Biotic and Abiotic stress
Zohreh Hajibarat; Abbas Saidi; MohammadReza Ghaffari; Mehrshad Zeinalabedini
Abstract
Plants use a variety of strategies to cope with abiotic stress, depending on the species and the growth of the plant. Abiotic stresses such as drought is the most important stress that affects yield of agricultural products. In addition, drought stress is one of the main limiting factors in plant growth, ...
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Plants use a variety of strategies to cope with abiotic stress, depending on the species and the growth of the plant. Abiotic stresses such as drought is the most important stress that affects yield of agricultural products. In addition, drought stress is one of the main limiting factors in plant growth, it can also inhibit respiration, photosynthesis, and thus affects the growth and physiological metabolism of plants. Plants activate several mechanisms such as morphological and structural changes as well as the expression of drought-resistant genes, the synthesis of hormones and osmotic regulators to reduce drought stress. Drought accelerates grain leaf senescence, altering the expression of thousands of genes and ultimately affecting grain protein content and grain yield. However, the genotypic variability exists for drought induced disruption and tolerance in barley. In this review, the approaches can help for improving barley genotypes in response to drought stress through breeding and physiological traits, genetic engineering, and marker-assisted selection (MAS). We detected genes and proteins involved in response to drought-tolerance using proteomics, transcriptomics and metabolomics approaches. Also, the introduced Quatitatives Traits Loci (QTLs) related to yield and Stay green and physiological traits found in this study can be used for MAS in barley improvement for drought tolerance in the future. In particular, comparative studies of genetically diverse germplasm exposed to adverse conditions such as drought provide valuable insights into plant responses to stress and create information on biochemical pathways involved in adaptation to environmental limitations. Proper evaluation of omics data can help the biomarker discovery.
Molecular Plant Breeding
Samira Bakhtiari; Hossein Sabouri; Mehdi Mollashahi; hossein hossein moghaddam
Abstract
Barley (Hordeum vulgare L.) is a model plant for genetical and physiological studies and has a high adaptability to different conditions. In order to locate QTL, the genomic areas controlling barley agronomic traits under experimental conditions were conducted in 104 families with their parents (Badia ...
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Barley (Hordeum vulgare L.) is a model plant for genetical and physiological studies and has a high adaptability to different conditions. In order to locate QTL, the genomic areas controlling barley agronomic traits under experimental conditions were conducted in 104 families with their parents (Badia and Kavir) in the Research Farm of Gonbad-e-Kavous College in 2013-2014. Agronomic traits such as biomass, spike weight, spike number, spike length, grain yield, peduncle length, stem diameter, flag leaf length, flag leaf width, flag leaf weight, grain numbers, grain weight, and awn length for all families were measured. For the saturation of map, 19 (93 alleles), the ISSR marker used that assigned to 7 groups of attachment to 7 chromosomes with a genome length of 617.5 cM and the average between markers equal to 5.41 cM Morgan. A total of 21 locations with QTL were identified for the agronomic traits. Thirteen major effect QTLs that controlled a large proportion of phenotypic variation were identified. Major QTLs The effects of controlling the desired attributes and their linked markers can be used in selection programs using the marker.
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.
Proteomics
Mohammad Reza Ghaffari; Nicolaus von Wirén; Klaus Humbeck; Phillip Franken
Volume 6, Issue 13 , May 2016, , Pages 27-39
Abstract
Deciphering of network correlation operating in the plant biomass accumulation and yield production is a pre-requisite for understanding the relationships between omics data and growth rate in plants. To investigate the relationship among transcripts and their regulation for lignocellulose biomass formation ...
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Deciphering of network correlation operating in the plant biomass accumulation and yield production is a pre-requisite for understanding the relationships between omics data and growth rate in plants. To investigate the relationship among transcripts and their regulation for lignocellulose biomass formation at the generative stage of barley, transcript profiling was applied on three contrasting spring barley lines two weeks after flowering. A custom barley cDNA Microarray (Agilent Technologies, Germany) containing 56000 barley oligonucleotides was used for transcriptome analysis on flag leaves of spring barley. The network correlation of transcripts involved in secondary and RNA metabolism revealed a higher number of positive than negative correlations of which a signal molecule, ABH1-Cap binding protein showed the highest node degree centrality. Statistical test showed a strong positive interrelation between ABH1-Cap binding protein and a key gene of phenylpropanoid pathway, Cinnamoyl-CoA reductase. The integrated data suggested Cinnamoyl-CoA reductase (CCR) might be used as putative biomarker for engineering of lignocellulose biomass improvement at the generative stage in barley.
Molecular Plant Breeding
Marouf Khalili; Rahim Mohammadian
Volume 6, Issue 13 , May 2016, , Pages 41-55
Abstract
Salinity is one of the main osmotic stresses that limit plants growth and development through changes in osmotic and ionic balances. In order to mapping of genomic regions of controlling quantitative trait locus (QTLs), related to salinity tolerance in grain barley and assessment of associated indices, ...
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Salinity is one of the main osmotic stresses that limit plants growth and development through changes in osmotic and ionic balances. In order to mapping of genomic regions of controlling quantitative trait locus (QTLs), related to salinity tolerance in grain barley and assessment of associated indices, an experiment was conducted during 2015 using 72 double haploid lines of barley along with their parents (Stepto and Morex) in randomized complete block design (RCBD) with two replications, at three conditions including normal and two salinity levels of NaCl (100 and 200 mM NaCl). Investigated traits in this study were coefficient of velocity of germination, final germination percentage, mean germination time, germination rate index and average germination speed. QTL analysis using composite interval mapping (CIM) was performed based on mean of three environments. Overall, for different traits 47 QTL with LOD≥2.5 was identified and 7 additive-by-additive significant epistatic effects were observed. Total phenotypic variance explained by the QTLs varied from 29.97 to 77.15 percent, which the lowest related to germination rate index under stress conditions of 200 mM and the highest related to coefficient of velocity of germination in normal conditions. The highest LOD (8.27) was obtained for coefficient of velocity of germination on chromosome of 4Hb under 100 mM stress conditions. Stable QTLs in three environments as well as linked markers could be used in the marker assisted selection (MAS) to improve germination characteristics under salinity conditions at different trials replicated over years.
Bioinformatics
Yaser Panahi Fakoor; Zahra-Sadat Shobbar; Ehsan Pourabed; Farzan Ghane Golmohamadi; Seyed Morteza Razavi
Volume 5, Issue 12 , February 2016, , Pages 25-38
Abstract
Abiotic stresses are among major factors limiting crop yields, and SnRK2 protein kinases are one of the key regulators of plant response to abiotic stresses. Due to the economic importance, cultivation area, and tolerance of barley to the abiotic stresses, identification and characterization of SnRK2 ...
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Abiotic stresses are among major factors limiting crop yields, and SnRK2 protein kinases are one of the key regulators of plant response to abiotic stresses. Due to the economic importance, cultivation area, and tolerance of barley to the abiotic stresses, identification and characterization of SnRK2 family members in barley is performed in present research. SnRK2 conserved sequences were used as a query for tBLASTn analysis in different databases such as NCBI and international barley sequencing consortium against all of the reported barley sequences. As a result, 10 members were identified (HvSnRK2.1 to HvSnRK2.10) which 8 of them were not yet reported. These HvSnRK2 members were aligned with AtSnRK2s and OsSnRK2s and a phylogenetic tree was constructed. Detection of chromosomal localization, promoter analysis and gene structure determination was also performed. Half of the family members were located on chromosome 2 and the rest on chromosomes 1, 4, 5 and 6. Number of introns in the gene family members varied from 0 to 8. Totally, 19 sorts of cis elements including abiotic stress responsive elements were found in HvSnRK2s promoter sequences. Expression pattern of the family members were evaluated in different tissues, treatments and genotypes, based on the microarray data. Expression of HvSnRK2.6 was up-regulated by drought, salt and cold stresses implementing its important role in signal transduction of these stresses and tolerance induction to them. It is expected that this gene could be used in plant manipulation and breeding programs aimed for tolerance enhancement to abiotic stresses especially drought.
Biotic and Abiotic stress
Roya Heidari; Raheem Haddad
Volume 5, Issue 9 , June 2015, , Pages 65-76
Abstract
Silicon is accounted as one of the elements that induces resistance to different kinds of stresses especially drought stress in plants. In this study, the effect of silicon was analyzed on the activity of antioxidant enzymes Catalase, Ascorbate peroxidase and Superoxide dismutase and also related genes ...
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Silicon is accounted as one of the elements that induces resistance to different kinds of stresses especially drought stress in plants. In this study, the effect of silicon was analyzed on the activity of antioxidant enzymes Catalase, Ascorbate peroxidase and Superoxide dismutase and also related genes expression pattern and H2O2 content on two varsities, NIMROOZ (drought resistant) and GORGAN (semi-resistant) under three treatments of drought, silicon-drought and control in a completely randomized design with three replications in four leaf developmental stage in a green house. Based on the results of factorial test, catalase activity was decreased in semi-sensitive varity and silicon treatment increased such activity in both varieties under drought stress. While the activity of two other enzymes (Ascorbat peroxidase and Superoxide dismutase) was increased under drought stress and silicon treatment intensified their activity in comparison with control. Their pattern of gene expression changed in a similar way of enzyme activity. It might be concluded that, the role of silicon in enhancing drought tolerance in barley plant is because of increasing activity of antioxidant enzymes and expression of stress responsible genes, and therefore, causes reduction in activity of reactive oxygen spices produced under drought stress.
Molecular Plant Breeding
M Rahimi; F Ebrahimpour; R Eshghi
Volume 2, Issue 3 , January 2013, , Pages 35-48
Abstract
In this study, an F2:3 population derived from the cross between Hiberna and Pfyner was used to analyze the inheritance of yield and its components in barley by generation mean analysis and to map the corresponding QTLs (quantitative trait loci) by microsatellite markers. Generation mean analysis suggested ...
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In this study, an F2:3 population derived from the cross between Hiberna and Pfyner was used to analyze the inheritance of yield and its components in barley by generation mean analysis and to map the corresponding QTLs (quantitative trait loci) by microsatellite markers. Generation mean analysis suggested that both additive and dominance effects were important for most of the traits evaluated, but dominance and non-allelic interaction had a more pronounced effect for days to maturity, number of grains per spike, spike length and plant height. The highest heritability was obtained for number of tillers, indicating that this trait is controlled by additive effects. The additive effects played major role in the inheritance of grain yield per plant, since heritability of this trait was low. The linkage map constructed by 159 microsatellite markers covered a total length of about 1030.5 cM. Using the method of composite interval mapping 2, 4, 2, 4, 1, 4 and 7 QTLs were detected for days to maturity, number of tillers, 1000-grain weight, plant height, spike length, number of grains per spike and grain yield, respectively. Ten QTLs had corresponding occurrences with the QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. The results of this study also showed that, grain yield per plant controls with several minor genes.
