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Briefing paper 2 | Published: 30 Sept 2023 | DOI: 10.6084/m9.figshare.24220930.v1

Breeding wheat for soil health

Emmrich P

DOI: doi.org/10.6084/m9.figshare.24220930.v1

Summary

Wheat is a global staple crop and the health of soils under wheat crops is critical for food security, biodiversity and the reduction of greenhouse gas emissions. Researchers at the John Innes Centre and partnering institutes are identifying root traits for breeding future wheat varieties that modulate soil microbial metabolism on carbon and nitrogen transformation to improve carbon storage and nitrogen use efficiency, thereby improving yields under low nitrogen inputs, reducing N2O emissions and nitrate runoff, and enhancing overall soil health. This briefing paper, based on an expert stakeholder consultation convened by NISD in March 2023, considers strategies for aligning stakeholder interests in adopting this novel technology for economic and environmental benefits and outlines policy measures to support this process.

Recommendations

  1. Establish nationally agreed measuring approaches for agricultural soil health, which correlate with desired outcomes including nitrogen use efficiency, biodiversity gain and carbon sequestration. These approaches must be scalable, for example through the use of remote sensing.
  2. Support farmers in trialling and adopting new agricultural technologies through a matched funding system to accelerate farming innovation. Currently, deployment of new technologies is hampered by high costs of technologies prior to scaling and first-mover advantages are frequently outweighed by the risk of adopting new practices.
  3. Integrate soil nitrogen cycles in emission calculations. This is necessary to create incentives to reduce N2O emissions from agricultural systems and meet net zero obligations. In addition, good soil nitrogen management can support soil carbon stocks, further benefiting GHG balance.
  4. Support deployment of crop varieties with traits benefiting soil health by highlighting the economic and environmental benefits of these traits to farmers, and by subsidising soil health improvements.

Introduction

Wheat is the UK’s most important crop and forms the foundation of the nation’s food system. Globally, wheat provides 20% of food calories (Gutierrez, 2017). Modern wheat varieties are highly productive, but are reliant on agricultural inputs, including nitrogen fertilizers. Yet, globally, about half of the N-fertilisers applied to wheat fields is lost to nitrification (Lassaletta et al., 2014). This results in environmental damage due to fertiliser runoff, and contributes to global warming due to emissions in the form of the potent greenhouse gas N2O, energy cost of fertiliser manufacture and damage to soil ecosystems. In the UK, fertiliser production and use accounts for 88% of CO2eq. emissions from wheat production (Achten and Van Acker, 2016). 

Root traits are becoming a breeding target to improve root systems and associated functions in plants, including abiotic stress tolerance, resource use efficiency, yield and more recently biodiversity and soil health parameters (Reynolds et al., 2021). Work under the WISH-Roots programme led by the John Innes Centre aims to address this vital issue by developing wheat breeding material that carries root traits that influence soil microbial communities in a way that increases nitrogen use efficiency of the wheat cropping system (Martinez-Feria et al., 2018; Congreves et al., 2021). To this end, the researchers are investigating a global diversity collection of traditional wheat cultivars (the Watkins collection) to characterise compounds exuded from the wheat roots into the soil immediately surrounding them – the rhizosphere – and their effect on soil nitrogen processes. This work uses metagenomic analysis to characterise the changes in soil microbial ecosystems, measures effects on soil carbon emissions and on crop performance. 

The programme has identified breeding markers that can be used to breed new wheat varieties with improved nitrogen use efficiency (NUE) and that can be grown successfully with reduced nitrogen inputs and with improved agricultural GHG balance (Leon et al., 2022). The program will provide quantification of the increase in nitrogen use efficiency over the next two years. Pre-breeding material will be available to breeders over the next two seasons. Wheat varieties with these traits could be available to farmers within 15 years. These breeding traits can be introduced into elite varieties using conventional, marker-assisted breeding approaches, but it may be possible to accelerate this process through the use of gene editing, which the England now provides for under the Genetic Technology (Precision Breeding) Act 2023, pending implementing secondary legislation. 

This briefing paper considers three avenues to driving adoption of this technology: direct agronomic benefits for farmers, enhanced marketability due to a claim of environmental benefits and subsidy support for improved agricultural carbon balance.

The policy challenge of measuring soil health

Multiple definitions for “soil health” exist (Tahat et al., 2020), taking into account both the composition and the functions of soils. While positive correlations exist between many desirable functions of soil, those relationships can be complex and dependent on soil type and management. Research revealing the enormous complexity and importance of soil microbial ecosystems for various soil functions has made rapid advances in recent years, in part driven by new genomic technologies to understand the diversity and dynamics of these ecosystems. 

Measurements of soil carbon emissions are being conducted under laboratory conditions.  It is possible, but costly at scale to measure soil carbon stocks and fluxes in the field (Smith et al., 2020). This is currently not part of the research project but was identified by the roundtable participants as necessary future work to support any claims regarding soil carbon benefit. Ultimately, landscape-wide measurements will only be possible on the basis of proxy measurements that are cost-effective to collect at scale, such as satellite imagery. Several companies are developing systems to do this (Bowles and Dauksta, 2023), but in the opinion of the roundtable participants, none of them are sufficiently reliable at present.

Targeted research is necessary and timely to develop efficient proxy measurements to assess a number of aspects of soil health and which can serve as indicators to evaluate interventions (includin new crop varieties, inputs or agricultural practices) and policies (e.g. regarding agricultural GHG balance), to enable high-integrity future soil carbon markets (Paustian et al., 2019; Black et al., 2022).

Demonstrating economic benefits to farmers and breeders

In most cases the yield order of wheat varieties remains the same across N-application regimes (Mahjourimajd et al., 2016). Hence the aim of the research programme is to either find genetics that improve yield across N-application regimes, in which case adoption would likely be rapid or find the rare exceptions, where the genetics of a variety cause it to have unusually stable yields across N-application regimes, meaning it performs better than other varieties under low N-application. However, a sole focus on yield might not capture the benefits of this technology: Ultimately, profitability, not yield, is the most important economic measure for farmers, and if these traits are able to reduce fertiliser input costs, they may make farms more profitable even if a (small) yield-penalty is incurred. But unless these can be quantified (in terms of £/ha) these benefits remain too abstract to inform farmers’ decision-making. 

“Some of the things I am asked continuously by farmers are: how much will I get out of my crop if I reduce nitrogen application? How much damage am I doing by applying agrichemicals? How long is the road to recovery?”

– Ben Taylor-Davis, Global Regenerative Farming

Specific, quantitative evidence for economic benefits of these traits to farmers is the most direct route to drive adoption by farmers, which in turn allows breeders and seed manufacturers to recoup their investments. This requires agronomic trials in collaboration with commercial wheat breeders, in parallel to the ongoing research work. The economic risk for the breeders would be outweighed by the potential benefit of bringing these traits into marketable varieties sooner. However, the technology also needs to be tested under a wide variety of field conditions and farming practices (from conventional to organic). While it may be possible to find progressive farmers willing to take the risk to test these at limited scale (such as the “soil squad” of 70 farms organised by the British On-Farm Innovation Network – BOFIN), any first-mover advantages for farmers likely do not make up for the costs of trialling this new technology. This is part of a general problem that the adoption of new agricultural technologies (prior to sector-wide scale-up) frequently does not pay for itself for farmers, making the sector slow to respond to technological and policy change. A matched funding system to support on-farm trials and adoption of new agricultural technologies by farmers would thus be highly beneficial.

Adding complexity to this is the variety of farming contexts in which the technology could see implementation in the future. Applications rates of different fertilisers, soil types, crop rotations, irrigation and rainfall, among other factors, are likely to affect the performance of the technology. In the current study, the population of traditional wheat varieties is being tested under zero, low (48kg/ha) and moderate (2x 48kg/ha) N-fertiliser application, and without fungicide treatment. The benefits of high NUE wheat lines supporting soil health are likely to be greatest under low-input farming systems. Under the EU Green New Deal, agricultural inputs are to be reduced by 50%, with organic production systems to account for 25% of acreage by 2030. Policy environments such as this create advantageous framing conditions for high NUE wheat varieties.

Integrating nitrogen use and GHG balance

Nitrogen use and agricultural GHG balance are connected in two major ways. Firstly, nitrous oxide (N2O) is a major GHG with a 100-year global warming potential 265 times that of carbon dioxide (Myhre et al., 2013). Agricultural use of nitrogen-based fertilisers is a major source of N2O and other NOx (Achten and Van Acker, 2016). Limiting these emissions has not received widespread attention from policymakers yet, but this is likely to change as global efforts towards carbon neutral agricultural systems accelerate. If agricultural NOx emissions were to be captured in carbon pricing (either in the form of a tax or permit cost for emission or a subsidy for emission abatement), this would create a powerful incentive to improve soil N management, e.g. by the use of this technology. But at present, the significant cost resulting from agricultural NOx emissions remains an externality to the agricultural system, meaning incentives for technological change are not realised.

Secondly, soil nitrogen is a crucial component of the living soil ecosystem and, through the interaction of micro- and macroorganisms and crops, contributes to soil carbon and phosphate retention, as shown by relatively stable N:C:P ratios (Cleveland and Liptzin, 2007). However, fertiliser N addition generally harms microbial diversity and biomass (Wang, Liu and Bai, 2018). By reducing N loss (to runoff and gas emissions), it may be possible to improve soil organic carbon retention as well, resulting in improvement in the agricultural carbon balance – a sector that is dragging behind other sectors in its progress towards net zero emissions. If the economic value of this emissions abatement/carbon sequestration achieved through N retention were to be captured via an effective soil carbon pricing mechanism it would provide a powerful incentive for action. In addition to these, improving the carbon balance of agriculture is essential for meeting the UK’s legal obligation under its 2050 net zero goal, which underlines the value of these breeding traits to the UK government. Nitrogen use and agricultural GHG balance are connected in two major ways. Firstly, nitrous oxide (N2O) is a major GHG with a 100-year global warming potential 265 times that of carbon dioxide (Myhre et al., 2013). Agricultural use of nitrogen-based fertilisers is a major source of N2O and other NOx (Achten and Van Acker, 2016). Limiting these emissions has not received widespread attention from policymakers yet, but this is likely to change as global efforts towards carbon neutral agricultural systems accelerate. If agricultural NOx emissions were to be captured in carbon pricing (either in the form of a tax or permit cost for emission or a subsidy for emission abatement), this would create a powerful incentive to improve soil N management, e.g. by the use of this technology. But at present, the significant cost resulting from agricultural NOx emissions remains an externality to the agricultural system, meaning incentives for technological change are not realised.

Secondly, soil nitrogen is a crucial component of the living soil ecosystem and, through the interaction of micro- and macroorganisms and crops, contributes to soil carbon and phosphate retention, as shown by relatively stable N:C:P ratios (Cleveland and Liptzin, 2007). However, fertiliser N addition generally harms microbial diversity and biomass (Wang, Liu and Bai, 2018). By reducing N loss (to runoff and gas emissions), it may be possible to improve soil organic carbon retention as well, resulting in improvement in the agricultural carbon balance – a sector that is dragging behind other sectors in its progress towards net zero emissions. If the economic value of this emissions abatement/carbon sequestration achieved through N retention were to be captured via an effective soil carbon pricing mechanism it would provide a powerful incentive for action. In addition to these, improving the carbon balance of agriculture is essential for meeting the UK’s legal obligation under its 2050 net zero goal, which underlines the value of these breeding traits to the UK government. 

Policy support may be needed to drive adoption of crop varieties to enhance soil health

Environmental considerations influence consumer food choices. While these are often stated as an important preference in consumer surveys, they appear to feature much less strongly at the decision point of which product to buy in a supermarket (Hoek et al., 2017). In addition, a claim based on the carbon and biodiversity benefits of improved system NUE, through a better interaction between wheat and soil microorganisms, requires a complex explanation and may struggle to cut through in a market of many already competing environmental claims. If wheat products produced from varieties with traits enhancing soil health and reducing inputs were to be marketed at a price premium (e.g. due to the costs of maintaining a separate supply chain), they would likely remain niche products. If improved NUE wheat varieties were to become widespread in the sector, the marginal cost of maintaining a separate supply chain would decrease, but so would the uniqueness of the selling point for products derived from these varieties. 

Due to these factors, the expert roundtable considered the option of using environmental claims at the point of retail to be a weak driver of adoption of the technology throughout the wheat value chain. This is analogous to the slow adoption of crop varieties with improved nutritional values, which are often forced into a niche premium market by supply chain costs, economies of scale and yield trade-offs.

Conversely, as outlined above, this technology promises significant economic value to farmers (by reducing input costs) and landholders (by improving the quality of the soil) and to the public by enhancing GHG balance, biodiversity and ecosystem services in agricultural systems. An expectation of future demand from farmers would be sufficient to drive use of these breeding traits by wheat breeders and seed manufacturers. But for this demand to materialise, the value of these varieties (in terms of farm profitability, land value and environmental benefits) must be made apparent to farmers and landholders. A promising route to disseminating this information is the AHDB Recommended List of wheat varieties, which compares yield and a limited number of performance characteristics for a number of commercial wheat varieties. As this is the most important document informing farmer decisions on which varieties to grow, it would be the ideal place to include data on the benefits of high NUE varieties, e.g. by including observed yields under low N-inputs, or selected measurements of impacts on soil health. 

Because breeding improved NUE wheat varieties is a multi-year process, long-term clarity in the policy environment regarding support for improving agricultural GHG balance through crop breeding (alongside other measures) is critical to encourage the necessary investments from the private sector.

Conclusions

Crop breeding holds great potential for improving the sustainability of agriculture, but little of this has been realised so far, as the focus of breeders has been overwhelmingly on yield characteristics. Deployment of future wheat varieties with traits that support soil microbial ecosystems and enhance nitrogen use efficiency is one promising route to improving agricultural GHG balance while maintaining yields, but the stakeholders considered policy support to be necessary to accelerate and encourage the adoption of this technology.

Roundtable participants

The roundtable was organised by the John Innes Centre in collaboration with the Norwich Institute for Sustainable Development and made possible by a grant from the NBI Grand Challenges Fund awarded by BBSRC/UKRI.

  • Tom Allen Stevens, Arable farmer in Oxfordshire, Founder of BOFIN
  • Daniel Knevitt, Project manager for the Delivering Sustainable Wheat ISP, JIC
  • Nicholas Bird, Wheat Research Lead UK, KWS
  • Luke Williams, BBSRC
  • Falk Hildebrand, group leader, Earlham Institute
  • Jon Clarke, Knowledge Exchange and Communications, KIC
  • Tony Miller, group leader, JIC
  • Jez Fredenburgh, Agrifood for Net Zero Network+
  • Simon Griffiths, group leader in wheat genetics, JIC
  • Tim Martin, self-employed agronomist, APEX agronomy
  • Luzie Wingen, quantitative geneticist, JIC
  • Chris Darby, research coordinator, NISD
  • Ben Taylor-Davis, global regenerative farming
  • Fred Warren, group leader, Quadram Institute of Biology
  • Maria Hernandez-Soriano, research lead WISH-Roots, JIC
  • Brian Reid, professor of soil science, UEA
  • Peter Emmrich, senior research associate, NISD

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