Plant Phenomics Education

There are many ways to learn about and develop skills in plant phenomics. The APPF offers Postgraduate Internship Awards, assistance in accessing facilities, as well as research publications, events and network linkages, and teaching resources.

Study

We offer support for students to access to our plant phenotyping capabilities

The APPF is committed to facilitating world-class plant phenomics research. To assist with access to our state-of-the-art plant phenotyping technology and growth environments, we offer support to postgraduate students from varied disciplines to access the very best tools and experience to accelerate their research.

In addition, we list grant directories below that may assist both researchers and students in finding further support. If you know of other international directories that should be included on this list, please let us know.

Postgraduate Internship Awards (PIA)

The Postgraduate Internship Awards (PIA) involve students joining the APPF team as interns, learning about experimental design, and image and data analysis, as they undertake collaborative projects using our cutting-edge plant phenotyping technology. This is an excellent opportunity for students to investigate their plant science questions with the support of the highly skilled APPF team.

Learn more

Watch

TEDxKAUST Talk by Professor Mark Tester

Professor Tester elegantly articulates the current problem of depleting fresh water resources and increasing food demand. His solution to solving food and water security issues is to unlock the salt-tolerant capabilities of various agricultural crops.

Further reading

Papers on phenotyping and related topics

The following papers will provide further information on phenotyping and related topics. If you wish to suggest topics and references, please contact us.

Towards recommendations for metadata and data handling in plant phenotyping
Krajewski P, Chen DJ, Cwiek H, van Dijk ADJ, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S (2015). Journal of Experimental Botany, 66, 5417-5427. DOI: org/10.1093/jxb/erv271

Agronomic data: advances in documentation and protocols for exchange and use
Hunt LA, White JW, Hoogenboom G. (2001). Agricultural Systems, 70, 477-492. DOI: org/10.1016/S0308-521X(01)00056-7

Field-based phenomics for plant genetics research
White JW, Andrade-Sanchez P, Gore MA, Bronson KF, Coffelt TA, Conley MM, Feldmann KA, French AN, Heun JT, Hunsaker DJ, Jenks MA, Kimball BA, Roth RL, Strand RJ, Thorp KR, Wall GW, Wang G (2012). Field Crops Research, 133, 101-112. DOI: org/10.1016/j.fcr.2012.04.003

Field high-throughput phenotyping: the new crop breeding frontier
Araus J.L. & Cairns J.E. (2014). Trends in Plant Science, 19, 52-61. DOI: org/10.1016/j.tplants.2013.09.008

Field high-throughput phenotyping:  The new crop breeding frontier
Araus JL, Cairns JE (2014). Trends in Plant Science vol 19 issue 1, 52-61. DOI: org/10.1016/j.tplants.2013.09.008

A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects
Arvidsson S, Perez-Rodriguez P, Mueller-Roeber B. (2011). New Phytologist, 191, 895-907. DOI: 10.1111/j.1469-8137.2011.03756.x

Integrating image-based phenomics and association analysis to dissect the genetic architecture of temporal salinity responses in rice
Campbell MT, Knecht AC, Berger B, Brien CJ, Wang D, Walia H (2015). Plant Physiology 168(4), 1476-1489. DOI: 10.1104/pp.15.00450

Dissecting spatiotemporal biomass accumulation in barley under different water regimes using high-throughput image analysis
Neumann K, Klukas C, Friedel S, Rischbeck P, Chen D, Entzian A, Stein N, Graner A, Kilian B (2015). Plant Cell and Environment, 38, 1980-1996. DOI: 10.1111/pce.12516

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up
Fahlgren N, Gehan MA, Baxter I (2015). Current Opinion in Plant Biology, 24, 93-99. DOI: org/10.1016/j.pbi.2015.02.006

Other reading

Book chapter: Perspectives in High-Throughput Phenotyping of Qualitative Traits at the Whole-Plant Level

Remote sensing of vegetation: principles, techniques, and applications
Jones HG, Vaughan RA (2010). Oxford University Press, New York.

A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in setaria
Fahlgren N, Feldman M, Gehan Malia A, et al. (2015). Molecular Plant, 8, 1520-1535. DOI: org/10.1016/j.molp.2015.06.005

Integrated analysis platform:  An open-source information system for high-throughput plant phenotyping
Klukas C, Chen D, Pape J-M (2014). Plant Physiology, 165, 506-518. DOI: org/10.1104/pp.113.233932

The iPlant collaborative: cyberinfrastructure for plant biology
Goff SA, Vaughn M, McKay S, et al. (2011). Frontiers in Plant Science, 2. DOI: org/10.3389/fpls.2011.00034

A semi-automatic system for high throughput phenotyping wheat cultivars in-field conditions: description and first results
Comar A, Burger P, de Solan B, Baret F, Daumard F, Hanocq J-F (2012). Functional Plant Biology, 39, 914-924. DOI: org/10.1071/FP12065

High-throughput non-destructive biomass determination during early plant development in maize under field conditions
Montes JM, Technow F, Dhillon BS, Mauch F, Melchinger AE (2011). Field Crops Research, 121, 268-273. DOI: org/10.1016/j.fcr.2010.12.017

Development and evaluation of a field-based high-throughput phenotyping platform
Andrade-Sanchez P, Gore MA, Heun JT, Thorp KR, Carmo-Silva AE, French AN, Salvucci ME, White JW (2014). Functional Plant Biology, 41, 68-79. DOI: org/10.1071/FP13126

BreedVision – a multi-sensor platform for non-destructive field-based phenotyping in plant breeding
Busemeyer L, Mentrup D, Möller K, Wunder E, Alheit K, Hahn V, Maurer H, Reif J, Würschum T, Müller J, Rahe F, Ruckelshausen A (2013). Sensors, 13, 2830. DOI: 10.3390/s130302830

Development of a field-based high-throughput mobile phenotyping platform
Barker J, Zhang N, Sharon J, Steeves R, Wang X, Wei Y, Poland J (2016). Comput. Electron. Agric., 122, 74-85. DOI: org/10.1016/j.compag.2016.01.017

Quantification of plant stress using remote sensing observations and crop models: the case of nitrogen management
Baret F, Houles V, Guerif M (Jan 2007). Journal of Experimental Botany 58(4): 869-880, DOI: 10.1093/jxb/erl231

Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance
Messina CD, Podlich D, Dong ZS, Samples M, Cooper M (Nov 2010), Journal of Experimental Botany 62(3): 855-868. DOI: 10.1093/jxb/erq329

Future scenarios for plant phenotyping
Fiorani F, Schurr U (Feb 2013). Annual Review of Plant Biology 64: 267-291, DOI: 10.1146/annurev-arplant-050312-120137

Phenomics – technologies to relieve the phenotyping bottleneck
Furbank RT, Tester M (Nov 2011).  Trends in Plant Science, 16, 635-644.10, DOI: 1016/j.tplants.2011.09.005

Thermal and narrowband multispectral remote sensing for vegetation monitoring from an unmanned aerial vehicle
Berni JAJ, Zarco-Tejada PJ, Suarez L, Fereres E (2009). IEEE Transactions on Geoscience and Remote Sensing, 47, 722-738. DOI: 10.1109/TGRS.2008.2010457

Unmanned aerial systems for photogrammetry and remote sensing: A review
Colomina I, Molina P (2014). Isprs Journal of Photogrammetry and Remote Sensing, 92, 79-97. DOI: org/10.1016/j.isprsjprs.2014.02.013

Global learning:  Online plant science courses

Distance learning

Learn from the best around the world with online plant science courses:

  • Plant Breeding  (Wageningen University & Research)
    Are you looking for more theoretical background on plant breeding? This online course includes five modules, both basic, more complex breeding and selection methods, new technological developments, and underlying biological concepts. Distance learning offers you a flexible learning process and the possibility to compose your own course. It is ideal for professionals and enables them to study the lecture material at their own pace and place. This distance learning course has been successfully followed by a broad audience from more than twenty different countries and are well-rated.
  • Plant Pathology and Entomology  (Wageningen University & Research in cooperation with the Royal Netherlands Society of Plant Pathology (KNPV) and the Foundation Willie Commelin Scholten for Phytopathology (WCS))
    Are you looking for more theoretical background on plant pathology and entomology? This online course includes modules on phytopathology, nematology, entomology and virology. Distance learning offers you a flexible learning process and the possibility to compose your own course. It is ideal for professionals and enables them to study the lecture material at their own pace and place.

Helping students learn about plant phenomics

Phenomics is an area of biology concerned with the measurement of phenomes — the physical and biochemical traits of organisms — as they change in response to genetic mutation and environmental influences. The phenome being all the possible phenotypes of an organism and the phenotype being the observable characteristics of an organism.

Captured phenomics data enables the more rapid discovery of molecular markers and faster germplasm development, aimed at improving crop yields including the tolerance of major crops and other agriculturally important plants to biotic and abiotic stresses such as drought, salinity and a broad spectrum of plant diseases.

Plant phenomics specifically was defined by Furbank and Tester (2011) as:

“Plant phenomics is the study of plant growth, performance and composition. Forward phenomics uses phenotyping tools to ‘sieve’ collections of germplasm for valuable traits. The sieve or screen could be high-throughput and fully automated and low resolution, followed by higher-resolution, lower-throughput measurements. Screens might include abiotic or biotic stress challenges and must be reproducible and of physiological relevance. Reverse phenomics is the detailed dissection of traits shown to be of value to reveal mechanistic understanding and allow exploitation of this mechanism in new approaches. This can involve reduction of a physiological trait to biochemical or biophysical processes and ultimately a gene or genes.”

Furbank RT & Tester M (2011) Phenomics – technologies to relieve the phenotyping bottleneck. Trends in Plant Science, 16, 635-644.

Who undertakes phenotyping?

A whole range of people carry out phenotyping, even if they don’t call it that. Plant breeders, farmers, growers, agronomists, viticulturists, plant scientists, ecologists and environmental scientists all do phenotyping in various forms.

The recent interest in phenomics has been in part due to the rapid development of the other -omics technologies: genomics, metabolomics, transcriptomics, and proteomics. The cost of these technologies has decreased enough to allow routine use, which has in turn led to a “phenotyping bottleneck”, a need to be able to better understand gene function and plant response to environment.

However, phenomics has been around for a long time and is fundamental to plant science. There are very few papers published by plant scientists that don’t incorporate some phenomics (e.g. plant biomass measurements). Precision agriculture is heavily dependent on measuring plant performance. Growers are increasingly using new technologies to measure plant growth and yield. Plant breeders are dependent on good phenomics in measuring yield and quality traits in new varieties.

Modern phenomics is simply using new technologies to do what was done previously with greater accuracy or with greater ease, and to measure aspects of plant growth and physiology that previously were not possible or were not possible with high throughput and precision.

Plant phenomics is a science that has the power to transform our lives. By exploring how the genetic makeup of an organism determines its appearance, function and performance, phenomics can help us tackle these pressing challenges.

With a rapidly growing world population, a transformational advance in grain production must occur to increase yield by 50-60% to meet projected global food demand. Groundwater sources are declining around the world, increasing soil salinity and causing losses in crop production and grazing land in many countries.

These global production issues are particularly pertinent to Australia which faces long periods of heat, drought and increasing salinity, undermining farm productivity. Increasing the yield in crops, particularly in these marginal environmental conditions, using novel approaches that exploit robotics, machine learning, computer vision and genetics technologies will significantly increase global food quality and production, and reduce environmental degradation.

Australia is in an outstanding position in plant science. Australian agriculture is amongst the most innovative in the world and has tremendous growth opportunities, and Australian farmers are highly qualified and eager to adopt novel systems for efficient and sustainable farming. This is an exciting time for plant phenomics and plant science.

Humanitarian
According to the Food and Agriculture Organization of the United Nations (FAO), an expected population increase to 9 billion by 2050 will require our food production to double (1). As one of the most food secure nations in the world, Australia will need to play a major role in contributing to the food production demand.

Nutritional
Malnutrition and undernutrition as well as overweight and obesity impose high economic and social costs on countries at all income levels (2). Whilst the human and social consequences of poor nutrition are immeasurable, the costs of undernutrition and micronutrient deficiencies are estimated at 2-3 percent of global GDP, equivalent to US$1.4-2.1 trillion per year. The economic costs of overweight and obesity were estimated to be about US$1.4 trillion in 2010 (3).

Environmental
Crop production is aimed at increasing the quality and quantity of yield. This is a major challenge in the face of climate change, declining arable land and biotic and abiotic plant stresses. In addition, the overuse of fertilisers is causing environmental pollution. Watch this short story to learn more about the challenges of developing plant varieties that can better cope with drought and salinity.

Economic
Australia is one of the most food secure nations. Approximately 60% of our food production is exported to other countries. The food production export value in 2011/12 was $30.5 billion (4).

1  High level exert forum “How to feed the world 2050”, Rome, October 2009 http://www.fao.org/wsfs/forum2050/en/
2  FAO (Food and Agriculture Organization of the United Nations), “The State of Food and Agriculture”, 2013, p. ix
3  FAO (Food and Agriculture Organization of the United Nations), “The State of Food and Agriculture”, 2013, p. ix
4  Australian Government, Department of Agriculture, Food and Fisheries, “Australian Food Statistics 2011-12, p.2

Teaching aids

The Plant Phenomics Teacher Resource booklet and Powerpoint presentation

The Plant Phenomics Teacher Resource provides background knowledge about plant phenomics research and technology for upper secondary school teachers. The resource describes current Australian plant phenomics research and the technology behind the research, in the form of short background ‘briefing notes’ with accompanying images. We hope it helps you create interest among your students in this new and important field of science.

Download the resources here:

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