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A Molecular Framework for Plant Cell Totipotency

Periodic Reporting for period 1 - POTENTIATE (A Molecular Framework for Plant Cell Totipotency)

Reporting period: 2015-06-01 to 2017-05-31

The plant kingdom is characterized by a high level of developmental plasticity, including the ability of plants to form embryos (totipotency) in the absence of fertilisation. Microspore embryogenesis (ME) is a form of totipotency in which immature (haploid) pollen is induced to form embryos in vitro. Haploid embryos can be converted to diploid homozygous (doubled-haploid, DH) plants in a single generation, placing ME in the centre of numerous breeding and trait discovery applications. ME was described more than 50 years ago, but a deep mechanistic understanding of ME and other forms of induced totipotency is lacking. It is, therefore, essential that we know the final fate of the different cell types in culture to be able to link these fates to specific signalling pathways and to understand their role in totipotency. Main objective in this project has been to isolate and characterize the different embryogenic cell types in Brassica napus microspore culture using a set of fluorescently-tagged gene reporters. The project has three main objectives:
1. Define and collect the different embryogenic cell types present in microspore culture using GFP-based reporters, time-lapse imaging, and cell sorting.
2. Define the transcriptional landscape of embryogenic cells using high throughput mRNA sequencing.
3. Determine the function of candidate microspore embryogenesis genes.
Objective 1: Define and collect the different embryogenic cell types present in microspore culture using GFP-based reporters, time-lapse imaging, and cell sorting.
The three GFP reporters mark an overlapping set of embryogenic cells, each with different fates i) differentiated embryos (DR5, LEC1 and GRP) and ii) unorganized callus (LEC1 and GRP) (Figure 1).
Time lapse imaging:
Time-lapse imaging of the embryo-expressed GFP reporter lines was used to determine the fate of the different embryogenic cell types in culture. We designed an efficient immobilization system to fix the position ofembryogenic structures and to follow them in time without interfering with their development. We optimized the imaging parameters by testing different microscopes/imaging platforms and different software packages for data handling and image processing. Time-lapse imaging of GFP-positive embryogenic structures at day 5 indicated that only the compact structures develop into differentiated embryos (Figure 2). Embryogenic callus-like structures never form differentiated embryos; the majority of these both stop growing and lose their embryo identity, visualized by a loss GFP embryo marker expression.
Cell sorting:
We tested two systems for their utility in sorting GFP-positive and GFP-negative cells from microspore culture: 1) the BioSorter (Union Metrica); and 2) Fluorescence Activated Cell Sorting or FACS. In addition, we tested filtering as a means to enrich for differentiated embryos in older cultures. The BioSorter was not useful for sorting GFP-positive and negative populations in microspore embryo cultures. Using FACS, we could separate 100% GFP-positive and 100% GFP-negative cell populations in the GRP:GFP and LEC1:GFP lines until day 6 of culture (Figure 3). However, DR5: GFP expression was too weak to allow cell sorting. Filtering was the most efficient method for isolating older embryogenic structures, around 94% of the filtrate corresponded to GFP-positive embryogenic structures (compact and callus-like), while the remaining 6% was pollen(Figure 4).

Objective 2: Transcriptome analysis
We used freshly isolated microspores, which can be easily isolated in large numbers, to optimise different steps in the mRNA-seq protocol, including mRNA isolation, mRNA amplification and mRNA-seq library construction before proceeding with the FACS samples.
After many trials we decided to use the Picopure kit (Thermo Fisher)) for RNA isolation in combination with the MessageAmp kit (Thermo fisher) for mRNA amplification. 40,000 cells/sample was set as the lower limit for each sample. We collected GFP-positive and GFP-negative cells by FACS or filtering during 6 months. Samples were collected from microspore culture with and without TSA, at day 0, 2, 4 and six days after stress treatment, using three replicates from two different Brassica napus lines. Most samples are ready for sequencing. Objective 3: Determine the function of candidate genes
Due to the large amount of time needed to set up the FACS system and to collect the samples we did not have time to study the function of candidate genes.

New objective: Study the cellular characteristics of embryogenic cells.
We prepared samples for light and transmission electron microscopy (Figure 5). We observed differences between the different types of embryogenic structures. Embryogenic calli, which do not form embryos, are characterized by loss of cell adhesion (Figure 6), most likely resulting from a decrease in the amount of pectins, arabinogalactan proteins and callose in the cell wall. Moreover in embryogenic calli we observed a massive increase in endoplasmic reticulum, ER stress and autopgahy-related markers (Figure 7), including lipohagy (Figure 8), as well as cell death. These abnormalities may explain why these structures do not continue with the embryogenic pathway.
There is very little known at a mechanistic level about how plant cells regenerate, due to the difficulty in linking the cellular/molecular observations to specific cell fates. I have developed a time lapse imaging system and used it to show identify the fate of the different embryogenic structures found in microspore culture. We now know that of all the initially embryogenic structures only the compact structures form differentiated embryos. However less than half of these compact structures form embryos, and although the remainder of the compact structures retain their embryo identity, they fail to differentiate. By contrast, most callus-like structures tend to lose their embryo identity as they age. It is not only important to understand the molecular-cellular processes in cells that successfully form haploid embryos in culture, but also to study the processes that take place in cells that are initially converted to embryos, but fail to complete this developmental pathway.. This knowledge can help us to understand what goes wrong and what we have to modify to help these structures to continue with the embryogenic pathway. Such knowledge can be directly translated to agronomically important crops that are recalcitrant for microspore embryogenesis.
The cell-sorting system that we have set up will allow us to specifically analyse the transcriptome of these different cell types to unambiguously assign specific signalling pathways to specific cell fates. These data are unique in the plant community and will allow us to answer a classical plant tissue culture question: how does a single differentiated cell regenerate in the absence of stem cells.
The output of this project can also be used in applied crop research to understand genotype-specific bottlenecks underlying recalcitrance for DH production and to develop biomarkers for marker assisted breeding of responsive germplasm.
Processing microspore cultures for light and transmission electron microscopy
Lipid accumulation and lipophagy
Biosorter versus filtering for cell sorting in older developmental stages
Examples of embryogenic growing during time laspse imaging
Type of embryogenic structures in brassica napus microspore culture
Pectin detection with Ruthedium Red
Endoplasmic reticulum stress and lytic activity in microspore embryogenesis
Fluorescence Activated Cells Sorting in early stages