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Arizona Phenotyping Network

Arizona Phenotyping Network

Feb 13, 2015

Arizona Phenotyping Network (AZPN)

Purpose

Bring all interested parties together to:

  • understand the original AZPN vision that Rod, Chieri, Kurt, and Matt developed and get a sense of what they were able to accomplish
  • determine the phenotyping needs for each location and, based on this information, determine if the vision has changed/should change and how
  • determine if it makes sense to move forward as a collective and, if so, the next step forward

During discussions on the feasibility of the network, consider the following issues:

  • how do we identify a unique contribution for the UA/USDA?
  • who will lead the endeavor as we move forward and how will it be managed?
  • how will we ensure network sustainability?

Agenda

  • 9:00-9:30 Chieri Kubota – AZPN, the original vision
  • 9:30-10:00 Jeff White and Kurt Nolte – what are the phenotyping needs and what is currently being done in Maricopa and Yuma?
  • 10:00-10:30 – Matt Rahr and Robert McArthur – IT needs and resources
  • 10:30-11:00 Chieri Kubota and Martha Narro – what are the phenotyping needs in Tucson and how can iPlant interface with the network?
  • 11:00 working lunch
  • 11:00---12:00 what should the AZPN look like?
  • 12:00-1:00 what resources are needed and what are the potential barriers?
  • 1:00-2:00 – wrap up and next step(s)

Participants (partial list)

  • UA CALS: Karen Schumaker, Robert Macarthur, Matt Rahr, Jennifer Smith, Chieri Kubota, 
  • UA YAC: Kurt Nolte
  • UA MAC: Rick Ward, Pedro Andrade, 
  • USDA ARS Maricopa: John Dyer, Jeff White
  • iPlant: Martha Narro

Key Points

USDA ARS Maricopa and UA MAC (Maricopa Agriculture Center)

These two groups have clear strong common goals related to field-based proximal sensing and have already begun to work together. MAC is converting a building for the groups to work in together on this phenotyping effort. Both groups have scientists with a research expertise spanning the science and remote sensing technologies. The crops studied are grains and cotton. Breeders are interested in the Maricopa site for studies on (no surprise) heat and drought tolerance. Candidate crops for this phenotyping effort are some wheat lines from Italy and some USDA cotton lines. Rick Ward also thinks a cross UA site collaborative phenotyping effort on lettuce in Yuma would have the advantage of studying individual plants (heads of lettuce) instead of communities of plants as is the case in grains. However, would need a person with lettuce breeding expertise.

Network capability: The MAC facility now has fiber optic network, but the electronics on the end of it would need to be rebuilt to handle the large amounts of phenotyping data that would need to be transferred out. For example, a Gantry platform would generate a TB per day. They will need CALS (College of Agriculture and Life Sciences at UA) and iPlant IT support to handle that. It isn’t currently in place at MAC. Will need GB connection to Tucson campus, then from there to Illinois can be handled by Internet 2.

UA YAC (Yuma Agriculture Center)

Yuma, AZ is a major producer of fresh produce (in contrast to grains and cotton) in the U.S. with a number of ag companies located there (those heads of lettuce in the grocery stores now). YAC is focused on supporting the growers and ag companies in the area. YAC is not research focused (not breeding or research on phenotyping), but rather has very strong working relationship with the ag companies in the area. They do phenotyping, just not for research purposes. What would be of use at YAC is a equipment with sensor-based technology platform they could lease to industry for their own studies. YAC would need collaborative expertise from MAC on phenotyping. They's also need a highly skilled technical support person to support the equipment (maintain it, explain it, train people to use it) and work with industry. 

UA Campus and Farm

The strengths are greenhouse-based research. The lack of correlation between performance of lines developed in greenhouses compared with those lines' performance in the field is well know. Chieri Kubota's expertise in greenhouse engineering and breeding could be paired with the field-based breeders at MAC and USDA ARS to study the root causes the failure of greenhouse lines in the field thereby improving the utility of greenhouse breeding and phenotyping. They would like to get the UA Optical Science involved in development of phenotyping technologies.

The group is keen to leverage iPlant for data management and analytics. Martha suggested starting with some small datasets and analyses to become familiar with using iPlant. Robert Macarthur and Matt Rahr in CALS will be strong partners and Matt could provide the support to the group after learning to use iPlant's CI.

Followup

  • Andy French will outline steps for beginning to move LIDAR data to iPlant for analysis. The idea is to begin with a small dataset, a visualization tool and then move on the analysis tools as a way of becoming familiar with using iPlant's CI.
  • Jeff White will outline a plan to an send association data set to iPlant for analysis. As with Andy, the idea is just to get started with something as a way of learning to use iPlant.
  • Rick Ward would like to send CYMMIT data to iPlant.
    • Martha will work to leverage Matt Rahr at UA on the above bullet items so he becomes sufficiently familiar with iPlant to support the AZPN group going forward.
  • Not related to the phenotyping meeting per se, but good:
    • Martha to work with Kelly Thorp (USDA ARS Maricopa) and Shelley Littin to create a news article describing Kelley's modeling work as a possible success story from the modeling workshop at TACC. Keep Matt Vaughn and Doreen Ware in the loop. The paper titled "Proximal hyperspectral sensing and data analysis. 2 approaches for eld-based plant phenomics." will be published this week or next in Computers and Electronics in Agriculture.