Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression

Author summaryIn the face of world population growth and climate change, the development of crops with increased yield and stress resilience is more urgent than ever. A major bottleneck in this process is translating the results of lab experiments to the field, in part because plant growth conditions in a lab are very different from field conditions. Here, we assess the merits of an alternative approach in which data is generated directly in the field, thereby bypassing the translation step. We profiled the gene expression and trait variability of a population of genetically (nearly) identical rapeseed plants grown in the same field, and used machine learning models to link the individual plants' gene expression to their phenotypic traits. We find that the plants' yield traits in spring can be predicted to a considerable extent from gene expression profiled > 5 months earlier in autumn. More importantly, we find that the top predictors in these models function in processes known to affect autumnal plant growth and development. This shows that our single-plant omics approach can be used to identify genes and processes influencing crop yield in the field. In the plant sciences, results of laboratory studies often do not translate well to the field. To help close this lab-field gap, we developed a strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants. Here, we use this single-plant omics strategy on winter-type Brassica napus (rapeseed). We investigate to what extent early and late phenotypes of field-grown rapeseed plants can be predicted from their autumnal leaf gene expression, and find that autumnal leaf gene expression not only has substantial predictive power for autumnal leaf phenotypes but also for final yield phenotypes in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. Our results show that single-plant omics can be used to identify genes and processes influencing crop yield in the field.

Automated summary

In this study, the authors developed a strategy for studying plant traits directly in the field, bypassing the translation step from lab experiments. They found that gene expression in autumn can predict yield traits in spring for rapeseed plants. The top predictor genes are involved in developmental processes that occur in autumn, indicating the influence of autumnal development on crop yield.