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Under appropriate tissue culture conditions, somatic plant cells can be induced to form embryos in a process called somatic embryogenesis (SE). SE provides a way to clonally propagate desirable plants and is therefore an important plant breeding tool. SE has also fascinated scientists for decades as an expression of plant ‘totipotency’, the ability to regenerate a whole new individual through embryogenesis. This thesis aims to obtain a deeper understanding of somatic embryo induction in Arabidopsis by the transcription factor BABY BOOM (BBM), through identification and functional analysis of BBM-binding proteins and BBM target genes. Chapter 1 introduces the concept of somatic embryogenesis, describes the different SE systems in Arabidopsis, and discusses the role of the plant hormone auxin and chromatin modifying proteins in this process. An overview is presented on the current knowledge on SE-induction through ectopic overexpression of certain transcription factor genes. These include BBM, as well as other genes that are studied in this thesis in relation to BBM. BBM is part of the eight member AIL subfamily of AP2/ERF domain transcription factors. Chapter 2 reviews the role of AIL proteins during embryogenesis, stem cell niche specification, meristem maintenance and organ positioning and growth. We summarize the gene regulatory networks in which AILs function and describe how these transcription factors integrate multiple hormonal inputs, with special emphasis on the interactions between AILs and auxin. Finally, we conclude that although the functions of AILs in plant development are well described, knowledge on the molecular mode of action of AIL proteins and the identity of AIL target genes is still limited. Transcription factors function in protein complexes and in Chapter 3 we show that members of the HOMEODOMAIN GLABROUS (HDG) transcription factor family physically interact with BBM and other AILs. HDG genes are expressed in the epidermis, the outer cell layer of the plant, where they promote differentiation of cells into specialized epidermal cell types, such as trichomes or stomata. We show that ectopic overexpression of HDG1 leads to loss of root and shoot meristems, phenotypes that had previously been reported for loss-of-function ail mutants. Conversely, down-regulation of HDG genes led to reduced cell differentiation, enhanced cell proliferation and SE phenotypes, phenotypes that resemble those found in AIL overexpression lines. Moreover, we found that co-overexpression of BBM and HDG1 reduces the overexpression phenotypes of both proteins. These results suggest opposite functions of AIL and HDG transcription factors, with AILs stimulating cell proliferation and HDGs stimulating cell differentiation, with the ratio between the two proteins determining the developmental outcome. Finally, we show that HDGs and AILs regulate each other on a transcriptional level and that they share common target genes. A variety of AIL overexpression phenotypes has been described in the literature, with BBM and PLT5/AIL5 being the only known AILs that induce SE upon overexpression. We show in Chapter 4 that all AIL proteins except AIL1 and ANT are able to induce SE, but that this phenotype relies on a high AIL protein dosage. Using BBM and PLT2 as AIL representatives, we show that an intermediate AIL concentration induces organogenesis (ectopic root and shoot formation) and that a low concentration inhibits cellular differentiation. In addition, we show that BBM and PLT2 induce direct SE when activated at seed germination, while post-germination activation leads to indirect SE from callus. The LEAFY COTYLEDON (LEC)/LAFL genes, which also encode SE-inducing transcription factors, are direct targets of BBM/PLT2 during direct SE, showing that these two SE pathways are linked. Using LAFL gene mutants, we show that the LAFL pathway is an important downstream component of BBM-mediated SE. Chapter 5 presents the in vivo, genome-wide analysis of BBM DNA binding sites in somatic embryos using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Our ChIP-seq and gene expression analysis reveal that BBM binds and positively regulates auxin biosynthesis genes and the recently discovered positive regulators of SE, the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) genes. Knock-out of either pathway reduced BBM-mediated SE, showing that auxin biosynthesis and the AHL genes are important components of the BBM pathway. We also show that BBM binds to a consensus DNA motif that resembles the reported ANT binding motif. Chapter 6 reviews methods for identifying the direct target genes of a plant transcription factor using microarrays, as was done for HDG1 (Chapter 4). We describe which different systems can be used to control transcription factor activity, and how these can be combined with microarray analysis to identify target genes. In addition, we provide guidelines for the statistical analysis of microarray data and for the confirmation of candidate target genes. In plant biology, protein-protein interactions are often studied using bimolecular fluorescence complementation (BiFC) or split-YFP. In my BBM-HDG interaction studies I encountered problems using this method, which lead to the cautionary note on the use of BiFC presented in Chapter 7. BiFC is based on the restoration of fluorescence after the two non-fluorescent halves of a fluorescent protein are brought together by a protein-protein interaction event. However, because the fluorescent protein halves are prone to self-assembly, it is crucial to use proper controls and a quantitative read-out of fluorescence to avoid false positive interactions. We present a guideline for the setup of a BiFC experiment, discussing each step in the protocol. Chapter 8 discusses how the results presented in this thesis contribute to our knowledge on AIL transcription factors and somatic embryo induction, as well as the questions that still remain. An extended model of dose-dependent AIL function is proposed, as well as mechanisms by which the AIL-HDG interaction could function at the molecular level. Finally, an overview is provided of the molecular-genetic intersection between the different transcription factor-induced SE pathways.

Microspore embryogenesis is an expression of plant cell totipotency that leads to the production of haploid embryos. Besides being a widely exploited plant breeding tool, microspore embryogenesis is also a fascinating system that can be used to obtain a deeper mechanistic understanding of plant totipotency. This thesis aims to provide more insight into the process of microspore embryogenesis, from the formation of embryogenic cells to the outgrowth of differentiated embryos. In Chapter 1 background information is provided on the various aspects of Brassica napus microspore culture and plant development that intersect with the topics that are studied in this thesis. Emphasis is placed on the basic requirements and limitations for successful microspore embryo culture, as well as on the roles of the plant hormone auxin and epigenetic regulation in the development of plant embryos, during both zygotic and in vitro embryo development. Chapter 2 reviews the recent advances that have been made in understanding the developmental and molecular changes that take place during microspore embryogenesis in model systems. The commonly reported cellular changes associated with the establishment of embryo cell fate are summarized and evaluated. The subsequent differentiation of the embryo is also discussed, specifically, what is known about the establishment of polarity, with emphasis on the importance of exine rupture as a positional clue, and the processes that influence meristem maintenance during culture. Finally, the studies on the molecular changes during microspore embryo induction are put into context of male gametophytic development. Overall, the current perspective on microspore embryo initiation presents a landscape in which several routes can lead to the same final destination. Stress treatments are widely applied to induce embryogenic growth in microspore culture. Chapter 3 explores the role of histone acetylation status in stress-induced microspore embryogenesis in Brassica napus. Inhibition of histone deactylases (HDACs) using the HDAC inhibitor trichostatin A (TSA), phenocopies the heat stress treatment that is normally used to induce embryogenic cell proliferation in B. napus microspore culture. Arabidopsis is recalcitrant for haploid embryogenesis, yet treatment with TSA also induced embryogenic cell divisions in this model species. Our observations suggest that the totipotency of the male gametophyte is kept in check by an HDAC-dependent mechanism and that the stress treatments used to induce haploid embryo development in culture impinge on this HDAC-dependent pathway. The repression of HDACs or HDAC-mediated pathways by stress and the accompanying changes in histone acetylation status could provide a single, common regulation point for the induction of haploid embryogenesis. Chapter 4 builds on the knowledge developed in Chapter 3 on the role of HDAC proteins in plant totipotency. A wide variety of chemically distinct HDAC inhibitors was evaluated and additional inhibitors that enhance embryogenic cell induction and/or embryo yield were identified. One surprising observation was made during the course of this study: the initial donor microspore/pollen stage affects the quality of the embryo that is formed. In control cultures, embryos from progressively older stages of donor microspores/pollen became progressively compromised in their basal (axis region) region, characterized by a shift from normal embryos with apical (cotyledons) and basal (root) polarity to abnormal embryos with a reduced basal pole and ball-shaped embryos. These abnormal phenotypes could be partially complemented by treatment with HDAC inhibitors, which promoted growth of the basal region of the embryo. Progressive enhancement of embryo basal identity was accompanied by enhanced and broadened expression of the DR5 auxin response reporter. The embryo phenotypes observed in control and HDAC inhibitor treated microspore cultures are similar to the phenotypes induced by altered expression of the Arabidopsis TOPLESS (TPL)/HDAC19/BODENLOS (BDL) repressor complex, which acts to restrict expression of the AUXIN RESPONSE FACTOR ARF5/MONOPTEROS (MP) to the basal region of the embryo during zygotic embryo development. To understand why most embryogenic callus failed to develop further, we examined the transcriptome of globular-shaped embryos that have started to histodifferentiate and compared it with embryogenic callus. The transcriptome analysis showed that the expression of many genes that regulate (auxin-related) embryo patterning were downregulated in embryogenic callus compared to globular stage embryos. This result may simply reflect the lack of patterning in these embryos or might indicate a role of auxin-signalling in embryogenic callus formation. Chapter 5 examines how embryo identity and patterning is established in two B. napus microspore embryo pathways, a zygotic-like pathway, characterized by suspensor and then embryo proper formation, and a pathway characterized by initially unorganized structures that lack a suspensor. We specifically asked the question: how can embryo patterning be established in the absence of an initial asymmetric division and in the absence of a suspensor, two key events in zygotic embryo development. Analysis of embryo fate (GRP) and auxin (PIN1, PIN7 and DR5) markers showed that embryo fate was established prior to cell division, and independent of subsequent division pattern. The suspensorless embryo program was marked by a transient auxin maximum, followed by establishment of the apical and basal poles at the globular stage, coincident with release of the embryo from the pollen exine. Unlike zygotic embryo development, polar auxin transport (PAT) was not required for embryo initiation or polarity establishment in this system. Suspensor embryos developed in a similar fashion as zygotic embryos, PAT was required for specification of the embryo proper from the suspensor. Haploid embryogenesis therefore follows at least two programs, a PAT-dependent program that requires embryo proper specification from the suspensor, and an alternative PAT-independent program marked by an initial auxin maximum. In the final chapter, Chapter 6, the work presented in this thesis is put in context of the broader plant development field. The epigenetic regulation of developmental transitions that respond to stress and during pollen development are highlighted. A model is provided that histone acetylation levels mediated by HAT and HDAC regulate pollen fate.