Biology subjects

Jouannic, S.

Publications and source records attributed to Jouannic, S..

5 recordsLinked to original sources

bioRxiv2026

Spatial Decoupling of the Endodermal Functions Establishes the Innermost Cortex as the Gravity Sensor in Rice Stems

Gravitropism is a remarkable example of coordinated growth, enabling plants to perceive gravity and generate asymmetric cell expansion that restores organ orientation. In Arabidopsis, gravity sensing in shoots occurs within starch-rich endodermis cells. In rice, however, the stem must accommodate gravitropic bending while preserving integrity of tissues surrounding emerging crown roots, raising the possibility that gravity sensing relies on distinct structural and physiological adaptations. Here, using high-resolution imaging together with auxin-response analyses, we identify a specialized cell layer at the inner boundary of the rice stem cortex, operationally defined by its position adjacent to the lignified endodermis and associated with gravitropic responses. This layer is characterized by circumferentially elongated cells, starch sedimentation, a confined auxin-response domain, and expression of gravity-sensing markers. Following gravistimulation, starch granules realign and the auxin response domain expands asymmetrically within this layer, coinciding with differential growth during stem bending. Our results further indicate that this response depends on polar auxin transport and conserved components of the gravitropic regulatory network. Together, these findings support a model in which gravity sensing and signaling in rice stems are spatially separated from the lignified endodermal barrier. Such tissue organization may represent a developmental adaptation that allows the stem to reconcile barrier integrity with growth flexibility.

plant biology↗

bioRxiv2026

Connecting gene expression and cytokinin signaling during meristem determinacy transition in the rice panicle

Structural complexity in the rice inflorescence (panicle) is determined by the activity of indeterminate meristems, which allow sequential branching events to occur but later acquire a determinate character that precludes the initiation of new growth axes. To better understand the underlying regulatory processes, we combined a detailed time-course of panicle development with tissue-specific sampling of meristems before and after the determinacy switch, monitoring global gene expression programs and hormone accumulation. This allowed the delineation of three dynamic transcriptional modules and the inference of gene regulatory networks highlighting hormone regulatory hubs associated with the indeterminate-to-determinate meristem transition. Our data confirm the importance of known regulators of inflorescence development and identify novel actors, notably genes encoding transcription factors, that were not previously described in the regulation of flowering. The combined biochemical and transcriptomic data support a model in which cytokinin signalling is particularly active during the proliferative branching phase, during which meristem maintenance is promoted while a feedback mechanism is also triggered, ultimately leading to the acquisition of determinate meristem fate later in development. HighlightInvestigating the molecular nature of rice inflorescence meristem determinacy, we studied temporal and spatial gene expression alongside hormone accumulation, identifying novel regulatory interactions and a key role for cytokinins.

plant biology↗

bioRxiv2023

African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the identification of key QTLs

BackgroundDeveloping high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The genetic interactions that govern the diversity of panicle complexity within and between the two species are still poorly understood. ResultsTo identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapo. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12 and QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. ConclusionOur analysis led to the detection of genomic variations between O. sativa cv. Caiapo and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.

plant biology↗

bioRxiv2021

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice

The architecture of the rice inflorescence is an important determinant of seed yield. The length of the inflorescence and the number of branches are among the key factors determining the amount of spikelets, and thus seeds, that will develop. Especially the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem regulates the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in rice. Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq we observed that two ALOG genes, Oryza sativa OsG1-like 1 (OsG1L1) and OsG1L2, have an expression profile similar to TAW1. Here we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes as the taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the datasets were also used for the construction of a gene regulatory network (GRN) proposing interactions between genes potentially involved in controlling inflorescence development in rice. The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of the homeodomain-leucine zipper transcription factor gene OsHOX14 suggest that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development. One-sentence summaryOsG1L1 and OsG1L2 control panicle architecture through delaying the transition from indeterminate branch- to determinate spikelet-meristem identity.

developmental biology↗

bioRxiv2020

Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima

BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

plant biology↗