Stripe rust resistance gene Yr48

Contributed by Josh Hegarty, Iago Hale and Jorge Dubcovsky

Lowe et al. (1) mapped and characterized a novel source of partial resistance to stripe rust, designated Yr48, in a population of 186 recombinant inbred lines (RILs) developed from a cross between UC1110 and PI610750. UC1110 [Chukar /// Yding // Bluebird / Chanate] is a hard white spring wheat breeding line from the UC Davis breeding program. PI 610750 [CIMMYT No.CYG90.248.1, Croc1 / Aegilops tauschii (Synthetic 205) // Kauz] is a synthetic derivative and the donor of Yr48.

Yr48 was initially mapped to a 5.3 cM region on the distal end of the long arm of chromosome 5A (1); subsequent high-density mapping work has developed additional markers and located Yr48 to the extreme distal end of 5AL. Closely-linked markers recommended for marker-assisted breeding programs are SNF-A2 (0.18 cM proximal of Yr48), BE495011 (0.09 cM proximal of Yr48) and cfa2149 (0.06 cM distal of Yr48).

In field studies in CA over four seasons, Yr48 accounted for approximately 10% of the total variation in disease severity and was associated with an average of 63% reduction in disease severity, compared to fully susceptible lines (1).

map of chromosome 5A near Yr48
Genetic map of the Yr48 region. The map to the left shows the original map presented by Lowe et al. (1). The map on the right shows the reduced Yr48 region resulting from high-density mapping. 

Markers for Yr48

Primer sequences

SNF-A2

SNF-A2-F       5'- TCC GTC TCC ATC ATT CAA CA -3'

SNF-A2-R       5'- GTG TTG CGC AAG TTT GTG AC -3'

BE495011

BE495011-F       5'- TGA TTA CTG TAG CTA CCT CCT CCT -3'

BE495011-R       5'- GGT GCA AGA TGT GCC TGT AA -3'

cfa2149

cfa2149-F       5'- CTT GGA GCT CGG GTA GTA GC-3'

cfa2149-R       5'- AAG GCA GCT CAA TCG GAG TA -3'

Amplification conditions

SNF-A2

  • Denaturing step: 94°C, 3 min
  • Amplification cycles (40 cycles)
    • 95°C, 30 sec
    • 58°C, 30 sec
    • 72°C, 30 sec
  • Extension step: 72°C, 5 min

BE495011

  • Denaturing step: 94°C, 3 min
  • Amplification cycles (40 cycles)
    • 95°C, 30 sec
    • 60°C, 30 sec
    • 72°C, 30 sec
  • Extension step: 72°C, 5 min

cfa2149

  • Denaturing step: 94°C, 3 min
  • Amplification cycles (40 cycles)
    • 95°C, 30 sec
    • 59°C, 30 sec
    • 72°C, 30 sec
  • Extension step: 72°C, 5 min

Expected products in the RILs

In the Yr48 donor lines, cfa2149 amplifies a ~225 bp fragment.  SNF-A2 amplifies an ~ 150 bp fragment in lines carrying Yr48 and a ~200 bp fragment in the line without Yr48. BE495011 amplifies a fragment of 236 bp fragment in lines carrying Yr48 and of ~ 228 bp in the RIL without Yr48.  The PCR products presented below were separated in a 6% (w/v) polyacrylamide gel running at 300 V.

Yr48 markers

Yr48 markers. 1 = Yr48 absent2 = Yr48 present, 3 = heterozygous. Red arrows point to the bands linked to the presence of Yr48. The PCR products were separated in a 6% (w/v) polyacrylamide gel running at 300 V.

Available germplasm

The following two RILs are recommended as donors of all three significant sources of stripe rust resistance (Yr48QYr.ucw-3BS, and QYr.ucw-2BS) identified in the UC1110 / PI610750 mapping population: GSTR 13606 and GSTR 13634.  For donors of Yr48 in an otherwise stripe rust susceptible background, the following two RILs are recommended: GSTR 13504 and GSTR 13618. All lines are maintained by and can be requested from the National Small Grains Collection.

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

References

1. Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Lowe I, Jankuloski L, Chao SM, Chen XM, See D, Dubcovsky J. In: Theoretical and Applied Genetics, 2011,123:143-157.DOI 10.1007/s00122-011-1573-0.

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