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

Global food security is 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 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.
Onion (Allium cepa L.) is a key vegetable crop, with global production in 2021 of over 106 Mt. It has a very large genome size (16Gb) meaning that development of DNA sequence and other similar resources has not matched those in other crops. Onions are also outcrossing crops, and the pace of breeding is reduced 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 link genetic diversity with physical and life history traits such as bulb colour, shape and daylength sensitivity. The project will develop links with stakeholders such as commercial onion breeders to better understand their needs.