Crop traits enabling yield gains under more frequent extreme climatic events

Costs of transitioning the livestock sector to net-zero emissions under future climates

Land managers are challenged with the need to balance priorities in production, greenhouse gas (GHG) abatement, biodiversity and social license to operate. Here, we develop a transdisciplinary approach for prioritising land use, illustrated by co-designing pathways for transitioning farming systems to net-zero emissions. We show that few interventions enhanced productivity and profitability while reducing GHG emissions. Antimethanogenic feed supplements and planting trees afforded the greatest mitigation, while revenue diversification with wind turbines and adoption of livestock genotypes with enhanced feed-conversion efficiency (FCE) were most conducive to improving profit. Serendipitously, the intervention with the lowest social licence-continuing the status quo and purchasing carbon credits to offset emissions-was also the most costly pathway to transition to net-zero. In contrast, stacking several interventions to mitigate enteric methane, improve FCE and sequester carbon entirely negated enterprise emissions in a profitable way. We conclude that costs of transitioning to net-zero are lower when interventions are bundled and/or evoke productivity co-benefits.

Historic rewiring of grass flowering time pathways and implications for crop improvement under climate change

Grasses are fundamental to human survival, providing a large percentage of our calories, fuel, and fodder for livestock, and an enormous global carbon sink. A particularly important part of the grass plant is the grain-producing inflorescence that develops in response to both internal and external signals that converge at the shoot tip to influence meristem behavior. Abiotic signals that trigger reproductive development vary across the grass family, mostly due to the unique ecological and phylogenetic histories of each clade. The time it takes a grass to flower has implications for its ability to escape harsh environments, while also indirectly affecting abiotic stress tolerance, inflorescence architecture, and grain yield. Here, we synthesize recent insights into the evolution of grass flowering time in response to past climate change, particularly focusing on genetic convergence in underlying traits. We then discuss how and why the rewiring of a shared ancestral flowering pathway affects grass yields, and outline ways in which researchers are using this and other information to breed higher yielding, climate-proof cereal crops.

An assessment of the relationship between spring frost indicators and global crop yield losses

Reports on the influences of spring frost on crop losses are not consistent, which may be because insufficient indicators of spring frost were included in the analysis. To bridge this gap, we analyzed global temperature datasets and production data for the three major crops of maize, winter wheat, and rice from 1981 to 2016. Five indicators of spring frost events: temperature fluctuation (Tv), temperature difference (Td), duration (Thour), occurrence date (Tdate), and frequency (Tnum) were considered to assess their relationship with yield losses. Linear regression was employed to analyze the change trends in five indicators and random forest was utilized to investigate the relationship between yield loss and indicators of spring frost. Our findings reveal that, despite a decline in the number of spring frost events during global warming, not all the five indicators declined over time. Tv is the most important indicator for yield losses in maize and winter wheat, which shows an increasing trend in their growing regions and provides an explanation for the increasing yield losses of maize and winter wheat over time. Td is the most important indicator of rice yield losses but it shows a decreasing trend in rice-growing areas, which explains why rice yield losses from spring frosts in recent years are not significant.

Developing functional relationships between waterlogging and cotton growth and physiology-towards waterlogging modeling

Cotton crop is known to be poorly adapted to waterlogging, especially during the early growth stages. Developing functional relationships between crop growth and development parameters and the duration of waterlogging is essential to develop or improve existing cotton crop models for simulating the impact of waterlogging. However, there are only limited experimental studies conducted on cotton specifically aimed at developing the necessary functional relationships required for waterlogging modeling. Further research is needed to understand the effects of waterlogging on cotton crops and improve modeling capabilities in this area. The current study aimed to conduct waterlogging experiments and develop functional relationships between waterlogging and cotton growth and physiology. The experiments were conducted in pots, and the waterlogging was initiated by plugging the drain hole at the bottom of the pot using a wooden peg. In the experiments, eight waterlogging treatments, including the control treatment, were imposed at the vegetative growth stage (15 days after sowing). Control treatment had zero days of water-logged condition; other treatments had 2, 4, 6, 8, 10, 12, and 14 days of waterlogging. It took five days to reach zero oxygen levels and one to two days to return to control after the treatment. After a total treatment duration of 14 days (30 days after sowing), the growth, physiological, reproductive, and nutrient analysis was conducted. All physiological parameters decreased with the number of days of waterlogging. Flavonoid and anthocyanin index increased with increased duration of waterlogging. Photosynthesis and whole plant dry weight in continuously waterlogged conditions were 75% and 78% less compared to 0, and 2-day water-logged plants. Plant height, stem diameter, number of main stem leaves, leaf area, and leaf length also decreased with waterlogging duration. When waterlogging duration increased, leaf, stem, and root macronutrients decreased, while micronutrients showed mixed trends. Based on the experimental study, functional relationships (linear, quadratic, and exponential decay) and waterlogging stress response indices are developed between growth and development parameters and the duration of waterlogging. This can serve as a base for developing or improving process-based cotton models to simulate the impact of waterlogging.

Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance

Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.

Impacts of recent climate change on crop yield can depend on local conditions in climatically diverse regions of Norway

Globally, climate change greatly impacts the production of major crops, and there have been many attempts to model future yields under warming scenarios in recent years. However, projections of future yields may not be generalisable to all crop growing regions, particularly those with diverse topography and bioclimates. In this study, we demonstrate this by evaluating the links between changes in temperature and precipitation and changes in wheat, barley, and potato yields at the county-level during 1980-2019 in Norway, a Nordic country with a range of climates across a relatively small spatial scale. The results show that the impacts of climate variables on yield vary widely by county, and that for some crops, the strength and direction of the link depends on underlying local bioclimate. In addition, our analysis demonstrates the need for some counties to focus on weather changes during specific crucial months corresponding with certain crop growth stages. Furthermore, due to the local climatic conditions and varying projected climate changes, different production opportunities are likely to occur in each county.

Silver lining to a climate crisis in multiple prospects for alleviating crop waterlogging under future climates

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.

Biostimulants alleviate water deficit stress and enhance essential oil productivity: a case study with savory

Water deficit stress exposure frequently constrains plant and agri-food production globally. Biostimulants (BSs) can be considered a new tool in mitigating water deficit stress. This study aimed to understand how BSs influence water deficit stress perceived by savory plants (Satureja hortensis L.), an important herb used for nutritional and herbal purposes in the Middle East. Three BS treatments, including bio-fertilizers, humic acid and foliar application of amino acid (AA), were implemented. Each treatment was applied to savory plants using three irrigation regimes (low, moderate and severe water deficit stress FC100, FC75 and FC50, respectively). Foliar application of AA increased dry matter yield, essential oil (EO) content and EO yield by 22%, 31% and 57%, respectively. The greatest EO yields resulted from the moderate (FC75) and severe water deficit stress (FC50) treatments treated with AA. Primary EO constituents included carvacrol (39-43%), gamma-terpinene (27-37%), alpha-terpinene (4-7%) and p-cymene (2-5%). Foliar application of AA enhanced carvacrol, gamma-terpinene, alpha-terpinene and p-cymene content by 6%, 19%, 46% and 18%, respectively. Physiological characteristics were increased with increasing water shortage and application of AA. Moreover, the maximum activities of superoxide dismutase (3.17 unit mg^-1 min^-1), peroxidase (2.60 unit mg^-1 min^-1) and catalase (3.08 unit mg^-1 min^-1) were obtained from plants subjected to severe water deficit stress (FC50) and treated with AA. We conclude that foliar application of AA under water deficit stress conditions would improve EO quantity and quality in savory.

Effects of plant density on the aboveground dry matter and radiation-use efficiency of field corn

The amount of solar radiation intercepted by the plant canopy drives crop plant photosynthesis and the formation and development of plant organs. Radiation-use efficiency (RUE) is an index used to quantify the relationship between solar radiation and biomass, and crop yield can be increased by increasing RUE. The main goals of this study were to initially investigate the effects of plant densities on the aboveground dry matter of corn, and subsequently examine the effects of plant densities on RUE and leaf area index (LAI), and the effects of LAI on RUE. Finally, we provide a comparative assessment of the approaches used to determine RUE. Analyses were conducted using growth and meteorological data obtained for two field corn varieties (TNG1 and TNG7) grown under four different plant density conditions in central Taiwan in 2017. The RUE values obtained in this study were primarily estimated from the slope of the linear relationship between aboveground dry matter measured at periodic harvests and the corresponding cumulative intercepted photosynthetically active radiation up to the time of harvest. TNG1 and TNG7 with a row spacing of 37.5 cm × 20 cm had the largest amounts of aboveground dry matter and highest RUE values of 4.41 and 4.55 g MJ-1, respectively. We established that the higher the plant density, the higher were the values obtained for RUE and LAI. We also compared the different methods of estimating RUE and make recommendations in this regard. Our findings in this study will enable farmers to gain information on the dynamics of crop yield variation at an early stage of growth, and also provide reference values that can be incorporated in future crop yield models.

Identification of agro-physiological traits of lentil that reduce risks of drought

Ideotype breeding is an essential approach for selection of desired combination of plant traits for testing in crop growth model for potential yield gain in specific environments and management practices. Here we parameterized plant traits for untested lentil cultivars for the APSIM-lentil model in phenology, biomass, and seed yield. We then tested these against independent data and applied the model in an extrapolated analysis (i) to assess the impact of drought on productivity across different rainfall environments; (ii) to identify impactful plant traits and (iii) to design new lentil ideotypes with a combination of desirable traits that mitigate the impact of drought, in the context of various agronomic practices across a wide range of production environments. Desirable phenological and physiological traits related to yield were identified with RUE having the greatest effect on yield followed by HI rate. Leaf size significantly affected seed yield (p< 0.05) more than phenological phases. The physiological traits were integrated into four ideotype designs applied to two baseline cultivars (PBA Hallmark XT and PBA Jumbo2) providing eight ideotypes. We identified a combination of genetic traits that promises a yield advantage of around 10% against our current cultivars PBA Hallmark XT and PBA Jumbo2. Under drought conditions, our ideotypes achieved 5 to 25% yield advantages without stubble and 20 to 40% yield advantages with stubble residues. This shows the importance of genetic screening under realistic production conditions (e.g., stubble retention in particular environments). Such screening is aided by the employment of biophysical models that incorporate both genetic and agronomic variables that focus on successful traits in combination, to reduce the impact of drought in the development of new cultivars for various environments. Stubble retention was found to be a major agronomic contributor to high yield in water-limiting environments and this contribution declined with increasing growing season rainfall. In mid- and high-rainfall environments, the key drivers of yield were time of sowing, physiological traits and soil type. Overall, the agronomic practices, namely, early sowing, residue retention and narrow row spacing deceased the impact of drought when combined with improved physiological traits of the ideotypes based on long term climate data.

Rice Paddies Reduce Subsequent Yields of Wheat Due to Physical and Chemical Soil Constraints

Yields of wheat crops that succeed rice paddy crops are generally low. To date, it has been unclear whether such low yields were due to rice paddies altering soil physical or mineral characteristics, or both. To investigate this quandary, we conducted field experiments in the Jianghan Plain to analyze differences in the spatial distribution of wheat roots between rice-wheat rotation (RW) and dryland-wheat rotations (DW) using a range of nitrogen treatments. Dryland wheat crops were preceded by either dryland soybean or corn in the prior summer. Biomass of wheat crops in RW systems was significantly lower than that of DW for all N fertilizer treatments, although optimal nitrogen management resulted in comparable wheat yields in both DW and RW. Soil saturated water capacity and non-capillary porosity were higher in DW than RW, whereas soil bulk density was higher in RW. Soil available nitrogen and organic matter were higher in DW than RW irrespective of N application, while soil available P and K were higher under RW both at anthesis and post-harvest stages. At anthesis, root length percentage (RLP) was more concentrated in surface layers (0-20 cm) in RW, whereas at 20-40 cm and 40-60 cm, RLP was higher in DW than RW for all N treatments. At maturity, RLP were ranked 0-20 > 20-40 > 40-60 cm under both cropping systems irrespective of N fertilization. Root length percentage and soil chemical properties at 0-20 cm were positively correlated (r = 0.79 at anthesis, r = 0.68 at post-harvest) with soil available P, while available N (r = -0.59) and soil organic matter (r = -0.39) were negatively correlated with RLP at anthesis. Nitrogen applied at 180 kg ha^-1 in three unform amounts of 60 kg N ha^-1 at sowing, wintering and jointing resulted in higher yields than other treatments for both cropping systems. Overall, our results suggest that flooding of rice paddies increased bulk density and reduced available nitrogen, inhibiting the growth and yield of subsequent wheat crops relative to rainfed corn or soybean crops.

Modelling Waterlogging Impacts on Crop Growth: A Review of Aeration Stress Definition in Crop Models and Sensitivity Analysis of APSIM

Currently, crop physiological responses to waterlogging are considered only in a few crop models and in a limited way. Here, we examine the process bases of seven contemporary models developed to model crop growth in waterlogged conditions. The representation of plant recovery in these models is over-simplified, while plant adaptation or phenotypic plasticity due to waterlogging is often not considered. Aeration stress conceptualisation varies from the use of simple multipliers in equations describing transpiration and biomass to complex linkages of aeration-deficit factors with root growth, transpiration and nitrogen fixation. We recommend further studies investigating more holistic impacts and multiple stresses caused by plant behaviours driven by soils and climate. A sensitivity analysis using one model (a developer version of APSIM) with default parameters showed that waterlogging has the greatest impact on photosynthesis, followed by phenology and leaf expansion, suggesting a need for improved equations linking waterlogging to carbon assimilation. Future studies should compare the ability of multiple models to simulate real and in situ effects of waterlogging stress on crop growth using consistent experimental data for initialisation, calibration and validation. We conclude that future experimental and modelling studies must focus on improving the extent to which soil porosity, texture, organic carbon and nitrogen and plant-available water affect waterlogging stress, physiological plasticity and the ensuing temporal impacts on phenology, growth and yield.

Effects of Selenium on Growth and Selenium Content Distribution of Virus-Free Sweet Potato Seedlings in Water Culture

Understanding the selenium tolerance of different sweet potato [Dioscorea esculenta (Lour.) Burkill] is essential for simultaneously for breeding of new selenium-tolerant varieties and improving the selenium content in sweet potato. Therefore, a greenhouse experiment was conducted from February to April 2022 to evaluate the effect of sweet potato cultivars and selenium (Na₂SeO₃) concentrations (0-40 mg/L) on plant growth, physiological activities and plant selenium content distribution. The results showed that when the selenium concentration was more than 3 mg/L, the plant growth was significantly affected and the plant height and root length were significantly different compared to the control. While the selenium concentration was 20 and 40 mg/L had the greatest effect on plant growth when the number of internodes and leaves of the plant decreased, the root system stopped growing and the number of internodes of the plant, the number of leaves and the dry-to-fresh weight ratio of the plant a very significant level compared to reached control. The relative amount of chlorophyll in leaves under treatment with a selenium concentration of 1 mg/L was increased, and the relative amount of chlorophyll in 3 mg/L leaves gradually increased with the increase in the selenium concentration. The values of the maximum photochemical efficiency PSII (fv/fm) and the potential activity of PSII (fv/fo) compared to the control under treatment with 40 mg/L selenium concentration and photosynthesis of plants was inhibited. The selenium content in root, stem and leaf increased with the increase in selenium concentration, and the distribution of selenium content in the plant was leaf <stem <root, and the selenium content in root was significantly higher than that in stem and leaf. In summary, the appropriate concentration of selenium tolerance has been determined to be 3 mg/L. The aquatic culture identification method of selenium tolerance of sweet potatoes and growth indices of various selenium tolerant varieties (lines) established in this study will provide a technical basis for selenium tolerant cultivation and mechanism research.

Genotype by Environment Interaction on Tropical Maize Hybrids Under Normal Irrigation and Waterlogging Conditions

Unpredictable rainfall in the tropics often increases the risk of waterlogging or even flooding in agricultural lands, hindering the efforts to fulfill maize demands. Breeding maize for waterlogging tolerance is necessary yet challenging since performing varietal testing on a set of hybrids might be biased toward the presence of genotype and environment interaction (GEI). This study aimed to elucidate the GEI effects on yield and related agronomic traits of tropical maize hybrids under normal irrigation and waterlogging conditions and to assess the adaptability of these hybrids in such conditions using several stability models. Ten hybrids including two commercial checks were evaluated across 14 environments under normal and waterlogging conditions in Indonesia from 2018 to 2020. Waterlogging imposed at the V6 stage for ten consecutive days significantly hampered the plant height and ear height, slightly delayed flowering dates, and reduced yield and yield components. The genotype, location, and genotype by location effects were significant on yield, but the genotype by waterlogging effect was not. Stress tolerance index is highly significantly correlated (p &lt; 0.01) with yield in both normal (r = 0.90) and waterlogging (r = 0.96) conditions. The GGE biplot analysis on yield revealed five sectors, two mega-environments, and five vertex genotypes. This study indicated the possibility of breeding maize hybrids tolerant to waterlogging (G05), as well as high-yielding hybrids under both conditions (G07).

Shifting Rice Cropping Systems Mitigates Ecological Footprints and Enhances Grain Yield in Central China

Intensive cereal production has brought about increasingly serious environmental threats, including global warming, environmental acidification, and water shortage. As an important grain producer in the world, the rice cultivation system in central China has undergone excessive changes in the past few decades. However, few articles focused on the environmental impacts of these shifts from the perspective of ecological footprints. In this study, a 2-year field trial was carried out in Hubei province, China, to gain insight into carbon footprint (CF), nitrogen footprint (NF), and water footprint (WF) performance. The three treatments were, namely, double-rice system (DR), ratoon rice system (RR), and rice-wheat system (RW). Results demonstrated that RR significantly increased the grain yield by 10.22-15.09% compared with DR, while there was no significant difference in the grain yield between RW and DR in 2018-2019. All of the calculation results by three footprint approaches followed the order: RR < RW < DR; meanwhile, RR was always significantly lower than DR. Methane and NH3 field emissions were the hotspots of CF and NF, respectively. Blue WF accounts for 40.90-42.71% of DR, which was significantly higher than that of RR and RW, primarily because DR needs a lot of irrigation water in both seasons. The gray WF of RW was higher than those of DR and RR, mainly due to the higher application rate of N fertilizer. In conclusion, RR possesses the characteristics of low agricultural inputs and high grain yield and can reduce CF, NF, and WF, considering the future conditions of rural societal developments and rapid demographic changes; we highlighted that the RR could be a cleaner and sustainable approach to grain production.

How Does Crop Rotation Influence Soil Moisture, Mineral Nitrogen, and Nitrogen Use Efficiency?

Rice-wheat (RW) cropping systems are integral to global food security. Despite being practiced for decades, Chinese RW cropping systems often suffer from low productivity and poor nitrogen use efficiency (NUE), reflecting management approaches that are not well-contextualized to region and season. Here, we develop the best management guides for N fertilizer in RW systems that are designed to help raise the productivity, NUE, and environmental sustainability of winter wheat over the long term. 2-year field experiments were conducted with four N fertilizer rates (0, 135, 180, and 225 kg N ha-1), allowing contrasts of yields, soil moisture, and NUE of wheat in RW in the humid climates zones on the Jianghan Plain. We compared RW systems with soybean/maize dryland wheat (DW) systems that are similarly endemic to China: after soybean/maize is harvested, soils are often drier compared with moisture content following rice harvest. With high seasonal N application rates (180-225 kg N ha-1), wheat crop yields increased by 24% in RW which were greater than comparable yields of wheat in DW, mainly due to greater kernels per spike in the former. Across treatments and years, N accumulation in plant tissue and kernel dry matter of DW was higher than that in RW, although mean agronomic efficiency of nitrogen (AEN) and physiological efficiency of nitrogen (PEN) of RW systems were greater. As N application rates increased from 135 to 225 kg ha-1, AEN and PEN of DW decreased but changed little for RW. Soil ammonium N was much lower than that of nitrate N; changes in NH4 + and NO3 - as a consequence of increasing N fertilization were similar for RW and DW. We recommend that tactical application of N fertilizer continue seasonally until midgrain filling for both the DW and RW systems. At fertilization rates above 180 kg N ha-1, yield responses disappeared but nitrate leaching increased significantly, suggesting declining environmental sustainability above this N ceiling threshold. Collectively, this study elicits many functional and agronomic trade-offs between yields, NUE, and environmental sustainability as a function of N fertilization. Our results show that yield and NUE responses measured as part of crop rotations are both more robust and more variable when derived over multiple seasons, management conditions, and sites.

Soybean Crops Penalize Subsequent Wheat Yield During Drought in the North China Plain

Contemporary wisdom suggests that inclusion of legumes into crop rotations benefit subsequent cereal crop yields. To investigate whether this maxim was generically scalable, we contrast summer soybean-winter wheat (SW) with summer maize-winter wheat (MW) rotation systems in an extensive field campaign in the North China Plain (NCP). We identify heretofore unseen interactions between crop rotation, synthetic N fertilizer application, and stored soil water. In the year with typical rainfall, inclusion of soybean within rotation had no effect on wheat ear number and yield, while N fertilization penalized wheat yields by 6-8%, mainly due to lower dry matter accumulation after anthesis. In contrast, in dry years prior crops of soybean reduced the rate and number of effective ears in wheat by 5-27 and 14-17%, respectively, leading to 7-23% reduction in wheat yield. Although N fertilization increased the stem number before anthesis in dry years, there was no corresponding increase in ear number and yield of wheat in such years, indicating compensating reduction in yield components. We also showed that N fertilization increased wheat yield in MW rather than SW as the former better facilitated higher dry matter accumulation after flowering in dry years. Taken together, our results suggest that soybean inclusion reduced soil available water for subsequent wheat growth, causing yield penalty of subsequent wheat under drought conditions. We call for more research into factors influencing crop soil water, including initial state, crop water requirement, and seasonal climate forecasts, when considering legumes into rotation systems. Graphical AbstractResponse of wheat population and yield to soybean inclusion under limited-irrigation.

iTRAQ Proteomic Analysis of Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance

Transient and chronic waterlogging constrains crop production in many regions of the world. Here, we invoke a novel iTRAQ-based proteomic strategy to elicit protein synthesis and regulation responses to waterlogging in tolerant (XM 55) and sensitive genotypes (YM 158). Of the 7,710 proteins identified, 16 were distinct between the two genotypes under waterlogging, partially defining a proteomic basis for waterlogging tolerance (and sensitivity). We found that 11 proteins were up-regulated and 5 proteins were down-regulated; the former included an Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like and CBS domain-containing protein. Down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9, 10 (9', 10')-cleavage dioxygenase-like, psbP-like protein 1 and mitochondrial ATPase inhibitor. We showed that nine proteins responded to waterlogging with non-cultivar specificity: these included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Sixteen of the 28 selected proteins showed consistent expression patterns between mRNA and protein levels. We conclude that waterlogging stress may redirect protein synthesis, reduce chlorophyll synthesis and enzyme abundance involved in photorespiration, thus influencing synthesis of other metabolic enzymes. Collectively, these factors accelerate the accumulation of harmful metabolites in leaves in waterlogging-susceptible genotypes. The differentially expressed proteins enumerated here could be used as biological markers for enhancing waterlogging tolerance as part of future crop breeding programs.