RESEARCH ARTICLE Major haplotype divergen s

DOI 10.1186/s12870-014-0379-zvated emmer wheat cv Yaroslav from crosses initiated in1CSIRO Agriculture Flagship, Canberra, ACT 2601, Australia Full list of author information is available at the end of the articleBackground Wheat stem rust caused by the fungal pathogen Puccinia graminis Pers. f. sp. tritici (Pgt) is a major worldwide threat to wheat crops. The re-appearance of stem rust epidemics in East Africa and their spread eastward to Yemen and Iran, based on Ug99- a wheat stem rust iso-late virulent on a large proportion of the world’s current wheat varieties, has alarmed the global wheat commu-nity [1,2]. More recently, new epidemics of stem rust caused by a different race of Pgt have been reported in Germany and Ethiopia (2013–2014