Characterization of Stripe Rust Resistance in Wheat Lines with Resistance Gene Yr17 and Implications for Evaluating Resistance and Virulence.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been the most important foliar wheat disease in south central United States since 2000 when a new strain of the pathogen emerged. The resistance gene Yr17 was used by many breeding programs to develop resistant cultivars. Although Yr17 was classified as a seedling (all-stage) resistance gene conferring a low infection type, seedlings with Yr17 frequently had intermediate to high infection types when inoculated with isolates that caused little or no disease on adult plants of the same wheat lines. The objectives of this study were to determine how to best evaluate Yr17 resistance in wheat lines and to determine which factors made seedling tests involving Yr17 so variable. Stripe rust reactions on wheat seedlings with Yr17 were influenced by temperature, wheat genotype, pathogen isolate, and the leaf (first or second) used to assess the seedling reaction. The most critical factors for accurately evaluating Yr17 reactions at the seedling stage were to avoid night temperatures below 12°C, to use the first leaf to assess the seedling reaction, to use multiple differentials with Yr17 and known avirulent, partially virulent and virulent isolates as controls, and to recognize that intermediate infection types likely represent a level of partial virulence in the pathogen that is insufficient to cause disease on adult plants in the field.

Race-Specific Adult-Plant Resistance in Winter Wheat to Stripe Rust and Characterization of Pathogen Virulence Patterns.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat in the Great Plains and southeastern United States. Growing resistant cultivars is the preferred means for managing stripe rust, but new virulence in the pathogen population overcomes some of the resistance. The objectives of this study were to characterize the stripe rust resistance in contemporary soft and hard red winter wheat cultivars, to characterize the virulence of P. striiformis f. sp. tritici isolates based on the resistances found in the cultivars, and to determine wheat breeders' perceptions on the importance and methods for achieving stripe rust resistance. Seedlings of cultivars were susceptible to recent isolates, indicating they lacked effective all-stage resistance. However, adult-plants were resistant or susceptible depending on the isolate, indicating they had race-specific adult-plant resistance. Using isolates collected from 1990 to 2013, six major virulence patterns were identified on adult plants of twelve cultivars that were selected as adult-plant differentials. Race-specific adult-plant resistance appears to be the only effective type of resistance protecting wheat from stripe rust in eastern United States. Among wheat breeders, the importance of incorporating stripe rust resistance into cultivars ranged from high to low depending on the frequency of epidemics in their region, and most sources of stripe rust resistance were either unknown or already overcome by virulence in the pathogen population. Breeders with a high priority for stripe rust resistance made most of their selections based on adult-plant reactions in the field, whereas breeders with a low priority for resistance based selections on molecular markers for major all-stage resistance genes.

Characterization of Resistance to Stripe Rust in Contemporary Cultivars and Lines of Winter Wheat from the Eastern United States.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, has been an important disease of winter wheat (Triticum aestivum) in the eastern United States since 2000, when a new strain of the pathogen emerged. The new strain overcame the widely used resistance gene, Yr9, and was more aggressive and better adapted to warmer temperatures than the old strain. Host resistance is the most effective approach to manage stripe rust. Winter wheat lines with resistance to the new strain in the field are common, but the genes conferring this resistance are mostly unknown. The objectives of this research were to characterize the all-stage resistance and adult-plant resistance (APR) to stripe rust in a representative group of contemporary winter wheat cultivars and breeding lines and to identify the resistance genes when possible. Of the 50 lines evaluated for all-stage resistance at the seedling stage, nearly all were susceptible to the new strain. Based on a linked molecular marker, seven lines had resistance gene Yr17 that confers resistance to both old and new strains; however, this resistance was difficult to identify in the seedling stage. Of the 19 lines evaluated for APR, all expressed APR compared with a very susceptible check. Nine had race-specific APR to the new strain and nine had APR to both old and new strains. The remaining line, 26R61, had all-stage resistance to the old strain (conferred by resistance gene Yr9) and a high level of APR to the new strain. APR was expressed as low infection type, low percent leaf area diseased, and long latent period at heading stage under both low and high temperature regimes and could be identified as early as jointing stage. Based on tests for linked molecular markers, the most widely used slow-rusting APR genes, Yr18 and Yr29, were not present in any of the lines. The results of this research indicate that effective all-stage resistance was conferred only by Yr17 and that APR was common and likely conferred by unknown race-specific genes rather than genes conferring slow rusting that are more likely to be durable.

Nivalenol-type populations of Fusarium graminearum and F. asiaticum are prevalent on wheat in southern Louisiana.

U.S. populations of the Fusarium graminearum clade cause head blight on wheat and barley and usually contaminate grain with the trichothecene mycotoxin deoxynivalenol (DON). Recently, however, individual nivalenol (NIV)-type isolates from the United States were described that belonged to either the newly described species F. gerlachii or the genetically distinct Gulf Coast population of F. graminearum sensu stricto (s.s.). Here, we describe the discovery of NIV-type F. graminearum s.s. populations that were found in high proportion (79%) among isolates from small-grain-growing regions of Louisiana. We genotyped 237 isolates from Louisiana with newly developed polymerase chain reaction (PCR) restriction fragment length polymorphism markers and multiplex PCR primers that distinguish among the three trichothecene types: the two DON types (15ADON and 3ADON) and NIV. These isolates were compared with 297 isolates from 11 other U.S. states, predominantly from the Midwest. Using Bayesian-model-based clustering, we discovered a southern Louisiana population of F. graminearum s.s. that was genetically distinct from the previously recognized pathogen population in the Midwest (MW15ADON population). Population membership was correlated with trichothecene type. Most isolates from the southern Louisiana population were of the NIV type, while the majority of the isolates from the Midwest were of the 15ADON type. A smaller proportion of isolates from Louisiana belonged to the previously described Gulf Coast population that was mostly of the 3ADON type. The NIV type was also identified in collections from Arkansas (12%), North Carolina (40%), and Missouri (2%), with the collections from Arkansas and North Carolina being small and unrepresentative. F. asiaticum was detected from the two southern Louisiana parishes Acadia and Alexandria. All identified 41 F. asiaticum isolates were of the NIV type. Greenhouse tests indicated that U.S. NIV types accumulated four times less trichothecene toxin than DON types on inoculated wheat. This is the first report of NIV-type populations of F. graminearum s. s. and F. asiaticum in the United States.

Resistance in Winter Wheat Lines to Initial Infection and Spread Within Spikes by Deoxynivalenol and Nivalenol Chemotypes of Fusarium graminearum.

Head blight of wheat in the United States is caused primarily by the deoxynivalenol (DON)-producing chemotype of Fusarium graminearum. However, the discovery of the nivalenol (NIV) chemotype of F. graminearum in Louisiana and Arkansas necessitates having resistance in wheat to both chemotypes. The objectives of this research were to quantify resistance of selected winter wheat lines to initial infection and pathogen spread within spikes, to determine whether wheat lines selected for resistance to the DON chemotype also have resistance to the NIV chemotype, and to improve the methods for quantifying resistance to initial infection. A susceptible check (Coker 9835) and 15 winter wheat lines, which are adapted to the southeastern United States and possess diverse sources of head blight resistance, were evaluated for head blight resistance in a series of greenhouse and growth-chamber experiments. Significant levels of resistance to both initial infection and spread within a spike were found among the lines, and lines with resistance to isolates of the DON chemotype had even higher levels of resistance to isolates of the NIV chemotype. Quantifying resistance to initial infection was improved by standardizing the inoculum and environmental conditions. Additional information related to resistance to spread within a spike was obtained by calculating the area under the disease progress curve from 7 to 21 days after inoculation.

Evidence for increased aggressiveness in a recent widespread strain of Puccinia striiformis f. sp. tritici causing stripe rust of wheat.

Stripe rust (yellow rust) of wheat, caused by Puccinia striiformis f. sp. tritici, has become more severe in eastern United States, Australia, and elsewhere since 2000. Recent research has shown that this coincided with a global spread of two closely related strains that were similar based on virulence phenotype and amplified fragment length polymorphism. The objective of this research was to quantify differences in aggressiveness among isolates representative of the pre-2000 and post-2000 populations. Representative isolates were evaluated at low (10 to 18 degrees C) and high (12 to 28 degrees C) temperature regimes for latent period, lesion length, lesion width, lesion area, and spore production on adult plants of a susceptible wheat cultivar with no known genes for resistance to stripe rust. "New" isolates (since 2000) were significantly more aggressive than "old" isolates (before 2000) for all variables. At the low temperature regime, new isolates sporulated 2.1 days (16%) sooner, grew 0.3 mm per day (18%) faster, produced 999 (140%) more spores per inoculation site per day, and produced 6.5 (71%) more spores per mm2 of lesion per day compared with old isolates. At the high temperature regime, new isolates sporulated 3 days (26%) sooner, grew 0.2 mm per day (18%) and 2.2 mm2 per day (88%) faster, grew 1.2 mm (50%) wider, produced 774 (370%) more spores per inoculation site per day, and produced 6.2 (159%) more spores per mm2 of lesion per day than old isolates. New isolates showed significant adaptation to the warm temperature regime for all variables. Based on these results and previously published models for stripe rust epidemics, recent severe stripe rust epidemics were most likely enhanced by the pathogen's increased aggressiveness, especially at higher temperature. Furthermore, these results demonstrate that wheat rust fungi can adapt to warmer temperatures and cause severe disease in previously unfavorable environments.

Rapid global spread of two aggressive strains of a wheat rust fungus.

Rust fungi can overcome the effect of host resistance genes rapidly, and spores can disperse long distance by wind. Here we demonstrate a foreign incursion of similar strains of the wheat yellow rust fungus, Puccinia striiformis f. sp. tritici, in North America, Australia and Europe in less than 3 years. One strain defined by identity at 15 virulence loci and 130 amplified fragment length polymorphism (AFLP) fragments was exclusive to North America (present since 2000) and Australia (since 2002). Another strain of the same virulence phenotype, but differing in two AFLP fragments, was exclusive to Europe (present since 2000-2001) as well as Western and Central Asia and the Red Sea Area (first appearance unknown). This may be the most rapid spread of an important crop pathogen on the global scale. The limited divergence between the two strains and their derivatives, and the temporal-spatial occurrence pattern confirmed a recent spread. The data gave evidence for additional intercontinental dispersal events in the past, that is, many isolates sampled before 2000 in Europe, North America and Australia had similar AFLP fingerprints, and isolates from South Africa, which showed no divergence in AFLP, differed by only two fragments from particular isolates from Central Asia, West Asia and South Europe, respectively. Previous research has demonstrated that isolates of the two new strains produced up to two to three times more spores per day than strains found in USA and Europe before 2000, suggesting that increased aggressiveness at this level may accelerate global spread of crop pathogens.

Genes for Adult-Plant Resistance to Leaf Rust in Soft Red Winter Wheat.

Host plant resistance in wheat (Triticum aestivum) has been the principal means of managing leaf rust caused by Puccinia triticina. The need for durable resistance has changed the focus from the use of seedling resistance to adult-plant resistance. The objectives of this study were to determine the genetic basis for adult-plant resistance and to determine the most effective method to identify adult-plant resistance genes Lr12, 13, and 34 among 116 contemporary soft red winter wheat cultivars and breeding lines. Adult-plant resistance was detected by inoculating flag leaves with a race that was virulent on seedlings. Approximately 90% of the lines expressed resistance under controlled conditions. It was postulated that the adult-plant resistance in 67 lines was due in part to either Lr12, 13, or 34; the adult-plant resistance detected in 17 lines was attributed to Lr12 based on a distinctive low infection type very similar to that on the isoline TcLr12; the adult-plant resistance in 27 lines was attributed to Lr34, as all of these lines expressed a "leaf tip necrosis" in the field (a phenotype controlled by a gene known to be tightly linked with Lr34); and the adult-plant resistance in 23 lines was attributed to Lr13 based on a high infection type at 18.1°C and low infection type at 25.5°C with one or more pathogen isolates that were virulent on Lr13 at 18.1°C and avirulent on Lr13 at 25.5°C. The adult-plant resistance detected in the remaining 40% of the lines was due to one or more unidentified genes for adult-plant resistance. In a 4-year field study at several locations, nearly 29% of the lines were resistant at all locations, no line was susceptible at all locations, and only 30% of the lines were susceptible at one or more locations. Given that many of the lines in this study were resistant to all known races of P. triticina before being released as cultivars, the high frequency of adult-plant resistance in this study demonstrates that adult-plant resistance can be incorporated even in the presence of highly effective seedling resistance.

Seedling Resistance Genes to Leaf Rust in Soft Red Winter Wheat.

Seedling and adult-plant resistance have been used to manage leaf rust, caused by Puccinia triticina, but there is little information on resistance genes in contemporary cultivars and advanced breeding lines of soft red winter wheat (Triticum aestivum). Lack of information on the genetic basis for resistance leads to uncertainty about durability of resistance and makes pyramiding resistance genes more difficult. The objective of this study was to determine the genetic basis for race-specific seedling resistance to leaf rust among the 116 contemporary lines from the 1998-99 Arkansas Wheat Cultivar Performance Test and the Uniform Eastern and Southern Soft Red Winter Wheat Nurseries. To postulate the presence of genes for leaf rust resistance (Lr genes), seedlings of each line and 24 isolines in a Thatcher background were evaluated for infection type in growth chambers at 22/18°C (day/night) or constant 17 or 18°C using 22 races of P. triticina. A computer program was used to analyze infection type data and facilitate identification of Lr genes. Genes Lr1, 2a, 2c, 3, 3ka, 9, 10, 11, 14a, 18, 20, 23, 24, and 26 were identified among the lines tested. Genes Lr3, 10, and 11 were the most common. Genes Lr15, 28, and 30 were postulated as possibly present in some lines but were not likely to be important among the lines. Genes Lr16, 17, 21, 32, 36, 38, and 39 were not detected. Fifty-four lines had one or more unidentified Lr genes that were not included in the set of 24 isolines. Only four lines (Agripro Marion, APD94-5282, NC94-7197, and VA97W-375) were resistant to all races used in this study, and these were postulated to have the combination of Lr9, 24, and 26.

A Computer Program to Improve the Efficiency and Accuracy of Postulating Race-Specific Resistance Genes.

Gene postulation has been the most widely used technique to determine the presence of particular rust resistance genes in lines of small grains. It applies the principles of gene-for-gene specificity to determine the most probable race-specific resistance genes present in host lines. As the numbers of lines, resistance genes, and races increase, postulation based on visual comparisons of infection types becomes more complex and laborious, and errors may occur. A computer program was developed to facilitate identification of race-specific leaf rust (Lr) genes in wheat (Triticum aestivum). Seedlings of 116 contemporary lines of soft red winter wheat and 24 Thatcher isolines (each Thatcher isoline with a single Lr gene) were inoculated with 22 races of Puccinia triticina. Infection types were recorded on the standard 0 to 4 scale where infection types 3 and 4 were considered high (line was susceptible; race was virulent) and others were low (line was resistant; race was avirulent). Based on the gene-for-gene concept, lines susceptible to a particular race cannot have an Lr gene for which the race is avirulent. For each line, step 1 of the program summarized results from races that were virulent on the line to definitively exclude Lr genes from the line, and this exclusion resulted in a relatively short list of Lr genes that could be present. Step 2 of the program utilized data from races that were avirulent on the line, and the output listed the low infection types produced on the line and the isolines with Lr genes that were not excluded in step 1. Of these Lr genes, a gene was considered present if the low infection type produced on the line by one or more races matched the low infection type on the corresponding isoline. Otherwise, the gene was considered possibly present. Epistatic effects of one or more Lr genes prevented definitive inclusion or exclusion of genes considered possibly present. If the low infection type produced on the line was lower than that on any of the isolines listed in step 2, then the line was considered to have an unidentified Lr gene; i.e., a gene that was not in the set of 24 isolines. This program facilitated the objective and accurate postulation of Lr genes and could be adapted to other host-pathogen systems.

Wheat Stripe Rust Epidemics and Races of Puccinia striiformis f. sp. tritici in the United States in 2000.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is most destructive in the western United States and has become increasingly important in the south-central states. The disease has been monitored by collaborators through field surveys and in disease nurseries throughout the United States. In the year 2000, stripe rust occurred in more than 20 states throughout the country, which was the most widespread occurrence in recorded history. Although fungicide applications in many states reduced yield losses, the disease caused multimillion dollar losses in the United States, especially in Arkansas and California. One of the prevalent cultivars, RSI 5, had a yield loss of about 50% in the Sacramento-San Joaquin Delta region of California. In the Pacific Northwest, wheat losses due to stripe rust were minimal because cultivars with durable resistance were widely grown and the weather in May 2000 was not favorable for the disease. To identify races of the pathogen, stripe rust collections from 20 states across the United States were analyzed on 20 wheat differential cultivars, including Clement (Yr9, YrCle), Compair (Yr8, Yr19), and the Yr8 and Yr9 near-isogenic lines. In 2000, 21 previously identified races and 21 new races were identified. Of the 21 new races, 8 were pathotypes with combinations of virulences previously known to exist in the United States, and 13 had virulences to one or more of the lines Yr8, Yr9, Clement, or Compair. This is the first report of virulence to Yr8 and Yr9 in the United States. Most of the new races were also virulent on Express. Races that are virulent on Express have been identified in California since 1998. The races virulent on Yr8, Yr9, and Express were widely distributed in California and states east of the Rocky Mountains in 2000. The epidemic in 2000 demonstrates that increased efforts to breed for stripe rust resistance are needed in California, the south-central states, and some other states in the Great Plains. Diversification of resistance genes and use of durable resistance should prevent large-scale and severe epidemics.