Genome Mapping in the Flax Rust Fungus Melampsora lini Reveals Novel Avirulence Genes

Rust fungi such as Melampsora lini (flax rust) and Puccinia graminis fsp tritici (wheat stem rust) form specialised haustoria structures during infection that serve as nutrient uptake sites as well as delivering effector proteins to the host cell. We have been investigating the molecular basis and cellular location of the recognition events between R and Avr proteins, as well as characterising Avr protein structure and function. Four avirulence (Avr) loci are known in flax rust and encode effectors that are recognised by host nucleotide-binding and leucine-rich repeat (NB-LRR) resistance proteins. Recently we generated a draft genome sequence of 190Mbp for flax rust represented in 21,000 contig sequences. Using RADseq, we have scored ~13,000 SNP markers in an M. lini F2 family to generate a large scale linkage map that has allowed anchoring of 67% of the genome sequence onto 28 linkage groups. This process identified physical regions co-segregating with several Avr genes and one avirulence inhibitor locus. Two new Avr genes have been cloned and confirmed by expression in resistance flax lines. Gene expression profiling during rust infection of flax reveals a common expression pattern for a subset of effector candidates that includes all of the known Avr genes.