Seminar 1 03242014 Phenomics Revolution Science 2013

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4 CSA News March 2013

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Taking thePhenomics Revolution

into the Field

By Karl Haro von Mogel


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March 2013 CSA News 5

started in 1990. The DNA in any plantvariety influences how it will developand grow in the face of multiple en-vironmental challenges including soiltype, weather, nutrition, and pests anddiseases. Plant breeders can use thisDNA information to associate the per-formance of plants, both in the green-house and the field, with the specificpieces of DNA carried by differentvarieties, even predicting performancebefore a seed is planted.

But with all the power of current

genotyping technologies, there is alimit to our ability to make strong con-nections between a plants genes andits traitsour ability to measure thetraits themselves.

This situation is changing rapidly.Scientists around the world are mak-ing new connections among disci-plines to develop and test technolo-gies that can bring a data revolution to

collecting plant phenotypes. And theyare doing it in the most difficult andimportant environmentthe field.

Balancing Technologies

Whether you are studying the basicbiology of a plant, or breeding newcrop varieties for farmers, the pheno-type is the center of attention.

Phenotypes are the physicalcharacteristics of an organism, whichresult from its genes, environment,

and how these two factors interact. Aphenotype can be everything from theheight of a plant, to its chemical com-position, yield, or response to specificenvironmental factors.

Long before the discovery of DNAand its role in heredity, farmers,breeders, and horticulturalists selecteddesirable plants based on the pheno-type. Even with todays sophisticatedgenetic research, which regularly seeswhole genomes published, it is what

the genes do to the phenotype thatmatters.

Measuring phenotypes of plantscan be challenging. The subtle effects

of genes that add up to determinequantitative traits can be easily missedand can require many repeated mea-surements to uncover. In addition,the structure of an entire plant can bedifficult to quantify. Edgar Spalding,a professor in the Botany Departmentat the University of WisconsinMadi-son, says that compared with DNAsequencing technology, phenotypingtechnology is still rather crude.

It is not much of an exaggerationto say that a ruler is used, and thatsnot high throughput.

Spalding is a principal investiga-tor for the Phytomorph project, whichseeks to turn delicate developmentalphenotypes into quantifiable mea-sures. One of his new tools is a roboticcamera that photographs growingseedlings and roots at regular inter-vals, with micron-level precision. Histeam tracks the root growth ofArabi-dopsis, maize, and tomato seedlings,looking for changes in their responseto gravity.

The genomics revolution is racing ahead at full speed.Complete genome sequences now cost a fraction ofwhat they were when the Human Genome Project

Center images above by Erica Seccombe, courtesy of the High Resolution Plant Phenomics Centre. Backdrop image: iStockphoto.

doi:10.2134/csa2013-58-3-1


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Through electronic image captureand computer analysis, we can seehow long even the tinyArabidopsisroot grows in five minutes, Spaldingsays.

It may not be obvious, but inmy view, when we have rich, high-throughput phenotyping, we aregoing to find out which componentof that phenotype set has predictivepower over something in the field.

Spalding stresses the importanceof raising the capabilities of pheno-typing tools. Anything we can do tomake the phenotyping activities moreautomated and more high throughputwill make studies of genotypepheno-type relationships more effective.

When was the last time you heardsomeone say that their phenotypedata was wonderfully large and com-plex, but their genotype informationneeds more detail?

The Phenomics Frontier

Phenomics, the study of completephenotypes and how they changeover time, is already underway.Companies such as Germany-basedLemnaTec have developed systemsfor phenotyping individual plantsin large, robotic greenhouses. Usingtechnologies combining photography,fluorescence imaging, 3D image anal-ysis, and data handling, thousands ofindividual plants can be grown and

automatically tracked through theirdevelopment. A conveyor constantlymoves potted plants around thegreenhouse and through a series of

scanning chambers.

With tools like these, physiologistscan study how different genotypes re-spond to stressful environmental con-ditions and efficiently observe the lifecycle of each plant. There are manysuch greenhouse facilities around theworld. However, there are many dif-ferences between the controlled condi-tions of a greenhouse and the variablenature of the field. Studying crucialtraits in the field will require turningit into a laboratory.

Its one thing to use a glass housefor a trait that is expressed early in de-velopment and at the individual plantlevel, but a lot of traits that we areinterested in are expressed at the com-munity scale, which means you haveto be working in field plots, saysASA Fellow Jeffrey White, a researchplant physiologist at the USDA Arid-Land Agricultural Research Center inMaricopa, AZ.

White was the lead author on areview of field-based phenomics for

plant genetics research recently pub-lished in Field Crops Researchand or-ganized a symposium on field-basedhigh-throughput phenotyping at lastyears ASA, CSSA, and SSSA Interna-tional Annual Meetings in Cincinnati,OH. He explains that many research-ers are developing ways to gatherphenotypic data in the field, usinga variety of approaches. These varyfrom tractor-based sensors to camerasmounted on irrigation cranes that roll

more effective.

Anything we can do to make the

phenotyping activities more automatedand more high throughput

will make studies of

genotypephenotype relationships

One of the new tools used by EdgarSpalding, principal investigator for the

Phytomorph project at the Universityof WisconsinMadison, is a roboticcamera that photographs growingseedlings and roots at regular inter-vals, with micron-level precision.


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1Short for Light Detection and Ranging. Its an

optical remote-sensing technology to study

canopy architecture.

across the field, imaging a crop like agiant flatbed scanner, or robots that

crawl along cables above the plants.From the air, cameras have beenmounted on blimps, full-sized aircraft,and remote-controlled helicopters.

The array of tools that can bedeployed is just as impressive. Tech-nologies can include visual light andinfrared cameras as well as ultrasonicsonar and its laser-based equivalentknown as LIDAR.1 Geographic Infor-mation Systems (GIS) can help aligndata to the right plots, and infraredthermometers can measure plant tem-

peratures. White raises the possibilityof low-power X-rays being tested. Helikens these developments to being inthe Wild West, where there are almostno rules.

There are so many great technolo-gies coming out all the time. Whowould have thought you could have a3D camera?

Wading through the availabletechnologies is the first hurdle, Whiteacknowledges.

How do you decide what is intel-

lectually neat but not useful? Theresgoing to be many years of researchfiguring out what works and whatdoesnt.

He adds that a given phenotypingapproach may work better for one

crop than for others.

Soybeans and corn are easy tar-gets, but it would be more challengingto examine every wheat plant becauseof the tillers.

Next, it takes testing the limits of asystem with real-world experiments.

Its one thing to have a proof ofconcept, and another thing to havesomething that will work robustly inthe field.

White is also part of a team at the

University of Arizona that is devel-oping a way to analyze phenotypesin the field from the seat of a tractor,which is already having good results.

Tracking Plants with Tractors

ASA, CSSA, and SSSA memberMichael Gore was formerly a researchgeneticist at the USDA Arid-LandAgricultural Research Center in Mari-copa, AZ and has recently accepted afaculty position in the Department ofPlant Breeding and Genetics at Cor-

nell University. He worked with PedroAndrade-Sanchez, an assistant profes-

sor in the Department of Agriculturaland Biosystems Engineering at theUniversity of Arizona, on developinga high-clearance tractor outfitted withan array of sensors to study droughtand heat tolerance in cotton. WhenGore first came to Arizona, he wasfaced with the challenge of quicklyand accurately measuring many phe-notypes in the field.

He needed to record several kindsof data at once, which he realizedwould require an army of techni-

cianseach with expensive equip-ment. One day, he saw a high-clear-ance tractor outfitted with a handhelddevice that can record the greennessof the crop based on its reflectance,a trait called normalized differencevegetation index (NDVI), and a lightbulb went on in his head.

The more I drilled into it I realizedit could be entirely possible to build ahigh-throughput platform to measurecanopy temperature, reflectance, andheight, Gore recalls.

Companies such as Germany-basedLemnaTec have developed systems forphenotyping individual plants in large,robotic greenhouses. Using technologiescombining photography, uorescenceimaging, 3D image analysis, and datahandling, thousands of individual plantscan be grown and automatically trackedthrough their development. A conveyorconstantly moves potted plants aroundthe greenhouse and through a series ofscanning chambers. Photo by LemnaTec.


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2See www.plantphenomics.org.au/HRPPC.

3See www.csiro.au/ICT.

The tractor they built can measurethe temperature of the plants them-selves with infrared thermometersand use ultrasonic proximity sensorsto get the height of the plants. Theyare also testing out LIDAR, an opticalremote-sensing technology to studycanopy architecture.

Driving the tractor through a fieldof cotton with more than 600 plots

that are 28 ft high takes less than anhour and allows Gore to preciselymeasure how the plants in his experi-ment respond to heat and droughtunder sufficient and limited irrigationregimes. And the system allows himto capture this data four times a daythroughout the growing seasonafeat never possible before.

Its greatest power is in visualizingtraits that cannot be easily scored.Canopy temperature can change veryrapidly, so there is a narrow windowfor robust measurements, Gore says.

He adds that his data give him atrue average of the whole plot, ratherthan measuring a few representa-tive plants. Since every data point isattached to its geographical position,the effects of edges and alleys onplants can be eliminated by trimmingit out of the data.

We have pretty good confidencein what were doing, Gore says.

With his recombinant inbred popu-lation and his phenotyping platform,Gore says these high-throughput traitsare heritable, and the quantitative traitloci for these traits can be mapped. Heis excited about the prospect of usingthis technology to measure pheno-types in many environments andanswer some fundamental biologicalquestions.

What I would love to do is tohave a high-throughput phenotypingplatform that can be cloned and thenused by breeders all over the UnitedStates. We can use the same platformto target the same traits and reallyinvestigate genotype by environmentinteractions on a national scale.

Flying High with the

Phenocopter

On the other side of the world,researchers at CSIRO (the Com-monwealth Scientific and IndustrialResearch Organisation) are also inter-ested in capturing field phenotypesen masse. CSIROs approach takesthem into the realm of automatedflying robotics. By modifying aremote-controlled gas-powered modelhelicopter, the researchers have devel-oped a versatile autonomous platformcalled the phenocopter.

ASA and CSSA member ScottChapman is a principal researchscientist at CSIRO and adjunct profes-sor at the University of QueenslandsQueensland Alliance for Agricultureand Food Innovation. Leading a teamworking on breeding for adaptation toclimate change, he is studying wheatand its response to environmentalstresses such as heat and drought.While CSIRO colleagues at the Aus-tralian Plant Phenomics Facility2workmainly on ground platforms, Chap-man wanted to measure the tem-peratures of an entire field of plantsquickly.

The only way I could think about

how to do it was to do it from the air,he says.

Hiring a piloted helicopter to flyover the field is expensive and disrup-tive to the plants. But Chapmans col-league, Torsten Merz from the CSIROICT Centre,3had already developedan autonomous helicopter-based sys-tem for surveying power lines, so theymodified it for applications in cropresearch. Underneath the helicopter,they installed several camerasvisual, near-infrared, and far-infrared

(thermal)and triggered them in pre-planned repeatable missions.

The phenocopter flies by itself,making multiple passes over a 1-hafield in just six minutes, providingdata that can help Chapman measureplant height, canopy cover, lodg-ing, and temperature throughout a

This high-throughput phenotypingsystem developed at the USDA Arid-

Land Agricultural Research Center inMaricopa, AZ is being used to collectplant height, canopy temperature, andcanopy reectance data from cottonplants. Photo by Michael Gore.


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4See www.iplantcollaborative.org.

day. Along with temperature sensorsplaced throughout the field, he saysthat he can see how plants respond tostress.

It allows us to see which plots areheating up faster, so we can see whichplants are modulating their wateruse. Over time, the ones that cantmodulate their water use will get hotbecause they run out of water supply.

Working with autonomous helicop-ters takes some additional software,Chapman notes.

You need software to plan mis-sions when you arrive, to gather theimages, and to extract data for plotswithin the images.

But this approach, he says, canafford some advantages. Phenotype-gathering helicopters can be pro-

grammed to measure experimentaltrials in farmers fields and return theneeded data. Because it is a fully auto-mated robot, the CSIRO helicopter canfly beyond visual range.

In the near future, Chapmanbelieves that small aerial robots willmake their own decisions about whento fly based on the weather or followa breeders instructions to fetch livephotos across the field and beam themto a field tablet.

Sorting Out the Data

Handling large amounts of dataand making sense of it presents a bigchallenge for high-throughput pheno-typing. The phenocopter, for instance,only generates about three gigabytes

of data per flight. Spalding has takenhundreds of thousands of images ofdeveloping seedlings with his roboticcamera, adding up to terabytes ofstorage. And while it currently gathersdata in the gigabyte range, Gore couldeasily see his tractor platform producea terabyte of data per run.

A major problem is that right nowwe dont have a good data manage-ment system in place, White says.

He is looking to the iPlant Col-laborative4and CGIARs IntegratedBreeding Platform for assistance withmanaging phenotypic data.

Spalding has an interest in devel-

oping the cyberstructure necessary tohandle the data being generated in thefield. He says scientists have to thinkabout how to move data from where itis collected to where it will be storedand processed for the investigator.Thumb drives are not the way to dothis efficiently. We have to conceive ofa set of technologies that will supportphenotyping activity in high through-put, robustness, and automation,Spalding says.

As a principal investigator on agrant from the Office of Cyberin-

frastructure at the National ScienceFoundation, Spalding is seeking toidentify the most limiting steps forhigh-throughput phenotyping.

Our goal is to come up witha blueprint for the kind of cyberinfrastructure that will make it moreefficient.

Thumb drives are not the way to

[manage data] effi ciently. We have to

conceive of a set of technologies

that will support phenotyping activity in

high throughput, robustness, and automation.

Researchers at CSIRO use a remote-controlled gas-powered model helicopter

called the phenocopter to measureplant height, canopy cover, lodging, andtemperature throughout a day. Picturedhere are Scott Chapman (left), a principalresearch scientist at CSIRO, and TorstenMerz, developer of the phenocopter.


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Plant height data collected by thenear-infrared camera on the pheno-copter can be used to estimate lodg-ing across plots. Images courtesy ofScott Chapman, CSIRO.

By collaborating with researchersworking in labs and fields, and withdifferent types of data, Spalding hopesto find patterns in what is rate limit-ing in this process.

If you have ideas, I would liketo invite you to participate in thisproject!

Ultimately, Chapman would like tosee the phenotype results right away.

With the many current systems,

it takes hours or days to process thedata, whereas if we can process it liveand extract all the data for each plot,then we can make a decision rightthere whether to fly the phenocopteragain for more measurements. Wegenerate even more phenotypes byrunning computer simulations of plotsbased on the image data.

Analyzing the data can also presenta significant challenge. Chapman iscurrently experimenting with extract-ing wheat flowering time and lodgingscores from aerial photographs, and

Whites colleagues in Arizona areworking on transforming LIDAR datainto a useful description of canopyarchitecture. These require a heavyinvestment in computer science.

With new sensors for measuringplants, we can derive new traits thatwere not considered before becausethey were not seen, Gore explains.

If you were to correlate a spikein reflectance with an important trait,

that is a new trait you can use forbreeding, he says. It changes yourconcept of what is a phenotype.

As computer science is increas-ingly used to assemble and describethe data, some associations will seemstrange and non-intuitive. Spaldingdescribes how this transition takesplace when he measures the pheno-type of a seed with a three-dimen-sional array of CCD (charge coupleddevice) cameras.

Imagine that seed now has40 numbers associated with it fromour three-dimensional image of theseed. We describe that seed with avector. We dont even have a physicalconcept of what some of those num-bers mean other than length, width,and color. Theyre all just mathemati-cal transformations of numbers, butperhaps some linear combination ofthem will actually, for reasons wedont understand, have some correla-tion with important traits such as leaf

angle, planting density, and so on.Thats the mind shift that phe-

notyping technologies are bringing.Theres value in measuring pheno-types together to get what we want,and later if you want to, you canfigure out why. It will lead to new hy-potheses. It is going to cause people tocome up with new ideas for explana-tions. What drives it will be its utilityin improving selection.

Sifting through all this data will beno easy task though, Gore points out.

Soon we will have hundredsto thousands of traits gathered bytechnologies such as fluorescence,imaging, and spectroscopy. What doyou do with that next? How do youcapture the most information contentfrom that and apply it to your breed-ing program? That question needs tobe answered sooner rather than laterbefore high-throughput phenotypingcan have a big impact on breeding.

Universally, they agree that de-veloping these technologies requiresconnections not only between plantscientists, but also with agriculturalengineers and computer scientists.For these pioneering efforts, a littlecreativity goes a long way.

Chapman, for instance, had onceconsidered being an engineer, but nowhe is able to bring that interest into hiswork in the field.

I get to see the most modern,cutting edge of wireless and roboticsapplied to food production, which isthe most ancient technology humansdeveloped. The molecular labs do thisall the time, but to do it live in thefield is something different.

Gore adds, The whole world isin a sense wide open. I think that in

the next few years, we will see somereally interesting advances in high-throughput phenotyping that peoplehavent even thought about yet andthat will be really fun.

Karl Haro von Mogel, contributing writer

for CSA Newsmagazine


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Seminar 1 03242014 Phenomics Revolution Science 2013