Biology subjects

Clerget, B.

Publications and source records attributed to Clerget, B..

6 recordsLinked to original sources

bioRxiv2026

Sunrise and sunset times are the main factors that determine the flowering time of photoperiod-sensitive sorghum

Crop photoperiodism models assume that flowering time is primarily controlled by daylength, yet many field observations contradict this view. We previously proposed an alternative framework integrating daily changes in sunrise and sunset times (dSR and dSS). Variety trials in Madagascar and in Argentina supported this concept: mid-late sorghum varieties from the northern hemisphere flowered late or very late when sown in November and December, consistent with the higher dSR/dSS values of the southern hemisphere summer. One Malian variety, sown monthly over six years in West Africa, exhibited high interannual variability in flowering time when sown between November and February. This revealed that up to four photoperiodic responses -- two quantitative and two qualitative, occurring at different times of the year -- may coexist within a single late photoperiod sensitive variety. All responses use only dSR and dSS cues. The qualitative responses are triggered by an internal phasic coincidence, which is set by a linear relationship between dSR and dSS at the onset of plant photoperiod sensitivity, and between dSR+dSS at panicle initiation. The research model fitted data from 28 varieties grown in Mali well. It also accurately fitted the duration to PI observed in three varieties sown at tropical and temperate latitudes. HighlightThe seasonal photoperiodic adaptation of flowering time in sorghum plants may rely on several signal transduction pathways regulated by sunrise and sunset times rather than day length.

Plant Biology↗

bioRxiv2026

Transformer-Based Phenotyping of Rice Root Aerenchyma Across Environments Enables Climate-Smart Rice Selection

Quantification of root anatomical traits such as cortical aerenchyma is key to understanding rice adaptation to diverse water regimes. Recently, the role of aerenchyma in regulating methane emissions has been demonstrated, making it a target for climate change mitigation. Despite its importance, breeding for root anatomical traits remains limited because manual analysis of root cross-sections is labor-intensive, inconsistent, and poorly scalable, and analysis pipelines do not generalize across heterogeneous imaging conditions. We present a deep learning pipeline based on a recent vision transformer architecture to automatically segment rice root anatomical structures and quantify aerenchyma. The model was trained on a multi-environment dataset of 1,760 annotated rice root cross-sections acquired across growth stages, cultivation systems, and countries, using a collaboratively defined annotation protocol. The model achieved high segmentation performance (mean Intersection-over-Union > 0.92) and near-perfect aerenchyma ratio quantification (R2 = 0.98), and was evaluated by two experts as performing on par with, and in some cases better than, expert annotators. Delivered as open-source software with an online interactive demonstrator, the pipeline revealed differences in aerenchyma across genotypes, water regimes, environments, and developmental stages. Overall, this work demonstrates that transformer-based segmentation enables high-throughput anatomical phenotyping, supporting scalable and climate-smart rice breeding. HIGHLIGHTSO_LITransformer-based segmentation enables robust aerenchyma phenotyping across environments C_LIO_LIA SegFormer model achieves expert-level accuracy on diverse rice root cross-sections C_LIO_LIAutomated analysis delivers near-perfect lacuna-to-cortex ratio quantification (R2 {approx} 0.98) C_LIO_LIOur online demonstrator supports scalable, climate-smart rice breeding applications C_LI

physiology↗

bioRxiv2022

Phyllochron duration and changes through rice development shape the vertical leaf size profile

O_LIWell-irrigated aerobic rice (Oryza sativa L.) plants are often shorter with smaller leaves, and the leaf appearance rate is slower in well-irrigated than in flooded environments. This observation questions the functional relationship between the leaf appearance rate, which is correlated with the apical cell production rate, and leaf length that is in turn correlated with the leaf division zone length. C_LIO_LIMeristem size, blade size, and appearance were monitored for all leaves from leaf 6 on the main stem of rice plants in field experiments using two varieties, two watering systems, and three sowing dates. C_LIO_LILeaf blade and division zone lengths were correlated in all leaves of the main stem of rice plants. New stable linear relationships were found between the leaf division zone growth duration and internal cell production rate, which changed after leaf 11. These stable relationships imply a stable link between the rates of cell production in the stem apex and leaf meristem, explaining the vertical leaf size profile. C_LIO_LIOverall, faster leaf appearance leads to shorter leaves and organs in rice because of a functional link, which is counterbalanced by additional acclimation in transplanted plants. C_LI

plant biology↗

bioRxiv2021

Bamboos flower after the return of an appropriate sun-moon phasing

All Asian woody bamboo species of economic importance are semelparous. They remain vegetative during time intervals that are specific to each species and range from three to 120 years, with notable concentrations around a series of values (3, 7-8, 14-17, 29-36, 42-48, 61-64, and 120 years). Then, they flower gregariously within a short period. Entire forests temporarily disappear during these periods, and the dates of these dramatic events have been recorded over the last 200 years. While searching for a correlated environmental cue, I have found that the concentrations of flowering cycles were highly correlated with the series of successive returns of almost the same sun-moon phasing as at seedling emergence. On basis of knowledge on plant photoperiod sensitivity, I hypothesize that bamboo plants i) run a lunar cellular clock that is set at the full moon, ii) retain in their cellular memory the exact sun-moon phasing of the year of their emergence as seedlings, and iii) inhibit flowering until the occurrence of a unique, species-specific sun-moon phasing that is shifted by a precise amount from the sun-moon phasing at their emergence. Recent evidence of plant responses to lunar cycles supports this hypothesis, for which experimental evidence is now anticipated. HighlightThe long-standing enigma of the triggering of the gregarious flowering of bamboos is possibly solved. Flowering would be inhibited until the occurrence of the species-specific sun-moon phasing.

plant biology↗

bioRxiv2021

Transplanting increases the leaf production rate in rice, consequently modifying plant development and growth

In Asia, direct sowing and water savings are major trends in previously transplanted and flooded irrigated rice systems because of the higher cost of wages and increasing water shortage. Previous experiments showed that the leaf appearance rate varies between aerobic and flooded cropping systems. This study aimed to further understand how the planting method affects the development rate, flowering time, and yield of lowland irrigated rice crops. A two-year experiment was undertaken at the International Rice Research Institute, Philippines, using three contrasting rice varieties and three planting methods (transplanted, wet direct-seeded, and dry direct-seeded; at a density of 25 plants m-2) in a field submerged in 3-5 cm water from two weeks after the transplanting date. The effect of the planting method was similar in the three varieties, mostly without interaction between the two factors. In 2013, the leaf number of seedlings grown in seedling trays was two leaves behind that of direct-seeded plants at the time of transplanting. However, the young transplanted plants recovered quickly; produced new leaves at a faster rate (with a shorter phyllochron); reached panicle initiation, flag-leaf emergence and flowering time 1 week later; and developed more leaves compared to the direct-seeded plants. In 2014, growing in the nursery induced no delay in leaf appearance due to temperatures lower than those in 2013; therefore, the planting method did not affect the leaf appearance rate. Thus, plant development was primarily delayed by the density stress in the seedling trays under warm temperatures; however, the transplanted rice plants had lower plastochron duration than the direct-seeded plants, which made up for the initial delay in leaf appearance. In both years and at similar plant density, the transplanted plants produced more tillers bearing larger upper leaves that led to a higher leaf area index; however, grain yields were similar for the transplanted and direct-seeded crops. Highlights- In seedling trays, leaf appearance stopped at the appearance of the fourth leaf. - After transplanting, leaf appearance resumed at a faster rate than in direct-seeded plants. - Transplanted plants had delayed panicle initiation and flowering time, more tillers, and more and larger leaves per tiller, but similar grain yield compared to direct-seeded plants at similar planting density.

plant biology↗

bioRxiv2020

Crop-photoperiodism model 2.0 for the panicle-initiation date of sorghum and rice that includes daily changes in sunrise and sunset times

Background and AimsDaylength determines flowering dates. However, questions remain regarding flowering dates in the natural environment, such as the synchronous flowering of plants sown simultaneously at highly contrasting latitudes. The daily change in sunrise and sunset times is the cue for the flowering of trees and for the synchronisation moulting in birds at the equator. Sunrise and sunset also synchronise the cell circadian clock, which is involved in the regulation of flowering. The goal of this study was to update the photoperiodism model with knowledge acquired since its conception. MethodsA large dataset was gathered, including four 2-year series of monthly sowings of 28 sorghum varieties in Mali and two 1-year series of monthly sowings of eight rice varieties in the Philippines to compare with previously published monthly sowings in Japan and Malaysia, and data from sorghum breeders in France, Nicaragua, and Colombia. An additive linear model of the duration in days to panicle initiation (PI) using day length and daily changes in sunrise and sunset times was implemented. Key ResultsSimultaneous with the phyllochron, the duration to PI of field crops acclimated to the mean temperature at seedling emergence within the usual range of mean cropping temperatures. A unique additive linear model combining daylength and daily changes in sunrise and sunset hours was accurately fitted for any type of response in the duration to PI to the sowing date without any temperature input. Once calibrated on a complete and an incomplete monthly sowing series at two tropical latitudes, the model accurately predicted the duration to PI of the concerned varieties from the equatorial to the temperate zone. ConclusionsThe results of the updated photoperiodism model strongly supported the hypothesis that photoperiodism could be a combined response to day length and daily changes in sunrise and sunset times.

plant biology↗