Genetic characterisation and fine mapping of sources of durable resistance to stripe rust in selected wheat genotypes

Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is one of the most important diseases of bread wheat (Triticum aestivum). In recent years the disease has reached a global distribution, also causing significant crop losses in South Africa since 1996. The deployment of disease resistant cultivars is recognised as an effective approach to minimise crop losses without the higher input costs associated with the application fungicides. The need for new sources of durable resistance has become apparent with the regular changes in the pathogen population and the emergence of more virulent races. Quantitative trait loci (QTL) mapping is a powerful tool for unravelling the genetic components responsible for disease resistance. For the purpose of this study, two cultivars have been identified with complete adult plant resistance (APR) to stripe rust. Previously, the South African spring wheat Kariega has been studied and the Lr34/Yr18/Pm38 gene and two major QTL, QYr.sgi-2B and QYr.sgi-4A, were identified in a Kariega X Avocet S doubled haploid (DH) mapping population. Cappelle-Desprez is an old European winter wheat for which resistance genes/QTL have been postulated. The objective of this study was to dissect the APR for stripe rust in these cultivars using a QTL mapping approach. The Kariega QTL were further characterised by increasing the DNA marker density in a more targeted approach. Additional simple sequence repeat (SSR) markers were incorporated in the genetic map and expressed sequence tag (EST) markers were developed for screening by means of single-strand conformation polymorphism (SSCP) analysis. The conversion of EST and Diversity Arrays Technology (DArT) markers to sequence tagged site (STS) markers were investigated to allow for high-throughput screening. In addition, selected SSR and DArT-STS markers were screened in a large Kariega x Avocet S F2 mapping population to improve the genetic map resolution in the QTL intervals. The QYr.sgi-2B and QYr.sgi-4A intervals have been delimited to 6.1 and 16.2 cM respectively, in the F2 mapping population with the aid of recombinant mapping. Resistance displayed by Cappelle-Desprez was studied in a Palmiet x Yr16DH70 recombinant inbred line (RIL) mapping population. The breeding line Yr16DH70, a Cappelle-Desprez derivative, is a more suitable parent in a spring wheat background. SSR and DArT markers were typed in the population. QTL were identified, and up to 75.2% of the phenotypic variance could be accounted for. A major QTL, QYr.ufs-2A, explaining up to 53.2% of the phenotypic variance was identified on chromosome 2A. The presence of the Yr16 gene on chromosome 2D was confirmed (QYr.ufs-2D) and additional minor QTL were detected on chromosomes 5B (QYr.ufs-5B) and 6D (QYr.ufs-6D). A minor QTL, QYr.ufs-4B was derived from Palmiet. Stripe rust resistance QTL from Kariega and Cappelle-Desprez provide valuable sources of resistance in adapted, spring wheat backgrounds to South African breeders. Improved characterisation of the QTL has led to the identification of QTL-associated markers, allowing for more efficient selection in marker-assisted breeding schemes, and it also paves the way for map-based cloning.