Leptosphaeria maculans Infection of Brassica spp.

Blackleg, caused by the fungal pathogen Leptosphaeria maculans is a devastating disease affecting canola plants (Brassica species), leading to significant economic losses every year. Effective and sustainable methods must be developed to manage this disease. Next generation sequencing (NGS) technology provides a variety of tools that enable us to scrutinise any organism at the genomic level. The identification of genes underlying important traits is extremely challenging in complex genomes such as Brassica napus (canola/oilseed rape). However, recent advances in next generation sequencing enable much quicker identification of candidate genes for traits of interest, including through a pan genome approach. These include skim based genotyping by sequencing (GBS), gene loss and presence-absence variation (PAV) analysis. Here we demonstrate the utility of these tools for the identification of candidate disease resistance genes from B. napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg), as well as to study the genomes of blackleg isolates. Avirulence (Avr) gene candidates. Analysis of the complete genome sequence of B. napus identified candidate CC-NBS-LRR and TIR-NBS-LRR family genes implicated in disease response, several of which were clustered around a region syntenic with major loci for blackleg resistance.  Molecular analyses of these candidate genes using skim-GBS in diverse cultivars and segregating populations, along with initial validation, will be presented. These methods are also being used to characterise the genomic diversity of the pathogen and to identify the difference in selection pressure in various regions of the genome, providing insights into the genome variation and function within this pathogen. Genomic information about this pathogen will better equip us to manage blackleg disease and reduce future crop losses.