A Co‐Dominant PCR‐Based Marker for Assisted Selection of Durable Stem Rust Resistance in Barley

Screening individual barley plants for resistance to stem rust is difficult and time consuming. The objective of this work was to develop PCR‐based markers for assisted selection of stem rust resistance in barley. Near isogenic barley lines (backcrossed 29 times) differing at the Rpg1 locus (where the gene that confers resistance to the stem rust pathogen Puccinia graminis t. sp. tritici is located) were screened for random amplified polymorphic DNAs (RAPDs) with 10 base primers. A total of 540 different primers were screened, and one was identified which amplified a DNA fragment closely linked to Rpg1. The DNA fragment was cloned, mapped, and sequenced. Specifically amplifying primers (SAPs) were designed to amplify related polymorphic DNA in other barley cultivars. The SAPs act as a co‐dominant marker suitable for marker assisted selection of the Rpg1 gene. Three different amplification patterns were observed in the various cultivars tested. Surprisingly, no specific banding pattern is diagnostic for the presence or absence of Rpg1, despite the demonstrated linkage. Of the three amplification patterns, only one (the 500‐bp banding pattern) was present in recently developed resistant cultivars. A similar amplification pattern is also found in many of the susceptible lines that have the cultivar Betzes in their pedigree. RFLP analysis can be used to differentiate the resistant and susceptible cultivars with this amplification pattern.