Synthetic auxin, indole-3-butyric acid (IBA), effectively promoted the rooting in Cinnamomum kanehirae cuttings. The easy-to-root genotype, H107, responded to IBA much earlier than the difficult-to-root genotype, L41. On day 5, the POD activity significantly decreased in the IBA-treated tissues as compared with the control. Similar phenomenon was observed in extract of L41 genotype showing that IBA inhibited POD activity. In addition, the variation in POD activity corresponds to an inverse variation in the concentration of free IAA. The levels of IAA in H107 genotype increased dramatically in IBA-treated tissues on day 5; while, in L41 genotype, the raise of IAA in IBA-treated tissues was observed on day 20. Moreover, the lignin content in IBA-treated H107 cuttings decreased is quite correlated with the decline of the POD activity; yet the lignin content in L41 genotype cuttings was almost unchanged. Hence, we suggest that the inhibition on POD may lead to the redifferentiation processes induced by IBA, then produce the new root primordia during the formation of adventitious roots.

Auxin can induce adventitious rooting. Synthetic auxin, indole-3-butyric acid (IBA), effectively promoted the rooting in Cinnamomum kanehirae. The peroxidase (POX) activity significantly decreased in the IBA-treated tissues as compared with the control. Hence, I suggest that the inhibition on POX activity may lead to the redifferentiation processes induced by IBA, which produces the new root primordia during the formation of adventitious roots. On this investigation, I cloned POX cDNA from the young roots. Degenerate primers were designed from the conservative regions of other published POX to amplify the expectant DNA fragment. Full-length cDNA of the POX gene designated CKPX1 and CKPX3 were cloned by the method of 5'and 3' RACE. The deduced amino acid of CKPX1 and CKPX3 were compared with the previously reported POX and showed between 40% and 60% identity with those plant species. Further studies on the promoter elements of CKPX3 were found out that elements related to auxin response, lignification, pathogen invasion and stress response. The results suggest that CKPX3 may be involved in the regulate process of adventitious rooting and defense against pathogens and environment stress.

Auxin can induce adventitious rooting. Synthetic auxin, indole-3-butyric acid (IBA), effectively promoted the rooting in Cinnamomum kanehirae. In Cinnamomum kanehirae, there are high (H) and low (L) rooting cultivar. The peroxidase (POX) activity significantly decreased in the IBA-treated tissues as compared with the control. The inhibition on POX activity may lead to the redifferentiation processes induced by IBA. In this investigation, we cloned POX cDNA from the young roots. Degenerate primers were designed from the conservative regions of other published POXs to amplify the expectant DNA fragment. We found that the H and L line have similar genes (>99%). The Full-length cDNA of the POX genes were cloned by the method of 5'and 3' Rapid Amplification of cDNA Ends (RACE). The deduced amino acid were compared with the previously reported POX and showed between 40% and 70% identity with other plant POXs. Further studies on the promoter elements of POX in High-rooting cultivar and Low-rooting line show that some elements are related to auxin response, lignification, pathogen invasion and stress response. The regulatory elements of the POX gene in High-rooting line contain sugar repression responsiveness (SRS) elements that might repress the expression of POX gene, causing the lower POX activity.

L’organogenèse post-embryonnaire des racines latérales joue un rôle essentiel dans l’établissement de l’architecture du système racinaire des plantes, et donc dans leur croissance et leur performance. L’objectif de cette thèse est de caractériser le réseau de gènes régulant le développement des racines latérales et en particulier, l’organisation fonctionnelle du primordium de racine latérale, formant un nouveau méristème racinaire, chez la plante modèleArabidopsis thaliana en combinant des études de biologie des systèmes appliquées à la dynamique du transcriptome lors de la formation des racines latérales avec la caractérisation fonctionnelle de gènes candidats pour la régulation de ce phénomène d’organogenèse.La première partie de la thèse concerne l’identification des cibles de PUCHI, un facteur de transcription de type AP2/EREBP impliqué dans le contrôle de la prolifération et de la différentiation cellulaire dans le primordium de racine latérale. Le phénotype liés à la parte de fonction de PUCHI a été caractérisé en détail et à mis en évidence un rôle de ce facteur de transcription dans l'initiation des racines latérales et le développement et l'organisation des primordia. Par l’analyse de profils spatiaux et temporels d’expression de gènes, nous avons pu mettre en évidence que l’expression de gènes codant des protéines impliquées dans la biosynthèse des acides gras à très longues chaînes (VLCFA) est transitoirement activée durant la formation de la racine latérale et que cette dynamique est dépendante de PUCHI. De plus, le mutant kcs1-5, perturbé dans la biosynthèse de VLCFAs, présente un phénotype de développement des racines latérales similaire à celui de puchi-1. Par ailleurs, la perte de fonction puchi-1 augmente fortement la formation de cals continus dans des racines cultivées sur milieu inducteur riche en auxine, ce qui est cohérent avec le rôle récemment décrit des VLCFA racinaires dans la formation et l’organisation de cals distincts lorsque la racine est cultivé sur milieu inducteur de cals. L'ensemble de nos résultats démontre que PUCHI régule positivement l’expression de gènes de biosynthèse de VLCFAs lors de la formation de racines latérales et la callogenèse. Nos résultats confortent également l’hypothèse selon laquelle la formation des racines latérales et celle de cals racinaires partagent des mécanismes de régulation communs.La seconde partie de la thèse s’intéresse à l’identification de facteurs régulateurs clés dans l’organisation fonctionnelle du primordium de racine latérale et particulièrement, l’organisation d’un nouveau méristème racinaire. J’ai contribué à produire de nouvelles lignées de plantes permettant de suivre en temps réel par microscopie confocale la mise en place des identités cellulaires caractéristiques d’un méristème racinaire dans le primordium de racine latérale en développement. En utilisant un algorithme d’inférence de réseau de gènes, j’ai produit puis analysé les relations prédites de régulation entre gènes d’intérêt, afin d’identifier des gènes candidats potentiellement impliqués dans la formation du centre quiescent, un élément clé dans l’organisation du primordium et la mise en place du nouveau méristème racinaire. La caractérisation fonctionnelle de certains de ces gènes candidats a été initiée.Ces travaux de thèse ont donc contribué à mieux comprendre les mécanismes de régulation de la formation des racines latérales chez Arabidopsis thaliana. / 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 .

In the wetter climates associated with the coastal forests of the Pacific Northwest, coarse woody debris (CWD) accumulations in the form of snags, downed boles, and large branches can be large in natural forest ecosystems. Although maintaining organic matter for sustainable site productivity is not in dispute, the importance of CWD as a source of soil organic matter is questionable. Forest managers attempting to optimize timber production need to know how CWD affects short-term forest tree growth and productivity. This study addresses the question of the immediate value of CWD for growth of mature (90 year old) western hemlock (Hw). Because of practical difficulty with mature trees growing in different substrates, we utilized fine root distribution or proliferation, as an indicator of important substrates.