Exploiting anatomical traits to accelerate breeding of novel stress tolerant crops

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Drought and low soil fertility are major constraints to global crop production. These constraints are becoming even more challenging over time due to deteriorating soil quality, increasing population pressure and changing climate. In this context, recent discoveries have identified several root anatomical traits that can substantially improve crop yield and climate resilience by improving water and nutrient uptake. For example, the formation of air spaces (termed aerenchyma) in root cortex tissue occurs when living cells undergo programmed cell death. This significantly reduces nutrient demand and respiration of root tissues, enables plant to acquire more soil resources and improve crop yield under drought and suboptimal nutrient conditions. In addition to aerenchyma formation, other traits such as reduced number and layers of living cells in the cortex tissue (termed cortical cell count and cortical cell file number respectively) confer similar benefits. However, despite this knowledge, anatomical traits have received little attention as selection criteria in crop breeding because of the challenges associated with sampling and quantification of anatomical phenotypes."Anatomics" is a novel interdisciplinary approach that now makes it possible for the first time to rapidly image and analyse plant anatomical traits in large numbers of crop varieties. Using this approach, my US collaborators generated root anatomical data for hundreds of maize varieties grown over 5 years in South Africa. Next, I analysed this dataset using an integrated gene-discovery pipeline that includes Genome wide association studies (GWAS), literature mining and enhanced data visualisation techniques. This analysis highlighted correlations between the anatomical data and hundreds of thousands of DNA polymorphisms in the maize diversity panel and thus pinpointed key genes that control root anatomical traits in maize. For instance, my pipeline identified two novel transcription factors functionally associated with aerenchyma formation. Mutation analysis of a maize mu insertion and a rice ortholog mutant for these transcription factors found a significant reduction in aerenchyma percentage in the mutants compared to the wild type. These studies confirmed the role of representative genes obtained from the Anatomics datasets in aerenchyma formation. However, the molecular mechanisms underlying the regulation of aerenchyma development are largely unknown. As a BBSRC Discovery Fellow, I will pioneer the use of anatomics and functional genomics approaches in cereal crops at University of Nottingham. My first objective will be to determine the molecular mechanism for aerenchyma mediated resilience in maize. Next, I will use Laser Capture Microdissection and Single-Cell RNA sequencing approaches to generate a cellular resolution gene expression atlas for the maize root and map genes and signals that control aerenchyma formation during root growth and development. Finally, I will translate the knowledge generated in maize to other important and often under-invested crops such as pearl millet to accelerate breeding and genetic improvement programmes. Aerenchyma formation is a developmental programme where specific cells within the same cortical layer undergo programmed cell death while neighboring cells survive. My spatiotemporal gene expression atlas of maize root at cellular resolution will be an unparalleled resource to characterise aerenchyma as well as other root anatomical traits and developmental programmes. Further, the gene regulatory mechanisms unravelled from this research will also help us to understand how such traits confer stress tolerance in maize and pearl millet crops which are economically important dietary staples. Thus, my research will also contribute to UK's global food security efforts.