Gene regulatory network for lateral root formation in Arabidopsis thaliana

Abstract : Post-embryonic lateral root organogenesis plays an essential role in defining plant root system architecture, and therefore plant growth and fitness. The aim of the thesis is to elucidate the gene regulatory network regulating lateral root development and de novo root meristem formation during root branching in the model plant Arabidopsis thaliana by combining a system-biology based analysis of lateral root primordium transcritome dynamics with the functional characterization of genes possibly involved in regulating lateral root organogenesis.The first part of the thesis deals with the identification the target genes of PUCHI, an AP2/EREBP transcription factor that is involved in controlling cell proliferation and differentiation during lateral root formation. We showed that loss of PUCHI function leads to defects lateral root initiation and primordium growth and organisation. We found that several genes coding for proteins of the very long chain fatty acid (VLCFA) biosynthesis machinery are transiently induced in a PUCHI-dependent manner during lateral root development. Moreover, a mutant perturbed in VLCFA biosynthesis (kcs1-5) displays similar lateral root development defects as does puchi-1. In addition, puchi-1 loss of function mutant roots show enhanced and continuous callus formation in auxin-rich callus induction medium, consistent with the recently reported role of VLCFAs in organizing separated callus proliferation on this inductive growing medium. Thus, our results show that PUCHI positively regulates the expression of VLCFA biosynthesis genes during lateral root development, and further support the hypothesis that lateral root and callus formation share common genetic regulatory mechanisms.A second part of the thesis specifically addresses the issue of identifying key regulators of root meristem organization in the developing lateral root primordium. Material enabling the tracking of meristem cell identity establishment in developing primordia with live confocal microscopy was generated. A gene network inference was run to predict potential regulatory relationships between genes of interest during the time course of lateral root development. It identified potential regulators of quiescent center formation, a key step in functional organization of the lateral root primordia into a new root apical meristem. The characterization of some of these candidate genes was initiated.Altogether, this work participated in deciphering the genetic regulation of lateral root formation in Arabidopsis thaliana .
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Duy Chi Trinh. Gene regulatory network for lateral root formation in Arabidopsis thaliana. Plants genetics. Université Montpellier, 2019. English. ⟨NNT : 2019MONTG003⟩. ⟨tel-02304191⟩

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