Combining modelling and experimental approaches to assess the feasibility of developing rice-oil palm agroforestry system.

Monoculture systems in SouthEast Asia are facing challenges due to climate change-induced extreme weather conditions, leading to significant annual production losses for rice and oil palm. To ensure the stability of these crops, innovative strategies like resilient agroforestry systems need to be explored. Converting oil palm monocultures to rice-based intercropping systems shows promise, but achieving optimal yields requires adjusting palm density and identifying rice varieties adapted to changes in light quantity and diurnal fluctuation. This paper proposes a methodology that combines a model of light interception with indoor experiments to assess the feasibility of rice-oil palm agroforestry systems. Using a functional-structural plant model (FSPM) of oil palm, the planting design was optimized to maximize transmitted light for rice. Simulation results estimated the potential impact on oil palm carbon assimilation and transpiration. In growth chambers, simulated light conditions were replicated with adjustments to intensity and daily fluctuation. Three light treatments independently evaluated the effects on different rice accessions. The simulation study revealed intercropping designs that significantly increased light transmission for rice cultivation with minimal decrease in oil palm densities compared to conventional designs. The results estimated a loss in oil palm productivity of less than 10%, attributed to improved carbon assimilation and water use efficiency. Changes in rice plant architecture were primarily influenced by light quantity, while variations in yield components were attributed to light fluctuations. Different rice accessions exhibited diverse responses to light fluctuations, suggesting the potential for selecting genotypes suitable for agroforestry systems.

Triose phosphate utilization in leaves is modulated by whole-plant sink-source ratios and nitrogen budgets in rice.

Triose phosphate utilization (TPU) is a biochemical process indicating carbon sink-source (im)balance within leaves. When TPU limits leaf photosynthesis, photorespiration-associated amino acid exports probably provide an additional carbon outlet and increase leaf CO2 uptake. However, whether TPU is modulated by whole-plant sink-source relations and nitrogen (N) budgets remains unclear. We address this question by model analyses of gas-exchange data measured on leaves at three growth stages of rice plants grown at two N levels. Sink-source ratio was manipulated by panicle pruning, by using yellower-leaf variant genotypes, and by measuring photosynthesis on adaxial and abaxial leaf sides. Across all these treatments, higher leaf N content resulted in the occurrence of TPU limitation at lower intercellular CO2 concentrations. Photorespiration-associated amino acid export was greater in high-N leaves, but was smaller in yellower-leaf genotypes, panicle-pruned plants, and for abaxial measurement. The feedback inhibition of panicle pruning on rates of TPU was not always observed, presumably because panicle pruning blocked N remobilization from leaves to grains and the increased leaf N content masked feedback inhibition. The leaf-level TPU limitation was thus modulated by whole-plant sink-source relations and N budgets during rice grain filling, suggesting a close link between within-leaf and whole-plant sink limitations.

Growth-defence trade-off in rice: fast-growing and acquisitive genotypes have lower expression of genes involved in immunity.

Plant ecologists and molecular biologists have long considered the hypothesis of a trade-off between plant growth and defence separately. In particular, how genes thought to control the growth-defence trade-off at the molecular level relate to trait-based frameworks in functional ecology, such as the slow-fast plant economics spectrum, is unknown. We grew 49 phenotypically diverse rice genotypes in pots under optimal conditions and measured growth-related functional traits and the constitutive expression of 11 genes involved in plant defence. We also quantified the concentration of silicon (Si) in leaves to estimate silica-based defences. Rice genotypes were aligned along a slow-fast continuum, with slow-growing, late-flowering genotypes versus fast-growing, early-flowering genotypes. Leaf dry matter content and leaf Si concentrations were not aligned with this axis and negatively correlated with each other. Live-fast genotypes exhibited greater expression of OsNPR1, a regulator of the salicylic acid pathway that promotes plant defence while suppressing plant growth. These genotypes also exhibited greater expression of SPL7 and GH3.2, which are also involved in both stress resistance and growth. Our results do not support the hypothesis of a growth-defence trade-off when leaf Si and leaf dry matter content are considered, but they do when hormonal pathway genes are considered. We demonstrate the benefits of combining ecological and molecular approaches to elucidate the growth-defence trade-off, opening new avenues for plant breeding and crop science.

The case for improving crop carbon sink strength or plasticity for a CO2-rich future.

Atmospheric CO2 concentration [CO2] has increased from 260 to 280µmolmol-1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550µmolmol-1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic 'feast-famine' sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.

Genotypic variation in source and sink traits affects the response of photosynthesis and growth to elevated atmospheric CO2.

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.

Is triose phosphate utilization involved in the feedback inhibition of photosynthesis in rice under conditions of sink limitation?

This study aimed to understand the physiological basis of rice photosynthetic response to C source-sink imbalances, focusing on the dynamics of the photosynthetic parameter triose phosphate utilization (TPU). Here, rice (Oriza sativa L.) indica cultivar IR64 were grown in controlled environment chambers under current ambient CO2 concentration until heading, and thereafter two CO2 treatments (400 and 800 µmol mol-1) were compared in the presence and absence of a panicle-pruning treatment modifying the C sink. At 2 weeks after heading, photosynthetic parameters derived from CO2 response curves, and non-structural carbohydrate content of flag leaf and internodes were measured three to four 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 CO2. This TPU reduction was explained by sucrose accumulation in the flag leaf resulting from the sink limitation. Taking together, our findings suggest that TPU is involved in the regulation of photosynthesis in rice under elevated CO2 conditions, and that sink limitation effects should be considered in crop models.

Overexpression of Hevea brasiliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation.

Ethylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF-IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting stress for better latex production. This study sets out to establish and characterize rubber transgenic lines overexpressing HbERF-IXc5. Overexpression of HbERF-IXc5 dramatically enhanced plant growth and enabled plants to maintain some ecophysiological parameters in response to abiotic stress such as water deficit, cold and salt treatments. This study revealed that HbERF-IXc5 has rubber-specific functions compared to Arabidopsis ERF1 as transgenic plants overexpressing HbERF-IXc5 accumulated more starch and differentiated more latex cells at the histological level. The role of HbERF-IXc5 in driving the expression of some target genes involved in laticifer differentiation is discussed.

Plasticity of Sorghum Stem Biomass Accumulation in Response to Water Deficit: A Multiscale Analysis from Internode Tissue to Plant Level.

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.

Juvenile Coffee Leaves Acclimated to Low Light Are Unable to Cope with a Moderate Light Increase.

The understorey origin of coffee trees and the strong plasticity of Coffea arabica leaves in relation to contrasting light environments have been largely shown. The adaptability of coffee leaves to changes in light was tested under controlled conditions by increasing the illumination rate on C. arabica var. Naryelis seedlings acclimated to low light conditions and observing leaf responses at three different developmental stages (juvenile, growing and mature). Only mature leaves proved capable of adapting to new light conditions. In these leaves, different major mechanisms were found to contribute to maintaining a good photosynthetic level. With increased illumination, a high photosynthetic response was conserved thanks to fast nitrogen remobilization, as indicated by SPAD values and the photorespiration rate. Efficient photoprotection was accompanied by a great ability to export sucrose, which prevented excessive inhibition of the Calvin cycle by hexose accumulation. In contrast, in younger leaves, increased illumination caused photodamage, observable even after 9 days of treatment. One major finding was that young coffee leaves rely on the accumulation of chlorogenic acids, powerful antioxidant phenolic compounds, to deal with the accumulation of reactive oxygen species rather than on antioxidant enzymes. Due to a lack of efficient photoprotection, a poor ability to export sucrose and inadequate antioxidant protection, younger leaves seemed to be unable to cope with increased illumination. In these leaves, an absence of induced antioxidant enzyme activity was accompanied, in growing leaves, by an absence of antioxidant synthesis or, in juvenile leaves, inefficient synthesis of flavonoids because located in some epidermis cells. These observations showed that coffee leaves, at the beginning of their development, are not equipped to withstand quick switches to higher light levels. Our results confirm that coffee trees, even selected for full sunlight conditions, remain shade plants possessing leaves able to adapt to higher light levels only when mature.

Expression of the Aeluropus littoralis AlSAP Gene Enhances Rice Yield under Field Drought at the Reproductive Stage.

We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50-90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions.

The qTSN4 Effect on Flag Leaf Size, Photosynthesis and Panicle Size, Benefits to Plant Grain Production in Rice, Depending on Light Availability.

Increasing rice yield potential is essential to secure world food supply. The quantitative trait locus qTSN4 was reported to achieve yield increases by enhancing both source and sink capacity. Three greenhouse experiments and one field experiment in the Philippines were conducted to study near-isogenic lines (NILs) in two genetic backgrounds, subjected to treatments with restricted light resources through shading (greenhouse) or population density (field and greenhouse). A consistent promotion of flag leaf width, leaf area and panicle size in terms of spikelet number was observed in the presence of qTSN4, regardless of environment. However, grain production per plant was enhanced only in one greenhouse experiment. An in-depth study demonstrated that increased flag leaf size in the presence of qTSN4 was associated with increased photosynthetic rates, along with lower SLA and greater N content per leaf weight and per area. This was emphasized under low light situation as the qTSN4-NILs did not express shade acclimation traits in contrast with the recipient varieties. The authors conclude that qTSN4 is a promising subject for further physiological studies, particularly under limited radiation. However, the QTL alone may not be a reliable source of increased yield potential because its effects at the plant and population scale are prone to genotype × environment interactions and the increased panicle size is compensated by the adaptive plasticity of other morphological traits.

Effect of carbohydrates and night temperature on night respiration in rice.

Global warming causes night temperature (NT) to increase faster than day temperature in the tropics. According to crop growth models, respiration incurs a loss of 40-60% of photosynthate. The thermal sensitivity of night respiration (R(n)) will thus reduce biomass. Instantaneous and acclimated effects of NT on R(n) of leaves and seedlings of two rice cultivars having a variable level of carbohydrates, induced by exposure to different light intensity on the previous day, were investigated. Experiments were conducted in a greenhouse and growth chambers, with R(n) measured on the youngest fully expanded leaves or whole seedlings. Dry weight-based R(n) was 2.6-fold greater for seedlings than for leaves. Leaf R(n) was linearly related to starch (positive intercept) and soluble sugar concentration (zero intercept). Increased NT caused higher R(n) at a given carbohydrate concentration. The change of R(n) at NT increasing from 21 °C to 31 °C was 2.4-fold for the instantaneous response but 1.2- to 1.7-fold after acclimation. The maintenance component of R(n) (R(m)'), estimated by assimilate starvation, averaged 28% in seedlings and 34% in leaves, with no significant thermal effect on this ratio. The acclimated effect of increased NT on R(m)' across experiments was 1.5-fold for a 10 °C increase in NT. No cultivar differences were observed in R(n) or R(m)' responses. The results suggest that the commonly used Q10=2 rule overestimates thermal response of respiration, and R(n) largely depends on assimilate resources.

Functional analysis of the durum wheat gene TdPIP2;1 and its promoter region in response to abiotic stress in rice.

In a previous work, we demonstrated that expression of TdPIP2;1 in Xenopus oocytes resulted in an increase in Pf compared to water injected oocytes. Phenotypic analyses of transgenic tobacco plants expressing TdPIP2;1 generated a tolerance phenotype towards drought and salinity stresses. To elucidate its stress tolerance mechanism at the transcriptional level, we isolated and characterized the promoter region of the TdPIP2;1 gene. A 1060-bp genomic fragment upstream of the TdPIP2;1 translated sequence has been isolated, cloned, and designated as the proTdPIP2;1 promoter. Sequence analysis of proTdPIP2;1 revealed the presence of cis regulatory elements which could be required for abiotic stress responsiveness, for tissue-specific and vascular expression. The proTdPIP2;1 promoter was fused to the ß-glucuronidase (gusA) gene and the resulting construct was transferred into rice (cv. Nipponbare). Histochemical analysis of proTdPIP2;1::Gus in rice plants revealed that the GUS activity was observed in leaves, stems and roots of stably transformed rice T3 plants. Histological sections prepared revealed accumulation of GUS products in phloem, xylem and in some cells adjacent to xylem. The transcripts were up-regulated by dehydration. Transgenic rice plants overexpressing proTdPIP2;1 in fusion with TdPIP2;1, showed enhanced drought tolerance, while wild type plants were more sensitive and exhibited symptoms of wilting and chlorosis. These findings suggest that expression of the TdPIP2;1 gene regulated by its own promoter achieves enhanced drought tolerance in rice.

Expression of the Aeluropus littoralis AlSAP gene in rice confers broad tolerance to abiotic stresses through maintenance of photosynthesis.

The expression of AlSAP, in rice cv. Nipponbare, enhances plant tolerance to cold, drought and salt stresses. AlSAP lines showed 100% survival rate and set seeds while control plants did not recover from the cold treatment. Under a severe drought stress treatment (fraction of transpirable soil water down to 0.1), AlSAP lines exhibited enhanced Transpiration Efficiency (TE) and maintained a high A (Assimilation rate) value (22 µmol·m(-2) s(-1) ) while these values dramatically decreased (A = 4 µmol·m(-2) s(-1) ) in control plants which were subsequently unable to recover from the stress. Of noteworthy is that AlSAP rice plants yielded a similar and a 60% seed set under control and stress conditions respectively, with regard to wild-type (WT) plants grown under control conditions. This indicates that AlSAP expression imposes no yield penalty and allows seed production even following a severe drought stress at the vegetative stage. Furthermore, AlSAP rice was shown to accumulate transcripts of a pilot set of eight stress-related genes at a significantly higher level than WT plants, both under control and stressed conditions. The results suggest that AlSAP expression generates stress tolerance in plants through maintenance of the photosynthetic apparatus integrity and by stimulating an endogenous adaptive potential which is not effectively accomplished in WT plants.

Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives.

Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

Model-assisted physiological analysis of Phyllo, a rice architectural mutant.

Studies of phenotype of knockout mutants can provide new insights into physiological, phenological and architectural feedbacks in the plant system. Phyllo, a mutant of Nippon Bare rice (Oryza sativa L.) producing small leaves in rapid succession, was isolated during multiplication of a T-DNA insertion library. Phyllo phenotype was compared with the wild type (WT) during vegetative development in hydroponics culture using a wide range of physiological and biometric measurements. These were integrated with the help of the functional-structural model EcoMeristem, explicitly designed to study interactions between morphogenesis and carbon assimilation. Although the phenotype of the mutant was caused by a single recessive gene, it differed in many ways from the WT, suggesting a pleiotropic effect of this mutation. Phyllochron was 25 (1-4 leaf stage) to 38% (>>4 leaf stage) shorter but showed normal transition from juvenile to adult phase after leaf 4. Leaf size also increased steadily with leaf position as in WT. The mutant had reduced leaf blade length : width and blade : sheath length ratios, particularly during the transition from heterotrophic to autotrophic growth. During the same period, root : shoot dry weight ratio was significantly diminished. Specific leaf area (SLA) was strongly increased in the mutant but showed normal descending patterns with leaf position. Probably related to high SLA, the mutant had much lower light-saturated leaf photosynthetic rates and lower radiation use efficiency (RUE) than the WT. Leaf extension rates were strongly reduced in absolute terms but were high in relative terms (normalised by final leaf length). The application of the EcoMeristem model to these data indicated that the mutant was severely deficient in assimilate, resulting from low RUE and high organ initiation rate causing high assimilate demand. This was particularly pronounced during the heterotrophic-autotrophic transition, probably causing shorter leaf blades relative to sheaths, as well as a temporary reduction of assimilate partitioning to roots. The model accurately simulated the mutant's high leaf mortality and absence of tillering. The simulated assimilate shortage was supported by observed reductions in starch storage in sheaths. Soluble sugar concentrations differed between mutant and WT in roots but not in shoots. Specifically, the hexose : sucrose ratio was 50% lower in the roots of the mutant, possibly indicating low invertase activity. Furthermore, two OsCIN genes coding for cell wall invertases were not expressed in roots, and others were expressed weakly. This was interpreted as natural silencing via sugar signalling. In summary, the authors attributed the majority of observed allometric and metabolic modifications in the mutant to an extreme assimilate shortage caused by hastened shoot organogenesis and inefficient leaf morphology.