Towards understanding Duckweed evolution - genomic and experimental approaches.

There is an urgent need for simplified plant systems for human and animal food production and synthetic biology applications. Accordingly, there has been growing interest in duckweeds, an eminently tractable system, with biomass doubling times of as little as 30 hours, massive worldwide diversity collections, and obvious synthetic biology potential, given their small, sequenced 150mb genome and amenability to genetic manipulation. Further, duckweed has the proven capacity to remediate polluted water and shows great potential as a feed resource, especially in developing nations where this is most needed. Recent evidence also supports its use in controlling mosquitoes and algae. Duckweed aquaculture fits easily into many crop/animal systems managed either by small farmers or on commercial scales. Duckweed farming does not require arable, fertile land and has the convenient ability to improve the quality of the nutrient-rich wastewater, minimizing the need for fertilization. This makes these plants a novel and exciting system of aquatic agriculture with high potential. Indeed, when effectively managed duckweeds yield 10-30 ton DW/ha/year containing up to 43% crude protein, 5% lipids and highly digestible dry matter. Additionally, duckweed grown on nutrient-rich water has a high concentration of trace minerals, K, P and pigments, particularly carotene and xanthophyll, that make duckweed meal an especially valuable supplement for poultry and other animals, and it provides a rich source of vitamins A and B for humans. However, much can be done now optimize the use of duckweed, as well as to leverage this system for fundamental studies in the evolutionary genomics of adaptation.
This project merges population genomic resequencing scans and phenotype-first elemental accumulation (~20-element 'ionomics') to explore the genomic basis of adaptation in duckweed populations and to characterise the potential of these plants. The project will involve collection of new duckweed accessions UK-wide and analysis of water ionomes and light environments. We will use and further develop as needed our established pipelines and techniques to duckweed diversity in order to understand the genomic basis of its adaptations to various environments. This work expands recent successful studies from the Yant Lab to this promising system.
Aim 1. Characterise the adaptation of duckweeds to extreme environmental conditions. This will include phenotyping up to 700 accessions (200 UK, 200 Iberian Peninsula and 300 'Landolt' lines available to us) in a novel high throughput phenotyping platform. Assays include multi-elemental 'ionomics' and growth parameters in diverse growth conditions using automated high-tech phenotyping platforms. Altered light environments and media manipulation are experimental techniques which will be used to explore physiological, ionomic and growth differences between different duckweed species. These data will feed directly into aim 2.
Aim 2. Population Genomics of adaptation in duckweeds. What is the genomic basis for the ionomic, physiological, morphological, and other traits we observe? What loci mediate these adaptations and what are the precise genomic signatures of local adaptation in this system? We have a quality reference for Spirodela polyrhiza and established pipelines for state-of-the-art population genomic analysis, as well as high throughput Illumina library preparation protocols in robotics systems for easy resequencing of hundreds of genomes. We begin by sequencing the most phenotypically extreme 400 genomes for in depth demographic analysis and selection scans (including high density GWAS) and assays for gene flow and hybridisation, a current major interest in the Yant Lab. This will produce a wealth of information on the genomics basis of diverse adaptations, as well as candidate alleles mediating consequential adaptations.