers as a useful strategy for the large-scale production of proteins with pharmaceutical importance, such as antibodies within a very short time period. Today, cancer is the second cause of death in human society. Compelling evidence suggests that vascular endothelial growth factor (VEGF), due to its essential role in angiogenesis, is a critical target for cancer treatment. In This study, Anti-VEGF (Nb42) nanobody different fragments were transiently expressed under the control of a viral strong promoter in cucurbit plant using ZYMV-based viral vector. These fragments included natural nanobody sequence (Nb42I) and optimized nanobody sequence (Nb42II) for expression in plant. After inoculation of plants, the presence of transcripts of the Nb42 gene fragments in cucurbit inoculated plants was detected by using RT-PCR. Also, the recombinant protein expression was confirmed by Dot blotting, SDS-PAGE, Western blotting and ELISA. Based on the ELISA results, the expression level of Nb42I and Nb42II nanobody fragments was 2 and 6.8 μg/g of leaf tissue respectively. Taken together, recombinant Nb42 nanobody could be efficiently expressed in cucurbit plant and ZYMV-based expression system would be an appropriate platform for production of recombinant proteins in cucurbit plantshttps://jab.uk.ac.ir/article_2016_95192c98732387165bf8e396c0f2dad2.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Transcriptome analysis of cumin (Cuminum cyminum L.) using RNA-SeqTranscriptome analysis of cumin (Cuminum cyminum L.) using RNA-Seq101116201710.22103/jab.2018.2017FADaruishSadeghiM.Sc student of Plant Breeding, College of Aburaihan, University of Tehran, Tehran, Iran.Mohammad-MahdiMortazavianAssociate Professor of Plant Breeding, College of Aburaihan, University of Tehran, Tehran, Iran.Mohammad-RezaBakhtiyarizadehAssistant Professor of Animal Science, College of Aburaihan, University of Tehran, Tehran, Iran.Journal Article20171010Cumin (<em>Cuminum cyminum</em> L.) is a flowering plant from Apiaceae family and native to the East Mediterranean to India. The main component of essential oil in cumin seeds is cumin aldehyde (63% of total oil). Despite the importance of the cumin derivative drugs little information is available on the genome and the molecular mechanisms involved in metabolic pathway of this plant. Transcriptomic studies have greatly contributed to better understand in metabolic pathways of medicinal plants. At the moment, the use of next-generation sequencing techniques, especially RNA-seq technique were considered as the suitable promising and most accurate methods of transcriptomic evaluation. In the present study, we report cumin transcriptome for the first time. Flower tissue was used to extract RNA from four samples for RNA-seq analysis. According to the results, more than 153000000 reads with length of 50 NT were achieved. Trinity software, using 25 and 32 K-mers, was used to assemble the reads. Selection of the best assembly was followed using BUSCO software based on the integer transcript sequences. After assembly of reads, 50973 genes with an average length of 725 NT and N50 value of 1136 NT were obtained. Moreover, 53103 transcripts were identified from all genes. From this number, 35860 transcripts had at least one homologous in Nr database. More than 66.7% of all transcripts had at least one homologous in GO database (biological process, molecular function, cellular compound). Most of the genes were related to transcriptional regulation and membrane activities. In the present study, the first transcriptome profile is reported in cumin which data can be used in subsequent studies to assess expression of genes and other genetic studies in this plant.Cumin (<em>Cuminum cyminum</em> L.) is a flowering plant from Apiaceae family and native to the East Mediterranean to India. The main component of essential oil in cumin seeds is cumin aldehyde (63% of total oil). Despite the importance of the cumin derivative drugs little information is available on the genome and the molecular mechanisms involved in metabolic pathway of this plant. Transcriptomic studies have greatly contributed to better understand in metabolic pathways of medicinal plants. At the moment, the use of next-generation sequencing techniques, especially RNA-seq technique were considered as the suitable promising and most accurate methods of transcriptomic evaluation. In the present study, we report cumin transcriptome for the first time. Flower tissue was used to extract RNA from four samples for RNA-seq analysis. According to the results, more than 153000000 reads with length of 50 NT were achieved. Trinity software, using 25 and 32 K-mers, was used to assemble the reads. Selection of the best assembly was followed using BUSCO software based on the integer transcript sequences. After assembly of reads, 50973 genes with an average length of 725 NT and N50 value of 1136 NT were obtained. Moreover, 53103 transcripts were identified from all genes. From this number, 35860 transcripts had at least one homologous in Nr database. More than 66.7% of all transcripts had at least one homologous in GO database (biological process, molecular function, cellular compound). Most of the genes were related to transcriptional regulation and membrane activities. In the present study, the first transcriptome profile is reported in cumin which data can be used in subsequent studies to assess expression of genes and other genetic studies in this plant.https://jab.uk.ac.ir/article_2017_8d8818c8e140c64c743113f563cf750f.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220The effect of drought stress on the expression of genes encoding phenylalanine ammonia lyase (PAL), eugenol synthase 1 (EGS1) and caffeic acid O-methyltransferase (COMT) enzymes in Basil (Ocimum basilicum)The effect of drought stress on the expression of genes encoding phenylalanine ammonia lyase (PAL), eugenol synthase 1 (EGS1) and caffeic acid O-methyltransferase (COMT) enzymes in Basil (Ocimum basilicum)117128201810.22103/jab.2018.2018FABabakAbdolahiAssociate professor and Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran.MohammadAlipourMSc students of Agricultural Biotechnology, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran.RezaDarvishzadehMSc students of Agricultural Biotechnology, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran.0000-0001-5991-4411BakhtiyarMajroomiMSc students of Agricultural Biotechnology, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, IranJournal Article20170528Basil (<em>Ocimum basilicum</em> L.) is one of the important medicinal plants belonging to the mint family which is a rich source of phenylpropanoid compounds such as methylchavicol and methyleugenol. Environmental stresses such as drought could change the percentage and content of the essential oils and expression level of the genes involved in their biosynthesis. In the current study, an experiment based on completely randomized design (CRD) with three replications was conducted in greenhouse to study the effect of drought stress on the expression of key genes involved in phenylpropanoids biosynthesis in <em>O. basilicum</em> c.v. Keshkeni luvelou. The genes studied, were phenylalanine ammonialyase (PAL), eugenol synthase 1 (EGS1) and caffeic acid O-methyltransferase (COMT). Plants were exposed to three levels of 100 (control), 75 and 50 % field capacity (FC) at the 6-8 leaf stage. The expression level of the studied genes were determined by real time PCR technique in plant leaves at the flowering stage. Analysis of gene expression data indicated that 50% FC increases the expression level of EGS1 by about 9.74, whereas those of COMT relatively remained unchanged. The expression level of PAL was increased 1.5 to 2 times under drought stress, although no significant difference for its expression was observed between 50% and 75% FC. Thus, it is possible to enhance the content of the phenylpropanoid compounds in basil through the application of controlled drought stress and consequently increasing the expression levels of EGS1 and PAL genes.Basil (<em>Ocimum basilicum</em> L.) is one of the important medicinal plants belonging to the mint family which is a rich source of phenylpropanoid compounds such as methylchavicol and methyleugenol. Environmental stresses such as drought could change the percentage and content of the essential oils and expression level of the genes involved in their biosynthesis. In the current study, an experiment based on completely randomized design (CRD) with three replications was conducted in greenhouse to study the effect of drought stress on the expression of key genes involved in phenylpropanoids biosynthesis in <em>O. basilicum</em> c.v. Keshkeni luvelou. The genes studied, were phenylalanine ammonialyase (PAL), eugenol synthase 1 (EGS1) and caffeic acid O-methyltransferase (COMT). Plants were exposed to three levels of 100 (control), 75 and 50 % field capacity (FC) at the 6-8 leaf stage. The expression level of the studied genes were determined by real time PCR technique in plant leaves at the flowering stage. Analysis of gene expression data indicated that 50% FC increases the expression level of EGS1 by about 9.74, whereas those of COMT relatively remained unchanged. The expression level of PAL was increased 1.5 to 2 times under drought stress, although no significant difference for its expression was observed between 50% and 75% FC. Thus, it is possible to enhance the content of the phenylpropanoid compounds in basil through the application of controlled drought stress and consequently increasing the expression levels of EGS1 and PAL genes.https://jab.uk.ac.ir/article_2018_84ddfb34126fc3a48ee38d7044e87276.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Induction of several Pathogenesis-Related genes in tobacco plants treated by salicylic and jasmonic acid after challenging with Pseudomonas syringae pv. TabaciInduction of several Pathogenesis-Related genes in tobacco plants treated by salicylic and jasmonic acid after challenging with Pseudomonas syringae pv. Tabaci129150201910.22103/jab.2018.2019FAFaridehFarajollahiMaster in Plant Pathology of Sari Agricultural Sciences and Natural Resources University, Sari, Iran.ValliolahBabaezadehAssociate Professor in Plant Protection Department of Sari Agricultural Sciences and Natural Resources University, Sari, Iran.HeshmatolahRahimianProfessor in Plant Protection Department of Sari Agricultural Sciences and Natural Resources University, Sari, Iran.Journal Article20170502Tobacco as a model plant (owing to certain features) is extensively used in molecular research with the aims to understand the fundamental plant and pathogen interactions. Fire blight bacterial disease of tobacco (Pseudomonas syringae pv. tabaci (Pst)) causes considerable damage to tobacco worldwide. Induction of genes associated with virulence that play a role in resistance to diseases can be effective in reducing the severity of disease. The evidence suggests that plant hormones are effective in gene expression in plants and increase the production of secondary metabolites. In addition, they stimulate the immune system of plant through the activation of transcription of genes linked with plant defense mechanisms that regulate the induced resistance. In this study, the expression of PR1, PR5, Pal, Catalase and WRKY12 in tobacco plants treated with salicylic acid at a concentration of 3 mM and tobacco plant treated with jasmonic acid at a concentration of 0.5 mM and also control plant in times 0, 12, 24, 48 and 72 after injection of Pseudomonas syrigae pv. tabaci was investigated by Quantitative Real-time PCR (QRT-PCR) technique. The results showed that jasmonic acid and particularly salicylic acid treatments caused significant changes in the expression of these genes after bacterial injection.
<strong></strong><em><br /></em>Tobacco as a model plant (owing to certain features) is extensively used in molecular research with the aims to understand the fundamental plant and pathogen interactions. Fire blight bacterial disease of tobacco (Pseudomonas syringae pv. tabaci (Pst)) causes considerable damage to tobacco worldwide. Induction of genes associated with virulence that play a role in resistance to diseases can be effective in reducing the severity of disease. The evidence suggests that plant hormones are effective in gene expression in plants and increase the production of secondary metabolites. In addition, they stimulate the immune system of plant through the activation of transcription of genes linked with plant defense mechanisms that regulate the induced resistance. In this study, the expression of PR1, PR5, Pal, Catalase and WRKY12 in tobacco plants treated with salicylic acid at a concentration of 3 mM and tobacco plant treated with jasmonic acid at a concentration of 0.5 mM and also control plant in times 0, 12, 24, 48 and 72 after injection of Pseudomonas syrigae pv. tabaci was investigated by Quantitative Real-time PCR (QRT-PCR) technique. The results showed that jasmonic acid and particularly salicylic acid treatments caused significant changes in the expression of these genes after bacterial injection.
<strong></strong><em><br /></em>https://jab.uk.ac.ir/article_2019_ea6b2efbdd4255a9f1b3bbc6399b58f4.pdfShahid Bahonar University of Kerman and Iranian Biotechnology SocietyAgricultural Biotechnology Journal2228-67059420180220Estimation of linkage disequilibrium and whole-genome scan for detection of loci under selection associated with body weight in Zandi sheep breedEstimation of linkage disequilibrium and whole-genome scan for detection of loci under selection associated with body weight in Zandi sheep breed151172202010.22103/jab.2018.2020FAHossinMohammadiPh.D Graduated Animal Science Department, Faculty of Agriculture, Tabriz University, Tabriz, Iran.AbbasRaffatProfessor Animal Science Department, Faculty of Agriculture, Tabriz University, Tabriz, Iran.HossinMoradiAssistant Professor Animal Science Department, University College of Agriculture and Natural Resources, Tehran University, Tehran, Iran.JalilShojaProfessor Animal Science Department, Faculty of Agriculture, Tabriz University, Tabriz, Iran.Mohammad HossienMoradiAssistant Professor Animal Science Department, Faculty of Agriculture, Arak University, Arak, Iran.Journal Article20170716Body weight is the most economically important trait in sheep industry. In genome-wide association study and genomic selection, determining of extent and level of linkage disequilibrium (LD) is critical in sample size and marker density. Moreover, selection for increasing of frequency in new mutations that are advantageous only in a subset of populations leaves some signatures in the genome. Locations of selection signatures are often correlated with genes and QTLs affecting economically important traits. Therefore, the objectives of this research were to study LD pattern and identify the genomic regions that have been under artificial and natural selection in Zandi sheep breeds with different body weight. For this purpose, the blood samples were collected form 73 Zandi sheep and 54241 markers were genotyped by using Illumina Ovine SNP50K BeadChip array based on latest assembly (Oar_4.0) sheep genome. After quality control, 40879 SNPs belonging to 71 animals were used in the final analysis. LD was calculated between all pairs were calculated with r<sup>2</sup> by PLINK software. To detect the selection sweep, due to linkage disequilibrium, associated with these signatures we carried out the cross-population Extended Haplotype Homozygosity (XP-EHH) test. In this study, the extent of LD in this study was 40 kb with r<sup>2</sup>=0.2. The results revealed ten genomic regions on 1, 2, 3, 5, 6, 9, 12, 13, 21 and 22 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes included in the growth traits, fat metabolism, development of the skeletal system, energy metabolism and meat quality traits such as FBP1, FAM184B, PKD2, FGF19, SPP1, MEPE CAPN2 genes.Body weight is the most economically important trait in sheep industry. In genome-wide association study and genomic selection, determining of extent and level of linkage disequilibrium (LD) is critical in sample size and marker density. Moreover, selection for increasing of frequency in new mutations that are advantageous only in a subset of populations leaves some signatures in the genome. Locations of selection signatures are often correlated with genes and QTLs affecting economically important traits. Therefore, the objectives of this research were to study LD pattern and identify the genomic regions that have been under artificial and natural selection in Zandi sheep breeds with different body weight. For this purpose, the blood samples were collected form 73 Zandi sheep and 54241 markers were genotyped by using Illumina Ovine SNP50K BeadChip array based on latest assembly (Oar_4.0) sheep genome. After quality control, 40879 SNPs belonging to 71 animals were used in the final analysis. LD was calculated between all pairs were calculated with r<sup>2</sup> by PLINK software. To detect the selection sweep, due to linkage disequilibrium, associated with these signatures we carried out the cross-population Extended Haplotype Homozygosity (XP-EHH) test. In this study, the extent of LD in this study was 40 kb with r<sup>2</sup>=0.2. The results revealed ten genomic regions on 1, 2, 3, 5, 6, 9, 12, 13, 21 and 22 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes included in the growth traits, fat metabolism, development of the skeletal system, energy metabolism and meat quality traits such as FBP1, FAM184B, PKD2, FGF19, SPP1, MEPE CAPN2 genes.https://jab.uk.ac.ir/article_2020_7b7a53e239400a13bd6be6c91c4f6c4e.pdf