2012 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 40,000 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. We derived over 1500 mutant wheat lines from the resistant plant Gabo 56 in order to facilitate the rapid identification of the resistance gene present in Gabo 56. Data were emailed via excel data files and pictures to collaborators at CIMMYT (Mexico), USDA-ARS Aberdeen, South Dakota State University, North Dakota State University, CSIRO (Australia), University of Nebraska, Washington State University, Kansas State University, and UC Davis. A graduate student and a postdoctoral research associate were recently hired for this project. A rapid DNA diagnostic assay for Pgt Ug99 race group was further optimized. Internal standard for the stage-1 assay was developed and tested. Set of SNP markers used in the stage-2 assay was modified to improve the overall performance of the assay. A total of 111 Ethanol killed samples collected from Kenya (2011 and 2012), Uganda (2012), Yemen (2011) and Zimbabwe (2012) were analyzed. Majority of the samples were identified to belong to Ug99 race group. Genotyping data predicted that these samples represent Pgt races PTKST, TTKSF, TTKSK and TTKST. Barberry as well as rust infections on barberry were surveyed in eastern Africa and Nepal. Samples from these surveys formed the basis for further studies through inoculation experiments and DNA sequencing. Results from these studies will help to explain the roles of barberry in pathogen variation and rust epidemiology in these regions and beyond. Stem rust infected wheat samples from Ethiopia and Kenya were analyzed for race identity and contributed to the understanding of population structure in eastern Africa. A high frequency of resistance to Ug99 was identified after screening a total of 1307 accessions of nine Aegilops spp. These resistant accessions will serve as valuable sources for identifying novel resistance genes and for introgression into adapted wheat germplasm. Genetics of Ug99 resistance in durum and related tetraploids wheat were investigated by evaluating parents and progeny with relevant stem rust races in seedling and adult plant stages. International wheat germplasm, especially those from CIMMYT, were assessed for resistance to Ug99 through multiple race testing.