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TGAC and JIC identify new genetic markers to combat yellow rust disease in wheat

A new study has identified genetic markers that signal resistance to the wheat yellow rust pathogen.

As the global population soars, there is a heightening pressure on agriculture to produce enough food to satisfy worldwide demand. Wheat is a major crop providing over 20% of the world's calorie and 25% of its protein intake. This vital crop's productivity is threatened by devastating diseases such as the wheat yellow rust pathogen (Puccinia striiformis f. sp. tritici) that infects bread wheat (Triticum aestivum L.).

Named after the yellow stripes that appear on the leaves of infected plants, yellow rust results in a heavily reduced or non-existent yield. Furthermore, there has been a recent upsurge in what are known as 'Warrior' strains of this disease that infect wheat variants that were previously believed to have resistance.

In order to counter the threat of wheat yellow rust, plant breeders have developed wheat variants that incorporate resistance genes (R-genes). Yr15 is an R-gene taken from wild emmer (Triticum dicoccoides) that provides resistance to this disease. Yet it remains difficult, due to the complex hexaploid structure of wheat DNA, to accurately identify which plants should be used in breeding schemes to ensure that the next generation of wheat will have the resistance gene.

The new research provides a new mechanism to identify whether or not a variant of wheat DNA contains this resistance gene. The team sequenced the RNA of wheat plants that were known to either be susceptible or resistant to wheat yellow rust.

By comparing the results, not only against each other, but also against existing models of bread wheat gene annotation, areas of genetic divergence were identified between the plants. These differences, known as single nucleotide polymorphisms (SNPs), were used to locate an allele (number of alternative forms of the same gene) that was very frequent in the resistant plants while rare in the susceptible plants. This indicated the chromosomal arm where Yr15 is located.

Further analysis identified the resistant gene out of the wheat's three closely related genomes, supported by the bioinformatics pipeline developed for the project, PolyMarker. This tool enabled the research team to select and design a set of genome specific primers to identify the genetic position of Yr15 and identify two SNPs that strongly indicate the presence of the resistance gene. 

The BBSRC-funded study was led by Ricardo Ramirez-Gonzalez and Dr Mario Caccamo at The Genome Analysis Centre (TGAC) and Dr Cristobal Uauy at the John Innes Centre (JIC), as part of an international team of scientists from agri-tech Institutes.

"This is a good example of how collaboration with business and public science can lead to exciting results that can be applied to industry", said Ricardo Ramirez-Gonzalez, lead author and PhD student at TGAC.

Ricardo added: "This study also shows that despite the complexity of the wheat genome, it is possible to take advantage of next-generation sequencing as an addition to existing techniques, such as Bulk Segregant Analysis."

The identification of these genetic markers facilitates a new method to ascertain if a bread wheat variant is resistant to wheat yellow rust. By checking for the presence of these markers within wheat plants, breeders will be more informed in their selection of which individuals to incorporate in their breeding strategy. In addition to this, the process used in this study may be applied to determine the location and markers for other genes within wheat and polyploid species.

Mario Caccamo, Director of TGAC and Ricardo's PhD supervisor, said: "This study is a great example on how multidisciplinary research focused on tackling a very complex problem can rapidly yield excellent results. We brought together expertise in plant disease resistance, advance genomics technologies and computational biology to advance in a field of science that will have direct impact on our ability to fight a devastating crop disease."

The paper, titled: "RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat" is published by Plant Biotechnology Journal (open access).

The project was coordinated by: TGAC, John Innes Centre, National Institute of Agricultural Botany, Limagrain UK Ltd and RAGT Seeds.

TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.


Story source: BBSRC/TGAC news release, 27 Nov 2014

Journal reference: Ricardo H. Ramirez-Gonzalez et al. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnology Journal. DOI: 10.1111/pbi.12281

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