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Genome-wide association study of stem rust resistance in a world collection of cultivated barley

Abstract

Key message

QTL conferring a 14–40% reduction in adult plant stem rust severity to multiple races of Pgt were found on chromosome 5H and will be useful in barley breeding.

Abstract

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an important disease of barley. The resistance gene Rpg1 has protected the crop against stem rust losses for over 70 years in North America, but is not effective against the African Pgt race TTKSK (and its variants) nor the domestic race QCCJB. To identify resistance to these Rpg1-virulent races, the Barley iCore Collection, held by the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection was evaluated for adult plant resistance (APR) and seedling resistance to race TTKSK and APR to race QCCJB and the Pgt TTKSK composite of races TTKSK, TTKST, TTKTK, and TTKTT. Using a genome-wide association study approach based on 6224 single nucleotide polymorphic markers, seven significant loci for stem rust resistance were identified on chromosomes 1H, 2H, 3H, and 5H. The most significant markers detected were 11_11355 and SCRI_RS_177017 at 71–75 cM on chromosome 5H, conferring APR to QCCJB and TTKSK composite. Significant markers were also detected for TTKSK seedling resistance on chromosome 5H. All markers detected on 5H were independent of the rpg4/Rpg5 complex at 152–168 cM. This study verified the importance of the 11_11355 locus in conferring APR to races QCCJB and TTKSK and suggests that it may be effective against other races in the Ug99 lineage.

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Acknowledgements

This research was funded, in part, by the Lieberman-Okinow Endowment at the University of Minnesota, American Malting Barley Association, the Bill & Melinda Gates Foundation, the UK Department for International Development to Cornell University for the Borlaug Global Rust Initiative Durable Rust Resistance in Wheat Project, USDA-ARS Cooperative Agreement 58-5062-5-012 (Understanding Stem Rust Resistance in Barley and Germplasm); and Triticeae-CAP project (2011-68002-30029) from the United States Department of Agriculture National Institute of Food and Agriculture. AJC acknowledges financial support from the following University of Minnesota fellowships: Norman E. Borlaug Graduate Fellowship for International Agriculture supported by the Vaale-Henry Endowment, the Minnesota Discovery, Research, and Innovation (MnDRIVE) Fellowship, and the Doctoral Dissertation Fellowship. We thank T. Szinyei and M. Martin for excellent technical assistance and Dr. A. Sallam and Dr. M. Muñoz-Amatriaín for assistance in data analysis.

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Austin Case and Brian Steffenson conducted the experiments in the USA and Kenya, performed the analyses, and wrote the manuscript. Sridhar Bhavani and Godwin Macharia coordinated and conducted the experiments in Kenya and revised the manuscript.

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Correspondence to Brian J. Steffenson.

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Communicated by Frank Ordon.

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Case, A.J., Bhavani, S., Macharia, G. et al. Genome-wide association study of stem rust resistance in a world collection of cultivated barley. Theor Appl Genet 131, 107–126 (2018). https://doi.org/10.1007/s00122-017-2989-y

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