Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

PloS One
Jérémy LavarennePascal Gantet

Abstract

Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. 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. We identified 3975 genes differentially expressed in crown root primordia. 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. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeli...Continue Reading

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Citations

Jul 27, 2021·Frontiers in Plant Science·Ai My LuongStefan Jouannic

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Datasets Mentioned

BETA
GSE133593

Methods Mentioned

BETA
laser capture microdissection
dissection
chips
chip

Software Mentioned

PageMan
Imaris
ZEN
TAC
GeneAtlas
Transcriptome Analysis Console ( TAC )
Mapman
BinTree RAPDB
Transcriptome Analysis Center
VisuaLRTC

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