My notes on Plant Biology Europe 2023 at Marseille (day 2)

04072023

Davide Bulgarelli's dream of personalized agriculture, inspired by personalized medicine.

 

 

 

Getting organised – the (re)evolution of fertility after genome duplication. Kirsten Bomblies.

Increased chr number -> increased cell size, this might affect organs such as stomata or xylem architecture. WGD might be a promising tool in agriculture, but often causes sterility (neo vs evolved polyploids). Her lab investigates how polyploids evolve using Arabidopsis thaliana and arenosa, that allow you to see the stages of polyploidization (https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.2154). She uses genome scan for selection, where allele freqs are plotted vs genome position, to find genes selected after polyploidization. 

Story 1 (fwd genomics of adaptation). Chiasmata formation in meiosis. They found that A. arenosa has amore efficient and lower crossover rate than neotetraploids (https://doi.org/10.1016/j.cub.2021.08.028 , https://doi.org/10.1073/pnas.1919459117).

 Story2 (rev genomics). Sterility of neopolyploids. They found genes under selection active during pollen tube formation (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8623246/).

P-bodies and post-transcriptional gene regulation in plant reproduction and stress response.  Karel Riha.

Describes their work on using microscopy and mutants to study the transition from meiosis to mitosis in gametogenesis in Arabidopsis thaliana (https://elifesciences.org/articles/52546 , https://www.frontiersin.org/articles/10.3389/fpls.2018.01602/full , https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009779). This transition requires suddenly stopping translation (https://pubmed.ncbi.nlm.nih.gov/35926014/).

The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements– Francois PARCY

UFO + LEAFY bind to specific LUBSO cis elements, which are a subset of those bound by LEAFY, as revealed by DAPseq. They found both monomeric and dimeric sited that contain half/entire  LEAFY sites plus an UFO site. They still don’t know whether UFO directly contacts DNA. They have also found that LEAFY K249 is crucial for the interaction with UFO + ubiquitination complex (https://pubmed.ncbi.nlm.nih.gov/36732360/). There hundreds of F-box proteins in A. thaliana, others might be doing the same, modifying targets of other TFs.

Timely endosperm elimination in Arabidopsis requires a programmed cell death pathway regulated by NAC transcription factors– Nicolas M. DOLL

Programmed Cell Death, controlled by several NAC transcription factors, plays a role in the embryo growth (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4453791). They saw that 4x NAC mutants (KIR1 and the others) produce larger, misshapen seeds, where the embryo does not take all the usual volume. These NACs are expressed in other tissues in the context of cell death (ie stigma development).

Predictable gene editing through Prime Editing in model plants and potential for crop breeding– Fabien NOGUE

Cas9 double-strand nicks phenotypes cannot always be predicted as they depend on subsequent DNA repair. Prime editing from 2019 allows susbtitutions and indels and has lower efficiency than Cas9 or base-editing tools. Needs to be improved for use in crops. He uses Physcomitrium as a model, which already has a T2T assembly, and the APT reporter gene. In their hands, prime editing was initially 30x efficient than Cas9 (https://pubmed.ncbi.nlm.nih.gov/35151447). Their strategy was to i) protect the PegRNA by fusing to it a viral pseudoknot [works], ii) use another reverse transcriptase [did not work], iii) split the nCas9 and RT in two proteins [a bit weaker]. They have now benchmarked their approach in A. thaliana, soybean, potato and grape, reporting an efficiency 2.5x smaller than classical Cas9.

CRISPR-based tool development to engineer plant genomes at the megabase scale– Júlia ARRAIZA RIBERA

She talks about her PhD OMEGA project where she uses P. patens to test Mb-scale, Cas9-dual targeting editions of the genome. Her goals are i) 5-10% genome reduction and ii) site-specific recombination. They find that large deletions (up to 100Kb) work in simplex, she is now testing multiplex epxeriments.

She is also testing Cre/lox to induce recombination, which requires inserting in the genome the loxPsym sites with CRISPR [works as expected in simplex, but tricky in multiplex settings or when sites are nearby on the same locus]. Recombination experiments to come.

Arabidopsis thaliana natural variation for photosynthesis: a model to guide improving crop photosynthesis? Mark Aarts.

Rubisco evolved when there was no much [O2] and suffers competition from oxygen in today’s conditions. Yield potential is a function of solar irradiance, interception efficiency (improved by breeding), harvest index (improved by breeding) and conversion efficiency into biomass (no targeted by breeding, potential for improvement, refers to Steve Long). Photosynthesis can be measured with gas analyzers, low throughput. Fluorescence imaging is much better for scaling up (ie MultispeQ), but this only a proxy for CO2 fixation, which is the real target. They have found natural variation for photosynthesis and and particular genes such as PPR YS1 (https://doi.org/10.1104/pp.114.252239) or Squalene epoxygenase-line (SQE) genes that have gained/lost exons and promoters across ecotypes and affect PSII performance. SQE are unique to Brassicaceae and Cleomaceae. There is also genetic variance in the cytoplasm, they have a protocol to swap plastids (https://www.nature.com/articles/s41477-019-0575-9). They then tested a set of plastotypes and measured their photosynthesis rates, finding a couple of outstanding plastotypes with mutations in cp gene ndhG. Overal so far they have documented 7 genes with natural variation related to photosynthesis efficiency (diff alleles contribute to a few % points of PS). He terminates by advertising the new Jan IngenHousz institute in Wageningen. Heritability of PS is 30% in optimal conditions, higher if you challenge the plants.

 

Comparative genomics session

1. The first pan-genome of a non-vascular plant broadens the understanding of land plants adaptation to their environment – Chloé BEAULIEU

Chloé is a 3rd year PhD student at the LRSV in Toulouse, in the EVO team lead by Pierre-Marc Delaux. She’s working on the genetic diversity of non vascular plant Marchantia polymorpha, in order to develop better knowledge of non-angiosperms. The overall goal is get new insights into the adaptation of landplants to their environment. Core < 10k genes acros > 100 ecotypes

2. Adapting CRISPR from Physcomitrium patens to sexually dimorphic moss, Ceratodon purpureus – Emilie-Katherine TAVERNIER

Emilie completed her PhD just two weeks ago. She has been working with the dioecious moss Ceratodon purpureus to evaluate sex linked genes. In this presentation, she’ll be tell us about about how she established CRISPR-Cas9 in tha species and some of the molecular barriers she had to overcome. 5x less efficiency than Physcomitrium. She won't talk about her latest upublished results.

3. The evolution of Arabidopsis centromeres – Fernando RABANAL

Fernando got a genomic sciences degree at UNAM, where I was fortunate enough to teach for some time. He became fascinated by the mysteries entangled in the repetitive fraction of the genomes since his PhD studies at the Gregor Mendel Institute in Vienna, where he investigated the natural variation and epigenetic regulation of ribosomal RNA gene clusters in A. thaliana with NGS data. Aware of the limitation of short-read data, for his postdoctoral research, I chose a group at the forefront of long-read sequencing technologies at the Max Planck Institute for Biology Tübingen. There he has been able to mine what has traditionally been inaccessible ‘dark matter’ in plant  genomes, namely, centromeres ribosomal RNA gene repeats. 10% innaceasible genome with HiFi. software for annotation:  https://academic.oup.com/bioinformatics/article/39/5/btad308/7159186

4. Divide and conquer: Evolutionary adaptations of the plant cytoskeleton during cell division – Katharina BÜRSTENBINDER

Her lab studies evolutionary adaptations and plant-specific functions of the cytoskeleton and she explain in depth recent, published work discovering a family of proteins involved in controlling cell divisions in plants that grow in 3D. This family expanded in angiosperms but goes back to some fungi (https://pubmed.ncbi.nlm.nih.gov/37068357).

 

Mural enfrente de la estación de Marsella.