2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 I 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Table of content Welcome . II Organizing committee . III Local organizers . IV Sponsors . V General information about COST Action FA 1306 . VI General information about the meeting and maps . VII Program . XI Abstracts for oral presentations . 1 Abstracts for posters Theme 1 – WG 1: Phenotyping at plant and field level . 35 Theme 2 – WG 2: Phenotyping at cell level . 69 Theme 3 – WG 3: Integration of phenotyping on both levels and translation translation into good practices for applied use . 95 Theme 4 – Data processing and integration . 107 Theme 5 – Stakeholder interactions . 113 List of participants. 115 I 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Welcome Dear participants of the 2nd General Meeting of the COST Action FA 1306 – PhenomenAll – The quest for tolerant varieties – Phenotyping at the plant and cellular level On behalf of the organizing committee of the COST Action and the local organizers we warmly welcome to Copenhagen. In Denmark we have a long tradition of collaboration bet- ween universities and this meeting is a joint arrangement between Department of Plant and Environmental Sciences (PLEN) at University of Copenhagen (UCPH) and Department of Food Science (FOOD) at Aarhus University (AU). We are looking forward to three days of new results, exchanging ideas and further developing our COST Action PhenomenAll by in- teresting discussions. We have experienced an overwhelming interest in the meeting. The program contains six keynote speakers, 24 oral presentations and 70 posters. All together we have 136 registered participants. We are particularly happy to welcome 15 stakeholder representatives represent- ting both breeders and hardware manufacturers. Based on requests after last years meeting we have not only one session per workgroup but we have also invited one keynote speaker on the topic of Data processing and integration and two keynote speakers representing Stakeholder interactions. Furthermore we have set aside time for group discussions about how to streng- then and further develop our COST Action and general networking. On Tuesday afternoon we will make an excursion to Campus Tåstrup, where Section of Crop Science of PLEN/UCPH resides and our phenotyping facilities are located. In the evening we will have the conference dinner in Tåstrup. We are particularly grateful to the six companies who are sponsoring this meeting. We would also like to thank three microbreweries on the island of Fyn (Funen), where the phenotyping facilities of FOOD/AU are located, for spon- soring a phenotyping session of beers. There would not have been a dinner without all of you. We would also like to thank the COST Organization for financially supporting the majority of participants and taking care of the administration. We will have three days with a tight and interesting schedule, looking forward to many inter- esting discussions! On behalf on the Organizing Committee and the Local Organizers Eva Rosenqvist Carl-Otto Ottosen PLEN/UCPH FOOD/AU II 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Organizing committee Eva Rosenqvist, University of Copenhagen, Denmark Carl-Otto Ottosen, Aarhus Universit, Denmark Sebastien Carpentier, KU Leuven, Belgium (Chair of COST Action FA 1306) Ulrich Schurr, Forschungszentrum Jülich, Germany (Co-chair of COST Action FA 1306) Andreas Voloudakis, Agricultural University of Athens, Greece Carla Pinheiro, ITQB, Portugal Diego Rubiales, Institute for Sustaniable Agriculture, CSIC, Spain Dyonisia Fasoula, Agricultural Research Institute, Cyprus Estelle Goulas, UMR 8567 CNRS/Université Lille 1, France Rick van de Zedde, Wageningen UR, The Netherlands III 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Local organizing committee University of Copenhagen Aarhus University Eva Rosenqvist Carl-Otto Ottosen Dominik Groβkinsky Benita Hyldgaard Dorthe Horn Larsen Jesper Svensgaard Jesper Cairo Westergaard IV 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Sponsors V 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 General information about COST Action FA 1306 The quest for tolerant varieties – Phenotyping ant plant and cellular level – PhenomenAll Mission Phenotyping is an emerging science that characterizes plant behaviour and quantifies features such as growth and stress tolerance in a precise and reproducible manner that allows linking to genetic control. As a highly interdisciplinary research area, phenotyping covers a wide range of methodological approaches from imaging based whole plant phenotyping (character- rization of morphological and physiological plant features), over molecular phenotyping ap- proaches on a cellular level (transcriptomics, proteomics, metabolomics) up to computational methods for image analysis, plant growth modeling and statistical data analysis and data inte- gration. The FA1306 work plan is divided into three work groups (WG). WG 1: Phenotyping at plant level This WG will collect information and novel devselopments in: • Sensors and image analysis • Plant physiology/pathology • Modelling plant growth and real time monitoring • Data management & statistics • Screening the biodiversity of European gene bank collections • Screening the parents and the offspring of breeding programs and different genetically modified plants WG 2: Phenotyping at cell level This WG will collect information and novel developments in: • Metabolomics and flux analysis • Proteomics • Transcriptomics • Genomics WG3: Integration of phenotyping on both levels and translation into good practices for ap- plied end use This WG will follow up the developments made in systems biology by integrating phenoty- ping on different levels and will collect the developments in translational research. • Phenotyping in practice (greenhouse/field) • Integration of different ‘omics’ technologies VI 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 General information about the meeting and maps The meeting will be held in auditorium A2-81.1 at Campus Frederiksberg, University of Co- penhagen, Thorvaldsens vej 40, 1871 Frederiksberg C (see map on page VIII)). The excursion and conference dinner will be held at Campus Tåstrup, Højbakkegård Allé 17, 2630 Tåstrup (see map on page IX and X). The buses departs 12:50 (sharp!) from Grønne- gårdsvej (see map on page VIII) Those who participate in the excursion but not in the dinner can take the free shuttle bus from Campus Tåstrup 16:35, arriving at the bus stop at Grønnegårdsvej 17:10. Those who does not want to participate in the excursion but in the dinner can take a IC train from Copenhagen Central Station and bus 116 to bus stop Agrovej. It is 8 minutes walk from Campus Tåstrup. Consult Eva Rosenqvist about it. Internet connection via WiFi Eduroam is available on campus. Employees from other scientific institutions that participate in Eduroam can use their home login name (username@homedomain) and password. For participants who do not have Eduroam a Guest Login will be provided (see separate paper in the conference bag). VII 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Map Campus Frederiksberg VIII 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Campus Frederiksberg and Campus Tåstrup IX 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Map Campus Tåstrup X 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Program Monday April 18, 2016 08.00 Registration, mounting of posters, buying lunch tickets Welcome: Svend Christensen (UCPH), Sebastian Carpentier 09.00 (COST), Eva Rosenqvist (convener) Achim Walter, ETH 09.10 WG 1: Phenotyping at plant/field level - new methods Zürich, CH 10.00 Coffee, poster viewing, buying lunch tickets 10.30 Stefan Gerth, DE Maize root growth tracking using X-ray CT segmentation Gerd Patrick Bienert, Screening for and development of boron-efficient rapeseed 10.50 DE and Arabidopsis genotypes Pirjo Peltonen-Sainio, Phenotyping nutrient use efficacy and resistance to seed borne 11.10 FI diseases for conventional and organic breeding Theoharis Ouzounis, Phenotyping tomato genotypes under four LED light en- 11.30 NL vironments for energy efficient use of light Danijela Vukadinovic, Fully automated detection of western flower thrips Frankli- 11.50 NL niella occidentalis damage in chrysanthemum leaves 12.10 Lunch, poster viewing Björn Usadel, Data processing: Ontologies to link genomics and pheno- 13.10 RWTH, DE typing Christiaan Biemond, How to manage and explore large and diverse datasets in Di- 14.00 NL gital Phenotyping? Non-invasive phenotyping of postharvest quality traits in to- 14.20 Gerrit Polder, NL mato and strawberry Angelika Czedik- Non-invasive phenotyping of plant fungal infections during 14.40 Eysenberg, AT the asymptomatic stage 15.00 Coffee, poster viewing 15.40 Workshop – four groups (appointed conveners) 1. Development of collaboration in the COST Action 2. + 3. Standards and procedures WG1 + WG2 4. Stakeholders – future 17.00 Main conclusions presentation by group conveners 17.40 MC meeting Free evening for sightseeing XI 2nd General Meeting of COST FA1306, PhenomenAll, Copenhagen April 18-20, 2016 Program Tuesday April 19, 2016 08.00 Registration, poster viewing WG 2: Phenotyping