Leaf rust caused by Puccinia triticina is the most common and widely distributed of the three wheat rusts. Losses from leaf rust are usually less damaging than those from stem rust and stripe rust, but leaf rust causes greater annual losses due to its more frequent and widespread occurrence. Yield losses from leaf rust are mostly due to reductions in kernel weight. Many laboratories worldwide conduct leaf rust surveys and virulence analyses. Most currently important races (pathotypes) have either evolved through mutations in existing populations or migrated from other, often unknown, areas. Several leaf rust resistance genes are cataloged, and high levels of slow rusting adult plant resistance are available in high yielding CIMMYT wheats. This paper summarizes the importance of leaf rust in the main wheat production areas as reflected by yield losses, the complexity of virulence variation in pathogen populations, the role cultivars with racespecific resistance play in pathogen evolution, and the control measures currently practiced in various regions of the world.

Three members of the Puccinia genus, Puccinia triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.

Relatively little is known about the genetic control of agronomic traits in common wheat (Triticum aestivum L.) compared with traits that follow Mendelian segregation patterns. A doubled-haploid population was generated from the cross RL4452x'AC Domain' to study the inheritance of the agronomic traits: plant height, time to maturity, lodging, grain yield, test weight, and 1000-grain weight. This cross includes the genetics of 2 western Canadian wheat marketing classes. Composite interval mapping was conducted with a microsatellite linkage map, incorporating 369 loci, and phenotypic data from multiple Manitoba environments. The plant height quantitative trait loci (QTLs), QHt.crc-4B and QHt.crc-4D, mapped to the expected locations of Rht-B1 and Rht-D1. These QTLs were responsible for most of the variation in plant height and were associated with other agronomic traits. An additional 25 agronomic QTLs were detected in the RL4452x'AC Domain' population beyond those associated with QHt.crc-4B and QHt.crc-4D. 'AC Domain' contributed 4 alleles for early maturity, including a major time to maturity QTL on 7D. RL4452 contributed 2 major alleles for increased grain yield at QYld.crc-2B and QYld.crc-4A, which are potential targets for marker-assisted selection. A key test weight QTL was detected on 3B and prominent 1000-grain weight QTLs were identified on 3D and 4A.

In hexaploid wheat, leaf rust resistance gene Lr1 is located at the distal end of the long arm of chromosome 5D. To clone this gene, an F(1)-derived doubled haploid population and a recombinant inbred line population from a cross between the susceptible cultivar AC Karma and the resistant line 87E03-S2B1 were phenotyped for resistance to Puccinia triticina race 1-1 BBB that carries the avirulence gene Avr1. A high-resolution genetic map of the Lr1 locus was constructed using microsatellite, resistance gene analog (RGA), BAC end (BE), and low pass (LP) markers. A physical map of the locus was constructed by screening a hexaploid wheat BAC library from cultivar Glenlea that is known to have Lr1. The locus comprised three RGAs from a gene family related to RFLP marker Xpsr567. Markers specific to each paralog were developed. Lr1 segregated with RGA567-5 while recombinants were observed for the other two RGAs. Transformation of the susceptible cultivar Fielder with RGA567-5 demonstrated that it corresponds to the Lr1 resistance gene. In addition, the candidate gene was also confirmed by virus-induced gene silencing. Twenty T (1) lines from resistant transgenic line T (0)-938 segregated for resistance, partial resistance and susceptibility to Avr1 corresponding to a 1:2:1 ratio for a single hemizygous insertion. Transgene presence and expression correlated with the phenotype. The resistance phenotype expressed by Lr1 seemed therefore to be dependant on the zygosity status. T (3)-938 sister lines with and without the transgene were further tested with 16 virulent and avirulent rust isolates. Rust reactions were all as expected for Lr1 thereby providing additional evidence toward the Lr1 identity of RGA567-5. Sequence analysis of Lr1 indicated that it is not related to the previously isolated Lr10 and Lr21 genes and unlike these genes, it is part of a large gene family.

Rust fungi are devastating plant pathogens and several Puccinia species have a large economic impact on wheat production worldwide. Disease protection, mostly offered by introgressed host-resistance genes, is often race-specific and rapidly overcome by newly-emerging virulent strains. Extensive new genomic resources have identified vital pathogenicity genes but their study is hampered because of the biotrophic life styles of rust fungi. In cereals, Barley stripe mosaic virus (BSMV)-induced RNAi has emerged as a useful tool to study loss-of-function phenotypes of candidate genes. Expression of pathogen-derived gene fragments in this system can be used to obtain in planta-generated silencing of corresponding genes inside biotrophic pathogens, a technique termed host-induced gene silencing (HIGS). Here we test the effectiveness of BSMV-mediated HIGS in the wheat leaf rust fungus Puccinia triticina (Pt) by targeting three predicted pathogenicity genes, a MAPK, a cyclophilin, and a calcineurin regulatory subunit. Inoculation of BSMV RNAi constructs generated fungal gene-specific siRNA molecules in systemic leaves of wheat plant. Subsequent Pt inoculation resulted in a suppressed disease phenotype and a reduction in endogenous transcript levels of the targeted fungal genes indicating translocation of siRNA molecules from host to fungal cells. Efficiency of this host-generated trans-specific RNAi was enhanced by using BSMV silencing vectors defective in coat protein coupled with introducing fungal gene sequences simultaneously in sense and antisense orientation. The disease suppression indicated the likely involvement of these fungal genes in pathogenicity. This study demonstrates that BSMV-mediated in planta-generated RNAi is an effective strategy for functional genomics in rust fungi.