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.