Genotyping Puccinia striiformis f. sp. tritici Isolates with SSR and SP-SNP Markers Reveals Dynamics of the Wheat Stripe Rust Pathogen in the United States from 1968 to 2009 and Identifies Avirulence-Associated Markers

Populations of Puccinia striiformis f. sp. tritici in Winter Spore Production Regions Spread from Southwestern Oversummering Areas in China

Stripe rust, caused by Puccinia striifomis f. sp. tritici (Pst), is one of the most destructive wheat diseases in China. Understanding the interregional dispersal of Pst inoculum is important for controlling the disease. In the present study, wheat stripe rust samples collected from the winter spore production and oversummering regions in November 2018 to March 2019 were studied through virulence testing and molecular characterization. From 296 isolates, 96 races were identified using a set of 19 Chinese wheat cultivars and 111 races were identified using 18 Yr single-gene lines as differentials. The isolates from Hubei province in the winter spore production area had the highest similarity in virulence with those from eastern Yunnan in the oversummering area. Molecular characterization using 13 simple-sequence repeat and 43 Kompetitive allele specific PCR-single nucleotide polymorphism markers supported the conclusion that the Pst populations in the winter spore production regions were from Guizhou and eastern Yunnan, key oversummering areas in the southwest. Furthermore, an analysis of wind movement at the 700-hPa high altitude also supported the conclusion of spore dispersal from the southwestern oversummering region to the south-central winter spore production region. The results of this study provide an epidemiological basis for deploying various effective resistance genes in different regions to control stripe rust.

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.

Two Main Routes of Spore Migration Contributing to the Occurrence of Wheat Stripe Rust in the Jiangsu and Zhejiang Coastal Sporadic Epidemiological Region in 2019, Based on Phenotyping and Genotyping Analyses

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive disease in many countries. In China, wheat stripe rust generally occurs in northwestern and southwestern China and sporadically in the Jiangsu and Zhejiang coastal epidemiological region (JZER), where an outbreak of the disease occurred in 2019. To understand the population structure and potential inoculum sources of the pathogen in this region, 171 isolates collected from 93 wheat fields of 53 counties in 10 provinces were phenotyped with two sets of wheat differentials and genotyped with 20 pairs of single-nucleotide polymorphism primers. Phenotype tests indicated that identical races (CYR34, CYR33, Su11-139, and Su11-14-1) detected in Jiangsu and Zhejiang were shared with the oversummering regions (Gansu), overwintering regions (Hubei, Henan, and Shaanxi), and Yun-Gui epidemiological regions (Yunnan and Guizhou). In JZER, races CYR32, G22-14, and G22-68 were detected in Jiangsu, but not in Zhejiang, and Su11-208 was identified in Zhejiang, but not in Jiangsu. Genotypic analysis revealed remarkable gene flows among the Jiangsu, Yunnan, Henan, and Anhui populations, as well as those of Zhejiang, Guizhou, and Sichuan, showing that wheat stripe rust in Zhejiang and Jiangsu was from spores that migrated from different routes. Major gene flows were detected between the Jiangsu and Zhejiang populations. P. striiformis f. sp. tritici from both overwintering regions (Yunnan, Sichuan, Guizhou, Henan, Hubei, and Shaanxi) and oversummering regions (Gansu) contributed to the wheat stripe rust epidemic in the JZER region in 2019.

Countrywide inter-epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China

Understanding countrywide pathogen population structure and inter-epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration route of P. striiformis f. sp. tritici across China based on sampling from 15 provinces representing six epidemic zones, viz., over-summering, over-wintering, eastern, Yun-Gui, Xinjiang and Tibet epidemic regions. High genotypic diversity was recorded in over-summering, Tibet and over-wintering epidemic regions. Epidemic regions partly explain population subdivision with variable divergence (F_ST  = 0.005-0.344). Xinjiang and Tibet epidemic regions were independent epidemic zones with least sharing of genotypes. Among other epidemic zones, i.e. over-summering, over-wintering, eastern and Yun-Gui epidemic zones, re-sampling MLGs, clustering-based structure, DAPC analyses, relative migration and low divergence (F_ST from 0.006 to 0.073) revealed frequent geneflow. Yun-Gui epidemic regions, with a potential for both over-summering and over-wintering, could play an important role in causing epidemics in main wheat-cultivating areas of China. High diversity, recombination signatures and inter-epidemic region migration patterns need to be considered in host-resistant cultivar development in China and neighbouring countries, considering risk of long-distance migration capacity of pathogen.

Genetic Characterization of Puccinia striiformis f. sp. tritici Populations from Different Wheat Cultivars Using Simple Sequence Repeats

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important fungal diseases affecting wheat (Triticum aestivum L.) worldwide. In this study, the genetic diversity and population structure of Pst isolates were analyzed using 15 microsatellite markers. Isolates were collected from five wheat cultivars with different levels of resistance from Yanting county and Fucheng district, Mianyang city, Sichuan province, China. The aim of this study was to investigate whether Pst populations are differentiated by wheat genotype or geographic origin. Seventy-six multilocus genotypes (MLGs) were identified from all 289 single uredinial isolates. In general, the genotypic diversity of Pst populations from five wheat cultivars in Fucheng was higher than that in Yanting. In addition, the genetic diversity was highest in the Pst populations from Mianmai 367, a cultivar considered to be highly resistant. The unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree, Bayesian clustering analysis, and minimum spanning network for the MLGs revealed two major genetic clusters based on geographical location. Greater differentiation was observed between the populations from the two sampling locations than between the populations from different hosts in the same location. The results suggest that geographic and environmental differences could partially explain the genetic differentiation of Pst more than wheat genotype. This study provides novel insight into the interactions between Pst populations and their hosts. The results could be helpful in designing more effective management strategies for stripe rust in wheat production.

Race Characterization of Puccinia striiformis f. sp. tritici in the United States from 2013 to 2017

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat. In this study, 1,567 isolates collected from the United States from 2013 to 2017 were tested for virulence on 18 wheat Yr single-gene lines to differentiate races. In total, 72 races, including 20 new, were identified, and their frequencies in different years and different epidemiological regions were determined and compared. The 20 new races had low frequencies, and 7 of them each were detected from only one sample and 10 only in a single year. Frequencies of virulence to Yr10, Yr24, and Yr32 were low (<10%); to Yr1, Yr76, YrTr1, and YrSP were moderate (10 to 40%); and to Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, and Exp2 were high (>70%), although they varied from year to year and from region to region. No virulence was detected to either Yr5 or Yr15, indicating that these genes were still effective against the pathogen in the United States. Based on the virulence data, the diversity of the U.S. P. striiformis f. sp. tritici population was the highest in 2016 and lowest in 2015, and the diversity of the regional population was the highest in region 1 and lowest in region 11. The yearly populations between consecutive years were closer than nonconsecutive years, and the eastern populations were closer to each other than those among the western populations. The findings are useful for understanding the pathogen evolution and for developing resistant cultivars for control of the disease.

Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.

Molecular Characterization of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Collections from Nine Countries

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. To understand the worldwide distribution of its molecular groups, as well as the diversity, differentiation, and migration of the Pst populations, 567 isolates collected from nine countries (China, Pakistan, Italy, Egypt, Ethiopia, Canada, Mexico, Ecuador, and the U.S.) in 2010–2018 were genotyped using 14 codominant simple sequence repeat markers. A total of 433, including 333 new multi-locus genotypes (MLGs), were identified, which were clustered into ten molecular groups (MGs). The MGs and country-wise populations differed in genetic diversity, heterozygosity, and correlation coefficient between the marker and virulence data. Many isolates from different countries, especially the isolates from Mexico, Ecuador, and the U.S., were found to be identical or closely related MLGs, and some of the MGs were present in all countries, indicating Pst migrations among different countries. The analysis of molecular variance revealed 78% variation among isolates, 12% variation among countries, and 10% variation within countries. Only low levels of differentiation were found by the pairwise comparisons of country populations. Of the 10 MGs, 5 were found to be involved in sexual and/or somatic recombination. Identical and closely related MLGs identified from different countries indicated international migrations. The study provides information on the distributions of various Pst genetic groups in different countries and evidence for the global migrations, which should be useful in understanding the pathogen evolution and in stressing the need for continual monitoring of the disease and pathogen populations at the global scale.

Population Diversity, Dynamics, and Differentiation of Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici From 2010 to 2017 and Comparison With 1968 to 2009 in the United States

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious disease on wheat in the United States, especially after 2000. In the present study, 2,247 Pst isolates collected over all stripe rust epidemiological regions in the United States from 2010 to 2017 were genotyped at 14 simple sequence repeat (SSR) loci to investigate the population diversity, dynamics, and differentiation. A total of 1,454 multilocus genotypes (MLGs) were detected. In general, the populations in the west (regions 1-6) had more MLGs and higher diversities than the populations in the east (regions 7-12). The populations of 2010 and 2011 were more different from the other years. Genetic variation was higher among years than among regions, indicating the fast changes of the population. The divergence (Gst) was bigger between the west population and east population than among regions within either the west or east population. Gene flow was stronger among the regional populations in the east than in the west. Clustering analyses revealed 3 major molecular groups (MGs) and 10 sub-MGs by combining the genotypic data of 2010-2017 isolates with those of 1968-2009. MG1 contained both 1968-2009 isolates (23.1%) and 2010-2017 isolates (76.9%). MG2 had 99.4% of isolates from 1968-2009. MG3, which was the most recent and distinct group, had 99.1% of isolates from 2010-2017. Of the 10 sub-MGs, 5 (MG1-3, MG1-5, MG3-2, MG3-3, and MG3-4) were detected only from 2011 to 2017. The SSR genotypes had a moderate, but significant correlation (r = 0.325; p < 0.0001) with the virulence phenotype data. The standard index values of association (rbarD = 0.11) based on either regional or yearly populations suggest clonal reproduction. This study indicated high diversity, fast dynamics, and various levels of differentiation of the Pst population over the years and among epidemiological regions, and the results should be useful for managing wheat stripe rust.