Sequencing the seaweeds: Using population genomic models to improve seaweed crop breeding

1. Overview
This studentship will look at the genetic basis of growth and development in green seaweeds, developing and strengthening an existing RCUK-funded collaboration between supervisors in Durham and Liverpool. The student will be based in Durham, but will work alongside a BBSRC-funded transnational network that links groups in the UK and India (the lead PI’s SuBBSea programme) and full training will be given to develop and encourage the student as an independent researcher. We are keenly aware of the importance of equality in science and would encourage any qualified candidates to apply.

2. Scientific background
The green macroalgae, or seaweeds, have intrinsic ecological value as the main ecosystem engineers across most UK and European coastlines and are also widely accepted to be one of the best potential second generation biofuel and biotechnology feedstocks. For these reasons, the past few years have seen a surge of interest in developing sustainable seaweed cultivation practices (= seaweed farms): seaweeds can be cultivated at low cost and grow more rapidly than terrestrial plants without competing for land or water resources.

However, for such cultivation to work, we need to develop selective breeding strategies that will maximise yield while minimising biosecurity risks (= spread of invasive species, effects of monocultures on coastal ecosystems). This will involve adapting modern crop breeding approaches (including quantitative genetic and genomic approaches) for use with marine crops and in marine ecosystems.

3. Specific aims and plan of work
The overarching aim of this studentship is thus to establish and develop quantitative genomic approaches to understand phenotypic variation in the commercially important green seaweed, Ulva spp. We will work towards applying the well-established mixed-effects model of selective breeding (the ‘animal model’) to understand how genetics influence seaweed growth, combining Durham’s seaweed expertise with Liverpool’s NBAF and bioinformatics facilities. Specific aims are:

a) To use whole-genome polymorphism data to identify loci associated with adaptation and growth in green seaweed populations worldwide. Relative to plants, very little is known about how seaweed phenotypes depend on genotypes, so work will assume Fisher’s model of many alleles, each having small effects. The student will begin by developing a bioinformatics pipeline (STACKS/Floragenex) to identify worldwide SNPs from existing RADseq data; the location of these SNPs (coding or non-coding) will be inferred from the Ulva reference genome being sequenced by the PI and co-I. The focus during this work will be on scanning for selection (identifying sweeps, etc.) using well-established genetic tools (Q-Q plots, single point/haplotype analysis) to highlight associations between geography and genotype.

b) To consolidate the scans for selection in a), above, with lab and mesocosm studies (in collaboration with current industrial partners) to identify causal genes involved in seaweed growth and development. Strains with desirable alleles of these genes will then be used to establish breeding populations and to develop sustainable seaweed aquaculture practices.