LiDAR

Collaborating for the common good: CIMMYT and CSIRO meet to capitalise on strengths

Plant scientists around the world share a common goal:  understanding plants to improve their tolerance of environmental stresses, resist disease and ultimately, increase yield. Global collaborations that share knowledge and technology are rich in experience and are essential to help accelerate our understanding to meet future challenges.

A recent meeting in El Batán, Mexico, is an excellent example of great minds coming together. Three team members from the Australian Plant Phenomics Facility joined host institution, CSIRO, and CIMMYT in a two-day workshop aimed at achieving critical steps towards a common framework for field phenotyping techniques, data interoperability and sharing experience.

CSIRO at CIMMYT

Front row:  Warren Creemers (4th from left), Xavier Sirault (5th) and Michael Schaefer (7th)

“Capitalising on our respective strengths, we developed basic concepts for several collaborations in physiology and breeding, and will follow up within ongoing projects and through pursuit of new funding,” said Matthew Reynolds, CIMMYT wheat physiologist, signaling the following:

  • Comparison of technologies to estimate key crop traits, including GreenSeeker and hyperspectral images, IR thermometry, digital imagery and LiDAR approaches, while testing and validating prediction of phenotypic traits using UAV (drone) imagery.
  • Study of major differences between spike and leaf photosynthesis, and attempts to standardise gas exchange between field and controlled environments.
  • Work with breeders to screen advanced lines for photosynthetic traits in breeding nurseries, including proof of concept to link higher photosynthetic efficiency/performance to biomass accumulation.
  • Validation/testing of wheat simulation model for efficient use of radiation.
  • Evaluation of opportunities to provide environment characterisation of phenotyping platforms, including systematic field/soil mapping to help design plot and treatment layouts, considering bioassays from aerial images as well as soil characteristics such as pH, salinity, and others.
  • Testing the heritability of phenotypic expression from parents to their higher-yielding progeny in both Mexico and Australia.
  • Extraction of new remote sensed traits (e.g., number of heads per plot) from aerial images by machine learning (ML) of scored traits by breeders and use of ML to teach those to the algorithm.
  • Demonstrating a semantic data framework’s use in identifying specific genotypes for strategic crossing, based on phenotypes.
  • Exchanging suitable data sets to test the interoperability of available data management tools, focusing on the suitability of the Phenomics Ontology Driven Data (PODD) platform for phenotypic data exchanges, integration, and retrieval.

CSIRO and CIMMYT share a long history in crop modelling and physiology, spanning more than 40 years. CIMMYT works throughout the developing world to improve livelihoods and foster more productive, sustainable maize and wheat farming. The centre’s portfolio squarely targets critical challenges, including food insecurity and malnutrition, climate change and environmental degradation. Through collaborative research, partnerships, and training, the centre helps to build and strengthen a new generation of national agricultural research and extension services in maize- and wheat-growing nations. As a member of the CGIAR System composed of 15 agricultural research centres, CIMMYT leads the CGIAR Research Programs on Maize and Wheat, which align and add value to the efforts of more than 500 partners.

 

Canberra, Camille and the Cropatron…

As the sun rises over another crisp autumn morning in Canberra, you will find French intern, Camille Mounier, keenly watching over her rice lines in the Cropatron at the Australian Plant Phenomics Facility’s node at CSIRO Agriculture and Food.

Her project, ‘A complex system biology approach to understand the factors affecting canopy photosynthesis’, is being led by Dr Xavier Sirault, Director of the node, in partnership with the Chinese Academy of Sciences.

The project team aim to develop system models of canopy photosynthesis for both rice and wheat, in particular, developing novel methods to combine these system models with phenomics data. This approach will help in the identification of the critical factors controlling photosynthetic energy conversion efficiency in C3 species with the view to improving canopy photosynthetic efficiency, and subsequently, crop yields in small grain cereals.

Using the Cropatron platform, Camille will acquire data on canopy growth, gas and energy exchange in order to validate the biophysical photosynthetic model developed by Prof Xinguang Zhu, Head of Plant Systems Biology Group at the CAS-MPG Partner Institute for Computational Biology.

The Cropatron is a PC2 compliant, fully environmentally controlled (temperature, CO2 and humidity) greenhouse equipped with an automated gantry system (operating at 3.5m above the floor) for proxy-sensing imaging of plants grown in mini canopies. The sensing head is composed of an hyperspectral camera (400-1000nm) for measuring chlorophyll pigments, Far IR imaging for proxy sensing of canopy conductance, LiDAR for quantifying canopy architecture and monitoring growth over time, lysimeters for measuring water use at plot level and a gas exchange chamber at canopy level for measuring canopy assimilation.

Academic and commercial plant scientists are welcome to access the Cropatron platform – find out about pricing, availability and bookings here.