Functional phenomics is an emerging discipline that utilizes phenotyping, physiology, multivariate statistics, and simulation modeling to generate and test new hypotheses about how plant traits integrate to influence crop performance and other attributes. Open science is a philosophy of increasing access to scientific practice and knowledge. Open science will be discussed in the context of best practices for plant phenomics research, including sharing preprints, software code and executables, data, images, and statistical analysis using examples from the speaker’s work. The speaker’s presentation is scheduled to last about 30 minutes, leaving ample time for community discussion about phenomics and open science. More information and speaker bios

This webinar was organized by ASPB’s Environmental and Ecological Plant Physiology (EEPP) Section. For more information about this group and how to become a member visit https://eepp.aspb.org/

Link to Webinar Transcript 


Resources Shared During the Webinar: 

York, L. M. (2018). Functional phenomics: an emerging field integrating high-throughput phenotyping, physiology, and bioinformatics. Journal of experimental botany, 70(2), 379-386.

York, L. M., Slack, S., Bennett, M. J., & Foulkes, M. J. (2018). Wheat shovelomics I: A field phenotyping approach for characterising the structure and function of root systems in tillering species. BioRxiv, 280875.

Seethepalli, A., Guo, H., Liu, X., Griffiths, M., Almtarfi, H., Li, Z., ... & Ma, X. (2019). RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping. bioRxiv, 569707.

Mattupalli, C., Seethepalli, A., York, L. M., & Young, C. A. (2019). Digital imaging to evaluate root system architectural changes associated with soil biotic factors. Phytobiomes Journal, PBIOMES-12.

Teaching Tool in Plant Biology: Phenomics of root system architecture: Measuring and analyzing root phenes by Larry York and Guillaume Lobet


Upcoming Meetings and Opportunities 




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Questions Asked During the Webinar: 

Question Asked Answer Given
please clarify if you get the roots out of the soil , whash it, and then image it with the RhizoVision sysF9:G13tem? how do you image the root? i mean in which environment you image the root? The RSA will be in the same orientation as in the soil? Thanks. Fully described in preprint, but dug up with shovel, washed and imaged. Search for rhizovision on biorxiv.
What is the main difference between RhizoVision and other availabale software for root imaging analysis like DIRT and GiARoot? Thanks, Amir RhizoVision Crown encompasses both a specific hardware platform and associated software, including Imager and Analyzer. Analyzer itself offers some of the same trait outputs but is designed to be used on the user's own desktop and has a multi-purpose design for both root crown and disconnected roots (scanned roots)
Is there any potential to use color imaging for root phenotyping, such that you could quantify the unsuberized vs suberized root length or volume (i.e., white vs brown roots)? Or does the automated segmentation not work well with color imagery? This is a really important characteristic for trees in a number of different environmental contexts. Color imagery can be problematic when mixed with uncontrolled lighting, but there is definitely potential. My work in maize indicated that when imaged on dark backgrounds, highly pigmented brace roots were so dark as to cause problems with segmentation. 
Can you use pictures obtained from different means and put them into Rhizovision? Do you have to use your specific set-up?  We assume high contrast images to solve the problems of difficult segmentation that our hardware platform addresses. However, you can provide segmented images from any platform.
Larry kindly share the root imaging tools Check https://quantitative-plant.org... and I have followed up with Jayne on twitter about the root phenotyping working group of IPPN
how about non-invasive imaging using x-ray? X-ray is a very promising direction, but currently expensive, slow, and requires substantial manual intervention (more than digging up and washing roots if you can believe it!)
can you monitor root growth over time? We have done some work with agar plates and blue paper or pouch methods.
How do we measure root branching density? branching density requires the length of the parent root and the number of children roots. Can be estimated pretty easily from single axial roots with laterals automatically, can also be counted manually. Difficult to measure on a whole root system
When measuring root angle, do we measure the angles of all the roots branching from the main root ? There are many ways to measure angles. Our software gives averages of all angles along all roots currently.
Can you talk about your career path to get where you are now, and what are the biggest things you learned from Undergrad -> Grad -> current role that aren't technical? Keep trying.
I would like to know for how long you were able to use the medium-throughput platfrom for multiple ion uptake kinetics if it is only for the early stage of growth?  We focus on seedlings but you can study older plants by excising roots or just placing part of the plant. Most methods are destructive as you need to get root length or mass to standardize the uptake rates
How can you analyze root traits from trees? What kind of challenges could we face? Soil coring might be useful. Rhizotrons are windows in the ground. Ground penetrating radar works with thicker roots.
What is mean by performance index? When I talk about performance I basically mean indicators of yield for crops or fitness for natural systems, but could be other 'functions'
Can't see bottom of your slides Sorry about that. I'm still working with my institute for how to share this material while protecting IP.
How much variation is there in root CO2 respiration among different crop plants and different crop plants under different streses, like drought and temperature variation We saw substantial variation within wheat, several fold. It is affected by stress for sure.
In your opinion, what can replicates better the root phenotype: Solid medium or hydroponics? Soil. The growth platform can be adapated to your needs but should be kept in mind to eventually confirm in soil.
what are the root characters that should be taken into account for cold tolerance studies in pulses I believe diameter influences cold tolerance and you might think of depth as a way to escape cold soil?
Is Rhizovision analyzer working with images from smaller plants in media plates, like Arabidopsis? As long as it's a whole root system by itself, then it meets the condition. We have used it for medicago on plates here
Is Rhizovision analyzer measuring root angle? Which type of angle? We currently measure angle of all points along all roots so it's very different from many angle measurements. We provide an average and frequencies of 'shallow' 'medium' 'steep'. Described in preprint. The new version will be more versatile and we can provide a beta within a month.
What method you use to study deeper roots, I mean roots at depth. Ashish rajurkar From U of Illinois, Urbana-Champaign Soil coring is the gold standard I'd say. Stable istopes can be used.
How does the Rhizo Vision handle relatively fine roots? On the hardware side, it's a limitation of camera resolution and the working distance which can be changed. For very fine roots, a flatbed scanner may work best. For the software, as long as you have a few pixels for the width of a root it is OK.
I work on Miscanthus, how would RhizoVision handle the rhizome? Would I need to separate the roots off? Could I make the software ignore it? You would have to manually crop it. We are working on adding regions of interst functionality.
FYI: There's a great tool for logging Github clones and views from Noah Fahlgren (on the subject of open science): https://github.com/nfahlgren/g... Thanks, that is useful 
What's your opinion on the usefulness and accuracy of minirhizotrons for studying roots in the field? I'm aware of the literature for minirhizotrons but haven't used them personally. Of course it's known they are  non-destructive, allow time series imagery.
Some plants have hard root system so the chances are less of loosing the actual orientation but what about rice crop being grown in hydroponics. As they are very delicate and get tangled easily. How can we manage imaging them?  Very carefully! No easy answer, but carefully tease apart with plastic tips.
Can we do this mapping in soil or water itself?  Difficult.
or map the growth pattern with time and nutrient availability? Also difficult. We have scanned switchgrass roots from living plants over time by just laying the shoot out of the plastic tray with water in which we spread the roots. Seems to work OK but not fast or easy.
is the raw image used in RhizoVision a composite of various angles or do you choose only one ''promising'' angle from which to take the picture? It's the subjectively widest perspective to the user that we use. Check out our preprint on M-PIP on biorxiv

Have Suggestions for Future Webinar Topics? Let us know in the comments or email Community@Plantae.org