Genotypic variation of Puccinia graminis infecting barberry and grasses

Abstract: Stem rust on cereals is a large problem in parts of the world, and it may reduce the yields significantly. It is caused by Puccinia graminis, a heteroecious basidiomycete with 365 known telial host grass species. Puccinia graminis reproduces asexually on the grass host. The sexual reproduction is completed on the alternate hosts barberry or mahonia. In Sweden, due to harsh winters, sexual reproduction is crucial for maintaining the population and spreading the disease. This has lead to the Swedish population of P. graminis being very genetically diverse. The most efficient way to avoid infection of P. graminis is the use of resistant cultivars. In places with a high rate of sexual reproduction eradication of barberry is a good management strategy. Puccinia graminis has undergone genetic differentiation in relation to their host species. This has given rise to the concept of formae speciales (f. sp.). A forma specialis is adapted to infect one or a few host species. The agronomically most important ones are P. graminis f. sp. tritici (Pgt), P. graminis f. sp. avenae (Pga) and P. graminis f. sp. secalis (Pgs) who infect wheat, oats and rye respectively. Barley is susceptible to both Pgt and Pgs. This thesis aims to examine which formae speciales are present in Sweden and also se if they can be distinguished using molecular techniques. The samples in the study were collected from barberry, cereals and grasses at different locations in Sweden. According to established definitions on the host species of the formae speciales Pgt, Pga and Pgs are present in Sweden. By sequencing the Internal Transcribed Spacer (ITS) region along with genes Elongation Factor 1 alpha (EF1-α) and Cytochrome Oxidase Subunit 1 (COI) the phylogenetic relationships of the different formae speciales was investigated. The sequences only distinguish between two phylogenetic clades; one containing samples collected from hosts susceptible to Pga and the other with hosts susceptible to Pgt and Pgs. Within Pga, a subclade of P. graminis f. sp. dactylis forms. The role of barberry in the epidemiology of stem rust was investigated by using microsatellites (SSR) and examine if the same multilocus genotypes (MLG) are found on barberry and nearby grasses at the same location. The same MLG:s were not found but some of the populations from the respective locations proved to have a common ancestry. The SSR data was also used to try to confirm the results from the phylogenetic study. There were statistically significant differences in genotype between the Pgt and Pga clades but not as consistent as for the phylogenetic study. In addition to the common disease management strategies the use of crop rotations alternating between cereals susceptible to Pgt and Pga would decrease the risk of infection as well. Future studies should focus on further investigate the differences between Pgt and Pga in order to determine if they could be regarded as two different species. The differentiation within Pga is also an interesting future study.