An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

Knowledge of the natural patterns of genetic variation and their evolutionary basis is required for sustainable management and conservation of wheat germplasm. In the current study, the genetic diversity and population structure of 100 individuals from four Triticum and Aegilops species (including T. aestivum, Ae. tauschii, Ae. cylindrica, and Ae. crassa) were investigated using two gene-based markers (start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP)) and simple-sequence repeats (SSRs). The SCoT, CBDP, and SSR markers yielded 76, 116, and 48 polymorphism fragments, respectively. The CBDP marker had greater efficiency than the SCoT and SSR markers due to its higher polymorphism content information (PIC), resolving power (Rp), and marker index (MI). Based on an analysis of molecular variance (AMOVA) performed using all marker systems and combined data, there was a higher distribution of genetic variation within species than among them. Ae. cylindrica and Ae. tauschii had the highest values for all genetic variation parameters. A cluster analysis using each marker system and combined data showed that the SSR marker had greater efficiency in grouping of tested accessions, such that the results of principal coordinate analysis (PCoA) and population structure confirmed the obtained clustering patterns. Hence, combining the SCoT and CBDP markers with polymorphic SSR markers may be useful in genetic fingerprinting and fine mapping and for association analysis in wheat and its germplasm for various agronomic traits or tolerance mechanisms to environmental stresses

An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

Knowledge of the natural patterns of genetic variation and their evolutionary basis is required for sustainable management and conservation of wheat germplasm. In the current study, the genetic diversity and population structure of 100 individuals from four Triticum and Aegilops species (including T. aestivum, Ae. tauschii, Ae. cylindrica, and Ae. crassa) were investigated using two gene-based markers (start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP)) and simple-sequence repeats (SSRs). The SCoT, CBDP, and SSR markers yielded 76, 116, and 48 polymorphism fragments, respectively. The CBDP marker had greater efficiency than the SCoT and SSR markers due to its higher polymorphism content information (PIC), resolving power (Rp), and marker index (MI). Based on an analysis of molecular variance (AMOVA) performed using all marker systems and combined data, there was a higher distribution of genetic variation within species than among them. Ae. cylindrica and Ae. tauschii had the highest values for all genetic variation parameters. A cluster analysis using each marker system and combined data showed that the SSR marker had greater efficiency in grouping of tested accessions, such that the results of principal coordinate analysis (PCoA) and population structure confirmed the obtained clustering patterns. Hence, combining the SCoT and CBDP markers with polymorphic SSR markers may be useful in genetic fingerprinting and fine mapping and for association analysis in wheat and its germplasm for various agronomic traits or tolerance mechanisms to environmental stresses

Effects of Drought Stress on Some Agronomic and Morpho-Physiological Traits in Durum Wheat Genotypes

Durum wheat performance in the Mediterranean climate is limited when water scarcity occurs before and during anthesis. The present research was performed to determine the effect of drought stress on several physiological and agro-morphological traits in 17 durum wheat genotypes under two conditions (control and drought) over two years. The results of analysis of variance indicated that the various durum wheat genotypes responded differently to drought stress. Drought stress significantly reduced the grain filling period, plant height, peduncle length, number of spikes per plot, number of grains per spike, thousand grains weight, grain yield, biomass, and harvest index in all genotypes compared to the control condition. The heatmap-based correlation analysis indicated that grain yield was positively and significantly associated with phenological characters (days to heading, days to physiological maturity, and grain filling period), as well as number of spikes per plant, biomass, and harvest index under drought conditions. The yield-based drought and susceptible indices revealed that stress tolerance index (STI), geometric mean productivity (GMP), mean productivity (MP), and harmonic mean (HM) were positively and significantly correlated with grain yields in both conditions. Based on the average of the sum of ranks across all indices and a three-dimensional plot, two genotypes (G9 and G12) along with the control variety (G1) were identified as the most tolerant genotypes. Among the investigated genotypes, the new breeding genotype G12 showed a high drought tolerance and yield performance under both conditions. Hence, this genotype can be a candidate for further multi-years and locations test as recommended for cultivation under rainfed conditions in arid and semi-arid regions.Peer reviewe

Wild Relatives of Wheat Respond Well to Water Deficit Stress : A Comparative Study of Antioxidant Enzyme Activities and Their Encoding Gene Expression

Previous studies have revealed that some wild wheat accessions respond well to water deficit treatments and have a good potential in terms of photosynthetic parameters, root system architecture, and several physiological properties. However, the biochemical responses and molecular mechanisms of antioxidant-encoding genes remain to be elucidated. Herein, we investigated the most tolerant accessions fromA. crassa,Ae. tauschii, andAe. cylindricapreviously identified from a core collection in previous studies, along with a control variety of bread wheat (T. aestivumcv. Sirvan) through measuring the shoot fresh and dry biomasses; the activities of antioxidant enzymes (including ascorbate peroxidase (APX), catalase (CAT), guaiacol peroxidase (GPX), and peroxidase (POD)); and the relative expression ofCAT, superoxide dismutase (MnSOD), andGPXandAPXgenes under control and water deficit conditions. Water deficit stress caused a significant decrease in the shoot biomasses but resulted in an increase in the activity of all antioxidant enzymes and relative expression of antioxidant enzyme-encoding genes. Principal component analysis showed a strong association between the shoot dry biomass and the activity of CAT, POD, and APX, as well asMnSODgene expression. Thus, these traits can be used as biomarkers to screen the tolerant plant material in the early growth stage. Taken together, our findings exposed the fact thatAe. tauschiiandAe. crassarespond better to water deficit stress thanAe. cylindricaand a control variety. Furthermore, these accessions can be subjected to further molecular investigation.Peer reviewe

Wild Relatives of Wheat Respond Well to Water Deficit Stress: A Comparative Study of Antioxidant Enzyme Activities and Their Encoding Gene Expression

Previous studies have revealed that some wild wheat accessions respond well to water deficit treatments and have a good potential in terms of photosynthetic parameters, root system architecture, and several physiological properties. However, the biochemical responses and molecular mechanisms of antioxidant-encoding genes remain to be elucidated. Herein, we investigated the most tolerant accessions from A. crassa, Ae. tauschii, and Ae. cylindrica previously identified from a core collection in previous studies, along with a control variety of bread wheat (T. aestivum cv. Sirvan) through measuring the shoot fresh and dry biomasses; the activities of antioxidant enzymes (including ascorbate peroxidase (APX), catalase (CAT), guaiacol peroxidase (GPX), and peroxidase (POD)); and the relative expression of CAT, superoxide dismutase (MnSOD), and GPX and APX genes under control and water deficit conditions. Water deficit stress caused a significant decrease in the shoot biomasses but resulted in an increase in the activity of all antioxidant enzymes and relative expression of antioxidant enzyme-encoding genes. Principal component analysis showed a strong association between the shoot dry biomass and the activity of CAT, POD, and APX, as well as MnSOD gene expression. Thus, these traits can be used as biomarkers to screen the tolerant plant material in the early growth stage. Taken together, our findings exposed the fact that Ae. tauschii and Ae. crassa respond better to water deficit stress than Ae. cylindrica and a control variety. Furthermore, these accessions can be subjected to further molecular investigation

Effect of Water Deficit Stress on Seedling Biomass and Physio-Chemical Characteristics in Different Species of Wheat Possessing the D Genome

Wild relatives of wheat serve as an extraordinary source of variability for breeding programs due to their capabilities to respond to various environmental stresses. Here, we investigated some species possessing a D genome (T. aestivum, Ae. tauschii, Ae. crassa and Ae. cylindrica) in terms of relative water content (RWC), stomatal conductance (Gs), relative chlorophyll content, initial fluorescence (Fo), maximum quantum yield of PSII (Fv/Fm), maximum primary yield of PSII photochemistry (Fv/Fo), as well as shoot fresh and dry biomasses under control and water deficit conditions. Our results revealed that water deficit negatively affected all traits; shoot fresh weight, Gs and RWC showed the highest reduction compared to the control condition. Principal component analysis (PCA) identified two PCs that accounted for 53.36% of the total variation in the water deficit conditions. Correlation analysis and PCA-based biplots showed that stress tolerance index (STI) is significantly associated with Fv/Fm and Fv/Fo under water stress conditions, suggesting that these are the best parameters to evaluate when screening for tolerant samples at the seedling stage. We identified 19 accessions from Ae. crassa and one from Ae. tauschii as the most tolerant samples. In conclusion, Ae. crassa might provide an ideal genetic resource for drought-tolerant wheat breeds

Effect of Water Deficit Stress on Seedling Biomass and Physio-Chemical Characteristics in Different Species of Wheat Possessing the D Genome

Wild relatives of wheat serve as an extraordinary source of variability for breeding programs due to their capabilities to respond to various environmental stresses. Here, we investigated some species possessing a D genome (T. aestivum, Ae. tauschii, Ae. crassa and Ae. cylindrica) in terms of relative water content (RWC), stomatal conductance (Gs), relative chlorophyll content, initial fluorescence (Fo), maximum quantum yield of PSII (Fv/Fm), maximum primary yield of PSII photochemistry (Fv/Fo), as well as shoot fresh and dry biomasses under control and water deficit conditions. Our results revealed that water deficit negatively affected all traits; shoot fresh weight, Gs and RWC showed the highest reduction compared to the control condition. Principal component analysis (PCA) identified two PCs that accounted for 53.36% of the total variation in the water deficit conditions. Correlation analysis and PCA-based biplots showed that stress tolerance index (STI) is significantly associated with Fv/Fm and Fv/Fo under water stress conditions, suggesting that these are the best parameters to evaluate when screening for tolerant samples at the seedling stage. We identified 19 accessions from Ae. crassa and one from Ae. tauschii as the most tolerant samples. In conclusion, Ae. crassa might provide an ideal genetic resource for drought-tolerant wheat breeds

Molecular diversity and phytochemical variability in the Iranian poppy (Papaver bracteatum Lindl.): A baseline for conservation and utilization in future breeding programmes

In the present investigation, 72 accessions of the Iranian poppy (Papaver bracteatum Lindl.) were analyzed for genetic diversity and population structure using start codon targeted polymorphism (SCoT) and inter simple sequence repeat (ISSR) markers along with four important phytochemical traits to provide baseline knowledge for the Iranian poppy’s breeding and conservation plans. Twelve ISSR and thirteen SCoT primers generated a total of 98 and 186 fragments with a mean of 8.17 and 14.31 fragments per primer, respectively. Polymorphic information content for ISSR and SCoT primers ranged from 0.39 to 0.45 and 0.28 to 0.34, with the resolving power ranging from 21.61 to 3.97 and 13.08 to 28.02, respectively. Neighbour-joining (NJ) based clustering grouped 72 accessions into three main groups based on two markers studied (ISSR and SCoT) and the combined data (ISSR + SCoT), which associated with their eco-geographical regions. Population structure based analysis divided 72 accessions into 3 subpopulations using ISSR markers, when SCoT was used eight subpopulations were observed. However, when the combined data was used only three subpopulations were found, which corresponded to the grouping observed with the NJ method and these results were supported by principal coordinate analyses (PCoA). Phytochemical analysis revealed that plant capsule has higher total amounts of the alkaloids; thebaine, morphine and oripavine than stem tissues. Interestingly, for the geographical parameters, latitude showed a significant and positive correlation with thebaine extracted from both stem and capsules and the regression results confirmed these associations. Taken together, our results indicated that three populations Ploor, Eil-Teymoor and Anjomane due to their high contents of alkaloids like thebaine as well as the Taham population due to its high content of morphine and oripavine have a strong enough potency to be used in the pharmacy industry.Peer reviewe

Applications of CRISPR-Cas9 as an Advanced Genome Editing System in Life Sciences

Targeted nucleases are powerful genomic tools to precisely change the target genome of living cells, controlling functional genes with high exactness. The clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) genome editing system has been identified as one of the most useful biological tools in genetic engineering that is taken from adaptive immune strategies for bacteria. In recent years, this system has made significant progress and it has been widely used in genome editing to create gene knock-ins, knock-outs, and point mutations. This paper summarizes the application of this system in various biological sciences, including medicine, plant science, and animal breeding.Peer reviewe