UG99 Stem rust (aka TTKSK, African stem rust races in the UG99 lineage)

Thanks to USDA-ARS NACA funding, we are working with colleagues at the USDA-ARS Forage Seed and Cereal Research Unit , Corvallis, OR; ARS, Raleigh, NC; and University of Minnesota - St. Paul, MN to characterize levels of barley seedling and adult plant resistance to stem rust UG99, identify the QTLs/genes responsible for the resistance phenotype, and to deploy resistance alleles in new genetic backgrounds.

 

 

In this project, we are developing germplasm resistant to race TTKSK (UG99) of stem rust. By leveraging resources provided by the Barley Stripe Rust NACA, we are also assessing this germplasm for resistance to other rusts. We are now into our fifth cycle of doubled haploid resistance allele introgression and deployment. To access phenotype and genotype data, please send a request*  for access to the Box folder containing a treasure trove of phenotype and genotype data.

Cycle I

  • Parents

Resistance donors: The donors were spring habit varieties, both hulled (TR02272, SB97197) and hull-less (MC0181-11, MC0181-31, SH98076, SH98073). This germplasm was developed by Drs. Brian Rossnagel and Aaron Beattie (University of Saskatchewan) and Bill Legge (Agriculture and Agri-food Canada, Manitoba). Seed of each accession, harvested from plants verified for resistance phenotype, was provided by Dr. Brian Steffenson (University of Minnesota).
Adapted germplasm:  The rpg4/Rpg5 donors were crossed with a range of germplasm from the OSU Barley Breeding Program, including winter and spring growth habit; hulled and hull-less; 2-row and 6-row; malting and food types.

  • Doubled haploid germplasm array

123 doubled haploids were generated from 14 cross combinations among the Cycle 1 parents. Genotype data were generated using the Illumina 9K and allele-specific primers for Rpg1 and rpg4/Rpg5. Phenotype  data for UG99 resistance at the seedling stage were generated at the Steffenson lab (University of Minnesota). 

Cycle 2

  • Parents

Resistance donors: The donors were TTKSK-resistant selections from Cycle I.
Adapted germplasm:  The Cycle I selections were crossed with winter/facultative malting and multi-use germplasm from the OSU program and the UC Davis Program.

  • Doubled haploid germplasm array

384 doubled haploids were generated. The DH and parents were genotyped with the Illumina 50K and allele-specific genotyping was conducted for rpg4/Rpg5. The array was phenotyped for TTKSK resistance at the seedling stage and for QCC-J resistance at the adult stage at the Steffenson lab (University of Minnesota). 

Cycle III:  An array of 373 doubled haploids was generated from crosses among OSU germplasm that exhibited resistance to race TTKSK at the seedling stage. None of this germplasm amplified for rpg4/Rpg5. These are, therefore, potential new sources of resistance to TTKSK. These resistance donors were crossed with winter/facultative malting and winter/facultative malting barley germplasm from OSU Barley Breeding Program. The array was phenotyped for stripe rust and scald under field conditions at Corvallis, OR (2 years) and Davis, CA (1 year). Stem rust at the seedling stage was assessed under controlled environment conditions at University of Minnesota. In addition, the array was phenotyped for vernalization sensitivity under field conditions at Corvallis, OR in the spring of 2021 to validate allele-specific KASP assays for vernalization and photoperiod sensitivity genes. The array was genotyped at the USDA-ARS Fargo Genotyping Lab using using the Illumina 50K SNP platform.

  • Report
  • Publication (in progress)
     

Cycle IV: An array of 661 genotypes (primarily doubled haploids and their parents) was assembled for phenotyping and genotyping. The array consists of germplasm from five sources within the OSU barley program (1) elite malting 2-row winter and facultative types with resistance to multiple diseases and potential for brewing and distilling end-uses; (2) 2-row winter and facultative selections developed for the US Wheat and Barley Scab Initiative with potential malting quality; (3) 2-row and 6-row winter and facultative selections from the USDA-OREI fall naked diversity panel with potential multi-purpose end uses; (4) 2-row winter and facultative selections from the AMBA LTT panel; (5) 2-row and 6-row winter selections from Cycle 2; (5) 2-row winter, facultative, and spring selections from Cycles 1 and 2.  Selected subsets were phenotyped at Bozeman, MT, and Pullman, WA. Some of the germplasm in Cycle 4 has already been genotyped with the Illumina 50K. The remainder of the germplasm will be genotyped with the same platform (or a new SNP platform under development at the USDA-ARS Fargo Lab) in 2022. Phenotypic data was generated on vernalization sensitivity using a spring-planted field trial at Corvallis, OR and to prevailing disease (notably stripe rust and scald) at Corvallis, OR and Davis, CA. Malting quality will be assessed on a subsample of lines from the Corvallis, Bozeman, and Pullman trials. A subsample of entries will be assessed for stem rust at the seedling stage under controlled environment conditions at University of Minnesota.

  • Report
  • Publication (in progress)

Cycle V: An array of 267 genotypes (primarily doubled haploids and their parents) was assembled for phenotyping and genotyping. The array consists of germplasm from two sources within the OSU barley program (1) elite malting 2-row winter and facultative types with resistance to multiple diseases and potential for brewing and distilling end-uses; (2) naked 2-row winter and facultative naked selections with potential for malting and downstream uses. The array will be phenotyped for prevailing diseases under fall-planted field conditions at Corvallis, OR and Davis, CA; for low temperature tolerance at Lincoln, NE; and for vernalization sensitivity under spring-planted conditions at Corvallis, OR. Samples from the 2021 crop at Corvallis (also the seed source for Cycle 5) will be the target of a collaborative effort to map genes determining malting quality and water sensitivity (a key climate change-related trait) with the Hartwick Center for Craft Food and Beverage. A subsample of entries will be assessed for stem rust at the seedling stage under controlled environment conditions at University of Minnesota. The array will be genotyped with the new SNP platform under development at the USDA-ARS lab at Fargo, ND.

Additional Outcomes:

*Please send requests for data access, and any questions/suggestions to franciscojavier.hernandezvasquez@oregonstate.edu