job offer MMT24-EEAD-01-01 "High resolution agroclimatic variables for field trials and adaptation of cereal crops (CLIMACER)"

[see PD18092024 below]

Program: https://momentum.csic.es

Project: High resolution agroclimatic variables for field trials and adaptation
of cereal crops (CLIMACER)

Location: Zaragoza, Aragón, Spain (Estación Experimental de Aula Dei-CSIC)

Principal Investigators:

• Bruno Contreras Moreira (Computational and Structural Biology , GitHub, bcontreras at eead.csic.es , +34 976716089) 
• Santiago Beguería (Erosion and Soil and Water Evaluation , GitHub, sbegueria at eead.csic.es, +34 976716158)

PROJECT SUMMARY
Understanding how crops respond and adapt to climate change is critical to ensuring food security and agricultural sustainability. Despite the existence of climatic data repositories, it is still challenging to calculate agroclimatic variables appropriate to the phenology of each crop, such as days of vernalization of winter cereal crops. This hinders the development of effective adaptation strategies. CLIMACER project addresses these limitations with two objectives. The first consists on developing open source tools for customized calculation of high-resolution agroclimatic indices based on public data, which will be used in two case studies of genotype-environment association with barley and Sinapis alba populations sequenced in previous projects. The second is to compile a FAIR database that will aggregate cereal trial data from the GENVCE network along with agroclimatic indices for diverse trial locations. 

Distribution of 4 barley subpopulations in mainland Spain, from https://doi.org/10.1111/mec.15009.

Tech and scientific fields: Climate change and biodiversity, platform of climate services, high-throughput data processing, data integration and analysis, computational biology 

PROFESSIONAL PROFILE

Minimum requirements:

• Fluency in Spanish and English.
•  Science university degree (computer science, biology, biochemistry, maths, physics, …).
• Programming ans scripting languages.

Other skills to be considered:

• R and/or Python programming skills.
•  Software development skills (API creation, source code repositories, etc).
•  Document digitalization skills (OCR).
•  Database management and/or data science skills.
•  Bioinformatics and/or geo-information science skills.

WHAT WE OFFER
A training program will be customized for the hired person, with two alternative paths: a) enrolling on a Master’s program; or, b) attending courses on scripting, bioinformatics, computer programming and data science. We also plan for the hired person to c) attend conferences on climatology, geoscience and genomics, d) organize a workshop in collaboration with CIHEAM Zaragoza to teach how to use the resulting API and d) to take part in research secondments for training in diverse national and international labs from 2025 to 2027.

Contract conditions
Indefinite contract for a University Graduate associated with the Momentum Project of 4 years' duration according to Spanish science law. Gross annual salary (37.000 € - 41.000 €).
Start of contract: before 31 December 2024
 

Application instructions and help

• https://momentum.csic.es
  
• Register and upload your qualifications at https://sede.csic.gob.es/tramites/bolsa-de-trabajo by September 20th 27th
• Titulado Superior FC1 / University Graduate FC1 (Out-of-Agreement Labour Exchange).
• Choose at least one of the following areas and topics/ámbitos:
  
• 8903 Recursos Naturales: Procesos de la geohidrosfera, Ejes transversales: Cambio Global, Biología de Organismos y Sistemas: Bioinformática
• 8905 Ciencia y Tecnologías Físicas: Sistemas Complejos, Informática, Tecnologías de la Información y Comunicaciones 
• Select our research center "Estación Experimental de Aula Dei (EEAD-CSIC)"
  
• Please pay attention to requirements of foreign degrees.
  
• The status of candidates at the bolsa is updated weekly or even less prequently in August.
  
• Questions to: momentum at csic.es or the PIs

 

We will update this post as more information becomes available. 

PD18092024: hemos comprobado que en la aplicación de la bolsa es posible seleccionar dos áreas, así que podéis apuntaros a otras áreas, por ejemplo "8905 Ciencia y Tecnologías Físicas", y ámbitos como Sistemas Complejos, Informática o Tecnologías de la Información y Comunicaciones

 

My notes on Plant Biology Europe 2023 at Marseille

Hi, in this and following posts I will be sharing my notes of the sessions of the Plant Biology Europe 2023 at Marseille: https://europlantbiology2023.org

day2 day3 day4

Note: access here the slides of the "Learning to build and interrogate the pangenome of Brachypodium distachyon" talk.

03072023 

Uncovering the hidden half of plants: discovering novel ways roots sense and adapt to heterogeneous environments. Malcolm Bennet.

Talks about xerobranching (https://pubmed.ncbi.nlm.nih.gov/30270188), a mechanism to control root branching in water-deprived soil layers. This is initially controlled by phloem-produced ABA [compamion cells] that travels to the root and triggers an auxin response in the epidermis [plasmodesmata] (https://doi.org/10.1126/science.add3771). They have used air-gap experiments to show this is conserved across angiosperms.

In the 2^nd part of the talk he talks about how soil compaction inhibits root growth and produces actually wider roots. However, in mutants unsensitive to ethylene, roots can actually overcome compaction. It seems that growth arrest is actually an ethylene response. Plants sense compaction by gauging gaseous ethylene diffusion in the soil (root radar signal). He is asked whether growing through compact soil actually damages the root. His answer is that natural variability suggests that damage is not the main driver or these mechanisms.

He goes on to stress we need to consider plant + soil + microbes to answer any root questions, so we should all talk to soil and microbe scientists.

 

A central role of root symbionts: the plant response to environmental stresses. Raffaella Balestrini.

Explains how strigogalactones produce by the root trigger the fungus infection during mycorrhiza establishment. Transcriptional landscape changes before -> after, revealing that [plant, fungus]  redundant transcripts encoding P-transporters ate upregulated. She shows experiments with Lotus japonica + Gigaspora. She moves to explain that AM symbiosis increases drought resilience, but it’s a process we still know little about, as responses depend on genotype interactions. She mentions https://doi.org/10.1126/science.aaz5192 and https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18281. She explains that infection in tomato affects also stomata density.

They are now working in a consortium that will produce tomato seeds coated with priming chemicals [including salicylic acid, which affect spore germination] and fungal spores to maximize stress resilience of adult plants.  She mentions https://doi.org/10.1016/j.tplants.2022.06.004 .

 

Fusing genome simulation and crop models for computer-aided breeding in future environments – Arnaud DESBIEZ-PIAT

Talks about training genomic prediction models with 10-cross validation as part of a virtual breeding platform. They get the genotypes ranked correctly, but has a 3d biass in anthesis date. Explores the effect of simulated and real recombination and models (rrBLUP vs Bayes) on the correlation of traits. He says that automatic phenotyping of germination rates is very hard. The goal is to keep genetic gain > errors.

Pervasive Under-Dominance in Gene Expression Underlying Emergent Growth Trajectories in Arabidopsis thaliana Hybrids– Wei YUAN

As Daniela Ristova, uses Biorender.com to make summaries. In her experiments comparing F1 hybrids to inbreds she finds less additive genes than dominant ones [hybrids have larger rosette areas]. She finds that promoters with more rare alleles have lower expression [allele freq as a proxy of deleteriousness], with hybrids with less rare alleles performing best. Paper soon out in Genome Biol?

Reconsidering photoperiod-sensitivity (PS) for maize adaption to climate change– Justine DROUAULT

Hypothesis: tropical maize could be re-introduced into temperate maize to increase adaptation in the face of climate change. She shows that selection towards PS indirectly selected also for other traits, such as plant height, etc. She classifies haplotypes according to their PS. She finds that tropical genotypes can reduce thermal time to flowering, but effect depends on background genotype.

Plasticity of root permeability for nutrient acquisition. Marie Barberon.

She explains the plastic role of suberin diffusion barrier in the root, citing https://www.pnas.org/doi/10.1073/pnas.2101730118.  A set of at least 4 MYB factors control (ectopic) suberization: 41,53,92,93. They cannot do single-cell as they cannot produce viable protoplasts of their root cells.

Polygenic selection and the evolution of gene expression in Arabidopsis Iyrata. Juliette de Meaux.

Inspiring talk on how her group is taking advantage of the Arabidopsis genomes (thaliana, halleri and lyrata) to study gene dominance. She starts by explaining that most genetic variance is deleterious and probably cannot be removed due to drift and the inability of selection to eliminate it. She shows that genes that show dominance display less Ks (more constrained) and that, conversely, additive genes, with smaller phenotypic effects, show larger Ks values (https://europepmc.org/article/ppr/ppr453330). She refers to https://www.nature.com/articles/s41467-021-23558-2, where they compare sterile hybrids of those species to classify cis variation. In outlokk, she favors future focus on many genes with small additive effect but large collective weight.

Changes in competitive ability over the course of durum wheat domestication are mediated by plant functional traits– Taïna LEMOINE

She studies Triticum monococcum, T. dicoccoides, T. turgidum landraces and T. turgidum elite varieties to measure their i) performance and ii) trait plasticity in the face of stress. She finds that domesticated materials performs better overall, but in terms of individual trait plasticity, wild material show larger variability, which suggests that breeding with a view of individual traits can still make gains from wild materials.

Horizontal gene transfer in Hordeum species– Marek SZECÓWKA

Hordeum species acquired DNA from panicoid sources via at least 9 events 5-1My ago. These lineages diverged 50Myr ago (https://pubmed.ncbi.nlm.nih.gov/33484020/). He asks how many accessory genes are from panicoids and what are their roles. So he chops Hordeum  genomes in 1Kb bits which are then mapped onto reference panicoid genomes, requiring at least 500b matches (BLASTN, 175b for BLASTX) and high % identity. He then requires >=70% identity and fragments >=5Kb for further analysis.  

They have also tracked panicoid TEs in Hordeum genomes and they seem to follow the segments and chromosomes previously shortlisted. They behave effectively as additional confirmation. They have built consensus panicoid TE library for this work.

---

Notes on Plant and Animal Genomes conference #PAG30 (V)

Wednesday 18012023

Oliver Ryder, San Diego Zoo Institute for Conservation Research. He talks about conservation genomics. For instance, he explains how the genomes of extinct species can be used to estimate genetic load and effective population size. On extant species, genome sequences can be used to estimate heterozygosity for instance (Californian condor > Andean condor). He then moves to technological possibilities to rescue/clone[nearly-]extinct species if we are able to crioperserve DNA and tissues. San Diego’s zoo has its own FrozenZoo for this.

Thomas Blein, Institute of Plant Sciences Paris-Saclay. MARS lncRNA regulates the coexpression of a gene cluster, recruits a TF to a promoter, controls a chromatin loop and coordinates epigenetically the expression of neighbor genes, in response to ABA: https://pubmed.ncbi.nlm.nih.gov/35150931 . You can read there that “The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways”.

Peijian Cao, China Tobacco Gene Research Center. Starts by presenting lncRNAs that encode small peptides (https://academic.oup.com/bib/article/20/5/1853/5047384, http://14.139.61.8/PlantPepDB/index.php). In his experiments they track the expression of lncRNAs in response to herbivores. They find that different lncRNAs coexpress with genes in the biosynthetic pathway to that produces JA. They also have evidence of encoded small peptides being produced upon binding to ribosomes. These peptides are as stable as common proteins.

Hikmet Budak, Montana BioAg Inc. Presents work on lncRNAs on different wheats to try and control pest insects.

Josephine Herbst, VIB-UGent Center for Plant Systems Biology.

Notes on Plant and Animal Genomes conference #PAG30 (IV)

Tuesday 17012023

Ian D Godwin, QAAFI, The University of Queensland. While he introduces sorghum, he recommends the book https://drunkenbotanist.com, which can be used for drinks, food and chicken fodder. In Australia it is grown in the driest area on the E. They are using gene editing to improve it and require high quality genomic resources, such as https://www.nature.com/articles/s41477-021-00925-x . They are particularly interested in high resolution PAV maps, as PAV is a main driver of diversity in this crop. Also they use a non-reference assembly for their work, although transformation still needs to be optimized.  They have selected their own promoters that also work well in barley and maize. They are using these to optimize may trais, mostly plant and root architecture, but also starch composition, which is naturally in a tight protein matrix that make it undigestible (https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13284). The plants have to be tested in the field, root reach the bottom of a pot in 10 days. The obtained lies with increased protein and larger grains. They have also tested them for poultry feeding, and observed that digestible, high protein content reduces the amount of soy-based fodder required by chicken. They further improved protein digestability by knocking out gamm-kapharin. He mentions that a VRN1 homolog in Sorghum controls root angle. In questions he says they are now introgressing their edited genes in parental lines used for Sorghum hybrids.

Viviane Slon, Tel Aviv University. She extracts ancient DNA from sediments. Previous work have extracted plant and animal DNA 400K yr old (permafrost). Such experiments allow to find out first/last appearance dates in sediments, which can be correlated to past biodiversity, history, climate change and human activity. A few weeks ago researchers have been able to go back 2M yr in Greenland. About 90% of the successfully extract DNA has no BLASTN hits. To improve yield they use mammalian mtDNA capture. What does differentiate ancient DNA from modern? It is shorter, C in single-stranded ends deaminate -> T (this is actually as a sanity check by counting nt substitution pero position). They are now able to extract hominid mtDNA from the soil even when there are no bones, as they have shown in the Denisova cave (https://www.nature.com/articles/s41586-021-03675-0). They have also managed to extract nuclear DNA in Galería de las estatuas, Atapuerca (https://www.science.org/doi/10.1126/science.abf1667) and distinguished two Neanthertal populations. What next? Her lab is now developing methods to improve field sampling, the wet lab and data analyses. With this toolbox we should be able to fill the gaps in the biodiversity history, particularly for plants. With high density sampling in sediment transects we should be able to estimate changes in allele frequencies with help from coalescent theory.

Samuel P. Hazen, University of Massachusetts Amherst. Talks about their experiments to find TFs that might be controlling cell wall thickening in Brachupodium distachyon., such as the bZIP named SWIZ. This is one among other TFS that are thigmotropic, relocating and locally expressing to the nucleous when the plant is touched/perturbed (this depends on calmodulin and Ca being released). Expression lasts about 1h.  They find that 7-9K genes are differentially expressed (DE) upon touching the plants and they have also discovered a couple of DNA motifs for SWIZ using ATAC-Seq analysis. They have also done de novo discovery of motifs upstream of DE genes. Adding external GA hormone represses movement to the nucleous. There’s a preprint at https://www.biorxiv.org/content/10.1101/2021.02.03.429573v2.abstract

Melissa Bredow, Department of Plant Pathology and Microbiology, Iowa State University. Frost is still an important stress for crops despite global warming. Freeze damage starts by seed ice crystal that end up piercing cell membranes. Gradual expose to cold expressed ice-binding proteins (IBP) that protect membranes upon freeze. She uses brachy as model to study the protection provided by IBPs. There are seven IBPs in B. distachyon (BdIRI1-7), none in A. thaliana. These protein are only stable < 4ºC (disordered otherwise) and theire folds are different across species. Apparently is not just cold what matters, but also bacterial (Xanthomonas, Pseudomonas sp) ice nucleation proteins that favour freeze and membrane destruction. Their current modela is that BdIRI proteins actually bind to bacterial nucleation proteins to inhibit their function.

Todd Blevins, Centre national de la recherche scientifique, University of Strasbourg. Studies the role of RNA polymerase IV in brachy, which silence transposons by transcribing non-coding RNAs that drive AGO-based silencing, as reviewed in https://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-093020-035446. Mutants of these genes (nrpd1) have reduced leaf elongation via regulation of cell production and via cell cycle exit. In addition, mutation causes higher expression of some genes, including bZIP TFs, which are silenced in the wild type. These have differentially methylated promoters. This varies across ecotyopes and depends on the presence/absence of a TE. They have screened methylated sequences with Illumina and Nanopore and found very comparable results, although ONT is superior when it comes to check individual TEs, as Illumina reads multimap.

Birkett Clay, USDA-ARS. Talks about integrating into https://breedbase.org Practical Haplotype Graphs built from exome data for wheat and barley. He uses code at https://github.com/TriticeaeToolbox/PHGv2 and imputation protocols at https://wheat.triticeaetoolbox.org/static_content/files/imputation.html. Imputation accuracy at the PHG in barley is > 93% if #markers > 2000. Details and converted VCF files are available at https://files.triticeaetoolbox.org . They display the resulting PHG with JBrowse (https://triticeaetoolbox.org/jbrowse). The PHG is built on a single reference genome, so you might need to select the appropriate reference to optimize imputation (or build a mosaic reference). Creating the PHG is computationally intensive, but the imputation is quite fast.

Karen A Sanguinet, Washington State University. She talks about buzz mutants that affect root biomass and hair formation in brachy. The A. thaliana ortholog rescue the mutant phenotype. She saw that BUZZ expression responds to N availability, although primary root growth is not N-responsive. It is expressed in the root epidermis.

Kapeel Chougule, Cold Spring Harbor Laboratory. Presents (PanOryza) efforts to consistently annotate gene models in the rice pangenome. Canonical isoforms are called with TRaCE (https://academic.oup.com/bioinformatics/article/38/1/261/6326792). At Gramene they have rice subsite and plan to build pan-gene indexes.

Andrew Olson, Cold Spring Harbor Laboratory. After a little history of the Gramene project (2022), he presents the pangenome sites (2021-22), which currently represent the larger bulk of new genes being added to Gramene (maize, rice, Vitis and Sorghum). He goes to summarize all the tasks involved in setting up and maintaining the sites, the import of data from Ensembl Plants (https://plants.ensembl.org) and Expression Atlas, and mentions they are now following the standards agreed at https://data.nal.usda.gov/ag-data-commons-collection-development-policy.

Sushma Naithani, Dept. of Botany and Plant Pathology, Oregon State University. She presents her work on curating plant reactome pathways using omic datasets (https://plantreactome.gramene.org). These pathways are linked to genes in Ensembl Plants and Gramene, which in turn often link to gene expression data. The curation protocols are illustrated at https://peerj.com/articles/11052. Currently they 126 species and 326 pathways, which have been project to 39K genes.

My turn. I presented our recent work "Building pangene sets from plant genome alignments confirms presence-absence variation", from the PanOryza project. The preprint can be read at https://www.biorxiv.org/content/10.1101/2023.01.03.520531v1 and code and documentation obtained here: https://github.com/Ensembl/plant-scripts/tree/master/pangenes.

[Source: Agata]  

Jonathan Cahn, HHMI-Cold Spring Harbor Laboratory. Talks about regulatory elements in maize inferred from diverse omics datasets (ie ChIP-seq, H3K4-me1) as part of http://www.maizecode.org, which follows ENCODE guidelines. Raw data can be downloaded, I cannot see the DNA motifs though. Superenhancers are delimited by methylated areas and enriched in H3K27ac and accumulate binding sites.The results of this project are described at https://www.frontiersin.org/articles/10.3389/fpls.2020.00289/full. Shows really nice plots made with https://cran.r-project.org/web/packages/ggalluvial

Sarah Dyer, EMBL-EBI. Talks summarizes the current status of the wheat pangenome at Ensembl Plants: https://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core. The main addition since last time I checked is that now wheat genes have a cultivar-based Compara section, where you can see orthology to genes in other pangenome wheats, ie: https://plants.ensembl.org/Triticum_aestivum/Gene/Strain_Compara_Tree?g=TraesCS3D02G273600;r=3D:379535906-379539827

Josh Clevenger, HudsonAlpha Institute for Biotechnology. https://www.hudsonalpha.org/khufudata/plant-improvement

On Twitter I heard about a talk I missed by Katie Jenike were she presented Panagram, K-mer based software for alignment-free visualization & analysis of pan-genomes. There’s code (https://github.com/kjenike/panagram) and even slideas at https://twitter.com/mike_schatz/status/1615440857980899328