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| http://brachypodium2019.unizar.es |
Here I will be posting my notes on the talks I attend.
PS: The abstract book has been published at https://zaguan.unizar.es/record/79582
Tuesday
Keynote by Elizabeth Kellog . I missed the first part of the talk, but she presented a whole range of data (histological, genomic, genetic) showing that the abscission zone (AZ), which is where florets in the spikelet shed, is fundamentally different in three grasses: Brachypodium, Oryza and Setaria. A key result was that only 3 genes are differently expressed in all three species, including yabby2 and myb26, and that lignin does not seem fundamental for abscission. However, later GWAS work on a wide Setaria panel found a single locus explaining abscission phenotypes, and it was a different myb transcription factor. A key question arising is why grasses have developed different genetic mechanisms to control abscission. You can read more about this at:https://onlinelibrary.wiley.com/doi/10.1002/9781119312994.apr0619
https://www.ncbi.nlm.nih.gov/pubmed/27257006
Wednesday
Session: Natural diversity and evolution
Robert Hasterok, University of Silesia
He speaks
about the evolution of the grass karyotype, which is 100-150Myr old, with a
basic chr number n=5, and the species in the Brachypodium genus, with a variety
of ploidy levels and chr numbers. He focus first on barcoding of annual B.
stacei, B. distachyon and B. hybridum using dozens of BACs from B. distachyon
to track chr regions (https://academic.oup.com/aob/article/122/3/445/5034913). Then he moves to more complex
perennials, showing unpublished results. Although showing conserved syntenic
chr regions, perennials have larger genomes. Regarding B. mexicanum, their data
cannot so far tell whether it is allopolyploid or perhaps underwent
whole-genome duplication.
Liang Wu,
Zhejiang University, Hangzhou
He talks
about divergent roles of FTs in flowering control in Brachypodium distachyon,
building on previous published work (https://www.nature.com/articles/ncomms14320). While there are only 2 homologues
in Arabidopsis thaliana, there are 6
copies in B. Distachyon. He then goes
on to show experimental results on some of them. For instance, FT2 alternative
splicing and dimerization seem to be involved with age flowering. Instead, FT5
is induced in short days and has a weak flowering inductivity. In fact it
represses flowering in long days and it is itself repressed by CO1, although
they don’t have an antibody to directly check the interaction (https://www.nature.com/articles/s41467-019-08785-y).
Sinead Dread, U Leicester
She talks
about Brachypodium distachyon grains
in a comparative (flat, little starch vs creased grain) and evolutionary
context. Brachy are sister to core pooids (Bromeae, Triticeae, Aveneae, Poeae).
Compared to Triticeae, brachy aleurone cannot be separated from the grain as
easily. Most of these observations have been published at https://www.ncbi.nlm.nih.gov/pubmed/24723396 . They have available reference
transcriptomes of the grain (that they hope to host at the EBI) which they are
using to study the expression of transcription factor families relevant in the
grain (FIL2/6,YABBY22/5, INO). She terminates with in situ pics showing
similarities between brachy and rice.
Benoit Lefebvre, INRA Toulousse
Brachypodium distachyon genetic variability for beneficial
interaction with arbuscular mycorrhizal fungi (AMF), a kind of associations
that have been shown to protect against diseases in rice (Magnaporthe oryzae) and that in brachy seems to depend on the
availability of both P and N in the root. They work first with ecotype Bd3-1 to
set up an automated phenotyping system to assess the effect of AMF on growth.
Now they are analyzing all ecotypes sequenced at the JGI. Clearly there seems
to be a positive response in some ecotypes (particularly those with low
biomass) and also negative on others (affects resource allocation). He has
published several papers on this: https://www.ncbi.nlm.nih.gov/pubmed/28548654 , https://www.ncbi.nlm.nih.gov/pubmed/30405668,https://www.ncbi.nlm.nih.gov/pubmed/30347445.
Errol Véla,
U Montpellier
His talk is
taxonomic, about the typification of names and their taxonomic assignment
within the Brachypodium distachyon
complex, a work they are carrying out in collaboration with the group of Pilar
Catalán. He shows very nice pics of morphological traits that clearly
differentiate the three annual Brachypodium
species. Their main result is that B.
stacei had been described earlier on a wider distribution area including
France and Algerie, and should be renamed to B. rigidum.
Session: Comparative genomics and
transcriptomics
Robin Buell, Michigan State U
She talks
about “Life with 1000 genomes: Defining the pan-genome in maize” after a short
intro on bacterial pan-genomes. Structural variation is impacted by
reproductive mode, TEs, ploidy, with outcrossers so far showing more
variability (maize vs potato). What’s an allele? Structural variants are
usually lowly expressed, shorter, and a subset of them have roles in
adaptation, and should be considered in genotype-phenotype analyses. They have
done GWAS/eQTL studies to identify genes/alleles that confer higher ethanol
content from corn stover. They use transcriptomes as pangenoma proxies and map
accessory transcript based on LD and have confirmed the PAV patterns in
whole-genome assemblies which have been produced since (http://www.plantcell.org/content/26/1/121 , https://dl.sciencesocieties.org/publications/tpg/abstracts/0/0/180069). She expects PAV genes to be able
to complement absent genes in hybrids. She also shows results on clustering
pangenes in terms of protein sequences, confirming that the variability is
still there, with lots of unique proteins found in some cultivars (B73, PH207,
PHJ89). The found a PAV explaining resistance to mosaic virus resistance, while
SNPs could not provide signal. Expression data is critical to remove PAV genes
not relevant in a particular condition of interest. They have built a broad
expression atlas of B73 with 79 tissues: over 4K pangenes have FPKM larger than 1,
apparently enriched in the seed (https://onlinelibrary.wiley.com/doi/10.1111/tpj.14184). They have also done WGNCA and
found modules enriched in particular functions which include PAV genes and a
few are highly connected. They use stringent criteria (I believe araound 80%
identity) to remove “copies” of existing genes.
Keiichi Mochida, RIKEN
Starts by
summarizing virtues of hybrid crops in terms of vigor or biomass, as happens
with B. hybridum. He then moves to the transcriptome analysis
of gene regulatory network reveals differential organization of rhythmic
transcriptome between sub-genomes in the allopolyploid grass B. hybridum. This work has been
published at https://academic.oup.com/gigascience/article/7/4/giy020/4924998. The main message is that in their
experiment they found thousands of genes (about 20% of genes) with differential
expression when comparing the hybrid and the parental diploids (B. distachyon,
B. stacei).
Alexander Betekhtin, U Silesia in Katowice
He talks
about his work on CRISPR/Cas9-based targeted mutagenesis in B. distachyon and B. hybridum and its application to study the model grass genome organization,
a field in which they have relevant experience (https://www.ncbi.nlm.nih.gov/pubmed/29893795). Their hypothesis is that genome stability
depends on the CDKG/Ph1 pathway, as seen in bread wheat and Arabidopsis thaliana. They are 4 copies
of this genes. They induce mutants in several of them and are now trying to
understand the cytogenetic phenotypes.
János Györgyey, Hungarian Academy of Sciences
He explains
he moved from wheat work on root architecture to brachy and then starts talking
about the LOB-domain transcription factor gene family in B. distachyon, a work they published at https://www.ncbi.nlm.nih.gov/pubmed/27686461. LOB stands for lateral organ
boundary. These TFs contain a Leu zipper domain as part of the larger LOB
domain (https://www.sciencedirect.com/science/article/abs/pii/S1360138510002050). They are characterizing the
expression of all the gene copies of this family across tissues.
Bruno Contreras
Moreira, Ensembl Plants, EBI
My talk is
“A pan-genome perspective on the co-expression response of genes to drought in
the model grass B. distachyon”, which was mainly the work of Rubén Sancho, a
former PhD student. Here we analysed the osmotic stress responses of 33 B. distachyon ecotypes under two
conditions, mild drought (D) and well-watered (control, C). Leaf transcripts
were sequenced and pseudo-aligned to the Bd21 reference genome with a double
purpose: i) to estimate their abundance and, ii) to assess the proportions of
core and accessory genes expressed in response to drought. We built weighted
co-expression networks from the transcriptome data and were able to dissect two
distinct network topologies in drought and control conditions, respectively.
While transcripts of control plants could be clustered in 30 modules with 839
hub genes, plants under mild drought yielded 38 modules with 628 genes
annotated as hubs. By comparing the resulting modules we identified five
exclusive D modules containing over-expressed genes enriched in Gene Ontology
terms such as proline synthesis, response to water deprivation, phosphate
starvation and temperature stimulus. In those exclusive D modules we performed de novo DNA motif discovery in upstream
sequences and identified putative cis-regulatory elements of an ABA inducible
leucine zipper transcription factor. In addition, we observed that some genes
in these modules display different expression levels among tolerant and
susceptible ecotypes. Finally, pan-genome analysis indicated that most
expressed transcripts are encoded by core genes, present in all ecotypes, while
14%, including some hubs, correspond to accessory genes.
Charles Solomon, U Leicester
He talks
about his PhD project on programmed cell death in developing B. distachyon caryopsis. He takes us on
a nice comparison of caryopsis development in brachy, A. thaliana and crops such as wheat and barley. His experiments
involve histological sections, dyes and RNA-seq to track the expression of
particular gene families, such as proteases A1, C1/13/14, in vegetative and
grain tissues.
Session:
Development and growth
David des Marais, MIT
He talks about natural diversity in patterns
of biomass allocation in annual (live fast, die young) and perennial
(bet-hedging) Brachypodium species. Most human calories are coming from
annuals, but there are some important perennials as well (ie sugarcane).
Perennials must compute how many meristems to commit; some also produce
rhizomes. In their experiment they see that perennial brachy species produce
more seeds, but annuals grow faster (dry mass over days in a single
session). This also holds for relative
growth rate, which can be decomposed as the product of leaf area x leaf mass
ratio x net assimilation rate. They also see that dark photosynthesis
significantly faster in B. distachyon vs perennials. He gets asked
whether comparing to B. mexicanum, being also polyploid, makes sense.
General idea: there’s more than one way to evolve a perennial into an annual.
Daniel Woods, UC Davis
He starts by describing his current work in comparing genotypes of both
brachy and wheat in terms of flowering-related traits, which builds from early
work (https://www.ncbi.nlm.nih.gov/pubmed/23619014). His
goal is to accelerate flowering gene discovery; he’s fished so far 14 genes! He
goes on to tell a story about a splice site mutant in a predicted DNA
polymerase subunit Cdc-27 (ZAO1) that caused rapid flowering of B. distachyon.
He discovered ZAO1 is a plant-specific gene, but there are other AAO genes
elsewhere. ZAO1 mutants seem to have altered the expression of few genes,
including most flowering control genes and MADS-box TFs. He’s now doing Y2H
assays in both brachy and wheat to fish proteins interacting with ZAO1.
John Doonan, Aberystwyth U, Wales
He talks about grain trait
variation in Brachypodium, which has lower starch content than crop grasses.
He describes a QTL analysis of populations from several ecotypes of B. distachyon and different traits. The best peak on shattering
maps next to a gene homologous to a shattering gene described in rice. They are
now working on phenotyping as part of EPPN (https://eppn2020.plant-phenotyping.eu) and verifying the candidate genes.
Michael Raissig, U Heidelberg
His talk is about evolutionary innovations of stomatal form and
function in Brachypodium. Grasses have bell-shaped guard cells that are
fundamentally different than those in dicots, opening significantly faster (https://science.sciencemag.org/content/355/6330/1215). A
stomata requires 6 cycles of cell division/differentiation. If I got that correctly, his lab is currently going
through a large mutant collection to identify more genes involved in stomata
development.
Richard Sibout, INRA Nantes
His talk intends to highlight the role of vascular tissues in grasses.
In this context his lab are studying mutants in B. distachyon that
affect the vascular development and auxine content, such as as vac1. When they mapped the mutant, it turns out it
affects a Leucine Rich Repeat Receptor Kinase (LRRRK) that regulates
vasculature patterning, phloem-xylem polarity and cell wall composition. He
shows beautiful pics but there is no paper or preprint to get them just yet.
Thiel Lehman, U Zurich
He explains that some B. distachyon genes (BdRSL) have previously
been shown to rescue A. thaliana root hair mutants (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006211).
He then moves on to talk about the molecular and cell biological
characterization of another gene, the BUZZ cell division kinase, which is also involved
in root hair development are somehow causes misexpression of BdRSL genes.
Session:
Tolerance and adaptation to abiotic stresses
Pubudu Handakumbura, U Massachusetts
Amherst
She talks about genotypic and phenotypic diversity for drought
tolerance in B. distachyon. She shows significant differences among
ecotypes in their responses to freshwater limitation, with very little shared
proteins/metabolites (6 ecotypes) being expressed. Metabolite response is strong
in the root and moderate in the leaf.
Mhemmed Gandour, U Sidi Bouzid, Tunisia
He talks about screening B. hybridum genotypes for drought
tolerance. His data shows high germination rates in dry conditions and conversely
a significant reduction under max soil moisture. They have also measured water
content in the leaf and root.
Shira Penner, Tel Aviv U
She describes her PhD work with around 30 Brachypodium populations
with variant ploidy along the aridity gradient in Israel (from 700l N to 200l S)
in order to assess their adaptation to stress. After analyzing her common
garden results she believes those plants escape drought but face competition
and finishes with a hint that endophytes might increase fitness. They could not
separate B. distachyon from B. stacei plants, both diploids.
Johannes Metz, U Hildesheim , U Potsdam
Following the previous talk, he speaks about ecology of annual Brachypodium
in Israel, sampling populations at the same elevation on a precipitation gradient.
He focus only on B. hybridum and finds that arid genotypes have less
roots and are less plastic, with no significant bet-hedging (https://www.sciencedirect.com/science/article/abs/pii/S1433831917300872
, https://www.sciencedirect.com/science/article/pii/S1439179117302311).
Eviatar Nevo, U Haifa
http://brachypodium2019.unizar.es/eviatar-nevo
https://www.youtube.com/watch?v=UhNzH39zLbk
Videoconference on Evolution Canyon: sympatric evolution through niche adaptation.
https://www.youtube.com/watch?v=UhNzH39zLbk
Videoconference on Evolution Canyon: sympatric evolution through niche adaptation.
Thursday
Session: Regulatory elements, networks and
epigenomics
Anne Roulin, U Zurich
She talks about population genomics of
transposable elements (TE) in B. distachyon. The effects of TE jumps can be
disruptions, the creation of new promoters or rather the epigenetic silencing
of neighbor regions. She shows that TEs in B. distachyon are not concentrated
exclusively in the centromeres, and rather colonize all chromosome regions. Her
team has developed a pipeline to analyze TE insertions polymorphism (TIPs), and
can now compare the rate of fixation of TIPs and SNPs in the 3 Mediterranean
populations on B. distachyon. The results were published at https://academic.oup.com/gbe/article/10/1/304/4769669 . She concludes that both recent activity of TE families and purifying
selection explain the current distribution of TEs along the pangenome. Then she
moves a more recent study on the effect on the expression/silencing of neighbor
genes in parallel in brachy and A. thaliana. They observe families of TE
that have a distance-related effect while other do not.
Mexia Li, KU Leuven
Her talk is about RNA interactome capture (RIC)
in B. distachyon, a protocol that has only been tested in Arabidopsis so
far (https://www.ncbi.nlm.nih.gov/pubmed/29339797) and that she says still needs to be optimized in plants (https://www.life-science-alliance.org/content/1/3/e201800088). Her results reveal a collection of core RBPome of RNA binding
proteins conserved in A. thaliana and B. distachyon and by
extension in flowering plants.
Joshua Coomey, U Mass Amherst
He talks about a transcription factor, SECONDARY
WALL INTERACTING bZIP (SWIZ), which regulates secondary cell wall biosynthesis
in B. distachyon in (thigmomorphogenic?) response to mechanical stress.
In particular SWIZ overexpression produces thicker walls and is translocated to
the nucleus in the root after stress (in histological preparations and confocal
videos). This behavior seems to be linked to GA synthesis rates. Using DAP-seq
they have characterized the bZIP-like motif of SWIZ, which binds to 3500 loci
in the genome (800 have the consensus), similar to AtbZIP52: CAGn*CTG.
Michael Thieme , U Zurich
Follows on a previous talk by Anne Roulin. His
is about stress-induced mobilization of transposable elements (TE) in natural
accessions of B. distachyon. This work is after previous work on rice
and A. thaliana ONSEN LTR TE (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1265-4), but he says A. thaliana is not really the best plant to study
the effect of TEs on natural populations. He is now performing mobilome-seq
after applying stress using a published protocol (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006630). Preliminary results suggest
TEs get mobilized in some ecotypes but not others after applying the same
stress condition.
Christoph Stritt, U Zurich
He talks about this study on the high sequence
turnover and GC between retrotransposon copies, which possibly indicate frequent
ectopic recombination. I had already cited his work (https://academic.oup.com/gbe/article/10/1/304/4769669). There are in total 11 (7 copia + 4 gipsy) LTR lineages in the B.
distachyon genome, which vary widely in age and abundance. Among them, the
Angela lineage is the most dynamic and responsible for a within-species
polymorphisms, while the Retand lineage is significantly richer in GC% than the
genome.
Kirankumar Mysore, Noble Research Institute
He describes an insertional mutagenesis in B.
distachyon Bd21-3 using the Tnt1 retrotransposon, based on https://www.ncbi.nlm.nih.gov/pubmed/29039003, and its potential use to identify novel sources of disease resistance.
On average, each line test has 12 Tnt1 insertions, of which 4 are genic. They
estimate they need 22K TnT1 lines to target any gene with 0.95 probability.
Session: Polyploidy and perenniality
Pamela Soltis, U
Florida
She talks about polyploidy as integrator
across levels of biological organization: from cells to ecosystems. She talks mainly
about her microevolution work on Tragopogon, which has unveiled a
variety on mechanisms of novelty in polyploids: non-additive gene content (gene
loss), expression, karyotupes, mosaics, etc. Then she moves to the macroevolutionary
scale, starting with this tree: https://genomevolution.org/wiki/index.php?title=Whole_genome_duplication,
which summarizes whole genome duplications (WGD) events. She claims that all
genomes probably contain ancient WGD which have diploidized later on. We would just
need to recognize them to better understand species. Not all WGD can be
associated to radiation events in evolutionary time. They have published a
paper in this: https://www.ncbi.nlm.nih.gov/pubmed/27234228
Ruben Sancho, U
Zaragoza, EEAD-CSIC, Arnold Arboretum
His talk is about his PhD work on i) reference-genome
syntenic mapping and ii) multigene-based phylogenomics to reveal the ancestry
of homeologous subgenomes in Brachypodium allopolyploids. This work is
still unpublished and proposes plausible hypothesis for the evolutionary
processes that produced the different allopolyploid species.
Virginia Markham, JGI, UC Berkeley
She presents her work on chr territories with Hi-C
data on B. hybridum. After analyzing that data she sees both D & S
subgenomes clearly segregated, with very little contacts. She reports that
neither subgenome dominates in terms of gene expression, although it is known
that there is nucleolus dominance in the hyrid. She observed that chromatine
topology in the diploid parents D&S is conserved in the hybrid as well. There
is one outstanding region in the chromatine which resembles a transposon trap/hotspot
described in A. thaliana?
Antonio Manzaneda, U Jaén
He presents his team’s work on homoeologous
gene expression and subgenome dominance in response to water stress in the
allotetraploid B. hybridum, which they have published at https://www.ncbi.nlm.nih.gov/pubmed/29893879.
The used 3 lines (Bd-30-1), Larva-20 (B. hybridum) and Alsur-1 (B.
stacei). They observe greater expression changes with respect to the
diploid parents under stress. He suspects these differences are epigenetic, but
they haven’t checked yet.
Natalia
Borowska-Zuchowska, U Silesia
She talks about nucleolar dominance (35S rRNA
genes) in allotetraploid B. hybridum, which was observed for the first
time in roots: https://www.ncbi.nlm.nih.gov/pubmed/18438442.
More recently they have seen that stacei
nucleoli are switched off during much of the life cycle, are methylated and
stay at the outside margin of the nucleous: https://www.ncbi.nlm.nih.gov/pubmed/30481334.
They also observe variance in the content of 35S genes in different B.
hybridum ecotypes. They hypothesize that the stacei nucleoli might have
pseudogenized instead of being silenced due to dominance.
Nir Sade, Tel Aviv U
He talks about his work on the perennial model
grass B. sylvaticum under stress
tolerance. He tests two accessions from Tunisia & Norway in terms of their
ability to produce biomass. He’s published some of this recently: https://www.ncbi.nlm.nih.gov/pubmed/29322303.
Using WGNCA he identified a candidate HdZIP TF that might regulate winter
hardiness.
He describes recent collaborative efforts (Harmonia7) to analyze the genetic, epigenetic and metabolomic differentiation of Turkish B. distachyon accessions into two geographically distinct populations. Their main finding is that genotypes from separate regions have specific responses. By analyzing RNAseq data they conclude that epialleles affect expression; he explains the VRN1 locus as an example to show that SNP variation correlates with CpG variation. His main message is that genetic, epigenetic and metabolomics variation seems to be linked in two populations.
Friday
Session:
Ecology and Environment
David Lowry, Michigan State U
He speaks
about environmental gradients and the genetic and physiological basis of local adaptation
and how his team and collaborators have chosen switchgrass (Panicum virgatum)
as the “worst ever model species” (outcrossing, long cycle, perennial, really
tall, large genome). He shows a figure correlating switchgrass latitude of
collection point (X) and days to flowering (Y), taken from https://www.jstor.org/stable/10.1086/675760.
By using outbred mapping populations and cloning plants in a latitudinal
gradient in the US they are now studying QTL X environment interaction (https://www.pnas.org/content/116/26/12933)
and puzzling rust resistance phenotypes.
Megan Korte, U Groningen
She talks about her PhD work on facilitation (positive species
interaction) as a driver of within population variation in Brachypodium.
She finds that nurse shrubs modify the microclimate and affect the abundance of
brachy plants that she’s genotyping.
Pedro Rey, U Jaén
He talks about his work about the influence of leaf functional trait
variation on the response to insect herbivory in the B. distachyon
species complex. Grasshoppers are the main invertebrate herbivorous. In their
experiments they observe natural variation across populations in their
tolerance to insects which appear genetic-based, not geographical, with B.
stacei being less tolerant than the other two species.
Xavier Picó, Estación
Biológica Doñana-CSIC
He talks about the value of regional collections of natural populations
to unravel the ecological and genetic basis of adaptive variation in Arabidopsis
thaliana on their sampled population in Iberia and Morocco. They have done
natural transplant experiments to show that Northern populations can adapt to
warmer southern conditions (https://www.ncbi.nlm.nih.gov/pubmed/29947421).
He insists on the idea that increasing sampling efforts is required to detect
adaptative alleles which are geographically localized. In his experience min T
is the key variable explaining natural variation.
Agnieszka Gladala-Kostarz, Aberystwyth U
She talks on her work assessing the impact of wind stress/mechanical
stimulation on the growth and composition of B. distachyon stems. This
response is mediated in part by pectin methylase activity and saccharification.
She carried out her work with two contrasting ecotypes.
Luis Mur, Aberystwyth U
He describes recent collaborative efforts (Harmonia7) to analyze the genetic, epigenetic and metabolomic differentiation of Turkish B. distachyon accessions into two geographically distinct populations. Their main finding is that genotypes from separate regions have specific responses. By analyzing RNAseq data they conclude that epialleles affect expression; he explains the VRN1 locus as an example to show that SNP variation correlates with CpG variation. His main message is that genetic, epigenetic and metabolomics variation seems to be linked in two populations.
Session:
Adaptation to abiotic and biotic constrains
Borjana Arsova,
Julich
She talks on the dynamic patterns of root nutrient
uptake (N, P, Zn) as observed using non-invasive phenotyping, molecular
approaches and beneficial microbes, which her group has started to publish at https://www.ncbi.nlm.nih.gov/pubmed/31127613.
In conditions with limited N they observe brachy plants grow better when
controlled amounts of growth-promoting bacteria are added. She also shows very
nice root images of the beneficial barley fungal endophyte Sebacina
vermifera.
Yusuke Kouzai, RIKEN, Japan
He works on B. distachyon sheath blight pathogen, Rhizoctonia
solani. His results, including transcriptomics on Bd3-1 and Tek-3 ecotypes,
suggest that activation of WRKY-dependent immunity facilitates native
resistance. He looks for dynamically expressed genes (DYGs, defined in terms of
i) RPM > 5 and ii) RPM ratio max/min > 2) during infection. The WRKY
genes are downstream of salicylic acid signaling and were characterized as hubs
in those genotypes but not in Bd21. The compute pathogen biomass with qPCR.
Macarena Mellado-Sanchez, U Hertfordshire
She talks about the SNF2 family of chromatin remodelers, which are conserved
in B. distachyon, rice and A.
thaliana. She has done transcriptome analysis to monitor the expression
levels of family genes in a variety of tissues and has observed that most of
them are involved in the response to
combinatorial abiotic stresses.
Emma Aronson, UC Riverside, USA
She talks about B. distachyon and B. hybridum root,
rhizosphere and bulk soil bacterial communities differ between native (where
they mix with other species) and invaded ranges (where they seem to colonize
whole hillsides, as in CA, USA). She shows PCA plots indicating that bulk soil
and rhizospheres retrieve different root microbiomes. She shows the native
microbiomes of Bdis and Bhyb are similar (but apparently more different between
them than with respect to Bromus if I got that correctly). She also
shows data that suggests microbiomes can change substantially in successive years.
Rajiv Kumar Tripathi, McGill U
He describes his unpublished work on the molecular characterization of
SPL/miR156, a regulator of 10 BdSBP genes (out of 18). He has done computational,
transcriptomic and molecular biology work with mutants.
Marlon De la Peña
Cuao, U País Vasco
His work is on using B. distachyon as a model to study ammonium
assimilation, nutrition and stress in cereals. He chooses a 2.5mM [NH4] in his
experiments and observes changes in the expression of enzymes involved in Met
biosynthesis. He then did a large-scale hydroponic experiment with 52 ecotypes
and found significant variability drove ongoing transcriptomic experiments to
see differences in expressed genes.
Session:
Crop and biomass crop translation
Klaus
Mayer
His talk “From genome to
genomes. Charting the genome landscape(s) of western civilization” starts by
reminding the domestication of wheat and barley on the fertile crescent. Why has
the wheat assembly taken so long? Complete wheat LTR are 8-20Kb, compared to
300b of Alu repeats. The genome of B. distachyon in 2010 was a major
step forward due to the synteny, followed by barley a couple of years later,
paving the way to genome zippers (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101540).
He also mentions the breakthrough of DeNovoMAGIC2.0 to assemble wheat with a
combination of sequencing libraries with different insert sizes and
complementary data. He mentions the ongoing pangenome work and discusses
findings the modern (war) history captured in the wheat genome diversity
explored at https://www.nature.com/articles/s41588-019-0393-z
Manuel Becana,
EEAD-CSIC, Zaragoza
He takes on a nice review around hemoglobins of vascular plants both in
model plants and crops. He starts with rhizobia and legumes, then moves to Frankia
and actinorhiza species such as Alnus. Finally he presents non-symbiotic
hemoglobins, which actually likely are the evolutionary precursors of the
former. He concludes by showing recent results showing that monocots, including
B. distachyon, have two copies of class 1 hemoglobines.
Miguel Alfonso-Lozano,
EEAD-CSIC, Zaragoza
He talks about his work on the functional analysis of fatty acid
elongase TaFAE1 gene from biofuel feedstock pennycress (Thlaspi arvense).
Their results reveal differences in seed-oil biosynthesis among Brassicaceae.
Ernesto Igartua,
EEAD-CSIC, Zaragoza
Diversification of cultivated barley and selection footprints in the
landraces of the Iberian Peninsula. He presents recently published work on environmental
adaptation of landraces (https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15009)
from the Spanish barley core collection at http://www.eead.csic.es/barley . He
shows plots that support that Temperature-related variables are the best to explain
the population stratification on the landraces. 23 regions associated to env
variables are now being further dissected within an exome capture panel of over
70 lines. Finally, he shows the allele frequencies on major flowering control
genes that separate the landraces subpopulations (PpdH1-2, VrnH1-3,Btr).
Aurora Díaz, CITA, Zaragoza
She talks about developing a molecular passport for a new Zea
weed emerged in the maize fields of Huesca and Lleida in Spain, which is molecularly
related to teosinte (ssp. mexicana and parviglumis). Her results shows that
more work and data are required to fully disentangle the evolutionary origins
of this weed.
Thomas Girin, INRA Versailles
His talk is about using B. distachyon Bd21-3 to do fundamental
research on ways to improve N Use Efficiency in cereals, so that farmers can
reduce the amount of fertilizers. He shows results on tillering stimulation
with NO3 addition and explains that brachy plants keeps producing tillers even
after flowering, unlike barley and wheat.
John Vogel, JGI & UC Berkeley
His talk “More, more, more, the genus Brachypodium
as a sequence-enabled functional genomics model” starts by inviting everyone
one to use JGI facilities (20% of current 1K users are from EU). He goes on to
list the upcoming sequence resources. He singles out the Bd1-1 assembly, with
99.96% of the sequences in 16 contigs and the highest BUSCO score for a diploid
at JGI.
He then moves on to discuss the implications
of PAV for polyploids and how he and collaborators are trying to analyze that
with B. hybridum, Bdis and Bsta. He mentions software polyCRACKER which
can be used to separate subgenomes in polyploids with no prior knowledge, based
on K-mer composition (https://www.biorxiv.org/content/10.1101/484832v2),
which was used to annotate and track transposable elements before and after the
hybridization. The PAV pattern in Bhyb is comparable to some Bdis lines.
Finally he talks about his recent efforts to develop model lab
microbiomes (http://eco-fab.org) which would
help produce reproducible microbiome research, as long the microbes that you want to mix
can be grown in the lab (he quotes about 80% for plant-associated bacteria).
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