Extreme weather events threaten food security, yet global assessments of impacts caused by crop waterlogging are rare. Here we first develop a paradigm that distils common stress patterns across environments, genotypes and climate horizons. Second, we embed improved process-based understanding into a farming systems model to discern changes in global crop waterlogging under future climates. Third, we develop avenues for adapting cropping systems to waterlogging contextualised by environment. We find that yield penalties caused by waterlogging increase from 3–11% historically to 10–20% by 2080, with penalties reflecting a trade-off between the duration of waterlogging and the timing of waterlogging relative to crop stage. We document greater potential for waterlogging-tolerant genotypes in environments with longer temperate growing seasons (e.g., UK, France, Russia, China), compared with environments with higher annualised ratios of evapotranspiration to precipitation (e.g., Australia). Under future climates, altering sowing time and adoption of waterlogging-tolerant genotypes reduces yield penalties by 18%, while earlier sowing of winter genotypes alleviates waterlogging by 8%. We highlight the serendipitous outcome wherein waterlogging stress patterns under present conditions are likely to be similar to those in the future, suggesting that adaptations for future climates could be designed using stress patterns realised today.

Climate change will drive increased frequencies of extreme climatic events. Despite this, there is little scholarly information on the extent to which waterlogging caused by extreme rainfall events will impact on crop physiological behaviour. To improve the ability to reliably model crop growth and development under soil waterlogging stress, we advanced the process-basis of waterlogging in the farming systems model Agricultural Systems Production Systems sIMulator. Our new mathematical description of waterlogging adequately represented waterlogging stress effects on the development, biomass and grain yield of many commercial Australian barley genotypes. We then used the improved model to examine how optimal flowering periods (OFPs, the point at which long-term abiotic stresses are minimal) change under historical and future climates in waterlogging-prone environments, and found that climate change will reduce waterlogging stress and shift forward OFP (26 d earlier on average across locations). For the emissions scenario representative concentration pathway 8.5 at 2090, waterlogging stresses diminished but this was not enough to prevent substantial yield reduction due to increasingly severe high temperature stress (−35% average reduction in yield across locations, genotypes and sowing dates). It was shown that seasonal waterlogging stress patterns under future conditions will be similar to those occurring historically. Yield reduction caused by waterlogging stress was 6% and 4% on average across sites under historical and future climates. To adapt, both genotypic and management adaptations will be required: earlier sowing and planting waterlogging tolerant genotypes mitigate yield penalty caused by waterlogging by up to 26% and 24% under historical and future climates. We conclude that even though the prevalence of waterlogging in future will diminish, climate change and extreme climatic events will have substantial and perverse effects on the productivity and sustainability of Australian farms.

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As one of the most important crops, rice provides the major food for more than half of the world population. However, its production is limited by many environmental factors, among which high temperature stress (HS) frequently occurs during anthesis and reduces its spikelet fertility. To explore the mechanism of HS tolerance in rice, we conducted a comparative proteomics analysis on the anthers between HS resistant and sensitive cultivars under different levels of high temperature. Under the same HS treatment, the resistant cultivar showed much higher spikelet fertility than the sensitive cultivar. Proteomic data showed that HS lead to the degradation of ribosomal proteins in the sensitive cultivar but not in the resistant one, which might result in the injury of protein biosynthetic machinery. In contrast, HS induced the increase of sHSP, β-expansins and lipid transfer proteins in the resistant cultivar, which might contribute to its ability to tolerate HS. The results provide some new insights into the mechanism of rice HS response.