Biology subjects

Palaffre, C.

Publications and source records attributed to Palaffre, C..

7 recordsLinked to original sources

bioRxiv2026

Disentangling shape and size variation to compare canopy architecture in maize

{middle dot} Comparing maize canopies is confounded by two problems: plants differ in the number of phytomers they produce, and phytomer size scales with that number. Position along the shoot is therefore an unreliable basis for comparison, confounding shape with size. {middle dot} We first position the floral transition (tassel initiation, T.I.) within shoot development, revealing it as the landmark that organizes a conserved canopy shape. This provides the foundation for aligning canopies that differ in phytomer number. {middle dot} Focusing on the leaf blade, we used functional data analysis on a maize panel across controlled and field environments to decompose variation in blade-length profiles, which was dominated (77%) by overall amplitude, identifying scaling as the major source of size variation. Because blades enlarge with each phytomer until the transition, later T.I. yields a larger maximum; this T.I.-linked component explains up to one-third of scaling variation, reinforced by a shared genetic association between T.I. and blade size with the flowering-time gene ZmCCT10. {middle dot} Regressing out this component leaves a residual that defines a new, heritable axis of intrinsic scaling, independent of flowering time. It distinguishes hyper- and hypo-scaling genotypes consistently across environments, offering a selection target decoupled from phenology.

plant biology↗

bioRxiv2026

Dissecting the phenotypic and genetic determinants of maize-bean interactions in intercropping

O_LICereal-legume intercropping is a cornerstone of agroecological systems because interactions between species can enhance agroecosystem resilience. Yet, the mechanisms underlying these interactions remain poorly understood. To address this gap, we investigated the maize-bean association under low-input conditions. C_LIO_LIWe conducted a two-year intercropping experiment with 200 climbing bean lines grown alongside three maize landraces in France and Romania. We evaluated bean phenotypic responses above- and below-ground to 3 maize landraces, treated as distinct biotic environments (E). Direct and indirect genetic effects were assessed by mapping bean and maize phenotypic traits onto the bean genome (G), with G x E interactions tested using contrasts among maize landraces. C_LIO_LICompetitive interactions dominated, maize acting as the stronger competitor. Maize landraces created distinct biotic environments affecting bean traits. Best-performing partners varied across experimental fields, with no evidence of bean local adaptation. The most productive and balanced mixtures were obtained with the traditionally intercropped maize landrace. Genome-wide association analyses identified loci underlying direct and indirect genetic effects, including candidate genes associated with neighbor perception. C_LIO_LIThese findings reveal the genetic complexity of maize-bean interactions and highlight competitive tolerance in bean and reduced aggressiveness in maize as key traits for improving cereal-legume intercrop performance. C_LI

genetics↗

bioRxiv2026

How to be dispensable: genomic and transcriptomic determinants in maize genes

BackgroundPlant genomes harbour a substantial proportion of dispensable genes - present only in a subset of individuals - that differ from ubiquitously shared core genes in multiple genomic and expression features. While these differences have been repeatedly documented, the factors shaping gene dispensability remain poorly understood. ResultsWe assembled a pan-gene set from eight maize inbred lines from American and European germplasms, together with their transcriptomic profile across 22 tissues/conditions, revealing the genomic and transcriptomic determinants of maize gene dispensability. Multivariate analysis demonstrates that gene expression level and purifying selection - rather than gene size - are the primary factors distinguishing core from dispensable genes. Dispensable genes overlap Helitrons at 4.6 times the rate of core genes, implicating Helitron-mediated gene capture as a major mechanism of dispensable gene formation. Classifying genes into stably expressed, variably expressed, and on-off categories shows that all three classes contain dispensable genes, though in different proportions than for core genes. Contrary to previous assumptions, we show that dispensable genes can participate in basal biological functions just as core genes, and that gene duplication likely provides only a partial mechanism for functional complementation of accessory genes absence. ConclusionsOur results provide novel insights into the molecular and evolutionary factors distinguishing core from dispensable genes and into the biological mechanisms shaping gene dispensability in maize, and demonstrate that classifying genes by transcriptional patterns provides a powerful framework for understanding the biological functions and evolutionary dynamics of both core and dispensable genes.

plant biology↗

bioRxiv2024

A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation

Understanding how plant phenotypes are shaped by their environments is crucial for addressing questions about crop adaptation to new environments. This study focused on analyzing the genetic variability underlying genotype-by-environment interactions and adaptation for flowering time in maize. We present a physiological reaction norm for flowering time plasticity (PRN-FTP), modeled from multi-environment trial networks and decomposed into its physiological components. We show how genotype-specific differences in developmental responses to temperature fluctuations condition differences in photoperiod perceived among genotypes. This occurs not only across but also within common environments, as the perception of photoperiod is altered by variation in rates of development and durations for becoming sensitized to photoperiod. Using a new metric for envirotyping sensed photoperiods for maize, it was found that, at high latitudes, different genotypes in the same environment can experience up to hours-long differences in photoperiod. This emphasizes the importance of considering genotype-specific differences in the experienced environment when investigating plasticity. Modeling the PRN-FTP for globally representative breeding material showed that tropical and temperate germplasm occupy distinct territories of the trait space for PRN-FTP parameters. Placed in the historical context of maize, our findings suggest that the geographical spread and breeding of maize was mediated by a specific modality of ecophysiological adaptation of flowering time. Our study has implications for understanding crop adaptation and for future crop improvement efforts. Article SummaryMaize adjusts its flowering time across environments using genetic pathways tuned to cues like temperature and day length. This study models how different varieties perceive and respond to these factors, revealing that genotypes can perceive the same environment in distinct ways. By disentangling the ecophysiological basis of genotype-environment interactions, the research explores maize diversity and highlights how adaptation and breeding have shaped distinct strategies for flowering time regulation in tropical and temperate varieties.

plant biology↗

bioRxiv2024

A multidisciplinary on-farm survey of maize-bean intercropping shows that revival of traditionalagricultural systems requires careful consideration of partner varieties and agronomic practices.

O_LICereal-legume intercropping is a promising strategy for sustainable agroecosystems. The traditional intercropping of maize and bean is experiencing a revival in some modern agricultural settings, such as in southwestern France, where maize hybrids are intercropped with the commercialized Tarbais bean. We conducted on-farm surveys and a field assay to address the following questions: How does the cropping system impact yield, nutrient uptake, and rhizosphere bacterial assemblages? Do positive or negative interactions between maize and beans dominate in intercropping? What is the effect of intercropping on plant transcriptomics? C_LIO_LIWe recorded farming practices, conducted yield and nutrient measurements, and characterized soil bacterial assemblages to compare sole-cropped maize and beans with intercropped plants. A controlled field assay was also established to extend this comparison to plant gene expression differences. C_LIO_LIIntercropping was associated with a trend towards increased bacterial diversity. The cropping system significantly influenced agronomic traits, with frequent farm-by-cropping system interactions underscoring the critical role of farming practices. Competition dominated maize-bean intercropping, with 34 negative correlations among the 47 significant ones between maize and bean traits. This competition affected yield and nutrition, but primarily impacted beans, which produced fewer but bigger/heavier seeds. Transcriptomic results concurred with these findings, revealing no differentially expressed genes in maize but 5,070 in beans under competition. C_LIO_LIOverall, our findings suggest that beneficial interactions between the two crops are hindered under current field conditions, underscoring the importance of carefully considering partner varieties and farming practices to revive traditional agricultural systems. C_LI Societal Impact StatementCereal-legume intercropping is a promising strategy for sustainable agroecosystems that leverages the biological complementarities between plant species, reducing the need for chemical inputs while enhancing field biodiversity. Here, we focused on maize-bean intercropping, which is experiencing a revival in modern conventional agricultural settings. We found a trend towards an increased soil bacterial diversity in intercropping. However, competition between the two crops dominated and primarily impacted yield and gene expression in beans. Despite lower yield, bean seeds exhibited greater size. Our study indicates that implementing variety selection of both species and adapting farming practices is essential to fully harness the potential of intercropping.

plant biology↗

bioRxiv2024

Effects of maize development and phenology on the field infestation dynamics of the European Corn Borer

Phenological match/mismatch between cultivated plants and their pest could impact pest infestastion dynamics in the field. To explore how such match/mismatch of plant and pest phenologies may interact with plant defense dynamics, we studied the infestation dynamics of maize by one of its main pests in Europe, the European Corn Borer (Ostrinia nubilalis; Lepidoptera: Crambidae). A two-year field experiment was carried out on a collection of 23 maize inbred lines contrasted for their earliness. Each inbred line was sown at three different dates in order to expose different developmental stages of maize to natural European corn borer infestation. The effect of the sowing date depended on the inbred line, the pest generation and the year. In 2021, the final pest incidence ranged from 36% to 91% depending on inbred lines and sowing date. In 2022, it ranged from 2% to 77%. This variability in final pest incidence can be related to variations in plant development during plant exposure to pest infestation. However, this relationship was not straightforward. Indeed, the shape and intensity of the relationship depended on the timing of the onset of the pest infestation. When infestation occurred while plants were in a vegetative stage, a non-linear relationship between development and pest incidence was observed with the least and most developed plants being the most infested. When infestation occurred when all plants were in the mature phase, the most developed plants were the least infested. Our results highlight the effect of plant-pest phenological match/mismatch on pest infestation dynamics and underline the importance of taking plant-pest interactions into account to propose relevant control strategies.

ecology↗

bioRxiv2021

EARBOX: An open tool for high-throughput measurements of the spatial organization of maize ears and inference of novel traits

BackgroundCharacterizing plant genetic resources and their response to the environment through accurate measurement of relevant traits is crucial to genetics and breeding. The spatial organization of the maize ear provides insights into the response of grain yield to environmental conditions. Current automated methods for phenotyping the maize ear do not capture these spatial features. ResultsWe developed EARBOX, a low-cost, open-source system for automated phenotyping of maize ears. EARBOX integrates open-source technologies for both software and hardware that facilitate its deployment and improvement for specific research questions. The imaging platform consists of a customized box in which ears are repeatedly imaged as they rotate via motorized rollers. With deep learning based on convolutional neural networks, the image analysis algorithm uses a two-step procedure: ear-specific grain masks are first created and subsequently used to extract a range of trait data per ear, including ear shape and dimensions, the number of grains and their spatial organisation, and the distribution of grain dimensions along the ear. The reliability of each trait was validated against ground-truth data from manual measurements. Moreover, EARBOX derives novel traits, inaccessible through conventional methods, especially the distribution of grain dimensions along grain cohorts, relevant for ear morphogenesis, and the distribution of abortion frequency along the ear, relevant for plant response to stress, especially soil water deficit. ConclusionsThe proposed system provides robust and accurate measurements of maize ear traits including spatial features. Future developments include grain type and colour categorization. This method opens avenues for high-throughput genetic or functional studies in the context of plant adaptation to a changing environment.

plant biology↗