Latex diagnosis is widely adopted in natural rubber-producing countries to optimize the natural rubber production through a physiological-based latex-harvesting system management. This study is the first bibliographical searching and meta-analysis on the variation of latex physiological parameters i.e. sucrose, inorganic phosphorus, thiols, and total solid content. The study used information extracted from 158 scientific papers. Descriptive statistics, agglomerative hierarchical clustering, and principal component analysis were performed to characterize applications of latex diagnosis, how often parameters are used and interpreted as well as the variation of its parameter values. From 158 papers, latex diagnosis parameters were used in 114 agronomy, 22 in physiology, and 22 in breeding papers. The agglomerative hierarchical clustering analysis indicated that sucrose and inorganic phosphorus contents were clustered together and total solid and thiols contents were located in another cluster. The average values of the total solid content, sucrose, inorganic phosphorus and thiols were 43.9%, 9.4 mM, 16.5 mM, and 0.52 mM, respectively. The percentage of interpretation is 63.3% for sucrose, 54.4% for inorganic phosphorus, 47.5% for thiols, and 41.1% for the total solid content. The low interpretation of thiols and total solid contents question their relevance in latex diagnosis. The low adoption of latex diagnosis in breeding could hinder the selection of activities leads to a limitation of selection for long-term high yielding and stress-adapted clones.

Latex diagnosis (LD) is applied to optimize the natural rubber production and prevent tapping panel dryness (TPD), a physiological syndrome affecting latex production in Hevea brasiliensis. The reduced thiol content (RSH) is one of the biochemical parameters associated with the risk of TPD. However, RSH is difficult to interpret because of the influence of the environment. In order to better understand the regulation of antioxidants and to better interpret RSH, a key parameter of LD, this study analysed in latex both oxidised and reduced forms of ascorbic acid (AsA) and glutathione, and their cofactors as well as other latex diagnosis parameters in response to harvesting stress (tapping and ethephon stimulation) and TPD occurrence. The content of antioxidants in latex had a high variability among five rubber clones. The concentration in AsA was about ten times higher than GSH in laticifer, GSH accounting for about 50% of RSH. For short-term harvesting stress, RSH increased with tapping frequency and ethephon stimulation. TPD is associated with high latex viscosity and bursting of lysosomal particles called lutoids, as well as for several rubber clones with lower RSH and GSH contents. These results suggest that a high level of RSH shows the capacity of laticifer metabolism to cope with harvesting stress, while a drop in RSH is the sign of long stress related to lower metabolic activity and TPD occurrence. RSH remains an essential physiological parameter to prevent TPD when associated with reference data under low and high harvesting stress. This study paves the way to understand the role of AsA and GSH, and carry out genetic studies of antioxidants.

[This corrects the article DOI: 10.1016/j.heliyon.2022.e09840.].

Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

In coffee, fruit production on a given shoot drops after some years of high yield, triggering pruning to induce resprouting. The timing of pruning is a crucial farmer's decision affecting yield and labour. One reason for fruit production drop could be the exhaustion of resources, particularly the non-structural carbohydrates (NSC). To test this hypothesis in a Coffea L. arabica agroforestry system, we measured the concentrations of NSC, carbon (C) and nitrogen (N) in leaves, stems and stumps of the coffee plants, 2 and 5 years after pruning. We also compared shaded vs full sun plants. For that purpose, both analytical reference and visible and near infrared reflectance spectroscopy (VNIRS) methods were used. As expected, concentrations of biochemical variables linked to photosynthesis activity (N, glucose, fructose, sucrose) decreased from leaves to stems, and then to stumps. In contrast, variables linked more closely to plant structure and reserves (total C, C:N ratio, starch concentration) were higher in long lifespan organs like stumps. Shading had little effect on most measured parameters, contrary to expectations. Concentrations of N, glucose and fructose were higher in 2-year-old organs. Conversely, starch concentration in perennial stumps was three times higher 5 years after pruning than 2 years after pruning, despite high fruit production. Therefore, the drop in fruit production occurring after 5-6 years was not due to a lack of NSC on plant scale. Starch accumulation in perennial organs concurrently to other sinks, such as fruit growth, could be considered as a 'survival' strategy, which may be a relic of the behaviour of wild coffee (a tropical shade-tolerant plant). This study confirmed that VNIRS is a promisingly rapid and cost-effective option for starch monitoring (coefficient of determination for validation, R-val(2) = 0.91), whereas predictions were less accurate for soluble sugars, probably due to their too similar spectral signature.

Rice crop is known as particularly sensitive to water deficit, especially during the reproductive phase when growth of vegetative organs and formation of spikelets are simultaneous. Many works have focused on the response of rice plants to water deficits varying in timing, duration and intensity. Oppositely, the impact of the environmental conditions on the response to a given water deficit remains largely unknown. In order to test it, two experiments under contrasted conditions of temperature, radiation and VPD were conducted on six genotypes in greenhouse in Brazil (S) and in growth chamber in France (GC). The plants were submitted to the same mild water deficit at the reproductive phase, by adjusting FTSW at 0.4. Under irrigation, plant growth rate was reduced and crop duration extended in GC in relation to S: ultimately, this trade-off resulted in similar plant height and biomass in both environments. Under water deficit and in both environments, elongation rate decreased and was associated with an increase in soluble sugars in stem and flag leaf, while starch was reduced in S and negligible in GC because of the low radiation. This common biochemical response displayed a large gradient of values across environments and genotypes, but differentially impacted the branch and spikelet formation on the developing panicle: in carbon limiting conditions (GC), the increase in soluble sugars was associated with the reduction in branch and spikelet number, and conversely in S. At the morphological level, the maintenance of spikelet number on the panicle was correlated with the maintenance of flag leaf width in all genotypes and conditions, that was discussed according to the maintenance of the apical meristem size. Genotypes were discriminated and the study underlined the global tolerance of Cirad 409 and sensitivity of IAC 25.

This study aimed to understand the response of photosynthesis and growth to e-CO2 conditions (800 vs. 400 μmol mol-1 ) of rice genotypes differing in source-sink relationships. A proxy trait called local C source-sink ratio was defined as the ratio of flag leaf area to the number of spikelets on the corresponding panicle, and five genotypes differing in this ratio were grown in a controlled greenhouse. Differential CO2 resources were applied either during the 2 weeks following heading (EXP1) or during the whole growth cycle (EXP2). Under e-CO2 , low source-sink ratio cultivars (LSS) had greater gains in photosynthesis, and they accumulated less nonstructural carbohydrate in the flag leaf than high source-sink ratio cultivars (HSS). In EXP2, grain yield and biomass gain was also greater in LSS probably caused by their strong sink. Photosynthetic capacity response to e-CO2 was negatively correlated across genotypes with local C source-sink ratio, a trait highly conserved across environments. HSS were sink-limited under e-CO2 , probably associated with low triose phosphate utilization (TPU) capacity. We suggest that the local C source-sink ratio is a potential target for selecting more CO2 -responsive cultivars, pending validation for a broader genotypic spectrum and for field conditions.

The integrative capacity of crop models is of great value to identify in-silico optimal combinations of traits (ideotypes) and traits x cultu ral practices in targeted agro-environments. This approach becomes even more challenging when considering the multiple environ mental factors constituting future agro-climatic scenarios : increasing stress frequency and severity (e.g., heat, drought, wind, flooding); enhanced atmospheric C02 concentration (e-COzl, and also adoption of more sustainable and resilient cultural practices (agroecology) combining of productivity with ecosystem services. Several studies reported the weaknesses of crop models in predicting crop performance in response to climate change. While these limitations were until now mainly explained by poor simulation by crop models of physiological responses to heat and drought, crop model shortcomings of the representation of Carbon (C) source-sink relations and interactions, involving phenotypic plasticity of both source and sink, should explain this limitations and have received less attention (Chang and Zhu 2017). Recent studies reported a down-regulation of C source capacity (i.e. photosynthesis) in C3 crops under e-C02 by sink lim itation in the afternoon, involving low TPU levels (Triose Phosphate Utilization) (rice: (Fabre et al. 2019). (Fabre, in prep) indicated that high constitutive source-sink ratios increase photosynthesis under e-C02 • Finally, (Kikuchi et al. 2017) demonstrated in a FACE trial that rice plants with high adaptive plasticity of tillering and panicle size respond better to e-C02 • Although particularly relevant to C3 crops that respond strongly to e-C02 , this also applies to C4 crops when they are C-sink limited (Oszvald et al., 2018). Therefore, Carbon source-sink relationships and their physiological and morphological adaptability (feedbacks) are pivotai in predicting crop ideotypes in a climate change context. ln addition, the agro-ecological transition needs better crop models to design solutions for improving (1) crop energy and carbon use, (2) resilience under abiotic stresses, and (3) ecosystem services such as channeling assimilates into the roots/soil (4p1000 initiative: C sequestration and soil improvement). This implies to further model plantplant and/or plant-soil interactions and related impacts on C source-sink relationships and competitions for (light) resources. Crop models should indeed be able to predict trade-offs among several crop performance objectives such as multiple production purposes (e.g., grain and biomass), between potential productivity and adaptation, and between productivity and ecosystem services such as C sequestration into the soil. For this, we will provide examples of analytical and modeling concepts. More quantitative, extrapolatable evidence is needed to understand the importance of C source and sink traits, their adaptive plasticity as they interact during plant development, and their impact on crop performance under anticipated agro-climatic conditions. This requires a dialogue between experimental and modeling research for which we are presenting concepts here. Our laboratory focuses on rice (C3) and sorghum (C4) model cereals using crop models simulating sink- and source driven phenotypic plasticity, namely SAMARA (Kumar et al., 2016) and Ecomeristem (Larue et al., 2019). Sorne (experimental, modelling) preliminary resu lts will be shown but a broader dynamics is needed. Once further improved, the models will be used to (i) estimate in silico the prediction errors caused by ignoring source-sink feedbacks and plasticity; (ii) predict the potential of improved trait combinations and plasticity on the performance of future crops; and (iii) propose how existing, generic crop models should be improved and what type of data will be needed for that.

Background: Rice crop is known as very sensitive to water deficit, especially during the reproductive phase when growth of vegetative organs and formation of spikelets are concomitant. The present study questioned whether the maintenance of vegetative organ expansion during a water deficit at the reproductive phase affects the reproductive structure organogenesis, and if relevant traits for adaptation can be identified. To answer these queries, the response to a same reproductive water deficit of six contrasted japonica genotypes has been analyzed under two contrasted climates differing in incident radiation, air hygrometry and temperature (greenhouse in Brazil, Sitis, and growth chamber in France, GC).Results: Under irrigation, plant growth rate was reduced in GC while crop duration was extended: the trade-offs resulted in similar plant height and biomass. From a method able to determine a posteriori the date of panicle initiation (PI), elementary processes were positioned in time, allowing to evaluate how much each process was affected, despite the diversity in phenology across genotypes. Elongation rate decreased with water deficit and was highly associated with an increase in soluble sugars in stem and flag leaf in both experiments, while starch was reduced in Sitis and negligible in GC. This unique response, however, induced a different effect across experiments on branch and spikelet formation. In short, in both experiments, maintenance of spikelet number was highly associated with maintenance of flag leaf and internode width. All variables, including branch and spikelet number, were highly affected with IAC 25 in both experiments, while variations were non-significant with Cirad 409. In addition, some other genotypes expressed a differential response between Sitis and GC, conveying a specific sensitivity to low radiation or to high air temperature. Conclusions: This study highlighted the importance of finely mapping in time elementary growth processes, thanks to PI date determination, in order to detect key traits of adaptation to abiotic stress through phenotyping across genotypes of diverse phenology. The maintenance of flag leaf width or internode diameter under a mild water deficit was highlighted here as a trait associated with the maintenance of yield components.

Huit ans de travaux de recherche sur les services ecosystemiques dans une grande ferme cafeiere du Costa Rica (observatoire collaboratif Coffee-Flux, en systeme agroforestier a base de cafeiers sous de grands arbres d'Erythrina poeppigiana, surface projetee de couronne de l'ordre de 16 %) ont suggere plusieurs applications pour les agriculteurs et les decideurs. Il est apparu que de nombreux services ecosystemiques dependaient des proprietes du sol (ici des Andisols), en particulier de l'erosion, de l'infiltration, de la capacite de stockage de l'eau et des elements nutritifs. Nous confirmons qu'il est essentiel de lier les services hydrologiques et de conservation au type de sol en presence. Une densite adequate d'arbres d'ombrage (plutot faible ici) permet de reduire la severite des maladies foliaires avec, en perspective, une reduction de l'usage de pesticides-fongicides. Un simple inventaire de la surface basale au collet des cafeiers permet d'estimer la biomasse souterraine et la moyenne d'âge d'une plantation de cafeiers, ce qui permet d'evaluer sa valeur marchande ou de planifier son remplacement. Le protocole de calcul actuel pour la neutralite carbone des systemes agroforestiers ne prend en compte que les arbres d'ombrage, pas la culture intercalaire. Dans la realite, si on inclut les cafeiers, on se rapproche tres probablement de la neutralite. Des evaluations plus completes, incluant les arbres, les cafeiers, la litiere, le sol et les racines dans le bilan en carbone du systeme agroforestier sont proposees. Les arbres d'ombrage offrent de nombreux servies ecosystemiques s'ils sont geres de maniere adequate dans le contexte local. Par rapport aux parcelles en plein soleil, nous montrons qu'ils reduisent l'erosion laminaire d'un facteur 2, augmentent la fixation de l'azote (N2) atmospherique et le pourcentage d'azote recycle dans le systeme, reduisant ainsi les besoins en engrais. Ils reduisent aussi la severite des maladies foliaires, augmentent la sequestration de carbone, ameliorent le microclimat et attenuent substantiellement les effets des changements climatiques. Dans notre etude de cas, aucun effet negatif sur le rendement n'a ete enregistre.

This study aimed to understand the physiological bases of rice photosynthesis response to C source-sink imbalances, with focus on dynamics of the photosynthetic parameter TPU (Triose Phosphate Utilization). A dedicated experiment was replicated twice on IR64 indica rice cultivar in controlled environments. Plants were grown under the current ambient CO 2 concentration until heading, thereafter, two CO 2 treatments (400 and 800 μmol mol −1 ) were compared in the presence and absence of a panicle pruning treatment modifying the C sink. At two weeks after heading, photosynthetic parameters derived from CO 2 response curves, and nonstructural carbohydrate content of flag leaf and internodes were measured 3-4 times of day. Spikelet number per panicle and flag leaf area on the main culm were recorded. Net C assimilation and TPU decreased progressively after midday in panicle-pruned plants, especially under 800 μmol mol −1 . This TPU reduction was explained by sucrose accumulation in the flag leaf resulting from the sink limitation. It is suggested that TPU is involved in rice photosynthesis regulation under elevated CO 2 conditions, and that sink limitation effects should be considered in crop models. Highlight This study provide new insights in the effect of C source-sink relationships on rice photosynthesis. TPU should be considered in photosynthesis studies under severe source-sink imbalance at elevated CO 2 .

Triose phosphate utilization is involved in the regulation of photosynthesis under elevated CO2 conditions, and it should be considered in photosynthesis studies under severe source–sink imbalance at elevated CO2.

Abstract Sweet and biomass sorghum are expected to contribute increasingly to bioenergy production. Better understanding the impacts of the genotypic and environmental variabilities on biomass component traits and their properties is essential to optimize energy yields. This study aimed to evaluate whether traits contributing to stem biomass growth and biochemical composition at different biological scales (co)vary with the genotype and the water status in sorghum. Height genotypes were studied over two years in field conditions in southern France under two water treatments (well watered vs. 25 days’ dry down during stem elongation). Main stem internode number, size, (non)structural carbohydrate, and lignin contents were measured at the end of the stress period and/or at final harvest, together with biochemical and histological analyses of the youngest expanded internode. The tallest genotypes showed the highest stem dry weights and lignin contents. Stem (structural) biomass density was positively correlated with lignin content, particularly in internode parenchyma. Stem soluble sugar and lignin contents were inversely proportional across genotypes and water conditions. Genotypes contrasted for drought sensitivity and recovery capacity of stem growth and biochemical composition. The length and cell wall deposition of internodes expanding under water deficit were reduced and did not recover, these responses being weakly correlated. Genotypic variability was pointed out in the growth recovery of internodes expanding under re‐watered conditions. According to the observed genotypic variability and the absence of antagonistic correlations between the responses of the different traits to water availability, it is suggested that biomass sorghum varieties optimizing their responses to water availability in terms of growth and cell wall deposition can be developed for different bioenergy targets.

Sorghum can significantly contribute to growing needs in ligno-cellulosic biomass for bio-sourced product diversification, particularly in water-limited conditions. However, the genotypic and environmental variability of stem biomass production and quality is still poorly understood, limiting its genetic improvement. This study aimed to identify the morphogenetic, biochemical and histological traits underlying at internode level the genotypic and environmental variability of stem biomass accumulation by sorghum. Three field experiments were organized to compare 8 genotypes under irrigated and drought (applied during stem elongation). The eco-physiological model Ecomeristem was used to explore trait impact for different cropping situations and production targets. Both stem biomass production and quality were affected by water deficit due to the reduction of the number, length and ligno-cellulosic content of expanded internodes, whereas their soluble sugar content was increased and diameter unaffected. Internodes developed after re-watering observed a remarkable recovery whereas those developed under stress did not recover. Genotypic variability for drought sensitivity and recovery was highlighted but no correlation was found between them. The drought response of growth, biochemical and histological traits was slightly correlated, suggesting only partial trade-offs between stem biomass production and quality response to drought, obviously under complex physiological and genetic controls. Once validated on available data, the crop growth model Ecomeristem was used to in silico explore trait impact on biomass production depending on the variation in key cropping criteria for biomass sorghum worldwide: targeted production (structural, nonstructural carbohydrates), planting density and water availability. Different ideotypes were suggested for each simulated situation, mainly defined by the trade-off between tillering propensity and internode sink capacity (related either to size or biomass density). It is suggested that not only internode biomass accumulation but also tillering capacity should be further considered for phenotyping and ideotyping biomass sorghum in its targeted cropping environments.

Breeding programs in Africa are generally based on growth criteria and rarely on wood chemical properties. Indeed, chemical analysis are often expensive, time-consuming and require several replicates. Then, using NIRS to predict these properties is a relevant solution. The research question focuses on the possibility of using multispecies models to predict properties of different species. This study considers 7 chemical properties (extractives, Klason lignin, acidosoluble lignin ASL, SG ratio, holocellulose, alphacellulose, hemicelluloses) based on 367 samples from 4 countries, belonging to 5 eucalypt species with hybrids (E. robusta, camaldulensis, urophylla, uropellita, urograndis). Established models were validated by cross- and test-set validation. Results shows that all R2CV are greater than 0.73, and all %RMSECV are less than 8.3% except for extractives and ASL. Prediction errors (%RMSEP) are always less than 9.5% except for these 2 properties, with respectively 23.6% and 18.1%. Prediction errors are always less than the double of the error of laboratory (%SEL). This study shows that multispecies NIRS models can be used to predict chemical properties, there is no significant difference between measurement error obtained with standardized method and %RMSEP. This method is particularly well-suited for a rapid wood phenotyping of multiple samples belonging to different species.

Oxidative stress occurring during in-vitro culture is detrimental for clonal propagation by somatic embryogenesis in particular in Hevea brasiliensis. In previous work, overexpression of the gene encoding the cytosolic reactive oxygen species detoxification enzyme HbCuZnSOD led to reduce somatic embryo regeneration in Hevea. In this study, the role of antioxidant was tested by overexpression of the E.coli GSH1 gene involved in glutathione biosynthesis in rubber embryogenic callus lines. Transgenic lines were successfully established and some plants were regenerated. Overexpression of EcGSH1 gene led to glutathione over-accumulation, and affected dramatically the somatic embryogenesis process and plant development. Upon a water deficit treatment, these plants displayed the greatest drop in photosynthetic nitrogen use efficiency, higher proline content, and higher glutathione reductase activity. Changes induced in transgenic lines overexpressing HbCuZnSOD and EcGSH1 were discussed as well as possible applications on plant material propagation, overcoming loss of natural rubber production through Tapping Panel Dryness, and tropical soil remediation.

The hypothesis made is that thermal resistance of sorghum and miscanthus stem pieces taken at well-defined positions of the stem is simply related to their biochemical composition. For miscanthus, two different genotypes and two internode levels were selected. For each region, the stem was divided into three radial layers. For sorghum, two different genotypes were selected and the stem was divided into the same three radial layers. The results show that the thermal analysis is only sensitive to very large variations of compositions. But aside of such large composition differences, it is impossible to correlate thermal effects to biochemical composition even on very small size, well-identified pieces of plant materials. The interplay between sugar-based components, lignin and minerals is totally blurring the thermal response. Extreme care must be exercised when willing to explain why a given plant material has a thermal behaviour different of another plant material.

Sorghum is increasingly used as a biomass crop worldwide. Its genetic diversity provides a large range of stem biochemical composition suitable for various end-uses as bioenergy or forage. Its drought tolerance enables it to reasonably sustain biomass production under water limited conditions. However, drought effect on the accumulation of sorghum stem biomass remains poorly understood which limits progress in crop improvement and management. This study aimed at identifying the morphological, biochemical and histological traits underlying biomass accumulation in the sorghum stem and its plasticity in response to water deficit. Two hybrids (G1, G4) different in stem biochemical composition (G4, more lignified, less sweet) were evaluated during 2 years in the field in Southern France, under two water treatments differentiated during stem elongation (irrigated; 1 month dry-down until an average soil water deficit of -8.85 bars). Plant phenology was observed weekly. At the end of the water treatment and at final harvest, plant height, stem and leaf dry-weight and the size, biochemical composition and tissue histology of internodes at 2–4 positions along the stem were measured. Stem biomass accumulation was significantly reduced by drought (in average 42% at the end of the dry-down). This was due to the reduction of the length, but not diameter, of the internodes expanded during water deficit. These internodes had more soluble sugar but lower lignin and cellulose contents. This was associated with a decrease of the areal proportion of lignified cell wall in internode outer zone whereas the areal proportion of this zone was not affected. All internodes for a given genotype and environment followed a common histochemical dynamics. Hemicellulose content and the areal proportion of inner vs. outer internode tissues were set up early during internode growth and were not drought responsive. G4 exhibited a higher drought sensitivity than G1 for plant height only. At final harvest, the stem dry weight was only 18% lower in water deficit (re-watered) compared to well-watered treatment and internodes growing during re-watering were similar to those on the well-watered plants. These results are being valorized to refine the phenotyping of sorghum diversity panels and breeding populations.

Eight years of monitoring ecophysiology and ecosystem services (ES) in a large coffee farm of Costa Rica yields a range of practical applications for the farmer and stakeholders, thanks to numerous scientific actors and disciplines contributing to our collaborative observatory (Coffee-Flux). • A lot of ecosystem services depend on the soil properties, such as runoff/infiltration, water and nutrient storage capacity. It is essential to relate hydrological and soil conservation services to the soil type, since this might have even more importance than the crop itself for ES. Regarding the use of fertilizer, we show that some soils may have a large storage capacity, allowing producing coffee at normal yields with just a reduced, or even a minimum amount of fertilizers, for instance when the economic conditions are unfavorable. Also, due to the soil variability within the farm, it is possible to adjust fertilization to micro-local conditions and reduce the total expenses and risks of leaching of N to the environment. VNIRS and MIR are promising broadband tools for screening the variability in soils. Adjusting N fertilizer to the optimum will also considerably reduce the N2O emissions and improve the GHG balance of the farm. • Pesticides-fongicides: we show that an adequate amount of shade trees allows reducing the severity of the whole complex of leaf diseases. This also should reduce expenses and impacts on the ecosystem. • Roots: a simple survey of basal area at collar allows estimating the belowground biomass and the average age of a plantation, to judge of its market value and to decide when to replace it. • Also starch plays a key role in the trophic equilibrium between the perennial parts of the coffee plant (aerial stump, belowground stump, coarse roots) and its ephemeral parts (resprout, leaves, fruits, fine roots). Coffee plants accumulate starch in the stumps by the end of the life of their resprout, as a strategy for survival. Breeding plants with less starch build-up capacity would probably allow increasing the fraction of productive years during the lifespan of the resprouts. • Coffee farms are probably much closer to C neutrality than currently admitted using the C-Neutrality protocol. We stress the prevailing role of coffee plants + litter + soil in the ecosystem C balance. If those are excluded from the calculations as done so far, coffee farms are GHG sources, by definition. We argue that either full assessments (as proposed here, at the ecosystem level, including trees, coffee, litter, soil and roots) or consensus on “sequestration factors” (the counterpart of emission factors) would allow performing a more realistic assessment of the GHG balance. • Finally, we bring new data confirming that shade trees offer numerous ecosystem services, when adequately managed for the local context. As compared to full sun conditions, they may (i) reduce laminar erosion by a factor of ca. 2, (ii) increase the atmospheric N2 fixation and the % of N recycled into the system, thus reducing the fertilizer requirements, (iii) reduce the severity of the leaf disease complex, (iv) increase C sequestration, (v) improve the microclimate, and (vi) be a large part of the solution to face climate changes. All this is possibly without negative effects on profitability or yield, if managed properly. In our particular case-study, we encount. (Resume d'auteur)