ICARDA'S phenotyping facilities: A game-changing solution for abiotic stress tolerance in crops

Global crop production faces significant obstacles such as abiotic stresses like heat, pests, and water scarcity due to climate change that can combine to significant yield reductions. Rapid population growth also increases demand beyond supply and further stresses production methods.

However, thanks to new image-based phenotyping methods that can determine a plant's genetic traits within specific environments, and sophisticated data analysis techniques such as machine learning, we can now dissect abiotic stress tolerance mechanisms in relevant plants and unlock new valuable traits to breed into new, resilient crop varieties. High-throughput phenotyping (HTP), which speeds up the phenotyping process, is revolutionizing breeding programs by increasing the intensity and accuracy of the selection processes.

PhysioTron Machine

ICARDA, with the support of the African Economic and Social Development Fund (AFESD), began modernizing its breeding programs in 2020. Initial work focused on integrating genomic prediction (forecasting the traits of plants) in the breeding pipelines before research moved to speed breeding technology to expedite breeding methods and HTP for increasing selection accuracy and intensity.

ICARDA's phenotyping facilities: a phenomenal breakthrough

ICARDA's phenotyping facilities are located in Morocco, with a phenomobile system (PhenoBuggy) based at the central research station in Marchouch (Rabat) and a precision phenotyping platform located at Sidi el Aidi (Settat). The precision phenotyping platform, created in collaboration with the National Institute for Agricultural Research of Morocco (INRA) and CIMMYT, hosts a rainout shelter fully automated lysimeter (PhysioTron) equipped with an HTP system designed for drought and heat stress tolerance studies. Data collected from those and other ICARDA strategic testing locations across its mandate region are combined and used to provide elite germplasm to our NARES partners.

The PhysioTron is a marvel of modern technology, housing up to 750 plots, 1.5 meters in depth, filled with soil according to soil profiles specified by the station. Its fully automated control system offers flexibility for designing a wide range of experiments that allow for applying various and controlled water regimes in each of the ten sectors. A mobile gantry will enable researchers to access middle plots without disturbing the earth of side plots. The system has a LiDAR and two RGB cameras for assessing green fraction, greenness, plant and spike counting, height, and biovolume.

a) Physiotron facilities overview, b) Details of the fully automated system, c) Details of the HTP system measurement head, d) Overview of the Sidi el Aidi Station.

Rooting for Root Architecture Traits

Roots are essential for plants to withstand abiotic stress caused by climate change, such as drought and waterlogging, as well as the knock-on effect on nutrient levels, especially nitrogen and phosphorus. These challenges will become more frequent and severe in the future, but we still don't fully understand how they affect crop production. Luckily, ICARDA's dedicated research on root phenotyping has already resulted in the development of drought-resistant crop varieties in its mandate regions.

ICARDA's researchers use advanced techniques, like "shovelomics" and "root coring," to uncover the secrets of root architecture and its impact on grain yield and drought tolerance. These efforts are crucial for ensuring that crops can thrive even in the harshest conditions, helping to safeguard food security in a changing world.

ICARDA is collaborating with other institutions under two EU-funded projects, Root2Res and BarleyMicroBreed, to develop faster and more efficient methods of identifying crop germplasm with beneficial root architecture traits. Roots2Res aims to design new tools for evaluating root traits, understanding the genetic control of root and rhizosphere function, and studying interactions between plant roots and microbiota to develop more sustainable and drought-adaptive crop varieties. BarleyMicroBreed will optimize the capacity of plant roots to interact with existing soil microbiota to improve resource use efficiency and stress resilience.

The projects will advance our mechanistic understanding of interactions between the crop plant genome, root phenotypic traits, and the root-associated microbiota to identify innovative breeding strategies that will lead to drought-adaptive barley varieties.