Stem rust resistance gene Sr49

The Watkins wheat collection is a set of landraces collected by A. Watkins in the 1920s (1).  The current collection has around 1200 accessions, and it is housed at the John Innes Centre Germplasm Resource Unit, in the UK, and at the Australian Winter Cereal Collection, in Tamworth, Australia. A genome-wide association study of a set of wheat landraces from the Watkins collection identified candidate stem rust resistance loci in chromosomes 1BL, 3A, 3B, 4BL, 5BL, 6BS and 7BS (2).

One of the landraces from the Watkins collection, landrace Mahmoudi (AUS28011) collected in Ghardimaou, Tunisia, carries a stem rust resistance gene that produces an all-stage response against all Australian pathotypes of Puccinia graminis f. sp. tritici that are virulent for other resistant genes currently deployed in commercial cultivars (3).

The stem rust resistance gene of Mahmoudi was designated Sr49 and it was mapped on the long arm of chromosome 5B.  Bansal et al (3) developed a mapping population from the cross of Mahmoudi and the susceptible cultivar Yitpi. Using this population they found two PCR markers flanking Sr49 that can be used for breeding, sun209, 1.5 cM on the distal side and sun479, 0.9 cM proximal.

Markers for Sr49

Primer sequences: 

sun479-F       5´- CAA ATG AAA TGT GAT CCT GTT -3´

sun479-R       5´- TCA TCT AAC CAG CAA TGG TAT -3´


sun209-F        5´- AGA CTA TGA GCT TCG CTA TTG -3´

sun209-R        5´- GTG ATT GGT TCG GAT TAC TTA -3´

PCR conditions

  • Denaturing step: 95°C, 10 min
  • Amplification step (35 cycles):
    • 92°C, 30 sec
    • 60°C, 40 sec
    • 72°C, 50 sec
  • Extension step: 72°C, 7 min

Expected products:

In the resistant Mahmoudi parent sun209 amplified a product of 148-bp and sun479 produced a band of 200-bp. These markers were validated in a set of 152 cultivars that did not carry Sr49. A few cultivars from the validation panel yielded a PCR product similar to that of Mahmoudi for one of the markers. However, none of those cultivars showed the alleles linked to Sr49 for both markers. In the case of sun479 PCR products can be separated on 2% agarose gel. For sun209, the different allele sizes differed in 2 to 10 bp, so a different separation method is required.

Conditions presented here should be considered only as a starting point of the PCR optimization for individual laboratories.


1. Establishing the AE Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat. Wingen LU, Orford S, Goram R, Leverington-Waite M, Bilham L, Patsiou TS, Ambrose M, Dicks J, Griffiths S. In: Theoretical and Applied Genetics, 2014, 127:1831-1842. DOI: 10.1007/s00122-014-2344-5.

2. Exploring wheat landraces for rust resistance using a single marker scan. Bansal UK, Arief V, Delacy IH, Bariana HS. In:Euphytica, 2013, 194:219–233. DOI: 10.1007/s10681-013-0940-0.

3. Mapping of a new stem rust resistance gene Sr49 in chromosome 5B of wheat. Bansal UK, Muhammad S, Forrest KL, Hayden MJ, Bariana HS. In: Theoretical and Applied Genetics, 2015, 128:2113–2119. DOI: 10.1007/s00122-015-2571-4.