![]() This type of approach led to the identification of new genes involved in root development and root physiology in Arabidopsis. Transcriptomic approaches, based on the quantification of gene expression at whole-genome level, overcome these limitations by identifying all the genes specifically expressed during a biological process. However, these approaches are impaired by functional redundancies, and by lethality of some mutants. Genetics and functional genomics approaches revealed several genes involved in CR development in rice. These roots develop post-embryonically from the stem and play an important role in the adaptation of plants to the soil hydro-mineral status. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.Ĭrown roots (CR) are a type of adventitious roots making up most of the root system in rice. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. We identified 3975 genes differentially expressed in crown root primordia. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Jérémy Lavarenne, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Writing – original draft, Writing – review & editing, 1, 2 Mathieu Gonin, Investigation, Methodology, 1 Antony Champion, Methodology, Supervision, Writing – review & editing, 1 Marie Javelle, Methodology, Supervision, Validation, Writing – review & editing, 2 Hélène Adam, Methodology, Supervision, 1 Jacques Rouster, Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Validation, Writing – review & editing, 2 Geneviève Conejéro, Methodology, 3, 4 Marc Lartaud, Methodology, 3, 4 Jean-Luc Verdeil, Methodology, 3, 4 Laurent Laplaze, Conceptualization, Writing – review & editing, 1 Christophe Sallaud, Conceptualization, Funding acquisition, Project administration, Resources, Supervision, Validation, 2 Mikael Lucas, Conceptualization, Supervision, Validation, Writing – review & editing, 1 and Pascal Gantet, Conceptualization, Funding acquisition, Investigation, Project administration, Resources, Supervision, Validation, Writing – review & editing 1, *Ĭrown roots constitute the main part of the rice root system.
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