notes on 1st Spanish Simposium on Physiology & Cereal Breeding (I)

These are my notes on  the first day of the 1st Spanish Simposium on Physiology & Cereal Breeding:

http://networks.iamz.ciheam.org/cerealsnetwork/en/summaries.html

AM Casas

Cereals are the most critical elements of food security, and future gains will be mostly genetic, as agriculture must be made more sustainable and less dependent on fertilizers and resources. She acknowledges main organizer Gustavo Slafer, who unexpectedly could not attend today.

Octavi Quintana, PRIMA foundation

PRIMA (http://www.prima4med.org) is a private foundation funded by 19 countries around the Mediterranean with long-term goals related to farming structure, water provision and food chain value, avoiding research fragmentation, aiming at projects with budget > 1M€ and supporting critical mass. They have a budget for funding calls in the next 6 years, with an emphasis on innovation and solving taxpayer problems. At least 1N & 1S non-European country must be involved in every proposals. Current stage 1 success rate of the 2018 call is 8%.

Ernesto Igartua, EEAD-CSIC

Talks about winter and spring cultivars, and their responses to T and daylength. Vernalization is the period of exposure to low T, which is essential for normal flowering of winters. Spring alleles are usually dominant. The divide between winter and spring is a simplification.  Neolithic cereals were exported from the Fertile Crescent to W Europe in two routes: i) continental; ii) Mediterranean basin.

Redundancy analysis of Spanish barley landraces and a collection of agroclimatic variables suggests that 1^st temperature and 2^nd waterfall/water balance explain most of the genotypic variance. Sorting of barley landraces matches different allelic combinations in flowering/vernalization genes (Vrn1, Ppdh1, Ppdh2), which actually cover a continuous gradient of vernalization and have an effect on yield.

Helga Ochagavia, Univ. Lleida

She talks about field experiments on bread wheat earliness, looking at three developmental phases. By comparing to published results, produced in the UK, she concludes that there is interaction between the genes underlying her loci and temperature. She describes results published at https://www.sciencedirect.com/science/article/pii/S0378429017305099.

Rubén Vicente, IRNASA-CSIC

Talks about plant responses to elevated [CO2] and cites durum wheat results from https://www.ncbi.nlm.nih.gov/pubmed/28827159. The used a gradient of 330 to 700ppm inside a glass house and perform a RNAseq experiment on flag leafs (http://msue.anr.msu.edu/news/flag_leaf_emergence_in_winter_wheat). They use MapMan to map DE genes to metabolism (http://mapman.gabipd.org/es/mapmanstore). They observe that sugar metabolism is enhanced but at the cost of reducing N and C compounds. They also see a decrease on photosynthesis with elevated T.

Pilar Testillano, CIB-CSIC

Talks about stress-induced embryogenesis and double-haploids. In barley cold is an inducer, and they have reported that autophagy is triggered in those conditions. She mentions a recently published article (https://www.ncbi.nlm.nih.gov/pubmed/29309624), where they check that the use of autophagy inhibitors and demethylating compounds improves embryogenesis in barley.

Priyanka Basavaraddi, Univ. Lleida

She present her PhD work on the study of fine-grain Earliness Per Se (EPS) genes in wheat adaptation. She is doing field experiments in last and current season in Lleida.

Arantxa Monteagudo, EEAD-CSIC

She presents her PhD results on the effect of light quality on barley. She observes that development of plants grown with metal halide bulbs is faster when compared to plants grown under standard incandescence bulbs.

Alejandro Pérez de Luque, IFAPA

Talks about plant symbiosis with microbial, particularly mycorrhiza and rhizobia, with recently published results (https://www.nature.com/articles/s41598-017-16697-4). He describes two wheat genotypes (Mercato, Avalon) which have a significantly different mycorrzhizal/rhizobia colonization competence and mentions that up to 20% of phtosynthates are exuded into the rhizosphere by the plant.

Bruno Contreras Moreira, EEAD-CSIC & ARAID

I talked about our recent work on the exploration of the pan-genome of Brachypodium distachyon and barley, with results from these papers: 

https://www.nature.com/articles/s41467-017-02292-8,  

https://www.frontiersin.org/articles/10.3389/fpls.2017.00184/full, 

https://dl.sciencesocieties.org/publications/tpg/abstracts/9/2/plantgenome2015.10.0101

Thorsten Schnurbusch, IPK-Germany

His keynote is about enhancing the yield potential of wheat by exploring spikelet architecture and grain number. Mentions that previous work (https://link.springer.com/chapter/10.1007/978-94-009-3131-2_10) has shown that in development of spike the number of spikelets is fixed, so it must be that floret fertility accounts for differences in grain number. However, they only find weak association between grain yield potential and grain number. He shows data suggesting that detillering does not increase grain number at harvest (https://www.ncbi.nlm.nih.gov/pubmed/26157170). Yet another recent paper studied the effect of ovary size of distal florets (F4 and beyond) on grain yield (https://www.ncbi.nlm.nih.gov/pubmed/25821074). He shows unpublished data on wheat lines with variable floret fertility (up to 6 florets per spikelet) and a QTL on chr 2A containing newly annotated gene GNI1, likely a floret inhibitor. His historical data shows that this gene has been selected for since 2000 in Germany. He shows data showing a 10-30% grain yield increase in field experiments. However, a strong source capacity is required to fill the gained grains.

These talks were followed by a round of flash poster summaries. Here's Carlos P Cantalapiedra talking about K-mer analysis of exome capture mapped reads in barley: https://github.com/eead-csic-compbio/kmeleon

final notes on EUCARPIA Cereals meeting (III)

Wednesday 21^st march 2018 (Spring)

Tatsuya IKEDA (NARO, Japan)

Starts by showing allelic variation in glutenin subunits, which form large complexes connected by SS-bonds. Different alleles (A1,B1,D1 & A3,B3,D3) produce different gluten networks, which are reflected on bread body and loaf volume. Combinations of glutenin alleles control dough quality. He refers to results published at http://dx.doi.org/10.1094/CCHEM-01-14-0009-R. He explains the http://www.wheatinitiative.org, which aims at improving wheat quality and safety and to integrate a research platform with shared materials and gene nomenclature (he shows examples of gene name searches in Ensembl Plants with no results due to lack of naming consensus). They already released glutenin master sets at CIMMYT Germplasm Bank. Starch/amylose content is also important for quality. Then he talks about safety and describes Fusarium toxin analysis.

Sebastian MICHEL (U Vienna, Austria)

His talk is about genomic selection for wheat breeding, aiming at simultaneous selection for grain yield and baking quality. He shows data showing a strong anti-correlation between yield and protein content (typical range 12-16%), which is clearly important for quality and trading. Therefore, they focus on outliers with high protein content. The develop yield and protein indexes, which allow selection of lines with excellent yield and good protein content, and lines with high-protein and acceptable yield, respectively.

Suong CU (Flinders U, Australia)

She talks about GWAS of Zn, Fe, Cu, Mn and P in wheat grain and rachis at two developmental stages with a bio-fortification perspective. She mentions partners CIMMYT and http://www.harvestplus.org. The calculate heritability of the uptake of those micronutrients and their correlation in mature grain and in the rachis, end they were low despite the experiments were done with fertilizer contributing enough of these. They perform GWAS correcting by Kinship and covariates and shows associated markers with most additive value. She shows some candidate genes and for Zn, for instance, there is one transporter and another annotated as a Zinc-finger.

Simon GRIFFITHS (JIC, UK)

His talk is about analysis of arabinoxylan (AX) soluble fibre in wheat grain. He mentions that in the UK there have been spectacular yield gains since 1885, but that nutritional quality has never been a breeding target until now. He focuses on fibre intake and fibre content in bread in the UK and explains that AX is the main fibre component of wheat grain endosperm, and is also part of the bran. He mentions that project https://healthgrain.org was concerned about genetic resources for improving wheat nutritional value. Shows that AX content is highly heritable. They have prepared populations with Yumai34 parent to discover QTLs for AX and found one. He explains that AX enrichment does not affect breadmaking functionality.

Peter ROGOWSKY (INRA Lyon, France)

Delivers a general lecture about CRISPR-Cas9 systems in breeding plants. Starts by explaining cellular DNA repair mechanism. The current success of Cas9 is that predicting RNA/DNA is much easier and reliable than protein-DNA binding. Stable transformation of Cas9 can be done with Agrobacterium, direct transfer (explants, protoplasts) or virus. Transient expression can be obtained by direct transfer of ribonucleoproteins. All these have been used successfully in wheat, with the bottleneck being generally plant regeneration after transformation. PAM-altered Cas9 have not yet been ported to plants, so targets must have a neighbor NGG site. Another option is to use CPF1, which recognizes TTTN sites.

Mutation and base edition have been mastered in plants, with frequencies less than 10%; gene editing still has frequencies below 1% in plants. However, currently genes can be edited by stacking base editions to modify coding sequences or promoters, when expression is important for the trait of interest. 

He also presents recent examples of gene inactivation in different crops, both monocot and dicot, still to be tested in the field, with the SDN1 (site directed nuclease) approach. He explains that Cas9 approaches are expect to have even more applications in terms of agronomic and quality traits. However, regulation is still not clearly defined for Cas9 editions at the EU (decision expected in 2018 by the European Court of Justice). He explains that this technique faces different ethical questions and their answers should be delivered case by case. He finishes with a table of promises/claims of Cas9 and the reality in 2018; this tech is still a long way from having an impact in the field and the EU market.

Fred VAN EEUWIJK (Wageningen U, Netherlands)

Presents methods for modelling genotype by environment (GxE) interactions in QTL mapping and genomic prediction, with applications to barley and wheat. How can we reduce the computing time of computing a linear mixed model per SNP when you have 10E5-E7 SNPs? With packages such as TASSEL P3D, GRAMMAR, FaST-LMM. He seems to prefer linear mixed models to Bayesian choices, as they are easier to customize. For multi-trait / environment modelling, he refers to https://dl.sciencesocieties.org/publications/cs/abstracts/56/5/2119 and this book: http://www.springer.com/gp/book/9783319205618. Fitting these multi models requires reducing the original complexity of the data. He mentions Haploview to merge SNPs in the same gene to build haplotypes/alleles and test them instead of individual SNPs. Finally, he mentiones that a software tool with their latest developments as part of the WHEALBI consortium will be available at the end of the year, and there will be training courses, but the modules will be available in CRAN as R packages (https://cran.r-project.org).

Andreas HUND (ETH Zürich, Switzerland)

Talks about GxE and modern field phenotyping techniques. He mentions that in the Swiss central plateau wheat yield (target 6-7T/ha) is limited by excess water, frost and then heat stress. They have set up all year round platform for phenotyping wheat. He shows canopy cover, height and senescence/reflectance data for winter wheat. They calculate heritabilities for their traits and obtain high values (H2>0.9) except for the duration of developmental stages. He shows data from a couple of papers (http://www.publish.csiro.au/fp/fp14226 and https://link.springer.com/article/10.1007/s10681-017-1940-2) showing, for instance, that earliest genotypes are not necessarily the tallest in terms of final height.

Friedrich LONGIN (U Hohenheim, Germany)

Just after lunch, he talks about genomic selection (GS) schemes for line breeding in wheat, are they really worth it? His simulation data suggest that direct phenotypic selection can yield higher genetic gain, but GS yield higher gains per year while having less plant material in the field. These trends depend on the GS accuracy, but with realistic values of 0.6 there seems to be a 16% annual gain advantage for GS if breeding cycle is sped up.

Daniela BUSTOS-KORTS (Wageningen U, Netherlands)

She talks about combining crop growth and statistical genetic modelling to evaluate phenotyping strategies, and shows wheat data. Genotyping is much cheaper than phenotyping, and she evaluates alternative phenotyping strategies with simulations, inspired by http://www.publish.csiro.au/cp/cp14007. She shows drought patterns observed in the Australia wheat belt, published in https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.12192.

Renaud RINCENT (INRA GDEC, France)

His talk is about genomic prediction of GxE interactions by coupling genetic and physiological modelling. He summarizes the challenges and opportunities of GxE in breeding and uses data grain yield from https://breedwheat.fr. His results indicate that considering GxE when doing phenotyping predictions provides more accurate models than simple models with no interaction. His AMMI model, which computed PCA on the residuals of the principal model, seemed promising but the gains were lost in the cross-validations, likely due to small dataset or to weak GxE in the data.

Philipp BOEVEN (Limagrain, France)

His talk discusses ways of breeding for favorable male floral traits, such as anther extrusion, in hybrid wheat. After GWAS he made BLUP genomic predictions (I had to read what Best Linear Unbiased Prediction is, a widely used genomic prediction method, at: https://www.ncbi.nlm.nih.gov/pubmed/23640517).

Funmi LADEJOBI (NIAB, UK)

The last talk of the meeting is about differentially penalized regressions, a modification of BLUP, which improve genomic prediction of wheat flowering time. She uses rrBLUP R package, documented at https://cran.r-project.org/web/packages/rrBLUP/index.html.

notes on EUCARPIA Cereals meeting 2018 (II)

Tuesday 20th March 2018

John FOULKES (U Nottingham, UK & CIMMYT collaborators)

Talks about genetic diversity and resource efficiency in wheat. Genetic gains in yield potential over the last decades has increased 0.5-1% per yr, now it is slowing down. Biomass acounts for a large part of that potential, while harvest index (HI, http://plantsinaction.science.uq.edu.au/content/641-harvest-index) is following an inverse trend. Therefore, we are not taking the full benefit of the genetic gains. Data from field assays indicates that the 2^nd internode that is competing with spike growth. He reckons that HI values of 0.6 are likely.

Then he moves on to N fertilization and the WISP project (http://www.wheatisp.org/Consortium/WISP.php), and shows some results about diversity on N uptake and also about photosynthetic efficiency published last year by Gaju et al,  https://www.sciencedirect.com/science/article/pii/S0378429016301022.

Finally, he summarizes experiments on root phenomics (shovelomics, extracting top 20 cm of crown root, see http://plantscience.psu.edu/research/labs/roots/methods/field/shovelomics) with the aim of redesigning root architecture. Using a Rialto x Savanah population, they discovered a great deal of variation in the root traits they were tracking. They also found correlation between root angle and root length under rain-fed conditions. They plan to set up a TILLING experiment to validate candidate genes. He shows nice images of root cuts of irrigated and non-irrigated plants that they’re using to train machine learning algorithms for image analysis.

 

Bruno CONTRERAS-MOREIRA (EEAD-CSIC, Spain)

That’s me. I talked about a series of experiments with pooled barleys designed with the aim of testing the agronomic advantage of the presence of flowering control gene PpdH2 in winter barleys proven through a natural selection approach. I took the chance to present the PpdH2 gene as ana accessory gene in the pan-genome context, using the terminology we have used in our papers (barley and A.thaliana & Brachypodium distachyon). I got questions by Frank Ordon and Simon Griffith: i) the number of seeds used to build the pools, and ii) could plant competition explain the results.

Gaëtan TOUZY (Arvalis, France)

He talks about his project on “Improving Water Use Efficiency in Bread Wheat by Multi-trait multi-Environment Genome-Wide Association Studies”.

Eric OBER (NIAB, UK)

The title of his talk is “Implementing large-scale field phenotyping in genomic selection to accelerate wheat breeding” which reports results of project GplusE (http://gtr.rcuk.ac.uk/projects?ref=BB%2FL022141%2F1). They do visual scoring plus drone and manned flight hyperspectral camera shots. They build Bayesian networks with a few traits and yield. They use data from a few years to predict phenotype (yield) with some success, but with different accuracies among sites and years. Average prediction is safer than predicting the best/worst performer genotypes. Best traits are hyperspectral data, development trains and late-measurements data.

Kerstin NEUMANN (IPK, Germany)

She talks about barley phenotyping at IPK, particularly about using high-throughput image analysis to study stress-adaptive and constitutive biomass QTLs in cereals. She shows data and results of spring barleys, published at https://www.ncbi.nlm.nih.gov/labs/articles/28797222, and winter wheats.

Ulrike LOHWASSER (IPK, Germany)

Her talk is about “Searching for Frost Tolerance in Wheat – A genome wide association study”. Frost tolerance is a complex trait, which involves winter survival, desiccation, anoxia, ice-encasement and even disease resistance. Heritability for frost tolerance is low in most locations when field trails are carried out in cold winters, but it is high in controlled conditions.

Heribert HIRT (KAUST, Saudia Arabia)

He talks about beneficial microbial endophytes to enhance abiotic stress tolerance and yield. He works mostly with Arabidopsis and is interested on plants living in deserts as part of project DARWIN 21 (http://www.darwin21.net). The do trials of Arabidopsis, but also wheat, barley, alfalfa and confirm beneficial effects under stress but not in normal conditions. In A. thaliana they actually observe that inoculation changes the stress response of the plant. They also did experiments to mimic microbial inoculation by adding external chemicals in A. thaliana. He shows data for one of their endophytes, Enterobacter spp. SA187, which was found in both monocot and dicot plants. They have no evidence of crop-specific strains, because they looked for generalists.

Ewen MULLINS (Teagasc, Ireland)

He talks about the impact (-30% in the last couple of years) of Septoria tritici blotch (STB) disease in wheat. They are carrying out intensive field phenotyping to support breeding of resistant lines. They did fungicide-free trials in Ireland and the UK, visually scoring plants, and concluded that different wheat genotypes have different latency periods. However, eventually disease progresses in all of them (https://onlinelibrary.wiley.com/doi/abs/10.1111/ppa.12780), so it would seem that a reasonable breeding target might be further extending the latency period.

Yvan MOËNNE-LOCCOZ (U Lyon, France)

Talks about interactions of plant-beneficial rhizosphere bacteria in cereals. Can breeding benefit from microbiome-based approaches? Does the plant genotype matter? Have modern cultivars lost their microbial partners? They have performed 16S rRNA scans of rhizosphere below different crops and wild plant species such as teosinte. They have data that suggest that some modern lines conserve the ability to interact with inoculated bacteria; others do not, perhaps for being counter-selected. They have used Pseudomonas kilonensis F113 to test root colonization in a panel of wheat cultivars and see that modern cultivars are relatively less colonized than old or landraces. He also mentions Azospirillum brasilense Sp245, which stimulates root growth by producing hormone IAA. He has a number of publications on these topics listed at https://scholar.google.fr/citations?hl=fr&user=rF48UsAAAAAJ.

Laetitia WILLOCQUET (INRA, France)

She talks about phenotyping methods for quantitative host plant resistance using simulation modelling and ROC curves. She reports results published at https://www.sciencedirect.com/science/article/pii/S1360138517300237. Phenotyping is now the bottleneck for breeding resistance. Nonetheless, data was produced to feed models of infection and resistance, estimate parameters and make predictions. Details on these simulation models can be found at this document published in 2014: https://goo.gl/VQpqK7

Hermann BUERSTMAYR (BOKU, Austria)

Genomics assisted improvement of Fusarium head blight resistance in bread wheat, durum wheat and triticale

Javier SANCHEZ-MARTIN (U Zürich, Switzerland)

His talk is about performing GWAS to reveal race-specific resistance genes to powdery mildew in wheats from the WHEALBI project (http://www.whealbi.eu). As in related talks, he discusses how exome capture platforms present mapping problems when aligning genes absent from the reference genome. He has published part of these results in 2016:  https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1082-1

Pierre-Antoine PRECIGOUT (U Paris-Saclay, France)

Pierre presents numerical, epidemiological models of foliar fungal pathogens in wheat, which have been described in detailed at https://www.ncbi.nlm.nih.gov/pubmed/28453406 . These model the latent period to predict potential evolutionary directions.