Genomics
Rezvan Mousivand; Mohammad Majdi; ّFoad Fatehi; Hamed ghobari
Abstract
One of the most harmful pests of Zagros forests is the Tortrix viridana (Lep. Tortricidae). Genetic diversity of Tortrix viridana host plant populations in the oak forests of northwestern Iran and the northern Zagros region was investigated using 28s gene sequence. The samples were collected from the ...
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One of the most harmful pests of Zagros forests is the Tortrix viridana (Lep. Tortricidae). Genetic diversity of Tortrix viridana host plant populations in the oak forests of northwestern Iran and the northern Zagros region was investigated using 28s gene sequence. The samples were collected from the forest areas of west Azarbaijan, Lorestan, Kurdistan and Kermanshah provinces. They were in the larval stage, were kept in laboratory conditions until they turned into pupa and then into a complete insect. DNA extraction was done by CTAB method. Also, in order to amplify the 28s region, the 28s gene sequence of Tortrix genus was used from NCBI for primer design. The desired region was amplified using the PCR method and the PCR products were sequenced. 21 samples were selected to investigate genetic diversity using the 28s gene, and 18 sequences DNAs were of suitable quality for further investigations. The DNA sequences were edited using Bioedit software and aligned using MegaX software, and the phylogenetic tree was drawn by UPGMA method with 1000 sampling repetitions. The evaluation of the genetic structure of populations showed that the diversity between populations is greater than within populations. The results of the phylogenetic tree also showed that different samples of the Tortrix viridana have genetic diversity based on geographical distance. Therefore, the time of appearance of the pest, their behavior and their type of control and management are also different.
Genomics
Parisa Daryani; Hadi Darzi Ramandi; Sara Dezhsetan; Zahra-Sadat Shobbar
Abstract
The root system architecture and the related traits are important factors for moisture uptake from deep soils. Information on QTLs controlling rice root system architecture was collected from the related papers and databases. A genome-wide meta-analysis was conducted on the QTLs using data from 28 independent ...
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The root system architecture and the related traits are important factors for moisture uptake from deep soils. Information on QTLs controlling rice root system architecture was collected from the related papers and databases. A genome-wide meta-analysis was conducted on the QTLs using data from 28 independent QTL mapping studies in 38 different rice populations. Among the 312 QTL regions that were mapped on the reference genetic map, 84 and 228 QTL regions were identified under normal moisture conditions and drought stress, respectively. After projection and displaying the QTLs on the reference consensus map, the meta-QTL analysis was performed using BioMercator software version 4.2. A total of 69 significant MQTLs regions were detected on the 12 rice chromosomes. The identified meta-QTL regions included 5-32 initial QTLs and reflecting multiple QTLs for 3-5 traits associated with root architecture. After evaluating the confidence intervals and the number of initial QTLs for each meta-QTL region, 23 meta-QTL regions were selected as the most important ones and the genes located in the MQTL regions were identified. WRKY, ARF, IAA, EXPA, WOX, HOX, YUCCA, RHL and NAC were among the important candidate genes involved in rice root system architecture, which were located in the MQTL regions. Interestingly, 60 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The promising candidate genes and MQTLs can be used for genetic engineering and MQTL-assisted breeding of root traits to improve yield potential, stability and efficiency in water deficit environments for rice.
Genomics
Reza Ataei; Majid Gholamhoseini; Valiollah Mohammadi
Volume 7, Issue 19 , November 2017, , Pages 25-37
Abstract
The phenotypic diversity of many important traits in plants is influenced by several loci, environmental factors and their interactions. Association mapping is one of the methods proposed in recent decades for genetic study and detection of quantitative trait loci (QTLs). Association mapping was used ...
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The phenotypic diversity of many important traits in plants is influenced by several loci, environmental factors and their interactions. Association mapping is one of the methods proposed in recent decades for genetic study and detection of quantitative trait loci (QTLs). Association mapping was used in human genetics and qualitative traits (such as diseases), but recently its use is increasing in the plant science because of advances in high throughput genomic technologies, interests in identifying novel and superior alleles, and improvements in statistical methods. Association mapping through linkage disequilibrium analysis is a purposeful method for identifying marker alleles and quantitative traits association. Unlike linkage mapping, this method identifies the association between phenotypic and polymorphic diversity in the genome by exploiting the diversity of natural populations and taking into account all the events that occurred during the evolution and is a promising approach for overcoming the limitations of linkage mapping. Despite association mapping has high statistical power, the application of this method in structured populations, species with low level of linkage disequilibrium and in traits controlled by rare alleles is complicated and difficult. In this review, we will present a comprehensive view, its application in population, current status and limitation of association mapping in plant science
Genomics
Asghar Mirzaie asl; Mishaneh Asgari; Maryam Alimirzaee
Volume 7, Issue 18 , November 2017, , Pages 57-72
Abstract
Transition from vegetative growth to reproductive phase is one of the most important developments in plants life. This phenomenon is influenced by many genetic and physiological factors in higher plants. Identification of these factors is an important aim in breeding of many plants. In recent decades, ...
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Transition from vegetative growth to reproductive phase is one of the most important developments in plants life. This phenomenon is influenced by many genetic and physiological factors in higher plants. Identification of these factors is an important aim in breeding of many plants. In recent decades, Arabidopsis has been used as a model plant in many studies related to flowering pathways and many paths has been found in this plant. Transition to flowering stage is regulated by flower causing genes including FT, TSF, SOC1 and AGL24 which induce identification of flowering meristem genes through the paths of photoperiod, vernalization, spontaneous and gibberellin. Photoperiodism is one of the most important environmental affecting factors in transition to flowering influenced by light receptors of phytochrome and cryptochrome, and CO and FT genes. FLC gene which is mainly responsible for vernalization in Arabidopsis, directly is as a repressor of FT and SOC1 flowering regulators and prevents the transition to flowering. Autonomous pathway genes are largely independent from the environmental conditions, and prevent the FLC expression by RNA-based control process or chromatin change. Finally, the gibberellin acts as a flowering accelerator when the photoperiodism pathway is inactive. In the present paper, the mechanism of flowering control for Arabidopsis plant is investigated and its importance in plant breeding is described.
Genomics
Atena Shadmehr; Hossein Ramshini; Mehrshad Zinalabedini; Masoud Parvizi Almani; MohammadReza Ghaffari; Aali Izadi darbandi; Maryam Farsi
Volume 6, Issue 16 , March 2017, , Pages 45-59
Abstract
Considering the potential of sugarcane in terms of energy and sugar production the study of genetic diversity is the best way to use available genetic germplasm for breeding programs in this plant. Thirty microsatellite primer pairs were used to screen 160 varieties. In total 169 alleles were recorded ...
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Considering the potential of sugarcane in terms of energy and sugar production the study of genetic diversity is the best way to use available genetic germplasm for breeding programs in this plant. Thirty microsatellite primer pairs were used to screen 160 varieties. In total 169 alleles were recorded with an average of 5.6 alleles per locus. The number of effective alleles per locus was ranged from 1.06 (locus AP-SSR03) to 1.921 (locus SMC119CG) with an average of 1.508. The PIC value was variable ranging from 0.06 (for AP-SSR03) to 0.5 (for SMC851MS). The principal coordinate analysis (PCoA) revealed six groups, so that the first three axes explained 15.20% of cumulative variation altogether. Clustering analysis was done using Neihbour-Joining algorithm and population structure analysis was performed using Bayesian method. The best number of sub-populations was identified as six. The grouping of genotypes in the sub-populations was not in consistent with their geographic origins. The grouping obtained from Bayesian method, phylogenetic relatedness analysis results and principal coordinates analysis grouping showed good agreement with each other. Analysis of molecular variance revealed that variation within subgroups was significantly higher than that of among subgroups. So it will be better to do selection within populations in order to select suitable parents in sugarcane breeding programs. The knowledge obtained in this study would be useful for breeding programs to improve the conservation and management of this valuable genetic resource to meet the demand of sugarcane cultivation for sugar and bioenergy production.
Genomics
Farzan Lahoot; Mehrshad Zeinalabedini; Jaber Karimi; Maryam Shahbazi; Behzad Sadeghzadeh
Volume 6, Issue 15 , December 2016, , Pages 25-35
Abstract
Genetic diversity is the best way to use available genetic potential for breeding programs in barley. In this study, genetic diversity of 63 Iranian and non-Iranian genotypes have been described. 29 out of 30 pairs microsatellite markers were polymorphic. A total of 225 alleles for different gene loci ...
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Genetic diversity is the best way to use available genetic potential for breeding programs in barley. In this study, genetic diversity of 63 Iranian and non-Iranian genotypes have been described. 29 out of 30 pairs microsatellite markers were polymorphic. A total of 225 alleles for different gene loci with an average of 2.7 per locus were identified. The highest number of alleles for Bmag0323, Hvm54 and EBmac679 (with 13 alleles) and the lowest number for the HVM0003 (with two alleles), respectively. The PIC amount and Shannon index value were variable ranging from 0.89 (for the EBmac679) to 0.21 (for the GBM1176) and from I=2.46 (for the Bmag0323) to I=0.48 (for the GBM1176), respectively. Genotype clustering was done using Neighbor-net and Cluster analysis was performed using Bayesian methods. The best number of sub-populations was identified 4 that were seen in most sub-populations genotypes originating from Iran. The results of clustering of Neighbor-net method showed good agreement with the model-based approach. The results showed that microsatellite markers well represented different genotypes of barley diversity. Also according to the results, native genotypes showed more diversity.
Genomics
Faramarz Hoshyardel; Reza Darvishzadeh
Volume 6, Issue 14 , August 2016, , Pages 61-72
Abstract
Tobacco (Nicotiana tabacum L.) is an industrial plant that play important role in economy of most countries. Oriental tobacco is a sun-cured, small-leafed, highly aromatic type of tobacco with limited information about its agronomic and chemical characteristics and their genetic control. This research ...
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Tobacco (Nicotiana tabacum L.) is an industrial plant that play important role in economy of most countries. Oriental tobacco is a sun-cured, small-leafed, highly aromatic type of tobacco with limited information about its agronomic and chemical characteristics and their genetic control. This research was conducted to prepare the genetic linkage map of oriental type tobacco in a recombinant inbred line population (103 lines) produced from the cross between SPT406 (male parent) and Basma seres 31 (female parent) and identification of genomic locations controlling some agronomic characteristics accompanied with chlorine content under field conditions. Markers including SSR, ISSR, REMAP and IRAP were utilized in construction of genetic linkage map. Linkage map comprising 46 markers was developed which covered 586.1 cM of tobacco genome and the average distance between two markers was 12.74 cM. Number of markers per linkage groups varied between 2 to 13. In this study, 19 QTLs with phenotypic variation between 13.2 to 40.1 were identified for characteristics including leaf length, leaf width, leaf number, plant height, internode distance, stem girth, dry leaf yield, photosynthesis value and leaf chlorine content using composite interval mapping. Co-localized QTLs were recognized in linkage groups 1, 3 and 5. Highest values of phenotypic variation achieved in the present study manifest the possibility for using identified retrotransposon and microsatellite markers in marker assisted selection programs of oriental type tobacco.
Genomics
Hamid Hatami Maleki; Marjan Jannatdoust; Reza Darvishzadeh
Volume 5, Issue 11 , December 2015, , Pages 51-63
Abstract
Salinity stress is one of the abiotic stresses which threaten plant species. Achieving any progress in breeding for tolerance to stresses needs existence of genetic diversity. In this research, reaction of 53 sunflower mutant lines seedlings accompanied by their parental line was studied in several salinity ...
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Salinity stress is one of the abiotic stresses which threaten plant species. Achieving any progress in breeding for tolerance to stresses needs existence of genetic diversity. In this research, reaction of 53 sunflower mutant lines seedlings accompanied by their parental line was studied in several salinity levels including 0, 2, 4, 6, 8 ds/m. Also, in molecular experiment, genetic diversity of mutant lines was inspected using AFLP markers. Results revealed significant differences among the studied lines in each of salinity level based on seedling characteristics. Two hundreds loci were amplified using 17 combinations of AFLP primers in the studied lines. Analysis of population structure classified studied mutant lines in two subgroups. Considering association mapping, 43 AFLP markers had significant relation with seedling characteristics. Phenotypic variance of the identified markers varied between 0.13 and 0.42.
Genomics
Fariba Morsali Aghajari; Reza Darvishzadeh; Naser Abbaspour
Volume 5, Issue 10 , September 2015, , Pages 1-16
Abstract
In order to study the effect of salinity on yield and physiological traits of sunflower and genetic analysis of these traits under salinity conditions, a factorial experiment based on completely randomized design with three replications were performed outside the greenhouse in an open air area under ...
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In order to study the effect of salinity on yield and physiological traits of sunflower and genetic analysis of these traits under salinity conditions, a factorial experiment based on completely randomized design with three replications were performed outside the greenhouse in an open air area under natural environmental conditions. The studied factors were included 2 salinity stress levels (normal and 6 dS/m) and sunflower recombinant inbred lines (102 lines derived from the cross PAC2 ×RHA266 together with parental lines). Traits such as grain yield per plant, chlorophyll content, net photosynthetic rate, leaf relative water content, Na+ and K+ concentrations were measured after flowering. The effect of salinity was significant on grain yield, leaf relative water content, Na+ and K+ concentrations as well as on Na+/K+ and K+/ Na+ ratios. For all traits, significant differences were observed between the genotypes studied. Genetic analysis of studied traits was done using a linkage map comprising 221 molecular markers (210 SSR/11 SNP) with an average distance of 7.44 cM between markers via composite interval mapping (CIM) procedure. Totally, 10 and 8 QTLs were detected for studied traits under normal and salt stress conditions, respectively. The phenotypic variance explained by QTLs (R2) ranged from 10.4%- 34.4%. The results showed the existence of co-localized QTLs for some of the studied traits under normal and salt stress conditions including Na+.S.4.1 with Na+/K+.S.4.1, Chl.NS.6.1 with K+.S.6.1. Using co-localized QTLs in different environmental conditions and different years could enhance the efficiency of marker-assisted selection in plant breeding programs.
Genomics
Reza Darvishzadeh
Volume 5, Issue 9 , June 2015, , Pages 15-28
Abstract
Since the economic value of cultivars depends on different characteristics, thus procedure of selection for several traits to maximizing the economic value always has been considered by plant breeders. Detailed knowledge on genetic behavior and association between economic traits will help breeders to ...
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Since the economic value of cultivars depends on different characteristics, thus procedure of selection for several traits to maximizing the economic value always has been considered by plant breeders. Detailed knowledge on genetic behavior and association between economic traits will help breeders to improve plant populations. In this study, 12 retrotransposons-based primers (7 IRAP and 5 REMAP primers) and general and mixed linear models (GLM and MLM) were used to identify molecular markers associated to 9 seed related important traits including oil yield, oil percentage, protein yield, protein percentage, grain length, grain diameter, grain weight, dehulled kernel weight, percentage of dehulled kernel weight to whole grain in 48 confectionery sunflower landraces under normal irrigation, mild and severe drought stress conditions. By applying Bayesian model, the whole confectionery sunflower populations were classified into two sub-populations. Based on general linear model, 2, 5 and 12 loci and through mixed linear model 2, 5 and 11 loci showed significant (P
Genomics
Hossein Sabouri; Sharifeh Mohammad Alegh; Abbas Biabani; Ahmad Reza Dadras; Atefeh Sabouri; Mahnaz Katouzi; Mahboubeh Najjar Ajam; Mahem Pirasteh; Rasoul Khatmi Nejad
Volume 4, Issue 8 , March 2015, , Pages 31-45
Abstract
Osmotic stress (such as drought stress) is a serious limiting factor to rice production and yield stability in worldwide. In order to locate the QTL associated with tolerance to osmotic stresses in germination stage and determine the contribution of each QTL on the phenotypic variation caused 96 lines ...
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Osmotic stress (such as drought stress) is a serious limiting factor to rice production and yield stability in worldwide. In order to locate the QTL associated with tolerance to osmotic stresses in germination stage and determine the contribution of each QTL on the phenotypic variation caused 96 lines of F8 Anbarboo × Sepeedrud (tolerant and sensitive to drought stress in germination stage, respectively) an experiment was conducted at Gonbad Kavous university in 2011-2013. For construction of genetic linkage map, 365 SSR marker and 32 primer combination were evaluated. 136 polymorphic SSR markers and 21 primer combination were used for providing of linkage map. Germination components including root length, shoot, coleoptile and the percentage of seed germination was recorded for 100 seed of each line in the osmotic stress resulting from sucrose, sorbitol and mannitol. For root length in all three stress conditions was found a QTL on chromosome 4 that had positive effect in all cases. Among the identified QTL, qSUC-5 (QTL for coleoptile length under sucrose stress) on chromosome 5, qSUR-2 (QTL for radicle length under sucrose stress) on chromosome 2 and qSUR-4 (QTL for radicle length under sucrose stress) on chromosome 4, respectively, 23, 23 and 26% of phenotypic variation for coleoptile and root length were justified in terms of osmotic stress. This QTL explained that due to the high percentage of candidates for marker-assisted selection programs recombinant line population of Iranian rice.
Molecular Plant Breeding
Mahdieh Safarzadeh; Reza Fotovat; Mohammadreza Azimi; Ehsan Mohsenifard; Behnam Bakhshi
Volume 4, Issue 6 , October 2014, , Pages 21-33
Abstract
Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this ...
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Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this study, the expression patterns of miR159a,b, miR160, miR167a,b and miR171a have been studied in both drought susceptible and drought tolerant varieties in wheat using qRT-PCR. miR159a,b, miR160, miR167a,b and miR171a could play important roles in MYB, ARF, ARF, and SCL, transcription factors regulation, respectively. High conservation among the studied miRNA families was observed in the mature miRNA producer regions by multiplex alignment of pre-miRNAs. Results of qRT-PCR analysis indicated that expressions of miR160 and miR167a,b in tolerant Variety and miR159a,b in susceptible Variety are increased significantly. However, no significant changes in expression were observed for miR171a in both tolerant and sensitive varieties. Presumably, up-regulation miR159a,b in susceptible variety could be resulted to reduction in the expression of MYB genes involved in drought response. On the other hand, up-regulation of miR160 and miR167a,b in tolerant variety, may lead to regulation of auxin and abscisic acid pathways interaction and probably these miRNAs could contribute in stress tolerance in tolerant variety. In addition, no significant change in miR171a expression demonstrated that expression of SCL could be regulated through other mechanisms in plant.
Genomics
Marjan Jannatdoust; Reza Darvishzadeh; Mohammad Ali Ebrahimi
Volume 4, Issue 6 , October 2014, , Pages 61-72
Abstract
In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) ...
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In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) to 1.468 (locus ORS1088) with an average of 1.825. The highest expected heterozygosity (0.484) was estimated for ORS785 locus and the lowest one (0.268) estimated for ORS1088. The mean of expected and observed heterozygosity was 0.435 and 0.722, respectively. Polymorphic information content varied between 0.572 in ORS785 locus and 0.334 in ORS1088 with an average of 0.503. A principal co-ordinates analysis (PCoA) showed that the first two Eigen-values explained 31.71% of the cumulative variation. Cluster analysis based on complete algorithm and Nei genetic distance grouped the studied populations in 3 main classes. Analysis of molecular variance revealed that the high part of total variation was due to within populations. So it will be better to do selection within populations in breeding programs.
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.
Genomics
Mohammad Ebrahimi
Volume 3, Issue 4 , September 2013, , Pages 133-148
Abstract
Today with appropriate understanding of economical, ecological, cultural and social importance of biodiversity, significant progresses have been made toward identification, quantification, finding distribution patterns and genetic relationships of this diversity. In addition, analysis of genetic variation ...
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Today with appropriate understanding of economical, ecological, cultural and social importance of biodiversity, significant progresses have been made toward identification, quantification, finding distribution patterns and genetic relationships of this diversity. In addition, analysis of genetic variation of various aspects such as distribution of allelic diversity, genetic structure and kinship relationships between and within populations, individuals and species is one of the main concerns in biological sciences. In this regard, and with respect to the importance of identification, preservation and maintenance of these genetic pools, to ensure the permanent existence of them and using those resources as a tool for facilitating management strategies and breeding processes, the efficiency of some different genetic and genomic methods including genome and transcriptome based microsatellites have been evaluated in some crop plants, i.e. saffron, and some species belonging to genus Prunus and Punica. Through the development of different molecular markers used in the above-mentioned studies, genome-based microsatellite markers have significantly improved our knowledge on the processes related to habitat segmentation and small populations, distribution of allelic diversity, patterns of germplasm management and finally genetic relationships in the field of genetic conservation. Recently, availability of next generation sequencing tools provided access to huge amount of transcriptomic and genomic sequences. This has allowed us to, a) investigate the diversity of gene functions caused by habitat segmentation, b) assess diversity of responses to biotic and abiotic stresses as well as environmental changes and, c) identify suitable markers to be used in studies such as marker-assisted selection. Here we discuss how the integration of genomic and transcriptomic variations backed up with new bioinformatic tools could improve the identification of relative influences of genetic and environmental threats and open up new frontiers in conservation studies.
Biotic and Abiotic stress
Behnam Bakhshi; Mohmmad Reza Bihamta; Ghasem Hosseini Salekdeh; Masoud Tohidfar
Volume 3, Issue 5 , February 2013, , Pages 93-102
Abstract
Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating ...
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Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating plant gene expression in biotic and abiotic stress. In this study, we selected five miRNAs for promoter analysis and evaluation of differential expression of them under drought stress in roots. Three of them including miR162, miR169 and miR172 are conserved in many plants and the others including miR1425 and miR1880 are rice specific miRNAs. In addition, upstream screening of MIRNA genes showed that upstream region of some MIRNA genes like MIR172 are enriched with important regulatory elements like DRE and ABRE. Quantitative Realtime-PCR was used in this study for analyzing differential expression of evaluated miRNAs. Studying the differential expression of miRNAs in roots under drought condition showed that miR169 was up-regulated but conversely, miR172 was down-regulated. The rest of miRNAs in our study did not show significant differential expression under drought stress. It can be concluded that NF-YA and AP2 as the most important target genes for miR169 and miR172 respectively can play critical roles in response to drought stress. .
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
A Ebadi; E Farshadfar; B Rabiei
Volume 2, Issue 3 , January 2013, , Pages 59-72
Abstract
Quantitative trait loci (QTL) mapping were carried out for 10 rice cooking and eating quality traits, by using a 144 recombinant inbred lines derived from cross between Hashemi and Neamat varieties with microsatellite markers. The ten traits included amylose content (AC), gelatinization temperature (GT), ...
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Quantitative trait loci (QTL) mapping were carried out for 10 rice cooking and eating quality traits, by using a 144 recombinant inbred lines derived from cross between Hashemi and Neamat varieties with microsatellite markers. The ten traits included amylose content (AC), gelatinization temperature (GT), and 8 parameters from the viscosity profile. A total of 23 QTLs were detected for the 10 traits, with at least one QTL and as many as 4 QTLs for each individual trait. At least one QTL for each trait detected on chromosome 6. Several QTL clusters were observed for multiple quality traits. Especially, one QTL cluster near the Alk locus on chromosome 6 includes four QTLs: qGT6, qFV6b, qCSV6 and qSBV6, which control GT, final viscosity (FV), consistency viscosity (CSV) and setback viscosity (SBV), respectively. Most of them were major QTLs. Another important QTL cluster was located at Wx locus on chromosome 6 includes 3 QTLs: qAC6, qMV6a and qBDV6, which control AC, MV (minimum viscosity) and breakdown viscosity (BD), respectively. Moreover, these QTLs were major QTLs. Our results showed some of cooking and eating quality controlled by tow region on chromosome 6, region of Wx locus and region of Alk locus. Markers linked to these two genes can be used as marker assisted selection in breeding programmes.
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 (
