Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Cloning agronomically important genes from large, complex crop genomes remains challenging. Here, we generate a 14.7-gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping, and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance against the devastating fungal stripe rust disease. We identified the race-specific disease resistance gene Yr27, encoding an intracellular immune receptor, as a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13, with the Yr27 and Lr13 proteins sharing 97% sequence identity. Our results thus demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes and also exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in future.