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Enhancing use efficiency of applied fertiliser increases farmers’ returns on fertiliser investment through reducing nutrient inputs and improving yields. We investigated on-farm how indigenous nutrient supply and management practices affected N, P, and K uptake, agronomic efficiency and recovery efficiency of fertiliser, and physiological efficiency of nutrients taken up, under irrigated lowland rice conditions in Uganda. Treatments included recommended agronomic practices (RAP) without fertilisation, farmers’ practice (FP), farmers’ selected intensification practice (FIP), and RAP with NPK fertilisation (RAP + NPK). Indigenous N, P, and K supply varied greatly among farmers’ fields. N, P, and K uptake were significantly higher under RAP + NPK than under RAP, FP, and FIP; however, physiological efficiency (PE; kg grain kg−1 nutrient uptake) was significantly lower under RAP + NPK by 19% (N), and 12% (P/K), due to a larger effect of NPK application on uptake than on yield, leading to higher tissue concentrations. Indigenous available N reduced apparent N recovery, and agronomic and physiological N efficiencies independent of treatment. Also, P and K PEs decreased with increasing indigenous supply. Delaying weeding beyond recommended time, in interaction with indigenous N supply, decreased agronomic N efficiency, but increased PE of N. Interaction between P rate and timing reduced its PE; K rate and weeding time interaction reduced its PE. The decrease in efficiencies at high indigenous supply and delayed weeding indicates a need for site-specific fertilisation strategies based on naturally available nutrient levels and proper weeding. Weeding and fertilisation timing directly affect nutrient use efficiency, and therefore, fertiliser use efficiency in rice production systems.

Vulnerabilities of the global fuel-fertilizer-food nexus have been revealed by a regional geopolitical conflict causing sudden and massive supply disruptions. Across over- and under-fertilized agricultural systems, nitrogen (N) fertilizer price spikes will have very different effects and require differentiated responses. For staple cereal production in India, Ethiopia, and Malawi, our estimates of N-fertilizer savings show the value of integrated organic and inorganic N management. N-deficient systems benefit from shifting to more cost-effective, high-N fertilizer (such as urea), combined with compost and legumes. N-surplus systems achieve N savings through better targeted and more efficient N-fertilizer use. Globally, there is a need to re-balance access to N-fertilizers, while steering the right fertilizer to the right place, and managing N in combination with carbon through near-term interventions, while striving for longer-term sustainable management. Nationally, governments can invest in extension and re-align subsidies to enable and incentivize improved N management at the farm level.

Crop productivity is poorly assessed globally. Here, we provide a deep learning-based approach for estimating rice yield using RGB images. During ripening stage and at harvest, over 22,000 digital images were captured vertically downwards over the rice canopy from a distance of 0.8 to 0.9 m, and rice yields were obtained in the corresponding area ranging from 0.1 and 16.1 t ha−1. A convolutional neural network (CNN) applied to these data at harvest predicted 70% variation in rice yield with a relative root mean square error (rRMSE) of 0.22. Images obtained during the ripening stage can also be used to forecast the final rice yield. Our work suggests that this low-cost, hands-on, and rapid approach can provide a breakthrough solution to assess the impact of productivity-enhancing interventions and identify fields where these are needed to sustainably increase crop production.

Nutrient deficiencies are considered major constraints to rice production in sub-Saharan Africa (SSA), but a systematic, continent-wide analysis of these constraints is lacking. The objective of this study was to assess responses of rice yields to macronutrients (N, P, and K) across major rice production systems [irrigated lowland rice (IL), rainfed lowland rice (RL), and rainfed upland rice (RU)] and diverse agro-ecological zones (semi-arid, sub-humid, humid, and highlands) in SSA. Diagnostic trials were conducted in 17 countries in 18–60 farmers' fields in each of 30 sites (totaling 1037 farmers' fields), of which 12 sites were in IL, 15 in RL and 3 in RU. All trials had an NPK treatment, and three treatments in which either nitrogen (N), phosphorus (P), or potassium (K) was omitted from the NPK treatment (minus N, P, and K plots). The trials were conducted during one or two seasons. Regression between yields in the NPK and minus N plots was used for calculating N fertilizer requirement, following the approach used for the development of a nutrient management decision support tool for rice (RiceAdvice) in SSA. Site mean yields in the NPK treatment ranged from 1.4 to 7.3 t ha−1. On average, these yields were 1.1 t ha−1 higher than farmers' yields previously observed in the same sites. N was generally the most limiting nutrient, followed by P. Rice yields without N, P, and K were 68, 84, and 89% of yields in the NPK treatment, and were positively correlated with those in the NPK treatment irrespective of production systems and agro-ecological zone (AEZ). Results from a regression model across sites indicated that achieving 3, 5, and 7 t ha−1 requires N fertilizer application at an average rate of 56, 91, and 122 kg N ha−1, respectively. However, there was significant treatment by site interaction on rice yield. Site mean yields were significantly lower without N, P, and K in 93, 60, and 50% of sites as compared to the NPK treatment. Yield response to macronutrients varied across sites and was not related to production system, nor AEZ. Results from this study will help further improvement of RiceAdvice for providing decision support tailored to the particular site, zone, or production system, thereby closing yield gaps, improving fertilizer nutrient efficiency and preventing negative environmental consequences of fertilizer use.

If future rice production is to contribute to food security for the increasing population of sub-Saharan Africa (SSA), effective strategies are needed to control weeds, the crop’s fiercest competitors for resources. To gain better insights into farmers’ access to, and use of, herbicides as part of weed control strategies, surveys were conducted in key rice production locations across SSA. Farm surveys were held among 1965 farmers across 20 countries to collect data on rice yields, farmer’s weed management practices, herbicide use, frequencies of interventions and information sources regarding herbicides. Markets were surveyed across 17 countries to collect data on herbicide availability, brand names and local prices (converted to US$ ha−1). Herbicides are used by 34% of the rice farmers in SSA, but adoption ranges from 0 to 72% across countries. Herbicides are more often used by men (40%) than by women (27%) and more often in irrigated (44% of farmers) than in rainfed lowland (36%) or upland rice growing environments (24%). Herbicides are always used supplementary to hand weeding. Following this combination, yield loss reductions in irrigated lowlands and rainfed uplands are estimated to be 0.4 t ha−1 higher than hand weeding alone. In rainfed lowlands no benefits were observed from herbicide use. Sixty-two percent of the herbicides sold at rural agro-chemical supply markets are unauthorized. These markets are dominated by glyphosate and 2,4-D, sold under 55 and 41 different brand names, respectively, and at relatively competitive prices (below average herbicide price of US $17 ha−1). They are also the most popular herbicides among farmers. For advice on herbicide application methods, farmers primarily rely on their peers, and only a few receive advice from extension services (

Upland rice production is often constrained by phosphorus deficiency (P) and drought events. Methods are needed to maximize P use efficiency, while promoting deep root development to mitigate drought. This study evaluates micro-dose P placement as a technique to enhance drought resilience of upland rice, thereby hypothesizing that P placement enhances deep root development, stimulated by the local P supply in the planting hole, compared to broadcast P. Two pot experiments were conducted using P deficient upland soil in Tanzania (Expt.1) and Madagascar (Expt.2), with factorial combinations of P doses (control and two P levels), application method (placement versus broadcast), rice varieties (DJ123 & NERICA4) and water regimes (field capacity and drying periods). Micro-dose P placement strongly boosted the establishment of upland rice and enhanced P recovery rates (4- to 5-fold) and fertilizer use efficiency (9- to 14-fold) compared to broadcast P. Micro-dose P placements significantly enhanced the fraction of roots found at largest depth (> 30 cm, Expt. 1; >15 cm, Expt. 2) by 22- to 33 %. Surprisingly, shoot P concentrations were markedly lower under P placement than under broadcast at equivalent P doses or equivalent biomass, indicating a Piper-Steenbjerg effect. This study is first in showing the enhanced deep rooting after basal P placement, and suggests replication at field scale where subsurface moisture may yield stronger benefits than in pots. The depleted shoot P concentrations induced by vigorous plant establishment under P placement may, however, counteract benefits at later growth stages and need further attention.

Rice is a staple food and cash crop for smallholder farmers in sub-Saharan Africa; however, yields are very low, with indications that both macro and micro-nutrients may limit rice productivity in East Africa next to the need for good agronomic practices. Diagnostic on-farm experiments were conducted in Uganda and Tanzania between 2015 and 2017 to assess the contribution of macro, secondary and micro-nutrients on lowland rice yield and identify options by which smallholder farmers can increase productivity. All treatments included good agronomic practices combined with: zero fertilisation as a control, NPK fertilisation with and without secondary and micro-nutrients (B, Mn, Zn, Cu, Mg, S), and/or treatments where B, Mn and Zn were omitted one at a time from the NPK + secondary and micro-nutrient treatment. NPK fertilisation significantly (p < 0.05) increased grain yield under irrigated condition by ca. 32 and 29 % during 2015 and 2016, and 24 and 100 % during 2016 and 2017 in Tanzania and Uganda, respectively; however, inconsistent effects were observed under rainfed condition. Observed higher yields corresponded mainly to higher panicle number with an additive effect of grains per panicle indicating major effects were at earlier growth stages supporting higher sink size development. Adding secondary and micro-nutrients to NPK enhanced yield significantly (p < 0.05) under irrigated condition in Tanzania 2015 and 2016 by 7 and 11 %, respectively, while varying results were obtained under rainfed condition. In Uganda, no significant (p> 0.22) effects of secondary and micro-nutrients were observed in both years and growing conditions. This study indicates that the first step to improving lowland rice productivity is proper water management, under otherwise also good crop management in terms of timely transplanting and weeding, and further yield gains can be realised with NPK fertilisation. Secondary and micro-nutrients were effective only when NPK were applied and on the fluvisols of Tanzania, and were not co-limiting yield on the plintosols of Uganda.

Organic amendments can reportedly sustain and increase lowland rice productivity in smallholder systems. Few studies have assessed locally-available substrates in hydrologically variable floodplain environments. We investigated the effects of green and farmyard manures on rice yields, and total soil C and N in the Kilombero floodplain, Tanzania. At both the fringe and the middle positions, five treatments were applied in 2016 and 2017, comprising (1) non-amended control, (2) farmyard manure, (3) pre-rice legumes, (4) post-rice legumes and (5) a combination of green and farmyard manures. Residual treatment effects were assessed in 2018 when rice plots were uniformly non-amended. Depending on the year and the position, organic amendments increased rice grain yields by 0.7&ndash, 3.1 Mg ha&ndash, 1 above the non-amended control. Sole green and farmyard manure applications had similar effects on grain yield, while a combination of green and farmyard manure led to a significant increase in grain yield above both the control and sole applications of organic amendments in both years. The contribution from biological N2 fixation by legumes ranged from 4 to 61 kg N ha&ndash, 1. Despite partial N balances being mostly negative, we observed positive residual effects on the yield of the non-amended rice in the third year. Such effects reached up to 4 Mg ha&minus, 1 and were largest with post-rice legumes, sole or combined with farmyard manure. Irrespective of the position in the floodplain, manures significantly increased soil C and N contents after two years, hence enhancing soil fertility and resulting in increased rice grain yields. Comparable benefits may be obtained along the hydrological gradients of other large river floodplains of the region and beyond.

The demand for rice in Eastern and Southern Africa is rapidly increasing because of changes in consumer preferences and urbanization. However, local rice production lags behind consumption, mainly due to low yield levels. In order to set priorities for research and development aimed at improving rice productivity, there is a need to characterize the rice production environments, to quantify rice yield gaps —i.e. the difference between average on-farm yield and the best farmers’ yield— and to identify causes of yield gaps. Such information will help identifying and targeting technologies to alleviate the main constraints, and consequently to reduce existing yield gaps. Yield gap surveys were conducted on 357 rice farms at eight sites (19-50 farmers per site) across five rice-producing countries in Eastern and Southern Africa —i.e. Ethiopia, Madagascar, Rwanda, Tanzania and Uganda— for one or two years (2012-13) to collect both quantitative and qualitative data at field and farm level. Average farm yields measured at the eight sites ranged from 1.8 to 4.3 t ha–1 and the average yield gap ranged from 0.8 to 3.4 t ha–1. Across rice growing environments, major causes for yield variability were straw management, weeding frequency, growth duration of the variety, weed cover, fertilizer (mineral and organic) application frequency, levelling and iron toxicity. Land levelling increased the yield by 0.74 t ha–1, bird control increased the yield by 1.44 t ha–1, and sub-optimal management of weeds reduced the yield by 3.6 to 4.4 t ha–1. There is great potential to reduce the current rice yield gap in ESA, by focusing on improvements of those crop management practices that address the main site-specific causes for suboptimal yields.

BackgroundBreeding towards resilient rice varieties is often constrained by the limited data on root system architecture obtained from relevant agricultural environments. Knowledge on the genotypic differences and responses of root architecture to environmental factors is limited due the difficulty of analysing soil-grown rice roots. An improved method using imaging is thus needed, but the existing methods were never proven successful for rice. Here, we aimed to evaluate and improve a higher throughput method of image-based root phenotyping for rice grown under field conditions. Rice root systems from seven experiments were phenotyped based on the “shovelomics” method of root system excavation followed by manual root phenotyping and digital root analysis after root imaging. Analyzed traits were compared between manual and image-based root phenotyping systems using Spearman rank correlations to evaluate whether both methods similarly rank the phenotypes. For each trait, the relative phenotypic variation was calculated. A principal component analysis was then conducted to assess patterns in root architectural variation.ResultsSeveral manually collected and image-based root traits were identified as having a high potential of differentiating among contrasting phenotypes, while other traits are found to be inaccurate and thus unreliable for rice. The image-based traits projected area, root tip thickness, stem diameter, and root system depth successfully replace the manual determination of root characteristics, however attention should be paid to the lower accuracy of the image-based methodology, especially when working with older and larger root systems.ConclusionsThe challenges and opportunities of rice root phenotyping in field conditions are discussed for both methods. We therefore propose an integrated protocol adjusted to the complexity of the rice root structure combining image analysis in a water bath and the manual scoring of three traits (i.e. lateral density, secondary branching degree, and nodal root thickness at the root base). The proposed methodology ensures higher throughput and enhanced accuracy during root phenotyping of soil grown rice in fields or pots compared to manual scoring only, it is cheap to develop and operate, it is valid in remote environments, and it enables fast data extraction.

Societal Impact Statement Fertilizer nutrients are essential for food and nutrition security, but a large proportion of nutrients applied to soil are lost because they are unavailable to plants. The extent of these nutrient losses exceeds safe and sustainable limits. Societal awareness of this is limited because it can take many seasons for nutrient‐loss impacts to become visible. We propose that Innovative Fertilizers and Application Technologies (IFAT) could help reduce nutrient losses and thus reduce pressure on resources, and provide important micronutrients for human health. However, transformation of the fertilizer sector through stakeholder engagement, policy interventions, and public–private initiatives will be required to unlock the full potential of IFAT. Summary Strategies for delivering sustainable food systems require significant reduction in yield gaps and food system inefficiencies. Mineral fertilizers will play a critical role in achieving both of these aims. However, reduction in nutrient losses from mineral fertilizer use to levels that are considered sustainable has not been achieved and has been estimated to be unachievable, even with optimized practices for current products. We argue that Innovative Fertilizers and Application Technologies (IFAT) are needed to address the daunting and interlinked food, agricultural, and environmental challenges facing humanity and the planet. We define IFAT as a set of fertilizer products and technologies that are designed by taking the physiological needs of plants (such as nutrient uptake, redistribution, and utilization) as the entry point in the fertilizer development process, rather than starting first with chemistry. This approach aims for the timely and targeted delivery of nutrients in balanced quantities. We propose that this can result in multiple food, agricultural, and environmental benefits, including increased yield, improvements in nutritional quality, enhanced crop resilience, and reduced emission of greenhouse gases (GHG), and leaching losses. However, the benefits of IFAT for human and environmental health have remained elusive. The major challenge for optimal use of IFAT is a transformation of the vast fertilizer sector by means of government policy interventions, societal responses, and significant investment in public and private research and development.

Phosphorus (P) deficiency is a major biophysical limitation to rice grain yields in sub-Saharan Africa, and low-cost P management strategies are needed by smallholder farmers to reverse soil fertility decline. On-station field and pot experiments were combined with on-farm testing to evaluate the effect of P micro-dose placement in dry-seeded, dibbled rice on emergence, early vigour and grain yield. Placing a micro-dose of 3–6 kg P ha−1 in the planting hole consistently increased early vigour and grain yield of both a P-efficient and less P-efficient rice genotype. An agronomic efficiency of P fertilizer (AEP) of 356–817 kg grains kg−1 P was achieved with a micro-dose of 3 kg P ha−1. A negative effect on emergence by placing a P micro-dose in the planting hole observed in one experiment was compensated by a higher grain weight per hill. In other experiments, no negative effect on plant emergence under both well-watered and water-stressed conditions and with different P sources was observed even when fertilizers were mixed with seeds. A micro-dose of 20–30 kg of DAP ha−1 placed in the planting hole resulted in an average net increase in profit of $91 to $136 ha−1 and benefit:cost ratio of 3–12 in on-farm experiments. Farmers’ appreciation of the technology was positive but lack of credit, availability of appropriate fertilizers in local agrodealers and increased labour requirements were identified as potential constraints for adoption. P micro-dose placement in the planting hole can be used as an entry point towards sustainable intensification in dry-seeded, dibbled rice systems in SSA, provided it is accompanied by institutional support and mechanization options to increase its adoption potential.

Lowland rice yields in East Africa remain low despite favourable hydro-edaphic conditions as benefits from improved cultural management vary between and within wetland types and interactions are poorly understood. Hence, multi-year agronomic field experiments were established to assess the differential responses of lowland rice to management (rainfed 0 and 60 kg N ha−1, and irrigated 120 kg N ha−1 + 60 kg PK ha−1) and field position within a floodplain in Tanzania (fringe and middle positions) and an inland valley in Uganda (valley-fringe, mid-valley and valley-bottom positions). We then calibrated and validated the Agricultural Production System Simulator (APSIM), evaluated the importance of external water table data as model input and assessed the relative effects of water and N stress on yield as affected by wetland type and field position. Yields of 3.2–9.2 Mg ha−1 were attained in the floodplain and of 1.9–6.3 Mg ha−1 in the inland valley, highlighting the substantial scope to boost yields beyond current regional means of around 2 Mg ha−1. The model estimated grain yields in both wetlands well within the experimental uncertainty during model validation (n = 12, r2 = 0.76, RMSEa= 0.92 Mg ha−1 in the floodplain; n = 18, r2 = 0.71, RMSEa= 0.72 Mg ha−1 in the inland valley). Results further emphasised the importance of external water table data for sound model performance as they evidently alleviated seasonal droughts. Simulated abiotic stress patterns additionally highlighted hydro-edaphic differences from field positioning within and between both wetlands. While low soil N was generally the main yield constraint, water stress was comparably more pronounced in the inland valley and supplemental irrigation thus more beneficial on yield. Hydro-edaphic field conditions favoured rice production in the floodplain’s fringe with comparably lower N stress, while large spatial-temporal variabilities prevented a distinct delineation based on toposequential field positions in the inland valley.