Biotic and Abiotic stress
Alireza Tarang
Abstract
Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression ...
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Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression of transcription factor genes DREB2A and ZFP252 at vegetative and reproductive stages were investigated in TH1 line (drought sensitive) and Neda (drought tolerant). Drought stress was induced by stopping irrigation at tillering and heading stages. Investigation of morphological traits showed tiller and panicle numbers as production indices were significantly higher in Neda cultivar than TH1 line. Real Time PCR Neda genotype showed a significant increase (3.217 expression ratio) in expression of transcript level of ZFP252 at vegetative stage under drought stress. This indicates the importance of this drought stress responsive gene in acquisition of drought tolerance in this genotype at this stage. Investigation of expression level changes in TH1 line showed significant increase in DREB2A and ZFP252 genes expression under drought stress at the vegetative stage. Gene expression analysis in this study suggesting that tolerant and sensitive plants may be using genetic regulations and different mechanisms to be exposed to stress conditions. Deciphering of these molecular mechanisms will aid to better understand stress tolerance and to select strategies for improving crop productivity facing climate change.
Molecular Plant Breeding
nadali bagheri; zeinab Masoudi Jozchal
Abstract
Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) ...
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Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) and IR-229R genotype (paternal parent). Also, molecular markers correlated with grain length were used to identify genotypes with longer grain length in the F2 population. The results of the evaluation of morphological traits showed that the average length of rice grain in the second generation L44 × IR-229R population is 11.16 mm, which is close to the average grain length in the mother genotype L44 (11 mm). Also, 10 genotypes showed longer seed length than the paternal parent, and among these genotypes, 6 genotypes (numbers 8, 10, 76, 82, 91 and 96) had greater seed width and 1000 seed weight than the population average. In the molecular evaluation, it was found that primers RM488 and RM234 (correlated with rice grain length on chromosome 1 and 7, respectively) showed polymorphism between parent’s genotypes. In examining the grain length trait with markers RM488 and RM234, genotypes 76, 82, 91 and 101 with grain length of 12.96, 12.66, 12.79 and 12.53 mm respectively were identified as long seed genotypes.
Molecular Plant Breeding
Morteza Oladi Ghadicolaei; Ghorban Ali Nematzadeh; Ali Ranjbar; Hamidreza Hashemi
Abstract
Marker-assisted selection (MAS), a selective method which is not influenced by environmental factors. The success of MAS-based breeding programs depends on the selection and validation of the markers used. In this study, to validate the gene(s) associated with salinity stress and evaluation of allelic ...
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Marker-assisted selection (MAS), a selective method which is not influenced by environmental factors. The success of MAS-based breeding programs depends on the selection and validation of the markers used. In this study, to validate the gene(s) associated with salinity stress and evaluation of allelic diversity of these markers in mutant rice lines, Band pattern of 18 SSR markers on a leaf sample of 14 mutant lines (M9) of rice, along with 2 susceptible controls (IR29 and Sepidrood) and 2 tolerant controls (Nonabokra and Dylmani) in 1398 in Genetics & Agricultural Biotechnology Institute of Tabarestan (GABIT). 11 primers were selected based on band pattern analysis in susceptible / tolerant cultivars. The molecular analysis results showed that OsMAPK4, OsCML11 and OsCPK17 had highest polymorphic information content (PIC). OsMAPK4 and OsCML11 had highest marker index (MI) at a rate of 0.23. The lowest PIC (0.05) and MI (0. 11) was accounted for OsCAX (D). Cluster analysis of molecular data, divided rice genotypes into three distinct groups. However, analysis of Biplot classified the genotypes into four different groups. In this study, 3 genes OsCML11, OsMAPK4 and OsCPK17 were identified on chromosomes 1, 6 and 7 respectively, as the most efficient primers in identifying the genetic diversity between the rice genotypes, considering that these primers have a very high linkage with salinity resistance genes, can be predicted that 3 lines G1 (M9-P1-7-2-1), G8 (M9-P3-21-1-1) and G9 (M9-P6 -7-1-1) have high tolerance to salinity stress.
Molecular Plant Breeding
Parvin Amani Daz; Hossein Hossein Moghaddam; Hossein Sabouri; Ebrahim Gholamalipour Alamdari; Sayedeh Masoomeh Hosseini; Somayeh Sanchouli
Abstract
Identification of the linked markers to drought tolerance genes are needed for the breeding of rice varieties. In order to mapping of QTLs controlling related to drought tolerance, 96 rice Inbred lines caused Ahlamitarom × Neda cross planted as complementary randomized design with 3 replications under ...
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Identification of the linked markers to drought tolerance genes are needed for the breeding of rice varieties. In order to mapping of QTLs controlling related to drought tolerance, 96 rice Inbred lines caused Ahlamitarom × Neda cross planted as complementary randomized design with 3 replications under drought stress in Gonbad Kavous University lab in 2014. Given the genetic variation among the studied lines, it was possible to the detection of QTLs in this study. In calculating the correlation of traits evaluated under drought stress, the highest correlation was for root diameter with root area density (0.96 **). The results of cluster analysis based on total traits under drought stress, lines assigned to four groups: tolerant, semi-tolerant, semi-sensitive and sensitive. Linkage map provided using F8 population, 30 SSR markers, and 20 ISSR markers and covered 1413.2 cM with an average distance between two markers 12.18. QTL analysis indicated that containing totally 13 distances were found, in this way, 2 QTL stem length, 1 QTL root number, 3 QTL leaf width, 1 QTL stem weight, 3 QTL leaf surface, 1 QTL stomata density before stress, 1 QTL stomata density after stress, 1 QTL ratio of total stomata surfaces total area after stress were controlled. Of the detected QTLs, qLL-2 and qSA-12, explained a high percentage of phenotypic variation for leaf area and stomata density after stress. The major QTLs detected in this study, can be used in marker-assisted selection breeding programs after validation
Molecular Plant Breeding
Bahareh Ghasemi; Hossein Sabouri; Hossein Hossein Moghaddam; Abbas Biabani; Mohamad Javad Sheikhzadeh
Abstract
Genetic diversity is of great importance for breeding programs. In order to study the genetic diversity of 102 different rice genotypes based on seedling traits and molecular experiments, an experiment was conducted in a Completely Randomized Design with three replications. The studied traits including ...
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Genetic diversity is of great importance for breeding programs. In order to study the genetic diversity of 102 different rice genotypes based on seedling traits and molecular experiments, an experiment was conducted in a Completely Randomized Design with three replications. The studied traits including Plumule length, radicle length, length of the largest leaf, width of the largest leaf, number of root, fresh shoot weight, fresh weight of root and root volume, and dry weight of shoot, dry weight of root were measured. The average of the Polymorphic of information content (PIC) was estimated to be 0.2716, indicating RM1029 with the of least 0.175 and the RM216 with the highest of 0.435 (PIC). The results of Association analysis between microsatellite marker and seeding traits at normal condition indicated that the RM60B allele for root length, RM127A allele for root, RM231G allele for the fresh weight of the stem explained high percentage of variations. In saline condition, RM129H allele for stem length trait, RM12091 B allele for root attribute, RM263G allele for stem fresh weight, RM127C allele for width of largest leaf explained high percentage of phenotypic variations and were identified as important markers. The results of this experiment can be used in breeding programs.
Molecular Plant Breeding
Omid Sofalian; Fatemeh Ajri; Atefeh Sabouri; Ali Asghari; Samira Hasanian
Abstract
One way to assessing the validity of recognized markers is studing the consistency of case grouping based on molecular markers and phenotypic data obtained from the normal and drought stress conditions. In this study in order to assessing probable relationship between SSR molecular markers and drought ...
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One way to assessing the validity of recognized markers is studing the consistency of case grouping based on molecular markers and phenotypic data obtained from the normal and drought stress conditions. In this study in order to assessing probable relationship between SSR molecular markers and drought tolerance indices in studding genotypes and grouping these genotypes based on SSR molecular markers and tolerance indices, 40 rice genotypes was used based on randomized complete block design with three replications in both normal and stress conditions. In addition, 26 microsattelite markers in relation with drought tolerance were used. Our results showed that 128 polymorphic alleles with 4.92 mean allele for each marker locus were amplified. The highest PIC value related to RM5672 (0.829) and the least related to RM523 (0.047). The corelation analysis between yield and tolerance indices in both two conditions confirmed that four indices; mean productivity (MP), geometric mean productivity (GMP), stress tolerance index (STI) and yield index (YI) were the best indices for sensitive and tolerant genotype discrimination. Grouping of genotypes based on cluster analysis using WARD method divided all of studding genotypes into three groups including tolerant, semi tolerant and sensitive. Considering the higher values of second group than the mean of the above indicators, they were introduced as tolerant genotypes, which often included upland genotypes and a Hashemi genotype. Based on our results thre firs group represent semi tolerant genotypes ant the third group represents sensitive genotypes. The cluster analysis based on microsatellite markers also divided genotypes into two groups. Comparison of these two types of grouping showed a significant correlation between them, so that in both groups the Hashemi genotype showed close proximity to the upland genotypes and was associated with them in one group.
Bioinformatics
Manzar Heidari; Zahra-Sadat Shobbar; Parisa Koobaz; Mohammad javad Heydari
Volume 6, Issue 14 , August 2016, , Pages 1-15
Abstract
Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. ...
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Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. EST libraries data under normal and drought stress conditions were downloaded from NCBI databank. Preprocessing, clustering and assembly of the EST sequences were done using EGassembler software. Generated contig and singleton sequences were used as template for BLASTx analysis against rice protein database and functional category assignment using CLC Protein Workbench software and AgriGO. The identified proteins in the normal and drought libraries were allocated to 70 and 82 functional categories, respectively. IDEG6 were used to identify significant differences between functional categories in control and drought stress libraries. Gene ontology analysis, revealed significant differences in 20 groups of molecular function, 35 groups of biological processes and 12 groups of the intracellular components. In order to find the significant differential expression between the two libraries, 4012 ESTs with unigene accession numbers were implemented through applying an algorithm by MATLAB software and were analyzed by IDEG6 software, where 42 genes were found to be differentially expressed between drought and normal conditions (31 up-regulated and 11 down-regulated genes). The up-regulated genes were involved in environmental and oxidative stress response, homestasis, proteolysis and glycolysis, while photosynthesis related genes were down-regulated.
Tissue culture and Micropropagation
Keyghobad Kaikavoosi; Altaf Hosseini Nadaf; Gholamreza Bakhshi khaniki
Volume 5, Issue 9 , June 2015, , Pages 29-38
Abstract
In most transformation studies it has been indicated that adding proline to the tissue culture medium can increase the callus induction frequency and reduce induction time. Adding proline to callus induction medium in this phase can affect the production of aromatic compounds in rice and if the goal ...
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In most transformation studies it has been indicated that adding proline to the tissue culture medium can increase the callus induction frequency and reduce induction time. Adding proline to callus induction medium in this phase can affect the production of aromatic compounds in rice and if the goal of exogenous gene transformation is increasing the rice aromatic associated secondary metabolites such as 2-acetyl-1-pyrroline (2AP), this amino acid can slipup the final results. Although, absence of amino acids such as proline can reduce callus induction percentage. In this research, callus induction from two indica rice varieties; Ambemohar 157 and Indrayani were optimized, using MS medium having various concentrations of 2,4-D, without using proline. The results revealed that 2.5 mgl-1 of 2,4-D for Ambemohar 157 and 4 mgl-1 for Indrayani can lead to better callus induction. These results indicated that absence of proline can be disregard by increasing of 2,4-D concentrations. Calluses obtained from the best hormone treatment were cultured on MS fortified with 0.01 mgl-1 NAA + (1, 2, 3, 4, 5) mgl-1 BAP for shoot regeneration. The highest percentage of regeneration was achieved on MS supplemented with 2 mgl-1and 3 mgl-1 for Ambemohar157 and Indrayani cultivar respectively. Proline contents in calli which were growth in MS medium supplemented with 500 mg/L of proline showed approximately 12 to 14 fold increase over the calli growth in non-proline added medium.
Biotic and Abiotic stress
Sepideh Torabi; Ghasem Hosseini Salekdeh
Volume 3, Issue 4 , September 2013, , Pages 1-14
Abstract
R Rice is one of most important crops feeding about half of the world population. Phosphorous is one of limiting factors of rice growth and its deficiency substantially decreases rice yield. In this study, we aimed to identify biochemical mechanisms of rice adaptation to phosphorous deficiency in leaf ...
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R Rice is one of most important crops feeding about half of the world population. Phosphorous is one of limiting factors of rice growth and its deficiency substantially decreases rice yield. In this study, we aimed to identify biochemical mechanisms of rice adaptation to phosphorous deficiency in leaf and root. We compared the metabolites in parental lines, Nipponbare, and its near isogenic line (NIL6-4) containing a major QTL for phosphorous uptake (PUP1) on chromosome 12. Phosphorous deficiency resulted in significant decrease in number of tillers and fresh weight in both parental line and its near isogenic line, however, this reduction was more pronounced in the parental line. Analysis of the level of several soluble sugars and activity of enzymes involved in energy production revealed that phosphorous deficiency could lead to some changes in glycolysis pathway in rice near isogenic line so that the plant could cope with the ATP shortage. It is most likely that enhancement of this biochemical pathways may increase rice adaptation to phosphorous deficiency and consequently increase plant production with less phosphorus fertilizer required.
Molecular Plant Breeding
hossein sabouri; Atefeh Sabouri; Mahnaz Katouzi
Volume 3, Issue 4 , September 2013, , Pages 15-24
Abstract
Due to the importance of mating system in plant fertilization ability, and in order to understand the genetic basis of floral traits associated with mating system in rice including pistil, stamen and glume, these traits were analyzed using a F2:3 population drived from a cross between Iranian cultivar ...
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Due to the importance of mating system in plant fertilization ability, and in order to understand the genetic basis of floral traits associated with mating system in rice including pistil, stamen and glume, these traits were analyzed using a F2:3 population drived from a cross between Iranian cultivar Gharib × Khazar. Quantitative trait loci (QTLs) affecting floral features were detected by Composite interval mapping using a linkage map constructed by using 111 SSR markers. Rate of exerted stigma, stigma length, stigma breadth, style length, anther length, lemma length, palea length, lemma thickness, palea thickness, lemma width and palea width were recorded. As many as 38 QTLs were detected to be associated with 11 traits. A total of 10, 5 and 23 QTLs were detected for trait related to pistil, stamen and size and shape of geumele, respectively. The result obtained revealed that QTLs of qSYL-1, qSYL-6 and qSTL-2a were able to explain 25.99, 30.67 and 24.61% of the total variation of style length and stigma length and distinguished as major effect QTLs. Through the identification of these QTLs, plant breeders would be able to gain more and deeper understanding and insights into the genetic basis of the traits associated with the combining ability in rice cultivars.
Molecular Plant Breeding
Meysam Alizadeh; Ghorban Ali Nematzadeh; Mohammad Ali Ebrahimi; Hamidreza Hashemi
Volume 3, Issue 4 , September 2013, , Pages 53-60
Abstract
Rice is the main source of carbohydrates for more than a third of the world's population. It is also a principal food stuff for the Iranian people. In this study, AFLP markers were used to evaluate and fingerprint a number of rice (Oryza sativa L.) genotypes, including 28 Iranian local varieties and ...
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Rice is the main source of carbohydrates for more than a third of the world's population. It is also a principal food stuff for the Iranian people. In this study, AFLP markers were used to evaluate and fingerprint a number of rice (Oryza sativa L.) genotypes, including 28 Iranian local varieties and 19 exotic varieties. Using 10 primer combinations, 675 bands were obtained out of which 429 bands (63.5%) showed polymorphism. Among the used primers, E-TTG, M-CAT with107 bands and E-AGG, M-CTG with 34 bands had the highest and the lowest band numbers, respectively. Average polymorphism information content (PIC) was at 0.34. The best primer combination to differentiate rice samples were E-TTG , M-CAT with the marker index of 24.1. The average genetic similarity based on Nei coefficient, was estimated at 0.67 (0.97 to 0.40). The dendrogram obtained by using the UPGMA determined three main groups among the investigated varieties which was in concordance with the PCR analysis results.In conclusion, AFLP markers could provide unique fingerprinting patterns for all the studied varieties. The finding of this study could be used in inbreeding programs to produce hybrid and promising varieties based on the genetic distances and the identification of heterotic groups.
Molecular Plant Breeding
Ehsan Mohseni fard; Mohammad Farsi; Ghasem Hosseini Salekdeh; Amin Mirshamsi Kakhki; Marayam Shahbazi
Volume 3, Issue 5 , February 2013, , Pages 105-115
Abstract
MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several ...
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MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several processes including tissue development, response to biotic and abiotic stress and induction of several other transcription factors and membrane proteins. In this study we selected miRNAs that regulate SPL transcription factors expression in rice. Later, the differential expression of these miRNAs are evaluated using qRT-PCR and Stem-loop primers. Results of shoot differential expression under drought stress showed that miR529 was down-regulated but conversely, miR535 was up-regulated. However, significant differential expression of miR156 was not observed in our study. Likewise, root differential expression under drought condition showed up-regulation of miR535, but miR529 and miR156 did not show any significant differential expression. Although all of these miRNAs are involved in regulating the expression of the same genes, but their diverse differential expressions highlight the complexity of gene-regulatory networks in various environmental conditions. Based on results of this study, it can be suggested that compared to miR535, miR156 and miR529 play more important roles in regulating the development and flowering process via controlling SPL transcription factors whereas, miR535, miR529 and relatively lesser miR156 are responsible for SPL transcription factor regulation under stress.
Molecular Plant Breeding
Ahmadreza Masomi; Hossein Askari; Abbas Saeidi; Masood Soltani-Najafabadi
Volume 3, Issue 5 , February 2013, , Pages 139-146
Abstract
Soil and water salinity is one of the limiting factors for rice cultivation in the worldwide. Among crops, rice is very sensitive to salinity but the sensitivity is higher at the seedling and heading stages. Study of gene expression patterns besides away of cellular proteins function, could be useful ...
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Soil and water salinity is one of the limiting factors for rice cultivation in the worldwide. Among crops, rice is very sensitive to salinity but the sensitivity is higher at the seedling and heading stages. Study of gene expression patterns besides away of cellular proteins function, could be useful to create of resistance plants to stress such as salinity. In this study, expression of the Coumaroyl coenzyme A -3hydroxylase (C3H) gene and physiological processes was surveyed under salinity stress in Oryza sativa cv. IR65192-4B cultivar, by Complete Randomized Design (CRD) in three replicates and qRT-PCR technique. Physiological results showed that, salinity stress reduced root length in 100mM but not significant in 0 and 50 mM NaCl. In addition, reduction of root dry weight was significant under salinity. On the other hand, data analysis of C3H gene expression shown, expression altered in differentages of the rice roots under one level of NaCl, and also, is variable in one age but in different of NaCl concentrations. Weak gene performance in one branch can lead the loss of other branches efficiency. Therefore, this point must be consider to create of salt resistance plant because can play a major role in overall resistance.
Biotic and Abiotic stress
R Amininasab; M.A Ebrahimi; A.A Ebadi; M Ghodsi
Volume 2, Issue 2 , September 2012, , Pages 15-25
Abstract
The study was designed to characterized the genetic diversity within subset of 20 Iranians rice (Oryza sativa L.) varieties using 19 microsatellite markers linked to genes controlling drought tolerance. Also drought resistance index as an important integrative trait in maturity stage was evaluated in ...
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The study was designed to characterized the genetic diversity within subset of 20 Iranians rice (Oryza sativa L.) varieties using 19 microsatellite markers linked to genes controlling drought tolerance. Also drought resistance index as an important integrative trait in maturity stage was evaluated in 20 varieties in two environments (stress and non stress). Results of combined analysis showed significant differences (
Proteomics
Ghasem Hosseini Salkade; Davood Nasr Abadi
Volume 1, Issue 1 , March 2012, , Pages 1-11
Abstract
Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. ...
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Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. To further understand the mechanism of plant response to salinity we employed a proteomic approach to profile the protein changes of rice 3th leaf and root under salt stress. Plants were grown in Yoshida nutrient solution and salt stress imposed after 25 days. Plants were treated by 100¬mM NaCl for 10. After that 3th leaves and total root were collected from control and salt stressed plants. The Na+ and K+ content of leaves/roots and several yield components changed significantly in response to short-term salt stress and their proteome patterns were analyzed using 2-DE in triplicates. The expression pattern of proteins significantly changed in all leaves/roots in response to stress. More than 488 and 345 protein were detected repeatedly in root and leaf 2Dgels respectively by software package. 107 proteins in root and 86 proteins in leaf of two genotypes showed significant response to stress. 3 protein in leaf gels and 2 protein in root gels were selected and identified by ESI-Q-TOF. The most important were Ferritin, Rubisco activase and ascorbat¬peroxidase in leaf and Peroxidase and Ascorbat¬peroxidase in root. All of them were enzyme and involved in detoxification and removal of reactive oxygen species (peroxidase, ascorbat¬peroxidase) Iron homeostasis (ferritin) or activation of other enzymes (rubisco¬activase).
Molecular Plant Breeding
Ghasem Mohammadi-Nejad; Rakesh Singh; AbdolMajid Rezaie; Ahmad Arzani; Babak Nakhoda; Mohammad Hossein Fotokian; Ali Moumeni; Glenn Gregorio
Volume 1, Issue 1 , March 2012, , Pages 49-59
Abstract
This research was conducted to validate and fine map the region attributed to salinity tolerance on chromosome1 in rice (Saltol) at International Rice Research Institute (IRRI) during 2005 to 2007. A major effect QTL (Saltol) which is responsible for Na+ and K+ uptake and their ratio was identified using ...
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This research was conducted to validate and fine map the region attributed to salinity tolerance on chromosome1 in rice (Saltol) at International Rice Research Institute (IRRI) during 2005 to 2007. A major effect QTL (Saltol) which is responsible for Na+ and K+ uptake and their ratio was identified using F8 recombinant inbred lines (RILs) of Pokkali/ IR29 cross on chromosome 1. This QTL explained around 64.3 to 80.2% of the phenotypic variation for the mentioned traits. Fine mapping was done using 10 SSR and EST-SSR markers and near isogenic lines (BC3F4), derived from IR29 × Pokkali that were produced for this trait. Random BC3F4 individuals were genotyped and phenotyped under two different electrical conductivities at seedling stage. QTL responsible for salinity tolerance at both ECs, were found in the same place in Saltol region, which explained 18 and 24% of the phenotypic variation for SES scores, respectively. According to the present results, possible location of Saltol was found in the interval around 1.2 cM on chromosome 1 that could physical map. It was around 350Kb. This QTL was mapped at the intervals of RM8094, RM3412 and CP6224. Therefore, molecular breeding for salinity tolerance in Iranian genotypes could be done using the mentioned markers.
