Climate Smart Agriculture Sourcebook

Genetic resources for Climate-Smart Agriculture Production

Production and Resources

Climate-smart management of plant genetic resources

Plant genetic resources are defined by the International Treaty on Plant Genetic Resources for Food and Agriculture as “any material of plant origin, including reproductive and vegetative propagating material, containing functional units of heredity of plant origin of actual or potential value for food and agriculture”. These resources are used, or have the potential to be used, for food and other agricultural purposes. They include crop wild relatives ; other species that could interbreed with crops; wild plants that are harvested for food; landraces and farmer varieties; and formally registered crop varieties. The diversity of plant genetic resources underpins global food security and nutrition. Plant genetic resources consist of a vast diversity of heritable traits that have enable crops to adapt to physical and biological stresses (e.g. drought, heat, cold, pests and diseases). This diversity needs to be harnessed to help crop production systems adapt to the consequences of climate change. However, despite the existence of diverse crops and their varieties, only 17 crops provide about 80 percent of human food energy needs met by plants out of the over 50,000 edible plant species (figures for 2013 as recorded in FAO’s statistical database FAOSTAT (FAO, 2017a). (see also chapter B1 - 1.1 on the need for sustainable production intensification and diversification). In fact, just seven of these (rice, wheat, sugarcane, maize, soyabean, potatoes and sugarbeet) account for about 55 percent of the energy intake of the world’s population (figures for 2013 as recorded in FAO’s statistical database FAOSTAT (FAO, 2017a).

B8 - 3.1 Impact of climate change on plant genetic resources

Climate change affects the concentration of carbon dioxide in the atmosphere, temperatures, precipitation patterns and the distribution of land suitable for cultivating many crops. See chapter B1 - 1.2 for the most universally accepted effects of climate change on crop production. It is predicted that in sub-Saharan Africa, the Caribbean, India and northern Australia, the amount of land suitable for crop production will decline. Without measures to adapt to these new conditions, production of the world’s major staple crops (wheat, rice and maize) will be negatively affected in these areas (FAO, 2015b). There is evidence that climate change has already reduced wheat and maize yields in many regions (Lobell, Schlenker and Costa-Roberts, 2011). Crop management practices and technologies for adaptation to climate change are presented in chapter B1 - 2, and these management practices in the context of specific farming systems are presented in chapter B1 - 3.

Genetic vulnerabilityxi results when a widely planted crop is uniformly susceptible to a pest, pathogen or environmental hazard as a result of its genetic constitution. This creates the potential for widespread crop losses. Genetic vulnerability threatens agricultural production in 60 countries (FAO, 2010). For example, of the 120 cultivars included in the Russian Official List of 2002, 96 percent of all the varieties of winter wheat in Russia were descendants of either one or both of two cultivars, Bezostaya 1 and Mironovskaya 808 (Martynov and Dobrotvorskaya, 2006). A new type of a particularly virulent pest or disease, which could emerge as a consequence of climate change, could conceivably cause considerable crop losses, as all the plants would be uniformly susceptible. An example of the dangers of genetic vulnerability is the infamous potato blight, which caused significant yield losses and contributed to unprecedented famine in Ireland in the mid-19th century. More recently, in the summer of 1970, corn fields in the middle and south central parts of the United States were devastated by a strain of Helminthosporium maydis. 

Climate change will also affect the ability of many crop wild relatives, which are potential gene donors for crop improvement programmes, to survive in their current locations. Species without alternative habitats will be vulnerable to extinction (Jarvis, Lane and Hijmans, 2008). Thomas et al. (2004) have predicted that by 2050, 15 to 37 percent of wild plant biodiversity, including the wild relatives of many crop species, will be threatened with extinction due to climate change. Of the 50 000 to 60 000 known species of crop wild relatives, it has been estimated that between 16 and 22 percent of these may be in danger of extinction by 2055 (Jarvis, Lane and Hijmans, 2008).

B8 - 3.2 Characterization, evaluation, inventory and monitoring of plant genetic resources

Characterization is the description of plant germplasmxii. It defines the expression of highly heritable characters including morphological, physiological or biochemical features, and entails the description of a minimum set of standard phenotypic, physiological and seed qualitative traits (FAO, 2014d). Some of the activities involved in characterization include true-to-type identification, gene flow studies and reference profiling. These activities can also assist in the detection of duplicates stored in genebanks (FAO, 2014d).

Evaluation is the study of environmental response traits and their function in diverse ecosystems. The evaluation of plant genetic resources, which is used to assess the agronomic performance of a crop, requires an analysis of agronomic data obtained through appropriately designed experimental trials. 

Characterizing and evaluating the variation of plants along environmental gradients is crucial for estimating their vulnerability to climate change. Having access to this information facilitates effective planning of how these resources could best be used and developed to harness production systems to climate change.  

Both characterization and evaluation are carried out using crop descriptor lists, such as those developed by FAO/Bioversity International, by International Union for the Protection of New Varieties of Plants and by United States Department of Agriculture’s National Plant Germplasm System.

Documentation plays an important role in the management of germplasm. The success or failure of a programme for the conservation and sustainable use of plant genetic resources depend to a large extent on the amount and quality of information that is available about these resources and the environments to which they are adapted, as well as on the effectiveness of the systems used to manage this information. This information is critical for making decisions about how to harness genetic resources to address the impacts of climate change.

In situ national inventories of crop wild relatives and wild food plants, and knowledge and information systems based on their genetic and eco-geographical analyses, can provide a solid foundation for establishing conservation priorities and monitoring the in situ diversity of these vulnerable plant groups (FAO, in press). 

In ex situ collections, passport dataxiii  represent the first basic information that helps document and characterize the plant diversity conserved. FAO and Bioversity International have recently published a revised set of passport descriptors widely used for documenting and exchanging germplasm (Alercia, Diulgheroff and Mackay, 2015). Descriptors associated with the location and date of collection are of particular relevance for crop wild relatives, wild food plants and, to a certain extent, landraces. Accurate data on these descriptors allow for the association of a conserved accessionxiv with its eco-geographical data of the area and habitat in which the population has evolved. A number of tools are freely available for eco-geographical analysis including CAPFITOGEN and DIVA-GIS.

Characterization and evaluation data are very important for the targeted use of germplasm. Information about germplasm allows for greater precision in the identification of sources of heritable traits for use in breeding programmes. Germplasm management systems, such as GRIN-Global, are increasingly being used for documenting not only passport but also characterization and evaluation data in genebanks. A number of national, regional and global specialized web portals currently publish information on ex situ collections, among these the United States Department of Agriculture  Germplasm Resources Information Network (GRIN), EURISCO, SESTO (NordGen) and GENESYS. USDA-GRIN and GENESYS provides access to passport data as well as characterization and evaluation data.

The World Information and Early-Warning System on Plant Genetic Resources for Food and Agriculture (WIEWS) is the information system used by FAO for the preparation of periodic, country-driven global assessments of the status of conservation and use of plant genetic resources for food and agriculture. WIEWS also monitors indicators on the implementation of the Second Global Plan of Action for Plant Genetic Resources for Food and Agriculture (FAO, 2011a) and contributes to the elaboration of the plant component of Sustainable Development Goal indicator 2.5.1.

B8 - 3.3 Sustainable use and development of plant genetic resources for climate change adaptation

The sustainable use of plant genetic resources encompasses trait evaluation; pre-breeding; plant breeding, including genetic enhancement and base-broadeningxv; diversification of crop production; development and commercialization of varieties; support to seed production and distribution; and development of new markets for local varieties and products. These activities can contribute to addressing the impacts of climate change on sustainable crop production. 

Farmer varieties and landraces are generally well adapted to current conditions in their local production environments and have been a successful source for adaptive genes in crop improvement (Mba, Guimaraes and Ghosh, 2012; Lopes et al., 2015). However, changing climatic conditions will mean that they may lose this adaptation (Bellon, Hodson and Hellin, 2011). The introduction of varieties of more suitable crops from elsewhere may not always be a practical solution (Bellon and van Etten, 2014). The breeding of new varieties may be the only viable option. 

An unintended consequence of the successes of genetic improvement is the increasingly narrow genetic base of cultivars, especially for the major crops (Tester and Langridge, 2010; Martynov and Dobrotvorskaya, 2006; Mba, 2013; Mba, Guimaraes and Ghosh, 2012; Nass and Paterniani, 2000). The increased homogeneity and uniformity (i.e. genetic vulnerability) render crops potentially more susceptible to the impact of climate change (see module B1 - 1.1 on the impacts of climate change on crop production). This genetic vulnerability may be reduced by incorporating into cultivars the novel traits (e.g. resistance to biotic and abiotic stresses) that are often found in crop wild relatives (Lane and Jarvis, 2007; Dwivedi et al., 2008; Maxted et al., 2008), and landraces and farmer varieties. Pre-breeding (i.e. the generation of intermediate materials that are used as parents in plant breeding) is a means to introgress novel alleles from non-adapted materials into crop varieties (Nass and Paterniani, 2000). The FAO e-learning course on pre-breeding (FAO, 2011b) is a useful capacity-building tool for this new crop improvement discipline. 

Some examples of the successful introduction of novel stress-tolerant traits into cultivars from crop wild relatives are presented in Table B8.1. 

Table B8.1.

Examples of traits obtained from crop wild relatives and the cultivated species to which they contributed resilience (Brozynska, Furtado and Henry, 2015; Maxted and Kell, 2008)




Water stress tolerance

Slender wild oats (Avena barbata

Oat (Avena sativa)

Leaf tolerance to cold stress

Wild grapevine species (Vitis amurensis)

Grape (Vitis vivifera)

Adaptation to high salinity and tolerance to submergence in saline water

Wild relative of rice (Oryza coarctata)

Rice (Oryza sativa)

Stress tolerance, nutritional and grain quality improvement

Wild rice (Oryza glaberrima)

Rice (Oryza sativa)

Early leaf spot resistance

Wild peanuts (Arachis appressipila, A. paraguariensis)

Peanut (Arachis hypogaea)

Resistance to nematods, Rust, early and late leaf spot

Grain size

Wild peanuts  (Arachis cardenasii)

Peanut (Arachis hypogaea)

Drought resistance

Wild plantain (Musa balbisiana, M. nagensium)

Banana and plantain (Musa acuminata, M. balbisiana)

Adaptation to high altitudes and cool temperatures

Wild cassava (Manihot rubricaulis)

Cassava (Manihot esculenta)

It is possible to use predictive characterization tools based on eco-geographic and climate data to determine remotely the diversity and geographical locations of crop wild relatives and landraces (Glaszmann et al., 2010; Redden, 2013). This approach is known as the Focused Identification of Germplasm Strategy. A useful tool for carrying out this strategy is the technical guideline developed by Bioversity International (Thormann et al., 2016). 

Increasing the yields of major food crops – or even maintaining them – in the face of climate change will depend to a large extent on the ability of plant breeders and geneticists to introduce adaptive traits found in plant genetic resources to breed locally adapted varieties (Jarvis et al., 2008). The active participation of farmers in crop varietal development significantly increases the adoption rates of new varieties (Sperling et al., 2001; Ashby, 2009; Efisue et al., 2008; Witcombe et al., 1996; TAC Secretariat, 2001). 

The development of crop varieties that tolerate the stressors brought about by climate change (Foresight, 2011; World Economic Forum, 2010) requires the use of a range of methodologies, such as induced mutations (Maluszynski et al., 2000; Ahloowahlia, Maluszynski and Nichterlein, 2004; Shu, 2009; Joint FAO/IAEA Mutant Varieties and Genetic Stocks Database); biotechnological applications, including cell and tissue biology, marker-assisted selection and genetic engineering; and novel plant breeding techniques, including genome editing procedures. The development of Scuba Rice, a flood-tolerant variety of rice, and its wide dissemination in flood-prone areas, such as those found in Bangladesh, India and the Philippines is an example of the successful breeding of a crop variety that supports climate-smart agriculture (Singh et al., 2010). The adoption of climate-ready varieties in locations where extreme events, such as flooding, are expected to increase as a result of climate change, can be a key component of climate-smart agriculture strategies.

Many edible plant species are neglected and underutilized but are resilient and adapted to marginal areas (Ebert, 2014; Kahane et al., 2013; Padulosi, Bergamini and Lawrence, eds., 2011; FAO, 2010). Examples include Bambara groundnut (Vigna subterranea), the jicama or yam bean (Pachyrhizus erosus) and Moringa (Moringa oleifera). In drought-prone regions, replacing staples, such as maize, with drought-resistant crops, such as cassava and millets, would make agronomic sense. However, this shift in production would become a viable climate-smart agricultural adaptation strategy only if farmers are willing to adopt these new crops (Burns et al., 2010; Rezaei et al., 2015). 

Farmers can only benefit from suitably adapted crop varieties if they can access the seeds and planting materials in a timely manner, in the right quantity and quality, and at an acceptable cost. For these diverse crops and crop varieties to contribute to climate change adaptation and sustain rural livelihoods, it is important to put in place effective seed delivery systems that cater to these new crops and can reach the remotest regions (Rubyogo et al., 2010; McGuire and Sperling, 2013; Sperling, Boettiger and Barker, 2014; Westengen and Brysting, 2014). Seed delivery systems involve variety release procedures, seed production, quality control, and marketing (Tripp, 2001; Louwaars and de Boef, 2012). As discussed in chapter B1 - 2, these systems are usually subject to national and international policies and regulations (FAO, 2015c), and involve diverse actors, such as government authorities, private firms, community-level cooperatives, input dealers, and contracted out-growers.

B8 - 3.4 Sustainable use and development of plant genetic resources for climate change mitigation

Overall, plant genetic resources contribute more significantly to climate adaptation than to climate change mitigation. A number of strategies, however, can improve the sequestration of greenhouse gases and contribute to mitigating climate change. One approach is to maintain or increase carbon content in plants, through the increased cultivation of crops that produce a four-carbon compound during photosynthesis (known as C4 plants), such as maize, sorghum, sugarcane and millets (Lara and Andreo, 2011). Studies have shown that increased carbon sequestration capacity, which is realized through improved photosynthesis, is a heritable trait that can be enhanced through conventional breeding (El-Sharkawy, 2016). Breeding activities in this area have led to varieties that are more productive and sequester more carbon. 

There is also significant diversity in the nitrogen-fixing capacity of legume crops, including pulses, such as garden pea, lentil, groundnut, mung bean, cowpea, pigeon pea and chickpea (Abi-Ghanem et al., 2013; Cernay, Pelzer and Makowski, 2016; Cook, 2014; Gresshoff et al., 2015). The cultivation of pulses and other legumes would provide additional support climate change mitigation, as increased nitrogen fixation is also correlated with increased carbon sequestration (see Box B1.7)  (Jensen et al., 2012; Mapope et al., 2016).

B8 - 3.5 Conservation of plant genetic resources

The conservation of plant genetic resources serves to maintain genetic diversity among and within plant species. Conservation strategies include safeguarding these resources in their natural habitats (in situ conservation), especially for crop wild relatives; managing these resources on farms (i.e. cultivating a diversity of crops and their varieties, especially farmer varieties and landraces); and storing accessions or samples in genebanks (ex situ conservation). Genetic studies provide tools for population monitoring and assessment that can be utilized for conservation planning (Govindaraj, Vetriventhan and Srinivasan, 2015). An efficient collaboration between genebank curators, breeders, and national programmes can help ensure the sustainable conservation of these resources.

In situ conservationxvi involves locating, describing the conservation status, and actively managing and monitoring targeted wild plant populations in their natural habitats. Many crop wild relatives are at risk of extinction from habitat loss, habitat fragmentation, changes in land use and land management practices, and introgression back from agricultural relatives. Climate change has become another threat to their survival. Species in some habitats, such as those found in montane environments and island or coastal areas, are especially vulnerable, as they tend to be highly specialized and/or isolated. These populations are likely to be the first casualties of climate change. 

Much of existing plant diversity, particularly of crop wild relatives and underutilized species, still needs to be secured. These species are fast disappearing due to the standardization of agricultural practices and changes in food habits (Rojas et al., 2009; FAO, 2010). There has been an overall increase in the awareness for conservation. However, significant issues still need to be resolved with regard to surveying, carrying out inventories and conserving plant genetic resources both in situ and on farms. Crop wild relatives remain a relatively low priority in germplasm collection, and significant gaps remain in their collection and conservation (Figure B8.1; Maxted and Kell, 2009).

Figure B8.1.

Global priority areas for conservation of crop wild relatives (CWR) of 12 food crops. 

Source: Maxted and Kell (2009)

The on-farm conservation and management of landraces and farmers’ varieties contribute to the continued evolution and adaptation of diversity. Activities in this area lead to the development of variants that are better suited to specific environments and are essential for future crop improvements. Farmers and indigenous and local communities play a critical role in the conservation and management of plant genetic diversity in situ and on farms.

Ex situ conservationxvii of plant genetic resources in genebanks safeguards a large and important amount of resources that are vital to global food security. Germplasm of crops and crop wild relatives is conserved in more than 600 genebanks worldwide and adds up to a total of about 4.7 million accessions maintained under medium- and long-term conditions globally (United Nations, 2017). Much of this plant diversity is important for breeding crop varieties that are adapted to climate change. The 11 genebanks of the Consultative Group for International Agricultural Research and the World Vegetable Centre maintain over 770 000 accessions comprising over 650 different genera. Since 1996, almost 2 million accessions have been added to ex situ genebanks with medium- and long-term collections, though gaps still exist (WIEWS, 2017).

Securing adequate storage conditions for the genetic materials already collected and providing for their regeneration and safety duplication are essential. Yet many of these collections are still vulnerable, exposed to natural disasters, including those caused by climate change, and man-made calamities such as civil unrest. Plant genetic resources are similarly vulnerable due to avoidable adversities resulting from lack of funding and/or poor management. To address these on-going issues, the Svalbard Seed Vault was created to provide backup (black box) storage for the global collections. The Seed Vault has the capacity to store 4.5 million varieties of crops, providing safeguarding for some 2.5 billion seeds. Currently, the Vault holds more than 930,000 samples, originating from almost every country in the world.