Field-based phenomics for plant genetics research

Authors: White, Jeffrey; ANDRADE-SANCHEZ, PEDRO - University Of Arizona; Gore, Michael; Bronson, Kevin; Coffelt, Terry; Conley, Matthew; FELDMAN, KENNETH - University Of Arizona; French, Andrew; HEUN, JOHN - University Of Arizona; Hunsaker, Douglas - Doug; Jenks, Matthew; Kimball, Bruce; ROTH, ROBERT - University Of Arizona; Strand, Robert; Thorp, Kelly; Wall, Gerard - Gary; WANG, GUANGYAO - University Of Arizona

Submitted to: Field Crops Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/7/2012
Publication Date: 5/1/2012
Citation: White, J.W., Andrade-Sanchez, P., Gore, M.A., Bronson, K.F., Coffelt, T.A., Conley, M.M., Feldman, K.A., French, A.N., Heun, J.T., Hunsaker, D.J., Jenks, M.A., Kimball, B.A., Roth, R., Strand, R.J., Thorp, K.R., Wall, G.W., Wang, G. 2012. Field-based phenomics for plant genetics research. Field Crops Research. 133:101-112.

Interpretive Summary: Perhaps the greatest challenge for crop research in the 21st century is how to better predict the performance of crops by taking advantage of information from genetics, physiology, climatology and other fields. Advances in “next generation” DNA sequencing have greatly reduced the cost of obtaining genetic data. Methods for characterization of plant traits (“phenotypes”), however, have evolved little over the past 30 years, and our ability to rapidly measure plant traits limits our ability to predict crop performance, especially for traits related to economic yield and stress tolerance. Specially prepared sets of research materials for genetic studies may involve 20 or more crosses, each represented by as many as 200 lines, so scenarios of field trials involving over 20,000 research plots at a single location are possible. This paper defines key criteria, experimental approaches, equipment and data analysis tools required for measuring plant traits at an unprecedentedly large scale. The focus is on simultaneous measurement of multiple traits related to plant color (reflectance), temperature and architecture. The proposed “field-based phenotyping” (FBP) system uses a vehicle to move replicated sets of sensors over four or more individual plots at once and has the potential to record data throughout the life of a crop. For traits such as drought or heat tolerance, we expect plots should be assessed several times during a single day. The complex set of raw data will be analyzed with novel techniques to obtain values of specific, useful traits. Many of the underlying methods and instruments exist and are used in precision crop management. Innovations are required in integrating the multiple sets of instruments and ensuring efficient, robust analysis of the large volumes of data that are anticipated. Further development of sensors and imaging systems will continue to improve our ability to phenotype large experiments or crop breeding nurseries, but the core FBP abilities appear to be achievable through a strong interdisciplinary effort drawing largely on assembling existing technologies in novel ways. Developing FBP capabilities is key to allowing researchers to advance our understanding of how genetics influences crop yields and thus is key to breeding new varieties that ultimately benefit farmers and consumers in numerous ways.

Technical Abstract: Perhaps the greatest challenge for crop research in the 21st century is how to predict crop performance as a function of genetic architecture and climate change. Advances in “next generation” DNA sequencing have greatly reduced genotyping costs. Methods for characterization of plant traits (phenotypes), however, have evolved little over the past 30 years, and phenotyping capability constrains genetic dissection of quantitative traits, especially those related to economic yield and stress tolerance. Mapping populations for major crops may consist of 20 or more crosses, each represented by as many as 200 lines, so scenarios of field trials involving over 20,000 plots at a single location are possible. Here, we define key criteria, experimental approaches, equipment and data analysis tools required for robust, high throughput field-based phenotyping (FBP). The focus is on simultaneous proximal sensing for spectral reflectance, canopy temperature, and plant architecture where a vehicle carrying replicated sets of sensors records data on four or more individual plots at once and with the potential to record data throughout the crop life cycle. For traits such as adaptations to water deficits or acute heat stress, plots should be assessed several times during a single diurnal cycle to quantify stress recovery. Raw data are analyzed via inverse modeling to estimate values of specific physiological traits such as leaf area expansion rate. Many of the underlying techniques and requisite instruments already exist and are used in precision crop management. The main innovations required are in integrating multiple sets of instruments and ensuring efficient, robust analysis of the large volumes of data that are anticipated. Parallel with the core proximal sensing should be capabilities for high-throughput phenotyping of specific traits such as root architecture and seed composition and for “ground truthing” results with conventional field measurements. Further development of sensors and imaging systems undoubtedly will continue to improve our ability to phenotype very large experiments or breeding nurseries, but the core FBP abilities appear to be achievable through a strong interdisciplinary effort drawing largely on assembling existing technologies in novel ways.