Omics in Plant Breeding

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Omics can inform you if the steak you are about to enjoy will be tender and juicy or if your glass of wine will be sweet or dry before your first sip and can provide you a genetic map to growing the deepest-red tomato possible. The panomic arsenal of omic tools is enhancing the quality, taste, and nutritional composition of food crops; increasing agricultural production for food, feed, and energy; playing a significant role in crop protection; and significantly affecting agricultural economics.

Through the use of genomics, proteomics, transcriptomics, and metabolomics, the consistency and predictability in plant breeding have been improved, reducing the time and expense of producing better quality food crops that are resistant to stress but still exhibit a high nutritional value.

Omics has provided insights to the molecular mechanisms of insect resistance to pesticides, and the tolerance of plants to herbicides for better pest management. Linking genes to traits provides more scientific certainty leading to improved cultivars and understanding the mechanisms of insect and weed resistance.

Omics enables a systems biology approach toward understanding the complex interactions between genes, proteins, and metabolites within the resulting phenotype.

This integrated approach relies heavily on chemical analytical methods, bioinformatics, and computational analysis and many disciplines of biology, leading to crop protection and improvements. This in part would create rural and urban job opportunities; improve the quality of air, water, and soil; improve the healthfulness of food; and produce human health-related products in plants, microbes, and animals.

The genetic makeup of plants has been intentionally altered since the initial start of agriculture, estimated to have its beginnings — years ago. The evolution of crop domestication, which was essentially genetic manipulation, was based on selective breeding to produce better plants and animals and resulted in genetic modifications, although not recognized at the time.

In these early experiments, only the seeds from the best-looking plants were saved for the next planting cycle. Traits such as higher yields, pest and disease resistance, larger fruits or vegetables, and faster growth were commonly selected. Farm animals were also selectively bred for higher yields of milk and meat.

Broccoflower, another well-known genetic modification, is said to have more vitamins than either the broccoli or cauliflower parent. Products of plant genetic manipulations based on chemical treatment and radiation are also well-known commodities. When the seeds from seeded watermelons are treated with colchicine, a triploid seed is produced that is sterile, leading to no seeds in the fruit.

This may be convenient for eating, but it takes away one of the pleasures of eating watermelon—the seed-spitting contests. Chemicals such as sodium azide and ethyl methanesulfonate are also used to produce mutagenic plants. Over mutagenic plant varietals have been officially released between and A popular variety of red grapefruit was created via thermal neutron radiation at Brookhaven National Laboratory. These nonspecific genetic manipulations have a high potential to result in unintended and perhaps adverse compositional changes.

However, the successful products of these genetic manipulations have led to searches for more efficient and controllable ways to transfer genetic traits among plants while lowering risks of adverse mutations using precision genetic modifications. The world of omics is quickly becoming a vast field and impossible to cover properly in just one paper.

Omics can enable the further expansion of agricultural research in food, health, energy, chemical feedstock, and specialty chemicals while helping to preserve, enhance, and remediate the environment. Omic technologies focus on key traits of interest with precision. Omics can lead to enhancement of the nutritional properties of food for consumer benefit, such as a tomato that is high in lycopene, fruit with delayed ripening characteristics, and produce with potent antioxidant capabilities. Omics enables us to learn more about the genes and biochemical pathways that control such attributes for added health benefits, moving beyond basic nutrition and into the development of functional foods, for example, seed oils that do not produce trans-fats but rather contain heart healthy omega-3 fatty acids or cassava melons with increased protein content to help fight malnutrition.

Improvements in protein quality and content for better human and animal nutrition, increased vitamin and mineral levels to address nutrient deficiencies, and reduction of allergens and of antinutritional substances that diminish food quality can all be explored through omics. Foodomics, another omics term, encompasses studies of food and nutrition through integrated omic approaches. Omic technologies allow the visualization or monitoring of all of the changes that take place when the genetics, nutritional state, or environment of an organism is altered, 8 thus revealing an understanding of the alterations in plant metabolism resulting from environmental interactions.

Omics can provide insights into species that we thought we knew everything about. The central Asian wild apple was long thought to be the main progenitor of the domesticated apple. However, using genomic markers it has been found that the European crabapple made an unexpectedly large contribution to the genome of the domestic apple Malus domestica. Using omics, the genes responsible for proteins that confer or block the desired traits can be determined. Thus, a transgenic plant contains a gene or genes i. Transgenic crop varieties possess a variety of useful agronomic traits. Simplified description for making a transgenic plant that is both drought tolerant and high in nutrient content.

In agriculture, the bacteria Agrobacterium tumefaciens is often used as a vector to deliver genes into plants. The bacteria are parasites with the natural ability to transfer their genes into plants. In the s researchers developed more precise and controllable methods of genetic engineering to create plants with desirable traits. In , the U. The FlavrSavr was developed to have more flavor and to have a longer shelf life. These modified traits now account for the majority of soybeans, cotton, and corn grown in the United States.

The Human Genome Project revealed that there are about human genes, whereas A. GenBank is an annotated collection of publicly available DNA sequences that is frequently updated to provide the latest DNA sequence information. Genomics provides knowledge-based approaches for crop plant biotechnology, enabling precise, and controllable methods for molecular breeding and marker-assisted selection, accelerating the development of new crop varieties. However, time is not the only advantage as new attributes not imagined before the omics era can be introduced into plants, such as the production of biopharmaceuticals and industrial compounds.

By adding a specific gene or genes to a plant, or knocking down a gene with RNAi, the desirable phenotype can be produced more quickly than through traditional plant breeding. The complete set of RNA, also known as the transcriptome, is edited and becomes mRNA, which carries information to the ribosome, the protein factory of the cell, translating the message into protein.

Transcriptomics has been described as expression profiling, as it is a study of the expression levels of mRNAs in a given cell population. Unlike the genome, which is roughly fixed for a given cell line, with the exception of mutations, the transcriptome is dynamic as it is essentially a reflection of the genes that are actively expressed at any given time under various conditions.

Transcriptomics determines how the pattern of gene expression changes due to internal and external factors such as biotic and abiotic stress. Transcriptomics is a powerful tool for understanding biological systems. Transcriptomic techniques such as next-generation sequencing NGS provide capability for furthering the understanding of the functional elements of the genome.

Proteins are everywhere in plants and are responsible for many cell functions. Through proteomics it can be determined whether expression of mRNA results in protein synthesis to further illuminate gene function. The hundreds of thousands of distinct proteins in plants play key functional roles for the texture, yield, flavor, and nutritional value of virtually all food products.

Comparative proteomics can determine the molecular mechanisms for susceptibility or resistance to enhance resistance traits. Protein patterns have been used to study the foam stabilization of Champagne and sparkling wines and the effect of fungal pathogens on grapes and wine authentication and to determine if grapes were indeed grown in the appropriate appellation. Translational plant proteomics is an expansion of proteomics from expression to functional, structural, and finally the translation and manifestation of desired traits.

Through translational proteomics the outcomes of proteomics for food authenticity, food security and safety, energy sustainability, human health, increased economic values, and environmental stewardship can be applied. Metabolomics is the study of chemical processes providing a linkage between genotypes and phenotypes. The metabolome is dynamic and subject to environmental and internal conditions. The simultaneous monitoring of metabolic networks enables the association of changes resulting from biotic or abiotic stress, which can aid in the development of improved crop varieties and a basic understanding of systems biology.

Monitoring changes in metabolite patterns can lead to quality improvements for nutrition and plant health. Metabolomics can provide an indication of the equivalency or compositional similarity between conventional and altered plants and determine if undesirable changes have occurred in the overall metabolite composition. Metabolic profiling through mass spectrometry MS and nuclear magnetic resonance NMR analyses have been used to ascertain metabolic responses to herbicides and investigate metabolic regulation and metabolite changes related to environmental conditions of light, temperature, humidity, soil type, salinity, fertilizers, pests and pesticides, and genetic perturbations.

The field of omics and particularly proteomics has been driven by major improvements in MS instrumentation, advanced data analysis, bioinformatics, and rapid analytical methods such as DNA microarrays to screen thousands of samples within a short time. High-resolution NMR spectroscopy has also been applied to omic studies. However, complex spectra are often obtained, and it is typically not as sensitive as MS.

An in-depth review of NMR theory and its applications to omics has been published.


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The two major analytical proteomic approaches are termed top-down and bottom-up. In a top-down approach intact proteins are analyzed by MS. The masses of the resulting peptides are compared with theoretical peptide masses. Matrix-assisted laser desorption ionization MALDI imaging enables the visualization of the spatial distribution of proteins and metabolites.

These types of proteomic studies further the understanding of the genetic regulation of fruit ripening and the changes that occur during storage to identify key parameters for maintaining nutrition upon storage and to prevent spoilage. Although wines are not known for their protein content, proteins are important factors in the quality of individual wines.

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Plant OMICS and Crop Breeding

In addition to the effect of wine proteins on foaming, important for sparkling wines, they also influence astringency, color stability, and other factors leading to the overall quality of the wine. Two-dimensional electrophoresis 2-DE with immunochemical and tandem MS detection can highlight differences in protein profiles of wine from healthy and diseased grapes. Advances in analytical methods will further advance the applications of omics. Second-generation proteomics employs stable isotope labeling of amino acids in cell culture SILAC and other quantitative methods for high-throughput measurement of protein dynamics and interactions rather than just identification by MS.

Third-generation techniques look at and compare entire proteomics over time and space, which requires large-capacity data analysis.

Plant OMICS and Crop Breeding - CRC Press Book

Accelerator MS has proven useful for metabolic profiling in humans, and it is anticipated that it will play an increasing role in plant metabolomics. Herbicides typically work by binding to plant enzymes to inhibit their action.

Omics Technologies and Crop Improvement

Crops modified to make different proteins or target sites that are not inhibited by a particular chemical can provide herbicide resistance to the crop, leaving weeds vulnerable. For example, plants that are resistant to glyphosate have been engineered to express a different protein that is not inhibited by the herbicide.

The planting of herbicide -resistant HT soybeans, cotton, and corn has dramatically risen in the United States since when they were first introduced. Frontiers in plant science, 12 september Proteome analysisProteome analysis Frontiers in plant science, 12 september Completion of the drought regime RAC tolerant had the most number of protein changes with Excalibur tolerant intermediate and Kukri intolerant; the least.

RAC has the highest capacity of the three cultivars for a cellular protein response to drought. Down regulation of proteins involved in photosynthesis and the Calvin cycle, consistent with avoidance of ROS generation in all three cultivars was observed. This highlights the importance of proteomics as a complementary tool for identifying candidate genes in abiotic stress tolerance in cereals. Protein changes during drought stress Why Phenomics?

Plant OMICS and Crop Breeding

Maize leaf, laser confocal microscopy reveals a clear distinction between high activity of photosystem II in mesophyll cells pink fluorescence and low activity in bundle sheath cells purple —a distinction typical of C4 plants. Phenomics provide snapshots of cellular structure — Required to understand the contrasting cellular features among C3 and C4 plants. IRRI- screening rice varieties with a cellular architecture best suited to house C4 enzyme assembly and those with muted photosystem II in bundle sheath cells.

Chlorophyll fluorescence, a measure of photosynthesis, in Arabidopsis seedlings and a wheat ear inset using a car engine dynamometer The emerging discipline of phenomics will help foment the next green revolution. Inductively coupled plasma mass spectrometry SummarySummary Integrated data set for quick and precise breeding Finkel You just clipped your first slide!

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