Abstract

Current food systems are challenged by relying on a few input-intensive, staple crops. The prioritization of yield and the loss of diversity during the recent history of domestication has created contemporary crops and cropping systems that are ecologically unsustainable, vulnerable to climate change, nutrient poor, and socially inequitable. For decades, scientists have proposed diversity as a solution to address these challenges to global food security. Here, we outline the possibilities for a new era of crop domestication, focused on broadening the palette of crop diversity, that engages and benefits the three elements of domestication: crops, ecosystems, and humans. We explore how the suite of tools and technologies at hand can be applied to renew diversity in existing crops, improve underutilized crops, and domesticate new crops to bolster genetic, agroecosystem, and food system diversity. Implementing the new era of domestication requires that researchers, funders, and policymakers boldly invest in basic and translational research. Humans need more diverse food systems in the Anthropocene—the process of domestication can help build them.

Why is Domestication Critical to Address the Agricultural Challenges of the Anthropocene?

The Process of Domestication Shapes Diversity.

Crop domestication is an ongoing process of building and sustaining dynamic, coevolutionary relationships between plants and humans (1). The degree of interdependence in such relationships varies over time and across human practices and cycles of selection, ranging from use of wild harvested species to human cultivation to selective breeding programs, with crops shifting across a spectrum of “wild,” “semi-domesticated,” “domesticated,” and “improved”/”elite” (SI Appendix, Table S1). The domestication triangle [sensu (2, 3)], which comprises (i) the genetic and phenotypic particularities of crop plants, (ii) human agronomic and cultural practices, and (iii) ecological and geographical factors, illustrates the complexity of ongoing crop domestication processes across scales [(4); Fig. 1]. Together, the three elements of domestication (i.e., crops, humans, and ecosystems) help explain how the beginnings of agriculture resulted in major transitions in human history, facilitating the rise of dominant contemporary societies and food systems (5, 6). Yet while crop domestication enabled intensified production regimes that could sustain large populations, it has also contributed to the depletion of genetic, agroecosystem, and dietary diversity, and subsequent negative ecological and social impacts, as summarized below.
Fig. 1.
The domestication triangle [sensu (2, 3)] provides a framework for describing the diversity of factors present within the process of domestication. The triangle is comprised of the genetic particularities of crop plants, ecological and geographical factors, human agronomic and cultural practices, and the interrelations between these three elements. Diversity within the domestication process is hierarchical (4). Crop diversity encompasses diversity within lines/varieties, within the crop as a whole, and across the entire crop genepool, which includes crop wild relatives. Ecological diversity spans from the level of a single field, to agroecosystems, which incorporate multiple fields and their surrounding areas, to regions and landscapes. Human diversity includes the tools and interventions used in domestication, agricultural practices and forms of labor, and culture and cuisine that drive domestication. The domestication triangle acknowledges that genetic diversity and biodiversity at the species level interacts with diversity in human systems to shape diversity in domesticates and agroecosystems. For example, the agricultural practice of polyculture increases ecological diversity within a field and can drive the demand for new crop diversity that maximizes yield under this cultivation scheme. Alternatively, cultural demands for specific nutrient content in food such as “complete proteins” or vitamin A can drive breeding programs for underutilized crops that fill these gaps, thereby increasing the species richness of ecological systems. This depiction of domestication makes it clear that the challenges facing modern food systems–creating crops that are resilient, sustainable, nutritional, and equitable–lie at the intersection of the three elements of domestication, and can only be overcome by engaging factors from across each of these elements to improve whole system diversity in domestication.
Crop diversity—from genetic diversity within crops, to diversity within fields and agroecosystems, to diversity of foods within diets and across regions—has frequently been proposed as an answer, even a panacea, to the problems faced by modern agricultural and food systems (3, 715). There is a general agreement that we do not have enough—or the right kinds of—crop diversity in current agricultural systems to drive the adaptation necessary to sustain yields under changing climates (3, 9). And, although crop diversity is linked to improved nutrition (13, 15) as well as economic resilience (16), current major crops are the foundation of agricultural and food systems that diminish, rather than enhance, diversity at the landscape scale (17).
Given the scientific consensus that increased crop diversity is an important solution to many, though not all, of the challenges facing our global food systems, it is now time to shift the conversation to key processes through which we can realize this goal. Food systems encompass the full suite of people and actions that produce, process, distribute, market, and consume foods. Narrowing in on agricultural crop production systems, two primary pathways for change are evident: agronomic management and crop domestication. Cropping system diversity will play a critical role in the future success of agriculture and agronomic management practices have become increasingly rich—including polyculture and crop rotation alongside organic, no till, hydroponic, vertical, and biodynamic farming (4, 18, 19). However, in this perspective, we focus on the second pathway, outlining the possibilities for broadening the palette of food crop diversity through a new era of crop domestication that engages and benefits the three elements of domestication: crops, ecosystems, and humans.

Current and Future Food Systems Are Challenged by Relying on a Few Input-Intensive, Staple Crops.

In 1983, the preeminent American agronomist Norman Borlaug wrote, “I am convinced that the eight billion people projected to be living 40 to 50 years from now will continue to find most of their sustenance from the same plant species that supply most of our food needs now” (20). Not only was Borlaug’s prediction correct, but in the past five decades, our reliance on these staple crop species has intensified: Human diets have become 36% more similar across the globe (21). As of 2019, the global population relied on rice, wheat, and maize for more than 40% of its calories, with a handful of crops—annual cereals, legumes, sugarcane, and roots/tubers—making up more than 75% of plant-based calories (22). Furthermore, the increased cultivation of and reliance on just a few crops has contributed to the loss and imperilment of critical agrobiodiversity (23) and accompanying biocultural knowledge (24).
For millennia, crop domestication was primarily directed by small-scale farmers. However, in the twentieth century, centralized agricultural programs sought to improve global food security. These programs prioritized yield gains through intensive breeding practices, the development of hybrid crops, investments in irrigation schemes, the invention and subsidization of synthetic fertilizers, mechanized crop management, and the release of “Green Revolution” wheat and rice cultivars bred to take advantage of these modern inputs (2527). Such efforts, which focused on a handful of staple crop species, were, by some numbers, wildly successful: between 1940 and 1980, production of major crops in the United States increased 242% while using only 3% more cropland (20). Since that time, a feedback loop of funding, research, breeding, and markets and trade has developed that promotes and preserves production of these crops at the global scale (25). However, over the past three decades, yield plateaus have been observed in many staple crops, including rice, wheat, and maize (28). These plateaus are predicted to be exacerbated by climatic changes (29), and current projections indicate that production will not keep pace with rising demand in the coming years (30, 31).
Furthermore, yield improvements for staple crops have often come at the expense of genetic diversity underlying beneficial traits, including abiotic stress tolerance, nutritive value, and pest or disease resistance (7, 26, 32). Today, we face many unanticipated challenges resulting from the history of domestication, including but not limited to: 1) high energetic input costs of agricultural and food systems and unsustainable ecological impacts on the land, water, air, and biodiversity of a limited planet; 2) vulnerability of existing crops and agricultural systems to climate change; 3) lack of adequate nutrition in our food systems; and 4) social inequities arising from the interactions of the first three factors; all of which contribute to the need to change agriculture (33).

1. Unsustainable.

Food systems are key contributors to the loss of biodiversity, including agrobiodiversity, seen around the globe (3, 27, 31, 3438). Agriculture acts as a primary sink for water, nitrogen, and pesticides, and is a leading cause of eutrophication, soil degradation, and land cover and land use change (37, 3941). The construction of agricultural niche space (42) has led to the simplification of ecosystems and loss of ecosystem functions (17, 19, 43, 44). Globally, agriculture represents a major driver of environmental change, contributing 23% of greenhouse gas emissions (40, 45, 46).

2. Climate vulnerable.

Agricultural systems are extremely vulnerable to changes in climate, including increasing temperatures and declining precipitation (4749), which can affect the intensity and distribution of pest and disease outbreaks (5052). Collectively, these impacts are expected to reduce yields for a number of primary crops in the next two decades, particularly in semi-arid regions (53, 54). Although individual crops may be more or less vulnerable to changes in climate, dependence on a small number of crops (with limited genetic diversity) and the need for increased investment in reactive adaptation of those species may limit society’s ability to explore and develop alternatives (9).

3. Nutrient poor.

The lack of diversity in food systems has a negative impact on diet quality and nutrient adequacy (55). We have not made adequate progress toward the UN’s Sustainable Development Goal 2, “Zero Hunger” (56). In 2020, some 768 million people faced hunger; this includes 21% of the human population in Africa, 9% of the populations of Asia and Latin America and the Caribbean (57), and 40% of people living in the world’s mountainous regions (58). Beyond sheer caloric content, the displacement of nutrient-dense crops with calorie-dense starches has left billions of people lacking adequate nutrients, from protein to critical micronutrients such as iron and vitamin A (26, 38, 59). Malnutrition due to overconsumption of high-calorie foods is also increasingly common, particularly in populations with low socioeconomic status, and the number of countries facing both types of malnutrition is on the rise (31, 38).

4. Inequitable.

The benefits of agriculture and threats that impact agriculture are not equally distributed. Many parts of the world, particularly in the tropics and subtropics, have been underserved by modern agriculture: Cultivars bred for high-input and mechanized regimes perform poorly under low-input conditions and suitable lines are not widely accessible (20, 26). Climate change is already impacting geographic regions unequally (60). Agricultural systems in developing regions of Africa, Southeast Asia, Central America, the Pacific, and the Caribbean are predicted to be most severely affected (9) because of their reliance on low-input, rain-fed cropping systems which are contingent upon regular weather patterns (61). These regions are among those facing the fastest growth in both population size and affluence, placing greater pressure on agricultural production and increasing food security risks (57).
The next era of crop domestication must engage the reality of our current social-ecological crisis. Humans need to sustain and accelerate the domestication of new and better crops while remembering past insights and avoiding past mistakes. The livability of the earth, home or “domus” to humans and many other forms of life, including an array of plant species, critically depends on the choices humans make about how we live, including how we eat. As Boivin et al. remind us, “Highlighting a long-term human role in shaping biodiversity does not absolve present day populations of taking responsibility for Earth’s environments. Instead, it … suggests that we should own up to our role in transforming ecosystems and embrace responsible policies befitting a species that has engaged in millennia of ecological modification” (36). Crop domestication has contributed to the challenges food systems now face—yet going forward, it may serve as an important process to build solutions.

How Can Domestication Increase Diversity to Enable Agricultural Change? What Might the Next Era of Crop Domestication Look Like?

Crop Domestication Can (and Must) Be Done Differently to Build Diverse Future Food Systems.

Starting now, our food systems must face the demands of the future, shifting focus from maximizing caloric production to maximizing nutrient density, sustainability, climate resilience, and equity (Fig. 1), with the ultimate goal of global nutritional resilience (26, 59, 62). Meeting this goal requires a new era of domestication that will build more diverse food systems. Crop domestication efforts, such as leveraging plant microbiomes and the development of perennial cereals and agroforestry systems, are among the important research goals laid out for this decade that will support long-term resilience (8, 3335, 63, 64).
Creating crops that support global nutritional resilience requires that we engage in different—meaning at once novel and alternative—methods that benefit interdependent ecological and human systems. We can utilize different technological interventions and breeding approaches across different levels of crop diversity, target different types of crop species and traits that provide ecosystem services, and engage different human systems in diverse geographic locations.

We can utilize different tools and interventions across multiple levels of crop diversity.

Diversity within a crop, both genetic and phenotypic, is hierarchical: There is diversity among individuals, among crop lines or varieties, and across the entire genepool, which includes landraces and wild relatives of the same or closely related species (Fig. 1). The tools and technologies that we have available (SI Appendix, Table S2) can be used to identify, utilize, and foster diversity across these levels.
Rapid developments in next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies over the past decade have permitted the proliferation of genetic and genomic datasets for a growing number of plant species (65). While sequencing costs and/or the assembly of a reference genome remain a barrier in some cases (particularly for underutilized crops), the limiting factor for other crops is now the collection of phenotypic data. High-throughput phenotyping (“phenomics”) represents an important advance (6670), utilizing sensors on autonomous ground or aerial vehicles to impute plant traits including height and yield in the field, or to complement (or perhaps replace) DNA “fingerprints” with multidimensional phenomic profiles to enable rapid, prediction-based breeding.
The availability of inexpensive sequence data and high-density marker sets has revolutionized our understanding of genotype–phenotype associations and the genetic architecture of agronomically important traits, which is critical for plant breeding (3, 71, 72). Genomic data increase efficiency and mapping resolution in genome-wide association studies [GWAS (73, 74)]. Additionally, examining selective sweeps and population subdivision can also reveal genes underlying less obvious morphological, physiological, and biochemical traits, particularly those with polygenic underpinnings (74, 75), while genome–environment associations (or “environmental GWAS”) identify loci correlated with environmental factors, such as precipitation, soil type, or temperature (76, 77). To date, many of these analyses have focused on single-nucleotide polymorphisms (SNPs), but as resequencing and the production of pangenomes has increased in prevalence, so has recognition that structural variants (e.g., inversions, copy number variation, and transposable elements) play an important role in plant adaptation and evolution, including in crop species (7881).
Genomics-assisted breeding (e.g., marker-assisted selection, genomic selection) enables the prediction of phenotypic performance in genotyped individuals and accelerates crop domestication and improvement (65, 66, 8285). Genome editing technologies, including CRISPR/Cas9, also have the potential to fast-track both the domestication of new crops and the improvement of existing ones (65, 8689) through precise alterations to genes underlying traits of interest. For example, de novo domestication might be facilitated via the editing of loci known to be associated with desired domestication traits in nondomesticated plants (86, 90). For existing crops, a new era of “breeding by editing” has been envisioned (91) where novel diversity is introduced into elite lines without transgenesis, deleterious mutations are purged, and novel beneficial variants are created using editing technologies. However, many important traits of interest for breeding (e.g., aspects of yield and quality) are polygenic, while editing approaches are limited to traits controlled by only one or a few loci, and further complexities may arise due to editing-imposed genetic bottlenecks, epistasis, gene-by-environment interactions, and polyploidy (discussed in ref. 90). Practical limitations include the requirement for tissue culture regeneration and transformation protocols (not yet available even for all major crops) and regulatory hurdles. While genome editing techniques represent a boon for research (e.g., for gene discovery and to elucidate genotype–phenotype associations), they provide neither a simple nor complete solution for current breeding challenges.
New technology could also reduce the number of traits to alter genetically in new domesticates and semi-domesticates, focusing breeding attention on yield and quality traits and accelerating the adoption of latecomer crops. For example, many grain crops were bred to be harvested en masse by scythe or by machine, necessitating architectural uniformity and phenological synchronicity. Innovations in small autonomous machines (92) may someday allow asynchronous harvesting (and weeding and planting), thereby reducing the soil compaction and fuel use associated with heavy machinery. Machine vision-based “smart” harvesting (e.g., of individual heads or fruits as they ripen) (93) would allow the design of modern cropping systems that feature greater plasticity of individual plants, genetic variation within crops, and multispecies intercropping: All features of traditional cropping systems with higher habitat complexity than today’s simplified agroecosystems.
Of course, to take advantage of agrobiodiversity, we must also heed the urgent calls to conserve it, both in and ex situ (94, 95). While progress toward comprehensive conservation of crop genetic resources is essential, curation and characterization of these genetic resources is also needed to facilitate informed selection of individuals for breeding pipelines (9698).

We can prioritize different types of crop diversity.

The species that make up our current food systems are remarkably homogeneous. While it is estimated that tens of thousands of plant species are edible to humans, only around 2,500 species from 170 taxonomic families have undergone some degree of domestication, with fewer than 300 considered “fully domesticated” (99, 100). To build our future food systems, we must leverage the diversity of plant forms, life histories, and functional traits to support ecosystem services (14, 17, 101, 102).
Our current food systems are dominated by annual crop species. However, with roots that develop over multiple years, perennial plants provide an array of ecosystem services that have the potential to benefit agricultural systems, including carbon sequestration, stabilization of soil, water conservation, and the development of soil microbiomes (40, 103107). For herbaceous species, efforts toward the perennialization of annual species and the domestication of new perennial crops are in progress (106, 108), and numerous species have been suggested as candidates (see “We Can Domesticate New Species” below). In addition to their ecological benefits, woody crops have been targeted for improvement because of their important role in small-scale and subsistence agriculture, particularly in tropical regions (107, 109).
Root systems, which have the potential to improve yield, decrease fertilizer and irrigation needs, and mitigate the impacts of pathogens and soil conditions (e.g., drought or salinity), are coming into focus as targets for crop improvement (110113). Grafting, a practice already widely employed for many cucurbit, solanaceous, and woody perennial crops, enables independent selection of traits within root and shoot systems, and can expedite root system breeding (110, 111, 113). The recent advance of grafting in monocots (114), once thought to be biologically impossible, suggests it may soon be applied in important staple crops, including wheat, rice, and bananas (114).

We can work with diverse human systems in different geographic locations.

Humans are a critical component of and reason for crop domestication, and our choices have important implications for diversity. There are a range of available choices with regard to the domestication and breeding locations for crops and suites of crops; the sociocultural and agronomic contexts for which crop domesticates are targeted; and the methods for engaging diverse human systems in domestication processes.
Over the past century, public and private plant breeding have been the driving force behind crop domestication (24). Green Revolution rice and wheat cultivars have been rolled out across many locations, but there have been geographic disparities, namely in Africa, and marginal environments in particular have not been effectively served by modern varieties that were bred for favorable conditions (25). Perhaps, this is because programs to revolutionize crop yield have focused on annual cereals that are not able to thrive (despite breeding efforts) on depleted, fragile, or degraded soils—soils in some cases degraded by millennia of raising annual cereals. The next era of domestication can better serve Africa and farmers with limited access to or limited interest in commercial fertilizers by investing in multifunctional agricultural systems that include food crops with a broader range of lifespans, rooting depths, nitrogen acquisition strategies, mycorrhizal associations, and other functional traits. New domestication could lead to a richer set of agroecological options that would allow better matching between crops and cropping systems and diverse geographies, farm sizes, economic systems, and nutritional needs (55, 110).
Meanwhile, domestication performed informally and at the local scale by farmers continues (115). Home gardens also continue to be sites where agrobiodiversity is stewarded (3, 116). Across locations and scales, human systems have traditions of culturally valuing particular plants, and therefore knowledge of these plants, that can contribute to catalyzing and sustaining domestication processes (90). The diversity of humans’ plant knowledge can make a difference for domestication. For example, in Africa, many wild fruit and nut trees and herbaceous orphan crops are already known by humans and have great potential for further domestication (27, 107).
Different methods can support work with diverse human systems in both localized and decentralized geographies. Integrative research and education efforts can be led by, or codesigned with, the specific human communities who hold relevant plant knowledge and tend key wild and domesticated landscapes. Participatory modeling approaches may support agrobiodiversity through building stakeholders’ understanding and ideas about management (117), and participatory plant breeding may support agrobiodiversity through engaging many agronomic environments (118). Citizen science can be used to collaboratively collect crop and ecology data and to invite social learning, all of which may be useful for studying and advancing domestication (90, 119, 120), though agricultural citizen science efforts need to consider low-income contexts and the Global South (121).

Nutrition, resilience, sustainability, and equity are at the intersections of the elements of domestication.

Asking questions about geographies and locations—i.e., asking “where” questions—can be a way to investigate the intersections of the genetic, ecological, and human diversity elements of domestication (Fig. 1). To guide different choices in domestication that advance nutrition, resilience, sustainability, and equity, domesticators and funders can consider:
Assets: Where are hotspots of plant biodiversity, agrobiodiversity, and landscape diversity? Where are human communities with sustained, revitalizing, or emergent food cultures? Where are past centers of domestication, regional assemblages, and domesticated landscapes? Where are human systems with knowledge and resources to motivate and maintain domestication now?
Needs: Where are ecologically threatened and degraded landscapes? Where are human communities most vulnerable to climate injustice? Where are regional food systems with low nutritional densities? Where is early stage or ongoing domestication possible or already happening with limited resources?

The Next Era of Domestication Can Feature Existing, Underutilized, and New Crops.

Transformation of our food systems depends on engagement with each of the three elements of domestication—crops, ecosystems, and humans—to diversify the palette of species, we grow and consume. Below, we describe how efforts targeting species across the domestication continuum (e.g., domesticated, semi-domesticated, and wild) can begin to realize such change.

We can introduce new diversity into major and minor crops.

The classic “domestication syndrome,” or suite of phenotypic traits associated with domestication, varies among crops, but often includes larger seed size and loss of seed shattering, reduction of lateral branching, and modification of reproductive timing (122, 123); collectively, these traits enhance yield and facilitate harvest. However, domestication has also resulted in undesirable changes in many of our major crops, such as the loss of genetic diversity (124, 125) and accumulation of deleterious mutations (i.e., the “cost of domestication”) (81, 126, 127), as well as altered metabolomic profiles and decreased nutritional content (32, 86, 122, 128). The challenge ahead is to introduce new diversity, reduce the mutation load, and increase overall crop resilience (e.g., improving photosynthetic capacity, water use efficiency, nutrient retention, and disease resistance), while maintaining important agronomic traits acquired during domestication.
Traits associated with stress adaptation, including pest and pathogen resistance and tolerance to drought, heat, salinity, and flooding, are often present in crop wild relatives and landraces, and can be introduced into elite lines via introgressive hybridization (11, 20, 129, 130). However, introgressed segments are typically large and may include undesirable traits and deleterious alleles alongside beneficial targets, a phenomenon known as “linkage drag.” To diminish these effects, complex breeding and backcrossing schemes are utilized in combination with marker-assisted selection and genomic selection (130, 131). However, introgression breeding has proven challenging and expensive, even for singular, known targets, and the types of traits that are introgressed from wild species tend to be limited (132).
As the complex interactions between genome, transcriptome, and proteome [i.e., the interactome sensu (133)] become more apparent, there is a growing realization that the introgression of a single or even a few genomic regions from a wild species may not be sufficient to overcome the challenges facing our crops. Rather than moving wild diversity into cultivated lines, some authors have proposed a reversal of this gene flow, transferring genes from cultivated lines into crop wild relatives to explore the potential role of genetic background effects and epistasis in agronomic trait variation (86, 134). This method may also serve to counteract the accumulation of deleterious mutations in our crops, as wild species are expected to carry lower genetic loads (129).
New methods show promise for improving the efficiency of introgression breeding. For example, genome–environment associations can facilitate selection of the most environmentally appropriate wild materials to use in breeding programs (76, 77). Feralized populations of crops and landraces may also serve as important genetic resources for locally adaptive traits, as well as potential targets for “de novo redomestication” (135). Similarly, screening cultivated material, especially landraces, for wild introgressions can identify admixed populations that have reduced linkage drag (129).

We can improve underutilized crop species.

Humans have developed agricultural relationships with many crop species that are not considered major crops and have not received organized, concerted breeding and improvement efforts (59, 136). Individually, these species make up a relatively small portion of global agricultural production, but collectively, they play an important role as cash crops and/or subsistence or famine foods in many of the world’s poorest regions, which are underserved by major crops (38, 136). These species, often considered “semi-domesticated,” are referred to as “neglected,” “orphan,” or “promising” crops (8, 59). Additionally, harm to indigenous human communities and the erosion of biocultural knowledge and agrobiodiversity has contributed to the loss of entire agricultural systems and their traditional food plants, termed “lost crops” (32, 137). Here, we use the term “underutilized crops” to collectively refer to both of these categories of plants.
Underutilized crops are recognized as an important resource for agricultural diversification that supports food security, nutrition, and sustainable practices (8, 10, 38, 59). While major crops require an infusion of diversity (see above), underutilized crops have plenty to choose from, with forms ranging from trees, vines, shrubs, and herbs; annual and perennial life histories; and products that include sweet and starchy fruits, nuts, oilseeds, grains, legumes, vegetables, leafy greens, succulents, woody perennials, roots and tubers, and more (reviewed in ref. 138). Many underutilized crops contain high levels of both macro- and micronutrients, and may therefore offer an avenue toward combating malnutrition (32, 38, 59). Because underutilized crops are primarily grown using low-input traditional practices, often in harsh conditions and in food-insecure regions, many of these species are well suited for sustainable, climate-resilient systems (8, 32, 136, 139). Other underutilized crops and traditional foods, such as macroalgae and seagrasses, can expand our ideas of agriculture to include new cultivation schemes (140, 141).
The majority of resources directed toward crop improvement focus on major and minor crop species, and underutilized crops suffer from a lack of genomic resources (86). However, having already undergone some level of human selection, underutilized crops have the potential for great gains with only modest investments of time and resources (38). Therefore, the first step for many of these species is the collection of genotypic and phenotypic data, including critical data on reproductive habits (32), and the creation of genetic maps and reference genomes that can facilitate genome-wide association studies (GWAS), genomic selection, and phenomic selection (8). As the costs of sequencing continue to drop, advanced tools and resources like machine learning, population genomic datasets, and pan-genomes, and in some cases even genetic modification, will also become more readily available for underutilized crops (8, 142).
For underutilized species, breeding targets will likely include traits that are important to scaling up cultivation, such as productivity, reproductive synchronicity, palatability, harvestability, and durability/storage capacity (143). But, in order to ensure we do not repeat the missteps of past domestication efforts, we must be more intentional. For example, domestication via natural selection, in which humans played the role of seed dispersers, led to the evolution of both larger fruits and seeds but also, in some cases, an intraspecific arms-race leading to excessive height (144). Preference for more palatable seeds may have led to a loss of defense compounds in both seeds and stems, and the practice of shifting cultivation and seasonal nomadism may have selected against plant investments in belowground structures and longevity (144). We now have the opportunity to domesticate species with the benefit of evolutionary genetics. We can practice artificial selection, in which plants lose individual fitness (e.g., semi-dwarf stature) in favor of greater collective yield. Importantly, we can also monitor and select against negative genetic correlations to avoid unintended alterations in plant defenses or ecosystem services.
Bringing underutilized species to a broader audience will require coordinated efforts between local farmers, researchers, and national food systems, as well as acknowledgment of the biocultural context in which they were domesticated (59, 90). There are lessons to be learned from other underutilized species such as avocado, quinoa, and açaí, which, marketed as “superfoods,” have seen a rapid rise in global importance (145147). Supporting the agricultural and social infrastructure required to increase crop production is critical, as are efforts to mitigate environmental impacts of agricultural expansion, and ensuring equity of monetary and dietary benefits within the areas of traditional cultivation (145149).

We can domesticate new species.

Due to economic investment in improving and tailoring major staple crops, which most people around the world rely upon for the majority of their calories, the “domestication of new crops has nearly stopped” (86). Alternatively, and as a result of limited support of the needed basic research (39), we propose that domestication of new crops has barely started.
Domestication of new plant species in the twenty-first century has been initiated despite resource constraints, and these efforts span plant families and types: bioenergy crops (150), cacti (151), ferns (152), halophytes (153160), tree fruits and nuts (161, 162), macroalgae (163166), marine grasses (141, 167), microalgae (168), palms (169, 170), perennial grasses (171173), perennial groundcovers (174), perennial oilseeds (90, 175, 176), and perennial tree and grain legumes (177179).
Wild species targeted for domestication typically face many of the same challenges as underutilized crops: A lack of essential genetic and phenotypic data, including reference genomes. Exceptions are the wild relatives of major crops, which can leverage genomic resources to enable advanced techniques such as gene editing (180). In such cases, genes of major effect that underlie the primary domestication traits of the major crop may be modified. However, this method does not account for the effects of minor alleles and genetic interactions (epistasis), which, while poorly understood at the mechanistic level, are known to impact agriculturally relevant traits. While gene editing may in some cases yield important advances, domestication processes that will help realize diversity still require engagement with all the three elements of crops, ecosystems, and humans (90).
Selection on new domesticates can target novel uses and innovative cultivation schemes, but it must also consider downstream needs, such as harvestability, storage capacity, and nutrient retention (143). Furthermore, breeding programs must select for limited tradeoffs between stress tolerance and yield, a goal that may be best accomplished by domesticating species that are already adapted to the environmental/climatic conditions in which they will be cultivated (143). Careful attention should also be paid to maintaining genetic diversity, including cryptic variation (i.e., not observed/expressed in domesticates) and that of important polygenic traits such as pest and pathogen resistance (181). The use of genomic selection and breeding strategies, including introgression breeding with wild relatives, and independent selection in multiple breeding populations may help achieve these goals. While the timeframe for neo-domestication is often portrayed as a drawback, new methods like speed breeding may facilitate more rapid domestication and improvement of new crop species (182, 183).
Ecologically, new crop domestication could be targeted for functions in addition to human use and consumption, such as the restoration of degraded and threatened ecosystems and for the provision of ecosystem services (73). New crop domestication for human food and to meet additional ecological sustainability goals may be compatible with simultaneous efforts to restore biodiverse landscapes. Because domestication of new species involves the sustained cultivation and production of large supplies of seeds, a domestication-based approach can generate the scientific knowledge, agronomic practices, and cultural valuation for seed harvest, processing, and storage that are also needed to accelerate restoration and rewilding. An example of this approach has been envisioned for domesticated seagrass (184).
Socially, new crop domestication could prioritize “identifying new plant sources for nutritional improvement” (35), particularly in regions and cultures vulnerable to climate change. New crop domestication could also advance equity. Communities with plant knowledge can grow that knowledge and their food cultures as they steward landscapes and pursue culturally appropriate domestication projects—and they may choose to collaborate with, and utilize knowledge and resources from, scientific and transdisciplinary research institutions and organizations around the world. However, additional hurdles besides funding of basic research include the time, labor, and skill involved in making strategic and collective decisions about new crop domestication, particularly the work involved in spanning and integrating disciplines, human behaviors, and diverse communities.

Discussion: What Will It Take to Advance the Next Era of Crop Domestication?

Which crop domestication strategies will make the most impact on building the diverse food systems needed in the Anthropocene? A multifaceted approach is recommended depending on the type of crop and geographic region, as explored above. In all cases, there is a need to accelerate crop domestication and/or improvement in the face of climate change while maintaining genetic diversity during the breeding process.
While some traits desired in our future crops will certainly be species specific, others should be universally sought after. Unmet needs and examples of related traits that could be addressed in domestication pipeline strategies (108, 143) include:
increased ecological benefits such as for soil health, by targeting carbon sequestration and perenniality, and for biodiversity, by targeting pollinator services and habitat stability and complexity;
decreased reliance on inputs, by targeting nitrogen production and efficiency and pest and pathogen resistance;
hardiness in the face of climate variability and weather extremes, by targeting water use efficiency and cold and heat tolerance;
adaptation for degraded, detrimental, and novel environments, by targeting carbon sequestration, length of life, and/or salt tolerance;
fit of the crop into innovative and valuable cropping systems and rotations (with other plants, microorganisms, etc.), by targeting growth habit for harvestability, resource partitioning traits, micronutrient and high protein content for human use, and multipurpose uses along with human food, such as fiber, lumber, forage, medicine, or fuel;
fit of the crop into more resilient and sustainable supply chains and food economies, by targeting storability and durability of the harvested crop, including nutrient content and retention.
If the next era of crop domestication is to start now, we must recognize barriers to change in the form of currently dominant systems and landscapes. Sustaining the domestication and widespread cultivation of a few input-intensive staple crops requires effort. For humans to gain access to edible energy (in the form of plants powered by the sun and fed by soils and fossil fuels), our societies deploy energy—particularly fossil fuel energy—in activities ranging from scientific research and development, to plowing and fertilizing and harvesting, to trading and storing and cooking foods.
Despite being vulnerable to climate change and other environmental crises, currently dominant annual grain crops and cropping systems are also resilient in the sense that they are relatively resistant to change; this is due to the investments they have already received, and the investments that they continue to receive, of both biophysical and sociocultural energetic resources (103, 185). As overall relative investment in agriculture is decreasing (186), there is increasing competition for research and development resources simply to maintain current crops and yields (34).
Yet we must grow investments in basic and translational research to enable bold advances in crop domestication that support diversity. Some effort and energy will need to be reallocated and repurposed. In addition to basic knowledge such as scientific tools and reference genomes (39), investments are needed to develop the context in which domestication emerges (123), including physical infrastructure, social networks, and cultural interest. Translational research–i.e., applying basic knowledge to pursue practical results, often through interdisciplinary and international collaboration–is needed across the elements of domestication, including to advance crop genetic improvement (187). Because domestication relationships have to be not just started but sustained, we recommend strategically targeting investments based on assets and needs, while simultaneously building a network across which social learning can be accelerated and maintained over time.
Many of the dramatic yield gains in major crops in the twentieth century were made possible by foundational public investments in innovative technologies and institutions—including land-grant universities and agricultural extensions, plant material centers, research stations, and international research centers and global partnerships—that transformed landscapes as well as agricultural and food systems. The next generation of crop domestication will similarly require materials and mechanisms for agricultural transformations that increase diversity (34, 36). It is now possible to do crop domestication differently, combining new genomic and geospatial technologies, interdisciplinary approaches (188), the rediscovery of place-based public agronomy and selective breeding, and innovative public–private partnerships. Humans need more diverse food systems in the Anthropocene—the process of domestication can help build them.

Data, Materials, and Software Availability

No data was collected or analyzed for this perspective.

Acknowledgments

We thank the organizers and participants of the 2021 workshop “Tapping the wild to feed the future” for helpful discussion prior to the formulation of this manuscript. E.J.W. is supported by a grant from the Wallace Genetic Foundation and USDA-NIFA Award 2020-67034-36879.

Author contributions

A.S.K., E.B.M.D., and E.J.W. conceptualized the paper; A.S.K., E.B.M.D., D.L.V.T., and E.J.W. wrote the paper.

Competing interests

The authors declare no competing interest.

Supporting Information

Appendix 01 (PDF)

References

1
M. D. Purugganan, What is domestication? Trends Ecol. Evol. 37, 663–671 (2022).
2
P. Gepts, “Crop domestication as a long-term selection experiment” in Plant Breeding Reviews, J. Janick, Ed. (John Wiley & Sons, Inc., 2004).
3
M. B. Hufford, J. C. B. M. Teran, P. Gepts, Crop biodiversity: An unfinished magnum opus of nature. Annu. Rev. Plant Biol. 70, 727–751 (2019).
4
J. M. Bullock et al., Resilience and food security: Rethinking an ecological concept. J. Ecol. 105, 880–884 (2017).
5
O. Smith et al., A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nat. Plants 5, 369–379 (2019).
6
M. D. Purugganan, D. Q. Fuller, The nature of selection during plant domestication. Nature 457, 843–848 (2009).
7
V. Chable et al., Embedding cultivated diversity in society for agro-ecological transition. Sustainability 12, 784 (2020).
8
M. A. Chapman, Y. He, M. Zhou, Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. New Phytol. 234, 1583–159 (2022).
9
V. Labeyrie et al., The role of crop diversity in climate change adaptation: Insights from local observations to inform decision making in agriculture. Curr. Opin. Env. Sust. 51, 15–23 (2021).
10
F. Massawe, S. Mayes, A. Cheng, Crop diversity: An unexploited treasure trove for food security. Trends Plant Sci. 21, 365–368 (2016).
11
E. Warschefsky, R. V. Penmetsa, D. R. Cook, E. J. B. von Wettberg, Back to the wilds: Tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am. J. Bot. 101, 1791–1800 (2014).
12
S. Brumlop, W. Reichenbecher, B. Tappeser, M. R. Finckh, What is the SMARTest way to breed plants and increase agrobiodiversity? Euphytica 194, 53–66 (2013).
13
C. Lachat et al., Dietary species richness as a measure of food biodiversity and nutritional quality of diets. Proc. Natl. Acad. Sci. U.S.A. 115, 127–132 (2018).
14
S. L. Cappelli, L. A. Domeignoz-Horta, V. Loaiza, A.-L. Laine, Plant biodiversity promotes sustainable agriculture directly and via belowground effects. Trends Plant Sci. 27, 674–687 (2022).
15
L. Hattersley, B. Cogill, D. Hunter, G. Kennedy, “Evidence for the role of biodiversity in supporting healthy, diverse diets and nutrition” in Biodiversity, Food and Nutrition: A New Agenda for Sustainable Food Systems, D. Hunter, T. Borelli, E. Gee, Eds. (Routledge, ed. 1, 2020), pp. 40–63.
16
D. Renard, D. Tilman, National food production stabilized by crop diversity. Nature 571, 257–260 (2019).
17
B. J. Cardinale et al., The functional role of producer diversity in ecosystems. Am. J. Bot. 98, 572–592 (2011).
18
G. Galluzzi, A. Seyoum, M. Halewood, I. L. Noriega, E. W. Welch, The role of genetic resources in breeding for climate change: The case of public breeding programmes in eighteen developing countries. Plants 9, 1129 (2020).
19
J. Hendrickson, J. C. Colazo, "Using crop diversity and conservation cropping to develop more sustainable arable cropping systems" in Agroecosystem Diversity, G. Lemaire, P. C. D. F. Carvalho, S. Kronberg, S. Recous, Eds. (Academic Press, 2019), pp. 93–108.
20
N. E. Borlaug, Contributions of conventional plant breeding to food production. Science 219, 689–693 (1983).
21
C. K. Khoury et al., Increasing homogeneity in global food supplies and the implications for food security. Proc. Natl. Acad. Sci. U.S.A. 111, 4001–4006 (2014).
22
FAO, FAOSTAT Food Balances (2010). www.fao.org/faostat/. Accessed 12 June 2022.
23
C. K. Khoury et al., Crop genetic erosion: Understanding and responding to loss of crop diversity. New Phytol. 233, 84–118 (2022).
24
A. Argumedo et al., Biocultural diversity for food system transformation under global environmental change. Front. Sustain Food Syst. 5, 685299 (2021).
25
P. L. Pingali, Green revolution: Impacts, limits, and the path ahead. Proc. Natl. Acad. Sci. U.S.A. 109, 12302–12308 (2012).
26
J. Bailey-Serres, J. E. Parker, E. A. Ainsworth, G. E. D. Oldroyd, J. I. Schroeder, Genetic strategies for improving crop yields. Nature 575, 109–118 (2019).
27
R. R. B. Leakey, A re-boot of tropical agriculture benefits food production, rural economies, health, social justice and the environment. Nat. Food 1, 260–265 (2020).
28
P. Grassini, K. M. Eskridge, K. G. Cassman, Distinguishing between yield advances and yield plateaus in historical crop production trends. Nat. Commun. 4, 2918 (2013).
29
C. Zhao et al., Temperature increase reduces global yields of major crops in four independent estimates. Proc. Natl. Acad. Sci. U.S.A. 114, 9326–9331 (2017).
30
D. K. Ray, N. D. Mueller, P. C. West, J. A. Foley, Yield trends are insufficient to double global crop production by 2050. Plos One 8, e66428 (2013).
31
M. C. Hunter, R. G. Smith, M. E. Schipanski, L. W. Atwood, D. A. Mortensen, Agriculture in 2050: Recalibrating targets for sustainable intensification. Bioscience 67, 386–391 (2017).
32
P. Smýkal, M. N. Nelson, J. D. Berger, E. J. B. von Wettberg, The impact of genetic changes during crop domestication. Agronomy 8, 119 (2018).
33
Q. Chen, W. Li, L. Tan, F. Tian, Harnessing knowledge from maize and rice domestication for new crop breeding. Mol. Plant 14, 9–26 (2020).
34
S. Anders et al., Gaining acceptance of novel plant breeding technologies. Trends Plant Sci. 26, 575–587 (2021).
35
N. Henkhaus et al., Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future. Plant Direct. 4, e00252 (2020).
36
N. L. Boivin et al., Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions. Proc. Natl. Acad. Sci. U.S.A. 113, 6388–6396 (2016).
37
J. A. Foley et al., Solutions for a cultivated planet. Nature 478, 337–342 (2011).
38
T. Borelli et al., Local solutions for sustainable food systems: The contribution of orphan crops and wild edible species. Agronomy 10, 231 (2020).
39
Z. Tian, J. Wang, J. Li, B. Han, Designing future crops: Challenges and strategies for sustainable agriculture. Plant J. 105, 1165–1178 (2021).
40
IPCC, “Summary for Policymakers” in Climate Change and Land: An IPCC Special Report on Climate Change, Desertification, Land Degradation, Sustainable Land Management, Food Security, and Greenhouse Gas Fluxes in Terrestrial Ecosystems, P. R. Shukla et al., Eds. (IPCC, 2019).
41
P. J. A. Withers, C. Neal, H. P. Jarvie, D. G. Doody, Agriculture and eutrophication: Where do we go from here? Sustainability 6, 5853–5875 (2014).
42
M. A. Zeder, Domestication as a model system for niche construction theory. Evol. Ecol. 30, 325–348 (2016).
43
P. Balvanera et al., Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol. Lett. 9, 1146–1156 (2006).
44
F. van der Plas, Biodiversity and ecosystem functioning in naturally assembled communities. Biol. Rev. 94, 1220–1245 (2019).
45
W. F. Ruddiman et al., Late Holocene climate: Natural or anthropogenic? Rev. Geophys. 54, 93–118 (2016).
46
E. C. Ellis, Ecology in an anthropogenic biosphere. Ecol. Monogr. 85, 287–331 (2015).
47
P. K. Thornton, P. J. Ericksen, M. Herrero, A. J. Challinor, Climate variability and vulnerability to climate change: A review. Global Change Biol. 20, 3313–3328 (2014).
48
V. Vadez “Responses to increased moisture stress and extremes: Whole plant response to drought under climate change” in Crop Adaptation to Climate Change, S. S. Yadav et al. (Blackwell Publishing Ltd., Ed. 1, 2011), pp. 186–197.
49
D. B. Lobell et al., Prioritizing climate change adaptation needs for food security in 2030. Science 319, 607–610 (2008).
50
T. Oszako, J. A. Nowakowska, Climate change and food security: Challenges for plant health, plant breeding and genetic resources. Folia For Polonica 57, 194–197 (2015).
51
S. C. Chapman, S. Chakraborty, M. F. Dreccer, S. M. Howden, Plant adaptation to climate change opportunities and priorities in breeding. Crop. Pasture Sci. 63, 251–268 (2012).
52
N. Maxted, S. Kell, Establishment of a Global Network for the in situ Conservation of Crop Wild Relatives: Status and Needs (FAO Commission on Genetic Resources for Food and Agriculture, 2009).
53
S. S. Yadav, R. J. Redden, J. L. Hatfield, H. Lotze-Campen, NA. E. Hall, Eds., Crop Adaptation to Climate Change (Wiley-Blackwell, 2011).
54
R. Wassmann et al., "Climate change affecting rice production the physiological and agronomic basis for possible adaptation strategies" in Advances in Agronomy, D. L. Sparks, Ed. (Academic Press, 2011), pp. 59–122.
55
M. Herrero et al., Farming and the geography of nutrient production for human use: A transdisciplinary analysis. Lancet Planet. Heal 1, e33–e42 (2017).
56
Global Panel on Agriculture and Food Systems for Nutrition, “Future Food Systems: For people, our planet, and prosperity” (Global Panel on Agriculture and Food Systems for Nutrition, 2020).
57
FAO, IFAD, UNICEF, WFP, WHO, “The state of food security and nutrition in the world 2020: Transforming food systems for affordable healthy diets” (FAO, 2020).
58
A. Hussain, F. M. Qamar, Dual challenge of climate change and agrobiodiversity loss in mountain food systems in the Hindu-Kush Himalaya. One Earth 3, 539–542 (2020).
59
D. Hunter et al., The potential of neglected and underutilized species for improving diets and nutrition. Planta 250, 709–729 (2019).
60
IPCC, "‘Summary for policymakers’ in climate change 2021: The physical science basis" in Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change, V. Masson-Delmotte et al., Eds. (Cambridge University Press, 2021).
61
J. Barron, S. Skyllerstedt, M. Giordano, Z. Adimassu, Building climate resilience in rainfed landscapes needs more than good will. Front. Clim. 3, 735880 (2021).
62
C. Béné et al., When food systems meet sustainability – Current narratives and implications for actions. World Dev. 113, 116–130 (2019).
63
R. J. Henry, E. Nevo, Exploring natural selection to guide breeding for agriculture. Plant Biotechnol. J. 12, 655–662 (2014).
64
I. Negrutiu, M. W. Frohlich, O. Hamant, Flowering plants in the anthropocene: A political agenda. Trends Plant Sci. 25, 349–368 (2020).
65
R. K. Varshney et al., Designing future crops: Genomics-assisted breeding comes of age. Trends Plant Sci. 26, 631–649 (2021).
66
N. Fahlgren, M. A. Gehan, I. Baxter, Lights, camera, action: High-throughput plant phenotyping is ready for a close-up. Curr. Opin. Plant Biol. 24, 93–99 (2015).
67
P. Song, J. Wang, X. Guo, W. Yang, C. Zhao, High-throughput phenotyping: Breaking through the bottleneck in future crop breeding. Crop. J. 9, 633–645 (2021).
68
W. Yang et al., Crop phenomics and high-throughput phenotyping: Past decades, current challenges, and future perspectives. Mol. Plant 13, 187–214 (2020).
69
C. Zhao et al., Crop phenomics: Current status and perspectives. Front. Plant Sci. 10, 714 (2019).
70
D. L. Van Tassel et al., Re-imagining crop domestication in the era of high throughput phenomics. Curr. Opin. Plant Biol. 65, 102150 (2022).
71
M. Thudi et al., Genomic resources in plant breeding for sustainable agriculture. J. Plant Physiol. 257, 153351 (2021).
72
R. K. Varshney, R. Terauchi, S. R. McCouch, Harvesting the promising fruits of genomics: Applying genome sequencing technologies to crop breeding. Plos Biol. 12, e1001883 (2014).
73
L. T. Cortes, Z. Zhang, J. Yu, Status and prospects of genome-wide association studies in plants. Plant Genome. 14, e20077 (2021).
74
P. Gepts, The contribution of genetic and genomic approaches to plant domestication studies. Curr. Opin. Plant Biol. 18, 51–59 (2014).
75
S. D. Turner-Hissong, M. E. Mabry, T. M. Beissinger, J. Ross-Ibarra, J. C. Pires, Evolutionary insights into plant breeding. Curr. Opin. Plant Biol. 54, 93–100 (2020).
76
J. R. Lasky et al., Genome-environment associations in sorghum landraces predict adaptive traits. Sci. Adv. 1, e1400218 (2015).
77
D. J. Gates et al., Single-gene resolution of locally adaptive genetic variation in Mexican maize. Biorxiv [Preprint] (2019). https://doi.org/10.1101/706739 (Accessed 17 June 2022).
78
M. Todesco et al., Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602–607 (2020).
79
A. Dolatabadian, D. A. Patel, D. Edwards, J. Batley, Copy number variation and disease resistance in plants. Theor. Appl. Genet. 130, 2479–2490 (2017).
80
R. K. Saxena, D. Edwards, R. K. Varshney, Structural variations in plant genomes. Brief. Funct. Genom. 13, 296–307 (2014).
81
B. S. Gaut, D. K. Seymour, Q. Liu, Y. Zhou, Demography and its effects on genomic variation in crop domestication. Nat. Plants 4, 512–520 (2018).
82
J. Crossa et al., Genomic selection in plant breeding: Methods, models, and perspectives. Trends Plant Sci. 22, 961–975 (2017).
83
E. L. Heffner, M. E. Sorrells, J. Jannink, Genomic selection for crop improvement. Crop. Sci. 49, 1–12 (2009).
84
P. Bajgain, X. Zhang, J. A. Anderson, Genome-wide association study of yield component traits in intermediate wheatgrass and implications in genomic selection and breeding. G3 Genes Genomes. Genetics 9, 2429–2439 (2019).
85
J. Crain, A. Haghighattalab, L. DeHaan, J. Poland, Development of whole-genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding. Plant Genome. 14, e20089 (2021).
86
A. R. Fernie, J. Yan, De novo domestication: An alternative route toward new crops for the future. Mol. Plant 12, 615–631 (2019).
87
C. Gao, Genome engineering for crop improvement and future agriculture. Cell 184, 1621–1635 (2021).
88
M. Pourkheirandish, A. A. Golicz, P. L. Bhalla, M. B. Singh, Global role of crop genomics in the face of climate change. Front. Plant Sci. 11, 922 (2020).
89
M. A. Steinwand, P. C. Ronald, Crop biotechnology and the future of food. Nat. Food 1, 273–283 (2020).
90
D. L. Van Tassel et al., New food crop domestication in the age of gene editing: Genetic, agronomic and cultural change remain co-evolutionarily entangled. Front. Plant Sci. 11, 789 (2020).
91
H. Wang, E. Cimen, N. Singh, E. Buckler, Deep learning for plant genomics and crop improvement. Curr. Opin. Plant. Biol. 54, 34–41 (2020).
92
A. G. Millard, R. Ravikanna, R. Groß, D. Chesmore, "Towards a swarm robotic system for autonomous cereal harvesting" in Towards Autonomous Robotic Systems, 20th Annual Conference, K. Althoefer, J. Konstantinova, K. Zhang, Eds. (Springer International Publishing, Cham, 2019), pp. 458–461.
93
L. Afsah-Hejri et al., "Mechanical harvesting of selected temperate and tropical fruit and nut trees" in Horticultural Reviews, I. Warrington, Ed. (Wiley, 2022), pp. 171–242.
94
N. P. Castañeda-Álvarez et al., Global conservation priorities for crop wild relatives. Nat. Plants 2, 16022 (2016).
95
S. McCouch et al., Feeding the future. Nature 499, 23–24 (2013).
96
M. Mascher, S. Wu, P. St, N. Amand, J. Poland. Stein, Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley. Plos One 8, e76925 (2013).
97
S. D. Tanksley, S. R. McCouch, Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277, 1063–1066 (1997).
98
S. McCouch et al., Mobilizing crop biodiversity. Mol. Plant 13, 1341–1344 (2020).
99
R. Dirzo et al., Defaunation in the anthropocene. Science 345, 401–406 (2014).
100
R. S. Meyer, M. D. Purugganan, Evolution of crop species: Genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013).
101
S. A. Wood et al., Functional traits in agriculture: agrobiodiversity and ecosystem services. Trends Ecol. Evol. 30, 531–539 (2015).
102
M.-P. Faucon, D. Houben, H. Lambers, Plant functional traits: Soil and ecosystem services. Trends Plant Sci. 22, 385–394 (2017).
103
T. E. Crews, W. Carton, L. Olsson, Is the future of agriculture perennial? Imperatives and opportunities to reinvent agriculture by shifting from annual monocultures to perennial polycultures. Global Sustain. 1, e11 (2018).
104
M. Kreitzman, E. Toensmeier, K. M. A. Chan, S. Smukler, N. Ramankutty, Perennial staple crops: Yields, distribution, and nutrition in the global food system. Front. Sustain. Food Syst. 4, 588988 (2020).
105
E. Isgren, E. Andersson, W. Carton, New perennial grains in African smallholder agriculture from a farming systems perspective: A review. Agron. Sustain. Dev. 40, 6 (2020).
106
S. R. Asselin, A. L. Brûlé-Babel, D. L. Van Tassel, D. J. Cattani, Genetic analysis of domestication parallels in annual and perennial sunflowers (Helianthus spp.): Routes to crop development. Front. Plant Sci. 11, 834 (2020).
107
R. R. B. Leakey, T. Mabhaudhi, A. Gurib-Fakim, African lives matter: Wild food plants matter for livelihoods, justice, and the environment—A policy brief for agricultural reform and new crops. Sustainability 13, 7252 (2021).
108
L. R. DeHaan et al., A pipeline strategy for grain crop domestication. Crop. Sci. 56, 917–930 (2016).
109
R. R. B. Leakey, “Tree domestication in agroforestry: Progress in the second decade (2003–2012)” in Advances in Agroforestry vol. 9 - The Future of Global Land Use, P. Nair, D. Garrity, Eds. (Springer, 2012), pp. 145–173.
110
A. Albacete et al., Unravelling rootstock×scion interactions to improve food security. J. Exp. Bot. 66, 2211–2226 (2015).
111
P. J. Gregory et al., Contributions of roots and rootstocks to sustainable, intensified crop production. J. Exp. Bot. 64, 1209–1222 (2013).
112
M. E. Isaac et al., Crop domestication, root trait syndromes, and soil nutrient acquisition in organic agroecosystems: A systematic review. Front. Sustain. Food Syst. 5, 716480 (2021).
113
E. J. Warschefsky et al., Rootstocks: Diversity, domestication, and impacts on shoot phenotypes. Trends Plant Sci. 21, 418–437 (2016).
114
G. Reeves et al., Monocotyledonous plants graft at the embryonic root–shoot interface. Nature 602, 280–286 (2022).
115
M. R. Bellon et al., Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos. Proc. Royal. Soc. B. 285, 20181049 (2018).
116
G. Galluzzi, P. Eyzaguirre, V. Negri, Home gardens: Neglected hotspots of agro-biodiversity and cultural diversity. Biodivers. Conserv. 19, 3635–3654 (2010).
117
V. Labeyrie et al., Networking agrobiodiversity management to foster biodiversity-based agriculture: A review. Agron. Sustain. Dev. 41, 4 (2021).
118
S. Ceccarelli, S. Grando, Return to agrobiodiversity: Participatory plant breeding. Diversity 14, 126 (2022).
119
M. E. Isaac, A. R. Martin, Accumulating crop functional trait data with citizen science. Sci. Rep. 9, 15715 (2019).
120
J. van de Gevel, J. van Etten, S. Deterding, Citizen science breathes new life into participatory agricultural research: A review. Agron. Sustain. Dev. 40, 35 (2020).
121
L. Ebitu, H. Avery, K. A. Mourad, J. Enyetu, Citizen science for sustainable agriculture – A systematic literature review. Land Use Policy 103, 105326 (2021).
122
R. S. Meyer, A. E. DuVal, H. R. Jensen, Patterns and processes in crop domestication: An historical review and quantitative analysis of 203 global food crops. New Phytol. 196, 29–48 (2012).
123
A. Bogaard et al., Reconsidering domestication from a process archaeology perspective. World Archaeol. 53, 56–77 (2021).
124
M. van de Wouw, C. Kik, T. van Hintum, R. van Treuren, B. Visser, Genetic erosion in crops: Concept, research results and challenges. Plant Genet. Resour. 8, 1–15 (2010).
125
S. Rauf, J. A. T. da Silva, A. A. Khan, A. Naveed, Consequences of plant breeding on genetic diversity. Int J. Plant Breed. 1, 1–21 (2010).
126
S. Renaut, L. H. Rieseberg, The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Mol. Biol. Evol. 32, 2273–2283 (2015).
127
B. T. Moyers, P. L. Morrell, J. K. McKay, Genetic costs of domestication and improvement. J. Hered. 109, 103–116 (2017).
128
S. Alseekh et al., Domestication of crop metabolomes: Desired and unintended consequences. Trends Plant Sci. 26, 650–661 (2021).
129
C. Burgarella et al., Adaptive introgression: An untapped evolutionary mechanism for crop adaptation. Front. Plant Sci. 10 (2019).
130
H. Dempewolf et al., Past and future use of wild relatives in crop breeding. Crop. Sci. 57, 1070–1082 (2017).
131
Md. Jamaloddin et al., Marker assisted gene pyramiding (MAGP) for bacterial blight and blast resistance into mega rice variety “Tellahamsa”. Plos One 15, e0234088 (2020).
132
R. Hajjar, T. Hodgkin, The use of wild relatives in crop improvement: A survey of developments over the last 20 years. Euphytica 156, 1–13 (2007).
133
L. Wu et al., Using interactome big data to crack genetic mysteries and enhance future crop breeding. Mol. Plant 14, 77–94 (2020).
134
E. J. B. von Wettberg et al., Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nat. Commun. 9, 649 (2018).
135
M. T. Pisias et al., Prospects of feral crop de novo re-domestication. Plant Cell Physiol. 63, 1641–1653 (2022).
136
P. Chivenge, T. Mabhaudhi, A. T. Modi, P. Mafongoya, The potential role of neglected and underutilised crop species as future crops under water scarce conditions in Sub-Saharan Africa. Int. J. Environ. Res. Pu. 12, 5685–5711 (2015).
137
N. G. Mueller, G. J. Fritz, P. Patton, S. Carmody, E. T. Horton, Growing the lost crops of eastern North America’s original agricultural system. Nat. Plants 3, 17092 (2017).
138
T. Ulian et al., Unlocking plant resources to support food security and promote sustainable agriculture. Plants People Planet 2, 421–445 (2020).
139
F. J. Massawe et al., The potential for underutilised crops to improve food security in the face of climate change. Procedia Environ. Sci. 29, 140–141 (2015).
140
L. Hayashi, S. d. J. Cantarino, A. T. Critchley, Challenges to the future domestication of seaweeds as cultivated species: Understanding their physiological processes for large-scale production. Adv. Bot. Res. 95, 57–83 (2020).
141
D. Burckhalter, Eelgrass: A traditional Comcaac (Seri) seafood and a revolutionary source of grain. J. Southwest. 63, 369–384 (2021).
142
Z. H. Lemmon et al., Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4, 766–770 (2018).
143
G. Luo et al., Accelerated domestication of new crops: Yield is key. Plant Cell Physiol. 63, 1624–1640 (2022).
144
D. L. Van Tassel, L. R. DeHaan, T. S. Cox, Missing domesticated plant forms: Can artificial selection fill the gap? Evol. Appl. 3, 434–452 (2010).
145
F. Andreotti et al., When neglected species gain global interest: Lessons learned from quinoa’s boom and bust for teff and minor millet. Glob. Food Sec. 32, 100613 (2022).
146
M. F. Bellemare, J. Fajardo-Gonzalez, S. R. Gitter, Foods and fads: The welfare impacts of rising quinoa prices in Peru. World Dev. 112, 163–179 (2018).
147
A. Magrach, M. J. Sanz, Environmental and social consequences of the increase in the demand for ‘superfoods’ world-wide. People Nat. 2, 267–278 (2020).
148
G. Alandia, J. P. Rodriguez, S.-E. Jacobsen, D. Bazile, B. Condori, Global expansion of quinoa and challenges for the Andean region. Global Food Security 26, 100429 (2020).
149
V. Angeli et al., Quinoa (Chenopodium quinoa Willd.): An overview of the potentials of the “golden grain” and socio-economic and environmental aspects of its cultivation and marketization. Foods 9, 216 (2020).
150
T. Sang, Toward the domestication of lignocellulosic energy crops: Learning from food crop domestication. J. Integra. Plant Biol. 53, 96–104 (2011).
151
Y. Mizrahi, Do we need new crops for arid regions? A review of fruit species domestication in Israel. Agronomy 10, 1995 (2020).
152
P. Brouwer et al., Azolla domestication towards a biobased economy? New Phytol. 202, 1069–1082 (2014).
153
J. M. Cheeseman, The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions. New Phytol. 206, 557–570 (2015).
154
F. R. Costa-Becheleni, Hydro-environmental criteria for introducing an edible halophyte from a rainy region to an arid zone: A study case of Suaeda spp. as a new crop in NW México. Plants 10, 1996 (2021).
155
T. Lombardi et al., Biological and agronomic traits of the main halophytes widespread in the mediterranean region as potential new vegetable crops. Hortic. 8, 195 (2022).
156
A. Razzaq et al., De-novo domestication for improving salt tolerance in crops. Front. Plant Sci. 12, 681367 (2021).
157
B. Duarte, I. Caçador, Iberian halophytes as agroecological solutions for degraded lands and biosaline agriculture. Sustainability 13, 1005 (2021).
158
J. E. Leake, V. Squires, S. Shabala, Rethinking rehabilitation of salt-affected land: New perspectives from australian experience. Earth 3, 245–258 (2022).
159
R. Martins-Noguerol et al., Crithmum maritimum seeds, a potential source for high-quality oil and phenolic compounds in soils with no agronomical relevance. J. Food Composition Analy. 108, 104413 (2022).
160
K. Negacz, P. Vellinga, E. Barrett-Lennard, R. Choukr-Allah, T. Elzenga, Eds., Future of Sustainable Agriculture in Saline Environments (CRC Press, ed. 1, 2021).
161
R. R. B. Leakey et al., The future of food: Domestication and commercialization of indigenous food crops in Africa over the third decade (2012–2021). Sustainability 14, 2355 (2022).
162
E. N. Kunene, K. A. Nxumalo, M. P. Ngwenya, M. T. Masarirambi, Domesticating and commercialisation of indigenous fruit and nut tree crops for food security and income generation in the kingdom of Eswatini. Curr. J. Appl. Sci. Technol. 37–52 (2020).
163
K. J. DeWeese, M. G. Osborne, Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement. J. World Aquacult Soc. 52, 1009–1030 (2021).
164
F. Goecke, G. Klemetsdal, Å. Ergon, Cultivar development of kelps for commercial cultivation—past lessons and future prospects. Front. Mar. Sci. 8, 110 (2020).
165
F. Rey et al., Domesticated populations of Codium tomentosum display lipid extracts with lower seasonal shifts than conspecifics from the wild—relevance for biotechnological applications of this green seaweed. Mar. Drugs 18, 188 (2020).
166
E. K. Hwang, N. Yotsukura, S. J. Pang, L. Su, T. F. Shan, Seaweed breeding programs and progress in eastern Asian countries. Phycologia 58, 484–495 (2019).
167
S. L. Pearlstein et al., Nipa (Distichlis palmeri): A perennial grain crop for saltwater irrigation. J. Arid. Environ. 82, 60–70 (2012).
168
E. Maréchal, Grand challenges in microalgae domestication. Front. Plant Sci. 12, 764573 (2021).
169
T. P. Pires, E. S. Souza, K. N. Kuki, S. Y. Motoike, Ecophysiological traits of the macaw palm: A contribution towards the domestication of a novel oil crop. Industrial. Crops. Products 44, 200–210 (2013).
170
R. Vargas-Carpintero et al., Acrocomia spp.: Neglected crop, ballyhooed multipurpose palm or fit for the bioeconomy? A review. Agron. Sustain. Dev. 41, 75 (2021).
171
N. Yan et al., Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. Commun. Biol. 5, 36 (2022).
172
A. Westerbergh, E. Lerceteau-Köhler, M. Sameri, G. Bedada, P.-O. Lundquist, Towards the development of perennial barley for cold temperate climates—Evaluation of wild barley relatives as genetic resources. Sustainability 10, 1969 (2018).
173
L. DeHaan, M. Christians, J. Crain, J. Poland, Development and evolution of an intermediate wheatgrass domestication program. Sustainability 10, 1499 (2018).
174
M. Griffiths et al., Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops. Plant Cell Environ. 45, 751–770 (2022).
175
M. B. Kantar et al., Neo-domestication of an interspecific tetraploid Helianthus annuus × Helianthus tuberous population that segregates for perennial habit. Genes 9, 422 (2018).
176
D. G. Tork, N. O. Anderson, D. L. Wyse, K. J. Betts, Domestication of perennial flax using an ideotype approach for oilseed, cut flower, and garden performance. Agronomy 9, 707 (2019).
177
D. L. Lauenstein et al., “Genetic breeding of Prosopis species from the ‘Great American Chaco’” in Low Intensity Breeding of Native Forest Trees in Argentina, M. J. Pastorino, P. Marchelli, Eds. (Springer International Publishing, 2021), pp. 271–293.
178
C. Pometti et al., “Species without current breeding relevance but high economic value: Acacia caven, Acacia aroma, Acacia visco, Prosopis affinis, Prosopis caldenia and Gonopterodendron sarmientoi” in Low Intensity Breeding of Native Forest Trees in Argentina, M. J. Pastorino, P. Marchelli, Eds. (Springer International Publishing, 2021), pp. 295–318.
179
C. Ciotir et al., Building a botanical foundation for perennial agriculture: Global inventory of wild, perennial herbaceous Fabaceae species. Plants People Planet 1, 375–386 (2019).
180
A. Zsögön, L. E. P. Peres, Y. Xiao, J. Yan, A. R. Fernie, Enhancing crop diversity for food security in the face of climate uncertainty. Plant J. 109, 402–414 (2022).
181
G. Charmet, Wheat domestication: Lessons for the future. C R Biol. 334, 212–220 (2011).
182
L. DeHaan et al., Roadmap for accelerated domestication of an emerging perennial grain crop. Trends Plant Sci. 25, 525–537 (2020).
183
A. Watson et al., Speed breeding is a powerful tool to accelerate crop research and breeding. Nat. Plants 4, 23–29 (2018).
184
M. M. van Katwijk, B. I. van Tussenbroek, S. V. Hanssen, A. J. Hendriks, L. Hanssen, Rewilding the sea with domesticated seagrass. Bioscience 71, 1171–1178 (2021).
185
A. Streit Krug, O. I. Tesdell, A social perennial vision: Transdisciplinary inquiry for the future of diverse, perennial grain agriculture. Plants People Planet 3, 355–362 (2021).
186
UN, “The sustainable development goals report” (UN DESA, 2020).
187
M. Reynolds et al., Translational research for climate resilient, higher yielding crops. Crop. Breed Genet. Genom. 1, e190016 (2019).
188
D. L. Van Tassel et al., Accelerating Silphium domestication: An opportunity to develop new crop ideotypes and breeding strategies informed by multiple disciplines. Crop. Sci. 57, 1274–1284 (2017).

Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 120 | No. 14
April 4, 2023
PubMed: 36972445

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Data, Materials, and Software Availability

No data was collected or analyzed for this perspective.

Submission history

Published online: March 27, 2023
Published in issue: April 4, 2023

Change history

September 11, 2023: The Acknowledgments have been updated. Previous version (March 27, 2023)

Keywords

  1. agriculture
  2. crops
  3. domestication
  4. perennials
  5. plant diversity

Acknowledgments

We thank the organizers and participants of the 2021 workshop “Tapping the wild to feed the future” for helpful discussion prior to the formulation of this manuscript. E.J.W. is supported by a grant from the Wallace Genetic Foundation and USDA-NIFA Award 2020-67034-36879.
Author Contributions
A.S.K., E.B.M.D., and E.J.W. conceptualized the paper; A.S.K., E.B.M.D., D.L.V.T., and E.J.W. wrote the paper.
Competing Interests
The authors declare no competing interest.

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Perennial Cultures Lab, The Land Institute, Salina, KS 67401
Emily B. M. Drummond1
Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
Perennial Crop Improvement, The Land Institute, Salina, KS 67401
William L. Brown Center, Missouri Botanical Garden, Saint Louis, MO 63110

Notes

2
To whom correspondence may be addressed. Email: [email protected].
1
A.S.K., E.B.M.D., and E.J.W. contributed equally to this work.

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