Exploring and utilization of rice resources
with broad-spectrum resistance against blast disease (Xuwei Chen, Sichuan
University, China)
He speaks
about their sampling effort to identify alleles in rice germplasm that confer
resistance to blast disease. A survey of 3K sequenced rice genomes discovered
through GWAS an allele in cultivar Digu with MAF=0.10. It is a SNP in the promoter of a Zinc Finger
TF. The results are published in https://www.ncbi.nlm.nih.gov/pubmed/28666113 . He then moves on to their work on
transcription factor IPA1 (Ideal Plant Architecture) , that represses
improductive tillers and enhances immune responses. Again, the selected allele (ipa1-1D)
carries a mutation that breaks a miRNA site. The results can be found in https://www.ncbi.nlm.nih.gov/pubmed/30190406
Do environmental changes induce retrotransposon
expression in plants? (Flavia Mascagni, University of Pisa, Italy)
She is
conducting work to determine to what extent retrotransposons (RTs) are
expressed in response to environmental changes in sunflower. Upon treatment
with hormones and chemicals, they observe higher expression in the leaf than in
the root, with some genotypes more prone than others. Overall they found 134
differentially expressed RTs. Then they used a similar approach in poplar,
again using public cDNA libraries. Some genotypes are more prone than others to
show RT expression in response to treatment. In both species, of the few
differentially expressed RTs, most belong to the Copia superfamily.
Functional genomics of European hazel (Corylus
avellana L.) to address an emerging, destructive powdery mildew pathogen (Stuart
Lucas, Sabanci University, Turkey)
For their
search of alleles conferring resistance they have completed a genome assembly yielding
11 scaffolds (370Mb) for a predicted size of 380Mb. They are now annotating MLO
and NLR genes. As for MLO genes, 5 clustered copies are good candidates for
disease resistance. For NLR they are using long-reads to sequence end-to-end
copies, on a pool of 363 genes with little overlap across populations.
Natural genetic variation in the response of
Arabidopsis to Plasmodiophora brassicae infection (William Truman, IPG PAS
Poznan, Poland)
He
describes this obligate pathogen protest (clubroot) that affects a wide range
of Brassica crops. Some of their previous results are at http://www.plantcell.org/content/30/12/3058 . They are testing candidate
resistant alleles in Arabidopsis thaliana
ecotypes. Some are being further studied in Y2H assays.
Daniele Filiault, Gregor Mendel Institute,
Austria
She
describes her Arabidopsis thaliana
experiments in a latitudinal gradient from Germany to Sweden. The measure
survival and slug susceptibility and observe local adaptation, with germplasms
from S latitudes doing badly when planted up North. They then do GWAS and
separate intra-specific and Genus-specific variants.
Pathogen-informed strategies for sustainable
broad-spectrum resistance in crops (Bart Thomma, University of Wageningen, The
Netherlands)
He talks
about how we can learn from pathogen molecules to obtain resistant crops. He
shows this video of tomato fungal pathogen Verticillium
dahlie: https://vimeo.com/222178738 . He then shows haplotypes of
different isolates of the pan-genome and refers to https://genome.cshlp.org/content/early/2016/07/12/gr.204974.116 and https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15168 . Each isolate has 10% lineage-specific
non-core genes and they are apparently more conserved across species of the
Gens than core genes. This could be due to horizontal transfer (unlikely),
selection (unlikely) or reduced error replicons (Hi-C experiments suggest
co-localized in nucleous, unmethylated, enriched in TE, etc). Their most recent
manuscript is https://www.biorxiv.org/content/10.1101/528729v1 . The find that a single effector
gene in the fungus is responsible for pathogenicity, and when removed infection
does not occur/progress. Conversely, when transformed into non-pathogenic
species of the genus they now cause a disease in tomato.
He ends
with another story, where they have seen that the fungus produces an
antimicrobial protein (VdAve1, is that an antibiotic?) that alters the plant root microbiome and ultimately
facilitate infection.
Beyond single genes: receptor networks underpin
plant immunity (Sophien Kamoun, The Sainsbury Laboratory, UK)
Most plants
are resistant to most pathogens, they have a very efficient immune system with
Pattern recognition receptors (PRR) and NLR receptors. Pathogens secrete
effectors to modulate plant defenses (https://www.ncbi.nlm.nih.gov/pubmed/23223409). Together, plant and pathogens
coevolve and drive diversification. The NLR diversification is much larger in
plants than in mammals (human vs muse, tomato vs coffee, 100Myr). In fact,
ultimately, pathogens alter plant genomes (gene-for-gene model). He proposes to
move from the single gene paradigm to the immune network, incorporating
redundancy, evolvability, robustness and epistasis (https://www.ncbi.nlm.nih.gov/pubmed/29930125).
Using data science to understand plant gene
regulation (Daphne Ezer, University of York, UK)
She starts
by asking how do we know that our experiments are relevant in the real world?
We need to correct for confounding variables and always put the data in its
context, right? For instance, for bulk RNA-seq you must sync plants/treatments to
make sure you are comparing tissues of the same age, same circadian point and
tissue ratio. She has developed tools for these tasks, such as https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2717-5
Structure, stability and phenotypic relevance
of DNA methylation in Thlaspi arvense natural populations (Dario Galanti, University
of Tubingen, Germany)
He talks
about his PhD project, which is concerned about heritable methylation as a
function of location of origin, and how that affects phenotypes. He is working
with pennycress (Thlaspi arvense). Populations
sampled across Europe. I'll see if we can load that genome in Ensembl.
Nanopore Direct RNA Sequencing Maps the
Arabidopsis m6A Epitranscriptome (Matthew Parker, University of Dundee, UK)
He starts
by enumerating the theoretical advantages of sequencing native RNA directly,
instead of sequencing cDNA. They are using it in several projects. The error
rate is 5-8% which is not a problem for polyAs, but it is for short exon
annotation and intron boundaries. In those cases they still use Illumina to
correct the long reads.
Improving gene regulatory network inference
from ATAC-Seq data using an ensemble motif mapping approach (Marc Jones, VIB /
Ghent University, Belgium)
This talk
complements yesterday’s talk by focusing on ATAC-Seq. They use ATAC read depth
to restrict genome regions where known motifs can be scanned to discover
relvant cis regulation.
No genome required: Finding genetic variants
associated with plant phenotypes without complete genome information (Yoav
Voichek, Max Plank Institute for Developmental Biology, Germany)
This talk
complements yesterday’s but with a focus on the biology and the comparison
between GWAS based on SNPs and kmers. He shows a Venn plot to show that noth
approaches miss have a large intersection. However, there are some SNPs
associated not found with kmers and also the converse (structural variants,
regions missing in reference, etc). He is asked how this would work with
heterozygous genomes.
Spain
