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Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes  [PDF]
Dechassa Duressa, Khairy M. Soliman, Dongquan Chen, Robert W. Taylor
American Journal of Molecular Biology (AJMB) , 2011, DOI: 10.4236/ajmb.2011.13016
Abstract: It is well documented that aluminum (Al) toxicity is the most important constraint to crop production on acid soils and soybean is one of the most Al sensitive plant species. To advance our understanding of the molecular and genetic mechanisms of Al-tolerance in soybean we compared root tip (1 cm long) transcriptome profiles of an Al-tolerant (PI 416937) and Al-sensitive (Young) soybean genotypes using a combination of DNA microarrays and quantitative real-time PCR gene expression profiling technologies, in a time-course experiment (2, 12, 48, 72 h post Al treatment). We observed many genes differentially expressed between the two genotypes in constitutive and non-constitutive manner. The most likely candidate Al-tolerance genes expressed at high level include the previously reported transcription factors, auxin down regulated-like protein (ADR6-like) and, basic leucine zipper (bZIP 94), sulfur transmembrane transport protein and lipid transfer protein; and several novel genes that include rare cold inducible protein (RCI2B ), GPI-transamidase, malonyl-COA: Isoflavone 7-O-glucoside-6"-O-malontransferase, a cell proliferation protein (WPP2), oleosin protein, pectinestrease inhibitor, and impaired sucrose induction1; whereas genes negatively correlated with Al-tolerance, namely cellulose synthase and calcium transporters were down regulated in Al-tolerant PI 416937 compared to the Al-sensitive Young. The possible mechanisms of how these genes contribute to Al-tolerance trait are discussed. In conclusion, transcriptome profile comparisons of Al-tolerant and Al-sensitive soybean genotypes revealed novel putative Al-tolerance genes. These genes deserve further functional characterization for eventual utilization in developing soybean germplasm adapted to high aluminum soils.
Identification of Aluminum Responsive Genes in Al-Tolerant Soybean Line PI 416937
Dechassa Duressa,Khairy Soliman,Dongquan Chen
International Journal of Plant Genomics , 2010, DOI: 10.1155/2010/164862
Abstract: Soybean is one of the most aluminum (Al) sensitive plants. The complex inheritance of Al tolerance trait has so far undermined breeding efforts to develop Al-tolerant soybeans. Discovering the genetic factors underlying the Al tolerance mechanisms would undoubtedly accelerate the pace of such endeavor. As a first step toward this goal, we analyzed the transcriptome profile in roots of Al-tolerant soybean line PI 416937 comparing Al-treated and untreated control plants using DNA microarrays. Many genes involved in transcription activation, stress response, cell metabolism and signaling were differentially expressed. Patterns of gene expression and mechanisms of Al toxicity and tolerance suggest that Cys2His2 and ADR6 transcription activators, cell wall modifying enzymes, and phytosulfokines growth factor play role in soybean Al tolerance. Our data provide insights into the molecular mechanisms of soybean Al tolerance and will have practical value in genetic improvement of Al tolerance trait. 1. Introduction Aluminum (Al) toxicity is a major constraint of crop production on acid soils. In view of the fact that 40% of world’s arable land is acidic [1, 2], Al toxicity remains a major hurdle for increasing world food, fiber, and fuel production particularly via expansion of cultivation into acid soils. Aluminum inflicts a wide range of cellular injuries in plants that ultimately result in reduced root growth, nutrient and water uptake, and productivity [1, 2]. Plants possess some degree of tolerance to Al toxicity that varies among species and genotypes [1, 3–6]. Al tolerance mechanisms include exclusion and internal detoxification. Al exclusion via rhizosphere Al-organic acid anion complex formation is the most widely documented physiological mechanism of Al tolerance in cultivated and wild plants alike [1, 7]. Root-exuded citrate, malate, and oxalate are the key organic acid anions involved in such mechanism. Genes involved in Al-induced root exudation of malate and citrate have been cloned in wheat [8] and sorghum [5], and their variants are being discovered in several plant species. Internal detoxification mechanisms involve the formation of Al complexes with organic acids, acidic polypeptides, and/or proteins and subsequent sequestration of Al in organelles away from sensitive sites in the cell [9, 10]. The genetic components of the internal detoxification pathways are yet to be elucidated. In soybean, Al tolerance is a complex trait perhaps involving several genes and pathways [11, 12]. Quantitative trait loci (QTL) mapping in a population derived from
Proteomic Analysis of Soybean Roots under Aluminum Stress
Dechassa Duressa,Khairy Soliman,Robert Taylor,Zachary Senwo
International Journal of Plant Genomics , 2011, DOI: 10.1155/2011/282531
Abstract: Toxic levels of aluminum (Al) in acid soils inhibit root growth and cause substantial reduction in yields of Al-sensitive crops. Aluminum-tolerant cultivars detoxify Al through multiple mechanisms that are currently not well understood at genetic and molecular levels. To enhance our understanding of the molecular mechanisms involved in soybean Al tolerance and toxicity, we conducted proteomic analysis of soybean roots under Al stress using a tandem combination of 2-D-DIGE, mass spectrometry, and bioinformatics tools and Al-tolerant (PI 416937) and Al-sensitive (Young) soybean genotypes at 6, 51 or 72 h of Al treatment. Comparison of the protein profile changes revealed that aluminum induced Al tolerance related proteins and enzymes in Al-tolerant PI 416937 but evoked proteins related to general stress response in Al-sensitive Young. Specifically, Al upregulated: malate dehydrogenase, enolase, malate oxidoreductase, and pyruvate dehydrogenase, in PI 416937 but not in Young. These enzymes contribute to increased synthesis of citrate, a key organic acid involved in Al detoxification. We postulate that simultaneous transgenic overexpression of several of these enzymes would be a robust genetic engineering strategy for developing Al-tolerant crops. 1. Introduction Toxic levels of aluminum (Al) in acid soils inhibit root growth and cause substantial reduction in yields of Al-sensitive crops [1, 2]. Its toxicity mechanisms include interference with nutrient and water uptake and translocation [3], disruption of calcium homeostatis [4], disruption of cytoskeleton [5, 6], callose deposition in apoplast that affects movement of substances from cell to cell [7], lipid peroxidation and reactive oxygen species production [8], and interference with cell division and elongation [9, 10]. In concert, these disorders thwart root growth and development that is typically manifested in stunted and swollen root system at the morphological level [11, 12]. Al disrupts cellular components and processes by high binding affinity to phosphate, sulfate, and carbonyl functional groups of cellular components in apoplast and symplast [11]. Perhaps as a direct and parallel evolutionary response to the nature of Al-ligand interaction, plants secret substances that possess these functional groups namely, organic acids [13], phenolics [14–16], and phosphate and polypeptides [17, 18] to bind and detoxify Al in the rhizosphere. Sequestration of Al in the rhizosphere with root secreted organic acids mainly citrate, malate, and oxalate is a common and well-documented physiological mechanism of
Effects of Farmyard Manure and Inorganic Fertilizer Application on Soil Physico-Chemical Properties and Nutrient Balance in Rain-Fed Lowland Rice Ecosystem  [PDF]
Tilahun Tadesse, Nigussie Dechassa, Wondimu Bayu, Setegn Gebeyehu
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.42041
Abstract: A field experiment was conducted to assess the effects of combined application of farm yard manure (FYM) and inorganic NP fertilizers on soil physico-chemical properties and nutrient balance in a rain-fed lowland rice production system in Fogera plain, northwestern Ethiopia. The study was carried out during the main cropping seasons of 2010 and 2011. Twenty-seven treatments comprising a factorial combination of three rates of FYM (0, 7.5, and 15 t·ha-1), three rates of nitrogen (0, 60, 120 kg·N·ha-1) and three rates of phosphorus (0, 50 and 100 kg·P2O5·ha-1) were tested. The experiments were laid out as a randomized complete block design with three replications. Bulk density, organic matter content, and available water holding capacity, total N, and available P of the soil were measured just after harvesting the rice crop. Results showed that application of 15 t·FYM·ha-1 significantly increased soil organic matter and available water holding capacity but decreased the soil bulk density, creating a good soil condition for enhanced growth of the rice crop. Application of 15 tFYM·ha-1 increased the level of soil total nitrogen from 0.203% to 0.349%. Combined application of 15 t·ha-1·FYM and 100 kg·P2O5·ha-1 increased the available phosphorous from 11.9 ppm to 38.1 ppm. Positive balances of soil N and P resulted from combined application of FYM and inorganic N and P sources. Application of 15·t ha-1·FYM and 120 kg·N·ha-1resulted in 214.8 kg·ha-1·N positive balance while application of 15 t·ha-1·FYM and 100 kg·P2O5·ha-1 resulted in a positive balance of 69.3 kg·P2O5·ha-1 available P. From the results of this experiment, it could be concluded that combined application of FYM and inorganic N and P fertilizers improved the chemical and physical properties, which may lead to enhanced and sustainable production of rice in the study area.
Effect of combined application of organic-P and inorganic-N fertilizers on yield of carrot
S Hailu, T Seyoum, N Dechassa
African Journal of Biotechnology , 2008,
Abstract: A study was undertaken to assess the effect of combined application of organic-P and inorganic-N fertilizers on yield and yield components of carrot (Daucus carota L.). The field experiment was conducted at Kombolcha ATVET College, South Wollo, Ethiopia. Seeds of carrot were sown on raised beds of a black clay soil. “Orga “and urea were used as sources of phosphorus and nitrogen, respectively, for the fertilizer treatments. The rates of fertilizers used in the experiment were, 309 kg “orga” ha-1 combined with six rates of urea (0, 68.5, 267.2, 274,342.5 and 411 kg urea ha-1). The field experiment was laid out in a randomized complete block design with seven fertilizer treatments, replicated five times. Yield and yield components of carrot were significantly influenced by the preharvest combined application of “orga” and urea treatments. Pre-harvest application of 309 kg “orga” ha-1 combined with 274 kg urea ha-1 increased yield of carrot by 46% compared to the control treatment. The values of yield components of carrot were also increased in response to the increased rate of combined “orga” and urea fertilizer application. The result showed that the combined application of 309 kg ha-1 “orga”and 274 kg ha-1 urea resulted in the maximum yield of carrot.
Effect of combined application of organic P and inorganic N fertilizers on post harvest quality of carrot
S Hailu, T Seyoum, N Dechassa
African Journal of Biotechnology , 2008,
Abstract: A study was undertaken to assess the effect of combined application of organic-P and inorganic-N fertilizers on post harvest quality of carrot (Daucus carota l.) stored at 1°C and ambient conditions (8.6 - 24.8°C). For the fertilizer treatments, 309 kg orga ha-1 (for P) in combination with each of six rates of urea (0, 68.5, 267.2, 274, 342.5 and 411 kg urea ha-1) was used. Carrot shelf life assessment was carried out in a factorial experiment with pre-harvest fertilizer treatments as one-factor and storage conditions as another factor. Pre-harvest fertilizer and post harvest storage treatments significantly affected the post harvest quality of carrot. The weight loss, contents of ascorbic acid, reducing sugar, total sugar, as well as titrable acidity and percentage marketability of carrot were significantly (p < 0.05) affected by the different pre-harvest combinations of fertilizer treatments both at harvest and during the storage period of 28 days at 1°C and ambient storage conditions. The storage temperature also showed significant (P < 0.01) influence on the weight loss, ascorbic acid, total soluble solids, total sugar, pH, titratable acidity and percentage marketability of carrots. After 28 days carrots subjected to 1°C storage had 51.4% less weight loss, 17.1% more ascorbic acid, 15.0% lower total soluble solids, 20.7% more total sugar and 30.1% more marketable compared to carrots stored under ambient conditions. This indicated that shelf life of carrots stored at 1°C exceeded that of samples stored under ambient conditions. Significant interaction was also observed between pre-harvest fertilizer treatments and post-harvest storage conditions in most of the quality parameters of carrot. The pre-harvest combined application of orga with urea at 309 kg ha-1 and 274 kg ha-1, respectively, and post harvest storage at 1°C is recommended for better postharvest quality maintenance of carrot.
Assessing the levels of food shortage using the traffic light metaphor by analyzing the gathering and consumption of wild food plants, crop parts and crop residues in Konso, Ethiopia
Ocho Dechassa,Struik Paul C,Price Lisa L,Kelbessa Ensermu
Journal of Ethnobiology and Ethnomedicine , 2012, DOI: 10.1186/1746-4269-8-30
Abstract: Background Humanitarian relief agencies use scales to assess levels of critical food shortage to efficiently target and allocate food to the neediest. These scales are often labor-intensive. A lesser used approach is assessing gathering and consumption of wild food plants. This gathering per se is not a reliable signal of emerging food stress. However, the gathering and consumption of some specific plant species could be considered markers of food shortage, as it indicates that people are compelled to eat very poor or even health-threatening food. Methods We used the traffic light metaphor to indicate normal (green), alarmingly low (amber) and fully depleted (red) food supplies and identified these conditions for Konso (Ethiopia) on the basis of wild food plants (WFPs), crop parts (crop parts not used for human consumption under normal conditions; CPs) and crop residues (CRs) being gathered and consumed. Plant specimens were collected for expert identification and deposition in the National Herbarium. Two hundred twenty individual households free-listed WFPs, CPs, and CRs gathered and consumed during times of food stress. Through focus group discussions, the species list from the free-listing that was further enriched through key informants interviews and own field observations was categorized into species used for green, amber and red conditions. Results The study identified 113 WFPs (120 products/food items) whose gathering and consumption reflect the three traffic light metaphors: red, amber and green. We identified 25 food items for the red, 30 food items for the amber and 65 food items for the green metaphor. We also obtained reliable information on 21 different products/food items (from 17 crops) normally not consumed as food, reflecting the red or amber metaphor and 10 crop residues (from various crops), plus one recycled stuff which are used as emergency foods in the study area clearly indicating the severity of food stress (red metaphor) households are dealing with. Our traffic light metaphor proved useful to identify and closely monitor the types of WFPs, CPs, and CRs collected and consumed and their time of collection by subsistence households in rural settings. Examples of plant material only consumed under severe food stress included WFPs with health-threatening features like Dobera glabra (Forssk.) Juss. ex Poir. and inkutayata, parts of 17 crops with 21 food items conventionally not used as food (for example, maize tassels, husks, empty pods), ten crop residues (for example bran from various crops) and one recycled food item (tat
Correlation and Path Analysis in Sweet Potato and their Implications for Clonal Selection
Engida Tsegaye,E.V. Devakara Sastry,Nigussie Dechassa
Journal of Agronomy , 2006,
Abstract: Understanding interrelationships among various agronomic traits is vital to plan an effective breeding program in sweet potato (Ipomoea batatas (L.) Lam.). This study was undertaken to determine associations among yield and yield related traits in the crop plant so as to identify the major traits of importance that could be used as a basis for clonal selection. A replicated field experiment was carried out using thirty sweet potato genotypes selected at random from the germplasm collection of diverse origin. Observations were made on ten characters. Phenotypic as well as genotypic correlation coefficient analyses revealed that storage root yield had positive and significant correlation with individual storage root weight, harvest index and storage root girth. Number of storage roots per plant was negatively and significantly correlated with individual storage root weight and storage root girth indicating the presence of compensatory relationship between number of storage roots per plant and the latter two traits. Path coefficient analysis for storage root yield also revealed that individual storage root weight, number of storage roots per plant and harvest index were the most important determinants of storage root yield. It could be concluded that due to the high estimated positive correlation and positive direct effect of individual storage root weight and harvest index on storage root yield, these traits would be most suitable for indirect selection in sweet potato improvement programs that aim at increasing storage root yield.
Genetic Variability for Yield and Other Agronomic Traits in Sweet Potato
Engida Tsegaye,Nigussie Dechassa,E.V. Devakara Sastry
Journal of Agronomy , 2007,
Abstract: Understanding the nature and magnitude of variability among sweet potato (Ipomoea batatas (L) Lam.) genotypes for traits of economic importance is vital to plan effective breeding programs. A replicated field experiment was carried out using thirty sweet potato genotypes selected at random from the germplasm collection of diverse sources. The specific purpose was to estimate the nature and magnitude of variability among yield and yield related traits in the crop plant. Observations were recorded on sixteen characters. The analysis of variance revealed that there were highly significant (p<0.01) differences among the genotypes for all the characters. Wide ranges of genotypic variability were observed among the genotypes for most of the characters. In vine traits, 32.4 to 82.5% of the observable variability was due to the genetic variation while in root traits this value ranged from 43.04 to 76.81% indicating the existence of immense inherent variability among the genotypes. The contributions of genetic variance to phenotypic variance were only 32.4 and 43.04%, for above ground dry matter content and storage root dry yield per plant, respectively suggesting the important role of environment in the expression of these traits. High genotypic coefficients of variation along with high heritability and expected genetic advances were recorded for vine length, vine internode length, leaf area, above ground fresh and dry weights, number of storage root per plant, individual storage root weight, storage root fresh yield per plant. Thus, future improvement of the crop plant should exploit the genetic variability available in the germplasm collection.
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