Stem rust resistance gene Sr43

Sr43 is a stem rust resistance gene discovered in Thinopyrum ponticum several years ago that is effective against Ug99 and related strains (1-3). Although it was transferred to hexaploid wheat (Triticum aestivum), it has not been used in breeding programs. The original translocations replaced large segments of wheat chromatin with Th. ponticum material carrying genes that negatively affected several quality traits. Among these genes there is one responsible for yellow color in flour.

Niu et al. (4) re-analyzed the original translocation lines carrying Sr43, KS24-1 and KS10-2 and confirmed that KS24-1 is a 7DS.7el2L Robertsonian translocation in which most of the chromatin of chromosome arm 7DL was replaced with Th. ponticummaterial. In contrast with its original description, the authors showed that KS10-2 is a 7DS-7el2S.7el2L translocation. Chromosome arm 7DL and a large part of 7DS were replaced with segments from chromosome 7 of Th. ponticum. Based on this information and to reduce the Th. ponticum chromatin accompanying Sr43, the authors developed a BC2F1 population of ph1b-induced homoeologous recombinant lines between wheat line Chinese Spring ph1b  and translocation line KS10-2. Two of these recombinant lines, designated RWG33 and RWG34 carry Sr43, the remaining Th. ponticum chromatin in these lines represent 17.5 and 13.7% of the original translocation chromosome. The authors also found two molecular markers linked to Sr43 in these lines.

Both lines, RWG33 and RWG34, have an increased flour yellow color, intermediate between the wheat parent and KS10-2.  They also present reduced kernel hardness. These traits turn these lines inappropriate for bread making, although they could be used in breeding programs for noodle varieties. The contents of ash and protein in flour did not show significant differences between wheat Chinese Spring, Thatcher, KS10-2, RWG33 and RWG34.

Niu et al. (4) reported that a project is underway to develop lines derived from RWG33 and RWG34 carrying Sr43 with a reduced amount of Th. ponticum chromatin and without the locus (or loci) responsible for the yellow color.

It has not been ruled out that Sr43 is an allelic variant of Sr25. Until further mapping data become available, users of these genes should be careful, check the parents and the responses to disease.

Markers for Sr43

In genetic backgrounds without ph1b mutations, the Th. ponticum translocations are not expected to recombine with wheat chromatin. In consequence, any marker located on the translocation, irrespective of its physical distance to Sr43, would be useful for monitoring transfer. Niu et al. (4) found two molecular markers specific for the translocation: SSR locus Xcfa2040 and EST-derived marker Xrwgs30.

Primers sequences: 


cfa2040-F        5'- TCA AAT GAT TTC AGG TAA CCA CTA -3'

cfa2040-R       5'- TTC CTG ATC CCA CCA AAC AT -3'


rwgs30-F       5'- CTC TTG GTG CCA CAC TCT GA -3'

rwgs30-R       5'- TCA GTT CCC TCC CAT TCA TC -3'

PCR conditions for both markers:

  • Denaturing step: 95°C, 5 min
  • Amplification step (45 cycles):
    • 95°C, 40 sec
    • 56°C, 40 sec
    • 72°C, 60 sec
  • Extension step: 72°C, 10 min

Expected products

The PCR products were separated on a 8% non-denaturing polyacrylamide gel.

Both molecular markers were validated with 32 wheat lines and cultivars. In all wheat germplasm lacking Sr43 Xcfa2040 amplified a PCR fragment of either 258-, 260-, 261- or 262-bp, while the allele linked to Sr43 produced a 233-bp fragment. At the Xrwgs30 locus a 1500-bp allele was detected in all wheat lines and a 1078-bp product in KS10-2 and derived lines carrying Sr43.

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


1. The transfer to wheat and homoeology of an Agropyron elongatum chromosome carrying resistance to stem rust. Knott DR, Dvorak J, Nanda JS. In: Canadian Journal of Genetics and Cytology, 1977, 19:75–79. [Journal link]

2. Transfer of stem rust resistance to wheat from an Agropyron chromosome having a gametocidal effect. Kibiridge-Sebunya I, Knott DR. In: Canadian Journal of Genetics and Cytology, 1983, 25:215–221. DOI: 10.1139/g83-035

3. Evaluation and characterization of seedling resistances to stem rust Ug99 races in wheat-alien species derivatives.Klindworth DL, Wang RRC, Cai X. In: Crop Science, 2009, 49:2167-2175. DOI: 10.2135/cropsci2009.02.0074

4. Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum. Niu Z, Klindworth DL, Yu G, L Friesen T, Chao S, Jin Y, Cai X, Ohm JB, Rasmussen JB, Xu SS. In: Theorical and Applied Genetics, 2014, 127:969-980. DOI: 10.1007/s00122-014-2272-4