EDITORIAL

 

Welcome from the Academia Section Chairs

 

As some of you may recall, the IPPN has structured itself into two sections, one focused on academia and one focused on industry. As the Inaugural Chairs of the Academia Section, we would like to take this opportunity to welcome all members of the IPPN.  

 

The goal of the IPPN is to increase the visibility and impact of plant phenotyping research and enable cooperation by fostering communication between stakeholders in academia, industry, government, and the general public. Consistent with this, the academia section of the IPPN aims to be an international leader in plant phenotyping by providing opportunities and value to its members in research, applications and education. As such, we would like to hear from you about how the section could best enable and inform your efforts in plant phenotyping.

For example,

• What do you see as the up-and-coming scientific challenges?

• How could the academia section support your educational needs?

• Where do you see growth potential in the discipline?

• Do you have ideas for cross-section collaboration and partnerships with other societies / domains?

 

Questions such as these will be included in the upcoming IPPN Phenotyping Survey 2021 (more information below). However, feel free to send suggestions directly to either of us (email here). Your input is critical to defining the mission of the section and the selection of strategic goals.
 
We hope to see you (virtually) at the NaPPN scientific conference (February 2021) and (in person!) at the next IPPS in Wageningen (October 2021)!

 

 

 

Jennifer Clarke and Rick van de Zedde 

(Chair & Vice Chair IPPN Academia Section)

 

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NEWS

 

 

First Results: New Field Phenotyping System Being Tested in Australia (& the Netherlands)

 

The Australian Plant Phenomics Facility recently purchased their first FieldExplorer field phenotyping platform from CropTraits to collect data for a range of applications. As an example, a project in collaboration with the CSIRO involves assessing the potential of remote sensing to provide farmers with decision-making tools for nitrogen fertiliser application. The trial is a paddock-scale set up, rather than the traditional plot set up and combines a number of different sensors for crop, weather and soil data collection. The trial design (bottom right) incorporates 1.5 km-long strips of ‘nitrogen rich’, ‘normal nitrogen’ and ‘nitrogen minus’ applications to barley. The FieldExplorer collected LiDAR and hyperspectral data along these long strips by dividing them into 10 m long ‘virtual plots’. Preliminary analysis of this data shows clear treatment differences for average crop height, percentage ground cover and biomass per area (topright). The data will be incorporated into the analysis of a larger data set from collaborators on the project with the goal of producing fertiliser management tools for farmers. 

 

Since June 2020 already, another FieldExplorer platform is also undergoing a trial phase for the "Netherlands Plant Eco-Phenotyping Centre" (NPEC), with first results waiting to be published later this year. 

 

 

First services for researchers as EMPHASIS moves into implementation phase

 

Once it is fully operational, EMPHASIS will enable researchers to use facilities, resources and services for plant phenotyping across Europe. Earlier this year, EMPHASIS has reached an important milestone: the establishment of the Interim General Assembly (IGA), a board of thus far ten countries that have formally declared their intention of moving EMPHASIS towards operation. This board acts as a main decision-making body on all strategic aspects with high-level importance for the future of EMPHASIS.

The aim of EMPHASIS is to integrate all European countries, and the IGA is open for participation of any further countries willing to work towards its setup. The IGA meeting in April 2020 marked the launch of the implementation phase which bridges the preparation of EMPHASIS to full operation. During this implementation period, the long-term legal framework of EMPHASIS will be developed and pilot services will be tested.

Plant researchers can already benefit from the first services, which can be found on the EMPHASIS website.

 

 

!!!Last Call#1: Final Round of Applications for Access to European Plant Phenotyping Facilities (DEADLINE: 26th October 2020)

 

The European Plant Phenotyping Network 2020 (EPPN2020) provides researchers belonging to academic and industry groups access to its 31 phenotyping facilities located all over Europe. The facilities can be used for experiments with either scientific or technological objectives. EPPN2020 has just launched its sixth (& last) call for application for transnational access, open to European groups but also open (to a limited extent) to groups originating from emerging countries or international research centers. The call closes on 26th of October 2020. Costs of such experiments are supported by the project.

 

 

!!!Last Call#2: Only a few days left to submit to the EMPHASIS Photo Competition (until end of August 2020)

 

EMPHASIS, together with DPPN, IPPN e.V. and LemnaTec, is looking for the best photograph portraying plant phenotyping.

 

The winning photographer will receive a high-end camera worth 2500 Euro.

 

Submissions may include (but are not restricted to) research images, photographs of researchers, plants, phenotyping facilities, equipment and also creative and artistic interpretations of the topic.

 

All short-listed photographs will be published by EMPHASIS and its partners and exhibited at various occasions.

Submit HERE, until August 31st!!!

 

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What we read... 

 

 

 

"Friday Hands-On: PhenomeForce" digital series will launch this fall

 

Joining the greater suit of conferences & workshops going digital this year, the NaPPN has decided to soon launch their free & online workshop series "Friday Hands-On".

According to the organizers, the intention of this digital series is to "build a broad network of experts & beginners, where users can easily connect and share knowledge, tools & discoveries (PhenomeForce)".

Especially highlighted is usage & training of open-source tools for working with functions, graphs, pipelines & workflows, Raspberry-pi and different programming languages (R, Python, Java, etc.).

Topical areas are plant breeding, plant growth & development, yield, soil, stress, conservation, organ morphology & others.

Main focus:

• Image analysis

• Data quality

• Statistics

• Machine learning (& A.I.)

• Results interpretation

 

Fridays Hands-On will take place every Friday (10am CDT) starting September 18th (check NaPPN homepage for any updates).

 

 

NPEC - Everything According to Plan

 

With huge effort & sound planning, the "Netherlands Plant Eco-Phenotyping Centre (NPEC)proceeds with its construction, originally started in late 2018. The timeline ranging from the proposal submission (2017) down to the yet-to-come official opening of NPEC @ WUR in combination with IPPS2021 (October 2021), can be followed -as it is continually being updated- on the NPEC homepage. 

Most recent progress in this 22 Mio. € project, funded by "The Netherlands Organisation for Scientific Research" (NWO):

• Ongoing construction works for the NPEC greenhouse, by Bosman van Zaal 

• Integration of hard- & software components for multi-sensor, custom-build gantries inside the greenhouse (WIWAM)

• Onset of the trial phase for the FieldExplorer (CropTraits) 

• Delivery of gravimmetric system by PlantDitech

 

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IPPN SERVICE

 

 

Back from Summer Break: The Phenomics Webinars continue on September 4th 

 

After taking a break during the summer, "The Phenomics Webinars" will continue their bi-weekly seminar series, providing insights given by different global experts in theory & practice, on topics involving plant phenotyping.

The Phenomics Webinars started off with a good reception among phenotyping communities worldwide. With mean audience sizes between 2K - 4K (!), mainly due to partnering with the AgriX-Forum for broadcasting in China, "The Phenomics Webinars" will continue throughout the rest of 2020 & likely beyond.

If you want to join our range of speakers, please submit your abstract, here!!

Next on the Phenomics Webinars:

Dr. Roland Schafleitner (Head of Molecular Genetics & Flagship Leader at AVRDC, Taiwan)- "Phenotyping at World Vegetable Center"

Past issues of "The Phenomics Webinars" can be accessed via the IPPN Youtube-Channel.
 

 

 

Come & visit our IPPN Youtube-channel, now also featuring non-IPPN resources!

 

During the Covid-19 crisis, many of us rely to a greater extend on digital content. May it be as creator of digital content for educational-, promotional- or other communicative reasons -or as user to learn about the newest trends in & around plant phenotyping. IPPN Office has thus started to re-model its Youtube -channel in order to provide high-quality, original content (>100 videos from the past 10 years).

Additionally, now it is possible for our IPPN Working Groups to showcase & highlight video-resources from 3rd-party creators also going beyond IPPNs original content. These videos are curated by the IPPN Working Groups & selected for high quality & content. You will find them in the channel overview under IPPN...Recommends, currently featuring two playlist with tutorials on "Low-Cost imaging" & "Imaging under Controled Environments"

 

 

Coming Soon: New IPPN Survey in 2021

 

For the past six years, IPPN launched it's bi-annual survey format "Plant Phenotyping Surveys". These surveys cover basic questions related to plant phenotyping in order to assess the status of emerging fields & usage of within the discipline. The surveys address participants from all geographic regions & professional disciplines.

These surveys form an important source of information for IPPNs knowledge base, communication & participation of its members, peers & associates worldwide. Data from these survey are being made available on the IPPN homepage & survey results have been extensively used for adressing the global status of plant phenotyping (such as in this review by Yang et.al.).

Participating in these surveys empowers everyone who contributes to add to the big picture of how phenotyping is being used & developed outside & between local & regional communities.

The Plant Phenotyping Survey 2021 is planned to start being sent out in the Q4 IPPN Newsletter.

If you happen to have ideas for questions you would like to find in this survey, feel free to send them to: IPPN@plant-phenotyping.org.

 

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Upcoming (E-)vents 

 

ECCV 2020 Workshop on Computer Vision Problems in Plant Phenotyping (CVPPP 2020): 28th August 2020, PM, Glasgow, UK

 

Due to Covid-19 ECCV and its workshops will be held online

After the successful CVPPP workshops from recent years at ECCV, BMVC, ICCV, and CVPR, CVPPP this year is held in conjunction with ECCV 2020. The goal of this sixth workshop is to continue to showcase the challenges raised by and extend the state of the art in computer vision for plant phenotyping.

The workshop is made possible through callaborative efforts & funding from IPPN, DPPN, Phenorob, Forschungszentrum Juelich, The University of Edinburgh & The University of Nottingham.

 

Current plans are:

• All papers, oral or poster, will have a pre-recorded video presentation, made available together with the paper to the attendees about a week before the workshop day

• Every workshop will have some scheduled individual interaction time during the workshop day

• This time will be split in two parts to allow attendees from all over the world to attend in good conditions

 

Check regular updates here 

 

 

 

SIBV/TOMRES Summer School 2020: 08.09.-10.09.2020

 

Exploring new strategies to help plants facing abiotic and biotic stresses is nowadays becoming even more crucial. Therefore the main aim of our Summer school is to improve students knowledge and awareness on this important topic, through lectures, workshops and discussions.  

 

The course will be held in English and is addressed to PhD students and young researchers in the fields of Plant Biology, Physiology, Biotechnology and Molecular Breeding.

Due to Covid-19 the whole event will be organized online. Preliminary program & details on how to participate

 

 

 

World Agri-Tech Innovation Summit: 15.09.-116.09.2020

 

The World Agri-Tech Innovation Summit is going virtual!  This year’s summit will be live online on September 15-16, 2020, providing a 1-1 meeting platform for our global agtech network, focused discussion groups, interactive panel discussions, start-up pitches, and critical intelligence from industry leaders on how our industry will emerge from the current crisis.

 

An expert international speaking faculty will present live, before hosting breakout virtual roundtables on the trends, opportunities and challenges that will shape your business in 2021:

• Carbon Neutrality: How are CPGs meeting their sustainability and responsible sourcing targets?

• Sustainable Inputs: Which bio-based inputs are on course for rapid growth over the next 10 years?

• Automation and Robotics: How are labour shortages accelerating the pace of automation?

• Supply Chain Resiliency: Where can technology reduce waste and inefficiency in the supply chain?

• Soil Health: How can we incentivise farming practices that improve carbon sequestration?

• Digital Platforms: How can we deliver greater value for farmers though supply chain digitisation?

• Localised Food Systems: What role will technology-driven production play in future food security?

• Investment Outlook: How are investors positioning themselves to brace against a downturn?

 

 

Update: Workshop postponed to July 2021

 

This workshop is being co-organized by IPPNs Affordable Phenotyping Working Group.

 

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CALLS & SPECIAL ISSUES

 

 

The Plant Phenome Journal Special Issue "Belowground Phenotyping": Submission deadline: 1st March 2021

 

This special section will be published in The Plant Phenome Journal (TPPJ), a trans-disciplinary, gold open access journal that focuses on original research, interpretations, and datasets investigating all aspects of plant phenomics. TPPJ is a forum that combines engineering, remote sensing, computer or data science with plant science, breeding, genetics, or agronomy.  

Scope: 
This special issue will focus on belowground phenotyping technologies and efforts to understand the function and variation of plant root systems. Root phenotyping is the high hanging fruit, and the purpose of this special section is to feature pioneering work in this area. 
 

We encourage contributions on the following topics:  

• Phenotyping technologies used to understand the function and variation of plant root systems 

• Work with novel sensors aimed at translating medical and defense imaging technologies into greenhouses and into the field to gather root traits

• Other indirect methods to observe root systems based on aboveground correlates 

 

Agronomy Special Issue "Improving Nutrient Use Efficiency from Lab to Field": Submission deadline: 30 July 2021

 

This special issue in Agronomy will primarily focus on the macro nutrients N and P, the study of all essential nutrients is welcomed. We are interested in latest studies that untangle plant uptake, nutrient allocation, and nutrient sensing and signalling in the plant. Furthermore, we welcome manuscripts on novel strategies for improving plant performance at limiting nutrient levels (at the molecular level or through the identification of novel root traits/phenotypes that facilitate uptake), and agricultural practices including but not limiting to the use of microorganisms.

Link to Special Issue Flyer

 

 

 

 

Ongoing: PlosOne Collection on "Plant Phenomics and Precision Agriculture": Submission deadline extended to December 14, 2020

 

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PUBLICATIONS

 

Research Spotlight: Phenotyping: New Windows into the Plant for Breeders
Michelle Watt, Fabio Fiorani, Björn Usadel, Uwe Rascher, Onno Muller, Ulrich Schurr  (2020) Annual Review of Plant Biology 71:1, 689-712

 

Out from their annual review in Plant Biology, Watt et. al. concluded following summary points:

1. Contemporary plant phenotyping is central to prebreeding in efforts to discover new complex traits, identify diversity that is heritable using high-capacity selection, and generate reusable data. While technologies are rapidly developing, access is being given to users from academia and industry to robust methodologies, technology development, protocols, and data integration.

2. Emerging and future phenotyping methods can be integrated within breeding, especially in the areas of field and early-generation germplasm development.

3. Phenotyping in controlled environments should not aim to mimic the complexity of field conditions; rather, it will contribute to our understanding of specific and dynamic plant– environment interactions, analyses of genetic diversity, and analyses of ex post routes of successful breeding.

4. Noninvasive field phenotyping—although still focused predominantly on aboveground traits—is developing into a robust and accessible tool that supports scientists and breeders in the analysis of crop features and the development of improved properties across heterogeneous and dynamic field situations.

5. Root phenotyping is developing rapidly to improve our understanding of key performance features in controlled environments. Recent developments show some advancement toward field phenotyping, especially in combination with root structure–function models. However, noninvasive root phenotyping in the field is still not possible, and significant advancements are needed to achieve this important target.

6. Data integration is paramount for the integration of plant phenotyping into present-day science and breeding domains. Ongoing community efforts toward this end include a wide range of standardization goals, from the level of generating quality data to their integration in large, diverse multiomics data landscapes.

7. Novel technical opportunities will emerge from the integration of robotics and data science to enhance accuracy and throughput in all aspects of noninvasive plant phenotyping, including integration with agronomy and on-farm management.

 

• Abeler-Dörner, L., Laing, A.G., Lorenc, A. et al. (2020) High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Nat Immunol 21, 86–100. https://doi.org/10.1038/s41590-019-0549-0

• Alahmad, S.; Kang, Y.; Dinglasan, E.; Mazzucotelli, E.; Voss-Fels, K.P.; Able, J.A.; Christopher, J.; Bassi, F.M.; Hickey, L.T. (2020) Adaptive Traits to Improve Durum Wheat Yield in Drought and Crown Rot Environments. Int. J. Mol. Sci., 21, 5260. https://doi.org/10.3390/ijms21155260

• Beres BL, Hatfield JL, Kirkegaard JA, Eigenbrode SD, Pan WL, Lollato RP, Hunt JR, Strydhorst S, Porker K, Lyon D, Ransom J and Wiersma J (2020) Toward a Better Understanding of Genotype × Environment × Management Interactions—A Global Wheat Initiative Agronomic Research Strategy. Front. Plant Sci. 11:828. https://doi: 10.3389/fpls.2020.00828

• Brown, D., Van den Bergh, I., de Bruin, S. et al. (2020) Data synthesis for crop variety evaluation. A review. Agron. Sustain. Dev. 40, 25. https://doi.org/10.1007/s13593-020-00630-7

• Honecker, A., Schumann, H., Becirevic, D. et al. (2020) Plant, space and time - linked together in an integrative and scalable data management system for phenomic approaches in agronomic field trials. Plant Methods 16, 55. https://doi.org/10.1186/s13007-020-00596-3

• X. Jin et al. (2020) High-throughput estimation of crop traits: A review of ground and aerial phenotyping platforms, in IEEE Geoscience and Remote Sensing Magazine, https://doi.org/10.1109/MGRS.2020.2998816

• M. Julkowska, Stephanie Saade, Gaurav Agarwal, Ge Gao, Yveline Pailles, Mitchell Morton, Mariam Awlia, Mark Tester (2020) MVApp—Multivariate Analysis Application for Streamlined Data Analysis and Curation. Plant Physiology Jul 2019, 180 (3) 1261-1276; https://DOI: 10.1104/pp.19.00235

• Lozano-Claros, D., Meng, X., Custovic, E. et al.  (2020) Developmental normalization of phenomics data generated by high throughput plant phenotyping systems. Plant Methods 16, 111. https://doi.org/10.1186/s13007-020-00653-x

• Jennifer Mack, Florian Rist, Katja Herzog, Reinhard Töpfer, Volker Steinhage (2020) Constraint-based automated reconstruction of grape bunches from 3D range data for high-throughput phenotyping,Biosystems Engineering, Volume 197, 285-305, ISSN 1537-5110, https://doi.org/10.1016/j.biosystemseng.2020.07.004

• Meireles, J.E., Cavender‐Bares, J., Townsend, P.A., Ustin, S., Gamon, J.A., Schweiger, A.K., Schaepman, M.E., Asner, G.P., Martin, R.E., Singh, A., Schrodt, F., Chlus, A. and O'Meara, B.C. (2020) Leaf reflectance spectra capture the evolutionary history of seed plants. New Phytol. https://doi.org/10.1111/nph.16771

• Nagel, K.A., Lenz, H., Kastenholz, B. et al. (2020) The platform GrowScreen-Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants. Plant Methods 16, 89. https://doi.org/10.1186/s13007-020-00631-3

• Parry, G, Provart, NJ, Brady, SM, Uzilday, B; (2020) The Multinational Arabidopsis Steering Committee. Current status of the multinational Arabidopsis community. Plant Direct. 00:1-9. https://doi.org/10.1002/pld3.248

• Raphael Petegrosso, Tianci Song, Rui Kuang (2020) Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants, Plant Phenomics, ArticleID 1969142, 16 pages, 2020. https://doi.org/10.34133/2020/1969142

• Matthew Reynolds, Scott Chapman, Leonardo Crespo-Herrera, Gemma Molero, Suchismita Mondal, Diego N.L. Pequeno, Francisco Pinto, Francisco J. Pinera-Chavez, Jesse Poland, et. al. (2020) Breeder friendly phenotyping.

• Plant Science, Volume 295, 110396, ISSN 0168-9452, https://doi.org/10.1016/j.plantsci.2019.110396

• Saade S, Brien C, Pailles Y, Berger B, Shahid M, et al. (2020) Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages. PLOS ONE 15(7)e0236037. https://doi.org/10.1371/journal.pone.0236037

• Anand Seethepalli, Haichao Guo, Xiuwei Liu, Marcus Griffiths, Hussien Almtarfi, Zenglu Li, Shuyu Liu, Alina Zare, Felix B. Fritschi, Elison B. Blancaflor, Xue-Feng Ma, Larry M. York, (2020) RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping, PlantPhenomics, ArticleID 3074916, https://doi.org/10.34133/2020/3074916

• Saoirse R. Tracy, Kerstin A. Nagel, Johannes A. Postma, Heike Fassbender, Anton Wasson, Michelle Watt (2020) Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. Trends in Plant Science, Volume 25, Issue 1, 105-118, ISSN 1360-1385, https://doi.org/10.1016/j.tplants.2019.10.015

• Thompson, A.L., Thorp, K.R., Conley, M.M. et al. (2020) A data workflow to support plant breeding decisions from a terrestrial field-based high-throughput plant phenotyping system. Plant Methods 16, 97. https://doi.org/10.1186/s13007-020-00639-9

• Hai Wang, Emre Cimen, Nisha Singh, Edward Buckler (2020) Deep learning for plant genomics and crop improvement. Current Opinion in Plant Biology, Volume 54, 34-41, ISSN 1369-5266, https://doi.org/10.1016/j.pbi.2019.12.010

• Röckel, F.; Moock, C.; Braun, U.; Schwander, F.; Cousins, P.; Maul, E.; Töpfer, R.; Hausmann, L. (2020) Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1. Genes, 11,891. https://doi.org/10.3390/genes11080891

• Ronghao Wang, Yumou Qiu, Yuzhen Zhou, Zhikai Liang, James C. Schnable (2020) A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis. Plant Phenomics, vol. 2020, Article ID 7481687, 8 pages, 2020. https://doi.org/10.34133/2020/7481687Whitcomb SJ, Rakpenthai A, Brückner F, Fischer A, Parmar S, Erban A, Kopka J, Hawkesford MJ and Hoefgen R (2020) Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. Front. Plant Sci. 11:1118.https://doi.org/10.3389/fpls.2020.01118

 

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PLANT

PHENOTYPING

JOBS

 

Open Positions

Head of Phenomics, Bayer, St. Louis, USA

Graduate Research Assistantship, Phenomics Lab, Washington State University, USA

4 Professorships-, 3 Junior Research Group Leader-, 2 Post-doc & 15 PhD Student Positions in the Excellence Cluster "PhenoRob"

 

Postdoctoral Positions

Post-doc position in plant ecophysiology or related field, BOKU, Vienna

Post-doc Scholar in Plant Sensors, North Carolina State University, NC, USA

Post-doc position in Precision Agriculture Lab, Washington State University, USA

Postdoc on the computing side of high-throughput phenotyping systems, Univesity of Georgia, USA

 

PhD positions

2 PhD positions at the Group “4D Crop Reconstruction” within the Cluster of Excellence PhenoRob – Robotics and Phenotyping for Sustainable Crop Production, Bonn, Germany

Research associate / Doctoral position (m/f/d): Optimizing Nitrogen use efficiency in agricultural production systems, KIT, Germany

35 PhD international fellowships for early-stage researchers  in the fields technology, engineering, physics, mathematics, life and health sciences, Spain/Portugal

Pre-PhD Internship & PhD position Studying the phenotypic plasticity of Vitis vinifera to water deficit, INRA, Montpellier, France