Following the appearance of stripe rust in South Africa in 1996, efforts have been made to identify new sources of durable resistance. The French cultivar Cappelle-Desprez has long been considered a source of durable, adult plant resistance (APR) to stripe rust. As Cappelle-Desprez contains the seedling resistance genes Yr3a and Yr4a, wheat lines were developed from which Yr3a and Yr4a had been removed, while selecting for Cappelle-Desprez derived APR effective against South African pathotypes of the stripe rust fungus, Puccinia striiformis f. sp. tritici. Line Yr16DH70, adapted to South African wheat growing conditions, was selected and crossed to the stripe rust susceptible cultivar Palmiet to develop a segregating recombinant inbred line mapping population. A major effect QTL, QYr.ufs-2A was identified on the short arm of chromosome 2A derived from Cappelle-Desprez, along with three QTL of smaller effect, QYr.ufs-2D, QYr.ufs-5B and QYr.ufs-6D. QYr.ufs-2D was located within a region on the short arm of chromosome 2D believed to be the location of the stripe rust resistance gene Yr16. An additional minor effect QTL, QYr.ufs-4B, was identified in the cv. Palmiet. An examination of individual RILs carrying single or combinations of each QTL indicated significant resistance effects when QYr.ufs-2A was combined with the three minor QTL from Cappelle-Desprez, and between QYr.ufs-2D and QYr.ufs-5B.

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The cloning of 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 to the devastating fungal stripe rust disease1. We identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity2,3. Our results demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes, and 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 the future.

The wheat cultivar Kariega expresses complete adult plant resistance to stripe rust in South Africa. The aim of this investigation was to determine the extent and nature of variability in stripe rust resistance in a population of 150 doubled haploid lines generated from a cross between Kariega and the susceptible cultivar Avocet S. Analysis of field data for adult plant stripe rust resistance identified two major QTLs and two minor QTLs in the resistant cultivar Kariega. The two major QTLs were located on chromosomes 7D ( QYr.sgi-7D) and 2B ( QYr.sgi-2B.1), contributing 29% and 30% to the phenotypic variance, respectively. QYr.sgi-2B.1 is primarily associated with a chlorotic and/or necrotic response, unlike QYr.sgi-7D, which is believed to be the adult plant resistance gene Yr18. These two QTLs for adult plant resistance in Kariega appear to represent different forms of resistance, where QYr.sgi-7D may represent potentially more durable resistance than QYr.sgi-2B.1. Mixture model analysis of the field leaf infection scores suggested a genetic model involving two independent genes combining in a classical, epistatic manner. The results of the QTL analysis demonstrate its higher resolution power compared to the mixture model analysis by detecting the presence of minor QTLs.

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