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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS, POPULATION BIOLOGY, AND HOST-PARASITE INTERACTIONS OF CEREAL RUST FUNGI AND THEIR DISEASES
2008 Annual Report


1a.Objectives (from AD-416)
Objective 1: Monitor and characterize races of cereal rust pathogens, particularly the new East African strain, Ug99. Sub-objective 1. A. Characterize races of cereal rust (stem rust–Puccinia graminis and Ug99, wheat leaf rust-Puccinia triticina, crown rust- Puccinia coronata) populations by testing on host differential lines with single genes for rust resistance. Identify races of cereal rusts that represent a threat to the production of wheat, oat, and barley cultivars in the United States. Sub-objective 1.B. Characterize populations of cereal rusts using molecular markers, such as microsatellites and single nucleotide polymorphism, combined with virulence polymorphism, to study race evolution, identify genetically distinct populations, and determine migration patterns of rust genotypes within and between continental regions. Sub-objective 1.C. Determine phylogenetic relationships within and between economically important cereal and grass rust fungi including P. coronata, P. graminis, P. hordei, P. recondita and P. triticina. Objective 2: Identify features essential for cereal rust pathogenesis. Sub-objective 2.A. Characterize avirulence genes and their corresponding gene products from the wheat stem rust fungus, Puccinia graminis. Sub-objective 2.B. Characterize the genome of Puccinia graminis. Objective 3. Identify resistance genes and develop effective strategies for deploying host-resistance genes to control cereal rust diseases. Sub-objective 3.A. Test wheat, oat, and barley germplasm from breeding programs throughout the United States for resistance to stem rust, leaf rust, and crown rust using the prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. Postulate presence of rust resistance genes in seedling tests using specific races of rust. Evaluate lines for adult plant resistance in field plots using a mixture of races with virulence to seedling resistance genes. Subobjective 3.B. Determine the genetic basis of rust resistance in wheat, barley, and oat cultivars and germplasm from the United States and world-wide that have had high levels of durable resistance to the rust pathogens. New rust resistance genes that condition durable rust resistance in cereal germplasm will be identified and characterized for chromosome location. Genes that confer resistance to new races with virulence to commonly grown cultivars will be identified. Resistance genes will be identified in segregating populations by rust infection type and using tightly linked molecular markers.


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
Isolates of Puccinia graminis f.sp tritici representative of races from North American were grouped into 8 distinct clades using SSRs. African isolates of P. graminis were also characterized and at least four distinct genotypes were observed. All members of the Ug99 (TTKS) race cluster had identical SSR genotypes. Approximately 15,000 EST reads from isolates representing the Ug99 race cluster were compared with ESTs and the assembled genome sequence from the NSF P. graminis genome project. cDNA libraries from two different stages of P. coronata were developed. Sequence of a rDNA gene repeat was determined for 65 rust samples collected in FY08. Analysis of rDNA from rusts collected from Panicum virgatium indicated that there are three members in this complex. Additional SNP markers for the AvrT6 and AvrT9a loci in P. graminis have been developed. ESTs from a haustorial enriched cDNA library were analyzed for potential avirulence genes. Systematic development of SNP markers across the current P. graminis genome assembly has begun. A microarray of approximately 21,000 predicted genes from the annotated genome sequence of P. graminis was developed. Specific chromosome locations of resistance genes to Ug99 wheat stem rust were identified based on the DArT markers: chromosome 4A for resistance in CnsSrTmp and CI15685, chromosome 2B in CI12499, chromosome 3A in CI14142, chromosome 6A in TA4152-37, and chromosome 2B in CI14035. Race QFCS of P. graminis f. sp. tritici was identified from most wheat growing areas of the US in 2007, but a diverse group of races (including virulence to Sr24) was identified in barley collections from Washington. US wheat regional nurseries were evaluated for resistance to TTKSK (Ug99), and its new variants, and genes effective against the TTKS lineage were postulated. A variant within race TTKS (or Ug99) that overcomes the resistance gene Sr36 was identified and characterized. Isolates of P. triticina from the U.S. and South America were analyzed using virulence to specific resistance genes and molecular markers. Over 90% of isolates in both continents were placed into two different groups, with no significant genetic differentiation between isolates from the two continents in either group. Two new leaf rust resistance genes, Lr63 and Lr64 were mapped to chromosomes 3AS and 6AL in wheat, respectively. 48 accessions from the USDA collection of Avena barbata have broad-spectrum resistance to crown rust, P. coronata and were crossed to hexaploid oat. Five recombinant inbred populations for mapping genes for adult plant partial resistance to crown rust of oat have been advanced to the F5 generation. Isolates of P. coronata from both the winter and spring oat regions of the US, and from around the world have been genotyped with 37 SSR markers developed in our lab.

This research addresses three of the four components of National Program 303, Plant Diseases; Component 1. Disease Diagnosis: Detection, Identification and Characterization of Plant Pathogens; Component 2. Biology, Ecology, Epidemiology, and Spread of Plant Pathogens and Their Relationships with Hosts and Vectors; and Component 3: Plant Disease Resistance.


4.Accomplishments
1. Identified and characterized a new variant within race TTKS (or Ug99) that overcomes the resistance gene Sr36.

Stem rust resistance gene Sr36 in wheat is important because it is highly effective against Ug99 and a major component for Ug99 resistance in U.S. soft winter wheat. The occurrence of a combination of virulence on Sr36 and Sr31 (as well as the virulence combination of Sr24 and Sr31 detected in 2006) has substantially increased the vulnerability of wheat to stem rust worldwide, raised serious concerns on the potential impacts.

NP 303 - Problem Statement 3B. Disease resistance in new germplasm and varieties.

2. New, effective crown rust resistance found in wild tetraploid slender oat, Avena barbata. Crown rust caused by Puccinia coronata is the most destructive disease of oat worldwide. Resistant oat varieties quickly succumb to new races of the pathogen, so new resistance genes are needed. The USDA collection of A. barbata was screened for resistance to a very diverse population of P. coronata. Forty-eight accessions were found to be resistant to this population which contained virulence to all the described crown rust resistance genes in cultivated oat. A. barbata represents a new, unexploited pool of novel resistance genes that can be used in oat improvement programs in the U.S. and elsewhere.

NP 303 - Problem Statement 3B. Disease resistance in new germplasm and varieties.

3. Microarray developed for the wheat stem rust pathogen, Puccinia graminis f. sp. tritici.

Stem rust is a potentially devastating disease, having been responsible for several historical, destructive epidemics. The development of genomic tools to better understand the genetic basis for pathogenicity and the obligate parasitic nature of P. graminis represents a significant advance. A microarray containing approximately 21,000 predicted genes from the annotated genome sequence of P. graminis f. sp. tritici was developed and preliminary analysis of the array has been completed. This microarray will be a crucial tool for dissecting genes involved in pathogenicity and their expression during disease development, and could pave the way for novel approaches to controlling rust diseases of crops.

NP303 - Problem Statement 2A: Pathogen Biology, Virulence Determinants, and Genetics of the Pathogen.

4. Genetic variation in populations of wheat leaf rust (Puccinia triticina) in North and South America indicate pathogen migration between the two continents.

Leaf rust of wheat, caused by Puccinia triticina is the most common disease of wheat in the U.S. and world-wide. Isolates of P. triticina from the U.S. and South America were analyzed using virulence to specific resistance genes and molecular markers. Over 90% of isolates in both continents were placed into two different groups, with no significant genetic differentiation between isolates from the two continents in either group. Isolates of leaf rust that first appeared in the mid 1990s in the U.S. were found to be closely related to isolates that first appeared in South America in the late 1990s. It is highly likely that recent migration of leaf rust between the U.S. and South America has occurred, although weather and wind patterns would not predict regular movement of spores between continents. Races of leaf rust selected by host resistance genes in one continent may easily migrate and infect wheat cultivars in the U.S. The high degree of virulence variation in P. triticina populations indicates the need for use of non-specific resistance in wheat cultivars to minimize yield losses.

NP 303 - Problem Statement 3B. Disease resistance in new germplasm and varieties.

5. Mapping and designation of leaf rust resistance genes in wheat.

Leaf rust of wheat, caused by Puccinia triticina is the most common disease of wheat in the U.S. and world-wide. Over 60 races of leaf rust are identified annually in the U.S. as a result most of the Lr resistance genes in wheat cultivars in the U.S. do not condition effective resistance. A leaf rust resistance gene in bread wheat line RL6137 that was originally derived from Triticum monococcum was mapped to chromosome 3AS in wheat, and was officially designated as Lr63. A leaf rust resistance gene in wheat line RL6149 originally derived from durum wheat was mapped to chromosome 6AL in wheat and officially designated as Lr64. Both genes Lr63 and Lr64 condition effective resistance to most of the leaf rust races in the U.S. and will be useful for improving leaf rust resistance in U.S. wheat cultivars.

NP 303 - Problem Statement 3B. Disease resistance in new germplasm and varieties.


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

Number of Non-Peer Reviewed Presentations and Proceedings5
Number of Newspaper Articles and Other Presentations for Non-Science Audiences1
Number of Other Technology Transfer1

Review Publications
Baenziger, P., Beecher, B., Graybosch, R.A., Ibrahim, A., Nelson, L., Jin, Y., Wegulo, S., Watkins, J., Chen, M., Bai, G. 2008. Registration of 'NE01643' Wheat. Journal of Plant Registrations 2:36-42.

Jin, Y., Szabo, L.J., Pretorious, Z., Singh, R., Fetch, Jr., T. 2008. Detection of Virulence to Resistance Gene Sr24 within Race TTKS of Puccinia graminis f. sp. tritici. Plant Disease. 92:923-926.

Zhang, X., Singh, R., Kolmer, J.A., Huerta-Espino, J., Jin, Y., Anderson, J. 2008. Inheritance of Leaf Rust Resistance in the CIMMYT Wheat Weebill 1. Crop Science. 47:1037-1047.

Zhang, X., Jin, Y., Rudd, J., Bockelman, H.E. 2008. New fusarium head blight resistance spring wheat germplasm identified in the USDA National Small Grain Collection. Crop Science. 48:223-235.

Fetch, T.G., Jin, Y. 2007. International system of nomenclature for Puccinia graminis f. sp. avenae. Plant Disease. 91:763-766.

Jin, Y., Singh, R.P., Ward, R.W., Wanyera, R., Kinyua, M., Njau, P., Fetch, T., Yahouyi, A., Pretorious, Z. 2007. Characterization of seedling infection types and adult plant infection responses of known Sr genes to race TTKS of Puccinia graminis f. sp. tritici. Plant Disease. 91:1096-1099.

Steffenson, B.J., Olivera, P., Roy, J., Jin, Y., Smith, K., Muehlbauer, G. 2007. A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Australian Journal of Agricultural Research. 58:532-544.

Tsilo, T.J., Jin, Y., Anderson, J.A. 2007. Microsatellite markers linked to stem rust resistance allele Sr9a in wheat. Crop Science. 47:2013-2020.

Kolmer, J.A., Ordonez, M.E. 2007. Genetic differentiation of Puccinia triticina populations in Central Asia and the Caucasus. Phytopathology. 97:1141-1149.

Zhang, X., Singh, R.P., Kolmer, J.A., Huerta-Espino, J., Jin, Y., Anderson, J.A. 2008. Genetics of leaf rust resistance in CIMMYT "Brambling" wheat. Plant Disease. 92:1111-1118.

Kolmer, J.A., Long, D.L., Hughes, M.E. 2008. Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2006. Plant Disease. 92:1241-1246.

Barnes, C.W., Szabo, L.J. 2008. A Rapid Method for Detection and Quantification of Bacterial DNA in Rust Fungal DNA Samples. Phytopathology. 98:115-119.

Castell-Miller, C., Szabo, L.J., Gale, L.R., O'Neill, N.R., Samac, D.A. 2008. Molecular variability of a Minnesota population of Phoma medicaginis var. medicaginis, the causal agent of spring black stem and leaf spot of alfalfa. Canadian Journal of Plant Pathology. 30:85-96.

Carson, M.L. 2008. Virulence Frequencies in Oat Crown Rust in the United States from 2001 through 2005. Plant Disease. 97:379-384.

Tsilo, T.J., Jin, Y., Anderson, J.A. 2008. Diagnostic microsatellite markers for detection of stem rust resistance gene Sr36 in diverse genetic backgrounds of wheat. Crop Science. 48:253-261.

Klindworth, D.L., Miller, J., Jin, Y., Xu, S.S. 2007. Chromosomal locations of genes for stem rust resistance in monogenic lines derived from tetraploid wheat accession ST464. Crop Science. 47:1441-1450.

Szabo, L.J., Koike, S.T., Hill, J.P. 2008. Rust. In: Schwartz, H.F, Mohan, S.K., editors. Compendium of Onion and Garlic Diseases and Pests. 2nd Edition. Minneapolis, Minnesota: APS Press. p. 41-44.

Bonman, J.M., Bockelman, H.E., Jin, Y., Hijmans, R.J., Gironella, A. 2007. Geographic Distribution of Stem Rust Resistance in Wheat Landraces. Crop Science. 47:1955-1963.

Last Modified: 10/25/2014
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