Validation and Marker-Assisted Selection of Stem Rust Resistance Gene Sr2 in Indian Wheat Using Gel-Based and Gel-Free Methods

Stem rust resistance gene Sr2 is an important slow-rusting gene which has provided resistance against stem rust for many years. The Sr2 gene has durable resistance against all stem rust pathogens including the Ug99 group of races. It shows recessive inheritance and is linked with two phenotypic markers, Pseudo Black Chaff (PBC) and High Temperature-Induced Seedling Chlorosis (HTISC). However, direct screening as well as phenotypic marker-based screening for selection of Sr2 is difficult due to the effect of environmental factors and genetic background. Microsatellite marker Xgwm533 linked to Sr2 gene is useful for rapid screening of large populations. Here we report validation and use of Xgwm533 for screening 21 wheat lines and 24 wheat genotypes for the presence of the Sr2 gene. Furthermore, we also report the presence of a new, smaller allele (97 bp) of Xgwm533 locus in a few genotypes that was also confirmed by sequencing. We also demonstrate a new SYBR green dye, melt-curve/profile-based assay for convenient screening of the Xgwm533 locus, where the presence of different alleles can be differentiated in a gel-free manner.