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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #350036
Title: Resistance gene cloning from a wild crop relative by sequence capture and association genetics

Author
item ARORA, SANU - John Innes Center
item STEUERNAGEL, BURKHARD - John Innes Center
item CHANDRAMOHAN, SUTHA - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item LONG, YUNMING - North Dakota State University
item MATNY, OADI - University Of Minnesota
item JOHNSON, RYAN - University Of Minnesota
item PERIYANNAN, SAMBASIVAM - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item HATTA, M - John Innes Center
item Szabo, Les
item Xu, Steven
item WULFF, BRANDE - John Innes Center

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2018
Publication Date: 2/4/2019
Citation: Arora, S., Steuernagel, B., Chandramohan, S., Long, Y., Matny, O., Johnson, R., Periyannan, S., Hatta, M.A., Szabo, L.J., Xu, S.S., Wulff, B.B. 2019. Resistance gene discovery and cloning by sequence capture and association genetics. Nature Biotechnology. 37(2):139-143. https://doi.org/10.1038/s41587-018-0007-9.
DOI: https://doi.org/10.1038/s41587-018-0007-9

Interpretive Summary: In modern agriculture, certain diseases have been one of the most serious threats to crop production. Although some chemicals such as fungicides are often used for disease control, genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, transfer of R genes into crops from their wild relatives is a lengthy process often associated with introduction of undesirable genes. In addition, the disease pathogens can rapidly evolve to overcome R genes when used singly in a crop variety. Introducing multiple cloned R genes into crops would avoid undesirable genes and delay emergence of resistance-breaking pathogen races. However, current R gene cloning methods require crop populations which are segregating for the R gene or its mutants. Such populations are difficult to generate for many wild relatives due to poor agronomic traits. In this study, we developed a new method (AgRenSeq) to rapidly clone four R genes in less than six months by using natural genome variation in a set of 151 wild diploid wheat lines. This method, combined with natural populations, genome sequencing, and gene-trait association analysis, is a major advance in discovering and isolating R genes for introducing resistance against a wide range of pathogen races in crops.

Technical Abstract: Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes and pathogens can rapidly evolve to overcome R genes when deployed singly. Introducing multiple cloned R genes into crops as a stack would avoid linkage drag and delay emergence of resistance-breaking pathogen races. However, current R gene cloning methods require segregating or mutant progenies, which are difficult to generate for many wild relatives due to poor agronomic traits. We exploited natural pan-genome variation in a wild diploid wheat by combining association genetics with R gene enrichment sequencing (AgRenSeq) to clone four stem rust resistance genes in <6 months. RenSeq combined with diversity panels is therefore a major advance in isolating R genes for engineering broad-spectrum resistance in crops.