The stem, leaf and stripe rust resistance genes Sr31, Lr26 and Yr9, located on the short arm of rye chromosome 1, have been widely used in wheat by means of wheat-rye translocation chromosomes. Previous studies have suggested that these resistance specificities are encoded by either closely-linked genes, or by a single gene capable of recognizing all three rust species. To investigate these issues, two 1BL.1RS wheat lines, one with and one without Sr31, Lr26 and Yr9, were used as parents for a high-resolution F2 mapping family. Thirty-six recombinants were identified between two PCR markers 2.3 cM apart that flanked the resistance locus. In one recombinant, Lr26 was separated from Sr31 and Yr9. Mutation studies recovered mutants that separated all three rust resistance genes. Thus, together, the recombination and mutation studies suggest that Sr31, Lr26 and Yr9 are separate closely-linked genes. An additional 16 DNA markers were mapped in this region. Multiple RFLP markers, identified using part of the barley Mla powdery mildew resistance gene as probe, co-segregated with Sr31 and Yr9. One deletion mutant that had lost Sr31, Lr26 and Yr9 retained all Mla markers, suggesting that the family of genes on 1RS identified by the Mla probe does not contain the Sr31, Lr26 or Yr9 genes. The genetic stocks and DNA markers generated from this study should facilitate the future cloning of Sr31, Lr26 and Yr9.

Stem rust susceptibility of European wheats under Australian conditions posed a significant threat to wheat production for the early British settlers in Australia. The famous Australian wheat breeder, William Farrer, tackled the problem of stem rust susceptibility through breeding fast-maturing wheat cultivars. South-eastern Australia suffered a severe stem rust epidemic in 1973, which gave rise to a national approach to breeding for rust resistance. The National Wheat Rust Control Program was set up in 1975, modelled on the University of Sydney’s own rust resistance breeding program, at the University of Sydney Plant Breeding Institute, Castle Hill (now Cobbitty). Back-crossing of a range of sources of resistance provided genetically diverse germplasm for evaluation in various breeding programs. Current efforts are directed to building gene combinations through marker-assisted selection. Major genes for resistance to stem rust and leaf rust are being used in the back-crossing program of the ACRCP to create genetic diversity among Australian germplasm. Stripe rust and to a lesser extent leaf rust resistance in the Australian germplasm is largely based on combinations of adult plant resistance genes and our knowledge of their genomic locations has increased. Additional genes, other than Yr18/Lr34 and Yr29/Lr46, appeared to control adult plant resistance to both leaf rust and stripe rust. Two adult-plant stem rust resistance genes have also been identified. The development of selection technologies to achieve genotype-based selection of resistance gene combinations in the absence of bioassays has evolved in the last 5 years. Robust molecular markers are now available for several commercially important rust resistance genes. Marker-assisted selection for rust resistance is performed routinely in many wheat-breeding programs. Modified pedigree and limited back-cross methods have been used for breeding rust-resistant wheat cultivars in the University of Sydney wheat-breeding program. The single back-cross methodology has proved more successful in producing cultivars with combinations of adult plant resistance genes.

The Puccinia striiformis f. sp. tritici (Pst) pathotype, 134 E16A?, detected in 2002 in Australia, produced relatively lower and higher adult plant stripe rust responses, respectively, on cultivars Kukri and Janz in comparison to the pre-2002 Pst pathotype 110 E143A?. Molecular mapping of adult plant stripe rust response variation among 180 Kukri/Janz-derived doubled haploid lines over 4 years, two each with Pst pathotypes 110 E143A? and 134 E16A?, was performed. QYr.sun-7B and QYr.sun-7D were consistently contributed by Kukri and Janz, respectively. QYr.sun-7D corresponded to the genomic location of Yr18 and QYr.sun-7B remains to be formally named. QYr.sun-1B, QYr.sun-5B, and QYr.sun-6B were detected during more than one season irrespective of the Pst pathotypes used, whereas QYr.sun-3B was identified only during the 2003 crop season. QYr.sun-1A contributed by Janz, and QYr.sun-2A from Kukri, were detected only against Pst pathotypes 110 E143A? and 134 E16A?, respectively. The DH lines showing better resistance than the either parent carried combinations of 4 to 6 QTL. These lines are currently being used as stripe rust resistance donors in wheat breeding programs.

Two Iranian common wheat landraces AUS28183 and AUS28187 from the Watkins collection showed high levels of seedling resistance against Australian pathotypes of leaf rust and stripe rust pathogens. Chi-squared analyses of rust response segregation among F(3) populations derived from crosses of AUS28183 and AUS28187 with a susceptible genotype AUS27229 revealed monogenic inheritance of leaf rust and stripe rust resistance. As both genotypes produced similar leaf rust and stripe rust infection types, they were assumed to carry the same genes. The genes were temporarily named as LrW1 and YrW1. Molecular mapping placed LrW1 and YrW1 in the short arm of chromosome 5B, about 10 and 15 cM proximal to the SSR marker gwm234, respectively, and the marker cfb309 mapped 8-12 cM proximal to YrW1. LrW1 mapped 3-6 cM distal to YrW1 in two F(3) populations. AUS28183 corresponded to the accession V336 of the Watkins collection which was the original source of Lr52. Based on the genomic location and accession records, LrW1 was concluded to be Lr52. Because no other seedling stripe rust resistance gene has previously been mapped in chromosome 5BS, YrW1 was permanently named as Yr47. A combination of flanking markers gwm234 and cfb309 with phenotypic assays could be used to ascertain the presence of Lr52 and Yr47 in segregating populations. This investigation characterised a valuable source of dual leaf rust and stripe rust resistance for deployment in new wheat cultivars. Transfer of Lr52 and Yr47 into current Australian wheat backgrounds is in progress.

BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases. Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920-1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker-trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.

A recombinant inbred line (RIL) population derived from the cross Arina/Forno was field tested for 2 years against Puccinia graminis f. sp. tritici under artificially created epidemic conditions. Both parents showed intermediate adult plant stem rust responses and the RIL population showed continuous variation for this trait. Composite interval mapping identified genomic regions controlling low stem rust response on chromosomes 5B and 7D consistently across all experiments. These genomic regions were named QSr.Sun-5BL and QSr.Sun-7DS and explained on an average 12% and 26% of the phenotypic variation in adult plant stem rust response, respectively. QSr.Sun-5BL mapped close to Xglk0354 and was contributed by Arina. The Lr34-linked markers csLV34 and swm10 were closely associated with QSr.Sun-7DS suggesting the involvement of Lr34 in controlling adult plant stem rust response of cultivar Forno. Additional minor and inconsistent QTLs explaining variation in adult plant stem rust response were identified on chromosome arms 1AS and 7BL. The QTL located on chromosome 7BL corresponded to the stem rust resistance gene Sr17 carried by cultivar Forno. A seedling stem rust resistance gene carried by Arina, SrAn1, was ineffective under field conditions and was mapped on the long arm of chromosome 2A. Genotypes carrying combinations of QSr.Sun-5BL and QSr.Sun-7DS based on positive alleles of the respective closest marker loci Xglk0354 and XcsLV34 or Xswm10 exhibited a lower response than either parent indicating an additive effect of these genes. Transfer of these genes into cultivars carrying Sr2 would provide a more effective and durable resistance against the stem rust pathogen. Markers csLV34 and/or swm10 could be used in marker assisted selection of QSr.Sun-7DS in breeding programs.

No abstract

Abstract:Genetic characterization of sources of durable resistance enables their strategic deployment in breeding programs. Genomic locations of uncharacterized adult plant resistance (APR) sources to leaf rust and stripe rust diseases of wheat were determined. Two genomic regions, 3DS (Halberd) and 5DS (Cranbrook) controlled APR to both leaf rust and stripe rust. Chromosomes 6B (Cranbrook) and 7B (Halberd) reduced leaf rust severity. Chromosomes 2DS, 3BS and 7A also reduced stripe rust severities in at least one crop season. Stem rust resistance genes Sr2 (3BS) and Sr30 (5DL) from Cranbrook explained stem rust response variation. Regression analysis also indicated strong positive interaction of these two loci in controlling stem rust. Expression of Sr2-linked psuedo black chaff (Pbc) was controlled by a major gene on chromosome 3BS and three modifiers located on chromosomes 6A, 3D and 7A. The chromosome 7A located region was not consistent across all seasons and sites. QTLs detected consistently in different experiments were temporarily designated as QYr/Lr3D, QYr/Lr5D, QLr6B and QLr7B