Functional physiological phenotyping with functional mapping: A general framework to bridge the phenotype-genotype gap in plant physiology

The recent years have witnessed the emergence of high-throughput phenotyping techniques. In particular, these techniques can characterize a comprehensive landscape of physiological traits of plants responding to dynamic changes in the environment. These innovations, along with the next-generation genomic technologies, have brought plant science into the big-data era. However, a general framework that links multifaceted physiological traits to DNA variants is still lacking. Here, we developed a general framework that integrates functional physiological phenotyping (FPP) with functional mapping (FM). This integration, implemented with high-dimensional statistical reasoning, can aid in our understanding of how genotype is translated toward phenotype. As a demonstration of method, we implemented the transpiration and soil-plant-atmosphere measurements of a tomato introgression line population into the FPP-FM framework, facilitating the identification of quantitative trait loci (QTLs) that mediate the spatiotemporal change of transpiration rate and the test of how these QTLs control, through their interaction networks, phenotypic plasticity under drought stress.

Automated summary

Recent years have seen the emergence of high-throughput phenotyping techniques for studying plant physiological traits in response to environmental changes, yet a general framework linking these traits to DNA variants is still lacking. Researchers have developed a framework that integrates functional physiological phenotyping with functional mapping to understand how genotype translates into phenotype. This framework was demonstrated in a study using a tomato introgression line population to identify quantitative trait loci and explore how these loci control phenotypic plasticity under drought stress.