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United States Department of Agriculture

Agricultural Research Service

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Location: Cereal Disease Lab

2009 Annual Report

1a. Objectives (from AD-416)
New funds will be used to expand the current research objectives for this ARS project to prepare for the possible appearance of Ug99 in North America. Those objectives are: Objective 1: Monitor and characterize races of cereal rust pathogens, particularly the new East African strain, Ug99. This includes the sub-objective of characterizing races of cereal stem rust, particularly Ug99 and related mutants, which represent a threat to the production of wheat, oat, and barley cultivars in the United States. Objective 2: Identify features essential for cereal rust pathogensis including sub-objectives of characterizing the genome of Puccinia graminis (stem rust). Research for this objective will be expanded to characterize the Ug99 genome sequence and to develop detection methods for the new Eastern African stem rust mutants. Objective 3: Identify resistance genes and develop effective strategies for deploying host-resistance genes to control cereal rust diseases. Research for this objective will be expanded to identify new sources of Ug99 resistance and to accelerate the development of Ug99-resistant wheat and barley varieties adapted for U.S. production.

1b. Approach (from AD-416)
Cereal rust pathogens continuously evolve to overcome existing host resistance genes in wheat, barley, and oats. Cereal germplasm with durable rust resistance, and other control strategies are needed to minimize yield losses due to cereal rusts. Variation in cereal rust populations will be analyzed by assessing virulence polymorphism to important rust resistance genes and by using molecular polymorphism to determine the relatedness and relationships between these populations. Migration patterns of cereal rust populations will be established using virulence and molecular markers. Virulence shifts in cereal rust populations in major cereal-producing areas of the U.S. in relation to use of rust resistance genes will be analyzed. Cereal germplasm with rust resistance will be evaluated in seedling plant tests and in adult plant field tests. Advanced germplasm lines with combinations of rust resistance genes will be selected. Cereal germplasm with durable resistance will be genetically analyzed to determine the identity and expression of the rust resistance genes. A genetic map of P. graminis will be constructed using AFLPs, SSRs, and SNPs. Physical maps of regions with avirulence genes will be developed using BAC and cosmid libraries. Genetic determinants of early infection processes in cereal rusts will be characterized. Crosses will be made with other cereal rust fungi to determine the genetics of avirulence/virulence to important rust resistance genes.

3. Progress Report
The wheat stem rust resistance gene SrTmp and a resistance gene in CI15685 have been mapped to the distal end of 4AL. Based on infection type data, the resistance gene in CI 15685 is different from SrTmp. Resistance in CI 12499 and CI 14142 were found to be conferred by Sr28 and Sr27, respectively. The stem rust resistance in TA4152-37 was found to be conferred by Sr13. Resistance in CI 14035 is conferred by a novel gene mapped to 2BL. Over 2000 breeding lines of wheat and barley were screened with stem rust to assist US breeders to develop stem rust resistant cultivars. 4400 accessions of cultivated and wild relatives of wheat were screened for resistance to Ug99. Molecular marker (SSRs) analysis indicated that a population of P. graminis collected from a barley field represented a mixture of asexual and sexual components. Isolates of P. graminis from Northeast Africa and Central Asia were genotyped and compared to Ug99. Isolates that belonged to the Ug99 race cluster showed identical SSR genotypes, confirming traditional race phenotyping demonstrating that Ug99 is spreading. DNA sequence analysis of several P. graminis f. sp. tritici genes was used to examine allelic variation in select isolates. Ug99 SNP data based has been used to identify 156 candidate regions for the development of Ug99 specific probes for real-time PCR assay. Primers and probes for 25 of these target sites have been developed and are being tested. Movement of soybean rust pathogen (Phakopsora pachyrhizi) spores was monitored across the major soybean production regions of the U.S. As observed in the previous years, major depositions of spores occurred in August through early September. The number of deposition events and spore load per event was lower in 2008 than in previous years, which correlated with the lower level of disease development. Approximately 70 collections of rust fungi were made and stored. DNA sequence analysis was performed on 30 collections. SNP (Single Nucleotide Polymorphism) markers were developed and mapped across the region containing the avirulence locus AvrT6. Additional SNP markers were developed and mapped for region believed to contain AvrT9a locus. Analysis of gene expression data for predicted P. graminis genes identified over 100 candidate effector genes. Illumina genomic sequence data has been generated for several isolates of P. graminis f. sp. tritici. P. graminis f. sp. tritici is highly polymorphic between strains as well as within strains between haploid genomes based on SNPs. In 2008-2009 52 races of wheat leaf rust (P. triticina) were identified from wheat growing areas in the U.S. Virulence to genes Lr11, Lr17, Lr24, Lr26 and Lr41 was common throughout the U.S. The predominant hard and soft red winter wheat cultivars are susceptible to the common races of leaf rust. In 2008 losses in Kansas due to leaf rust were estimated to be 5%. 1200 additional accessions of Avena barbata from the Canadian germplasm system were screened for wide-spectrum resistance to oat crown rust at both the seedling and adult plant stages. Initial crosses of selected A. barbata accessions with cultivated oat were completely resistant in field tests.

4. Accomplishments
1. Evidence for migration of leaf rust of wheat to the U.S. from the Middle East and Africa found. 118 isolates of P. triticina from the Middle East (Israel, Egypt, Turkey) and East Africa, (Ethiopia and Kenya) were tested for virulence to leaf rust resistance genes and molecular genotype with simple sequence repeat (SSR) markers. Four distinct groups of SSR genotypes were found. Two of the groups were very similar to the two most common groups of P. triticina isolates in North America, which may have resulted from recent intercontinental migration of wheat leaf rust. Migration of P. triticina from other continents may give rise to new virulence changes in rust populations in the U.S.

2. An alternate host of wheat stem rust found near origin of Ug99 wheat stem rust. Berberis holstii, a barberry species native to Eastern Africa, was found widely distributed in the highlands of Kenya where wheat and barley were grown. The species was determined to be susceptible to Puccinia graminis through greenhouse inoculation experiments. Research results implicated B. holstii as an alternate host for stem rust, thus could generate new variants of stem rust pathogen in areas of Eastern Africa such as Ug99.

3. A new quantitative trait locus for stem rust resistance is found in the old wheat cultivar Thatcher. Thatcher has long been known for having some degree of resistance to stem rust, but the genetic basis for this was elusive. The genetic locus for resistance was mapped to chromosome 2BL in wheat using molecular markers. This resistance is effective to all tested stem rust races, including Ug9 (TTKS) from Africa. This finding will help breeders select for this type of resistance in their breeding programs.

4. New sources of resistance to Ug99 wheat stem rust found in wild relatives of wheat. Several relatives of wheat, including Aegilops tauschii, Ae. speltoides, Triticum monococcum, T. urartu, T. timopheevii, T. dicoccoides, T. dicoccom, T. carthlicum, T. polonicum, T. turanicum, Secale cereale, and X Triticosecale sp. were found to be sources of Ug99 resistance in greenhouse tests. Many of these resistant sources likely have novel genes for resistance to Ug99, and can serve as sources of resistance for U.S. wheat germplasm enhancement and breeding programs.

5. New variants of wheat stem rust in Kenya were found to have arisen by mutation within the existing race Ug99. Ug99 is a highly virulent strain of the wheat stem rust pathogen Puccinia graminis f. sp. tritici. In 2006 and 2007 two new variants of Ug99 with additional virulence were discovered. DNA analysis demonstrated that these two variants represent different members of the same genetic lineage. In addition, DNA analysis confirmed Ug99 has spread into Central Asia. This confirms that this threat to world wheat production continues to mutate and spread, making it a great potential threat to U.S. agriculture.

Review Publications
Kolmer, J.A., Chen, X., Jin, Y. 2009. Diseases Which Challenge Global Wheat Production - The Cereal Rusts. In: Carver, Brett F., editor. Wheat: Science and Trade. Hoboken, NJ: Wiley Press. p. 89-124.

Faris, J.D., Xu, S.S., Xiwen, C., Friesen, T.L., Jin, Y. 2008. Molecular and cytogenetic characterization of a durum wheat Aegilops speltoides chromosome translocation conferring resistance to stem rust. Chromosome Research. 16(8): 1097-1105.

Bolton, M.D., Kolmer, J.A., Garvin, D.F. 2008. Wheat Leaf Rust Caused by Puccinia triticina. Molecular Plant Pathology. 9(5):563-575.

Kolmer, J.A., Singh, R.P., Garvin, D.F., Viccars, L., William, H.M., Huerta-Espino, J., Ogbonnaya, F.C., Raman, H., Orford, S., Bariana, H.S., Lagudah, E.S. 2008. Analysis of the Lr34/Yr18 Rust Resistance Region in Wheat Germplasm. Crop Science. 48(5):1841-1852.

Bolton, M.D., Kolmer, J.A., Xu, W., Garvin, D.F. 2008. Lr34-Mediated Leaf Rust Resistance in Wheat: Transcript Profiling Reveals a High Energetic Demand Supported by Transient Recruitment of Multiple Metabolic Pathways. Molecular Plant-Microbe Interactions. 21(12):1515-1527.

Graybosch, R.A., Peterson, C.J., Baenziger, P.S., Baltensperger, D.D., Nelson, L.A., Jin, Y., Kolmer, J.A., Seabourn, B.W., French, R.C., Hein, G.L. 2009. Registration of ‘Mace’ Hard Red Winter Wheat. Journal of Plant Registrations 3:51-56.

Jin, Y., Szabo, L.J., Rouse, M., Fetch, T., Pretorious, Z., Wanyera, R., Njau, P. 2009. Detection of Virulence to Resistance Gene Sr36 within Race TTKS Lineage of Puccinia graminis f. sp. tritici. Plant Disease. 93:367-370.

Tsilo, T., Chao, S., Jin, Y., Anderson, J. 2009. Identification and validation of SSR markers linked to the stem rust resistance gene Sr6 on the short arm of chromosome 2D in wheat. Theoretical and Applied Genetics. 118:515-524

Kolmer, J.A., Long, D.L., Hughes, M.E. 2009. Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2007. Plant Disease. 98:538-544.

Kolmer, J.A., Ordonez, M.E. 2009. Differentiation of Molecular Genotypes and Virulence Phenotypes of Puccinia triticina from Common Wheat in North America. Phytopathology. 99:750-758.

Kolmer, J.A. 2009. Genetics of Leaf Rust Resistance in the Soft Red Winter Wheat Caldwell. Crop Science. 49:1187-1192.

Haley, S.D., Johnson, J.J., Westra, P.H., Peairs, F.B., Stromberger, J.A., Heaton, E.E., Seifert, S.A., Kottke, R.A., Rudolph, J.B., Bai, G., Bowden, R.L., Chen, M., Chen, X., Jin, Y., Kolmer, J.A., Seabourn, B.W. 2009. Registration of 'Thunder CL' Wheat. Journal of Plant Registration. 3(2):181-184.

Barnes, C.W., Szabo, L.J., Bowersox, V.C. 2009. Detection of Phakopsora pachyrhizi Spores in Rain Using a Real-Time PCR Assay. Phytopathology. 99:328-338.

Zhong, S., Leng, Y., Friesen, T.L., Faris, J.D., Szabo, L.J. 2009. Development and characterization of expressed sequence tag (EST)-derived microsatellite markers for the wheat stem rust fungus, Puccinia graminis f.sp. tritici. Phytopathology 99:282-289.

Last Modified: 2/23/2016
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