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Key message Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Abstract Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.

Drought poses a serious threat to crop production worldwide, and is expected particularly to affect rice production and hence food security. Given that wheat is known to tolerate drought better than rice, we compare rice and wheat (cv. Weebill) to understand the species level differences in drought adaptive mechanisms. We also compare two contrasting rice genotypes (IR64, drought susceptible, and Apo, drought tolerant) for such mechanisms under well-watered (100% field capacity, 100%FC) and water-limited (60%FC) conditions. The reduction in biomass of wheat under water limitation was smaller due to a higher rate of photosynthesis associated with maintenance of tissue turgor compared to rice genotypes. Drought caused greater inhibition of Photosystem II quantum efficiency, carboxylation efficiency, and photosynthetic capacity parameters in IR64 than in Apo. Transcript levels of photosynthesis-related genes were also significantly more repressed by water limitation in IR64, whilst the wheat genotype showed smaller reduction than Apo. Despite higher non-photochemical quenching (NPQ), a smaller increase in scavenging enzymes in IR64 resulted in more accumulation of reactive oxygen species (ROS) in 60%FC than in 100%FC compared to Apo. As a photoprotection mechanism, increased levels of NPQ resulted in lower ROS accumulation in wheat despite the similar increase in scavenging enzyme transcript levels as in Apo, signifying the importance of preventing oxidative burst for enhanced drought tolerance. In Apo, upregulation of the 9-cis-epoxycarotenoid dioxygenase 2 gene implies the use of xanthophyll pool for the ABA biosynthesis. Our data suggest that regulating photosynthesis and oxidative protection in the wheat genotype enhanced drought tolerance. Improving these traits for rice is crucial to develop drought-tolerant rice genotypes.

In vitro-propagated potato plantlets are commonly used in potato seed tuber production. Four experiments were carried out to identify how the duration of the last in vitro phase (‘age’) before planting of in vitro-produced plantlets affects the early growth and development ex vitro, assessed 10–14 days after planting. Experiments included varying ranges in age of the in vitro plantlets at planting (10–40, 15–45, 14–28 and 14–56 days old at the moment of planting in the respective experiments) and different cultivars. Because in vitro plantlet size increases with age, the first experiment studied interactions between age and planting method. Planting ‘deep’ (the upper four visible leaves above the ground) seemed more robust than planting ‘shallow’ (all nodes/leaves above ground except the lowest two), and in later experiments, only deep planting was applied. Across experiments, plants grown from younger in vitro plantlets had smaller leaf areas 10–14 days after planting than those from older in vitro plantlets. The increase in leaf area levelled off with increasing age of the in vitro plantlets used, especially when plantlets were older than c. 28 days. Larger leaf areas 10–14 days after planting were related to the older in vitro plantlets having higher absolute growth rates after planting and a larger above-ground leaf area at planting, even though four leaves were kept above ground in all treatments. Below ground, plants from older in vitro plantlets had more stem nodes, initiated stolons earlier after planting and initiated more stolons per plant. Tuber initiation rarely occurred within 14 days after planting, but was observed in some plants from 42- and especially 56-day-old in vitro plantlets of the very early cultivar Gloria and a single plant from 56-day-old in vitro plantlets of the mid-early cultivar Bintje. The data show that planting older in vitro plantlets can enhance early leaf area growth. Plants from older in vitro plantlets also more readily initiate stolons below ground and may be more advanced in the tuber formation process, especially when from early cultivars.

The study was conducted to determine the dormancy and physiological age characteristics of diverse potato genotypes as influenced by growing altitudes and seasons for future breeding strategies and optimal patterns of use. Dormancy and sprouting characteristics have an impact on tuber production, storability and seed quality for planting and ware for consumption and the market. This study presents the results of dormancy and physiological age measurements conducted on 47 potato genotypes grown at three altitudes with three replications at each location and in two contrasting growing seasons. The seed tubers were evaluated at low altitude under darkness on moist sand storage conditions to assess their dormancy release, number of sprouts, sprout weight, sprout length and percentage tuber weight loss. Results showed significant (p

Lucerne (Medicago sativa L.) is a widely grown perennial legume worldwide which can provide high biomass and protein yields, biological N fixation, deep soil water extraction and a range of ecosystems services relevant to current and future agricultural systems. The potential to expand lucerne beyond its current cultivated areas in New Zealand, and its potential productivity across the country's contrasting climate zones, are currently unknown. To gain such insights, we estimated land suitability and spatial distribution of lucerne above-ground biomass across New Zealand lands considering contrasting growth conditions (rain-fed or irrigated for different soils types) and two simulation methods of different complexity (process- and GIS-based approaches). This aimed to assess yield-estimate spatial patterns and sensitivity to model selection for a wide range of combinations of water supply (i.e. irrigation and soil water storage) across New Zealand climate zones. For example, highly suitable areas for lucerne cultivation, were estimated in ∼21 thousand km2 when considering the exclusion of steep slopes, poor soil drainage and excess annual rainfall. The two crop-yield models were applied in response to 30 years of daily historical (1971–2000) weather data downscaled at 5 km resolution on suitable areas. Simulated average lucerne yields ranged from ∼4.5–28 t dry matter/ha per year. Simulations showed a distinct spatial pattern of yield decline from north to south, mainly in response to decreasing temperatures. Temporally, water limited yields were up to 4-fold more variable than under irrigation, depending on the degree of drought stress across different years. Results also unveiled systematic spatial patterns of model uncertainty quantified as yield sensitivity to model selection. For instance, simulated yields were most sensitive to model selection (6–31% of total variability, Ti) within high abiotic-stress environments (e.g. low temperature and limited water supply). Overall, soil type selection accounted for most of yield variability (58–78% Ti), being particularly important in warmer environments with variable seasonal rainfall regimes (e.g. northern regions). As expected, water supply (i.e. rain-fed or irrigated systems) was relatively more impactful on yield (8–20% Ti) for limited rainfall areas, where crops are most drought prone (e.g. east coast and central southern regions). Long-term regional scale comparisons of annual lucerne yield, between 30-year simulated distributions and point-based observations from the AgYields database, helped identify hotspots of yield overestimation. Such insights are useful to guide future research on high yield gap areas (e.g. southern colder and drier locations) and highlight key areas for model improvement (e.g. representation of multiple biotic stresses). Overall, our results provide a first gridded-model assessment of lucerne suitability and yield at national scale and quantify the share of variability explained by key climatic, management and methodological components in spatial analysis studies. These insights can inform future modelling efforts and support agricultural planning that considers the expansion of lucerne and other perennial legumes.

Research on diploid hybrid potato has made fast advances in recent years. In this review we give an overview of the most recent and relevant research outcomes. We define different components needed for a complete hybrid program: inbred line development, hybrid evaluation, cropping systems and variety registration. For each of these components the important research results are discussed and the outcomes and issues that merit further study are identified. We connect fundamental and applied research to application in a breeding program, based on the experiences at the breeding company Solynta. In the concluding remarks, we set hybrid breeding in a societal perspective, and we identify bottlenecks that need to be overcome to allow successful adoption of hybrid potato.

CONTEXTMillions of people living in the Eastern Gangetic Plains (EGP) of India engage in agriculture to support their livelihoods yet are income poor, and food and climate insecure. To address these challenges, policymakers and development programs invest in irrigation-led agricultural intensification. However, the evidence for agricultural intensification to lift farmers’ incomes above the poverty line remains largely anecdotal. OBJECTIVEThe main objective of this study is to use a large household survey (n=15,572; rice: 8,244, wheat: 7,328; 2017/18) to assess the link between agricultural intensification and personal daily incomes from farming (FPDI) in the rice-wheat systems of the EGP – the dominant cropping system of the region.METHODSWe use the Intensification Benefit Index (IBI), a measure that relates farm size and household size to FPDI, to assess how daily incomes from rice-wheat production change with irrigation-led intensification across the EGP.RESULTS AND CONCLUSIONSRelative to the international poverty line of 1.90 Purchasing Power Parity (PPP)$ day-1 and accounting for variations in HH size in the analysis, we found that small farm sizes limit the potential for agricultural intensification from irrigation to transform the poverty status of households in the bottom three quartiles of the IBI. The estimated median FPDI of households with intensified systems in the bottom three quartiles is only 0.51 PPP$ day-1 (a 0.15 PPP$ gain). The median FPDI increases to 2.10 PPP$ day-1 for households in the upper quartile of the IBI distribution (a 0.30 PPP$ gain). Irrigation-led agricultural intensification of rice-wheat systems in the EGP may provide substantial benefits for resilience to climatic change and food security but achieving meaningful poverty reduction will require complementary investments.SIGNIFICANCETransforming the poverty status of most smallholder farmers in the EGP requires diversified portfolios of rural on- and off-farm income-generating opportunities. While bolstering food- and climate security, agronomic intervention programs should consider smallholders’ limited monetary incentives to invest in intensification. Irrigation-led agricultural intensification programs and policies should explicitly account for the heterogeneity in household resources, irrigation levels, and degree of dependence on agricultural income.

In Ecuador, farmers poorly adopt practices to manage potato seed degeneration. This could be related to the deficient understanding of the farmers’ capacity to experience seed degeneration and respond to it. We contribute to this understanding by answering: How do farmers experience seed degeneration?; What practices do farmers implement when their seed is degenerated?; and Is experiencing degeneration the pivotal factor determining how farmers replace their seed regardless their income? We analysed data collected in Ecuador through farmers’ focus group discussions, farmers’ surveys and interviews, and the Ecuadorian employment status survey. We found that approximately half of the farmers experienced degeneration. Farmers experienced it through low yields, change in seed appearance, crop weakening, and seed physiological problems. When farmers experienced degeneration, they replaced their seed, sought for technical advice, applied more agricultural inputs, or grew other crops. Income was an important trigger for farmers to change their seed replacement practices.

Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.

CONTEXT: Wheat-maize (W-M) double cropping is the dominant land use system in the North China Plain (NCP). This system has high grain output but suffers from high fertilizer input and nitrogen (N) surplus. Meanwhile, the market demands more protein and oil crops, such as soybean or peanut. OBJECTIVE: Here, we assess whether incorporation of legumes into W-M via intercropping with maize can contribute to lower annual N input while maintaining high annual outputs and diversifying products with high yield stability. METHODS: We compared yield, yield stability, and profitability of six rotation systems: W-M30 (at the maize inter-plant distance of 30 cm), the density-increased W-M20, wheat-soybean (W-S), wheat-peanut (W-P), and wheat with an intercrop of maize (at the inter-plant distance of 20 cm) and soybean (W-MS) or peanut (W-MP). Four annual N input levels were compared: N0 (no N input), N1 (reduced N input), N2 (target practice), and N3 (current high input). RESULTS AND CONCLUSIONS: Results over four years showed that replacing maize by maize/legume intercrops had a similar wheat yield as that of W-M while the N input was intermediate between W-M and W-legume rotations. Total actual/equivalent grain yields and gross margins of W-MS or W-MP were consistently intermediate between W-M and W-legume rotations. Intercropping enhanced the yield and temporal yield stability of maize per plant, with benefits for both yield stability of the intercropping system of maize season and the annual rotation system. Averaged over six rotation systems, increasing N supply increased the annual total actual/equivalent grain yield, gross margin and yield stability to a plateau starting at N1 or N2, without a further significant increase at N3. Specifically, the response of total equivalent yield or gross margin of each annual system to increasing N supply could be fitted by the linear-plateau model. Compared to the response curve of W-M, W-MS and W-S reached the plateau with a lower N input and higher yield and profit, while W-MP and W-P reached the plateau with lower N input but decreased the yield and profit. Compared to W-M with 240–360 kg N/ha/year, W-MS used 210–320 kg N/ha/year saving 11.1–12.5% fertilizer N, while maintaining or improving production by 9.1–13.0%, and improving profitability by 12.1–15.6% and temporal yield stability by 12.8–50.6%. SIGNIFICANCE: W-MS diversifies products with lower N input and higher outputs, profitability, and temporal yield stability than conventional W-M, thus is highly recommended towards productive and sustainable agriculture in the NCP.

This study aimed to understand the morphophysiological responses and primary metabolism of tomato seedlings subjected to mild levels of nitrogen and/or water deficit (50% N and/or 50% W). After 16 days of exposure, plants grown under the combined deficit showed similar behavior to the one found upon exposure to single N deficit. Both N deficit treatments resulted in a significantly lower dry weight, leaf area, chlorophyll content, and N accumulation but in a higher N use efficiency when compared to control (CTR) plants. Moreover, concerning plant metabolism, at the shoot level, these two treatments also responded in a similar way, inducing higher C/N ratio, nitrate reductase (NR) and glutamine synthetase (GS) activity, expression of RuBisCO encoding genes as well as a downregulation of GS2.1 and GS2.2 transcripts. Interestingly, plant metabolic responses at the root level did not follow the same pattern, with plants under combined deficit behaving similarly to W deficit plants, resulting in enhanced nitrate and proline concentrations, NR activity, and an upregulation of GS1 and NR genes than in CTR plants. Overall, our data suggest that the N remobilization and osmoregulation strategies play a relevant role in plant acclimation to these abiotic stresses and highlight the complexity of plant responses under a combined N+W deficit.

Managing outbreaks of alien plant pests is key to preserving biodiversity and safeguarding crop production. Zoning strategies are applied by plant health authorities to tailor measures to the risk of spread in relation to distance from the outbreak epicentre and the biology of the pest. Here we synthesize information on outbreak management to evaluate the diversity and consistency of such approaches. We collected information on the zoning strategies of 121 outbreaks of 25 plant pests in the European Union (EU). According to the organism’s presence and the measures applied, five zones were distinguished: an infested zone (83% of cases), a buffer zone (76%), a clear-cutting zone (28%), an eradication zone (1%) and a containment zone (1%). Infested zones and buffer zones were adjacent non-overlapping zones, while the clear-cutting zone, eradication zone or containment zone was within either the infested zone or buffer zone. A combination of infested and buffer zones was used in 51% of recorded cases. Measures differed within different zones. Destruction of infested plants in the infested zone was done in 78% of the cases, while surveillance was always applied in the buffer zone. Regulation of an organism at EU level led to a convergence of zoning strategies applied by different member states. Regulations often prescribed the greatest widths used before regulations were issued. Further analyses are needed to explore the efficacy of different strategies including the costs of each strategy. Such analyses should combine insight from practice with bio-economic modelling.

Grazing exclusion changes soil physical-chemical characteristics, rapidly affects microbial community composition and function, and alters biogeochemical processes, e.g., carbon (C) cycle, over time. However, the temporal dynamics of CO2 emission and CH4 uptake during grassland restoration chronosequences remain poorly understood. We investigated soil CO2 emission and CH4 uptake, the genes related to CO2 and CH4 production and reduction (cbbL, cbbM, chiA, and pmoA), and associated microbial communities under different durations of grazing exclusion (0, 7, 16, 25, and 38 years) to reveal the mechanisms and potential of soil CO2 emission and CH4 uptake in a semi-arid steppe. The results showed that a proper exclusion period could significantly improve soil physical-chemical conditions, vegetation community, and soil C-cycling. The abundance of C-cycling functional genes (cbbL, cbbM, chiA and pmoA), CH4 uptake and CO2 emission rates showed a single-peak pattern with increasing duration of grazing exclusion, peaking at 16 years and then decreasing in the period between 25 and 38 years, indicating that the effect of exclusion weakened when the exclusion period was too long. The changes in C-cycling functional genes and microbial communities are primarily influenced by aboveground net primary productivity (ANPP), and are associated with CO2, CH4, soil water content (SWC), and soil organic carbon (SOC). Structural equation modeling showed that increases in SOC content and pmoA abundance caused by an increase in ANPP accelerated CO2 emission and CH4 uptake rates, respectively. Our results provide valuable insights into the critical role of grazing exclusion in promoting grassland restoration and carbon sequestration, and have potential implications for sustainable land management practices.

Intercropping, also known as mixed cropping, consists on simultaneously growingmore than one species on a field. It has a great potential for enhancing water- and nutrientuseefficiency and improving plant productivity, yield stability and resilience to biotic and abiotic stress, including those triggered by climate change. Despite their manifold benefits,the practice of intercropping has not risen above its niche status in many regions of theworld. The selection of varieties specifically adapted to intercropping remains a major practical challenge to its widespread deployment. This Editorial of a Research Topic hosted at Frontiersin Plant Sciences entitled “Breeding for intercropping” gathers a series of articles coveringnew insights in the areas of quantitative genetics, ecology, ecophysiology and agronomyintegrating theoretical, experimental as well as participatory approaches.

To identify if and how the age of in vitro potato plantlets at planting affects the later tuber formation, an extensive pot experiment was performed under controlled conditions. In vitro-derived plantlets of different ages (14, 28, 42 and 56 days old at planting) and cultivars varying in maturity type (Gloria, very early; Bintje, mid-early; Elkana, late) were grown after planting for 10 weeks at photo/thermoperiods of 16 h (standard conditions) or 12 h (short-day conditions). Plants raised from older in vitro plantlets produced higher total dry weights, harvest index and tuber dry and fresh weights than plants from younger in vitro plantlets when grown under standard conditions after planting. By contrast, total and tuber dry weights were not affected by plantlet age when grown under short-day conditions. The number of tubers per plant increased with increase in in vitro plantlet age in the later cultivars and in the oldest age classes of the very early cultivar when plants were grown under standard conditions. Short-day conditions resulted in fewer, but larger tubers than standard conditions. Results support the ideas that (1) plants from older in vitro plantlets and earlier maturing cultivars are more advanced in the tuber formation process; however, this may benefit tuber yield only when plants are grown under conditions that are not strongly inducing tuberization, and (2) higher tuber numbers can be achieved by more below-ground nodes—as in older in vitro plantlets—and/or by later or less strong tuber induction—as in less inducing conditions (16-h vs. 12-h), later cultivars or younger in vitro plantlets.

Context or problem: The reallocation of dry matter (DM) and nitrogen (N) from vegetative tissues to the grains are critical for both yield quantity and protein content of cereal crops. However, it is unclear to which extent the dynamics in DM and N reallocation depend on N availability, and how individual leaves within the maize canopy respond to different N availabilities in terms of these processes. Objective or research question: This study aimed to quantify DM and N accumulation, partitioning, and reallocation from vegetative to reproductive parts in maize in relation to soil N availability. Methods: A long-term N fertilizer trial was conducted in Jilin province, Northeast China, growing maize at three N fertilizer levels (low N availability, N0; intermediate N availability, N1; and high N availability, N2). The accumulation, partitioning, and reallocation of DM and N were quantified at the whole-plant, organs, and single-leaf scales in 2015 and 2016. Results: Although both post-silking DM accumulation and post-silking N uptake increased in response to higher N availability, 8.3–38.8% of grain N still needed to be reallocated from vegetative organs with a larger fraction coming from leaves (10.5 – 36.5%) than from stems (4.4 – 11.6%). This dependency of grain N on N reallocation from vegetative parts increased at lower soil N availability. Furthermore, the vertical patterns of reallocated leaf DM and reallocated leaf N changed with N availabilities. While in general leaves in the middle part of the canopy tended to reallocate more DM and N to the grains than leaves from the upper or lower canopy parts, these most-contributing leaves were higher in the canopy at low than at high N availability. Conclusions and implications: Grain N relies on reallocation more than does grain DM. At lower N availability, more grain DM and grain N need to be reallocated from vegetative organs. Furthermore, the leaf ranks from which most DM and N were reallocated, gradually increased from the bottom to upper ranks as N availability decreased. Together, our results on the dynamics of N and DM uptake and reallocation during the reproductive phase are important for plant and crop models that require these processes for accurate predictions of maize performance.

Improving the quality of seed potatoes that smallholder farmers plant continues to represent one of the most important challenges of the potato sector in most developing countries to counter the long-lasting poor yields. This study aimed to better understand the way farmers choose seed potato by exploring the attributes they look for and the benefits they expect from them. We used means-end chains analysis in combination with Kelly’s repertory grid as an elicitation technique and disaggregated data for male and female partners. In total, farmers named 38 attributes they look for when selecting seeds. Farmers associate “good” seeds to those that are well-sprouted, have many eyes, are of a variety they know, are medium in size, are certified, and are undamaged. Most preferred attributes lead to a higher yield and consequently higher income which is the most predominant avenue for farmers to achieve their desired values in life. Female farmers mentioned fewer attributes and also pursued fewer values than their male counterparts. Users and non-users of certified seed were shown to use the same attributes to select their potato seeds. Non-users of certified seed thus seem to be aware of the benefits of certified seed even though they are not using it. The results from this study indicate that increasing the availability of certified seed is not necessarily a straightforward way of improving the quality of seed potato planted by Kenyan smallholder farmers.

Cocoa is an important commodity crop and source of income for millions of small-holder farmers. Nonetheless, questions on cocoa tree functioning, best management practices and climate change responses remain. Modelling is a powerful tool to address these questions, complementing experimental work that is expensive and time consuming due to the long productive cycle of the cocoa system. However, compared to other crops, cocoa modelling has not received as much attention. OBJECTIVE: We reviewed existing cocoa models and identified the main gaps in the literature and possible strategies to advance models of cocoa production. METHODS: We first classified relevant research questions in cocoa production along three main axes (fundamental-applied, spatial organization, prediction horizon) and aligned modelling approaches along these. We then reviewed six published cocoa models using these axes as framework. This comparison revealed several modelling gaps for which we provide an overview of data availability for future model development. RESULTS: (i) Several plant processes (i.e., water stress responses, respiration, climate change responses, nutrient effects and phenology) are either missing from existing cocoa models or are simulated based on general plant physiological knowledge rather than cocoa-specific knowledge. (ii) The only currently existing 3D model of cocoa architecture has very limited scope and does not include physiological processes. (iii) There are no model-based decision support tools available for supporting the main management practices such as irrigation, fertilization and pruning. (iv) Data for model calibration and validation are often scarce. CONCLUSIONS: We conclude that data availability for model design, calibration and validation is currently the main bottleneck for further development of cocoa models. Extensive cooperation within the cocoa research community and a large network of long-term experiments under different climatic and management conditions are required to close the identified modelling gaps.

CONTEXT: To avoid excessive chemical-fertilizer application and improve agricultural productivity in rice, a fertilizer recommendation system called Nutrient Expert® (NE) was designed. However, the ability of NE to balance yield, profitability and environmental sustainability in rice production needs to be further evaluated, as it is still difficult for farmers to assess the proper nitrogen (N) application rate. OBJECTIVE: The objective of this study was to demonstrate the advantages of the NE system in balancing yield, profitability and N loss in rice production, and recommend proper N application rates for different cropping seasons of rice. METHODS: This study describes results from field experiments conducted in five main rice cropping provinces from 2017 to 2020 in China, to investigate any advantages of NE compared with local farmers' practice (FP), and to determine the proper N application rates for different cropping seasons of rice. RESULTS AND CONCLUSIONS: Compared with FP, NE had 12.1% lower N-fertilizer application, but increased rice grain yield by 4.3% and net profit by 7.4%, and decreased yield-scaled N loss by 20.7%. We showed how yield, profitability and N loss were affected by N balance (i.e., N applied to the field minus N removed from the field by the harvested crop biomass), and quantified relationships between N balance and N application rate, and between N output and input. Based on relationships between N balance and N application rate, we recommend N application rates in a range from 122 to 214 kg ha−1, depending on cropping seasons of rice. We demonstrated that NE can simultaneously improve yield, profitability and environmental sustainability. SIGNIFICANCE: Our study provided quantitative support for NE-based recommendations on the N application rate for smallholders farming in different rice cropping systems, and these recommendations can serve as a reference for avoiding excessive N application rate in paddy fields in other regions with similar eco-environment.

Combinability of species in intercrops depends on the production conditions and there is limited information on the potential of intercropping under conventional (i.e., non-organic) management in Western Europe. Here we determined productivity of four crop species (maize, Zea mays L.; wheat, Triticum aestivum L.; faba bean, Vicia faba L.; pea, Pisum sativum L.) in six different bi-specific mixture compositions. Species were spring-sown and fertilized in their strips according to common practice for monocrops. Strips were 1.5 m wide enabling strong interspecific interactions. Intercrops with maize, a species sown and harvested later than the other three species, had land equivalent ratio (LER) values that were in four out of six cases significantly greater than one, from 1.14 ± 0.04 to 1.22 ± 0.05 in 2018, and from 0.98 ± 0.06 to 1.15 ± 0.01 in 2019. Simultaneous intercrops comprising two of the other three species had LER values that tended to be lower than one, even though many LERs were not significantly different from one: from 0.94 ± 0.02 to 0.95 ± 0.04 in 2018, and from 0.80 ± 0.08 to 0.93 ± 0.04 in 2019. The yield gain (net intercropping effect; NE) in relay intercrops with maize ranged from 1.33 ± 0.59 to 2.01 ± 0.54 Mg ha−1 in 2018, and from 0.29 ± 0.41 to 1.04 ± 0.14 Mg ha−1 in 2019. The NE of simultaneous intercrops ranged from −0.43 ± 0.13 to −0.27 ± 0.22 Mg ha−1 in 2018, and from −1.17 ± 0.49 to −0.36 ± 0.22 Mg ha−1 in 2019. Results indicate that temporal complementarity between species drove the LER (or NE) in these experiments. On the other hand, values of the LER (or NE) were similar in species combinations with or without legumes, suggesting no major role for complementarity for nitrogen capture under the conditions of the study. Faba bean was the most competitive species and reached high partial LER and NE values in intercrops at the expense of the companion species. Competition from faba bean reduced the grain yield of wheat and pea more than it increased faba bean grain yield, resulting in negative net effects. Results suggest that relay strip intercropping can improve land use efficiency and total grain yield in conventional farming in Western Europe if species have temporal complementarity.

Preceding crop and nitrogen (N) fertilization affect N cycling and productivity of subsequent wheat in double cropping. However, the effects of preceding crop and N fertilization on relationships between yield and “mineral nutriome” or nutritional quality (amount and bioavailability) in wheat grains have not been well characterized, particularly not in the case of multiple mineral nutrient elements and when considering cumulative effects of fertilization strategies in long-term field experiments. Here we present effects of preceding crop (monocultures of maize, peanut or soybean, and intercropping of maize with peanut or soybean) at 4 levels of annual fertilizer N input (0–440 kg/ha) on yield traits, major mineral nutrients and their relationships in wheat grains in a 4-years continuous double-cropping field experiment in the North China Plain. Nitrogen fertilizer increased wheat grain yields, mass concentrations of N and copper (Cu), and micronutrient (mainly zinc: Zn and iron: Fe) bioavailability, while no N supply was associated with low grain yield, N and Cu concentrations and micronutrient bioavailability, high mass concentrations of Zn, manganese, phosphorus (P), calcium, magnesium and phytate-P, and a high ratio of phytate-P/P. Moderately lowering N input from the in-season 240 to 200 kg/ha (but not 120 kg/ha) would not harm grain yield and most nutritional traits. Compared to significant effects of N application level on almost all grain yield and nutritional traits, and soil properties, preceding crops had less impact and only grain yields and Zn concentrations were significantly affected. Grain yields, N and Zn concentrations varied dramatically from an average of 2.7 to 7.6 t/ha, 16.5–19.3 g/kg and 15.1–19.8 mg/kg with different N application levels, respectively; while varied relatively little from 5.9 to 6.6 t/ha, 17.8–18.3 g/kg and 16.1–18.1 mg/kg under different preceding crops, respectively. Compared to the conventional wheat-maize rotation, a legume pre-crop monoculture but not maize/legume intercropping increased grain yields by 5.0–11.9% on average, but reduced grain Zn concentrations from 17.5–17.8 to 16.1 mg/kg significantly. The legume effect was most significant at zero or low N supply. The relationship between grain yields and Zn concentrations was adequately described by a concave-up parabola (R2 = 0.3001, P < 0.0001, n = 288), suggesting appropriate N fertilization and rotation can achieve high-yield while ameliorating the dilution of grain Zn density. Therefore, our findings provide new insight in relationships among agronomic practices, wheat grain yield and grain nutritional quality (particularly for Zn).

A novel cropping system for potato was tested for two consecutive years under normal Dutch agronomic conditions. Seedlings from two experimental genotypes of hybrid true potato seeds were produced in a greenhouse nursery and transplanted into the field 5 weeks after sowing to assess tuber yield levels and to study effects of hilling on tuber yield and number, tuber size distribution and tuber greening. Field experiments had a split-plot design with hilling treatments as the main plots and genotypes as the sub-plots. Final harvest was at 122 and 132 days after transplanting in 2017 and 2018, respectively. Hybrid seedlings were transplanted into small initial ridges and irrigated straight after planting. Three hilling treatments were applied between transplanting and 100% canopy cover. Treatment ‘zero hilling’ did not receive any additional hilling after transplanting. Treatments ‘double hilling’ and ‘triple hilling’ received two and three additional hilling treatments, respectively. Total tuber yields at final harvest in both years were not affected by the hilling treatments. Yields for the respective genotypes were 26 and 30 Mg/ha in 2017 and 25 and 32 Mg/ha in 2018. Total tuber numbers were only affected by hilling treatments in 2017, where under hilled conditions, plants produced more tubers compared with plants under zero hilling. Plants under zero hilling yielded more tubers in size class > 40 mm compared with triple hilling in 2017. In 2018, no significant effects of hilling on tuber numbers were found, but the trend was similar to that in 2017.

Aim Recycling of cocoa pod husks has potential to contribute to mineral nutrition of cocoa. Yet little is known of the nutrient content and nutrient release patterns from the husks. The potassium (K) rich husks are usually left in heaps in cocoa plantations in Africa. We aimed to understand and quantify release patterns of K and other nutrients from husks under varying rainfall regimes and assessed the effects of partial decomposition and inundation on nutrient leaching rates. Methods We incubated chunks of cocoa pod husks to assess decomposition rates and we measured nutrient leaching rates from two sets of husk chunks: one set was placed in tubes that were submitted to simulated scheduled rainfall events while the second set was continuously inundated in beakers. Results Decomposition of husks followed a second-order exponential curve (k: 0.09 day−1; ageing constant: 0.43). Nutrient losses recorded within 25 days were larger and more variable for K (33%) than for other macronutrients released in this order: Mg > Ca ≈ P > N (less than 15%). Potassium leaching was mainly driven by rainfall frequency (P Conclusion Some initial decomposition of cocoa pod husks is required to expose K to intense leaching. As decomposition progresses, abundant K losses are to be expected under frequent and/or intense rainfall events.

Several constraints affect the performances of the farming system in Chencha suggesting the necessity of adjustments in the farm components. Therefore, an exploration was made to simultaneously optimize operating profit, labour and soil organic matter balances. Data from twelve farms and secondary data on improved technologies were used as bases for the exploration. Using the multi-objective model FarmDESIGN, the optimization was conducted for two scenarios for each farm, i.e., optimization based on the currently existing farm components and practices and by introducing new technologies and practices to amend the current farm management options. The results revealed that the farm operating profit, labour balance and organic matter balance were not yet optimized with the current farm configurations of all farms. But there is ample scope to improve and simultaneously optimize both the economic, social and environmental sustainability either through optimization of management within current farm resources, or through using improved technologies. The highest improvement could be made through combined optimization of management within current farm resources and improved technologies. The major important factor that influenced the optimization was the cropping plan, which might be associated with the management practices applied for a particular crop. However, adjusting areas of crops and implementation of some other optimized solutions may be difficult for individual farmers and requires advice through agricultural extension programmes. Therefore, there is a need to improve the awareness of farmers to wisely manage: crop area and associated crop and soil management practices, land use for eucalyptus, straw use and storage of farm yard manure. Moreover, it is important to diversify off-farm income sources, introduce alternative threshing machineries and improve market access for farm products.

Global dimming, a decadal decrease in incident global radiation, is often accompanied with an increase in the diffuse radiation fraction, and, therefore, the impact of global dimming on crop production is hard to predict. A popular approach to quantify this impact is the statistical analysis of historical climate and crop data, or use of dynamic crop simulation modelling approach. Here, we show that statistical analysis of historical data did not provide plausible values for the effect of diffuse radiation versus direct radiation on rice or wheat yield. In contrast, our field experimental study of 3 years demonstrated a fertilization effect of increased diffuse radiation fraction, which partly offset yield losses caused by decreased global radiation, in both crops. The fertilization effect was not attributed to any improved canopy light interception but mainly to the increased radiation use efficiency (RUE). The increased RUE was explained not only by the saturating shape of photosynthetic light response curves but also by plant acclimation to dimming that gradually increased leaf nitrogen concentration. Crop harvest index slightly decreased under dimming, thereby discounting the fertilization effect on crop yields. These results challenge existing modelling paradigms, which assume that the fertilization effect on crop yields is mainly attributed to an improved light interception. Further studies on the physiological mechanism of plant acclimation are required to better quantify the global dimming impact on agroecosystem productivity under future climate change.

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Bans on the use of synthetic herbicides require innovative management approaches to maintain the attractiveness and usability of turfgrass swards. Such measures should include the use of locally adapted cultivars that germinate and establish quickly, resulting in the densest possible stands. Additionally, a number of turfgrasses have been reported to produce allelopathic substances that inhibit common turfgrass weeds. Mowing heights should be set to achieve maximum weed suppression while still providing acceptable quality for desired use. Sustainable turfgrass management programs have led to a reduction in fertilizer inputs; however, without the availability of herbicides, fertilization regimes need to be re-examined. The literature suggests that broadleaf weeds are reduced but never fully controlled when more N is applied; therefore, finding a balance between what is needed and what is environmentally safe and sustainable is critical. Organic herbicides include plant pathogens from the fungus Phoma and strains of the bacterium Pseudomonas fluorescens. Both can be used to control several weeds common to turfgrasses. Acetic acid has also been shown to have herbicidal activity; however, it has limited residual activity, and its efficacy remains questionable on mature weeds. Thermal weed control can be used to sterilize a seedbank or spot treat existing weeds. Future turfgrass breeding programs could focus on understanding and enhancing the allelopathic potential of turfgrasses to outcompete weeds more effectively. Furthermore, more research should be directed at assessing the competitiveness of certain turfgrasses against weeds within the limitations of producing turfgrass areas of acceptable aesthetics and playing quality.

The metabolic-oxidative stress profile of the rice flag leaf during drought stress in the reproductive stage is highly predictive for grain yield loss sensitivity of 292 accessions at harvest time., Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate–glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.

Intercropping is the simultaneous cultivation of plant species in the same field for a considerable proportion of their growing periods. Interest in intercropping for sustainable agriculture is on the rise and the number of scientific studies on intercropping is strongly increasing. Here we assess the current status of knowledge on factors that determine yield, yield stability and resource use efficiency of intercropping as compared to sole cropping. Distinguishing resource use into acquisition and conversion shows that intercrops are mainly improving acquisition rather than conversion efficiency. We also make an attempt to quantify the importance of reduced biotic stresses through pests, diseases, and weeds. We particularly focus on blank spots in the knowledge and possible bias in existing literature and ask which research approaches are needed to advance the field and pave the way for a wider usage of intercropping in modern sustainable agriculture.

Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised brain tissue a substantial amount of information processing occurs in a centralised manner, most biological computing is distributed across multiple entities, such as cells in a tissue, roots in a root system or ants in a colony. Physical context, called embodiment, also affects the nature of biological computing. While plants and ant colonies both perform distributed computing, in plants the units occupy fixed positions while individual ants move around. This distinction, solid versus liquid brain computing, shapes the nature of computations. Here we compare information processing in plants and ant colonies, highlighting how similarities and differences originate in, as well as make use of, the differences in embodiment. We end with a discussion on how this embodiment perspective may inform the debate on plant cognition.

Semi-natural habitats in agricultural landscapes vary greatly in shape and vegetation characteristics. They can appear either as relatively large patches of several hectares or as narrow bands (less than 1 m wide) between fields and roads and between fields. Semi-natural habitats support biodiversity and associated ecosystem services on farmland, thereby contributing to sustainable agriculture. However, the effects of different semi-natural habitat types on the polytrophic level of epigaeic arthropods are still unclear. In this study, we classified semi-natural habitats into five types. (1) woody areal (WA), (2) woody line (WL), (3) herbaceous areal (HA), (4) herbaceous line (HL) and (5) isolate habitat (IH). We aimed to explore differences in epigaeic arthropod community composition in five different semi-natural habitats and the effects of different semi-natural habitats and different sampling locations on epigaeic arthropod activity-density and diversity. The results showed that epigaeic arthropod communities show significant differences, not only between farmland and semi-natural habitats, but also between different types of semi-natural habitats. Isolate habitats have the highest activity-density of epigaeic arthropods and Linear herbaceous maintain the highest epigaeic arthropod diversity. We also found in this study, both the activity-density and diversity of epigaeic arthropods showed edge-biased distribution. It may be possible to promote sustainable agricultural ecosystems by understanding the effect of semi-natural habitats on epigaeic arthropods, which is conducive to improving the quality of the agricultural ecological environment.

The technology of hybrid breeding in diploid potatoes creates opportunities to design novel and improved cultivation systems based on hybrid true potato seeds. A promising cultivation pathway to produce seed or ware tubers is by transplanting greenhouse-raised seedlings into the field. This study explored the effects of transplanting date and seedling age on tuber yield, using greenhouse-raised seedlings. Field trials with experimental hybrid genotypes were conducted in three consecutive years. In 2017 and 2018, 4- and 6-week-old seedlings were transplanted at four dates: March, April, May and June. In 2019, transplanting dates included April, May and June and seedling age was 5 weeks. In 2018, the March planting experienced severe frost during the initial field period resulting in crop failure. In 2017 and 2019, plants could withstand shorter and less severe frost events. Seedling age did not significantly affect tuber parameters. Transplanting in June resulted in lower marketable yield (> 28 mm) compared with earlier transplanting dates when crops were harvested in September. At full crop senescence, no differences in marketable yield were observed. The optimal transplanting window, taking into account weather-related risks, is approximately between early April and end May. For some genotypes, crop cycle length was observed to be a more important yield-determining factor than transplanting date.

Intercropping maize and soybean is renowned for improving crop production and resource use efficiencies. Interspecific competition and complementarity with respect to root plasticity is essential knowledge for understanding the mechanisms of overyielding and optimizing intercropping species selection. We conducted a three-year field experiment (2017–2019) to quantify land and water productivities in relation to above- and below-ground interspecific interactions, root growth and distribution under different nitrogen rates in maize/soybean intercropping. The land productivity in terms of land equivalent ratio (LER) in maize/soybean intercropping was 1.10 across all years and N rates. The yield increase in intercropped maize was mainly gained from an 45% increase in kernel numbers, while the yield loss of intercropped soybean was caused mainly by an 35% decrease in the pod numbers compared to sole cropping. The system level water use efficiency, defined as water equivalent ratio (WER) was also 1.10. Compared with sole stands, intercropped maize consumed more water during the vegetative stage, but intercropped soybean took up more during the reproductive stage. That indicated a temporal complementarity of water use in the intercrop, which benefited maize kernel formation and partially offset the negative shading effect of soybean grain filling. Soybean showed a marked increase in root length density (RLD). Compared to the produced aboveground biomass (DM) in the intercrop, the intercropped soybean invested more assimilates into root than shoot, as defined as root plasticity, the RLD/DM ratio of soybean in the intercrop was 76% more than sole system. However, the intercrop did not change root plasticity of maize. The overlap of maize and soybean roots, i.e. interspecific interaction interface, occurred mainly within the position between two border rows and at first soybean row. Under interspecific competition, soybean in the intercropping created both temporal and spatial differentiation for water uptake, which might be a key reason for enhancing intercropping land and water productivities. Our results contribute to understanding the mechanism of interspecific interaction for maximizing land and water productivities in rain-fed intercropping.

Pollination deficits can compromise fruit yield and quality and have been reported in several fruit crops. It is unknown whether there is a pollination deficit in the production of Korla fragrant pear, Pyrus sinkiangensis, in China, and if so, whether this deficit can be mitigated by the use of managed honeybees (Apis mellifera). We assessed insect communities, flower visitation, pollination deficit and honeybee contribution to pear pollination in Korla fragrant pear orchards in Xinjiang, China. Insect communities were monitored using colored pan traps, and pollination deficit was assessed by comparing fruit set with open pollination to that with hand pollination in orchards without beehives from 2018 to 2021. The contribution of honeybees to pollination was assessed by comparing flower visitation, fruit set and fruit quality in pear orchards with and without beehives in 2020 and 2021. In orchards without beehives, wild bees (72%) were the dominant pollinator group in pan traps, followed by honeybees (15%), moths, hoverflies, butterflies and wasps (Vespidae). Fruit set in these orchards was much lower with open pollination (8 ± 2%) than with hand pollination (74 ± 4%). When comparing pollination in orchards with and without beehives in 2020 and 2021, we found that honeybees were responsible for most of the flower visits in orchards with (96%) and without beehives (66%). Wild bees were responsible for 1% and 6% of flower visits in orchards with and without beehives, respectively. Fruit set was significantly higher in orchards with beehives (38 ± 9%) than in orchards without beehives (12 ± 3%), while fruit set and sugar content were positively associated with pollinator visitation rate. The findings reveal a large pollination deficit in Korla fragrant pear orchards, and show that this deficit can be mitigated using managed honeybees.

Arable land systems are complex ecosystems composed of cultivated land and semi-natural habitats. Retaining an appropriate proportion of semi-natural habitats in arable land systems is beneficial for enhancing landscape heterogeneity and biodiversity. However, it is unclear how many semi-natural habitats need to be retained in arable land systems to improve landscape heterogeneity. In this study, the land use data of four counties were used as the data source in the Lower Liaohe Plain, Liaoning Province, and Rao’s quadratic entropy index (Q) was used to quantitatively characterize the landscape heterogeneity. We aimed to explore the minimum proportion of semi-natural habitat required to maintain high landscape heterogeneity and determine the independent and interactive effects of semi-natural habitat composition and configuration on landscape heterogeneity. We found that (1) maintaining a 5% proportion of semi-natural habitats is the minimum threshold for achieving high landscape heterogeneity in arable land systems. Retaining a 10% share of semi-natural habitats is beneficial for both agricultural production and land ecology. (2) The combination of woodland, water and ditches was good for improving landscape heterogeneity. Connectivity in semi-natural habitats is critical to improving landscape heterogeneity. (3) The interaction of semi-natural habitat composition and configuration had a strong effect on landscape heterogeneity (53.1%). Semi-natural habitat configuration was found to be more important than composition for landscape heterogeneity. The role of semi-natural habitat composition and configuration in maintaining landscape heterogeneity and supporting the sustainability of land use therefore needs to be considered in arable land systems.

We assessed how the temperature response of leaf day respiration (Rd) in wheat responded to contrasting water regimes and growth temperatures. In Experiment 1, well-watered and drought-stressed conditions were imposed on two genotypes; in Experiment 2, the two water regimes combined with high (HT), medium (MT) and low (LT) growth temperatures were imposed on one of the genotypes. Rd was estimated from simultaneous gas exchange and chlorophyll fluorescence measurements at six leaf temperatures (Tleaf) for each treatment, using the Yin method for non-photorespiratory conditions and the non-rectangular hyperbolic fitting method for photorespiratory conditions. The two genotypes responded similarly to growth and measurement conditions. Estimates of Rd for non-photorespiratory conditions were generally higher than those for photorespiratory conditions but their responses to Tleaf were similar. Under well-watered conditions, Rd and its sensitivity to Tleaf slightly acclimated to LT but did not acclimate to HT. Temperature sensitivities of Rd were considerably suppressed by drought, and the suppression varied among growth temperatures. Thus, it is necessary to quantify interactions between drought and growth temperature for reliably modelling Rd under climate change. Our study also demonstrated that the Kok method, a currently popular method for estimating Rd, underestimated Rd significantly and should be abandoned.HighlightLeaf day respiration (Rd) acclimated little to growth temperature, but significantly to drought by reducing its thermal sensitivity. The Kok method underestimates Rd and should no longer be used.

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy-one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.

Potato production in low-income countries is threatened by seed degeneration, i.e., the accumulation of seed-borne diseases and pests in potato seed tubers when these are vegetatively propagated over consecutive cycles, leading to a reduction in seed quality and yielding ability. Agroecological settings and seed recycling (on-farm propagation over consecutive cycles) determine the process of seed degeneration. However, it is poorly understood how these factors affect this process. Therefore, to reduce this knowledge gap, we analysed two datasets collected in Ecuador, one from a multi-annual field experiment and one from a farmers’ seed study. The experiment, carried out from 2013 to 2016, aimed to assess seed degeneration at agroecological settings present in three different altitudes. The farmers’ seed study, in which 260 farmers were surveyed in 2018, aimed to understand potato seed degeneration in farmers’ fields under diverse agroecological settings. Our results of the multi-annual field experiment showed that agroecological settings have a heterogeneous influence on the presence of seed-borne diseases and pests. We also found that both the agroecological settings at the three altitudes and the number of on-farm propagation cycles affected the rates at which seed-borne diseases and pests on the seeds increased and yield decreased. However, the farmers’ seed study challenged these results by indicating that this was not clear on farms. Combining these results, this article shows that agroecological settings and seed recycling only partially explain the process of seed degeneration. This suggests that more research about seed degeneration needs to also take place under farmers’ conditions to fully understand the complex of potato performance factors. We expect that such research will support the design of improved seed interventions, while simultaneously it may generate discussion about when potato seed degeneration plays an important role in productivity.

CONTEXT: Studies in the Andes have demonstrated that seed degeneration of potato occurred in experimental conditions, but was negligible in farmers' conditions. There are two hypotheses for this difference: (1) farmers cultivate resistant varieties, or (2) they use on-farm practices that can manage seed degeneration. Farmers may replace some of the seed saved from their fields with outside seed, but it is an open question what level of benefit farmers experience from partial replacement. OBJECTIVES: The objective of this study was to investigate the role of the cultivated varieties, the on-farm seed management practices, and seed replacement in potato seed degeneration. Moreover, this study evaluated the potential effect of partial replacement of the farmers' seed lot each season with healthy seed, compared to less frequent nearly full replacement, in simulations. METHODS: We surveyed farmers in the Cotopaxi province, Ecuador, in 2008, 2010, and 2018, and performed a study on the incidence of pathogens and pests in farmers' seed lots in 2018. We also evaluated the potential effects of the timing of replacement of farmers' seed lots by healthy seed to manage degeneration, applying the seedHealth model. RESULTS AND CONCLUSIONS: We found that farmers experience no or only slow degeneration in their varieties. Analysing yield data reported by farmers to detect degeneration, we did not detect yield declines. The type of variety and year of data collection explained the variation in yield. These results seem to confirm the hypothesis that varieties cultivated in the Andes are resistant to the impact of seed degeneration on yield, and that seed degeneration depends on the agroecological conditions present within a cropping season or year. Because we did not find an impact on yield, we hypothesized that on-farm practices affect seed-borne pathogens and pests causing seed degeneration. We identified multiple on-farm practices playing a role in the process of seed degeneration: they either slowed down or accelerated this process depending on the seed-borne pathogen and pest causing seed degeneration. Our scenario analyses using the seedHealth model showed how replacing farmers' seed lots by healthy seed could usefully reduce seed degeneration compared to using the same amount of seed to periodically replace nearly all seed in a season. Our results showed that on-farm practices are also critical drivers in the process of seed degeneration. SIGNIFICANCE: This study demonstrated the importance of considering on-farm seed management practices (i.e., use of cultivated varieties) to strengthen seed systems interventions aiming to manage potato seed degeneration. Additionally, this study showed the potential of partially replacing farmers' seed with healthy seed as an alternative when complete seed replacement is not an option.

Potato is the second most important food crop after maize in Kenya. However, most farmers produce potatoes under sub-optimal management, resulting in low yields, despite the introduction of improved varieties. Potato production practices were documented and compared to contribute towards improved potato management and productivity in Kenya. The study was guided by the hypothesis that potato farming and management practices influence potato performance and can depend on the production environment. Focus group discussions and household surveys were conducted in three major potato growing areas in Kaptama, Saboti and Lelan in Bungoma, Trans Nzoia and Elgeyo Marakwet counties in Kenya. Farming was the main occupation of 58.2% of the respondents. Respondents across the study sites indicated that they grew potatoes with their main focus as a cash (83.6%) and food (16.4%) crop. Most respondents had planted potatoes during both the last long (96.4%) and short (92.4%) rainy seasons. The four most important constraints limiting optimal potato production according to respondents were lack of quality seed, diseases (specifically late blight and bacterial wilt), poor marketing and lack of adequate technical knowledge on potato management. Low yields realized by farmers were mainly influenced by poor farmer practices in the use of seed, fertilizers, pesticides and crop rotation. This was compounded by farmers’ perceptions on input quantities applied, frequencies and farmers’ access to agricultural extension information on potatoes, which heavily relied on family members and neighbouring farmers. Provision of quality seeds and training of farmers with the support of demonstrations on fertilizer and pesticide and appropriate crop rotation practices are recommended for improved potato production and yields. Use of irrigation where possible should be enhanced through government and development partners’ support to ensure sustainable potato production and supply. Also, the use of viable extension information channel(s) could enhance potato production for household food security, livelihoods and national goals.

Context: Global cocoa production is largely concentrated in West Africa where over 70% of cocoa is produced. Here, cocoa farming is largely a rain-fed, low-input system with low average yields, which are expected to decline with climate change. With increasing demand, there is a need to evaluate opportunities to increase production whilst avoiding deforestation and expansion to croplands. Thus, it is important to know how much additional cocoa can be produced on existing farmland, and what factors determine this potential for increased yield.Objective: The objective was to quantify the cocoa yield gap in Ghana and identify the factors that can contribute to narrowing the gap.Methods: We calculated the cocoa yield gap as the difference between potential yield (i. water-limited potential(Yw) quantified using a crop model, ii. attainable yield in high-input systems(YE), iii. attainable yield in low-input systems(YF)) and actual farmer yield. Both absolute and relative yield gaps were calculated. We then related each yield gap (absolute & relative) as a function of environment and management variables using mixed-effects models.Results and conclusions: There were considerable yield gaps on all cocoa farms. Maximum water-limited yield gaps (YGW) were very large with a mean absolute gap of 4577 kg/ha representing 86% of Yw. Attainable yield gap in high-input (YGE) was lower with mean absolute gap of 1930 kg/ha representing 73% of YE. The yield gap in low-input (YGF) was even lower with mean absolute gap of 469 kg/ha representing 42% of YF. Mixed-effects models showed that, absolute YGW were larger at sites with higher precipitation in the minor wet and minimum temperature in the minor dry season explaining 22% of the variability in YGW. These same factors and cocoa planting density explained 28% of variability in absolute YGE. Regardless of climate, absolute YGF and relative YGW, YGE and YGF were reduced by increasing cocoa planting density and application of fungicide against black pod. The models explained 25% of the variability in absolute YGF, and 33%, 33% and 25% in relative YGW, YGE and YGF respectively.In conclusion, climate determined absolute YGW in Ghana whilst absolute YGE were determined by both climate and management. In contrast, absolute YGF and relative YGW, YGE and YGF can be reduced by agronomic management practices.Significance: Our study is one of the first to quantify cocoa yield gaps in West Africa and shows that these can be closed by improved agronomic practices.

Increasing fresh water scarcity is a major constraint for rice (Oryza sativa) productivity under future climatic conditions. It is important to understand why rice cannot perform like other dryland cereals, when grown under drier soil conditions. The responses of plant growth, plant water status, leaf and stem anatomical attributes to soil water deficit were examined at two developmental stages of three rice and two wheat (Triticum aestivum) cultivars grown under three water regimes in a pot experiment. Yield and yield components were determined at plant maturity. The stress sensitivity of plant growth was slightly more prominent at vegetative than at flowering stages. Water deficit limited root growth but had little impact on above-ground growth in rice plants. The xylem system of the leaves was more developed in rice than in wheat, but the opposite was true for the root xylem system. Compared with stem xylem attributes, leaf xylem attributes played a larger role in modulating leaf water potential under water deficit. In addition, the variation in yield response to water deficit between various types of rice, and between rice and wheat was closely associated with the response of leaf water potential to water deficit. To grow rice in drier conditions, its xylem system should be balanced by increasing root growth and modifying leaf anatomy.

The Nutrient Expert system (NE) has been proposed to improve yield and nitrogen (N) use efficiency (NUE) in the double rice cropping systems in China. However, the advantage of the NE system has yet to be quantified experimentally. A four-year field experiment was conducted in a double rice cropping system in China, to evaluate the ability of NE in improving yield and NUE. The experimental treatments consisted of NE based fertilization, current farmers’ practices (FP) and soil test based fertilizer recommendation (ST), and a series of nitrogen (N) rate treatments. The NUE decreased with increasing N application, while the yield did not increase significantly beyond N application rates of about 140 kg ha−1 (corresponding to the amount proposed by NE) in both early and late rice. NE increased grain yield (by 10.3% and 6.3%) and N uptake (by 5.7% and 4.0%) compared with FP and ST, respectively. NE significantly increased NUE compared with FP, and decreased the N surplus in comparison to FP and ST. The N dilution curve was Nc = 34.50 W−0.55 for early rice and Nc = 37.71 W−0.59 for late rice (where Nc is the N concentration in g kg−1, and W is the dry matter accumulation in t ha−1). The relationship between relative yield and the nitrogen nutrition index derived from the dilution curves confirmed that NE offered an optimum N application rate (approximately 140 kg ha−1) for both early and late rice. Carbon (C) and N translocation from vegetative organs to grains was enhanced with increasing N rate, while NE significantly increased C and N translocation compared with FP. Overall, the NE system ensured a high rice yield, increased N uptake and NUE. Therefore, the NE, as a user-friendly tool, is a sustainable fertilizer recommendation approach suitable for double rice cropping system, especially when soil testing is not available or timely for smallholders.

Rising temperatures and more frequent droughts caused by global climate change reduce yields and increase climate risk, especially in rain-fed agriculture. Together with scarce land and water resources, this poses a serious threat to food security. Field experiments have shown that relay intercropping systems under irrigated conditions can improve productivity. However, little is known whether these improvements could also be obtained with simultaneous intercropping in rain-fed agriculture under water-limited conditions. To investigate this question, we analyzed a maize/soybean simultaneous intercropping system, using a modeling approach. A light interception model for strip intercrops was implemented into the APSIM classic model for simulating crop growth and yield in strip-intercropped maize and soybean and then calibrated and validated using field experiments conducted from 2017 to 2019 at 4 sites in Northeast China. We then ran a simulation using climatic data (1961–2020) from these sites. Model validation showed good agreements between observations and simulations. The results obtained from our simulation over the period from 1961 to 2020 showed that intercropping was predicted to increase total yields by 41.3% and subsequently enhanced total economic revenue by 23.8% compared to sole systems. It also reduced yield gap of maize by 33%, soybean by 56%, and the system by 45%. Attainable land equivalent ratio (LER) under rain-fed conditions was 1.27 over 60 years across the 4 sites, with a relative yield gain of maize of 0.35 and a relative yield loss of soybean of 0.08. Attainable LER was higher than potential LER. Yields and LER were significantly higher between 1991 and 2020, indicating a potential increase in land productivity with intercropping under a warming climate. Our results thus suggest that simultaneous intercropping offers great opportunities for yield enhancement in rain-fed agriculture under global climate change.

Low productivity of rice in Uganda is attributed to sub-optimal production practices related to soil nutrient, crop and weed management. Application of improved management practices could enhance productivity. Returning 1 year after a joint experimentation in which different components of recommended agronomic practices (RAP) for rice were tested, we assessed change in management practices and grain yield of participating farmers (participated in joint experimentation) and non-participating farmers (did not participate) with plots in the same irrigation scheme. Participating farmers belonging to the lower-yielding farmers under farmers' practice (FP) during joint experimentation improved their management practices, compared with the middle- and top-yielding farmers. Sixty-one, 24 and 7% of lower-, middle- and top-yielding farmers, respectively, weeded earlier after experimentation compared with weeding time under FP during joint experimentation. Seventy-nine percent of lower-yielding farmers used fertiliser after experimentation compared with 18% during experimentation, with a higher N rate increase than middle- and top-yielding farmers. Overall, participating farmers transplanted and weeded earlier, and applied slightly higher N rates compared with non-participating farmers. Top-yielding farmers had significantly (p = 0.03) higher grain yield, followed by middle- and lower-yielding farmers. However, lower-yielding farmers made significantly (p < 0.001) higher yield gain than middle- and top-yielding farmers. A paired t-test showed that average yield gain was 1,358 (1,027–1,689), 473 (252–695) and −91.7 (−397–213) kg ha−1, respectively, for lower-, middle- and top-yielding farmers. Participating farmers had higher grain yield (4,125 kg ha−1) than non-participating farmers (3,893 kg ha−1). Three farm types were identified that differed in application of RAP, however, with small differences in household characteristics. The farm type with higher fertiliser use in nursery and field, line transplanting, timely weeding and higher N rate had the highest grain yield. We conclude that joint experimentation had a larger effect on raising yield of lower-yielding farmers, bringing farmers closer in their management and outputs. Lack of differences among farm households could indicate that wealth is not crucial in innovation adoption in this production system.

In cocoa cultivation pruning is considered an essential yield-enhancing practice but its effects on cocoa tree growth and yield, and how these are mediated by tree size and competition are poorly understood. Here, we evaluate the impact of experimental pruning on: light interception, leaf flushing and the number of flowers and of developing, wilted and harvested pods. The pruning treatment removed an average 26.4% of cocoa tree aboveground biomass and was aimed to create an open cup-shaped crown. Stem basal area and sum of neighbor tree basal area were used as proxies for tree size and tree competition, respectively. All response variables were analysed at tree level as a function of pruning, tree size and tree competition using generalized linear mixed effect models. After one year, pruned trees recovered initial losses in whole-canopy light interception but maintained a more uniform distribution of light in the canopy. Pruning directly increased flushing activity, while the effect on the other variables was mediated by the interaction with tree size and competition. Pruning increased the positive effect of tree size and competition on flower number and similar effects were found for small pod number. The latter effect was counterbalanced by an increase of pod wilting in pruned trees under high competition, resulting in similar numbers of large and harvested pods on the stem in pruned and unpruned trees. For pods in the canopy, pruning did enhance the positive effect of tree size and strongly reduced the negative effect of competition on pod number. As canopy pods made up 60% of the total, similar pruning effects were found for the total number of harvested pods. The predicted net effect of pruning on the number of harvested pods varied greatly with tree size and competition, ranging from -58% for small trees under low competition, to +150% for large trees under high competition. This large variability stresses the importance of individual-level analysis to quantify pruning effects and calls for more attention to individual tree characteristics in training and practice of cocoa pruning. The pruning-induced reduction of negative competition effects suggests that pruning can contribute to realizing high-density cocoa stands.

CONTEXT: Sustainable cropping systems need to balance productivity and profitability with resource and environmental conservation. Within a population of cropping system observations, there might be positive deviants that outperform others in terms of sustainability, which could serve as “model systems” for future development. Wheat-maize double cropping is the dominant system in the North China Plain, which is facing multiple economic, societal, and environmental sustainability challenges. Identifying exemplary positive deviants out of a multitude of wheat-maize observations might provide solutions to enhance overall sustainability. OBJECTIVES: We aimed to 1) identify exemplary wheat-maize systems that reached optimal performance across seven sustainability indicators, 2) determine which factors regarding management practices and farming contexts resulted in the sustainability gaps between exemplary and other systems, and 3) propose a sustainable wheat-maize prototype. METHODS: Based on a farmer survey dataset (n = 344), we developed a cropping system-level positive deviance approach, including multi-criteria assessment, positive deviant identification (Pareto ranking) and positive deviant clustering, to identify exemplary wheat-maize systems. We then compared exemplary and other systems to quantify the sustainability gaps and identify the key variables explaining sustainability gaps. RESULTS AND CONCLUSIONS: Sixteen percent of wheat-maize cases were Pareto-optimal and were classified as positive deviants. These were sorted into seven clusters representing contrasting sustainability patterns. Among these clusters, one comprised exemplary systems due to the best compromise over the indicator set. Compared to remaining wheat-maize cases, exemplary systems, on average, resulted in 49% and 17% higher gross margin and dietary energy output, respectively, and 33–51% lower labor use, groundwater depletion, N loss, net greenhouse gas emission, and pesticide use. Key practices conferring exemplary system performance included higher maize seeding density, lower fertilizer N input in wheat, partial substitution of inorganic fertilizer with manure, a smaller number of irrigation events, and a lower frequency of pesticide and herbicide application. No significant difference in farming context was found between exemplary and other systems. SIGNIFICANCE: Since the practices of exemplary systems were already locally adopted and proven, we expect that farmers in the region can increase the sustainability of their wheat-maize production by adjusting their management to resemble the exemplary systems. The positive deviance approach thus provides a pragmatic bottom-up approach to identify practices that can improve the sustainability of cropping systems, and can be used for other cropping systems elsewhere.

Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8 . Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil.