Abiotic stresses associated with climate change that destabilize yields include flooding, drought, soil salinity and extreme temperatures (Fig. 1). Resilience mechanisms have been mobilized for crop improvement through the identification of genes that are associated with key traits and signal transduction pathways, followed by breeding or engineering46,47 (Fig. 2b–f). Attaining resilience without affecting overall yield is a considerable challenge.

Flooding

Floods regularly limit yields48. Rice is exceptionally resilient against flooding, yet over 30% of the acreage cultivated with rice suffers yield loss owing to plant submergence49. SUBMERGENCE 1 (SUB1), identified in a flooding-tolerant landrace of rice, encodes a cluster of genes for ethylene-responsive transcription factors, including the submergence-activated SUB1A-150. The SUB1A transcription factor curbs the activation of genes that promote the breakdown of leaf sugars and starch (photo-assimilate) that would otherwise fuel growth to escape an inundation51 (Fig. 2b). The introduction of SUB1A-1, through marker-assisted breeding, into high-yield varieties now provides an additional week or more of submergence tolerance—without compromising yields under non-submergence conditions52.

The submergence tolerance by growth quiescence provided by SUB1A-1 contrasts with the accelerated underwater elongation of the shoots of varieties of crops that are adapted to progressive seasonal floods in delta regions. Deepwater varieties invest photo-assimilate into the extension of submerged stem internodes (Fig. 2b). This requires the SNORKEL 1 (SK1) and SNORKEL 2 (SK2) genes that encode transcription factors that are similar to SUB1A53, as well as biosynthesis of the hormone gibberellin. Gibberellin biosynthesis involves a functional allele of SEMIDWARF1 (SD1)54, the gene that—when mutated—determines the short stature of Green Revolution rice55. This knowledge can improve yields in low-lying areas that affected by climate change.

The alleles of SUB1A, SK1, SK2 and SD1 that are key to flooding survival are found in wild Oryza species56, which indicates that they arose in ancestral populations in flooded ecosystems. Evolution has modified the same growth-response network involving the hormones ethylene and gibberellin to achieve submergence tolerance or escape in diverse species of wetland plants48. Pathways to improved flooding tolerance include manipulation of root traits associated with waterlogging tolerance that involve a conserved mechanism48 and the oxygen-dependent turnover of SUB1A-1-like transcription factors, accomplished in several species57,58,59,60. There are other opportunities to protect yields in wet climates. Torrential rain and hail can cause yield losses of 50% or more, owing to premature pod shattering in oil crops. The identification of genes that control pod shattering in Arabidopsis61 enabled the gene-targeted molecular breeding of optimized pod-shattering properties in canola that is now increasingly planted by farmers.

Drought

Drought and other dehydration or osmotic stresses (salinity and cold) stimulate the production of the hormone abscisic acid (ABA) in plants. Although the mechanisms of the initial sensing of osmotic stress and signalling in response to osmotic stress remain poorly understood, the elucidation of the ABA receptor and signal transduction mechanisms62,63 has exposed new avenues for the enhancement of dehydration tolerance. This includes ABA receptor overexpression64,65 and engineering to respond to exogenously sprayed small molecules66,67, the overexpression of signal transduction components68,69,70 or the drought-driven repression of negative regulators of ABA signal transduction69,71.

ABA closes the adjustable stomatal pores on the leaf surface that allow gas exchange and thus reduces the water lost from plants during drought, but this response can be weak in crop varieties69,72. ABA also helps to regulate root growth in response to water availability, including inhibition of lateral root growth and enhancement of primary and secondary root growth. This developmental reprogramming allows roots to seek water. The DEEPER ROOTING (DRO1) gene of rice provides a deep root architecture in paddy fields, which bolsters yields under water-limited conditions73,74,75 (Fig. 2c). The identification of the major loci that control root traits associated with drought resilience has proven challenging owing to their quantitative nature and low heritability, which requires sophisticated belowground phenotyping and analytical methods76. Yet roots grow laterally towards moisture in soil77. New roots that access moisture emerge only on the side of a root that is moist, as a modification of a key auxin-response transcription factor on the dry side of a root impedes the developmental program78 (Fig. 2c). Knowledge such as this can inform strategies for the advanced breeding and engineering of improved resilience to drought, which continues to limit yields79,80.

Salinity

Irrigation substantially expands growing seasons and increases crop yields in many regions. Salt (sodium chloride) gradually accumulates in irrigated soils and is toxic to most crops; sodium accumulation is particularly detrimental in leaves. Approximately 40% of irrigated lands worldwide are affected by increased salt levels, and expansion of soil salinization is a major threat to crop performance47.

Plants encode a sodium-transporter gene sub-family named HKT181 (high-affinity K+ transporter) that provides protection from the over-accumulation of sodium in leaves82 (Fig. 2d). HKT1 mediates the removal of sodium, mainly in roots, from the xylem83,84, the vascular conduits that transport water and nutrients from roots to leaves. Major quantitative trait loci that enhance salt tolerance in wheat, wheat relatives and rice possess distinct HKT1 alleles47,83,85. This knowledge has enabled the marker-assisted breeding of wheat with a higher salt tolerance, resulting in a yield improvement of 25% under salinity stress in field trials85. Beneficial alleles of HKT1 may enhance salinity tolerance in other species, as has been shown in rice83. It will be necessary to combine HKTs with other strategies to further boost salinity resistance as land salinization continues to rise. The effects of salinity on root development also need to be factored into intervention strategies86,87. Natural variation in transporter genes and their regulation has also provided field-tested solutions for other toxic elements, including aluminium88,89 and boron90.

Extreme temperatures

Higher atmospheric levels of CO 2 and other greenhouse gases are predicted to increase the frequency and duration of heat-waves91, which will lead to losses in crop yield—especially in arid regions92. Sensitivity to extreme temperatures varies during the plant lifecycle and across species. Low temperatures influence the germination, establishment, growth and viability of crops, except for those with temporal chilling or freezing resilience (such as winter wheat). Genetic variation in key transcriptional regulators of cold resilience is leveraged in breeding of several grain crops46. By contrast, warm temperatures promote growth until a threshold is reached above which yields precipitously diminish, especially when soil moisture is low or humidity is high93,94. Sensitivity to temperature extremes is heightened during reproduction, when it reduces male fertility and seed quality95. This presents a daunting challenge as protective responses are typically accompanied by reduced yield. Heat stress is an expanding threat in tropical regions, because, at high humidity, plants are less able to cool their leaves by transpiration via stomatal pores that control the trade-off between CO 2 intake and water loss96. There is an urgent need for research and for ensuing genetic and engineered solutions that preserve crop productivity at increased temperatures (Box 1).

Metabolic control of resilience and yield

Breeding or engineering plants for a high yield potential in varied and variable environments is a potential solution for capturing effective resilience. Plants typically dampen growth and accelerate reproductive development as a consequence of stress. Yield maintenance under moderate drought was significantly improved in AQUAmax corn hybrids produced by selective and marker-assisted breeding97. The underlying genetic variants and mechanisms that enable these lines to conserve soil moisture and delay the accumulation of biomass until grain filling remain to be characterized. Higher yields under well-watered conditions as well as under moderate drought at the time of flowering was achieved in corn that expresses a metabolic enzyme that converts the low-abundance metabolite trehalose-6-phosphate (T6P) to trehalose in the phloem companion cells at the base of the ear and developing florets98 (Fig. 2e). This cell-specific modulation of T6P augments the mobilization of photosynthate to the unfertilized floret, and prolongs the photosynthetic activity of leaves during grain filling. The spatial modulation of T6P levels also regulates the draw of seed reserves into young elongating shoots of rice, particularly when dry seeds are sown directly into a flooded paddy99. The application of plant-permeable T6P analogues to wheat leaves increased seed filling and improved recovery from drought100. These examples illustrate the critical integration of metabolism and stress resilience to improve crops that can be provided by genetic variation and engineering.