Physiological and Genetic Responses of Resistant and Susceptible Spring Wheat in Grain-Filling Stage of Development to Water Limitation - Essay Prowess

Physiological and Genetic Responses of Resistant and Susceptible Spring Wheat in Grain-Filling Stage of Development to Water Limitation

Physiological and Genetic Responses of Resistant and Susceptible Spring Wheat in Grain-Filling Stage of Development to Water Limitation

Physiological and Genetic Responses of Resistant and Susceptible Spring Wheat in Grain-Filling Stage of Development to Water Limitation

Introduction

Agriculture is one economic activity that most economic across the international borders upon which the society heavily relies. There are two basic segments on farming namely crop farming and animal farming. In a bid to ensure that food security is there in the world economies, attempts have been made to grow and nurture crop production activities and make agriculture relevant. Amongst these food crops includes wheat. Wheat is one amongst the most consumed wheat grains. It is cultivated from a worldwide context and is also traded either as raw material or even flour internationally or domestically. Arguably, a series of research has been conducted regarding the elements of growth of this crop. Most importantly, it is considered to grow in areas that do not receive consistent heavy rainfall. However, from a professional understanding, the there are aspects attributed to the crop that makes it suitable for food security especially in the context of its ability to contain the challenges it faces as a result of the changes in the climate (Oono et.al, 2013). The research attempts to take a professional approach in detailing the challenges faced and the potentiality of the crop regarding the natural issues such as drought.

Importance of wheat to world agriculture

Besides aiming at the increased level of income and improved life status, the world agriculture has focused on agriculture in the aspect of food security. Accordingly, the wheat crop is at the center of the agriculture’s list of necessary food crops that are meant to ensure that there is food security. Arguably, the wheat crop is considered to be a sufficient crop in providing food for human consumption and indirectly assist in supplementing food for the animals. From a historical perspective, the wheat grain has remained at the top of the list amongst the foods that are used to provide humans to people. An approximated timeline of about 8, 000 years ago. Further, the British Museum, one could see the actual loaves of bread that were baked in Egypt some 5, 000 years past. 

Growing and developing wheat under water limiting conditions

Generating a well-coordinated relationship between water and growth of wheat is essential for the management of this crop. Arguably, the wheat is grown under irrigation conditions in that it plays the role in the limitation of the entire water resource that is used to facilitate the growth of the crop. Particularly, the approach is used either in the highlands cross to the equator and even away from the equator (Claeys & Inzé, 2013). Further, in the subtropical areas, the crop is also grown under these limitation water conditions. The relationship here stipulates the level of sensitivity to water deficit occurs especially in the context of the winter wheat. The difference is attributed to the conditioning of the water resource. However, the most important aspect of this conditioning of the water resource for the wheat crop is that it facilitates its capacity to adjust the growth capacity. Particularly, it enables the plans to grow better under water deficit conditions (Claeys & Inzé, 2013). 

Besides the argument that the wheat crop, at times in the development stage requires growing in rain deficit condition, there is a stage where the crops attempt to use their adaptations when they need water. For instance, there are different categories of wheat. In this case, the spring wheat, for example, is adapted in a manner that it can generate water in the water limitation eras. For instance, they have a very active rooting system. From a statistical perspective, the depth of the root system is approximately 0.9 meters. It also has an optimal or maximum 1.2 to 1.5 meters, as well as, a spread of approximately 0.15 to 0.25 meters in all the direction from the mainstream plant (Fischer, 2011). That enables it to adapt to the limitation water seasons especially during the re-productivity stage.

Background on the essentiality of the drought tolerance genes

The wheat crop is adapted to the drought conditions even as it undergoes its development. Particularly, the dehydrin genes manifested in the wheat crop as expected to serve the role of enhancing tolerance of the crops to some harsh emergent conditions (Nezhadahmadi et.al, 2013). Plant stress is closely associated with the fact that the plant is genetically altered in such a manner that the plant’s equilibrium system can manage the water deficiency stress (Hassan et.al, 2013). These genes that are associated with assisting the wheat crop to cope with the drought conditions are said to be regulated at once especially when the drought conditions emerge. As such, they are produced to respond to the signal transduction, the stress response and assist the plant in withstanding the drought stress (Nezhadahmadi et.al, 2013). Therefore, the alteration of the genetic expression is essential in the context that the plants can easily prepare for the water deficit conditions.

How plants respond to water limitation genetically.

As stipulated above, the genes responsible for protecting the plants from adverse situations of water limitations. Initially, the genes are said to emerge especially when the conditions of water limitations become severe. However, there is an impact that the changes in the genetic formulation of the plants. As such, the plants tend to respond to the genetic modulation. For instance, it affects the photosynthesis process (Guóth et.al, 2009). Hence, growth is retarded. Precisely, the water stress conditions result in the closing of the stomata. Therefore, the rate in which the process of transpiration takes place is also affected. In most cases, there is permanent wilting if the other adaptations that are designed to help the plant cope with the situation are do not suffice. Hence, the runaway xylem cavitation emerge. They are closely followed by desiccation leading to the death of the plant. 

The drought conditions, from a general perspective, always have adverse implications on the magnitude in which the output of the plant is concerned (Mahpara et.al, 2014). Usually, the first thing that occurs the quality of output is depleted. For instance, the quality of the wheat crop product is assessed through the biomass weight, the length of the spikes, the weight of the very spikes and the weight, as well as, the number of seeds (Borrás et.al, 2004). However, drought minimizes the quality of the wheat crop products in each of these aspects. Accordingly, there is a likelihood that these crop qualities are depleted in such a manner that the weight, size, and the biomass value of the output is not of enough quality as expected during the normal harvesting conditions (Sivamani et.al, 2000).

Limitations of recent studies on Drought Stress

Recent studies regarding the issue of drought stress have been facing a series of challenges especially in the context of the reliability of the information provided. Most importantly, the research attempts have been using commonly understood perspectives regarding the possible impacts of drought to the quality of the produce (Fischer, 2011). Most research assumes or neglects the details that ought to be provided in a bid to understand the particular adaptations that the plants have in line with the genetics and genomics. Quite often, there are signs of studies being too ambitious, yet not permitted any effective dissection of the cases of drought response to cases of drought (Reddy et.al, 2004). As such, the facts and concepts regarding the adaptation of the crop to the climate have been further complicated. The complication occurs in such a manner that these research have only conducted studies on some scenarios and regime leaving out the others. Also, the research shows the massive absence of genome sequence, as well as, the poor genomics. Therefore, there is a research gap that ought to be filled in a bid to stipulate reliable agricultural understanding of all the elements associated with the growth and development of the wheat crop.

Literature Review

Introduction

RNA sequencing is a very common term in the context of food production and crop farming in the agricultural sector. Most importantly, it refers to the most effective approach or revolutionary tool responsible for an increase in productivity. Usually, it is an approach that assists in the evaluation of any changing cellular transcriptome (Duan et.al, 2012). It embraces the attempts to cross-hybrid the low-value genes with the high-value genes. Concerning the changes in the state of the crop genes. Research stipulates that sequencing in plants is associated with the replacement of the genetic expression of a plant from the recent generation of the forthcoming generation (Liu et.al, 2015). Usually, the professional RNA-sequence is a tool that assists in the discovery and profiling of the RNAs.  

Background information

There is rapid growth in the population in the world. Concurrently, there is an increase in the level of demand especially in the context that increases in population in such as scale that is not equitable to the food produced lead to increased food insecurity. Arguably, even to date, the sufficient levels of food production regardless of the use of the nitrogenous fertilizers (Ruuska et.al, 2008). As such, there is an emerging need for the plants to support or promote bacteria. Arguably, the PGPB or Plant Growth Promoting Bacteria could be an alternative to the elevation of the nitrogenous application efficiency in the essential food crops such as wheat (Ruuska et.al, 2008). From a professional point of understanding, the Azospirillum Brasilense is considered an excellent model in the process of investigating the molecular platform of the relative Plant-PGPB interaction. The interaction involves the movement in plant NUE.

The alternative practice to improve the value of NUE is supposed to engage the use of the plant growth promoting bacteria. The rationale for making this proposition is that the bacteria manage to elevate the root-system development, as well as, improve the rate in which the nutrients are acquired (Keulen, 1975). Most likely, the Azospiilla is one amongst preferable genera. The wheat food crop is one amongst the oldest food crop species. From a statistical perspective, there are approximately 630 million tons per year. Hence, the food crop manages to feed at least 35 to 40 percent of the global population. The modern biotechnology has supported substantial and reliable global efforts associated with wheat-breading. Therefore, there has been sufficiency in the magnitude through which the crop is yielding. However, it is imperative to denote that there exists a research gap as far as the application of the PGBP is concerned.

The research, accordingly, calls for a dual- RNA sequencing for the wheat products. Most importantly, the sequencing is influenced by the idea of increased fathoming of the wheat crop. As such, there is a need to establish a brasilense gene expression. Conducting this exercise could result in the provision of insights such as the molecular mechanisms associated with the host response (Reddy et.al, 2004). Besides, it provides essential research insights in the context of strategies associated with the bacterial colonization approaches. Finally, it provides an overview of the approach that is necessary to elevate the productivity of the plant.

As a result of the series of research conducted in relations to increase the level of yields, it is clear that the generic developments at times improve the yield and quality of the yield of the wheat crop. For instance, in the context of improving the growth of the wheat seedling especially in the context of the colonization of the Azospirillum Brasilense, it is clear that a series of adjustments were carried out in the non-inoculated wheat seedlings. Research associated with the RNA sequential of the wheat plant root by the use of the A. Brasilense bacteria demonstrated optimal and remarkable change especially in the context of the productivity. From a more complex perspective, the changes are first identified in the plant genes that take part in the process of transportation. That is reflected in the context that the plant manages to take up the nutrients including the important nitrogen gas (RNA, 2016). Further, the series of approaches tend to demonstrate the DNA replication, as well as, the cell division that is as a result of the presence or introduction of the bacteria to the plant’s generic system.

The alterations in the gene characterization link directly with the expected improvement of the growth of the wheat seedlings. Remember, the cases of drought are highly associated with depleted quality of the seeds produced by the wheat crop. Therefore, the addition of the bacteria to improve the quality of the products such as manipulating the wheat genes. From a professional point of understanding, the changes in the genetic character traits mean that there emerges the development of fresh cultivars. That ultimately means that there will be improved productivity. 

There are various ways through which the genetic modulation or modification of the wheat plants could lead to an alternative outcome when it comes to productivity. In this context, the adjustments are being made to the root part of the plant. Particularly, the adjustments in the plants through the alteration of the plant’s DNA through the introduction of the bacteria. However, out of the RNA-sequencing, the root biomass is increased (RNA, 2016). Particularly, the sequencing improves the nutrient acquisition by the plant hence increases the root surface area. That makes it possible for the nutrient transporters to be more efficient. Also, the hypothesis is improved, and there are a series of adjustments made to the root structure. First, the enhancement or root surface area. Further, there is an increase in the DNA synthesis in root cells, as well as, the regulation of the ESTs encoding cell regulators. The wide root network, therefore, assists in improving the rate of absorption of the nutrients and water even during the water resistance conditions.

Physiological effects

The assessment process of how effective an RNA sequencing is conducted by analyzing the physiological characteristics of the plants. In this case, the study provides an overview of the few elements regarding the introduction of a foreign substance, bacteria into the plant’s root system. In consideration of the fact that the assessment intends to evaluate the ability of the wheat plant to adjust to the changes associated with drought and water limitation condition, the sequencing approach is an excellent one (Ruuska et.al, 2008). Usually, the root system of any plant is essential in the process of absorption of water and nutrients. In most cases, the ability to absorb nutrient goes shoulder to shoulder with the ability to absorb water. Accordingly, the changes that could be conducted on the root system is most relevant here.

From a physiological perspective, the wheat plant requires adjustments in the root system for it to endure the harsh conditions that result from drought. There are limited water and nutrient resources. Particularly, the manner in which the plants increases the root system regarding the surface areas is very essential. The RNA sequencing, therefore, resulted in the improvement of the root surface area (Ruuska et.al, 2008). The network increases to an extent that the plant can easily absorb the water resources from the soil. During the water limitation durations, the plant attempts to absorb the water resource especially in the context of accessing water from a wide network.

Arguably, there are deeper adaptations that could be associated with the sequencing process and the dry spell. First, the dry spells that are characterized by water limitation tend to be saline in nature since there is little hydroxyl to diffuse and reduce the salinity. Therefore, the salinity condition is likely to be hazardous to the plant’s growth. That means that the scarcity of water and the condition where the salinity conditions are inappropriate means that the root system has to adapt a change that will assist it to protect the plant from the adverse effects of the related drought conditions. Wheat that is colonized through the process of sequencing is structured in such a manner that they can hold the stress resultant from the saline conditions (Yang et.al, 2003). Therefore, the root system that is inoculated get relieved from the osmotic stress and become tolerant to the saline conditions, as well as, water limitation tolerance (Hsiao et.al, 1997).

            Therefore, the sequencing process makes it possible for the wheat plant to adapt to the drought conditions genetically. The genes introduced into the root system, particularly, are essential in making the plant tolerant to stress (Ruuska et.al, 2008). Further, the plant also demonstrates the capacity to increase the amount and rate of absorption of the water and nutrient resources. Accordingly, the quality of output is improved as opposed to that which could have been expected under the normal, not colonized and non-inoculated conditions of the plant. The quality of the produce is analyzed concerning the weight and number of seeds harvested. Alternatively, the health of the plants is determined by the well-structured root system and the long and weighted spikes.

Objective and Objective significance

Transcriptomic analysis for spikes and flag leaf    

First, the spike is considered to be the imperative element of the foundation for the grain yield. Despite the fact that the genetic changes may not be clear in the cases of sequencing, it is clear that the locus in this aspects refers to the productivity of the different categories of wheat plant. There are several classification of the wheat product. In this case, the chosen varieties for analysis include the Alpowa and Idaho spring wheat varieties. A singular analysis will be conducted on both varieties.  The central aim of the study is to attempt and analyze the essentiality of the essential elements associated with the different varieties of the spring wheat crop.    

The Alpowa variety is known for its resistance to the drought conditions. There are a set of character traits and properties that result in the adaptation. For instance, the in the context of the transcriptomic analysis, it is essential to denote that the spikes and the flag leaf are essential and are subject to analysis. Besides, the research intends to conduct an analysis that will depict the reason behind the Idaho susceptible property especially considering the adversity of the drought conditions. From an analytical perspective, it is clear that this is a comparative approach between the two varieties of spring wheat.

Secondly, the study will conduct a critical analysis of the physiological effects of the two varieties. Each variety is subject to reflecting the outcomes of the poor or strong adaptability to the drought or harsh environmental conditions. Usually, the physiological effects are reflected in the character traits that the spikes and the flag leaf parts of the plant varieties have. Arguably, the physiological outcomes or characteristics are considered to be the most reliable factors that could be used to determine the best approach if there is a need to engage in any form of RNA sequencing in a bid to improve the ability to withstand the harsh conditions such as water limitation (Xue et.al, 2006).

Method Objective

The RNA extraction and synthesis of DNA

The process of RNA extraction is a procedural one. It requires the use of a series of reagents. However, the RNA extraction commonly embraces the use of the TRIzol or even the equivalent TRI. It is an approach that considers the extraction of the RNA from the cells. This inference is based on the professional proposition by Chomczynski (Ramalho et.al, 2004). Despite the fact that the process is time-consuming. It results in the extraction of more RNA than most other approaches of extracting it. Below is an overview of how the extraction and establishment of the DNA ought to be.

The regent in this protocol is the TRIzol reagent. Approximately 0.8 M of sodium citrate or 1.2 < NaCl is used. Isopropanol, chloroform, 75 percent of the EtOH within the DEP H2O are used. The process contains a series of steps. The first step is the cell lysis (Ramalho et.al, 2004). In this step, it is imperative to denote that the process takes several minutes. It is also imperative factor out that the RNA is stable in the trizol considering that it deactivates the RNases. During this phase, one can leave the sample in the freezer.

The second step is that of phase separation. The step takes approximately 15 to 45 minutes. However, that depends on the sample number and also whether there is a feasibility that an additional chloroform wash is deemed necessary. Usually, the step incorporates the use of the centrifuge. For instance, in case, the centrifuge does not exemplify sufficiency, the interphase that contains the DNA could remain cloudlike. That implies that it could be poorly compacted. The third step is the RNA precipitation and wash. In this case, the step takes approximately 20 to 40 minutes. However, that depends on the size of the sample. Here a series of additives and reagents are used. It is crucial to denote that the approach is better than alternative RNeasy especially because we are dealing with smaller amounts of RNA (Ramalho et.al, 2004). The choice minimizes the chances of organic solvent contamination leading to faulty results.     

The other step is that of RNA wash. The process requires approximately 15 to 30 minutes. Similarly, the process duration is determined by the number of samples being assessed. The final process, in this case, is that of re-dissolving the RNA.    

DNA quantification

Similarly, the quantification of DNA could be conducted differently. The DNAs that are extracted and sampled are now run on a 0.8 percent agarose minigel that contains approximately 0.5 µg / ml of the ethidium bromide. The samples, then, are run next to the differentiated DNA standards. These stands are recorded with regards to the already known concentrations. The levels are identified through the molecular mass markets. In a bid to sustain a stable and constant background of the gel staining, it is essential to incorporate approximately 0.5 µg / ml of the ethidium bromide within the running buffer. After that, one can run the ultraviolet light to get the photograph of the gel. It is after this that one can now compare the fluorescence intensities. Then, it becomes possible to make appropriate estimates of the DNA concentrations.

In a bid to quantitate the mixtures of DNA regarding the fragments and the sizes, it is essential that one makes spot samples on a 1 percent agarose slab gel. The slab gel contains the very 0.5 µg / ml of the ethidium bromide. The gel is supposed to stand for some hours at the normal room temperature. That allows for the minute contaminating molecules to exit. Finally, the use of the ultraviolet light is applied in taking the photograph of the gel. That way, it is easy to quantitate the DNA.

RNA-Seq library formation

There are a series of steps associated with the RNA sequencing library formation. The first one is that of designing the experiment. In that case, one sets up the experiment in a bid to address the questions on sequencing. Secondly, the RNA is prepared. Here the most appropriate way to understand the undertakings is by isolating and then purifying the RNA input elements (Kiefer et.al, 2007). Then, the libraries are prepared. Arguably, in this step, the RNA undergoes conversion to being CDNA. Here the sequencing adapters are used. The CDNA is sequenced by the use of a sequencing platform (Khodarev et.al, 2002). Then the ultimate results are analyzed as a result of the short-read sequences.

Hi-Seq Sequencing

Notably, the DNA technologies, as well as, the expression analysis operate the HiSeq2500 amongst others (DNA Technologies Core, 2016). The sequencing is essential since it results in synthesized data that is crucial in the context of ensuring that the information acquired is useful, for instance, in depicting the characteristic and adaptation difference two varieties of spring wheat as required by the research. In the context of the illumine library preparations, it is essential to understand that the approach is procedural (DNA Technologies Core, 2016). It involves a set of experimental manipulations such as data analysis, as well as, instrument runs. Therefore, in the context of conducting a professional sequencing, there is a need to create a sequencing library, seeding and finally the establishment of the flow cell regarding the illumine C-bot. two important concepts, in this case, are synthesis and bioinformatics.

Quality filtering of sequences

In a bid to establish the value of the sequencing activities, it is essential to sort and determine the best. Considerably, the process is used to single out elements such as the DNA and the RNA in a bid to determine the way to alter and modify them for the better. Usually, the next-generation sequencing machinery including the illumine is said to have a feasibility of error in line with each base that is indicated by the quality scores that whose acronym is (Q). According to this uncertainty, it is imperative to engage is solemn filtering of the sequencing. The process of engaging in the quality filtering Q30 is conducted using the fast filter command. The most recommended one is the expected error filtering.    

Sequence alignments

Despite the fact that there are only two crop varieties that are subject to analysis, it is imperative to ascertain that there are a variety of ways to input and align the sequence of the CDNA (Fischer, 2011). These include the use of developing sets that are closely related to each other regarding the spices, the same species or even different species. However, considering that the two varieties of crops belong to the spring wheat type of wheat, the most appropriate method to use is the unique gene alignment approach.

Differential Gene Expression Analysis

In a bid to identify, understand and differentiate the differentially expressed genes in the two crop varieties subject to research, it is imperative to denote that the use of the differential display techniques is essential. The most applicable methods of expressional analysis, in this case, could be the northern blot analysis and the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) (Camilios-Neto et.al, 2014).

Cufflinks program

The RNA-Seq library is developed from fragments of the CDNA raging between the 200 to 400 bp in the length. Therefore, the use of the Cufflinks is essential and reliable (Trapnell et.al, 2012). The program is associated with possessing a clever modeling, as well as, interface. The only challenge associated with the program is that it is quite complicated.

Statistical Analysis by using R program and R packages

The statistical data collected and that would require the analysis of recording could use the R-program and the R-packages. For instance, these program and packages are essential in fostering successful Gene extraction analysis and the functional analysis (Finotello et.al, 2015). The collected data is sorted out in the sequence alignment approach of choice.

Expected results      

In line with the past research, cases of sequencing have resulted in modification of the physiology traits of the plants (Xue et.al, 2006). In this case, the expected results ought to provide insights that are in line with the above proposition. Hence, the statistical inferences provided by the research are likely to portray a genetic difference between the Alpowa and Idaho varieties of spring wheat. As such, it is possible that Alpowa’s biomass weight, the lengths, and weights of the spikes and seeds are often of greater value than those of Idaho.     

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