Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system

Abstract

Nondestructive plant phenotyping is fundamental for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-through phenotyping facilities can further our understanding of plant development and stress responses, their high costs significantly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant growth and evapotranspiration. We paired these devices with a suite of computational pipelines for integrated and straightforward data analysis. We validated the suitability of our system for large screens by evaluating a cowpea diversity panel for responses to drought stress. The observed natural variation was subsequently used for Genome-Wide Association Study, where we identified nine genetic loci that putatively contribute to cowpea drought resilience during early vegetative development. We validated the homologs of the identified candidate genes in Arabidopsis using available mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of species.

Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis

“…To investigate SR3G's contribution to salt stress tolerance beyond seedling stage and agar plate conditions, we evaluated the performance of Col-0 and sr3g-5 mutant in soil. We exposed the soil-grown plants to salt stress and imaged the rosette size every 30 minutes for two weeks using the automated imaging platform (L. 'ang Yu et al 2023). As salt-induced changes depend on the developmental stage at which the stress is applied (Julkowska et al 2017), we examined the role of SR3G exposed to salt stress at 2 or 3 weeks after germination, corresponding to early and late vegetative stages.…”

“…We then allowed the pots to be drained for 2-3 h to eliminate excess moisture. The pots were placed under phenotyping rigs equipped with an automated imaging system (L. ’ang Yu et al 2023) and the pot weight was measured daily to maintain the reference weight corresponding to 50% of the soil water holding capacity throughout the experiment.…”

“…To evaluate the growth of soil-grown plants, we used an in-house developed automated imaging system using Raspberry Pi cameras to capture the growth dynamics over the period of two weeks (L. 'ang Yu et al 2023). The collected images were processed using PlantCV pipeline (Gehan et al 2017), followed by the data analysis in R, as described here (https://rpubs.com/mjulkowska/sr3g_Maryam2021OctNov).…”

Tapping into the plasticity of plant architecture for increased stress resilience

“…[237][238][239] Improving genomic resources for wild crop relatives and indigenous crops provide better resources for development of diversity panels and mapping populations. [240][241][242][243] Forward genetic studies, such as genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping, combined with more accessible plant phenotyping, [244][245][246] will help to identify new genetic regions associated with changes in plant architecture, productivity and stress resilience.…”