2013 Annual Report
1a.Objectives (from AD-416):
Identify molecular markers linked to stem rust resistance genes, identify new sources of resistance to stem rust, and characterize the molecular genetics of stem rust resistance in order to deploy resistant varieties of wheat to Ug99 stem rust in the United States and worldwide.
1b.Approach (from AD-416):
Seedling Phenotyping of Mapping Populations. Stem rust assays of seedling plants from mapping populations can be an efficient way to provide phenotypic data for use in the identification of markers linked to stem rust resistance. The Cereal Disease Laboratory has provided wheat geneticists with phenotypic data for mapping populations segregating for stem rust resistance genes including Sr13, Sr22, Sr35, SrTmp, and a number of populations being mapped by CIMMYT and other collaborators associated with the DRRW projects. We request support for further phenotyping of mapping populations segregating for new and unknown resistance genes.
Seedling Screening of Breeding Lines and Diverse Germplasm. Screening breeding lines at the seedling stage with diverse races of stem rust including Ug99 lineage and other important virulence combinations at the Cereal Disease Laboratory has helped to postulate Ug99-effective genes in various gene pools and breeding germplasm, including confirmation of APR resistance. This work has provided breeders in CIMMYT, ICARDA, Ethiopia, Kenya, and United States with information on the presence or absence of particular resistance genes and effective gene combinations. The Cereal Disease Laboratory can continue to provide seedling screening of breeding lines and germplasm with Ug99, variants of Ug99, and other virulent races in order to provide breeders with the necessary information to develop/improve stem rust resistance.
Molecular Genetics of Rust Resistance near the Sr9 locus. Recent data indicate the presence of a Ug99 resistance locus linked or allelic with the Sr9 locus (resistance genes temporarily designated as SrWeb and SrGabo56). Several stem rust alleles are present at the Sr9 locus which is also known to be allelic with stripe rust resistance genes Yr5 and Yr7. USDA-ARS scientists at Pullman, WA, are conducting studies in order to clone Yr5. The availability of markers and sequence information at the Yr5 locus will enable the development of markers potentially tightly linked with Sr9 and SrGabo56 in available mapping populations. In order to test for the allelism of SrGabo56 and Sr9, populations for testing allelism have been derived. Screening of these populations with both stem rust and molecular markers can determine whether or not SrGabo56 is an allele of Sr9.
The unique phenotypic diversity at the Sr9 locus makes this an appealing candidate for cloning. Understanding the variation responsible for five Sr9 alleles, Yr5, Yr7, and SrGabo56 will uniquely enhance our understanding of the molecular mechanisms of resistance and race-specificity and could provide base knowledge for long-term projects including the development of new resistance alleles and for the deployment of durable resistance. The marker information available from the mapping of Sr9a, SrWeb, SrGabo56, and Yr5, the sequence information available from the Yr5 mapping project, and the plant populations currently available make the molecular dissection of resistance at this locus feasible.
A total of over 62,700 datapoints were collected on the reaction of Ug99 stem rust to wheat lines. These data were used to determine resistant and susceptible wheat lines in order to provide stem rust disease data necessary for genetic mapping of stem rust resistance genes in wheat. Data were emailed via excel data files and pictures to collaborators at CIMMYT (Mexico), USDA-ARS Aberdeen and Fargo, CSIRO (Australia), Cornell University, The Central Research Institute for Field Crops (Turkey), Swedish University of Agricultural Sciences, South Dakota State University, Agriculture and Agri-Food Canada, UC Davis, Washington State University, University of Nebraska, and North Dakota State University. Three EMS-derived mutant wheat lines of resistant wheat line Gabo 56 were identified and validated as true mutants. A total of 145 SNPs that cosegregate with Ug99 resistance in Gabo 56 were identified through 90K SNP chip and RNAseq analyses. Monitoring for Pgt Ug99 race group using molecular diagnostic assay has expanded to include 302 samples from eight countries (Eritrea, Ethiopia, Kenya, Pakistan, South Africa, Uganda, Uruguay and Zimbabwe). Only samples from Africa tested positive for Ug99 race group. The majority of the samples collected from Africa were positive for Ug99 race group and the genotypes indicated that races TTKSK, TTKST, TTTSK and TTKSF were present. These four different race phenotypes were made up of seven different genotypes. Several new genotypes were found, and verification will be done once live representative Pgt isolates are obtained. Assay data were sent to collaborators who collected the samples and to the central data system at CIMMYT (Ethiopia). Data analysis of Pgt genome genotyping projected has continued for 75 DNA samples through collaboration with Broad Institute. Improvements to the SNP calling methods were developed to reduce errors. Phylogenetic analysis of 70 Pgt strains was completed. Infected barberry samples from Nepal, Pakistan, Ethiopia, and Kenya were inoculated onto the identification series consisting of wheat, barley and oat lines. All inoculations were negative except for one sample from Ethiopia that produced a positive infection on Prolific rye. Samples are analyzed using DNA markers. Stem rust samples from Kenya, Ethiopia, Turkey, Pakistan, and Uruguay were analyzed through race-typing experiments. Ug99 related races were detected in Kenya and Ethiopia. Stem rust samples from Turkey and Uruguay were negative for Ug99-related races. Samples from Pakistan were not viable. Efforts in identifying new sources of Ug99 continued. During this reporting period, two field seasons in Ethiopia and one field season in St. Paul were conducted to screen durum for stem rust resistance. This is a continuation to identify Ug99 resistance in tetraploids. Mapping populations are being developed for genetic studies of Ug99 resistance in durum, emmer, and other tetraploids.