Genomics accelerated isolation of a new stem rust avirulence gene - wheat resistance gene pair

Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled by genetic resistance in the latter half of the 20th century, new strains of Pgt with increased virulence, such as Ug99, have evolved by somatic hybridisation and mutation. These newly emerged strains have caused significant losses in Africa and other regions and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases. A number of race-specific rust resistance genes have been characterised in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class. These receptors recognize pathogen effector proteins often known as avirulence (Avr) proteins. However, only two Avr genes have been identified in Pgt to date, AvrSr35 and AvrSr50 and none in other cereal rusts, which hinders efforts to understand the evolution of virulence in rust populations. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale) which is a wheat-rye hybrid and is a host for Pgt. Sr27 is effective against Ug99 and other recently emerged Pgt strains. Here we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.