Population Genetic Structure of Puccinia striiformis in Northwestern China

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.

Virulence and Molecular Characterization Reveal Signs of Sexual Genetic Recombination of Puccinia striiformis f. sp. tritici and Puccinia striiformis f. sp. hordei in Tibet

Stripe rust of wheat and barley is caused by different formae speciales, Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), respectively. To understand the relationship between the populations of the two formae speciales, a total of 260 P. striiformis isolates, including 140 from barley and 120 from wheat collected from Linzhi, Tibet, China, from 2018 to 2020, were tested on 18 barley and 13 wheat genotypes and genotyped with 26 single-nucleotide polymorphism (SNP)-based Kompetitive allele-specific PCR (KASP) markers. As a result, 260 isolates were identified as 83 virulence phenotypes (VPs), 115 of which as 9 VPs and could infect only wheat (wheat population), 111 as 54 VPs and could infect only barley (barley population), and 34 belonged to 20 VPs that could infect both wheat and barley (mixed population). Of the 149 multilocus genotypes (MLGs) that were identified, 92 were from wheat, 56 from barley, and 1 from both wheat and barley. Phenotypic and genotypic diversity was high in the populations from wheat and barley. Low linkage disequilibrium was found in most of the sampling sites of both crops, indicating strong signs of sexual reproduction (|r̄d| = 0.022 to 0.393, P = 0.004 to 0.847), whereas it was not observed in the overall population (wheat and barley sources) and the wheat, barley, and mixed populations, which may be because of the complex composition of isolates. Population structure analyses based on phenotyping and SNP-KASP genotypes supported the separation of the two formae speciales. However, MLGs and clusters containing isolates from both wheat and barley obviously indicated sexual genetic recombination between the two formae speciales. The results of the study provided an insight into evolution of Pst and Psh and showed the importance of management strategies for stripe rust of wheat and barley in regions where both crops are grown.

Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from Shaanxi-Gansu-Ningxia-Xinjiang of Northwestern and Sichuan-Yunnan of Southwestern China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases worldwide. In China, wheat stripe rust generally occurs in the northwestern and southwestern regions; however, the genetic relationships of Pst populations between these regions are largely unclear. To determine the population structure and potential migration route in these regions, 235 isolates collected from Xinjiang (XJ), Gansu (GS), Ningxia (NX), Shaanxi (SX), Sichuan (SC), and Yunnan (YN) provinces in 2021 and 2022 were phenotyped using two sets of Pst differentials and genotyped using 20 competitive allele-specific PCR-single nucleotide polymorphism (KASP-SNP) markers. The phenotype tests indicated that CYR34, CYR32, and CYR33 were the predominant races with different occurrence frequencies in different regions and years. Genotypic analysis revealed that a total of 183 multilocus genotypes were identified, and the genetic diversity in the YN subpopulation was the highest. The genetic background in the SX subpopulation was similar to that in the GS and NX subpopulations, and the genetic background in the YN subpopulation was similar to that in the SC and SX subpopulations. A high level of gene flow (Nm) was found between the SX and GS, SX and NX, GS and NX, and SC and YN subpopulations, suggesting the migration of Pst among these regions, while a small amount of Nm existed between the SX and SC subpopulations. SC may serve as a bridge connecting Pst subpopulations between the northwestern provinces (SX, GS, and NX) and the southwestern provinces (SC and YN). With a relatively high genetic distance and low Nm values compared with other Pst subpopulations, XJ is considered a relatively independent epidemiological region in China. These results improved our current understanding of the wheat stripe rust epidemic in northwestern and southwestern regions of China.

Virulence and molecular genetic diversity, variation, and evolution of the Puccinia triticina population in Hebei Province of China from 2001 to 2010

Wheat leaf rust, caused by Puccinia triticina, is one of the most important fungal diseases of wheat in China. However, little is known about the dynamic changes of population structure and genetic diversity of P. triticina during a period of time. In this study, 247 isolates of P. triticina collected from Hebei Province from 2001 to 2010 were tested on 36 Thatcher near-isogenic lines for virulence diversity and detected by 21 pairs of Expressed Sequence Tag derived Simple Sequence Repeat (EST-SSR) primers for genetic diversity. A total of 204 isolates were successfully identified as 164 races, and THTT, THST, PHRT, THTS, and PHTT were the most common races in Hebei Province from 2001 to 2010. The cluster analysis based on virulence showed that P. triticina has a rich virulence polymorphism, which had a certain correlation with the years, while the cluster analysis based on EST-SSR showed that the genetic diversity of the P. triticina population was significantly different between years in Hebei Province from 2001 to 2010. In addition, the population structure of P. triticina may have changed greatly in 2007 and 2009, which was significantly different from that of 2001-2006 on either virulence or genetic characteristics. The variation frequency of the population structure had an increasing trend during this period. From 2001 to 2010, there was a certain degree of gene flow among the P. triticina populations. No significant correlation was found between virulence and molecular polymorphism. The genetic differentiation analysis of the 10 tested populations (each year as a population) showed that the coefficient of genetic differentiation (Gst) was 0.27, indicating that there was a certain genetic differentiation among or within populations of P. triticina in Hebei Province. The genetic variation within populations (73.08%) was higher than that among populations (26.92%), which indicated that the genetic variations were mainly found within populations. Our study provides the foundation for a better understanding of the population structure change and genetic diversity of P. triticina over a period in Hebei Province of China.

Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China

Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting disease development and establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens wheat production through its long-distance migration. Because of wide variation in geographic features, climatic conditions, and wheat production systems, Pst sources and related dispersal routes in China are largely unclear. In the present study, we performed genomic analyses of 154 Pst isolates from all major wheat-growing regions in China to determine Pst population structure and diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, and field surveys, we investigated Pst sources and their contributions to wheat stripe rust epidemics. We identified Longnan, the Himalayan region, and the Guizhou Plateau, which contain the highest population genetic diversities, as the Pst sources in China. Pst from Longnan disseminates mainly to eastern Liupan Mountain, the Sichuan Basin, and eastern Qinghai; that from the Himalayan region spreads mainly to the Sichuan Basin and eastern Qinghai; and that from the Guizhou Plateau migrates mainly to the Sichuan Basin and the Central Plain. These findings improve our current understanding of wheat stripe rust epidemics in China and emphasize the need for managing stripe rust on a national scale.

Clonal Expansion and Dispersal Pathways of Puccinia polysora in China

Southern corn rust (SCR) caused by Puccinia polysora is one of the most devastating diseases in the world. In recent years, SCR has been upgraded from a minor to a major disease around the world, including in China. However, little is known about its population genetics and structure in China. In this study, we analyzed 288 isolates collected from various localities during 2017 in seven Chinese provinces: Guangxi, Guangdong, Anhui, Hunan, Shandong, Henan, and Shaanxi. The isolates were analyzed using nine microsatellite markers. The population structure, genetic diversity, and reproduction mode of P. polysora were investigated based on genotype data. Strong genotypic diversity was detected and clonal reproduction was dominant. The populations collected from the pathogen's winter-reproductive regions harbored more genotypes than those collected from the pathogen's epidemic regions. The spatial differences in genotypic richness, and evenness among the populations were significant, and showed a decreasing trend from south to north. Most isolates were clustered into two clonal groups. Two high-frequency multilocus genotypes (MLGs), MLG1 and MLG2, were widely distributed in all populations. Our analyses confirmed that P. polysora employed clone dispersal from the pathogen's winter-reproductive regions to the pathogen's epidemic regions, and in addition to the sources from the pathogen's winter-reproductive regions, the pathogen in Anhui and Hunan might also have other sources from areas such as Taiwan, China, or/and Southeast Asia, and the pathogen went through a genetic bottleneck during its dispersal. These findings provide initial insights into the reproduction mode and dispersal pathways of P. polysora in China.

Changes of Barley Stripe Rust Populations in the United States from 1993 to 2017

Barley stripe rust is a relatively new disease in the United States. The pathogen, Puccinia striiformis f. sp. hordei (Psh), was first observed in Texas in 1991 and has spread north and westwards and mainly caused epidemics in the western United States. A total of 447 isolates collected from 1993 to 2017 were identified as 382 multilocus genotypes (MLGs) using 14 simple sequence repeat markers. The MLGs were clustered into six molecular groups (MGs) using the discriminant analysis of principal components and the hierarchical cluster analysis, and the MGs had significant differences in frequency in different years. MG1 was present in the population prior to the year 2000. MG2, MG3, and MG4 became predominate after 2000. MG5 was detected in all 24 years but more frequent from 2010 to 2017. MG6 was the most recent group detected mainly from 2011 to 2017 and had the highest correlation coefficient with the virulence phenotypes among the MGs. The heterozygosity and genotypic diversity of the Psh populations increased from 2000 to 2017, even more from 2010 to 2017. The results indicate rapid genetic changes from year to year, with major molecular group changes around 2000 and 2010. The possible mechanisms underlying the population changes are discussed.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from the Longnan, Longdong, and Central Shaanxi Regions of China

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases of wheat worldwide. In China, Longnan (LN) and Longdong (LD) in the south and east of Gansu province, respectively, are important P. striiformis f. sp. tritici oversummering areas and are a source of P. striiformis f. sp. tritici inoculum for the major wheat-growing regions in eastern China. Central Shaanxi (CS) is a wheat-growing region that acts as an important bridge zone for stripe rust epidemic development between LN and LD in the west and the Huanghuai wheat-growing region in the east, and thus, it plays an essential role in P. striiformis f. sp. tritici epidemics in China. To study the relationships among P. striiformis f. sp. tritici populations in the three regions (LN, LD, and CS), we sampled 284 isolates from different geographic locations. Based on 10 simple sequence repeat markers, the results demonstrated high genetic diversity in all three regions, although diversity did vary among regions, with LN > LD > CS. Genetic differentiation was lower, with more extensive gene flow between LD and CS. P. striiformis f. sp. tritici populations in the CS region were genetically closer to those from LD than those from LN, which may be a result of geographical proximity and topography. A positive and significant correlation existed between linearized fixation index (F_ST) and the log of geographical distances among all subpopulations. Linkage disequilibrium analysis showed that subpopulations of P. striiformis f. sp. tritici from Qinzhou, Qincheng, Beidao, and Maiji from LN and Qianyang and Longxian from CS were in equilibrium (P > 0.05), suggesting that somatic hybridization and/or sexual reproduction may exist in these subpopulations.

Analyses of Wheat Yellow Rust Populations Reveal Sexual Recombination and Seasonal Migration Pattern of Puccinia striiformis f. sp. tritici in Gangu, Northwestern China

Puccinia striiformis f. sp. tritici is the causal agent of wheat yellow rust with records of regular and severe epidemics in China. This study explored the population dynamics of the yellow rust pathogen in Gangu, northwestern China. In Gangu, the Weihe River runs from west to east and divides Gangu into three regions: North and South mountain, with the valley in between. To study the genetic structure of the pathogen in local populations, samples were collected over 3 years from the three regions at different altitudes both within and between the wheat cropping seasons. A total of 811 P. striiformis f. sp. tritici isolates were successfully genotyped using 16 simple sequence repeat markers. The results suggest that P. striiformis f. sp. tritici can survive year-round in Gangu. The P. striiformis f. sp. tritici populations migrated among the regions, and the migration pattern was not related to altitude. The oversummering populations in the North and South mountain regions were genetically different from each other; and the P. striiformis f. sp. tritici populations collected from the lower altitude in the valley had no relationship with any of the populations collected in the spring or fall, indicating that they too have a different origin. Signatures of random mating were found in the populations collected in both North and South mountain regions, but not in the valley populations.

Population Genetic Structures of Puccinia striiformis f. sp. tritici in the Gansu-Ningxia Region and Hubei Province, China

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a destructive wheat disease in China. The Gansu–Ningxia region (GN) is a key area for pathogen over-summering in China, and northwestern Hubei (HB) is an important region for pathogen over-wintering, serving as a source of inoculum in spring epidemic regions. The spatiotemporal population genetic structure of Pst in HB and the pathogen population exchanges between GN and HB are important for estimating the risk of interregional epidemics. Here, 567 isolates from GN and HB were sampled from fall 2016 to spring 2018 and were genotyped using simple sequence repeat markers. The genotypic and genetic diversity of Pst subpopulations in HB varied among seasons and locations. Greater genetic diversification levels were found in the spring compared with fall populations using principal coordinate analysis and Bayesian assignments. In total, there were 17 common genotypes among the 208 determined, as shown by a small overlap of genotypes in the principal coordinate analysis and dissimilar Bayesian assignments in both regions, which revealed the limited genotype exchange between the populations of GN and HB.

Genetic Structure and Asymmetric Migration of Wheat Stripe Rust Pathogen in Western Epidemic Areas of China

Puccinia striiformis f. sp. tritici causes severe global epidemics of wheat stripe rust primarily by airborne urediniospores. Understanding long-distance migration patterns of P. striiformis f. sp. tritici is critical for disease forecasting and management. Although the western epidemic areas in China have been considered as the source of inoculum spread eastward across the country, migration pathways among different populations within the western epidemic areas are poorly understood. In this study, we investigated the population genetics of 200 P. striiformis f. sp. tritici isolates from western epidemic areas using amplified fragment length polymorphism and simple sequence repeat markers. A coalescent approach was also used to calculate the migration rates among populations. Data analyses with both marker systems indicated high genetic diversity in each regional population. The Mantel test revealed significant positive correlation between genetic and geographic distances. Both discriminant analysis of principal components and STRUCTURE analysis supported moderate population structure shaped by seasonality and geography. The calculated migration rates indicated the presence of asymmetric migration between major populations in western epidemic areas, with greater migration rates from high elevation, oversummering areas to low elevation, overwintering areas. Sichuan Basin, one of the low elevation, overwintering areas, sampled in both fall and spring, was inferred as a recipient in fall but a donor in spring. Migration among P. striiformis f. sp. tritici populations may be partly attributable to terrace farming and prevailing wind direction in different seasons. Our study provides a better understanding of fine-scale population structure and the interregional migration pattern of P. striiformis f. sp. tritici in northwestern China and will inform future rust management.