Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis.

Long-distance migration and host adaptation by transboundary plant pathogens often brings detrimental effects to important agroecosystems. Efficient surveillance as a basis for responding to the dynamics of such pathogens is often hampered by a lack of information on incursion origin, evolutionary pathways and the genetic basis of rapidly evolving virulence across larger timescales. Here, we studied these genetic features by using historical isolates of the obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst), which causes one of the most widespread and devastating diseases, stripe (yellow) rust, of wheat. Through a combination of genotypic, phenotypic and genomic analyses, we assigned eight Pst isolates representing putative exotic Pst incursions into Australia to four previously defined genetic groups, PstS0, PstS1, PstS10 and PstS13. We showed that isolates of an additional incursion of P. striiformis, known locally as P. striiformis f. sp. pseudo-hordei, had a new and unique multilocus SSR genotype (MLG). We provide results of overall genomic variation of representative Pst isolates from each genetic group by comparative genomic analyses. We showed that isolates within the PstS1 and PstS13 genetic groups are most distinct at the whole-genome variant level from isolates belonging to genetic group PstS0, whereas the isolate from the PstS10 genetic group is intermediate. We further explored variable gene content, including putative effectors, representing both shared but also unique genetic changes that have occurred following introduction, some of which may additionally account for local adaptation of these isolates to triticale. Our genotypic and genomic data revealed new genetic insights into the evolution of diverse phenotypes of rust pathogens following incursion into a geographically isolated continental region.

Complementary resistance genes in wheat selection 'Avocet R' confer resistance to stripe rust.

KEY MESSAGE: Complementary genes for resistance to wheat stripe rust in an Avocet selection mapped to chromosome arms 3DL and 5BL. Susceptible Avocet selections lacked the 5BL gene due to a chromosomal deletion. This study reports the inheritance and genetic mapping of the YrA (temporary name of convenience to describe the specificity) seedling resistance to wheat stripe rust (caused by Puccinia striiformis f. sp. tritici; Pst) in a resistant selection of the Australian cv. Avocet [Avocet R (AvR)-AUS 90660]. Genetic analysis was performed on F2 populations and F3 generation families from crosses between wheats that carried and lacked the YrA resistance. Greenhouse seedling tests with two avirulent Pst pathotypes (104 E137 A- and 108 E141 A-) confirmed that the YrA resistance was inherited as two complementary dominant genes. Ninety-two doubled haploid (DH) lines from a cross between the Australian cv. Teal (Pst susceptible) and AvR were used for DArT-Seq genotypic analysis to map the seedling resistance. Marker-trait association analysis using 9035 DArT-Seq loci mapped the genes to the long arms of chromosomes 3D (3DL) and 5B (5BL), respectively. F2 populations from crosses between susceptible DH lines that carried either the 3DL or 5BL marker genotypes confirmed the complementary gene model. Fluorescence in situ hybridization (FISH) analysis determined that Teal carries a reciprocal T5B-7B translocation. FISH analysis also identified a 5BL chromosomal deletion in Avocet S relative to AvR that further validated the complementary gene model and possibly explained the heterogeneity of closely related wheats carrying the YrA resistance. The individual loci of the complementary YrA resistance were designated Yr73 (3DL) and Yr74 (5BL). Candidate single gene reference stocks will be permanently accessioned following cytological analysis to avoid the T5B-7B translocation.

The genetic basis of resistance to barley grass yellow rust (Puccinia striiformis f. sp. pseudo-hordei) in Australian barley cultivars.

KEY MESSAGE: Resistance to Puccinia striiformis in 18 barleys was conferred by one or more genes. In two genotypes, resistance mapped to chromosomes 5HL and 7HL (seedling), and 5HS (adult plant). Twenty barley genotypes were assessed for resistance to a variant of P. striiformis [barley grass yellow rust (BGYR)] that is adapted to wild Hordeum sp. (barley grass) and is known to be virulent on several Australian barley cultivars. With the exception of Biosaline-19, all of the genotypes tested were resistant to BGYR. Genetic analyses of 16 Australian and three exotic barley lines indicated that each carried at least a single gene for resistance. Seedling resistance genes identified in the doubled haploid population developed from a cross between Franklin and Yerong were mapped to the long arm of chromosomes 5H and 7H, respectively. These genes were given the temporary designations of Rpsp-hFranklin and Rpsp-hYerong. Three QTL were detected in the same population when tested at the adult plant stage, two of them being in a similar position to Rpsp-hFranklin and Rpsp-hYerong and the third one was mapped to 5HS. Allelism tests between genotypes that exhibited seedling infection type responses to BGYR that were similar to Franklin and Yerong revealed that resistance in most were genetically independent of Rpsp-hFranklin and Rpsp-hYerong.

Genetic and molecular analyses of resistance to a variant of Puccinia striiformis in barley.

Seedlings of 62 Australian barley cultivars and two exotic barley genotypes were assessed for resistance to a variant of Puccinia striiformis, referred to as "Barley Grass Stripe Rust" (BGYR), first detected in Australia in 1998, which is capable of infecting wild Hordeum species and some genotypes of cultivated barley. Fifty-three out of 62 cultivated barley cultivars tested were resistant to the pathogen. Genetic analyses of seedling resistance to BGYR in six Australian barley cultivars and one Algerian barley landrace indicated that they carried either one or two major resistance genes to the pathogen. A single recessive seedling resistance gene, rpsSa3771, identified in Sahara 3771, was located on the long arm of chromosome 1 (7 H), flanked by the restriction fragment length polymorphism (RFLP) markers Xwg420 and Xcdo347 at genetic distances of 12.8 and 21.9 cM, respectively. Mapping resistance to BGYR at adult plant growth stages using the doubled haploid (DH) population Clipper × Sahara 3771 identified two major quantitative trait loci (QTL), one on the long arm of chromosome 3 (3 H) and the second on the long arm of chromosome 1 (7 H), accounting for 26 % and 18 % of the total phenotypic variation, respectively. The QTL located on chromosome 7HL corresponded to seedling resistance gene rpsSa3771 and the second QTL was concluded to correspond to a single APR gene, designated rpsCl, contributed by cultivar Clipper.

Somatic hybridization in the Uredinales.

Rust fungi are cosmopolitan in distribution and parasitize a wide range of plants, including economically important crop species such as wheat. Detailed regional, national, and continental surveys of pathogenic variability in wheat-attacking rust pathogens over periods of up to 90 years have shown that in the absence of sexual recombination, genetic diversity is generated by periodic introduction of exotic isolates, single-step mutation, and somatic hybridization. Laboratory studies have provided evidence for somatic hybridization between many rust species and formae speciales, and there is evidence for the process in nature within and between rust species on Linum, poplar, Senecio, wheat, and several grass species. Although the mechanisms involved in somatic hybridization are not well understood, they are thought to involve the fusion of dikaryotic vegetative hyphae, nuclear exchange, and possibly exchange of whole chromosomes between nuclei or parasexuality via the fusion of the two haploid nuclei, followed by mitotic crossing over and vegetative haploidization. In three cases, hybrid isolates rendered resistant plant genotypes susceptible because of new combinations of virulence. Implications for resistance breeding and future prospects in understanding the process are discussed.

Pathogenic and molecular variation support the presence of genetically distinct clonal lineages in Australian populations of Puccinia graminis f. sp. avenae.

Previous studies of the causal agent of stem rust of oats (Puccinia graminis f. sp. avenae; P. g. avenae) in Australia have demonstrated a high level of pathogenic variability. In this work, the pathotypic structure of the Australian P. g. avenae population in 1999 was investigated, as well as the pathotypic and genetic diversity of a collection of 26 Australian isolates representing a 25-year period (1971-1996). In the 1999 sample, 16 races belonging to six international standard races were identified from 97 isolates, with standard race 94 predominant in all regions. Race 94+Pg-13,Pg-Sa,Pg-a, detected in southern New South Wales (sNSW) and northern New South Wales (nNSW), was virulent on all of the differential genotypes used. Detailed analyses of pathogenicity and AFLP variability among 26 isolates collected from 1971-1996 revealed that isolates of standard race 94 collected in 1999 were genetically distinct from other Australian races of P. g. avenae. This evidence, along with data from annual pathogenicity surveys, suggests that the group to which standard race 94 belongs appeared during the late 1980s, and that it increased in frequency to dominate P. g. avenae pathogen populations throughout Australia from 1992 onward. The existence of groups of P. g. avenae isolates in Australia that differ in pathogenicity and AFLP phenotype suggests that current populations have evolved from a number of isolates of the fungus that differ in their genetic backgrounds, which may have originated from independent introductions or from asexual hybridisational events.

The expression and genetics of resistance to stripe (yellow) rust in three European and four New Zealand wheat cultivars.

Adult plant resistance (APR) to stripe rust in three European (Pegaso, Victo and Aztec) and four New Zealand cultivars (Weka, Kopara, Kokart and Takahe) was characterised using hybrid analysis and tests of allelism. In agreement with earlier work, the APR in most of these cultivars appeared to be controlled by two or more genes with additive effects. It was suggested that heavy selection pressure should be avoided in early generations in breeding programs utilising APR, because lines in which APR genes are heterozygous may display lower levels of resistance due to the incompletely dominant and interactive nature of many APRs. Such lines are capable of generating more resistant progenies following selfing. It was also demonstrated that it is possible to misclassify F2 plants as susceptible if APR genes are in a heterozygous condition, especially in the case of gene(s) conferring intermediate levels of resistance. The presence of a common APR gene in Kopara and Takahe, and perhaps Weka, was suggested because all shared a common parent in their pedigree and no susceptible plants were observed in F2 populations derived from intercrossing them. The difficulties inherent in conducting genetic studies on APRs and the need for large population sizes for such studies were emphasised.

Molecular genetic variability of Australian isolates of five cereal rust pathogens.

Rust fungi cause economically important diseases of cereals, and their ability to rapidly evolve new virulent races has hindered attempts to control them by genetic resistance. PCR-based molecular tools may assist in understanding the genetic structure of pathogen populations. The high multiplex DNA fingerprinting techniques, amplified fragment length polymorphisms (AFLP), selectively amplified microsatellites (SAM) and sequence-specific amplification polymorphisms (S-SAP) were assessed for their potential in investigations of the genetic relationships among isolates of the wheat rust pathogens, Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and P. striiformis f. sp. tritici (Pst), the oat stem rust pathogen P. graminis f. sp. avenae (Pga), and a putative new P. striiformis special form tentatively designated Barley grass yellow rust (Bgyr). Marker information content, as indicated by the number of species-specific fragments, polymorphic fragments among pathotypes, percentage of polymorphic loci, and the marker index, was highest for the SAM assay, followed by the AFLP and S-SAP assays. UPGMA analysis revealed that all marker types efficiently discriminated the five different taxa and Mantel tests revealed significant correlations between the marker types. Within pathogen groups, the marker types differed in the amount of variation detected among isolates; however, the major differences were consistent and polymorphism was generally low. This was reflected by the AMOVA analysis that significantly partitioned 90% of the genetic variation between taxa. Of the three marker types, SAMS were the most informative, and have the potential for the development of locus-specific microsatellites.