While my colleagues @EEAD-CSIC attended a meeting on cereal breeding at Lleida, today I travelled to Barcelona to learn at the meeting 'At the forefront of plant research 2023'. This is organizaded by CRAG and the chosen venue is the CosmoCaixa up in the hill. I will be sharing my notes here.
Jump to the other days here: II, III
Monday 08
may
Britt Koskella ‘Leveraging the above ground (phyllosphere) microbiome for plant healt’
She talks about her work on phytosphere (aereal part) microbiome on tomato. They have found that tomato seeds contain a relatively conserved microbiome composition. When grown in controlled conditions in the greenhouse, plants seem to have really little bacteria. The seed bacteria can hel control the growth of Pseudomonas syringae.
In field experiments they observe that there is transmission from neighbors (https://pubmed.ncbi.nlm.nih.gov/35022514), in fact it is more important than the actual genotype of the plants.Further experiments show that drought induces a loss of bacterial/mycorr richness, targeting specific taxa.
Teva Vernoux ‘Auxin in development: where to respond, when to respond and how to respond?’
Shows a nice picture of shoot apical meristem to describe the parts where class A ARFs triggered to establish a spatial pattern. Permissive chromative marks surround the gene bodies; the repressive ones cover mainly the gene body. In protoplasts the observe that there’s a large network of TFs repressing ARFs. Using DAPseq & protoplast data they find that combinations of class A,B,C ARFS bind inverted repeats and direct repeats with spacers 8,13 and 5,15 respectively. Their model is that different tuples ARF,CRE have different roles.
Marja Timmermans ‘How to make a flat leaf: Pre-patterns, small RNA morphogens and Turing dynamics’
Describes a n=6 TF/miRNAs network that control how a flat leaf is made, 3 expressed adaxial and 3 abaxial (https://pubmed.ncbi.nlm.nih.gov/35318449). There are also two opposing gradients of miRNAs (https://www.cell.com/developmental-cell/pdfExtended/S1534-5807(17)30816-X) which control the translation of the TFs and control leaf polarity by defining robust developmental boundaries.
She and collabs explored Turing models / cell automata, which combine a short-range + loop and long-range – feedback loop, to create leafs and managed to bring it down to n=3 while maintaining the known n=6 interactions and adding a few new ones. Their best model predicts that AS2 has to be a mobile TF. She alsi mentions https://www.science.org/doi/10.1126/science.aay5433
Keith Slotkin ‘Targeted Transposition in Arabidopsis’
His lab works on target site integration. Context: HR has so low freq is unusable in plants. Homology-Directed Repais has medium precision. Another option is NEEJ, with low precision. For these reasons they are exploring using guided-transposition using the Pong/mPing system, a PIF/Harbinger element from rice, that have 1-order magnitude success rate of targeted integration when shipping with a long linker to full ds-cutting Cas9 genes.
What about precision of insertion? 0-7bp (mostly 1-4) changes at the junctions of insertion sites. Ping transposase is used to excise, Cas9 to cut new destination site. Offsites? Yes, apparently not using Cas9 but the transposase instead, which is still viable. So far mPing can integrate 430-1563bp cargos. They are currently testing it on soybean. There’s a preprint at https://assets.researchsquare.com/files/rs-2679086/v1_covered.pdf?c=1679325102
Angela Hancock ‘Adaptation to novel environments’
Walks us along the use of Arabidopsis thaliana projects on population genomics, first in Europe and more recently in Africa, including Cabo Verde (https://www.arabidopsis.org/servlets/TairObject?type=species_variant&id=98), where the growing season is very short (2-3m). They have studied the island (Santo Antao, Fogo) populations and found out that they represent a single migration from N Africa. CV populations flower rapidly to produce more seed (46% variance from a nonsynon mutation in FRIGIDA, see https://www.nature.com/articles/s41467-022-28800-z).
Plants from volcanic Fogo shows chlorosis in standard pots. Ionome experiments show those line have rebalanced Fe/Mn to adapt to their native soil by harboring two mutated transporters with different affinities, one of them a loss of function (https://www.science.org/doi/10.1126/sciadv.abm9385), the other a tandem duplication. These are nice examples of evolutionary innovations.
Hao Yu ‘RNA modification underlies plant development and stress responses’
There are over 170 chemical modifications to RNA, 3UTR m6A (N-methyladenosin) being the most common in A. thaliana as measured with nanopore direct RNA sequencing. He shows examples of roles of m6A modification during development (seed onset, proliferation of SAM, male meiosis [rice]). In the second part of his talk he focus on the rm1 mutant (disordered protein region) and the role of m6a in drought survival, possibly in the ABA range of action. They find that RM1 recruits m6A mRNA to stress granules.
Elena Monte ‘Photosignaling for plant adaptation to environmental challenges’
Two stories: rhythmic responses, cotyledon expansion, two processes regulated by PIF/phytochrome. She talks about the role of PIFs + basal ABA in closing stomate during the night and opening at dawn, a process that depends on blue light intensity. They found KAT1,a s K++ channel in guard cells, responds both to ABA (to close) and PIFs (to open at dawn, ChIP peaks upstream). https://www.biorxiv.org/content/10.1101/2023.01.14.524044v1
