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Mapping a Type 1 FHB resistance on chromosome 4AS of Triticum macha and deployment in combination with two Type 2 resistances

Burt, C., Steed, A., Gosman, N., Lemmens, M., Bird, N., Ramirez-Gonzalez, R., Holdgate, S. & Nicholson, P. (2015). Theoretical and Applied Genetics, 1-14.

Paper summary

In this paper by Burt et al., markers closely flanking a Type 1 FHB resistance gene in wheat were identified and the potential of combining this with Type 2 resistances to improve control of Fusarium head blight (FHB) was demonstrated.
Fusarium head blight (FHB) is a serious problem for commercial wheat production. It causes large reductions in grain yield and baking quality, and an even greater threat is due to mycotoxins which contaminate infected grain and pose a risk to human and animal health. Crop management and agrochemical measures are only partly effective in controlling the disease and the development of FHB resistant varieties is important.
Two forms of FHB resistance can be identified: Type 1 confers resistance to initial colonisation of Fusarium, and Type 2 provides resistance to spread within the wheat ear. Type 1 FHB resistance was previously located on chromosome 4 of Triticum macha but a lack of polymorphic markers and a limited number of recombinants has prevented accurate mapping of this QTL. Using KASP SNP genotyping assays in combination with new populations, the position of the resistance was determined to allow it to be tracked in breeding programmes.

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Highlights of the paper

  • Study lead by the John Innes Centre (part of the ‘Integrated Strategy to Prevent Mycotoxin Risk’ (INSPYR) Project, a Sustainable Arable LINK project)
  • Combinations of 1B, 3B and 4A FHB resistance QTL tested in a susceptible UK wheat background (Hobbit-‘sib’).
  • Use of a 288 line F4 population developed from Hobbit ‘sib’ to refine QTL localisation and identify SNP markers to aid MAS and pyramiding with other FHB resistance QTL for plant breeders
  • FHB resistance QTL combinations set up and evaluated for resistance in polytunnel and field trials over three years.

How KASP genotyping was used

  • Parent lines of the population and the single chromosome substitution line HS/Tm4A were screened at LGC Genomics with a wheat KASP™ SNP panel developed in conjunction with the University of Bristol, containing over 5,000 validated SNP assays (Allen et al. 2013). Polymorphic markers were selected for even coverage of chromosome 4AS and primer sets obtained to apply to subsequent populations and resulting recombinant lines.
  • Additional SNP markers were selected on the iSelect 90 k wheat SNP chip and converted to KASP assays. These KASP assays were run in-house at the John Innes Centre on a standard real-time PCR machine.
  • QTL combination lines were additionally screened for the presence of the 3B QTL using an Fhb1 linked KASP assay to confirm the presence of this resistance as determined by SSR markers (a marker previously developed by Gina Brown-Guedira (USDA) as part of a panel of KASP assays for MAS of agronomically important genes in wheat).

KASP SNP wheat library

The LGC wheat genotyping library offers easy access to more than 8,000 functionally validated KASP SNP genotyping assays. These assays are available to researchers and plant breeders to enable development of precision breeding in wheat (Triticum spp.) hybrids.
The library was developed in conjunction with the University of Bristol (UK), and the Integrated Breeding platform, respectively.
A ‘core set’ of 960 KASP SNP genotyping assays has been identified that provide an even distribution of SNP markers across the A, B and D genomes. Over 400 assays have been linked to known functional proteins in the NCBI database.