The global food system faces mounting vulnerabilities from climate change, pests and malnutrition, largely due to a historical reliance on a narrow range of staple crops that has reduced agricultural biodiversity and resilience
(Molotoks et al., 2020; Abberton et al., 2015). As climate change increases the vulnerability of agriculture worldwide, food security is urgently needed due to rising weather variability, depletion of resources and ecological disturbances
(Manjeet et al., 2023). Indigenous crops, which are adapted to local environments and cultures, offer a strategic pathway to diversify food production and enhance sustainability
(Mayes et al., 2012). Many underutilized species are well adapted to marginal lands and with low cost inputs and may thus be of great benefit for the survival of poor communities, employment generation and sustainability of agricultural ecosystems
(Barua et al., 2019). However, they remain underutilized due to socio-economic barriers such as inadequate policy, weak markets and limited research
(Akinola et al., 2020; Thakur, 2014). Their continued exclusion from formal agricultural systems accelerates genetic erosion and marginalization
(Lichun et al., 2018). For example, in Ethiopia, there is a growing concern about the loss of genetic diversity for ‘minor’ root and tuber crops, which reduces its contribution to food security of the people (
Zerihun, 2022).
Many indigenous species exist in an intermediate state between wild and fully domesticated forms, often maintained through farmer-led selection, a process that preserves valuable genetic diversity and local adaptation (
Goron and Raizada, 2015;
Razifard et al., 2020). These fruit crops have not undergone any conscious phase of domestication and selection and their cultivation is very restricted, yet they can thrive even under most adverse situations
(Barua et al., 2019). Effectively integrating these crops into contemporary agriculture therefore requires a dual focus: understanding their domestication pathways and addressing the socio-structural constraints that limit their scaling.
This review argues that advancing the cultivation of indigenous crops is critical for building resilient food systems in the face of climate change and population growth
(Mabhaudhi et al., 2022). Climate resilient agriculture (CRA) addresses these issues by focusing on conserving and optimizing soil resources and promoting biodiversity
(Kujur et al., 2026). To that end, it synthesizes current knowledge on the benefits, domestication processes and key barriers, from genetic improvement and participatory breeding to market access and policy reform, that shape their potential. By bridging the gap between domestication science and socio-economic analysis, this paper provides a cohesive framework for leveraging neglected and underutilized species (NUS) as catalysts for food security, agroecological resilience and sustainable livelihoods.
Theoretical framework and research approach
Theoretical framework
This review employs a holistic systems perspective, framing the process of domesticating underutilized indigenous crops as a confluence of biodiversity preservation, enhanced climate resilience, strengthened food and nutritional security and the perpetuation of cultural heritage. Informed by agroecological principles and resilience theory, domestication is conceptualized as a dynamic continuum. This continuum spans from wild progenitors through semi-domesticated varieties to cultivated modern breeds, driven by human selection and the intertwined co-evolution of culture and crops. This is supported by the work of
Meyer and Purugganan (2013).
This framework is structured around four interconnected dimensions:
i. Ecological and genetic dimension: This dimension focuses on adaptation, the maintenance of genetic diversity and the capacity for environmental resilience. It underscores the critical role of conserving genetic resources as both a foundational element and a direct outcome of sustainable domestication efforts
(Dempewolf et al., 2017; Bohra et al., 2022).
ii. Socio-cultural dimension: This aspect acknowledges domestication as a form of social innovation, intricately shaped by traditional knowledge systems, cultural values and localized food economies
(Modest et al., 2021).
iii. Economic and market dimension: Here, the focus is on the development of value chains, market accessibility and the diversification of livelihoods as key catalysts for adoption and the fair distribution of benefits (
Mgwenya et al., 2025).
iv. Governance and policy dimension: This dimension highlights the significance of institutional structures and policy interventions that influence research priorities, conservation strategies and equitable benefit-sharing mechanisms.
Sustainable domestication is considered achieved when these dimensions interact synergistically to preserve ecological integrity, safeguard genetic diversity and uphold cultural authenticity, while simultaneously improving food security and fostering socio-economic inclusion. The conceptual model thus connects foundational inputs, such as knowledge, research and policy, with the dynamic processes of domestication, participatory breeding and market development, ultimately leading to desirable outcomes like biodiversity stewardship, community empowerment and the establishment of climate-resilient systems.
Research methodology
A systematic review was undertaken, adhering rigorously to the PRISMA 2020 guideline. This approach combined bibliometric analysis with a qualitative synthesis to systematically examine the existing literature pertinent to the domestication and utilization of underutilized indigenous crops.
Literature search strategy
Peer-reviewed academic publications spanning the period from 2010 to 2025 were systematically retrieved from prominent databases including Scopus, Web of Science, ScienceDirect, PubMed and Google Scholar. The initial search identified 2,543 records. Searches were executed using Boolean operators to combine keywords such as:
(“indigenous crops” OR “underutilised crops” OR “orphan crops”) AND (“domestication” OR “crop improvement”) AND (“food security” OR “climate resilience” OR “biodiversity conservation”).
In addition to academic articles, relevant grey literature and institutional reports from organizations such as the FAO, CGIAR and IPBES were also incorporated into the review.
Criteria for study inclusion and exclusion
Studies were included if they met the following criteria:
- Centrally focused on the domestication, enhancement, or application of underutilized crops.
- Reported findings related to ecological, socio-economic, or policy impacts.
- Were published in English and had undergone peer review.
Studies were excluded if they:
- Primarily addressed major staple crops without a specific focus on underutilized varieties.
- Lacked sufficient methodological rigor in their design or reporting.
Following the removal of duplicates and a two-stage screening process (title/abstract, then full-text), 38 studies were included for the final qualitative synthesis.
Data extraction and analysis procedures
Data extracted from the selected studies were systematically coded using NVivo 14 software and subsequently organized into five primary analytical themes:
- Ecological and genetic diversity considerations.
- Domestication and crop breeding processes.
- Socio-cultural knowledge and practices.
- Market dynamics and economic systems.
- Governance structures and policy frameworks.
Thematic and narrative analysis techniques were then employed to synthesize patterns, identify emergent trends, address contradictions and pinpoint existing research gaps.
Synthesis of findings
A narrative synthesis approach was adopted to integrate the qualitative and quantitative findings derived from the reviewed literature. This process involved three distinct analytical stages:
- Mapping the existing body of evidence.
- Categorizing the benefits and challenges associated with domestication thematically.
- Synthesizing the findings within the established conceptual framework to discern and articulate sustainability outcomes.
Ethical considerations
This review did not involve the collection of primary data. Ethical principles were rigorously maintained through accurate attribution of sources and due recognition of indigenous knowledge. The study also operates in alignment with the principles of the Nagoya Protocol on Access and Benefit Sharing (ABS).
Anticipated contributions
This review is expected to yield the following significant contributions:
- The development of a comprehensive conceptual model that elucidates the interconnections between crop domestication processes and both ecological and socio-economic sustainability.
- The identification of critical research lacunae in areas such as genomics, participatory breeding approaches and market development strategies for underutilized crops.
- The provision of a policy-focused roadmap designed to guide the integration of underutilized crops into broader climate-smart agricultural initiatives.
Defining indigenous and underutilized crops in context
A variety of terms, such as underutilized species,
orphan crops,
underutilized species,
minor crops, traditional crops and
neglected species, are used to describe plant species that are not widely cultivated in mainstream agriculture. For the purposes of this discussion, “indigenous crops” refers to plant species that either originated in a specific region or have undergone significant diversification there and are strongly linked to the food systems, ecological knowledge and cultural traditions of local and indigenous communities
(Hunter et al., 2019). Passed down through informal seed systems and generations of farmer selection, these crops have developed unique adaptations to suit local environmental conditions and socio-cultural needs
(Mabhaudhi et al., 2019a).
The label ‘underutilized’ indicates that these species, despite their potential benefits for food and nutritional security, agrobiodiversity conservation and climate change resilience, receive limited attention in global agricultural research, policy and commercial development (
Tadele, 2019). Their potential remains largely unrealized due to historical neglect, limited genetic enhancement, weak value chains and insufficient institutional support
(Woldeyohannes et al., 2022).
While globally dominant crops like wheat, maize and rice are bred extensively for high-input agricultural systems, indigenous crops are often chosen for characteristics suited to traditional farming practices, such as drought resistance, pest immunity, minimal input needs and cultural or medicinal value. These crops, geographically and ecologically varied, include African leafy vegetables (Amaranthus spp., Corchorus spp.,
Solanum nigrum), climate-resilient grains like fonio (
Digitaria exilis) and finger millet (
Eleusine coracana), tuber crops like indigenous yams (
Dioscorea spp.) andean root vegetables (
oca, ulluco) and pseudo-cereals like quinoa and amaranth (
Chenopodium quinoa, Amaranthus spp.)
(Termote et al., 2021). Frequently, they function as biocultural keystone species, representing the combined ecological and cultural heritage of indigenous communities
(Mattalia et al., 2024).
Domestication, from a biological and evolutionary perspective, is a continuous and evolving process of human-driven selection that leads to heritable genetic changes, distinguishing cultivated plants from their wild relatives. Typical domestication traits encompass loss of seed dormancy, larger seed or fruit size, uniform ripening and reduced natural dispersal or toxicity (
Meyer and Purugganan, 2013). Many indigenous crops are still in this phase of domestication, an ongoing and non-linear process influenced by localized selection pressures and preferences. These prioritize versatility, adaptation to challenging environments and cultural significance over the limited productivity measures emphasized in industrial agriculture
(Modest et al., 2021). This creates a diverse range of semi-domesticated species that connect wild and cultivated ecosystems, especially within smallholder and traditional agroecological systems.
Significance of indigenous crops: A multifaceted perspective
Indigenous crops hold significance far beyond their direct role in local food production, serving vital ecological, nutritional, cultural and economic purposes. Experts increasingly acknowledge their essential contribution to sustainable agriculture, especially given current challenges like climate change, biodiversity loss and the vulnerability of global food systems (
IPBES, 2019). Table 1 below synthesizes these core advantages.
Biodiversity and genetic resources
The cultivation and preservation of indigenous, often underutilized, crops are crucial for boosting agrobiodiversity, which in turn strengthens ecosystem resilience and genetic variety within our food supply
(Hunter et al., 2019). Unlike single-crop monocultures, these diverse species possess a wealth of valuable traits for enduring environmental stresses such as drought, heat, salinity and pests-characteristics essential for crops to adapt to a changing climate
(Dempewolf et al., 2017; Jamnadass et al., 2020). Their genetic material is not only vital for improving the indigenous crops themselves but also provides specific genes (alleles) that can enhance major staple crops through techniques like pre-breeding and introgression (
Tadele, 2019). Losing these genetic resources, often due to widespread adoption of major crops and insufficient institutional backing, means a permanent loss of future adaptability
(Modest et al., 2021).
Ecological sustainability
Many indigenous crops flourish in challenging, marginal environments where traditional cash crops struggle. They are foundational to traditional agroecological practices, requiring minimal inputs and conserving resources effectively
(Chivenge et al., 2015; Altieri and Nicholls, 2017). Growing these crops offers significant ecological benefits, including restoring soil fertility, preventing erosion and improving water retention. When grown alongside other crops in polyculture systems, they boost overall biodiversity, attract beneficial insects and microbes and lessen the need for artificial fertilizers and pesticides
(Mabhaudhi et al., 2019).
Nutritional security and health
Often overlooked, indigenous crops frequently boast better nutritional content than many globally consumed staples. For instance, numerous leafy vegetables are packed with vital micronutrients like iron, zinc, calcium and vitamins A and C, while pseudocereals such as quinoa and amaranth provide complete proteins and essential fatty acids (
Smith and Maunder, 2022). Incorporating these crops into local diets can effectively address ‘hidden hunger,’ reduce widespread micronutrient deficiencies and help prevent non-communicable diseases linked to poor dietary balance (
John and Vicent, 2025). Expanding food diversity with these crops aligns perfectly with the concept of nutrition-sensitive agriculture, which aims to ensure both sufficient calories and high-quality diets (
Li and Siddique, 2020).
Socio-cultural heritage and traditional knowledge
Indigenous crops are intrinsically linked to cultural identity, traditional rituals, and vast systems of ethnobotanical knowledge
(Saensouk et al., 2025). They represent centuries of accumulated local wisdom concerning cultivation, food processing, seed preservation, and culinary traditions. Reintroducing and nurturing these species can foster cultural empowerment and facilitate the transfer of knowledge across generations, particularly when integrated into collaborative plant breeding programs and community-managed seed networks
(Modest et al., 2021). Nevertheless, obstacles like cultural resistance or inadequate institutional backing can impede their wider adoption; therefore, successful projects must be culturally sensitive and driven by the communities themselves
(Sperling et al., 2020).
Economic potential and livelihoods
Indigenous crops offer significant economic prospects, especially for smallholder farmers in difficult growing regions. Their minimal input requirements, attractiveness to niche markets, and inherent climate resilience can lead to reliable income streams, particularly if their value chains are enhanced through processing, branding, and certification
(Mgwenya et al., 2025). For instance, the commercial development of crops like fonio (
Digitaria exilis) and baobab (
Adansonia digitata) has demonstrably improved rural livelihoods across parts of Africa
(Jamnadass et al., 2020; Tadele, 2019). However, realizing these advantages is often hampered by hurdles like inadequate infrastructure, insufficient consumer knowledge, and disorganized markets (
John and Vicent, 2025;
Mmbando, 2025). Successful economic transitions will likely necessitate public investment in research and agricultural extension services, coupled with institutional frameworks that ensure fair distribution of value (
Mmbando, 2025;
Ohlin et al., 2024).
Benefits deriving from utilising indigenous crops
Harnessing the potential of native crops through proactive promotion and integration offers a multitude of interconnected advantages, ranging from enhanced food security and improved nutrition to environmental sustainability, biodiversity preservation and the empowerment of local communities. The significance of these benefits is increasingly acknowledged in global discussions about transforming food systems, achieving sustainable development and building resilience to climate change.
Bolstering food security and climate resilience
Indigenous crops are vital for climate-smart agriculture due to their inherent adaptation to local environments, including resistance to drought, heat, salinity and poor soils. Their resilience is crucial for ensuring food security amidst increasing climate variability, particularly in vulnerable regions reliant on rainfed agriculture. Incorporating indigenous species diversifies cropping systems, reducing reliance on a limited number of crops and increasing system stability and yield reliability, especially in challenging environments.
Enhancing nutrition and public health
Many native crops boast superior nutritional profiles, offering essential vitamins, minerals, proteins and fiber often lacking in staple foods. Leafy greens like Amaranthus and Corchorus are rich in iron and calcium, while pseudocereals such as quinoa and amaranth provide complete proteins. Integrating these crops into local diets is a cost-effective approach to combatting micronutrient deficiencies, particularly among women and children. Public health initiatives that promote their consumption can contribute to long-term health and prevent non-communicable diseases.
Promoting sustainable and regenerative agriculture
Indigenous crops are often grown in eco-friendly systems that require minimal chemical inputs and conserve soil and water. Utilizing them in polycultures and crop rotations enhances resilience, soil fertility and natural pest control. By supporting ecosystem services like pollination, nutrient cycling and carbon sequestration, they align with the goals of regenerative agriculture and climate change mitigation.
Facilitating dynamic on-farm conservation
Cultivating indigenous crops actively contributes to the in-situ conservation of plant genetic resources, allowing for continued evolution under farmer management. This on-farm approach not only preserves genetic diversity but also safeguards associated cultural and ecological knowledge. While gene banks play a vital role in
ex-situ conservation, maintaining these species within their native environments ensures adaptation to evolving climate and disease pressures.
Empowering local and indigenous communities
Revitalizing indigenous crops empowers communities by leveraging their cultural and economic significance. These crops are often deeply connected to local identities, traditions and knowledge, providing a valuable resource base. Promoting them can restore pride in traditional practices, facilitate knowledge transfer between generations and create inclusive value chains that prioritize smallholder participation and equitable benefit-sharing. Market development for indigenous crops is already improving livelihoods and empowering women in various regions.
The process, challenges and implications of domestication and improvement
Realizing the potential of indigenous crops often requires strategic domestication and genetic improvement to address traits that limit cultivation or consumption, such as seed shattering, anti-nutritional compounds, or laborious processing
(Bohra et al., 2022). Modern approaches like marker-assisted selection and participatory plant breeding (PPB) are effective, with PPB ensuring traits align with local preferences and environments (
Aziz and Masmoudi, 2025;
Lebot and Viquez-Zamora, 2025).
However, systemic barriers hinder progress. The following consolidated challenges are critical:
•
Limited R and D and genetic erosion: · Chronic underinvestment in research leaves agronomic, genomic, and nutritional profiles poorly understood (
Mphande, 2025). Paradoxically, domestication itself risks genetic homogenization, eroding the diversity that underpins resilience (
Dempewolf et al., 2017).
•
Weak seed systems and value chains: Formal seed systems often neglect indigenous varieties, while informal networks may lack scale. Coupled with underdeveloped processing infrastructure and market access, this stifles commercial viability (
John and Vicent, 2025).
•
Policy neglect and knowledge loss: Agricultural policies frequently favor major staples, creating disincentives. Simultaneously, the intergenerational erosion of traditional knowledge threatens the conservation of cultivation and utilization practices.
(Melash et al., 2023; Ngonzi and Lubenga, 2020).
•
Equity and access concerns: Commercialization raises issues of fair benefit-sharing and biopiracy, necessitating robust Access and Benefit Sharing (ABS) frameworks per the Nagoya Protocol to protect community rights (
Bob and Christine, 2025;
Ebert et al., 2023).
Implications
Responsible domestication must be guided by a socio-technical framework that integrates formal science with farmer-led innovation and traditional knowledge. The goal is not merely yield improvement but advancing food sovereignty, cultural integrity and ecological stewardship, ensuring that crop development strengthens rather than undermines the foundational benefits these species provide
(Kahane et al., 2021; Massawe et al., 2020).
Discussion: Navigating the path from recognition to integration
This review affirms that indigenous underutilized crops are vital resources for building sustainable and resilient food systems. However, their journey from marginalization to mainstream integration is fraught with systemic contradictions. The central challenge lies in navigating a path that enhances productivity and market viability without eroding the very genetic diversity, ecological adaptability and cultural embeddedness that constitute their core value. This discussion synthesizes the findings to highlight key tensions and propose a reframed approach for future action.
The core tension: Standardization vs. biocultural integrity
The findings reveal a fundamental tension. On one hand, domestication and improvement efforts often aim to standardize traits for wider adaptability and market appeal, a process aligned with conventional agricultural development. On the other hand, the unique value of these crops is inherently tied to their local specificity, maintained through decentralized seed systems and traditional knowledge
(Melash et al., 2023). This creates a critical dilemma: how to improve yields or processing efficiency without triggering genetic homogenization or disempowering the communities who are their custodians.
The erosion of traditional knowledge is not merely a collateral loss but a direct threat to the sustainability of improvement programs themselves. As
Lemchi et al., (2016) underscore, this knowledge is the operating manual for cultivating diverse landraces in variable environments. Therefore, future strategies must view knowledge co-creation and intergenerational transfer not as a separate challenge, but as the foundational pillar of any domestication initiative.
Reframing the framework: From linear improvement to socio-ecological innovation
The persistent challenges of underinvestment, weak seed systems and market neglect (
Tadele, 2019) are symptoms of a broader systemic failure to value biocultural diversity. Addressing them requires moving beyond a linear pipeline model of “crop improvement” toward a socio-ecological innovation framework. This entails:
1. Redefining ‘Improvement’: Success metrics must be expanded beyond yield to include nutritional density, ecosystem service provision, climate resilience and cultural relevance. Participatory Plant Breeding (PPB) is a critical methodology here, as it embeds farmer priorities and ecological context directly into the breeding agenda
(Colley et al., 2022).
2. Reconceptualizing seed systems: Formal and informal seed systems should not be seen as mutually exclusive but as complementary. Policy support is needed to legitimize, strengthen and link community seed banks and farmer networks with national gene banks and regulatory frameworks, creating a resilient, polycentric seed governance model.
3. Integrating ethical governance from the outset: The issues of Access and Benefit-Sharing (ABS) cannot be an afterthought. As
Elbert et al. (2023) argue, proactive engagement with the Nagoya Protocol and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) is essential to design value chains that ensure equitable returns and recognize traditional knowledge as intellectual innovation.
Strategic alignment for systemic impact
To translate this reframed approach into action, targeted efforts must be strategically aligned with broader sustainable development objectives. Table 2 synthesizes key challenges and proposed future directions, explicitly linking them to relevant Sustainable Development Goals (SDGs). This alignment provides a concrete framework for policymakers, researchers and funders to prioritize interventions that deliver compounded benefits across food security, environmental sustainability and social equity.
