Exploitation of the onion genome to develop breeding tools for resistance against three pathogenectic fungi

The goal of the project is to exploit the recently sequenced genome of onion (Allium cepa) to develop tools for disease resistance breeding.

We will analyse resistance gene sequences in onion and compare them with those of two related Allium species, Allium roylei and A. fistulosum that contain resistance traits to Fusarium, Botrytis or Stemphylium, through bio-informatic analyses of the available onion genome and the generation of new sequence data from resistance gene amplicons. These complementary approaches will generate an inventory of the absence/presence of resistance genes (or gene families) and of their allelic variation.

An interspecific cross population obtained between from a cross A. cepa x F1(A. roylei x A. fistulosum) is available and was used in the past to detect QTLs for resistance to Botrytis leaf blight and Fusarium basal rot. Co-localization and association analyses will be performed of gene sequences emerging from these analyses with QTLs conferring resistance to these fungi, in order to provide molecular markers for breeding programmes. In addition, we will perform transcript analyses of infected onion plants and (partially resistant) interspecific hybrids, to generate insight in resistance mechanisms.

Companies will use the developed plant materials for validation of resistance and for performing further crosses to introgress disease resistance into onion. The project will form an example to demonstrate how a genome sequence of an outbreeding crop may be used to screen for useful genetic variation in wild relatives, and how tools such as markers can be generated to speed up the introgression and selection steps and make them more precise.