Stem rust resistance gene Sr50

Sr50 is a stem rust resistance gene translocated into wheat from rye cultivar Imperial. It is effective against Ug99 races of Puccinia graminis f. sp. tritici and was introgressed into wheat chromosome 1D by translocation from the short arm of rye chromosome rye 1R (1). Two other stem rust resistance genes were also transferred from rye chromosome 1R, Sr31 and SrRAmigo. Using genetic and molecular analysis, Mago et al. (1) showed that Sr50 is a different gene.

Sr50 is homologous to barley locus Mla, a powdery mildew resistance gene, and codes for a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB- LRR) protein, which is a common feature of several rust resistance genes. The genomic region where Sr50 is located harbors seven related CC-NB-LRR genes. Using comparative genomic analysis with a susceptible sr50 deletion mutant, generation of additional EMS sr50 mutants and complementation tests with transgenic plants, Mago et al. (1) demonstrated that, out of those seven, ScRGA1-A was the CC-NB-LRR gene responsible for Sr50 resistance. The protein encoded by Sr50 recognizes an effector pathogen protein, AvrSr50, that is produced at the uredinial stage and delivered into the plant cells during infection (2).  

Markers for Sr50

Mago et al. (1) developed a perfect PCR marker for Sr50 (Sr50-5p-F3/R2) that was tested on a set of rye accessions, but until now it was not widely validated in wheat germplasm. There is another molecular marker, IB-267, that was developed several years before the gene was cloned, and tightly linked to Sr50 in rye (3). Since the rye translocation in wheat recombines as a single block, only one marker is necessary. We recommend to test these markers on the donor and recurring parents of the breeding program.

Primer sequences from Ref. 1:

Sr50-5p-F3       5'- TTC AGT GAA GTT GCC GCT GT -3'

Sr50-5p-R2       5'- GCA TGC TCT CAA GCT CCT TCT -3'

Primer sequences from Ref. 3: 

IB-267-F       5'- GCA AGT AAG CAG CTT GAT TTA GC -3'

IB-267-R       5'- AAT GGA TGT CCC GGT GAG TGG -3'

Amplification conditions for IB-267

  • Denaturing step: 94°C, 3 min
  • Amplification step (35 cycles):
    • 94°C, 30 sec
    • 55°C, 60 sec
    • 72°C, 60 sec
  • Final step: 25°C, 60 sec
Conditions presented here should be considered only as a starting point of the PCR optimization for individual laboratories.


1. Sr50 gene reveals rich diversity at a cereal disease resistance locus. Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo MC, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y. In: Nature plants, 2015, 1:15186. DOI:10.1038/nplants.2015.186.

2.AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R.  In: Science, 2017, 358(6370):1607-1610.DOI:10.1126/science.aao4810.

3. Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines. Mago R, Spielmeyer W, Lawrence G, Lagudah E, Ellis J, Pryor A.  In: TAG Theoretical and Applied Genetics, 2002, 104(8):1317-24. DOI:10.1007/s00122-002-0879-3.