Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust.

Agriculture and Agri Food Canada Morden Research and Development Centre 101 Route 100 Morden MB R6M 1Y5 Canada

Centre for Desert Agriculture KAUST Thuwal 23955 6900 Saudi Arabia

CSIRO Agriculture and Food Canberra ACT 2601 Australia

Department of Plant Pathology University of Minnesota St Paul MN 55108 USA

Department of Plant Sciences University of California Davis CA 95616 USA

Howard Hughes Medical Institute Chevy Chase MD 20815 USA

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research 77900 Olomouc Czech Republic

John Innes Centre Norwich Research Park Norwich NR4 7UH UK

Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at Weifang Weifang Shandong 261000 China

Plant Breeding Institute School of Life and Environmental Sciences University of Sydney Cobbitty NSW 2570 Australia

Plant Science Program Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology Thuwal 23955 6900 Saudi Arabia

School of Molecular Biosciences College of Medical Veterinary and Life Sciences University of Glasgow Glasgow G12 8QQ UK

State Key Laboratory of Wheat and Maize Crop Science National Wheat Innovation Centre Centre for Crop Genome Engineering and College of Agronomy Longzi Lake Campus Henan Agricultural University Zhengzhou 450046 China

US Department of Agriculture Agricultural Research Service Cereal Disease Laboratory St Paul MN 55108 USA

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