Exploiting anatomical traits to accelerate breeding of novel stress tolerant crops

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.

Root anatomical traits such as aerenchyma (RCA) formation enable plants to acquire more soil resources for less metabolic investment and significantly improves yield under drought and suboptimal nutrient conditions. 'Anatomics', a novel interdisciplinary approach, now makes it possible to rapidly image and analyse anatomical traits in large numbers of crop species. Using this approach, my US partners generated root anatomical data for hundreds of maize varieties grown over 5 years in South Africa. I recently analysed it using integrated Genome wide association studies, literature mining and enhanced data visualisation techniques.

My gene-discovery pipeline associated several candidate genes with RCA formation including bHLH (ROS signaling) and EIL (ethylene signaling) transcription factors. Further, maize bhlhtf transposon insertion line and rice oseil1 mutant showed significant reduction in RCA formation confirming their functional role.

As a BBSRC Discovery Fellow, I will first use CRISPR gene editing approach to determine molecular mechanisms by which these key genes regulate RCA formation under drought and nutrient stress. Next, I will generate a cellular resolution gene expression atlas using Laser Capture Microdissection coupled Single-Cell RNA sequencing approach to map cell-specific developmental programmes employed in RCA formation during root growth and development. This research in maize will uncover key genes that control RCA formation and help understand how this trait confers drought and nutrient stress tolerance. It will also provide a proof of principle for characterizing other root anatomical traits. Finally, I will develop "RCA Trait Molecular Markers" to translate the knowledge generated in maize to other important and often under-invested crops such as pearl millet. The marker-assisted selection of pearl millet varieties with improved RCA formation and stress tolerance will help accelerate the breeding and genetic improvement programmes.

My proposed research will determine molecular mechanisms controlling root cortical aerenchyma formation in maize that enables greater acquisition of soil resources and substantially improves crop yield. Additionally, the research outputs will provide timely avenues by identifying novel allelic variants in related cereals such as pearl millet that are drought tolerant and nutrient efficient. Thus my research will directly contribute to one of the key aims of BBSRC - exploiting genomics for agriculture and global food security.

Prospective beneficiaries and how they may benefit.

1. Farmers and breeders: Farmers and breeders are likely to be the direct beneficiaries of this research as it will identify stress tolerant genetic variants in maize and pearl millet. These varieties will be able to grow better on low nutrient soil without or with reduced fertilizer applications and thus would have major economic impact on developing countries, where a large proportion of farmers don't have ready access to fertilizers. Further, it will help to reduce fertilizer inputs to make agriculture environmentally sustainable. Thus, the improved crops will promote low input agriculture, better returns and likely have impact on farm income leading to improved nutritional, financial and social stability.

2. Breeding institutes and companies: The knowledge i.e. gene toolkit and molecular markers from my research in Maize and Pearl Millet could be transferred to other economically important crop plants such as sorghum, rice and wheat. Thus other breeding research institutes (International Maize and Wheat Improvement Center: CIMMYT, International Crops Research Institute for the Semi-Arid Tropics: ICRISAT, etc.) and companies (Syngenta, Monsanto, etc.) will also benefit from this research.

3. Academic and industrial researchers: The research will generate a number of new resources (mu insertion, CRISPR-Cas9 mutants, transcriptional and translational reporters, repression lines, Anatomics Molecular Markers, pear millet allelic variants with improved RCA and stress tolerance, etc.) and datasets (Gene expression atlas, Control versus Stress RNAseqs, LAT images for maize mutants and Pearl Millet inbred lines, field phenotype data, etc.) that will benefit a wide spectrum of researchers from other disciplines in academia as well as industry. Additionally, it provides an example of using Anatomics approach for studying other agronomic processes controlled at the anatomical scale (e.g. crop water use efficiency, xylem vessel diameter, etc.). Understanding key genes or signals in regulating root cortical traits under developmental and environmental cues will enable researchers to design new approaches to manipulate root anatomical traits in crops. This research will also create a knowledge base that will allow the commercial sector to exploit and generate IP and new products in the future.

4. Members of the public: They will benefit from the dissemination of my research outputs through science outreach activities specifically developed for distinct non-specialist audiences, such as children from local schools and members of general public. Such outreach will increase public awareness and understanding of global food security issues and the social and economic impact of plant and crop research. This will also inspire students to consider science, especially plant and agriculture research, as a future career option.