10 de abril de 2018

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

My notes on the second and final day of the 1st Spanish Simposium on Physiology & Cereal Breeding: http://networks.iamz.ciheam.org/cerealsnetwork/en/summaries.html

Omar Vergara-Diaz, Univ.Barcelona
He presents preliminary results on yield predictive models in water stress and control conditions based on metabolite profiles of leaves and spikes of field-grown wheat inferred from hyperspectral readings. He has recently presented this results at http://adsabs.harvard.edu/abs/2017AGUFM.B51A1782V.

Shawn Kefauver, Univ. Barcelona & CIMMYT Africa
He talks about methods of proximal UVA phenotyping/scanning maize using complex image processing software (MosaicTool, a plugin for FIJI, see more at this presentation in Spanish: https://ruralcat.gencat.cat/documents/20181/68301/Aplicacions%20i%20reptes%20dels%20drons%20en%20el%20fenotipatge1508158117144). 

Inès Zouari, INAT, Tunisia
She presents results on drought stress impact on durum wheat. Her work involves the development and use of drought (susceptibility and tolerance) indices, which were evaluated to ascertain their value in breeding. She concludes that selection must be based on different combinations of indices depending on whether breeding targets irrigated or rainfed materials. In all cases the number of spikes and high biomass seem diagnostic as traits to be selected.

John Foulkes, University of Nottingham-UK
His keynote is about exploring genetic diversity for rooting traits and tolerance of water & N stresses in wheat. He starts by explaining what N-use efficiency (NUE) is. He mentions that deep roots help plants under drought and that is reflected in C12/13 isotope ratios. He also mentions RootNav (http://www.plant-image-analysis.org/software/rootnav) and ImageJ (https://imagej.nih.gov/ij) which they have used to study root phenotypes (crown root angle, root length density) in lab experiments, observing high heritabilities in DH populations and significant association to yield in rainfed trials. He shows nice pics of aerenchyma formation in roots under drought.

Marta Lopes, CIMMYT, Turkey
She talks about winter wheat physiology and the optimization of resilience to a changing environment in rainfed crop systems of Turkey and Iran. She shows field data on grain yield when plots are exposed to heat spells and drought before and after heading. She mentions an article recently published in FPS, but I could not find, sorry. During questions, she explains that there is a database of CIMMYT genotypes so that anyone can query and order seeds.

Mariona Martínez-Subira, Univ. Lleida
She talks about her work, in collaboration with CSIC and SemillasBatlle, synthesis of bioactive compounds (beta-glucans, arabinoxylans) in barley during grain filling in response to late abiotic stress. She reports that growth under plastics reproduces terminal heat stress and that stress affects the composition of bioactive compounds.

Rubén Vicente, presents work done at Univ. Barcelona
Talks about C and N metabolism in laminar and non-laminar photosynthetic organs under contrasting water regimes in low- and high-yielding durum wheat cultivars (Sebastian & Pelayo) grown in ITACyL, Valladolid for 3 seasons. Under water stress they observe reduction of biomass, grain yield and senescence.

Damiano Martignano, CRAG, Barcelona
His talk describes approaches for Cas9 genome editing in Sorghum, which he applies to brassinosteroids (BS) engineering. He builds on previous observations in Arabidopsis thaliana showing that increasing BS receptors increases performance under drought. He mentions also the uzu mutant in barley, which is related. His protocol takes 10-14 weeks. They are producing NILs from Iberian landraces obtained from INIA. They are building a facility to perform high-throughput phenotyping (DroughtSpotter and PHENOSPEX).

David Soba, Univ. Navarra
He talks about the effect of elevated [CO2] on durum wheat grain quality during grain filling. Concludes that yield is increased, as well as gluten proteins. In contrats, free amino acids are reduced.

Elena Prats, IAS-CSIC, Córdoba
She delivers a keynote on the physiological dysfunctions of stomata (lock-up) under fungal infection and drought which affect both resistance to disease and drought responses. She explains a series of experiments in which plants were supplied with ABA and exposed to fungi, that allowed her team to conclude that infection does affect the stomatal movements. This behavior is part of what has been called hypersensitive response, which has been described in https://academic.oup.com/jxb/article/59/3/501/573771.

Francisco Ciudad- Bautista, ITACyL, Valladolid
Reports on the current incidence of fly Oscinella frit, which affects both wheat and barley, in Castilla y León, Spain. He shows fly curves and pictures of larvae and pupae in grains and explains how the symptoms can be distinguished from other diseases.

Yésica Pallavicini, ITACyL
She presents preliminary results on the use of aerial platforms and spectral indices to monitor the spread of  yellow rust in bread wheat along the growing season.

9 de abril de 2018

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:

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 1st temperature and 2nd 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: 

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