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= Plant Genetic Variation Under Domestication =

Traits that are being genetically improved
There are many challenges facing farmers who are trying to successfully grow crop plants. These challenges include but are not limited to climate change, pest incurrence ,soil salinity, drought, and irregular sunlight exposure. Researchers hypothesize that with appropriate genetic manipulation, an increase in photosynthesis, at the leaf level, could then be integrated into an increase in carbon gain at the canopy level and thus an increase in overall crop yield.

As mentioned above, drought is one of the most serious challenges facing farmers today. With shifting climates comes shifting weather patterns, meaning that regions that could traditionally rely on a substantial amount of precipitation were, quite literally, left out to dry. In light of these conditions, drought resistance in major crop plants has become a clear priority. One method for improving crop plant drought resistance is to find plants that have some kind of natural drought resistance, i.e. the Bambara Groundnut mentioned below, determining the genetic basis to this resistance, and then transferring them to otherwise vulnerable crop plants. One of the most vulnerable crop plants in terms of drought is rice, a crop commonly grown in a liquid medium. (Jiban, Mitra 2001) was able to document one such successful genetic transmission. Barley hva1 gene, responsible for late embryogenesis abundant (LEA) proteins, has been transferred to rice to produce drought-resistant transgenetics.

Hand in hand with drought resistance comes a plant's root orientation, or put another way its' Root System Architecture (RSA). A root orientation that maximizes water retention and nutrient uptake will mitigate many abiotic factors that a plant may be facing. It is hoped to accomplish this by using a series of techniques that have built upon computer tomography, which enables temporally continuous, 3D monitoring of roots, soil material and water content at high resolution (in the 100 μm range). There must be a continued focus on the efficient usage of available water on a planet that is expected to have a population in excess of nine-billion people by 2050.

One final, specific area of genetic improvement is focused on the crop plant's uptake and utilization of soil born Potassium, (K). Potassium is an essential element for crop plants to bring in as it has wide reaching effects not only on a plant's development and continued growth, but also on its' yield and overall quality. A plant's ability o effectively uptake Potassium and utilize it efficiently is known as its' Potassium Utilization Efficiency (KUE). It has been suggested that first optimizing plant root architecture and root K uptake activity may effectively improve plant KUE. Second, plant KUE is regulated by K transport and translocation in plant tissues and organs, which may also provide possibility for improvement of plant KUE. Finally, selection of the important natural variations in crops associated with high KUE may also give valuable information for genetic improvement of crops.

Crop plants that are being genetically improved
It is an incredibly important crop plant area that is often overlooked and taken for granted despite the fact that the Cereals, rice wheat and barley, make up a huge amount of the global diet across all demographic and social scales. These cereal crop plants are all autogamous, self- fertilizing, meaning that the generation of novel allele combinations is not only extremely difficult, but also very unlikely. In order to combat this issue the researchers suggest an "Island Model of Genomic Selection" (GS). As its' name suggests, this form of modeling breaks the single large population of cereal crop plants down into several smaller subpopulations which can receive "migrants" from the other subpopulations. This breakup of populations into smaller units, hence the island name, allows for new genetic combinations to be made. Finally this "island-model" can be maximized in efficiency by using Evolutionary Algorithms (EA's) which help researchers to mathematically predict which subpopulations will be the most effective.

The Bambara Groundnut, is an extremely durable crop plant that, like many underutilized crops, has up to now received very little attention in either an agricultural or a genetic sense. The Bambara Groundnut is drought resistant and is known to be able to grow in almost any soil conditions, no matter how impoverished an area may be. Using new genomic and transcriptomic approaches is allowing researchers to not only make improvements in this relatively small-scale crop but to also make the same improvements in the large-scale crop plants while ultimately broadening the global food-supply. The reduction in cost, and wide availability of both microarray technology and Next Generation Sequencing (NGS) have made it possible to analyze underutilized crops, like the groundnut, at at genome-wide level (Khan et. al. 2016).Not overlooking particular crops that don't appear to hold any value outside of the developing world will be key to not only overall crop improvement, but also to reducing the global dependency on only a few crop plants, which holds many intrinsic dangers to the global population's food supply.

Challenges facing genetic improvement
The semi-arid tropics, ranging from parts of North and South Africa,Asia especially in the South Pacific, all the way to Australia are notorious for being both economically destitute and agriculturally difficult to cultivate and farm effectively. Barriers include everything from lack of rainfall and diseases, to economic isolation and environmental irresponsibility. (Sharma and Ortiz 2000) are primarily interested in the continued efforts, of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Mandated crops of ICRISAT, including groundnut, pigeonpea, chickpea, sorghum and pearl millet, are the main staple foods for nearly one billion people in the semi-arid tropics. Where possible, some wild plant breeds are being used for transferring genes to cultivated genotypes or species by interspecific hybridization involving modern methods of embryo rescue and tissue culture. One example of early success has been work involving the very detrimental Peanut Clump Virus (PCV). Transgenetic plants containing the coat protein gene for Peanut Clump Virus have been produced successfully offering the plant protection against it, and work with other coat proteins and virus polymerases is ongoing. It is believed that the widespread implementation of new biotechnological approaches will finally help bring relief to one of the most densely populated and food poor regions on the planet.

Once again the food security of the Pacific Island Countries (PICs) is called into question, with special focus being paid to the economically poor regions ability to agronomically deal with the ever greater effects of climate change. The fact that the region in question is made up largely of a chain of islands is of critical importance. Island geography naturally has deficiencies in geographical area in which to farm, and irresponsible use of the land in this poor region is rampant. It has been predicted that there are only two remaining options for meeting the needs of the ever increasing Pacific Island Countries’ (PIC) populations: 1.) increase agricultural production or 2.) increase food importation. The latter of course runs into the issues of availability and economic feasibility, leaving only the first option as a viable means to solve the region's food crisis. Unfortunately there hasn't been a large degree of effort put forth to achieve option one. It is much easier to misuse the limited resources remaining, as compared with solving the problem at its' core.

Working with wild plants to improve domestics
Many of the differences listed above actually make wild plants the perfect vehicle, on a genetic level, to hybridize with existing crop plants to produce a wide array of favorable outcomes. These outcomes can range from newly formed perennials to crop plants of a higher yield, growth rate, and overall resistance to outside pressures. It is important to remember that these changes may take some length of time, indeed decades to achieve. In a stroke of Irony one of the greatest early successes wasn't with a crop plant at all, but rather a hybrid grass variant known as Kernza. Over the course of nearly three decades, work was done on an attempted hybridization between an already domesticated grass strain, and several of its wild relatives. While the domesticated strain as was more uniform, the wild strains where larger and faster propagating. In a painstaking process the researchers would select only the hybrid progeny which not only grew the best, but also showed the most successful hybrid inclusion. After the afore mentioned length of time the Kernza was born, bearing the uniform orientation and linearly vertical root system, along with the increased size and rate of propagation rate. Although it was for a non-crop grass plant, the Kernza example is just one of many exemplifying the genetic power behind this form of human-mediated evolution.

Work has also has been focusing on improving domestic crops through the use of what are refered to as Crop Wild Relatives (CWR). The amount and depth of genetic material available in CWR's is more immense than originally believed, and the range of plants involved, both wild and domestic, is ever expanding. Through the use of new biotechnological tools such as genome editing, cisgenesis/intragenesis, the transfer of genes between crossable donor species including hybrids, and other omic approaches.

Sources Used:

1.)Tassel, David van, and Lee DeHann. “Wild plants to the rescue: efforts to domesticate new, high-Yield, perennial grain crops require patience and persistence--but such plants could transform Agriculture .” American Scientist, 2013, pp. 218–226. Opposing viewpoints in context , doi:0003-0996. A very interesting review, which covers the process of hybridizing wild perennials with domesticated annuals in order to produce new crop perennials. Uses their work with the Kernza plant line as an example.

2.) Morrell, Peter, et al. “Plant Domestication, a Unique Opportunity to Identify the Genetic Basis of Adaptation.” National Academy of Sciences, 2007. JSTOR journals , doi:10.1073/pnas.0700643104. A review, that aims to answer the question: Are phenotypic changes driven by artificial means an apt analogy to adaptation in nature? Also provides an explanation of Top-Down versus Bottom-Up sequencing for the detection of adaptive genes in plants.

3.) Yabe, Shion, et al. “Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.” PLOS ONE, pp. 1–21. Academic Search Complete, doi:10.1371/journal.pone.0153945 . An interesting and comprehensive summary of the methods employed to genetically modify rice crops. Rice is a staple food crop and has become a reference of monocot plant material for functional genomic research. With the availability of high quality rice genome sequences, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis.

4.) Zhang, H, et al. “Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement.” Evolutionary Applications , 2016, pp. 5–24. Medline, doi:10.1111/eva.12434. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, the authors highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species.

5.) Kilian, B, et al. “Accessing genetic diversity for crop improvement.” Current Opinion in Plant Biology, 2010, pp. 167–173. ScienceDirect, doi:0.1016/j.pbi.2010.01.004. A relatively recent study covering the new advancements in work with crop plant germplasms, specifically techniques that have greatly improved their accuracy.Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, and bananas.

6.) Dillion, Sally L, et al. “Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae).” Annals of Botany, 2007, pp. 975–989. JSTOR journals , doi:03057364 10958290. Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe, and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programs to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species.

7.) Iran, Sharma K, and Rodomiro Ortiz. “Program for the Application of Genetic Transformation for Crop Improvement in the Semi-Arid Tropics.” In Vitro Cellular & Developmental Biology, 2000, pp. 83–92. JSTOR journals , doi:10545476 14752689. The semi-arid tropics are characterized by unpredictable weather, limited and erratic rainfall and nutrient-poor soils and suffer from a host of agricultural constraints. Several diseases, insect pests and drought affect crop productivity. Developing stress-resistant crops has been a worthwhile activity of the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Mandated crops of ICRISAT, including groundnut, pigeonpea, chickpea, sorghum and pearl millet, are the main staple foods for nearly one billion people in the semi-arid tropics. Genetic transformation provides a complementary means for the genetic betterment of the genome of these crops.

8.)Hayes, Patrick M, et al. “Barley genetic variation: implications for crop improvement.” Briefings in Functional Genomics , July 2014, pp. 341–350. Academic Search Complete , doi:2041-2649. Genetic variation is crucial for successful barley improvement. Genomic technologies are improving dramatically and are providing access to the genetic diversity within this important crop species. Diverse collections of barley germplasm are being assembled and mined via genome-wide association studies and the identified variation can be linked to the barley sequence assembly. Introgression of favorable alleles via marker-assisted selection is now faster and more efficient due to the availability of single nucleotide polymorphism platforms. High-throughput genotyping is also making genomic selection an essential tool in modern barley breeding.

9.) Mitra, Jiban. “Genetics and genetic improvement of drought resistance in crop plants.” Current Science , 2001, pp. 758–763. JSTOR journals , doi:edsjsr.24105661. Drought limits the agricultural production by preventing the crop plants from expressing their full genetic potential. Three mechanisms, namely drought escape, drought avoidance and drought tolerance are involved in drought resistance. Various morphological, physiological and biochemical characters confer drought resistance. This review covers these different resistances in detail.

10.) Horton, Peter . “Prospects for crop improvement through the genetic manipulation of photosynthesis: morphological and biochemical aspects of light capture.” Journal of Experimental Botany , 2000, pp. 475–485. JSTOR journals , doi:00220957 14602431. In this review the important interaction between photosynthetic capacity, acclimation to the light environment, nitrogen accumulation and canopy architecture are discussed. The possibility of genetic intervention to increase both biomass accumulation, and improve nitrogen economy are each considered. Finally, the numerous procedures for genetic manipulation of light harvesting are also discussed, with a view to improving radiation-use efficiency in crops.

11.) Khan, M H, et al. “Genetic Engineering for Crop Improvement.” Journal of Plant Science Research, 2013, pp. 5–13. Environment Complete, doi:0970-2539. In this interesting review, a number of commercialized, genetically engineered (GE) varieties in cotton, maize and soybean were created using this technology and at present the traits introduced are herbicide and/or pest tolerance. Gene technology enables the increase of production in plants, as well as the rise of resistance to pests, viruses, frost, etc. Gene transfer is used to modify the physical and chemical composition and nutritional value of food. The advantages of future applications could even be much bigger.

12.) Khan, F, et al. “Genomic and transcriptomic approaches towards the genetic improvement of an underutilized crops: the case of bambara groundnut.” African Crop Science Journal, 2016, pp. 429–458. BASE, doi:edsbas.D5BFBAA3. This review paper highlights how a number of recent technologies and approaches used for major crop research, can be translated into use in research of minor crops, using bambara groundnut as an exemplar species. Using drought tolerance as a trait of interest in this crop, the researchers demonstrated how limitations can affect genomic approaches for understanding traits in bambara groundnut, and, how genomic methodologies developed for major crops can be applied to underutilized crops for better understanding of the genetics governing important agronomic traits.

13.) Thakur, Ajay K, et al. “ROLE OF GENETIC ENGINEERING IN HORTICULTURAL CROP IMPROVEMENT - A REVIEW.” Agricultural Reviews, 2012, pp. 248–255. Academic Search Complete, doi:0253-1496. In this review the authors summarize the different ways in which genetic engineering creates plants with specific changes in the background of a proven cultivar without disturbing their genetic constitution. Expression of undesirable genes can be blocked by the application of antisense gene technology and RNAi technology. Finally, Genetic transformation provides the means for modifying horticultural traits in various horticultural crops without altering their phenotype.

14.) Forster, Brian, et al. “Root system architecture: opportunities and constraints for genetic improvement of crops .” Trends in Plant Science, 2007, pp. 474–481. ScienceDirect, doi:10.1016/j.tplants.2007.08.012. Abiotic stresses increasingly curtail crop yield as a result of global climate change and scarcity of water and nutrients. One way to minimize the negative impact of these factors on yield is to manipulate root system architecture (RSA) towards a distribution of roots in the soil that optimizes water and nutrient uptake. It is now established that most of the genetic variation for RSA is driven by a suite of quantitative trait loci. As the researchers discuss, marker-assisted selection and quantitative trait loci cloning for RSA are underway, exploiting genomic resources, candidate genes and the knowledge gained from Arabidopsis, rice and other crops.

15.) Clegg, Michael T. “Genetics of Crop Improvement.” American Zoologist, 1986, pp. 821–833. JSTOR journals , doi:edsjsr.3883007. Humans have been engaged in the genetic manipulation of crop plants for millennia. At its most elemental level, plant genetic manipulation has three requirements: 1.) a source of genetic variability that can be utilized for plant improvement; 2.) methods for propagating desirable plant genotypes; and 3.) strategies for the transfer and selection of useful genes or gene combinations. The modern science of genetics has provided many new approaches to each of these three aspects of plant improvement.

16.) Lebot, Vincent. “Coping with insularity: the need for crop genetic improvement to strengthen adaptation to climatic change and food security in the Pacific.” Environment, Development and Sustainability, Dec. 2013, pp. 1405–1423. Business Source Premier, doi:10.1007/s10668-013-9445-1. In this review the capability of Pacific Island countries' agriculture to adapt to climatic and environmental changes is analyzed. Additionally, biophysical and economic vulnerabilities of the food system are identified. For the major food crops, the needs for genetic improvement are detailed, and practical solutions for broadening genetic bases are suggested. The paper concludes by identifying areas for additional research on crops and agro-ecosystems adaptation aiming at increasing the flexibility of agriculture in the Pacific.

17.) Ning, Yang, et al. “Revolutionize Genetic Studies and Crop Improvement with High-Throughput and Genome-Scale CRISPR/Cas9 Gene Editing Technology.” Molecular Plant, Sept. 2017, pp. 1141–1143. ScienceDirect, doi:10.1016/j.molp.2017.08.001.A highly technical, but very recently completed look at how the CRISPR/cas9 gene editing technology has made it possible to edit any of the major crop plants at the M0 generation level in order to produce desired phenotypes by the M2 generation.

18.) Wang, Yi, and Wei-Hua Wu. “Genetic approaches for improvement of the crop potassium acquisition and utilization efficiency .” Current Opinion in Plant Biology, 2015, pp. 46–52. ScienceDirect, doi:10.1016/j.pbi.2015.04.007. Potassium (K) is one of the essential macronutrients for higher plants, not only important for plant growth and development, but also crucial for crop yield and quality. The deficiency in K in large areas of arable land worldwide has become a limitation for sustainable development of agriculture, and threatens the world food security. This review covers methods to enhance plants’ natural uptake of potassium through genetic improvement of the K utilization efficiency (KUE).

19.) Xie, Weibo. “Rice functional genomics research: Progress and implications for crop genetic improvement.” Biotechnology Advances, pp. 1059–1070. ScienceDirect, doi:10.1016/j.biotechadv.2011.08.013. An interesting and comprehensive summary of the methods employed to genetically modify rice crops. Rice is a staple food crop and has become a reference of monocot plant material for functional genomic research. With the availability of high quality rice genome sequences, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis.

20.) Vega-Sanchez, Miguel E, and Pamela C Ronald. “Genetic and biotechnological approaches for biofuel crop improvement.” Current opinion in Biotechnology, 2010, pp. 218–224. ScienceDirect, doi:10.1016/j.copbio.2010.02.002. Research and development efforts for biofuel production are targeted at converting plant biomass into renewable liquid fuels. Major obstacles for biofuel production include lack of biofuel crop domestication; low oil yields from crop plants as well as recalcitrance and enzymatic breakdown. Researchers describe their progress around these obstacles, including increasing fatty acid content and by optimizing the hydrolysis of plant cell walls to release fermentable sugars.