Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia

The Migration, Diversity, and Evolution of Puccinia triticina in China

Wheat leaf rust, caused by Puccinia triticina, is one of the most common fungal diseases of wheat in China and occurs widely in various wheat-growing regions. To clarify the epidemic, spread rules, and population structure of P. triticina among different regions, 217 isolates of P. triticina collected from Hebei, Shandong, Sichuan, and Xinjiang in China were tested by 34 Thatcher near-isogenic lines and 21 pairs of EST-SSR primers. A total of 83 races were identified, and THTT, PHTT, THTS, and PHJT were the most predominant races in the four provinces in 2009. We found enriched virulence and genetic diversity in the four P. triticina populations and a significant correlation between genetic polymorphism and geographic regions. However, no significant correlation was found between virulence phenotypes and molecular genotypes. Moreover, a notable high level of gene flow (Nm = 2.82 > 1) among four P. triticina populations was detected. The genetic relationship among Hebei, Shandong, and Sichuan populations was close, possibly due to the spread of P. triticina from Sichuan to Shandong and then to Hebei. In contrast, the Xinjiang population was relatively independent. Genetic differentiation analysis showed some level of differentiation among or within populations of P. triticina in the four provinces, and the genetic variation within populations (74.97%) was higher than across populations (25.03%). Our study provides a basis for a better understanding of the regional migration, epidemic, and population structure of P. triticina in China.

Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers

Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.

Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis

BACKGROUND

Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces.

RESULTS

Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions.

CONCLUSIONS

Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.

Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations

The wheat leaf rust fungus, Puccinia triticina Erikss., is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates and to gain insight into race evolution. The collection included isolates comprising of many different race phenotypes collected worldwide from common and durum wheat. One isolate from wild wheat relative Aegilops speltoides and two from Ae. cylindrica were also included for comparison. Based on 121,907 informative variants identified relative to the reference Race 1-1 genome, isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in 1311 predicted secreted protein genes. In gene-coding regions, all groups had high ratios of nonsynonymous to synonymous mutations and nonsense to readthrough mutations. Grouping of isolates based on two main variation principle components for either genome-wide variation or variation just within the secreted protein genes, indicated similar groupings. Variants were distributed across the entire genome, not just within the secreted protein genes. Our results suggest that recurrent mutation and selection play a major role in differentiation within the clonal lineages.

Genotyping-by-Sequencing for the Study of Genetic Diversity in Puccinia triticina

Leaf rust, caused by Puccinia triticina Erikss., is globally the most widespread rust of wheat. Populations of P. triticina are highly diverse for virulence, with many different races found annually. The genetic diversity of P. triticina populations has been previously assessed using different types of DNA markers. Genotyping technologies that provide a higher density of markers distributed across the genome will be more powerful for analysis of genetic and phylogenetic relationships in P. triticina populations. In this study, we utilized restriction-associated DNA (RAD) genotyping-by-sequencing (GBS) adapted for the Ion Torrent sequencing platform for the study of population diversity in P. triticina. A collection of 102 isolates, collected mainly from tetraploid and hexaploid wheat, was used. The virulence phenotypes of the isolates were determined on 20 lines of Thatcher wheat near isogenic for leaf rust resistance genes. Seven races were found among 57 isolates collected from tetraploid wheat, and 21 races were observed among 40 hexaploid wheat type isolates. This is the first study to report durum wheat virulent races to Lr3bg in Tunisia, Lr14a in Morocco, and Lr3bg and Lr28 in Mexico. Ethiopian isolates with high virulence to durum wheat but avirulent on Thatcher (hexaploid wheat) were tested for virulence on a set of durum (tetraploid) differentials. A subset of 30 isolates representing most of the virulence phenotypes in the 102 isolates were genotyped using RAD-GBS. Phylogenetic analysis of 30 isolates using 2,125 single nucleotide polymorphism (SNP) markers showed nine distinct clusters. There was a general correlation between virulence phenotypes and SNP genotypes. The high bootstrap values between clusters of isolates in the phylogenetic tree indicated that RAD-GBS can be used as a new genotyping tool that is fast, simple, high throughput, cost effective, and provides a sufficient number of markers for the study of genetic diversity in P. triticina.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

The progress of leaf rust research in wheat

Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.

Virulence of Leaf Rust Physiological Races in Iran From 2010 to 2017

The wheat leaf rust fungus, Puccinia triticina, has widespread geographical distribution in Iran within the Fertile Crescent region of the Middle East where wheat was domesticated and P. triticina originated. Therefore, it is of great importance to identify the prevalence and distribution of P. triticina pathotypes in this area. From 2010 to 2017, 241 single-uredinium isolates of P. triticina were purified from 175 collections of P. triticina made from various hosts in 14 provinces of Iran, and they were tested on 20 Thatcher near-isogenic lines carrying single-leaf rust resistance genes. In total, 86 pathotypes were identified, of which the pathotypes FDTTQ, FDKPQ, FDKTQ, and FDTNQ were most prevalent. No virulence for Lr2a was detected, whereas virulence for Lr1 was found only on bread wheat in a few provinces in 2016. Only isolates from durum wheat and wild barley were virulent to Lr28. Although virulence for Lr9, Lr20, and Lr26 was observed in some years, the virulence frequency for these genes was lower than that of the other Lr genes. P. triticina collections from host plants with different ploidy levels or genetically dissimilar backgrounds were grouped individually according to genetic distance. Based on these results, collections from barley, durum wheat, oat, triticale, and wild barley were different from those of bread wheat.

Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing

The wheat leaf rust fungus, Puccinia triticina, is found in the major wheat growing regions of the world and is a leading cause of yield loss in wheat. Populations of P. triticina are highly variable for virulence to resistance genes in wheat and adapt quickly to resistance genes in wheat cultivars. The objectives of this study were to determine the genetic relatedness of worldwide collections of P. triticina using restriction site associated genotyping by sequencing. A total of 558 isolates of P. triticina from wheat producing regions in North America, South America, Europe, the Middle East, Ethiopia, Russia, Pakistan, Central Asia, China, New Zealand, and South Africa were characterized at 6745 single nucleotide loci. Isolates were also tested for virulence to 20 near-isogenic lines that differ for leaf rust resistance genes. Populations that were geographically proximal were also more closely related for genotypes. In addition, groups of isolates within regions that varied for genotype were similar to groups from other regions, which indicated past and recent migration across regions. Isolates from tetraploid durum wheat in five different regions were highly related with distinct genotypes compared to isolates from hexaploid common wheat. Based on a molecular clock, isolates from durum wheat found only in Ethiopia were the first to diverge from a common ancestor form of P. triticina that is found on the wild wheat relative Aegilops speltoides, followed by the divergence of isolates found worldwide that are virulent to durum wheat, and then by isolates found on common wheat.

Multilocus Genotypes of the Wheat Leaf Rust Fungus Puccinia triticina in Worldwide Regions Indicate Past and Current Long-Distance Migration

Many plant pathogenic fungi have a global distribution across diverse ecological zones and agricultural production systems. Puccinia triticina, the wheat leaf rust fungus, is a major pathogen in many wheat production areas of the world. The objective of this research was to determine the genetic relatedness of P. triticina in different worldwide regions. A total of 831 single-uredinial isolates collected from 11 regions were characterized for multilocus genotype at 23 simple sequence repeat loci and for virulence to 20 lines of wheat with single genes for leaf rust resistance. A total of 424 multilocus genotypes and 497 virulence phenotypes were found. All populations had high heterozygosity and significant correlation between virulence and molecular variation, which indicated clonal reproduction. The populations from North America and South America, Central Asia and Russia, and the Middle East and Europe were closely related for multilocus genotypes and many individual isolates from other continental regions were closely related. Twenty-seven multilocus genotypes were found in more than one continental region, and 13 of these had isolates with identical virulence phenotypes. The wide geographic distribution of identical and highly related multilocus genotypes of P. triticina indicated past and more recent migration events facilitated by the spread of clonally produced urediniospores.

Genetic Differentiation of the Wheat Leaf Rust Fungus Puccinia triticina in Pakistan and Genetic Relationship to Other Worldwide Populations

Collections of Puccinia triticina, the wheat leaf rust pathogen, were obtained from Pakistan in 2008, 2010, 2011, 2013, and 2014. Collections were also obtained from Bhutan in 2013. Single uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes, and for molecular genotype with 23 simple-sequence repeat (SSR) primers. Twenty-four virulence phenotypes were described among the 89 isolates tested for virulence. None of the isolates had virulence to Thatcher lines with Lr9, Lr24, or Lr18. Virulence to most of the other Thatcher lines was over 50%. The two most common virulence phenotypes, FHPSQ and KHPQQ, had virulence to Lr16, Lr17, and Lr26. Twenty-seven SSR genotypes were found among the 38 isolates tested for molecular variation. The SSR genotypes had high levels of observed heterozygosity and significant correlation with virulence phenotype, which indicated clonal reproduction. Cluster analysis and principal component plots indicated three groups of SSR genotypes that also varied significantly for virulence. Isolates with MBDSS and MCDSS virulence phenotypes from Pakistan and Bhutan were highly related for SSR genotype and virulence to isolates from Turkey, Europe, Central Asia, the Middle East, North America and South America, indicating the possible migration of the rust fungus between continental regions.

Genetically Divergent Types of the Wheat Leaf Fungus Puccinia triticina in Ethiopia, a Center of Tetraploid Wheat Diversity

Collections of Puccinia triticina, the wheat leaf rust fungus, were obtained from tetraploid and hexaploid wheat in the central highlands of Ethiopia, and a smaller number from Kenya, from 2011 to 2013, in order to determine the genetic diversity of this wheat pathogen in a center of host diversity. Single-uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes and for molecular genotypes with 10 simple sequence repeat (SSR) primers. Nine virulence phenotypes were described among the 193 isolates tested for virulence. Phenotype BBBQJ, found only in Ethiopia, was predominantly collected from tetraploid wheat. Phenotype EEEEE, also found only in Ethiopia, was exclusively collected from tetraploid wheat and was avirulent to the susceptible hexaploid wheat 'Thatcher'. Phenotypes MBDSS and MCDSS, found in both Ethiopia and Kenya, were predominantly collected from common wheat. Phenotypes CCMSS, CCPSS, and CBMSS were found in Ethiopia from common wheat at low frequency. Phenotypes TCBSS and TCBSQ were found on durum wheat and common wheat in Kenya. Four groups of distinct SSR genotypes were described among the 48 isolates genotyped. Isolates with phenotypes BBBQJ and EEEEE were in two distinct SSR groups, and isolates with phenotypes MBDSS and MCDSS were in a third group. Isolates with CCMSS, CCPSS, CBMSS, TCBSS, and TCBSQ phenotypes were in a fourth SSR genotype group. The diverse host environment of Ethiopia has selected and maintained a genetically divergent population of P. triticina.

Collections of Puccinia triticina in Different Provinces of China Are Highly Related for Virulence and Molecular Genotype

Collections of Puccinia triticina, the wheat leaf rust pathogen, were obtained from seven provinces in China from 2009 and 2010. Single uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes, and for molecular genotype with 23 simple sequence repeat (SSR) primers. Forty-eight virulence phenotypes were described among the 155 isolates tested for virulence. All but four isolates were virulent to Lr26, and no isolates with virulence to Lr18 or Lr24 were found. The three most common phenotypes, FCBQQ, PCGLN, and PCGLL, were found in five, five, and three provinces, respectively. Thirty-six SSR genotypes were found among the 100 isolates tested for molecular variation. Isolates with identical virulence phenotypes and SSR genotypes were found in more than one province. Analysis of variation showed no overall differentiation of SSR genotypes or virulence phenotypes based on province of origin. The SSR genotypes had high levels of linkage disequilibrium, high levels of observed heterozygosity, and significant correlation with the virulence phenotypes, all measures that indicated clonal reproduction. Bayesian cluster analysis and principle component plots indicated three groups of SSR genotypes that also varied significantly for virulence. The seven provinces are continuously adjacent to each other and likely form a single epidemiological zone for P. triticina.

Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution

Co-evolution of fungal pathogens with their host species during the domestication of modern crop varieties has likely affected the current genetic divergence of pathogen populations. The objective of this study was to determine if the evolutionary history of the obligate rust pathogen on wheat, Puccinia triticina, is correlated with adaptation to hosts with different ploidy levels. Sequence data from 15 loci with different levels of polymorphism were generated. Phylogenetic analyses (parsimony, Bayesian, maximum likelihood) showed the clear initial divergence of P. triticina isolates collected from Aegilops speltoides (the likely B genome donor of modern wheat) in Israel from the other isolates that were collected from tetraploid (AB genomes) durum wheat and hexaploid (ABD genomes) common wheat. Coalescence-based genealogy samplers also indicated that P. triticina on A. speltoides, diverged initially, followed by P. triticina isolates from durum wheat in Ethiopia and then by isolates from common wheat. Isolates of P. triticina found worldwide on cultivated durum wheat were the most recently coalesced and formed a clade nested within the isolates from common wheat. By a relative time scale, the divergence of P. triticinia as delimited by host specificity appears very recent. Significant reciprocal gene flow between isolates from common wheat and isolates from durum wheat that are found worldwide was detected, in addition to gene flow from isolates on common wheat to isolates on durum wheat in Ethiopia.

Shared influence of pathogen and host genetics on a trade-off between latent period and spore production capacity in the wheat pathogen, Puccinia triticina

Crop pathogens are notorious for their rapid adaptation to their host. We still know little about the evolution of their life cycles and whether there might be trade-offs between fitness components, limiting the evolutionary potential of these pathogens. In this study, we explored a trade-off between spore production capacity and latent period in Puccinia triticina, a fungal pathogen causing leaf rust on wheat. Using a simple multivariate (manova) technique, we showed that the covariance between the two traits is under shared control of host and pathogen, with contributions from host genotype (57%), pathogen genotype (18.4%) and genotype × genotype interactions (12.5%). We also found variation in sign and strength of genetic correlations for the pathogen, when measured on different host varieties. Our results suggest that these important pathogen life-history traits do not freely respond to directional selection and that precise evolutionary trajectories are contingent on the genetic identity of the interacting host and pathogen.