Breeding Plants for Polycultures
Multicropping systems, defined as growing multiple species in the same field throughout a season, have potential to maintain high yields while reducing energy intensity and ecological damage. Layering multiple species onto the same plot often results in more efficient land utilization. The diversity of plant physical forms (height, root patterns) and differences in growth timing brought about by multi-species plantings allow for those plants to allocate resources more efficiently (Homulle et al. 2022). Additionally, plants can perform services for one another such as provisioning nitrogen or attracting pollinators, reducing the need for farmers to supplement deficiencies and boosting yields more cost-effectively (Vandermeer 1990).
Multicropping environments, which include a range of configurations from intercropping (planting two plants side-by-side), alley cropping (planting an understory crop between lanes of trees), and sophisticated permaculture designs involving dozens of plants, involve complex growing conditions.
In many circumstances, polycultures have been shown to have a yield advantage over monocultures for the reasons described above. A sample of intercropping systems, dominated by cereal-legume combinations, found that on average productivity was higher when crops were grown together. (Yu et al., 2015). There are situations where the theory does break down, however. In another analysis of 26 different polyculture systems, there was an average yield reduction of 24% (Iverson et al. 2014).1 Competition between species in mixed plantings can and does lead to significant yield reductions.
Amid these mixed results, it’s possible that polyculture performance has yet to achieve its full potential. The environmental pressures, or lack thereof, a plant faces during varietal development are what define a crop’s final characteristics. By breeding plants for monocultures, we are directing them to adopt traits optimized for that setting (Vandermeer and Perfecto 2025). Traits driving excessive resource acquisition or wasteful resource utilization may be promoted in an environment where a plant’s immediate vicinity is unburdened by a competing species, leading to genetics that are inadequate for multicropping.
In her excellent appraisal of the Green Revolution, Marci Baranski illustrates this process in action, showcasing how seed produced by the Green Revolution were optimized for input-intensive monocultures. Their strategy has been termed ‘wide adaptation’, which sought to develop crops that can grow successfully across a range of environments and climates. To achieve this, candidates in these breeding programs were heavily irrigated and fertilized so they could survive in mountains, rainforests, and deserts (Baranski 2022). This led to crop outputs that required expensive and energy-intensive inputs, which drove a series of environmental and social consequences (further reading) (Patel 2013). The experience of the Green Revolution shows that how a crop is bred shapes the range of environments in which it can thrive. Over time this influences the contours of the food system, such as our current reliance on fertilizers over a more diversified nutrient strategy.
If we desire landscapes with more diversity in species and function, tailoring plant genetics to better integrate into multicropping systems can be an important strategy in unlocking new potential. This idea can be termed ‘breeding for systems.’ By adapting crops to intercropping, alley cropping, and other polyculture planting schemes we may be able to boost yields, amplify ecosystem services, and realize more resilient landscapes.
While large-scale ‘breeding for systems’ programs have yet to be launched, there are some experimental examples showcasing this theory in action. One study of different grassland species found that plants grown in mixtures over several growing cycles had lower rates of competition between species and showed a propensity towards facilitation when compared to lineages grown in monocultures. Legumes were important drivers of the facilitation (Schöb et al. 2018). A similar experiment of cereals, legumes, and herbs found glimpses of a similar effect in domesticated plants. Specifically, coriander descended from mixed cropping lines produced 1.7 times more than those descended from monoculture lines. Moreover, wheat from similar heritages had a higher ratio of seed to biomass production, indicating more efficient use of nutrients and energy (Schmutz and Schöb 2024).
There are two directions a ‘breeding for systems’ approach could take. The first is, instead of investing heavily into a fully functioning breeding program, to assess existing varieties of target crops for their suitability under multicropping conditions. Here, researchers would identify traits of interest and conduct a trial assessing existing cultivars for the presence and magnitude of these traits.
An example of this work came from some of my former colleagues at the University of Missouri Center for Agroforestry. They were interested in characterizing black walnut suitability for alley cropping systems. A common limitation of these systems is the shade cast by trees can lower crop yields by reducing the amount of light available for photosynthesis. Black walnuts are already relatively well suited to alley cropping, as they leaf out later in the season than other trees, allowing for the understory crop to access a lot of light in early growth stages (Bishop et al. 2023). In this trial, they recorded the volume of light passing through the canopy of different walnut cultivars over the course of the growing season, which varies due to differences in tree shape or when leaves emerge from the bud. When this light availability data was paired with average nut yields, they were able to recommend economically optimal walnut varieties specifically for alley cropping systems (Bishop 2022).
A wide range of traits can be characterized in this way. A trial out of France found that when planted with wheat, Persian walnut roots grow deeper into the soil, with another study of the same duo out of China finding that wheat decreased its root density (Cardinael et al. 2015; Duan et al. 2019). While not eliminating competitive pressures, this flexibility in root traits when grown with a companion allows both the wheat and the walnut to reduce the impact competition has on yield. These traits can become targets for growers interested in such opportunities.
The other direction for a ‘breeding for systems’ program involves establishing proper selection trials leading to the development of crop varieties specially adapted to multicropping systems. Traits of interest depend on species but can focus on the shape, size, and architecture of different anatomical attributes (Moore et al. 2022). Things like leaf size, biomass density, root length, or canopy height influence the ability of a plant to access light, nutrients, or water which has downstream effects on the competitive pressure they exert on neighbors.
Additionally, traits related to developmental timing like day length sensitivity or early maturity can help make crops more suitable for multicropping by reducing the importance of time in a crop's development, allowing it to more easily align with the needs of other crops. Finally, a level of flexibility in trait expression allows plants to adjust their growth to the situation at hand (Francis et al. 1976; Callaway et al. 2003).
Breeding efforts would themselves take place in monocultural settings since selection for a range of traits is easier in homogenous environments (Moore et al. 2023). However, lacking specifically targeted traits, growing crops of interest in multicrops, and simply propagating the highest performing individuals is a reasonable alternative. Breeding programs should also integrate the limitations of target environments, both present and future. If local soils are persistently lacking in phosphorous, or a region will experience increasing aridity in coming years, breeding conditions should reflect that (Wade 2015).
One limitation of this work would be the atrophying of genetic diversity among existing crop varieties. Since most of our crops have been bred for and grown in monoculture settings, it appears they may have lost traits associated with success in multicropping systems (Vilela and González-Paleo 2015). It's possible that before a proper breeding program can be launched, it will be necessary to rebuild genetic diversity. Since many traditional farming systems use multicropping practices, particularly in the tropics, acquiring seeds from these groups can help to revitalize our genetic stock. Of course, royalty payments should be made to those who have stewarded any lines integrated into breeding programs.
While we can never be sure whether meaningful advancements in productivity or ecosystem functioning would result from putting this research agenda into practice, existing theoretical and experimental literature shows that this idea has a robust foundation. Taking a cropping system view to plant breeding would forge new directions in bringing about a more diverse and sustainable agriculture for the future.
What I’m Reading, Watching, and Listening to
Do Libraries Sink?: A wonderfully humorous video from the library interns at Oklahoma State.
Tired of Loosing: I never thought I would tear up over an essay about storage units.
Why Aren't There Snow Monkeys in North America or Europe?: For my fellow biogeography lovers.
References
Baranski M (2022) The Globalization of Wheat: A Critical History of the Green Revolution. University of Pittsburgh Press, Pittsburgh, PA
Bishop B (2022) Characterizing eastern black walnut (Juglans nigra) cultivars for alley cropping systems. Master’s Thesis, University of Missouri-Columbia
Bishop B, Meier NA, Coggeshall MV, et al (2023) A review to frame the utilization of Eastern black walnut (Juglans nigra L.) cultivars in alley cropping systems. Agroforest Syst. https://doi.org/10.1007/s10457-023-00909-0
Callaway RM, Pennings SC, Richards CL (2003) Phenotypic Plasticity and Interactions Among Plants. Ecology 84:1115–1128. https://doi.org/10.1890/0012-9658(2003)084[1115:PPAIAP]2.0.CO;2
Cardinael R, Mao Z, Prieto I, et al (2015) Competition with winter crops induces deeper rooting of walnut trees in a Mediterranean alley cropping agroforestry system. Plant Soil 391:219–235. https://doi.org/10.1007/s11104-015-2422-8
Duan ZP, Gan YW, Wang BJ, et al (2019) Interspecific interaction alters root morphology in young walnut/wheat agroforestry systems in northwest China. Agrofor Syst 93:419–434. https://doi.org/10.1007/s10457-017-0133-2
Francis CA, Flor CA, Temple SR (1976) Adapting Varieties for Intercropping Systems in the Tropics. In: Multiple Cropping. John Wiley & Sons, Ltd, pp 235–253
Homulle Z, George TS, Karley AJ (2022) Root traits with team benefits: understanding belowground interactions in intercropping systems. Plant Soil 471:1–26. https://doi.org/10.1007/s11104-021-05165-8
Iverson AL, Marín LE, Ennis KK, et al (2014) Do polycultures promote win-wins or trade-offs in agricultural ecosystem services? A meta-analysis. J Appl Ecol 51:1593–1602. https://doi.org/10.1111/1365-2664.12334
Moore VM, Peters T, Schlautman B, Brummer EC (2023) Toward plant breeding for multicrop systems. Proceedings of the National Academy of Sciences 120:e2205792119. https://doi.org/10.1073/pnas.2205792119
Moore VM, Schlautman B, Fei S, et al (2022) Plant Breeding for Intercropping in Temperate Field Crop Systems: A Review. Front Plant Sci 13:. https://doi.org/10.3389/fpls.2022.843065
Patel R (2013) The Long Green Revolution. The Journal of Peasant Studies 40:1–63. https://doi.org/10.1080/03066150.2012.719224
Schmutz A, Schöb C (2024) Coadaptation of coexisting plants enhances productivity in an agricultural system. Proceedings of the National Academy of Sciences 121:e2305517121. https://doi.org/10.1073/pnas.2305517121
Schöb C, Brooker RW, Zuppinger-Dingley D (2018) Evolution of facilitation requires diverse communities. Nat Ecol Evol 2:1381–1385. https://doi.org/10.1038/s41559-018-0623-2
Vandermeer J, Perfecto I (2025) Inherent suboptimality of monocultural crop breeding. Agroecology and Sustainable Food Systems 0:1–11. https://doi.org/10.1080/21683565.2025.2475459
Vandermeer JH (1990) Intercropping. In: Carroll CR, Vandermeer JH, Rosset P (eds) Agroecology. McGraw-Hill, New York
Vilela AE, González-Paleo L (2015) Changes in resource-use strategy and phenotypic plasticity associated with selection for yield in wild species native to arid environments. Journal of Arid Environments 113:51–58. https://doi.org/10.1016/j.jaridenv.2014.09.005
Wade L (2015) Agroecological approaches to breeding: Crop, mixture and systems design for improved fitness, sustainable intensification, ecosystem services, and food and nutrition security. In: Gliessman SR (ed) Agroecology for food security and nutrition. Food and Agriculture Organisation of the United Nations, France, pp 90–103
This result does seem to be driven by systems that failed to include a nitrogen fixing component. When combinations included legumes reductions from integration disappeared