Sequencing seeds for the future: development of tools for efficient utilisation of crop genetic diversity

   School of Life Sciences

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  Dr Charlotte Allender  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Global food security if facing multiple threats from climate change, population growth and the need to adopt farming methods that use fewer inputs such as irrigation. Fertilizer and pesticides. New crop varieties offering increased performance and resilience in changing environments will form a significant part of the solution to these issues. Crop genepool diversity is the raw material used by plant breeders; accumulating knowledge of comparative variation within crops is a valuable activity which can improve efficiency in plant breeding. Understanding how diversity is partitioned across different parts of a crop genepool (modern cultivars, traditional varieties and wild species, and over the geographical range of the crop in question) can help access novel variation. Genebanks such as the UK Vegetable Genebank hold collections of crop diversity in the form of large seed collections, often holding thousands of samples. Developments in sequencing technologies, approaches and bioinformatics mean that it is now feasible to obtain sequence information at a matching scale.

Some of the most important crops in the word pose significant challenges to such genomic characterisation, requiring a range of approaches to obtain key information on allelic diversity. Onion (Allium cepa L.) is a key vegetable crop, with global production in 2021 of over 106 Mt. It is a diploid species (2n=2x=16), however the large genome size of 16Gb means that development of sequence and other genomic resources has not matched those in other crops. Onions are also outcrossing crops exhibiting inbreeding depression, and the pace of breeding is reduce by a biennial life history. The UKVGB has >1100 samples of onion in its collections, spanning a wide range of geographic origins and morphological types. This project will use the UKVGB resources to understand onion genepool diversity, inter and intra varietal variation and develop tools and resources for future onion breeding and research. In particular the project will develop a GWAS (Genome Wide Association Study) approach in onion, linking genomic variation with key phenotype data related to morphology and life history such as bulb colour, shape, daylength sensitivity, and chemical composition. You will use techniques such as RNAseq as a technique to look at both allelic variation and gene expression in a panel of >300 samples. The project will build and develop links with key stakeholders such as commercial onion breeders to better understand their needs. The project will also utilise and develop a range of phenotyping methods including image analysis.


  • Transcriptome sequencing (RNAseq)
  • Whole genome sequencing
  • Phenotyping of plants under glasshouse or other controlled conditions – development of image analysis tools
  • Bioinformatic analysis

Principal Supervisor: Dr Charlotte Allender

Secondary Supervisor(s): Dr Graham Teakle

University of Registration: University of Warwick

Lab Page: Warwick Genetic Resources Unit

BBSRC Research Themes: Sustainable Agriculture and Food (Plant and Crop Science)

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Labate JA, Glaubitz JC, Havey MJ. Genotyping by sequencing for SNP marker development in onion. Genome. 2020 Dec;63(12):607-613. doi: 10.1139/gen-2020-0011. Epub 2020 Aug 27. PMID: 32853533.
Richard Finkers, Martijn van Kaauwen, Kai Ament, Karin Burger-Meijer, Raymond Egging, Henk Huits, Linda Kodde, Laurens Kroon, Masayoshi Shigyo, Shusei Sato, Ben Vosman, Wilbert van Workum, Olga Scholten, Insights from the first genome assembly of Onion (Allium cepa), G3 Genes|Genomes|Genetics, Volume 11, Issue 9, September 2021, jkab243,

 About the Project