Stripe rust resistance gene Yr54

Quaiu 3 is a spring wheat line (Babax/Lr42//Babax*2/3/Vivitsi) with high yields and high levels of resistance against leaf and stripe rust. It has a good level of adult plant resistance against stripe rust, but it shows seedling stage susceptibility.

Basnet et al. (1) developed a mapping population of 182 F5 recombinant inbred lines by crossing Quaiu 3 with the susceptible line Avocet-YrA and tested it in field trials for two years. A genetic linkage map of 650 DaRT (Diversity Arrays Technology) and 130 SSR polymorphic markers was constructed and used for QTL analysis of disease data.

Four major QTLs for stripe rust resistance derived from Quaiu 3 were identified. One of them, QYr.tam-2D, was the most significant, detected in the four environments and explained 49-54% of the phenotypic variation. QYr.tam-2D is located on the long arm of chromosome 2D, close to the telomere.

There are other stripe resistance loci on chromosome 2D. Yr16 maps near the centromere and account for a smaller fraction of the phenotypic variance (10%) (2). Other QTLs with smaller effects were reported on 2DL but they map far from Yr54 (1). On the other hand, Jagger et al.(3) found a QTL, QPtst.jic.2D, in the German cultivar Alcedo on chromosome arm 2DL, that explained 34-53% of phenotypic variation based on percentage infection and infection type. In addition to this similarity in the proportion of variation explained, there is some overlap between the markers defining the intervals for QYr.tam-2D and QPtst.jic.2D. However, Quaiu and Alcedo do not share any significant ancestral relationship, and in consequence it is difficult to determine at this point whether they are allelic variations of the same loci.

Marker for Yr54

Basnet et al. (1) determined that Yr54 was flanked by DArT markers wpt-667162 (proximal) and wpt-667054 (distal) at a distance of less than 0.5 cM. Microsatellite marker Xgwm301 was also found at a distance of 0.5 cM and could be useful for breeding.

Primers sequences:


WMS301-F       5'- GAG GAG TAA GAC ACA TGC CC -3'

WMS301-R       5'- GTG GCT GGA GAT TCA GGT TC -3'

PCR conditions:

  • Denaturing step: 94°C, 3 min
  • Amplification step (45 cycles):
    • 94°C, 1 min
    • 55°C, 1 min
    • 72°C, 2 min
  • Extension step: 72°C, 10 min
Conditions presented here should be considered only as a starting point of the PCR optimization for individual laboratories.


1. Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3. Basnet BR, Singh RP, Ibrahim AMH, Herrera-Foessel SA, Huerta-Espino J, Lan C, Rudd JC. In: Molecular Breeding, 2014, 33:385–399. DOI:10.1007/s11032-013-9957-2.

2. Mapping of durable adult plant and seedling resistance to stripe rust and stem rust diseases in wheat. Bariana HS, Hayden MJ, Ahmed NU, Bell JA, Sharp PJ, McIntosh RA. In: Australian Journal of Agricultural Research, 2001, 52:1247–1255. DOI:10.1071/AR01040

3. The genetic characterization of stripe rust resistance in the German wheat cultivar Alcedo. Jagger L, Newell C, Berry S, MacCormack R, Boyd L. In: Theoretical and Applied Genetics, 2011, 122:723–733. DOI:10.1007/s00122-010-1481-8