Location: Cereal Disease Lab2017 Annual Report
Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogens. Sub-objective 1.A. Monitor, collect, and characterize cereal rust pathogen populations in the U.S. for virulence to rust resistance genes in current cultivars. Sub-objective 1.B. Determine levels of genetic variation in Puccinia triticina, P. graminis and P. coronata populations. Sub-objective 1.C. Refine phylogenetics and systematics of P. graminis from Mahonia and other native Berberis spp. in North America. Objective 2: Further develop genomic resources of cereal rust pathogens and identify fungal genes involved in pathogenicity and development. Sub-objective 2.A. Identify effectors of P. graminis f. sp. tritici involved in fungal pathogenicity and host resistance. Sub-objective 2.B. Develop genomic resources and tools for more detailed analysis of P. coronata. Objective 3: Improve host resistance in cereal crops to rust pathogens through investigations in sources and genetics of rust resistance, characterization of various germplasm, and incorporation into adapted germplasm. Sub-objective 3.A. Evaluate wheat, oat and barley germplasm from U.S. breeding programs for rust resistance. Sub-objective 3.B. Identify and characterize new sources of rust resistance in wheat, barley, and oat; and incorporate into adapted germplasm.
Cereal rust fungi (Puccinia coronata, P. graminis, and P. triticina) are dynamic leading to constant changes in the U.S. population and erosion of effective rust resistance in cereal crops. In addition, introduction of foreign isolates, such as Ug99, further threaten cereal production. Development of cereal cultivars with effective rust resistance and management strategies of these diseases depend on monitoring, collection, virulence phenotyping, and genotypic characterization of cereal rust pathogen populations. Rust resistant cereal germplasm will be selected by testing wheat, oat, and barley lines from breeding programs throughout the U.S. and other sources for resistance to these pathogens using the prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. Testing with selected isolates of the cereal rust pathogens and host genetics studies will identify the rust resistance genes in breeding lines and germplasm. Advanced germplasm lines with combinations of rust resistance genes will be selected and released for further use in cultivar development. Rust fungi produce a large arsenal of effector proteins in order to infect and colonize the plant host. Genetic and genomic approaches will be used to identify and characterize effector genes from P. graminis and P. coronata.
Progress was made on all objectives. Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogens. 174 collections of wheat leaf rust (P. triticina) from the southern states, Ohio Valley, and central Great Plains had been received from collaborators and collected by staff at the USDA-ARS in St. Paul, Minnesota. Of isolates tested for virulence thus far in the survey, race TFTSB, with virulence to Lr1, Lr2a, Lr24, Lr26, Lr3ka, Lr11, Lr17, Lr30, Lr10, and Lr14a is the most common race in the southern United States. Other races with virulence to Lr17 and Lr39 are common in Texas and Oklahoma and in Louisiana. A total of 831 isolates of P. triticina (wheat leaf rust) have been genotyped using 23 SSR marker loci. The leaf rust collections are from North America, South America, Central Asia, Russia, China, Pakistan, the Middle East, and East Africa. Neighbor-joining analysis using Nei's genetic distance of 40 groups defined by SSR genotypes indicated that groups of P. triticina from the United States were highly related to groups of isolates from South America, and the Middle East. Another group of isolates from the United States are highly related to isolates from Ethiopia, Pakistan, Europe, and South America. Recent migration of P. triticina is occurring. All the international populations have characteristics of clonal reproduction. 21 collections of P. graminis f. sp. trtici (wheat stem rust), 23 collections of P. graminis f. sp. avenae (oat stem rust), and 3 collections of P. graminis f. sp. secalis (rye stem rust) from the United States were obtained by the USDA-ARS Cereal Disease Laboratory. Of the isolates tests thus far, all P. graminis f. sp. tritici isolates were race QFCSC and P. graminis f. sp. avenae isolates included races TJS and TGN. 90 collections of P. coronata (oat crown rust) from the southern (72) and northern (18) regions were received from collaborators and collected and by staff at the USDA-ARS, Cereal Disease Laboratory. From the first 50 collection we have obtained 118 single pustule isolates and data from differential lines is being collected. A total of 100 samples of P. graminis f. sp. tritici were genotyped from the Middle East. Objective 2: Further develop genomic resources of cereal rust pathogens and identify fungal genes involved in pathogenicity and development. Ninety isolates of P. graminis f. sp. tritici from United States, Europe and Africa were sequenced. The data will be used for phylogenetic analysis and mapping effector genes. The genome sequence assembly and annotation of P. coronata is nearly complete. Large isolate collections representing the diversity of this species are being prepared for sequencing to determine the level of sequence diversity. This re-sequencing effort will allow development of molecular tools for further characterization of this species and role of sexual vs. mutational derived variation in pathogenicity. Objective 3: Improve host resistance in cereal crops to rust pathogens through Investigations in sources and genetics of rust resistance, characterization of various germplasm, and incorporation into adapted germplasm. Recombinant inbred line (RIL) populations of Tc*3/Deliver, Tc*3/Bill Brown have been evaluated for segregation of leaf rust resistance. The RIL populations will be genotyped with the 90K SNP chip from Illumina, and the leaf rust phenotype data will be used to map the chromosome location of the adult plant leaf rust resistance. Double haploid populations of Linkert/LMPG6 and Linkert/Foremost have been evaluated for leaf rust segregation. Chromosome location of the segregating leaf rust resistance will be determined using the 90 K chip. Backcrossing of linkage blocks of two Ug99-effective Sr genes was initiated. Marker-assisted backcrossing facilitated the generation of BC4F1 seed of the Sr9h-Sr28 linkage block and BC2F1 seed of the Sr15-Sr22 linkage block. Crosses generated F1 and F2 seed for the purpose of combining additional Sr genes on chromosome 2B (Sr36, Sr39, Sr40, Sr47, Sr193883). Recurrent parents used for backcrossing were obtained from the University of Minnesota and South Dakota State University. A total of 583 oat breeding lines from different programs in the United States and Canada were evaluated for crown rust resistance in field plots. Additional 116 advanced oat breeding lines from the regional programs were analyzed for crown rust reaction. Nearly 328 lines from the Aberdeen USDA program were also evaluated for their adult plant resistance to oat crown rust in the buckthorn nursery. Additionally, we are assessing the effectiveness of several adult plant resistance genes in the buckthorn for future use in the effort to pyramid and develop more durable resistant germplasm. A total of 1620 wheat breeding lines from the uniform regional nurseries, preliminary regional nurseries, and individual breeding programs across United States were tested with multiple stem rust races in greenhouse and in the field. Seedling screening included tests with 4 races in the Ug99 races group and 5 other races of foreign origin with significant virulence combinations. Resistance genes effective against these races were postulated. Data were provided to nursery coordinators and individual breeders, and were posted at CDL website. About 500 lines of genetic materials from ARS and university scientists, who collaborated with us in stem rust resistance discovery and characterization, were tested with stem rust races in greenhouse and field experiments. Contributed to the documentation of germplasm/variety releases.
1. A new gene for durable leaf rust resistance in wheat. The wheat cultivar Toropi from Brazil, has had long lasting resistance to leaf rust, caused by Puccinia triticina. Long lasting leaf rust resistance in wheat has been difficult to achieve and maintain since the leaf rust pathogen is highly variable for virulence to leaf rust resistance genes in wheat, and populations of this rust fungus can adapt quickly to the resistance in the released cultivars. ARS scientists in St. Paul, Minnesota studied the identity of the leaf rust resistance genes in Toropi, identifying a major gene for adult plant leaf rust resistance on chromosome 5BS. This is a new gene for adult plant leaf rust resistance and has been designated as Lr78 in the wheat gene catalogue. Toropi had other genes with lesser effect on chromosomes 1BL, 3BS, and 4BS. A KASP marker for Lr78 can be used in wheat improvement programs to select for the new durable resistance gene.
2. Cloning of a durum wheat stem rust resistance gene. Wheat provides a substantial proportion of the calories and proteins consumed by the human population but further increases in wheat production are necessary to feed a growing human population. Reducing yield losses caused by pathogens can contribute to these increases. ARS scientists in St. Paul, Minnesota, report the identification of Sr13, a gene from durum wheat that confers resistance to the new virulent races of the stem rust pathogen that appeared in Africa at the beginning of this century including Ug99. Three different resistance forms of Sr13 were identified and developed perfect markers to accelerate their deployment in wheat breeding programs. The three resistant forms of Sr13 corresponded to two phenotypic alleles, Sr13a and Sr13b, that differ in their effectiveness to stem rust pathogen races. Both Sr13a and Sr13b confer resistance to Ug99. The perfect marker linked to Sr13 and knowledge of allelic differences will allow United States durum wheat breeders to more effectively develop Ug99 resistant cultivars. In addition, Sr13 can be a useful component of transgenic cassettes including multiple resistance genes.