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EASTBIO Adaptive introgression and cold tolerance in British Rhododendron ponticum – a genomic approach


School of Biological Sciences

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Dr R Milne No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Second Supervisor Dr Mario Vallejo-Marin University of Stirling
Project Description for Advert (max 500 words). This will be the text that is advertised to prospective students:

Rhododendron ponticum is invasively naturalised over much of the British Isles, which is much colder than its native range (Spain and Turkey). Naturalised material contains introgressed (transferred by hybridisation) DNA from the highly cold-tolerant American R. catawbiense, and such DNA is more frequent in colder regions of the UK, suggesting but not proving that introgression from R. catawbiense confers increased cold tolerance.
This project would make use of the full genome sequence of R. ponticum, recently generated by co-supervisor Dr Jianquan Liu’s group in China. This will be used as a basis for designing a set of RNA baits to capture sequence data from hybrid populations and herbarium samples. The bait set will comprise candidate cold tolerant genes, plus single copy genes well dispersed over the genome, to allow for FST scanning to detect frequency of introgressed regions from R. catawbiense, and to determine if cold-tolerance associated genes are over-represented in the introgressed set.

Hybridization with R. catawbiense happened in cultivation before naturalisation, followed by numerous plantings all over the country, >120 years ago. Flowering begins after ~12 years but plants live >100 years, making it unclear how many generations have passed, during which selection could have acted. Theoretically, invasive naturalised populations might have short generation times and reproduce mainly by seed due to leading edge effects as they expand their range, compared to native stands where seed establishment opportunities are few due to competition, leading to long generation times and a bigger role for clonal spread. To test this, age structures of native and naturalised populations can be determined using tree rings, and the proportion of catawbiense DNA in each individual can tell us the minimum number of generations since hybridisation; clonal spread can be inferred from morphological and DNA markers,

Every naturalised British population has an independent history in the wild, and each therefore will provide replicate tests for selection effects. Moreover, certain naturalised (“slope”) populations are spread over a range of altitudes, allowing for differential selection on cold-tolerance genes within such populations.

The student will collect and examine material of R. ponticum from naturalised populations, especially from the top and bottoms of slope populations, and from native sites; also R. catawbiense material for genetic reference. Genome regions and bait loci showing evidence of positive selection will be studied, using the full R. ponticum genome sequence and the literature, to identify the key cold tolerance loci.
This project combines fieldwork and evolutionary biology with NGS and bioinformatics. The student will also forge connections with China and professional rhododendron breeders.

https://www.ed.ac.uk/biology/people/profile/rmilne2
http://www.plant-evolution.org/wp/
https://www.rbge.org.uk/about-us/organisational-structure/staff/tropical-diversity/dr-catherine-kidner/
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The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity




Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants. Please refer to UKRI website (https://www.ukri.org/our-work/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions (https://www.ukri.org/wp-content/uploads/2020/10/UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf) for full eligibility criteria.

References

Milne RI, Abbott RJ (2000). Origin and evolution of invasive naturalized material of Rhododendron ponticum L. in the British Isles. Molecular Ecology, 5: 541-556.
Hart ML, Forrest LL, Nicholls JA, Kidner CA (2016) Retrieval of hundreds of nuclear loci from herbarium specimens Taxon, 65 1081-1092
Nicholls JA, et al. (2015). Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the the neotropical rain forest genus Inga (Leguminosae: Mimosoideae) Frontiers in Plant Biology 6:710. doi: 10.3389/fpls.2015.00710
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