Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2005

Physiological specialization of Puccinia triticina and genome-wide association mapping provide insights into the genetics of wheat leaf rust resistance in Iran

Leaf rust caused by Puccinia triticina Erikss. (Pt) is the most widely distributed and important wheat disease worldwide. The objective of the present study was to determine the frequency of Iranian Pt races, their virulence to key resistance genes and map quantitative trait loci (QTL) for resistance to different Pt races from 185 globally diverse wheat genotypes using a genome-wide association study (GWAS) approach. The virulence pattern of the 33 Pt isolates from various wheat-growing areas of Iran on 55 wheat differentials showed that the FKTPS and FKTTS were relatively frequent pathotypes among the 18 identified races. The weighted average frequency of virulence on the resistance genes Lrb, Lr3bg, Lr14b, Lr16, Lr24, Lr3ka, Lr11 and Lr20 were high (> 90%). However, low virulence on the resistant genes Lr2a, Lr9, Lr19, Lr25, Lr28 and Lr29 indicates that these genes are still effective against the pathogen population in Iran at present. GWAS on a panel of 185 wheat genotypes against 10 Pt races resulted into 62 significant marker-trait associations (MTAs) belonged to 34 quantitative trait loci (QTL) across 16 chromosomes. Among them, 10 QTLs on chromosomes 1A, 1B, 3B, 3D, 4A, 6D, 7A and 7D were identified as potential novel QTLs, of which four QTLs (QLr.iau-3B-2, QLr.iau-7A-2, QLr.iau-7A-3 and QLr.iau-7D-2) are more interesting, as they are associated with resistance to two or more Pt races. The known and novel QTLs associated with different Pt races found here, can be used in future wheat breeding programs to recombine different loci for durable resistance against leaf rust races.

Historical Development of the Puccinia triticina Population in South Africa

In contrast to many other countries, the virulence and genetic diversity of the South African Puccinia triticina population before 1980 is unknown, because of the absence of regular and systematic race analysis data and viable rust cultures. Herbarium specimens housed at the National Collection of Fungi, Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa (SA), provided the opportunity to investigate the genetic development of the population using isolates collected between 1906 and 2010. Five subpopulations that survived between 21 and 82 years in the field were found. While three of these could represent the original races that entered SA during European settlement, two appear to be recent exotic introductions into SA, most probably from other African countries. The demise of the three oldest subpopulations might be from the release of resistant wheat cultivars. The population is clonal, where new virulence develops through single step mutations and selection for virulence. Although a possible case of somatic hybridization was found, sexual reproduction appears to be absent in SA. This study confirmed the importance of annual surveys in SA and its neighboring countries for the timely detection of new virulent races that could threaten wheat production in SA.

Lr80: A new and widely effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars

A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3⁺. Genetic analysis based on Agra Local/Hango-2-derived F₃ families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these were mapped on the entire Agra Local/Hango-2 F₃ population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90 K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.

Virulence of Puccinia triticina, the Wheat Leaf Rust Fungus, in the United States in 2017

Samples of wheat leaves infected with the leaf rust fungus, Puccinia triticina, were obtained in 2017 from agricultural experiment station plots, demonstration plots, and farm fields in the Great Plains, the Ohio Valley, the southeastern states, California, and Washington in order to determine the prevalent virulence phenotypes present in the United States. A total of 65 virulence phenotypes were identified among the 469 single uredinial isolates that were tested on 20 near-isogenic lines of Thatcher wheat that differ for leaf rust resistance genes. Virulence phenotypes MBTNB at 11.3% of the overall population, and MCTNB at 7.0%, were the first and third most common phenotypes. Both phenotypes were found mostly in the southeastern states and Ohio Valley region. Phenotype TFTSB at 10.9% was the second most common phenotype and was found mostly in southern Texas. Virulence to leaf rust resistance gene Lr39, which is present in hard red winter wheat cultivars, was highest in the Great Plains region. Virulence to Lr11 and Lr18, which are present in soft red winter wheat cultivars, was highest in the southeastern states and Ohio Valley region. Virulence to Lr21, which is present in hard red spring wheat cultivars, was highest in the northern Great Plains region. The predominate P. triticina phenotypes from the soft red winter wheat regions of the southeastern states and Ohio Valley area differed from those in the hard red winter and hard red spring wheat areas of the Great Plains region. Collections from Washington had unique virulence phenotypes that had not been previously detected.

Resistance of Aegilops longissima to the Rusts of Wheat

Stem rust (caused by Puccinia graminis f. sp. tritici), leaf rust (P. triticina), and stripe rust (P. striiformis f. sp. tritici) rank among the most important diseases of wheat worldwide. The development of resistant cultivars is the preferred method of controlling rust diseases because it is environmentally benign and also cost effective. However, new virulence types often arise in pathogen populations, rendering such cultivars vulnerable to losses. The identification of new sources of resistance is key to providing long-lasting disease control against the rapidly evolving rust pathogens. Thus, the objective of this research was to evaluate the wild wheat relative Aegilops longissima for resistance to stem rust, leaf rust, and stripe rust at the seedling stage in the greenhouse. A diverse collection of 394 accessions of the species, mostly from Israel, was assembled for the study, but the total number included in any one rust evaluation ranged from 308 to 379. With respect to stem rust resistance, 18.2 and 80.8% of accessions were resistant to the widely virulent U.S. and Kenyan P. graminis f. sp. tritici races of TTTTF and TTKSK, respectively. The percentage of accessions exhibiting resistance to the U.S. P. triticina races of THBJ and BBBD was 65.9 and 52.2%, respectively. Over half (50.1%) of the Ae. longissima accessions were resistant to the U.S. P. striiformis f. sp. tritici race PSTv-37. Ten accessions (AEG-683-23, AEG-725-15, AEG-803-49, AEG-1274-20, AEG-1276-22, AEG-1471-15, AEG-1475-19, AEG-2974-0, AEG-4005-20, and AEG-8705-10) were resistant to all races of the three rust pathogens used in this study. Distinct differences in the geographic distribution of resistance and susceptibility were found in Ae. longissima accessions from Israel in response to some rust races. To P. graminis f. sp. tritici race TTKSK, populations with a very high frequency of resistance were concentrated in the central and northern part of Israel, whereas populations with a comparatively higher frequency of susceptibility were concentrated in the southern part of the country. The reverse trend was observed with respect to P. striiformis f. sp. tritici race PSTv-37. The results from this study demonstrate that Ae. longissima is a rich source of rust resistance genes for wheat improvement.

Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia

Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2013

Collections of Puccinia triticina were obtained from rust-infected leaves provided by cooperators throughout the United States and from wheat fields and breeding plots by USDA-ARS personnel and cooperators in the Great Plains, Ohio River Valley, and southeastern states in order to determine the virulence of the wheat leaf rust population in 2013. Single uredinial isolates (490 total) were derived from the collections and tested for virulence phenotype on 20 lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes. In 2013, 79 virulence phenotypes were described in the United States. Virulence phenotypes MBTNB, TNBGJ, and MCTNB were the three most common phenotypes. Phenotypes MBTNB and MCTNB are both virulent to Lr11, and MCTNB is virulent to Lr26. MBTNB and MCTNB were most common in the soft red winter wheat region of the southeastern states and Ohio Valley. Phenotype TNBGJ is virulent to Lr39/41 and was widely distributed throughout the hard red winter wheat region of the Great Plains. Isolates with virulence to Lr11, Lr18, and Lr26 were common in the southeastern states and Ohio Valley region. Isolates with virulence to Lr21, Lr24, and Lr39/41 were frequent in the hard red wheat region of the southern and northern Great Plains.

Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust) of wheat and is highly variable in virulence toward wheat with race-specific resistance. During 2010, wheat stripe rust was the most widespread in the recorded history of the United States, resulting in large-scale application of fungicides and substantial yield loss. A new differential set with 18 yellow rust (Yr) single-gene lines was established and used to differentiate races of P. striiformis f. sp. tritici, which were named as race PSTv in distinction from the PST races identified in the past. An octal system was used to describe the virulence and avirulence patterns of the PSTv races. From 348 viable P. striiformis f. sp. tritici isolates recovered from a total of 381 wheat and grass stripe rust samples collected in 24 states, 41 races, named PSTv-1 to PSTv-41, were identified using the new set of 18 Yr single-gene differentials, and their equivalent PST race names were determined on the previous set of 20 wheat cultivar differentials. The frequencies and distributions of the races and their virulences were determined. The five most predominant races were PSTv-37 (34.5%), PSTv-11 (17.5%), PSTv-14 (7.2%), PSTv-36 (5.2%), and PSTv-34 (4.9%). PSTv-37 was distributed throughout the country while PSTv-11 and PSTv-14 were almost restricted to states west of the Rocky Mountains. The races had virulence to 0 to 13 of the 18 Yr genes. Frequencies of virulences toward resistance genes Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, YrTr1, and YrExp2 were high (67.0 to 93.7%); those to Yr1 (32.8%) and YrTye (31.3%) were moderate; and those to Yr10, Yr24, Yr32, and YrSP were low (3.4 to 5.7%). All of the isolates were avirulent to Yr5 and Yr15.

Race and Virulence Dynamics of Puccinia triticina in China During 2000-2006

Wheat leaf rust, caused by Puccinia triticina, is an important foliar disease of wheat in China. The dynamics of races and virulence in P. triticina populations in China during 2000 to 2006 were studied. Leaf rust samples were collected during surveys of wheat fields and trap nurseries in 16 provinces, and provided by coworkers throughout China. The virulence of single-pustule isolates was determined on near-isogenic Thatcher lines for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17, and Lr30, and races were denominated using the Prt code system. During 2000 to 2006, 79 races were identified from a total of 613 isolates. Races PHT (23.7%), THT (14.7%), PHJ (11.4%), and THJ (4.2%) were the four common races, all avirulent to Lr9 and Lr24. The frequency of isolates with virulence to Lr1, Lr2c, Lr3, Lr11, Lr16, Lr17, and Lr26 was over 80%, and these isolates were widely distributed in China, whereas the frequencies of virulence to Lr9, Lr19, Lr24, Lr25, Lr28, and Lr29 were 0.2 to 2.5%. The diversity of virulence phenotypes of Chinese P. triticina populations appeared to increase from 2000 to 2006. P. triticina races and virulences in China appear to be isolated from those in other countries.

Genetic differentiation within the Puccinia triticina population in South America and comparison with the North American population suggests common ancestry and intercontinental migration

Leaf rust, caused by Puccinia triticina, is the most prevalent and widespread disease of wheat in South America. The objective of this study was to determine whether genetically differentiated groups of P. triticina are currently present in South America and to compare the South American population with the previously characterized population in North America. In total, 130 isolates of P. triticina from the wheat-growing regions of Argentina, Brazil, Chile, Peru, and Uruguay, mostly from the 1990s to 2008, were tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotypes with 23 simple-sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotypes, 99 isolates were included for further analysis. Principal coordinate analysis plots indicated five different groups of isolates based on SSR genotypes that also differed for virulence to leaf rust resistance genes. All pairs of groups, except for one pair, were significantly differentiated for SSR genotypes according to R(ST) statistics. All but two pairs of groups were significantly differentiated for virulence phenotype according to Phi(PT) statistics. Isolates in all five groups had high values of fixation index for SSR alleles and linkage disequilibrium was high across all isolates that indicated the clonal reproduction of urediniospores. Only one of the five P. triticina groups from South America was differentiated for SSR genotypes from all of the six P. triticina groups from North America. The high degree of similarity for SSR genotype of isolates from both South America and North America suggested a common European origin of P. triticina that was introduced to both continents. The emergence of the same P. triticina virulence phenotypes with highly related SSR genotypes in the United States in 1996 and in Uruguay in 1999 indicated the likely intercontinental migration of these genotypes from Mexico to both South America and North America.

Wheat leaf rust caused by Puccinia triticina

Leaf rust, caused by Puccinia triticina, is the most common rust disease of wheat. The fungus is an obligate parasite capable of producing infectious urediniospores as long as infected leaf tissue remains alive. Urediniospores can be wind-disseminated and infect host plants hundreds of kilometres from their source plant, which can result in wheat leaf rust epidemics on a continental scale. This review summarizes current knowledge of the P. triticina/wheat interaction with emphasis on the infection process, molecular aspects of pathogenicity, rust resistance genes in wheat, genetics of the host parasite interaction, and the population biology of P. triticina.

TAXONOMY

Puccinia triticina Eriks.: kingdom Fungi, phylum Basidiomycota, class Urediniomycetes, order Uredinales, family Pucciniaceae, genus Puccinia.

HOST RANGE

Telial/uredinial (primary) hosts: common wheat (Triticum aestivum L.), durum wheat (T. turgidum L. var. durum), cultivated emmer wheat (T. dicoccon) and wild emmer wheat (T. dicoccoides), Aegilops speltoides, goatgrass (Ae. cylindrica), and triticale (X Triticosecale). Pycnial/aecial (alternative) hosts: Thalictrum speciosissimum (= T. flavum glaucum) and Isopyrum fumaroides.

IDENTIFICATION

Leaf rust is characterized by the uredinial stage. Uredinia are up to 1.5 mm in diameter, erumpent, round to ovoid, with orange to brown uredinia that are scattered on both the upper and the lower leaf surfaces of the primary host. Uredinia produce urediniospores that are sub-globoid, average 20 microm in diameter and are orange-brown, with up to eight germ pores scattered in thick, echinulate walls.

DISEASE SYMPTOMS

Wheat varieties that are fully susceptible have large uredinia without causing chlorosis or necrosis in the host tissues. Resistant wheat varieties are characterized by various responses from small hypersensitive flecks to small to moderate size uredinia that may be surrounded by chlorotic and/or necrotic zones.

USEFUL WEBSITE

USDA Cereal Disease Laboratory: http://www.ars.usda.gov/mwa/cdl.

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2006

Collections of Puccinia triticina were obtained from rust-infected leaves provided by cooperators throughout the United States and from surveys of wheat fields and nurseries in the Great Plains, Ohio River Valley, southeast, California, and Washington State in order to determine the virulence of the wheat leaf rust population in 2006. Single uredinial isolates (718 in total) were derived from the collections and tested for virulence phenotype on lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3a, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17a, Lr30, LrB, Lr10, Lr14a, Lr18, Lr2, and Lr28 and winter wheat lines with genes Lr41 and Lr42. In the United States in 2006, 56 virulence phenotypes were found. Virulence phenotypes TDBJG, TDBGG, and TDBJH were among the four most common phenotypes and were all virulent to resistance gene Lr24. These phenotypes were found throughout the Great Plains region. Phenotype MLDSD with virulence to Lr9, Lr17, and Lr41 was also widely distributed in the Great Plains. In the soft red winter wheat region of the southeastern states, phenotypes TCRKG and MBRKG with virulence to genes Lr11, Lr26, and Lr18 were among the common phenotypes. Virulence phenotypes with virulence to Lr16 were most frequent in the spring wheat region of the northern Great Plains. Virulence to Lr21 was not found in any of the tested isolates.