by Emma J Devereux
Citation: Devereux, E.J.,(2021), “Genetics in Agriculture: An Introduction”, EcoFoodDev, https://www.ecofooddev.com/genetics-in-agriculture-an-introduction/
In this post I present an overview of some of the main issues surrounding genetic modification in crops, laying the groundwork for a conversation regarding gene editing of crops via their wild relatives.
Cover image from http://www.sci-news.com/genetics/barley-genome-04814.html: Phylogenetic tree of 68 full-length α-amylase protein sequences derived from amy genes identified in the genomes of barley, hexaploid wheat, B. distachyon, rice, sorghum and maize. Image credit: Mascher et al, doi: 10.1038/nature22043.
The Need for Global Crop Improvement
Why do scientists, agriculturalists and food production specialists practice crop improvement practices? A rapidly changing climate, combined with unpredictable geopolitical landscapes and mass migration, requires that sustainable methods of food production are urgently developed. The field of agricultural genomics has for decades been central to crop development, providing breakthroughs such as reference genome sequencing, genotyping for genome-wide association studies, and genomic prediction technologies essential in crop improvement. These innovations have resulted in cultivars able to withstand emerging and changing conditions, selecting for agriculturally desirable traits including high yield, stress tolerance and pest resistance (Editorial, Nature Genetics, 51, 2019). However, genetic modification of cereal crops remains a controversial topic in wider society, commonly misunderstood, with different methods of crop improvement all being placed under the “GMO” umbrella. The communication of the science and principles behind this method have been poorly communicated to the public, and the history of such techniques has only more recently been considered from a multi-disciplinary perspective (for example by experts from the fields of botany/biology and environmental archaeology working together).
Genetics, Geopolitics & Food Security
Like it or loath it, genomics has a vital role to play in future food security and food sustainability. By 2050, it is estimated that the global population will be between 9 – 10 billion people (UN, 2019 https://www.un.org/development/desa/en/news/population/world-population-prospects-2019.html). Such rapid population increase places great strain on global food production. At the same time, as a result of climate change and urbanization, available agricultural land is decreasing. The ‘Green Revolution’ heralded the innovation of dwarf crop varieties, allowing for increased yield in smaller areas. Yet this also facilitated urbanization and the establishment of protected ecological areas- both of which are difficult (and undesirable) to now dismantle or repurpose.
Genetic modification has been used to fill nutritional gaps in the food market. Scientists developed Golden Rice to produce beta-carotene (vitamin A) to tackle vitamin A deficiency (Paine et al., 2005).
Food poverty is not a thing of the future but is a critical issue in the present day. Famine is an urgent global threat due to desertification and war such as in Yemen and South Sudan. Recent geopolitical upheavals (the Arab Spring, the Taliban, Isis) have been attributed to crop failures in the years preceding their occurrence. It is predicted that increased food shortages in the future will lead to increased migration, further conflicts, and widespread famines (https://www.un.org/sustainabledevelopment/hunger/).
Hence crop improvement schemes that embrace genomic technology for the purposes of future food security will become ever more urgent. Genetics in agri food production offers comprehensive, extensive, universal technological methods in food production to provide solutions for a pressing worldwide problem (Genomics and our future food security. Nat Genet 51, 197 (2019). https://doi.org/10.1038/s41588-019-0352-8 https://www.nature.com/articles/s41588-019-0352-8).
Climate change
As detailed in various prior posts (https://bit.ly/3zcaGR3 ; https://bit.ly/36JYJpx ; https://bit.ly/2TiqUsA ; https://bit.ly/3ezw7nj ), a change in climate roughly 12,000 years ago precipitated the move to agriculture. However, current climate change is putting agriculture under threat. Increased aridification and reduction of water sources has led to a decrease of available agricultural land. Intensive farming of the remaining land will lead to soil degradation and land exhaustion.
Increasingly unpredictable weather has led to widespread farming difficulties. Waterlogging and soil compaction are major threats to agricultural production, leading to increased input costs and reduced outputs. For example, agronomist Simon Draper of the Maize Growers Association has warned that waterlogging will severely reduce the window to set seed for maize growers in the UK in 2020, with a potential 40% yield loss (Park, 2020).
Wet weather also hampers application of pesticides and fungicides. Agronomists are searching for new crop varieties that have been genetically modified to cope with higher rainfall while delivering higher yields, especially in Europe. Tom Dummett, Oil Seed Rape (OSR) product manager with RAGT Seeds, recently described a new variety of OSR which has been modified to be flexible in differing weather conditions and maintain yields (https://www.fginsight.com/ragt/resistance-and-genetic-potential-key-for-winter-wheat-107078).
Rising global temperatures will also cause an increase in insect populations placing further pressures on crop yields. Researcher’s project further losses of over 50% in wheat crops with a 2⁰C rise, and 30% further losses in maize (Bevan et al, 2017). With 800 million people chronically hungry today, increasing pestilence resistance is an emerging food security crisis (Deutsch et al, 2018).
Pathogen resistance
Development of cereal varieties with increased pathogen resistance but that require less inputs such as pesticides (and development of management practices to tackle crop pathogens) is a primary goal of agricultural research, and one in which genomics plays a pivotal role. Crop disease is a major economic and food security issue. A collaboration between The Zoological Society of London, Rothamsted Research and Sheffield University used computer models to predict the economic cost of pesticide-use on UK farms producing winter wheat. The weed ‘Black-grass’ (Alopecurus myosuroides) has forced UK farmers to abandon winter wheat crops, costing the UK economy ~£400 million, and 800,000 tonnes of lost wheat yield each year (Varah et al, 2019). The authors predict these costs to significantly rise and impact food production and call for an urgent reduction of pesticide use. However, this requires an alternative to pesticides to protect yield outputs.
Wikicommons
Agri-genomics has a key role to play in reducing the dependency of farmers on pesticides and seed coating chemicals. For example, the next horizon of genetic cereal cultivation is tackling the existence of “superweeds” which display resistance to multiple forms of herbicide (MHR). Research into MHR has revealed a gene that acts as a “switch” that turns on MHR in weeds, and scientists are actively searching for ways to “switch off” this gene. Scientists at the Universities of York and Durham have discovered a gene called AmGSTF1 that plays a key role in controlling multi-herbicide resistance (MHR) in black-grass and ryegrass. Chemicals that inhibit this gene can be used to make weed killers that are effective against resistant weeds (https://www.technologynetworks.com/genomics/news/blackgrass-resistance-gene-discovered-188956).
Biodiversity loss
Plant domestication is an evolutionary process. Limited numbers of progenitor species were used by early farmers and they selected for traits related to yield, harvesting ability, and edibility (Hua et al., 2015). This produced genetic bottlenecks that have resulted in a reduction in genetic variation among annual herbaceous crops (Zhang et al., 2016). This lack of genetic diversity in our economic crops is a food security threat, as we depend on only a few dozen species for the bulk of our nutrition and the few species we manipulate have limited ability to cope with environmental instability. However, their wild relatives display greater biodiversity and an adaptability to marginalised environments and extreme soil conditions.
For example, analysis of genetic variation in modern maize, early domesticated maize and wild populations of teosinte (wild, ancient maize) identified ~1,200 genes affected by domestication. Modern maize lines display only ~57% of the diversity of progenitor populations (Bevan et al, 2017).
Political pressure
Agricultural production is experiencing increasing pressure from policy makers with regards to methods. For example, Brexit will require the formation of entirely new agricultural policy in the UK as it leaves the European Union and the Common Agricultural Policy (CAP). Funding for farming is a central concern for UK farmers, as well as new directions on farming methods and standards (Kay, 2020, Farmers Guardian). Genomic solutions that cut input costs have a significant role to play in this new political and farming landscape.
Pesticide bans and environmental legislation are also key agricultural considerations. For example, Oil Seed Rape (OSR) has seen a dramatic increase in beetle pests due to the neonicotinoid ban, and farmers now unable to control these pests with insecticides are experiencing huge yield losses. Prescribed application windows for pesticides are difficult to adhere to due to increasingly unpredictable weather conditions, particularly recurring winter storms. The development of pathogen resistant crops is a potential solution to these obstacles.
The current Covid-19 crisis has highlighted gaps in the food supply chain. According to a report produced by the UN, at least 265 million people are being pushed to starvation by the Covid-19 crisis (https://www.theguardian.com/global-development/2020/apr/21/coronavirus-pandemic-will-cause-famine-of-biblical-proportions). Urgent interventions to improve food production, and secure food supply chains in times of lockdown, are a key element to tackling crises such as this.
Public perception & GMO controversy
Consumer buying habits ultimately direct how food is produced. Consumers increasingly gravitate towards “organic” and “non-GMO” products on supermarket shelves and are also concerned about the use of antibiotics and the potential role this plays in human antibiotic resistance. Alternative crop development techniques are also required to make farming more environmentally sustainable and environmentally friendly. A major concern of environmental policy, particularly in the EU (EU Nitrates Directive etc.) is chemical run off from the field (pesticides) into water courses, leading to pollution of waterways and biodiversity loss. Development of crop varieties resistant to pathogens and reducing the need for pesticides is hence of central environmental importance.
However, GMO is still viewed negatively by the public in general. More recently the potential of gene editing via the wild relatives of crops (the plants that grow within the natural community of the cereal crop), as distinct from genetic modification, has shown potential to be a fertile future avenue of research in crop development to confer the required resistance and biodiversity, as well as being a more “natural” solution to crop advancement. Foods produced through genetic editing via crop wild relatives (CWR), as opposed to synthesized via GMO, may be more palatable to the consumer. This distinction between Genetic Modification (GM) and Genetic Editing (GE) has been highlighted as an essential distinction to outline to the public (Dyer 2020, Farmers Guardian). In upcoming posts I will discuss gene editing and the concept of Crop to Wild Relative research (CWR).
References cited
- Bevan, M.W., Uauy, C., Wulff, B.B., Zhou, J., Krasileva, K. and Clark, M.D., 2017. Genomic innovation for crop improvement. Nature, 543(7645), pp.346-354.
- Deutsch, C.A., Tewksbury, J.J., Tigchelaar, M., Battisti, D.S., Merrill, S.C., Huey, R.B. and Naylor, R.L., 2018. Increase in crop losses to insect pests in a warming climate. Science, 361(6405), pp.916-919.
- Editorial: “Genomics and our future food security”. Nat Genet 51, 197 (2019). https://doi.org/10.1038/s41588-019-0352-8
- Fuller, D.Q., Willcox, G. and Allaby, R.G., 2012. Early agricultural pathways: moving outside the ‘core area’hypothesis in Southwest Asia. Journal of experimental botany, 63(2), pp.617-633.
- Hua, L., Wang, D.R., Tan, L., Fu, Y., Liu, F., Xiao, L., Zhu, Z., Fu, Q., Sun, X., Gu, P. and Cai, H., 2015. LABA1, a domestication gene associated with long, barbed awns in wild rice. The Plant Cell, 27(7), pp.1875-1888.
- Paine, J., Shipton, C., Chaggar, S. et al. Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nat Biotechnol 23, 482–487 (2005). https://doi.org/10.1038/nbt1082
- Varah, A., Ahodo, K., Coutts, S.R., Hicks, H.L., Comont, D., Crook, L., Hull, R., Neve, P., Childs, D.Z., Freckleton, R.P. and Norris, K., 2020. The costs of human-induced evolution in an agricultural system. Nature Sustainability, 3(1), pp.63-71.
- Vavilov, N.I., 1926. The origin of cultivated plants. News in Agronomy, pp.76-85.
- Zhang, H., Mittal, N., Leamy, L.J., Barazani, O. and Song, B.H., 2017. Back into the wild—Apply untapped genetic diversity of wild relatives for crop improvement. Evolutionary Applications, 10(1), pp.5-24.
- UN, “Goal 2: Zero Hunger”: https://www.un.org/sustainabledevelopment/hunger/
- UN, 2011. World Population Prospects, UN Department of Economic and Social Affairs, Population Division, New York. <http://esa.un.org/unpd/wpp/ index.htm> (accessed 10.04.2020)
- Dyer, A., February 2020, Farmers Guardian: https://www.fginsight.com/news/clear-conversation-needed-on-gene-editing-in-order-to-convince-public–106357
- Kay, A., February 2020, Farmers Guardian: https://www.fginsight.com/news/news/defras-environmental-land-management-scheme–everything-you-need-to-know–106108
- Kay, A., February 2020, Farmers Guardian: https://www.fginsight.com/news/news/farm-groups-express-fury-at-government-plans-to-accept-us-food-safety-standards-105724
- Park, April 2020, Farmers Guardian: https://www.fginsight.com/news/evaluating-maize-crop-establishment-this-year-107605
- RAGT, April 2020, Farmers Guardian: https://www.fginsight.com/ragt/news—ragt/resistance-and-genetic-potential-key-for-winter-wheat-107078
