Plant breeding for food safety

Project Rationale:

Food security often focuses on food production, but reduced food waste and enhanced quality and safety are important targets for food resilience. Leafy crops have the potential to provide nutrient dense and versatile fresh produce, but eaten raw, with minimal processing, they provide a risk to human health and are prone to losses from microbial spoilage. Leaves are host to diverse and numerous community microorganisms and with the availability of high throughput DNA sequencing approaches, new insights into the abundance and diversity of these plant-associated microorganisms are emerging. They have a significant impact on the quality, shelf-life and safety of fresh leafy produce, but they vary depending on climate, plant traits, agricultural practices and microbial colonisation. This project will focus on the extended phenotype that exists between leaf-based traits in lettuce and the abundance and diversity of microbes that form the unique leaf microbiome that sits in a biofilm across the leaf surface. The project will explore which leaf-based traits can be linked to safer, cleaner food production systems and the genetic basis of these plant-based traits will be identified using quantitative genetic approaches, as our latest research shows these to be tractable. At the same time we have access to wide GWAS populations of lettuce for leaf microbiome analysis. This project will provide novel pre-breeding insight into better food for the future through molecular plant breeding.

Methodology:

The project combines plant, microbial and genomic sciences, working in the field, laboratory and in significant data analysis bioinformatics pipelines. We will utilize the latest genomic technologies, focused on meta barcoding, including novel approaches developed in the laboratory of GT to sequence the microbiome of leaf surfaces, with successful protocols already in place. We will investigate leaf surface, anatomical and chemical profiles using molecular genetic approaches in mapping populations to map QTL for leaf and microbial traits. We will, test the hypothesis that leaves with large cells, high surface hydrophobicity and low stomatal numbers are less favorable for microbial growth. This will be complemented with amplicon (meta bar-coding) and shotgun sequencing of the microbiome, as approrpiate where a significant bioinformatic skill set will be developed during the project (for which training will be given). Interesting leaf genotypes will be explored in more detail and developed as ‘model leaves’ to investigate attachment and proliferation characteristics for pathogens (E. coli, Salmonella, Listeria) and spoilage organisms (Pseudomonas). At the same time, work on-farm growing crops in commercial systems will also be undertaken in the UK and California with input from both the California Leafy Green Research Board and Vitacress Salads Ltd (VSL).

Training:

The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at School of Biological Sciences but will also spend significant periods of time based in the laboratory of Gail Taylor at the University of California, Davis. Specific training will include attendance on taught courses in Quantitative Genetics, R, Plant Breeding and the specialist seminar series available in Agronomy and Horticulture, Plant Biology. Specialist training in DNA extraction and manipulation, field growing and salad horticulture, microbiome shotgun and metabarcoing sequencing, data handling, and bioinformatics will be given. At the same time, the CASE partner, Vitacress Salads is one of the largest suppliers of fresh cut leafy green and culinary herbs in Europe and the student will benefit from time spend with the company, with three former PhD student being employed there following PhD completion and through access to cutting edge commercial agronomy and interaction with major supermarkets.