Race Dynamics, Diversity, and Virulence Evolution in Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust in China from 2003 to 2007

Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici

The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.

Comparative analysis of stripe rust resistance in seedling stage and Yr gene incidence in spring and winter wheat from Xinjiang, China

Background

Stripe rust, caused by the fungus Puccinia striiformis f.sp. tritici (Pst), poses a significant threat to global wheat production.

Objectives

This study aims to analyze the distribution of stripe rust resistance genes, characterize resistance phenotypes at the seedling stage of 137 spring and 149 winter wheat varieties in Xinjiang, China, and discern differences in resistance between spring and winter wheat varieties.

Design

We used various Pst races (CYR23, CYR29, CYR31, CYR32, CYR33, CYR34) to characterize seedling resistance of spring and winter wheat varieties and to correlate resistance to the presence of wheat resistance genes (Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, Yr81) using molecular markers.

Results

Among spring wheat varieties, 62, 60, 42, 26, 51, and 24 varieties exhibited resistance to CYR23, CYR29, CYR31, CYR32, CYR33, and CYR34, respectively, with four varieties resistant to all varieties. Among winter wheat varieties, 66, 32, 69, 26, 83, 40 varieties demonstrated resistance to CYR23, CYR29, CYR31, CYR32, CYR33, and CYR34, respectively, with four varieties resistant to all varieties. Molecular testing revealed that, in spring wheat, 2, 17, 21, 61, 10, 0, 10, 79, and 32 varieties carried Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, and Yr81 genes, respectively. In winter wheat, 40, 20, 7, 143, 15, 1, 6, 38, and 54 varieties carried Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr80, and Yr81 genes, respectively. Notably, winter wheat exhibited a significantly higher resistance frequency than spring wheat, particularly in the incidence of Yr9, Yr10, Yr17, Yr18, and multi-gene combinations.

Conclusion

In summary, this study provides information on seedling stage resistance to stripe rust 286 Xinjiang wheat varieties, elucidates the distribution of resistance genes in this population, and offers a mechanistic basis for breeding durable resistance in wheat. varieties from Xinjiang.

Comparative Analysis of Virulence and Molecular Diversity of Puccinia striiformis f. sp. tritici Isolates Collected in 2016 and 2023 in the Western Region of China

Puccinia striiformis f. sp. tritici (Pst) is adept at overcoming resistance in wheat cultivars, through variations in virulence in the western provinces of China. To apply disease management strategies, it is essential to understand the temporal and spatial dynamics of Pst populations. This study aimed to evaluate the virulence and molecular diversity of 84 old Pst isolates, in comparison to 59 newer ones. By using 19 Chinese wheat differentials, we identified 98 pathotypes, showing virulence complexity ranging from 0 to 16. Associations between 23 Yr gene pairs showed linkage disequilibrium and have the potential for gene pyramiding. The new Pst isolates had a higher number of polymorphic alleles (1.97), while the older isolates had a slightly higher number of effective alleles, Shannon's information, and diversity. The Gansu Pst population had the highest diversity (uh = 0.35), while the Guizhou population was the least diverse. Analysis of molecular variance revealed that 94% of the observed variation occurred within Pst populations across the four provinces, while 6% was attributed to differences among populations. Overall, Pst populations displayed a higher pathotypic diversity of H > 2.5 and a genotypic diversity of 96%. This underscores the need to develop gene-pyramided cultivars to enhance the durability of resistance.

Molecular and Cytological Identification of Wheat-Thinopyrum intermedium Partial Amphiploid Line 92048 with Resistance to Stripe Rust and Fusarium Head Blight

Thinopyrum intermedium (2n = 6x = 42, EeEeEbEbStSt or JJJsJsStSt) contains a large number of genes that are highly adaptable to the environment and immune to a variety of wheat diseases, such as powdery mildew, rust, and yellow dwarf, making it an important gene source for the genetic improvement of common wheat. Currently, an important issue plaguing wheat production and breeding is the spread of pests and illnesses. Breeding disease-resistant wheat varieties using disease-resistant genes is currently the most effective measure to solve this problem. Moreover, alien resistance genes often have a stronger disease-resistant effect than the resistance genes found in common wheat. In this study, the wheat-Th. intermedium partial amphiploid line 92048 was developed through hybridization between Th. intermedium and common wheat. The chromosome structure and composition of 92048 were analyzed using ND-FISH and molecular marker analysis. The results showed that the chromosome composition of 92048 (Octoploid Trititrigia) was 56 = 42W + 6J + 4Js + 4St. In addition, we found that 92048 was highly resistant to a mixture of stripe rust races (CYR32, CYR33, and CYR34) during the seedling stage and fusarium head blight (FHB) in the field during the adult plant stage, suggesting that the alien or wheat chromosomes in 92048 had disease-resistant gene(s) to stripe rust and FHB. There is a high probability that the gene(s) for resistance to stripe rust and FHB are from the alien chromosomes. Therefore, 92048 shows promise as a bridge material for transferring superior genes from Th. intermedium to common wheat and improving disease resistance in common wheat.

Physio-Biochemical, Anatomical, and Molecular Analysis of Resistant and Susceptible Wheat Cultivars Infected with TTKSK, TTKST, and TTTSK Novel Puccinia graminis Races

Stem rust, caused by Puccinia graminis f.sp. tritici, is one of the most dangerous rust diseases on wheat. Through physiological, biochemical, and molecular analysis, the relationship between the change in resistance of 15 wheat cultivars to stem rust disease and the response of 41 stem rust resistance genes (Sr,s) as well as TTKSK, TTKST, and TTTSK races was explained. Some cultivars and Sr genes, such as Gemmeiza-9, Gemmeiza-11, Sids-13, Sakha-94, Misr-1, Misr-2, Sr31, and Sr38, became susceptible to infection. Other new cultivars include Mir-3 and Sakha-95, and Sr genes 13, 37, 40, GT, and FR*2/SRTT3-SRTT3-SR10 remain resistant. Some resistance genes have been identified in these resistant cultivars: Sr2, Sr13, Sr24, Sr36, and Sr40. Sr31 was not detected in any cultivars. Reactive oxygen species such as hydrogen peroxide and superoxide, enzymes activities (catalase, peroxidase, and polyphenoloxidase), and electrolyte leakage were increased in the highly susceptible cultivars, while they decreased in the resistant ones. Anatomical characteristics such as the thickness of the epidermis, ground tissue, phloem tissue and vascular bundle diameter in the midrib were decreased in susceptible cultivars compared with resistant cultivars. Our results indicated that some races (TTKSK, TTKST, and TTTSK) appeared for the first time in Egypt and many other countries, which broke the resistant cultivars. The wheat rust breeding program must rely on land races and pyramiding genes in order to develop new resistance genes that will survive for a very long time.

Virulence Characterization of Puccinia striiformis f. sp. tritici in China Using the Chinese and Yr Single-Gene Differentials

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat. Identifying Pst races is essential for developing resistant cultivars and managing the disease. In this study, 608 isolates collected from China in 2021 were tested with the Chinese set of 19 wheat variety differentials and the set of 18 Yr single-gene differentials. Of the 119 races detected with the Chinese set of differentials, 94 were new. A higher number (149) of races were identified using the Yr single-gene differentials. The frequencies of virulence factors to 17 of the 19 Chinese differential varieties and to 10 of the 18 Yr single-gene differentials were high (>60%). None of the isolates were virulent to the differentials Zhong 4 (Yr genes unknown) and Triticum spelta Album (Yr5) in the Chinese set and the Yr5 and Yr15 lines in the single-gene set of differentials, indicating that these genes or varieties are effective against the Pst population detected in 2021. Using Nei's genetic distance, the 16 provincial Pst populations were clustered into six groups based on the Chinese set and eight groups based on the Yr single-gene set of differentials. In addition, we found that the same races identified using the Chinese differentials could be further differentiated into different races using the Yr single-gene differentials, suggesting a higher differential capability than the Chinese set of differentials. The results provide a scientific basis for monitoring Pst populations and guiding resistance breeding in China.

Identification and Molecular Mapping of the Gene YrFL in Wheat Cultivar Flanders with Durable Resistance to Stripe Rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most severe diseases of wheat (Triticum aestivum L.) worldwide. Identification and characterization of resistance genes is advantageous to cultivating wheat varieties with durable resistance, which is the most economic and effective strategy to control stripe rust. Flanders, a common wheat cultivar released in France in 1986, confers effective resistance to stripe rust both at the seedling and adult plant stages. To elucidate the genetic basis of resistance in Flanders, F1, F2, and F2:3 generations derived from the cross Mingxian169 × Flanders were evaluated with the most prevalent Chinese Pst race CYR33 at the seedling stage. Inheritance analysis showed that the stripe rust resistance of Flanders was controlled by a single dominant gene, temporarily designated as YrFL. Bulked segregant analysis (BSA) combined with a wheat 660K single-nucleotide polymorphism (SNP) array indicated that polymorphic SNP markers were mainly located in the 0 to 150 Mb on wheat chromosome 5A. One hundred and eleven kompetitive allele-specific PCR (KASP) and 39 simple sequence repeat (SSR) markers on chromosome 5A were used to locate the YrFL. Linkage analysis mapped YrFL with 19 KASP and three SSR markers on wheat chromosome 5AS, and the genetic distances of the closest flanking markers AX108925494 and Xbarc56 to YrFL were 0.6 and 2.0 cM, respectively. Chromosome location, resistance characterization, and molecular marker positions indicated that YrFL is likely a novel stripe rust resistance gene on wheat chromosome 5AS and could be pyramided with other resistance genes to improve resistance in wheat breeding programs.

Mapping and validation of a novel major QTL for resistance to stripe rust in four wheat populations derived from landrace Qishanmai

Wheat yield has been constrained by stripe rust disease globally. A wheat landrace (Qishanmai, QSM) consistently showed lower stripe rust severities in multiple year studies than susceptible check varieties including Suwon11 (SW) at the adult plant stage. To detect QTL for reducing the severity in QSM, 1218 recombinant inbred lines (RILs) were developed from SW × QSM. QTL detection was conducted firstly using 112 RILs selected for similarity in pheno-morphological characters. The 112 RILs were assessed for stripe rust severity at the 2nd leaf, 6th leaf and flag leaf stages under field and greenhouse conditions, and genotyping was done primarily with a single nucleotide polymorphism (SNP) array. On the basis of these phenotypic and genotypic data, a major QTL (QYr.cau-1DL) was detected on chromosome 1D at the 6th leaf and flag leaf stages. Further mapping was conducted by genotyping 1218 RILs using new simple sequence repeat (SSR) markers, which were developed by referring to the sequences of the wheat line Chinese Spring (IWGSC RefSeq v1.0). QYr.cau-1DL was mapped within a 0.5 cM (5.2 Mb) interval delimited by the SSR markers 1D-320.58 and 1D-325.79. These markers were applied to select for QYr.cau-1DL by screening F₂ or BC₄F₂ plants of the wheat crosses RL6058 × QSM, Lantian10 × QSM and Yannong21 × QSM. F_2:3 or BC₄F_2:3 families derived from the selected plants were assessed for stripe rust resistance in the fields of two locations and in a greenhouse. Wheat plants carrying the resistant marker haplotype in homozygous state for QYr.cau-1DL showed lower stripe rust severities (by 44% to 48%) than plants lacking this QTL. The trial of RL6058 (a carrier of Yr18) × QSM also indicated that QYr.cau-1DL had larger effect than Yr18 on reducing severity; they acted synergistically, yielding an elevated level of stripe rust resistance.

Races CYR34 and Suwon11-1 of Puccinia striiformis f. sp. tritici Played an Important Role in Causing the Stripe Rust Epidemic in Winter Wheat in Yili, Xinjiang, China

Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease. Its pathogen frequently adapts to newly invaded regions and overcomes resistance in wheat cultivars. This disease is especially important in China due to its favorable conditions for the stripe rust epidemic and the recombination population structure of pathogens. Xinjiang is a vast epidemic region in China, but very limited research on this disease has been performed in this region. In this study, we identified 25 races from 129 isolates collected from winter wheat fields from five different regions (Nileke, Xinyuan, Gongliu, Huocheng, and Qapqal) of Yili, Xinjiang, using the Chinese set of 19 differential wheat lines. All isolates were virulent on the differentials Fulhad and Early Premium, but no isolates were virulent on Yr5. Among the 25 races, Suwon11-1 was the most prevalent, followed by CYR34. Both races were found in four out of the five locations. It is important to continue monitoring stripe rust and its pathogen races in this region, as it forms a pathway between China and Central Asia. Collaborative research is essential for controlling stripe rust in this region, other regions in China, and neighboring countries.

Genetic Characteristics and Linkage of Virulence Genes of the Puccinia striiformis f. sp. tritici TSA-6 Isolate to Yr5 Host Resistance

To understand the inheritance of the TSA-6 Puccinia striiformis f. sp. tritici (Pst) isolate that is virulent to Yr5 and was recently detected in China, we analyzed avirulence and virulence of 120 selfed progeny lines from Berberis shensiana. The results showed that the TSA-6 isolate is virulent against the Yr5 resistance gene, and overall progeny lines were categorized into 73 virulence phenotypes (VPs); of these, 72 VPs differed from the isolate TSA-6, and only one VP, including three progeny, was identical to the parental isolate. The analyses indicated that the TSA-6 isolate is homozygous for avirulence at the Yr10, Yr15, and Yr26 resistance loci and virulence at the YrA resistance locus. The TSA-6 isolate is heterozygous for avirulence at the Yr2, Yr3, Yr5, Yr7, and Yr8 resistance loci, which are controlled by a dominant/recessive relationship. The Yr1, Yr6, Yr9, Yr17, Yr27, Yr25, Yr28, Yr29, Yr32, YrTr1, and YrSP resistance loci are governed by two complementary dominant/recessive genes. Avirulence against heterozygous Yr4, Yr43, Yr44, Yr76, and YrExp2 resistance loci is regulated by a dominant and recessive or a dominant and suppressor gene pair. In total, 117 multilocus genotypes were detected at 24 KASP-SNP marker loci among the 120 progenies. Using these marker loci, we constructed a linkage map with a genetic distance interval spanning 624.5 cM. Quantitative trait loci corresponding to phenotypic segregation for virulence at 20 Yr resistance loci in addition to the Yr1 resistance locus were identified. These results facilitate our understanding of Pst virulence evolution and simplify breeding of wheat cultivars with effective resistance to wheat stripe rust.

Direct Evidence Demonstrates that Puccinia striiformis f. sp. tritici Infects Susceptible Barberry to Complete Sexual Cycle in Autumn

Wheat stripe rust is an airborne and destructive disease caused by a heteroecious rust fungus Puccinia striiformis f. sp. tritici (Pst). Studies have demonstrated that the rust pathogen accomplishes sexual reproduction on susceptible barberry under natural conditions in spring, whereas Pst infection on barberry is still in blank in other seasons. In late October 2016, aecial production on barberry shrubs were observed in Linzhi, Tibet, China. Therefore, experimental tests were conducted to verify the existence of sexual cycles of Pst in this season. By inoculating 52 aecial clusters from 30 rusted barberry leaves, four Pst samples, T1 to T4, were successfully recovered from the rusted barberry shrubs. Sixty-five single uredinium (SU) isolates were derived from the four Pst samples. Based on virulence tests on the Chinese differential hosts, T1 to T4 samples were unknown races and showed mixed reactions on some differentials. Twenty-one known races and 44 unknown races belonging to five race groups were identified among the 65 SU isolates. Meanwhile, the 65 SU isolates produced 26 various virulence patterns (VPs; called VP1-VP26) on 25 single Yr gene lines and 15 multilocus genotypes (MLGs) at nine simple sequence repeat marker loci. Clustering analysis showed similar lineage among subpopulations and different lineage between subpopulations. Linkage disequilibrium analysis indicated that the SU population was produced sexually. This study first reported that Pst infects susceptible barberry to complete sexual reproduction in autumn. The results update the knowledge of disease cycle and management of wheat stripe rust and contribute to the understanding of rust genetic diversity in Tibet.

Characterization and functional analyses of wheat TaPR1 genes in response to stripe rust fungal infection

The pathogenesis-related protein-1 (PR1) gene is important for plants to respond to various biotic and abiotic stresses. Unlike those in model plants, PR1 genes in wheat have not been systematically studied. Herein, we identified 86 potential TaPR1 wheat genes using bioinformatics tools and RNA sequencing. Kyoto Encyclopedia of Genes and Genomes analysis indicated that the TaPR1 genes were involved in the salicylic acid signalling pathway, MAPK signalling pathway, and phenylalanine metabolism in response to Pst-CYR34 infection. Ten of the TaPR1 genes were structurally characterized and validated by RT‒PCR. One particular gene, TaPR1-7, was found to be associated with resistance to Puccinia striiformis f. sp. tritici (Pst) in a biparental wheat population. Virus-induced gene silencing showed that TaPR1-7 is important for Pst resistance in wheat. This study provides the first comprehensive study on wheat PR1 genes, improving our overall understanding of these genes in plant defenses, particularly against stripe rust.

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.

Long-Distance Transport of Puccinia striiformis f. sp. tritici by Upper Airflow on the Yunnan-Guizhou Plateau Disrupts the Balance of Agricultural Ecology in Central China

Long-distance dispersal of plant pathogens in the air can establish diseases in other areas and lead to an increased risk of large-scale epidemics. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat in China. Hubei is an important overwintering region for Pst in China, and this overwintering region is a determinant of stripe rust severity in eastern China. In 2017, stripe rust disease caused a pandemic in the Hubei region and resulted in great yield losses of wheat. To explain the disease pandemic, a total of 595 single-lesion samples of stripe rust were collected in spring, including 204 in five provinces in 2017 and 391 in four provinces in 2018, and genotyped with 13 simple sequence repeat makers. The samples were classified into 12 subpopulations based on the locations and year of collection. Genetic diversity was determined for the collection and each subpopulation. Differentiation and gene flow were determined between subpopulations. STRUCTURE analyses and discriminant analysis of principal components were conducted, and the results were used to infer the relationships between subpopulations. Our study revealed a new route of Pst transmission from the Yunnan-Guizhou Plateau to the Hubei region. The Pst inoculum of northwestern Hubei came from Gansu in the northwest, whereas the inoculum in southern Hubei came from the Yunnan-Guizhou Plateau via upper airflow. After the initial inocula infected wheat plants and multiplied in northern and southern Hubei, urediniospores produced in these regions further spread together along the middle reach of Hanshui Valley and made exchanges there. The finding of the new transmission route of Pst is important for improving integrated stripe rust disease management, which should have a profound impact on the balance of agricultural ecology in China.

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.

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.

Identification and molecular mapping of YrBm for adult plan resistance to stripe rust in Chinese wheat landrace Baimangmai

A new adult plan resistance gene YrBm for potentially durable resistance to stripe rust was mapped on wheat chromosome arm 4BL in landrace Baimangmai. SSR markers closely flanking YrBm were developed and validated for use in marker-assisted selection. The wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) frequently acquires new virulences and rapidly adapts to environmental stress. New virulences in Pst populations can cause previously resistant varieties to become susceptible. If those varieties were widely grown, consequent epidemics can lead to yield losses. Identification and deployment of genes for durable resistance are preferred method for disease control. The Chinese winter wheat landrace Baimangmai showed a high level of adult plant resistance (APR) to stripe rust in a germplasm evaluation trial at Langfang in Hebei province in 2006 and has continued to confer high resistance over the following 15 years in field nurseries in Hebei, Sichuan and Gansu. A recombinant inbred line population of 200 F₁₀ lines developed from a cross of Baimangmai and a susceptible genotype segregated for APR at a single locus on chromosome 4BL; the resistance allele was designated YrBm. Allelism tests of known Yr genes on chromosome 4B and unique closely flanking marker alleles Xgpw7272₁₈₉ and Xwmc652₁₆₄ among a panel of Chinese wheat varieties indicated that YrBm was located at a new locus. Moreover, those markers can be used for marker-assisted selection in breeding for stripe rust resistance.

Molecular Mapping of a Recessive Gene for Stripe Rust Resistance at the YrCf75 Locus Using Bulked Segregant Analysis Combined with Single Nucleotide Polymorphism Genotyping Arrays and Bulked Segregant RNA-Sequencing

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases in wheat worldwide. Planting resistant varieties is the most economical, effective, and environment-friendly measure to control wheat stripe rust. Changfeng 75, a Chinese winter wheat variety, shows high stripe rust resistance in both seedling and adult-plant stages. The seedling tests of F₁, F₂, and F_2:3 populations derived from Mingxian 169/Changfeng 75 inoculated with Chinese predominant Pst race CYR34 showed that the stripe rust resistance of Changfeng 75 was controlled by a single recessive gene. The locus was temporarily designated as YrCf75. Bulked segregant analysis (BSA) combined with the wheat 660K single-nucleotide polymorphism (SNP) array and bulked segregant RNA-sequencing indicated that the proportion of polymorphic SNPs on wheat chromosome 2A was the highest, which suggested that YrCf75 was likely located on chromosome 2A. Two hundred and twenty-five Kompetitive allele-specific PCR (KASP) and 75 simple sequence repeat (SSR) markers on chromosome 2A were used to map YrCf75 using the BSA approach. Linkage analysis indicated that 31 KASP markers and one SSR marker were linked to YrCf75, and the genetic distances of the two closest flanking KASP markers, AX-1110060462 and AX-111004763, were 1.2 and 2.7 cM, respectively. YrCf75 was located on wheat chromosome 2AL. The molecular detection, resistance specificity, and chromosome location showed that YrCf75 is likely a new gene that is different from the known stripe rust resistance genes (Yr1 and Yr32) on wheat chromosome 2AL.

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.

Elucidating the Population Structure and Genetic Diversity of Indian Puccinia striiformis f. sp. tritici Pathotypes Based on Microsatellite Markers

In India, systematic wheat yellow rust survey and pathotype (race) analysis work began in 1930. However, information on population structure and genetic diversity of yellow rust pathogen has not been available. To address this, we conducted studies on population structure and genetic diversity of Puccinia striiformis f. sp. tritici (Pst) pathotypes using 38 simple sequence repeat primer-pairs. Bayesian assignment and discriminant analysis of principal components indicated the presence of two distinct Pst subpopulations (Pop1 and Pop2) along with 37.9% admixed pathotypes. The unweighted pair-group method with arithmetic mean also categorized these pathotypes into two major clusters. Principal coordinates analysis explained 20.06 and 12.50% variance in horizontal and vertical coordinates, respectively. Index of association (I_A) and the standardized index of association ([Formula: see text]) values showed that Pst subpopulations reproduced asexually (clonally). In total, 102 alleles were detected, with the expected heterozygosity (H_exp) per locus ranging from 0.13 to 0.73, with a mean of 0.47. The average polymorphic information content value of 0.40 indicated high genetic diversity among pathotypes. Analysis of molecular variance revealed 12% of the total variance between subpopulations, 11% among the pathotypes of each subpopulation, and 77% within pathotypes. A significant moderate level of genetic differentiation (F_ST = 0.122, P < 0.001) and gene flow (N_m = 1.80) were observed between subpopulations. The Pst virulence phenotypes showed a weak positive correlation (R² = 0.027, P < 0.02) with molecular genotypes.

Identification of Mahonia Species as Alternate Hosts for Puccinia striiformis f. sp. tritici and Determination of Existence of Sexual Propagation of the Rust Pathogen on Mahonia Under Natural Conditions in China

Many Berberis species have been identified as alternate hosts for Puccinia striiformis f. sp. tritici. Importantly, susceptible Berberis species are determined to play an important role in the occurrence of sexual reproduction, generation of new races of the rust pathogen. However, little is known about Mahonia serving as alternate hosts for P. striiformis f. sp. tritici and their role to commence sexual reproduction of the rust fungus under natural conditions. Herein, three Mahonia species or subspecies, Mahonia fortunei, M. eurybracteata subsp. ganpinensis, and M. sheridaniana, were identified as alternate hosts for P. striiformis f. sp. tritici, and seven Mahonia species were highly resistant to the rust pathogen. We recovered seven samples of P. striiformis f. sp. tritici from naturally rusted Mahonia cardiophylla plants. Totally, 54 single uredinium (SU) isolates, derived from the seven samples, generated 20 different race types, including one known race type, and 19 new race types. SNP markers analysis showed that all SU isolates displayed high phenotype diversity (H = 0.32) with a high Shannon's information index (I = 0.49). Analysis of linkage disequilibrium indicated an insignificant rbarD value (rbarD = 0.003, P < 0.1). As a result, all SU isolates are sexually produced, suggesting that P. striiformis f. sp. tritici parasitizes susceptible Mahonia to complete sexual reproduction under natural conditions. The role of Mahonia in occurrence of wheat stripe rust are needed to study for management of the disease.

Isolation, Identification and Hyperparasitism of a Novel Cladosporium cladosporioides Isolate Hyperparasitic to Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Simple Summary

Obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst) is a major threat to wheat production. Parasites of Pst can be used to develop biological agents for environmentally friendly control of this fungal disease. Here, we report a hyperparasitic fungus isolated from taupe-colored uredinia of Pst and identified as Cladosporium cladosporioides through molecular and morphological characterizations. The hyperparasitic isolate was able to reduce the production and viability of Pst. Therefore, Cladosporium cladosporioides may have potential in biological control of stripe rust on wheat.

Abstract

Wheat rust outbreaks have caused significantly economic losses all over the world. Puccinia striiformis f. sp. tritici (Pst) is an obligate biotrophic fungus causing stripe rust on wheat. Application of fungicides may cause environmental problems. The effects of hyperparasites on plant pathogens are the basis for biological control of plant pathogenic fungi and parasites of Pst have great value in biological agents development. Here, we report the isolation and characterization of isolate of Cladosporium cladosporioides from Pst based on morphological characterization and analysis of molecular markers. The hyperparasitic isolate was isolated from taupe-colored uredinia of Pst. Upon artificial inoculation, the hyperparasitic isolate was able to reduce the production and germination rate of Pst urediospores, and Pst uredinia changed color from yellow to taupe. Scanning electron microscopy demonstrated that the strain could efficiently colonize Pst urediospores. Therefore, the isolate has the potential to be developed into a biological control agent for managing wheat stripe rust.

Yield Losses Associated with Different Levels of Stripe Rust Resistance of Commercial Wheat Cultivars in China

Wheat stripe rust is one of the most destructive diseases to affect wheat. Although the major resistant wheat varieties have made a great contribution to global food security, yield losses from stripe rust still occur in large wheat growing areas when climatic conditions are unstable. Despite this threat, resistance levels and yield losses of these elite wheat cultivars under wheat stripe rust infection have not been well studied. Based on this investigation of natural infection conditions over 2 years, analysis of the area-under-the-disease-progress-curves differentiated the susceptible cultivars Mianmai 367 (MM367; 788.59), Jinmai 47 (JM47; 1,087.71), and Avocet Susceptible (AvS; 1,314.59) from resistant cultivars Xikemai 18 (XKM18; 177.50) and Xiaoyan 6 (XY6; 545.67). Stripe rust resulted in a 2-year mean yield loss of 32% for all tested varieties. The susceptible varieties JM47, AvS, and MM367 lost 64, 55, and 21% of grain yield, respectively. On the contrary, rust-resistant cultivars XKM18 and XY6 lost only 11 and 28%, respectively. In addition, stripe rust resulted in reduced kernel hardness, flour yield, and flour whiteness. Dough and gluten properties were also affected. Overall, results revealed that the grain yield and quality loss values of the resistant wheat cultivars were less than in the susceptible cultivars. Disease-resistant cultivars such as XKM18 should be promoted and recommended for application. It may also be suggested that growing a susceptible variety such as MM367 could be feasible in combination with fungicide application under high disease pressure.

Role of Sexual Reproduction in the Evolution of the Wheat Stripe Rust Fungus Races in China

Experimental and population genetic approaches have reshaped our view of how fungal pathogens reproduce, with consequences for our understanding of fungal invasions. Puccinia striiformis f. sp. tritici, the causal agent of stripe rust, poses a severe threat to wheat production worldwide. The sexual stage of P. striiformis f. sp. tritici was discovered >10 years ago, but how it affects the evolution of the pathogen, especially the emergence of the new virulent races, remains largely unknown. Here, using population genetic analyses, we demonstrate that sexual reproduction plays an important role in the evolution of P. striiformis f. sp. tritici races in China, specifically the newly emerged and devastating race virulent to resistance gene Yr26, which is widely used in China and exerts strong selective pressure on the pathogen population. Association analysis identified six genes encoding secreted proteins as candidates for virulence on wheat cultivars carrying the Yr26 resistance gene. Our results highlight the important role of sexual reproduction and selection exerted by hosts in the emergence of new virulent races in China.

Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety 'Neimai 836'

The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety 'Apav#1' and resistant variety 'Neimai 836' was used to develop a mapping population containing 148 F₅ recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico, in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico, in 2017 and in Mianyang, Ezhou, and Gansu, China, in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multipathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3 to 16% of the phenotypic variation in resistance to leaf rust and 7 to 14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high-level resistance to both leaf rust and stripe rust.

Molecular Cytogenetic Analysis of the Introgression between Agropyron cristatum P Genome and Wheat Genome

Agropyron cristatum (2n = 4x = 28, PPPP) is an important wild relative of common wheat (Triticum aestivum L., 2n = 6x = 42). A previous report showed that the wheat-A. cristatum 6P translocation line WAT655 carrying A. cristatum 6PS (0.81-1.00) exhibited high resistance to prevalent physiological races of stripe rust (CYR32 and CYR33). In this study, three disease resistance-related transcripts, which were mapped to A. cristatum 6PS (0.81-1.00) through the analysis of specific molecular markers, were acquired from among A. cristatum full-length transcripts. The BC₅F₂ and BC₅F_2:3 genetic populations of the translocation line WAT655 were analyzed by using three disease resistance-related gene markers, A. cristatum P genome-specific markers, and fluorescence in situ hybridization (FISH). The results revealed that the introgression between A. cristatum P genome and wheat genome was observed in progenies of the genetic populations of the translocation line WAT655 and the physical positions of the three genes were considerably adjacent on A. cristatum 6PS (0.81-1.00) according to the FISH results. Additionally, kompetitive allele-specific PCR (KASP) markers of the three genes were developed to detect and acquire 24 breeding lines selected from the progenies of the distant hybridization of wheat and A. cristatum, which showed resistance to physiological races of stripe rust (CYR32 and CYR33) and other desirable agronomic traits according to the field investigation. In conclusion, this study not only provides new insights into the introgression between A. cristatum P genome and wheat genome but also provides the desirable germplasms for breeding practice.

Genetic Diversity of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Yunnan, China

The stripe rust of wheat is one of the devastating diseases in China, which is caused by fungus Puccinia striiformis f. sp. tritici (Pst). The Yunnan Province of China is located in the south-western part, and holds distinctive geographical and climate features, while wheat growth and epidemics of stripe rust fungus are fully dissimilar to the major wheat-growing regions of China. It is important to discover its origin and migration to control the disease. In this study, 352 isolates were sampled from 11 spots of the Yunnan Province during the wheat growing season from 2004 to 2015 and analyzed with SNPs markers of housekeeping genes. Results revealed that 220 haplotypes were inferred from the concatenating sequences; among them, 5 haplotypes (viz., 'H86', 'H18', 'H8', 'H15' and 'H23') comprised over 24.5% of the population. The haplotype diversity, nucleotide diversity, mutation rate and recombination events were 0.992, 6.04 × 10^-3, 4.46 × 10^-3 and 18.0 respectively, which revealed the genetic diversity of Pst populations among all locations. Four grouping methods, such as UPGMA-tree, PCA, PLS-DA and STRUCTURE, were employed for the categorization of the Pst populations conferring to their races and topographical localities. All methods were found significant and mostly had co-linear relations with each other. The analysis of molecular variance (AMOVA) conferred total variation was 9.09%, and 86.20% of variation was within the populations. The current study also exposed a comparatively high genetic multiplicity within the population, while low genetic inconsistency among the populations. Furthermore, the molecular records on the gene pole (Nm = 18.45) established that the migration of the stripe rust pathogen occurred among all locations in Yunnan province. The ancestral haplotype was detected in Yuxi. Based on the trajectories of upper airflow and genetic diversity of Pst populations in different locations, it is suggested that the locations Dehong, Dali, Lincang and Baoshan are probably a major source of Pst in Yunnan.

Molecular Mapping of a Novel Quantitative Trait Locus Conferring Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Guangtoumai

Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat worldwide. Chinese wheat landrace Guangtoumai (GTM) exhibited a high level of resistance against predominant P. striiformis f. sp. tritici races in China at the adult plant stage. The objective of this research was to identify and map the major locus/loci for stripe rust resistance in GTM. A set of 212 recombinant inbred lines (RILs) was developed from a cross between GTM and Avocet S. The parents and RILs were evaluated in three field tests (2018, 2019, and 2020 at Chongzhou, Sichuan) with the currently predominant P. striiformis f. sp. tritici races for final disease severity and genotyped with the Wheat 55K single nucleotide polymorphism (SNP) array to construct a genetic map with 1,031 SNP markers. A major locus, named QYr.GTM-5DL, was detected on chromosome 5DL in GTM. The locus was mapped in a 2.75-cM interval flanked by SNP markers AX-109855976 and AX-109453419, explaining up to 44.4% of the total phenotypic variation. Since no known Yr genes have been reported on chromosome 5DL, QYr.GTM-5DL is very likely a novel adult plant resistance locus. Haplotype analysis revealed that the resistance allele displayed enhanced levels of stripe rust resistance and is likely present in 5.3% of the 247 surveyed Chinese wheat landraces. The derived cleaved amplified polymorphic sequence (dCAPS) marker dCAPS-5722, converted from a SNP marker tightly linked to QYr.GTM-5DL with 0.3 cM, was validated on a subset of RILs and 48 commercial wheat cultivars developed in Sichuan. The results indicated that QYr.GTM-5DL with its linked dCAPS marker could be used in marker-assisted selection to improve stripe rust resistance in breeding programs, and this quantitative trait locus will provide new and possibly durable resistance to stripe rust.

Genome-wide association mapping reveals potential novel loci controlling stripe rust resistance in a Chinese wheat landrace diversity panel from the southern autumn-sown spring wheat zone

BACKGROUND

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultivars are considered to be the most effective approaches to control this disease. In this study, we evaluated the infection type (IT), disease severity (DS) and area under the disease progress curve (AUDPC) of 143 Chinese wheat landrace accessions for stripe rust resistance. Assessments were undertaken in five environments at the adult-plant stage with Pst mixture races under field conditions. In addition, IT was assessed at the seedling stage with two prevalent Pst races (CYR32 and CYR34) under a controlled greenhouse environment.

RESULTS

Seventeen accessions showed stable high-level resistance to stripe rust across all environments in the field tests. Four accessions showed resistance to the Pst races CYR32 and CYR34 at the seedling stage. Combining phenotypic data from the field and greenhouse trials with 6404 markers that covered the entire genome, we detected 17 quantitative trait loci (QTL) on 11 chromosomes for IT associated with seedling resistance and 15 QTL on seven chromosomes for IT, final disease severity (FDS) or AUDPC associated with adult-plant resistance. Four stable QTL detected on four chromosomes, which explained 9.99-23.30% of the phenotypic variation, were simultaneously associated with seedling and adult-plant resistance. Integrating a linkage map of stripe rust resistance in wheat, 27 QTL overlapped with previously reported genes or QTL, whereas four and one QTL conferring seedling and adult-plant resistance, respectively, were mapped distantly from previously reported stripe rust resistance genes or QTL and thus may be novel resistance loci.

CONCLUSIONS

Our results provided an integrated overview of stripe rust resistance resources in a wheat landrace diversity panel from the southern autumn-sown spring wheat zone of China. The identified resistant accessions and resistance loci will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.

Characterization of the Durum Wheat-Aegilops tauschii 4D(4B) Disomic Substitution Line YL-443 With Superior Characteristics of High Yielding and Stripe Rust Resistance

Durum wheat is one of the important food and cash crops. The main goals in current breeding programs are improving its low yield potential, kernel characteristics, and lack of resistance or tolerance to some biotic and abiotic stresses. In this study, a nascent synthesized hexaploid wheat Lanmai/AT23 is used as the female parent in crosses with its AB genome donor Lanmai. A tetraploid line YL-443 with supernumerary spikelets and high resistance to stripe rust was selected out from the pentaploid F₇ progeny. Somatic analysis using multicolor fluorescence in situ hybridization (mc-FISH) revealed that this line is a disomic substitution line with the 4B chromosome pair of Lanmai replaced by the 4D chromosome pair of Aegilops tauschii AT23. Comparing with Lanmai, YL-443 shows an increase in the number of spikelets and florets per spike by 36.3 and 75.9%, respectively. The stripe rust resistance gene Yr28 carried on the 4D chromosome was fully expressed in the tetraploid background. The present 4D(4B) disomic substitution line YL-443 was distinguished from the previously reported 4D(4B) lines with the 4D chromosomes from Chinese Spring (CS). Our study demonstrated that YL-443 can be used as elite germplasm for durum wheat breeding targeting high yield potential and stripe rust resistance. The Yr28-specific PCR marker and the 4D chromosome-specific KASP markers together with its unique features of pubescent leaf sheath and auricles can be utilized for assisting selection in breeding.

TaClpS1, negatively regulates wheat resistance against Puccinia striiformis f. sp. tritici

BACKGROUND

The degradation of intracellular proteins plays an essential role in plant responses to stressful environments. ClpS1 and E3 ubiquitin ligase function as adaptors for selecting target substrates in caseinolytic peptidase (Clp) proteases pathways and the 26S proteasome system, respectively. Currently, the role of E3 ubiquitin ligase in the plant immune response to pathogens is well defined. However, the role of ClpS1 in the plant immune response to pathogens remains unknown.

RESULTS

Here, wheat (Triticum aestivum) ClpS1 (TaClpS1) was studied and resulted to encode 161 amino acids, containing a conserved ClpS domain and a chloroplast transit peptide (1-32 aa). TaClpS1 was found to be specifically localized in the chloroplast when expressed transiently in wheat protoplasts. The transcript level of TaClpS1 in wheat was significantly induced during infection by Puccinia striiformis f. sp. tritici (Pst). Knockdown of TaClpS1 via virus-induced gene silencing (VIGS) resulted in an increase in wheat resistance against Pst, accompanied by an increase in the hypersensitive response (HR), accumulation of reactive oxygen species (ROS) and expression of TaPR1 and TaPR2, and a reduction in the number of haustoria, length of infection hypha and infection area of Pst. Furthermore, heterologous expression of TaClpS1 in Nicotiana benthamiana enhanced the infection by Phytophthora parasitica.

CONCLUSIONS

These results suggest that TaClpS1 negatively regulates the resistance of wheat to Pst.

TaYS1A, a Yellow Stripe-Like Transporter Gene, Is Required for Wheat Resistance to Puccinia striiformis f. sp. Tritici

Yellow stripe-like (YSL) transporters are required for the transportation of metal-phytosiderophores and are structurally related to metal-nicotianamine complexes. Some studies also reported the involvement of YSL transporters in pathogen-induced defense. However, the molecular mechanisms of YSL genes involved in biotic stress responses are still not clear, especially in cereal crops. This study aimed to functionally characterize TaYS1A during the interaction of wheat and Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust disease. TaYS1A was localized in the cell membrane of wheat protoplasts and Nicotiana benthamiana cells. TaYS1A was significantly up-regulated in wheat leaves after being infected with the avirulent Pst isolate CYR23 and after treatment with salicylic acid (SA). Silencing of TaYS1A by the virus-induced gene silencing method enhanced the susceptibility of wheat to Pst accompanied by reducing the accumulation of SA and H2O2 and down-regulating the transcriptions of TaPR1 and TaPR2. In addition, TaYS1A was found to interact with TaNH2, a homolog of OsNH2, by yeast-two-hybrid assay, and silencing of TaYS1A diminished the expression of TaNH2. Our findings suggested the existence of positive regulation of TaYS1A in providing resistance against Pst by modulating SA-induced signaling and offered new insight into the biological role of YSL in wheat against pathogens.

Identification of an Elite Wheat-Rye T1RS·1BL Translocation Line Conferring High Resistance to Powdery Mildew and Stripe Rust

Wheat-rye T1RS·1BL translocations have been widely used worldwide in wheat production for multiple disease resistance and superior yield traits. However, many T1RS·1BL translocations have successively lost their resistance to pathogens due to the coevolution of pathogen virulence with host resistance. Because of the extensive variation in rye (Secale cereale L.) as a naturally cross-pollinating relative of wheat, it still has promise to widen the variation of 1RS and to fully realize its application value in wheat improvement. In the present study, the wheat-rye breeding line R2207 was characterized by comprehensive analyses using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization with multiple probes, multicolor GISH, and molecular marker analysis, and then was proven to be a cytogenetically stable wheat-rye T1RS·1BL translocation line. Based on the disease responses to different isolates of powdery mildew and genetic analysis, R2207 appears to possess a novel variation for resistance, which was confirmed to be located on the rye chromosome arm 1RS. Line R2207 also exhibited high levels of resistance to stripe rust at both seedling and adult stages, as well as enhanced agronomic performance, so it has been transferred into a large number of commercial cultivars using an efficient 1RS-specific kompetitive allele specific PCR marker for marker-assisted selection.

Molecular Marker Based Design for Breeding Wheat Lines with Multiple Resistance and Superior Quality

There has not been a major wheat stem rust epidemic worldwide since the 1970s, but the emergence of race TTKSK of Puccinia graminis f. sp. tritici in 1998 presented a great threat to the world wheat production. Single disease-resistance genes are usually effective for only several years before the pathogen changes genetically to overcome the resistance. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most common and persistent wheat diseases worldwide. The development of varieties with multiple resistance is the most economical and effective strategy for preventing stripe rust and stem rust, the two main rust diseases constraining wheat production. Plateau 448 has been widely used in the spring wheat growing region in northwest China, but it has become susceptible to stripe rust and is susceptible to TTKSK. To produce more durable resistance to race TTKSK as well as to stripe rust, four stem rust resistance genes (Sr33, Sr36, Sr-Cad, and Sr43) and three stripe rust resistance genes (Yr5, Yr18, and Yr26) were simultaneously introgressed into Plateau 448 to improve its stem rust (Ug99) and stripe rust resistance using a marker-assisted backcrossing strategy combined with phenotypic selection. We obtained 131 BC₁F₅ lines that pyramided two to four Ug99 resistance genes and one to two Pst resistance genes simultaneously. Thirteen of these lines were selected for their TTKSK resistance, and all of them exhibited near immunity or high resistance to TTKSK. Among the 131 pyramided lines, 95 showed high resistance to mixed Pst races. Nine lines exhibited not only high resistance to TTKSK and Pst but also better agronomic traits and high-molecular-weight glutenin subunit compositions than Plateau 448.

Using continous wavelet analysis for monitoring wheat yellow rust in different infestation stages based on unmanned aerial vehicle hyperspectral images

Yellow rust is the most extensive disease in wheat cultivation, seriously affecting crop quality and yield. This study proposes sensitive wavelet features (WFs) for wheat yellow rust monitoring based on unmanned aerial vehicle hyperspectral imagery of different infestation stages [26 days after inoculation (26 DAI) and 42 DAI]. Furthermore, we evaluated the monitoring ability of WFs and vegetation indices on wheat yellow rust through linear discriminant analysis and support vector machine (SVM) classification frameworks in different infestation stages, respectively. The results show that WFs-SVM have promising potential for wheat yellow rust monitoring in both the 26 DAI and 42 DAI stages.

Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust

First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.

Identification of Stripe Rust Resistance Genes in Common Wheat Cultivars From the Huang-Huai-Hai Region of China

Wheat stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious fungal disease worldwide, especially in the Huang-Huai-Hai region, a main wheat production area in China. Gene postulation, molecular testing, and pedigree analysis were conducted to determine the presence of stripe rust resistance genes to 15 Pst races in 66 selected commercial wheat cultivars released from 2000 to 2016. In addition, races CYR32, CYR33, and CYR34 were used to evaluate resistance to Pst at the adult-plant stage of wheat in the field. Four Yr genes (Yr9, Yr10, Yr26, and Yr32) were postulated in 24 wheat cultivars either singly or in combination. Thirty-six cultivars might contain unknown Yr genes, whereas no identified Yr gene was postulated in six cultivars. Yr9 was detected at a frequency of 28.8%, and no cultivars carried Yr5, Yr15, or Yr18. Ten cultivars (15.2%) exhibited adult-plant resistance in the field tests with three predominant races. Three cultivars (Langyan 43, Xinong 889, and Yunfeng 139) had all-stage resistance. These results are useful to growers selecting cultivars and to breeders aiming to use more resistance genes to develop new cultivars with effective resistance in order to reduce stripe rust damage.

Molecular Characterization of International Collections of the Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici Reveals High Diversity and Intercontinental Migration

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust), one of the most important wheat diseases worldwide. To understand the genetic variation of the pathogen in a global scale, 283 P. striiformis f. sp. tritici isolates collected from 16 countries in eight geographic regions were genotyped using 24 codominant simple sequence repeat markers. The overall collection had a high level of genetic diversity, and the diversity levels in the Asian populations were generally higher than those of the other regions. Heterozygosity of isolates ranged from 0 to 75%, with an average of 46%. Mean heterozygosity in individual countries ranged from 34 to 59%. A total of 265 multilocus genotypes (MLGs) were detected, which were classified into eight molecular groups. Some of the molecular groups were present in all geographic regions. Moreover, many isolates from different regions were found to be identical or very closely related MLGs. Analysis of molecular variance revealed high variation within countries and intermediate variation between countries, but it revealed low and insignificant variation among geographic regions. Pairwise comparisons of regional populations detected considerable effective migrants and only low to moderate levels of differentiation. The molecular genotypes had a moderate level of correlation with the virulence phenotypes, and some of the molecular/virulence groups contained isolates from different continents. The results indicate tremendous migrations of P. striiformis f. sp. tritici and warrant the development of management strategies considering the global pathogen population.

Study of Inheritance and Linkage of Virulence Genes in a Selfing Population of a Pakistani Dominant Race of Puccinia striiformis f. sp. tritici

Wheat stripe rust is a severe threat of almost all wheat-growing regions in the world. Being an obligate biotrophic fungus, Puccinia striiformis f. sp. tritici (PST) produces new virulent races that break the resistance of wheat varieties. In this study, 115 progeny isolates were generated through sexual reproduction on susceptible Himalayan Berberis pseudumbellata using a dominant Pakistani race (574232) of PST. The parental isolate and progeny isolates were characterized using 24 wheat Yr single-gene lines and ten simple sequence repeat (SSR) markers. From the one-hundred-and-fifteen progeny isolates, 25 virulence phenotypes (VPs) and 60 multilocus genotypes were identified. The parental and all progeny isolates were avirulent to Yr5, Yr10, Yr15, Yr24, Yr32, Yr43, YrSp, YrTr1, YrExp2, Yr26, and YrTye and virulent to Yr1, Yr2, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27, Yr28, YrA, Yr44, and Yr3. Based on the avirulence/virulence phenotypes, we found that VPs virulent to Yr1, Yr2, Yr9, Yr17, Yr47, and YrA were controlled by one dominant gene; those to YrSp, YrTr1, and Yr10 by two dominant genes; and those to YrExp2 by two complementary dominant genes. The results are useful in breeding stripe rust-resistant wheat varieties and understanding virulence diversity.

Evaluation of a global spring wheat panel for stripe rust: Resistance loci validation and novel resources identification

Stripe rust (incited by Puccinia striiformis f. sp. tritici) is airborne wheat (Triticum aestivum L.) disease with dynamic virulence evolution. Thus, anticipatory and continued screening in hotspot regions is crucial to identify new pathotypes and integrate new resistance resources to prevent potential disease epidemics. A global wheat panel consisting of 882 landraces and 912 improved accessions was evaluated in two locations in Egypt during 2016 and 2017. Five prevalent and aggressive pathotypes of stripe rust were used to inoculate the accessions during the two growing seasons and two locations under field conditions. The objectives were to evaluate the panel for stripe rust resistance at the adult plant stage, identify potentially novel QTLs associated with stripe rust resistance, and validate previously reported stripe rust QTLs under the Egyptian conditions. The results indicated that 42 landraces and 140 improved accessions were resistant to stripe rust. Moreover, 24 SNPs were associated with stripe rust resistance and were within 18 wheat functional genes. Four of these genes were involved in several plant defense mechanisms. The number of favorable alleles, based upon the associated SNPs, was significant and negatively correlated with stripe rust resistance score, i.e., as the number of resistances alleles increased the observed resistance increased. In conclusion, generating new stripe rust phenotypic information on this panel while using the publicly available molecular marker data, contributed to identifying potentially novel QTLs associated with stripe rust and validated 17 of the previously reported QTLs in one of the global hotspots for stripe rust.

Wheat-associated microbiota and their correlation with stripe rust reaction

AIMS

This study was aimed at revealing the composition of microbiota in leaves, roots and rhizosphere soil of wheat plants that are resistant or susceptible to stripe rust, one of the most widely destructive leaf diseases in wheat production.

METHODS AND RESULTS

A total of 36 wheat plants that showed resistant or susceptible reactions to stripe rust were sampled. Three compartments of each plant including leaves, roots and rhizosphere soil were used for whole-genomic DNA extraction and the DNA samples were subjected to high-throughput 16S rRNA gene sequencing. A total of 2885 operational taxonomic units (OTUs) were revealed from the sequencing, and they mainly distributed in the phylum of Proteobacteria. Twenty-nine OTUs formed the core microbiota of wheat plants. The differences between above- and below-ground environments could explain most of the dissimilarity of wheat-associated microbial communities. Therefore, those microbes that were able to adapt to the above-ground (leaf) environment might be more important resources for biocontrol agents against stripe rust, and they could be from genera Hymenobacter, Flavobacterium, Chitinophage, Flavisolibacter, Niastella, Mucilaginibacter, Pedobacter, Aquincola, Massilia, Citrobacter, Cronobacter, Ewingella, Acinetobacter and Pseudomonas. No matter the microbial taxa were significantly selected by the resistant or susceptible wheat plants, they contained the members with plant growth promoting (PGP) features and could be used as potential biocontrol agents to reduce stripe rust damage.

CONCLUSIONS

The core microbiota associated with wheat plants and microbial taxa that were significantly correlated with reactions to stripe rust were identified in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

Few studies had been done on the microbiota associated with wheat so far. Our study will not only provide fundamental knowledge about the composition of wheat-associated microbiota but also reveal the microbial taxa that have the potential to be integrated into the strategy of stripe rust management.

A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance

Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.

Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

BACKGROUND

Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments.

RESULTS

In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci.

CONCLUSIONS

Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.

Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces

Background

Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China.

Results

Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage.

Conclusions

The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0736-x) contains supplementary material, which is available to authorized users.

Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance

A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines (RILs) derived from the cross Thatcher (TC) × HQM and 138 RILs from Luke × AQ were assessed for disease severity in six field trials. A genetic map of TC × HQM was constructed by genotyping these RILs using the 90 K wheat single-nucleotide polymorphism chip. Luke × AQ map was previously constructed for another disease study and also utilized here. Based on these maps and disease data, a quantitative trait locus (QTL) was detected on the chromosome arm 2AL from both TC × HQM and Luke × AQ and designated as QYr.cau-2AL. The resistance allele at QYr.cau-2AL came from HQM and AQ. QYr.cau-2AL was significantly effective across all the test environments and different genetic backgrounds, with its effect magnitude being higher than that of Yr18. QYr.cau-2AL synergistically acted with Yr18 and a QTL for high-temperature adult-plant resistance on 2BS, resulting in an elevated resistance from the juvenile plant growth stage onward, although QYr.cau-2AL alone displayed no substantial resistance at juvenile stage. Evidence indicates that QYr.cau-2AL is novel and confers durable resistance, and thus, should have high potential value for practical breeding.

Microsatellite Analysis and Urediniospore Dispersal Simulations Support the Movement of Puccinia graminis f. sp. tritici from Southern Africa to Australia

The Australian wheat stem rust (Puccinia graminis f. sp. tritici) population was shaped by the introduction of four exotic incursions into the country. It was previously hypothesized that at least two of these (races 326-1,2,3,5,6 and 194-1,2,3,5,6 first detected in 1969) had an African origin and moved across the Indian Ocean to Australia on high-altitude winds. We provide strong supportive evidence for this hypothesis by combining genetic analyses and complex atmospheric dispersion modeling. Genetic analysis of 29 Australian and South African P. graminis f. sp. tritici races using microsatellite markers confirmed the close genetic relationship between the South African and Australian populations, thereby confirming previously described phenotypic similarities. Lagrangian particle dispersion model simulations using finely resolved meteorological data showed that long distance dispersal events between southern Africa and Australia are indeed possible, albeit rare. Simulated urediniospore transmission events were most frequent from central South Africa (viable spore transmission on approximately 7% of all simulated release days) compared with other potential source regions in southern Africa. The study acts as a warning of possible future P. graminis f. sp. tritici dispersal events from southern Africa to Australia, which could include members of the Ug99 race group, emphasizing the need for continued surveillance on both continents.

Complete genome sequence of a novel mitovirus from the wheat stripe rust fungus Puccinia striiformis

The complete genome of a novel mycovirus, Puccinia striiformis mitovirus 1 (PsMV1), derived from the wheat stripe rust fungus Puccinia striiformis strain SCSN-10, was sequenced and analyzed. The full-length cDNA sequence is 2496 bp in length with a predicted AU content of 57.65% in the genomic RNA. Sequence analysis indicated that a single large open reading frame (ORF) is present on the positive strand when the fungal mitochondrial genetic code is used. The single ORF encodes a putative RNA-dependent RNA polymerase of 743 amino acids with a molecular mass of 84.9 kDa that shares the closest similarity with the corresponding proteins of Cronartium ribicola mitovirus 5 and Helicobasidium mompa mitovirus 1-18 (34% and 35% aa sequence identity, respectively). Phylogenetic analysis further indicated that PsMV1 is a new member of the genus Mitovirus within the family Narnaviridae. This is the first report of the full-length nucleotide sequence of a novel mitovirus, PsMV1, from the causal agent of wheat stripe rust.

TaRPM1 Positively Regulates Wheat High-Temperature Seedling-Plant Resistance to Puccinia striiformis f. sp. tritici

RPM1 is a CC-NBS-LRR protein that was first shown to be required for resistance to Pseudomonas syringae pv. maculicola in Arabidopsis thaliana. Our previous study showed that TaRPM1 gene in wheat was upregulated about six times following infection by Puccinia striiformis f. sp. tritici (Pst) under high temperature, compared with normal temperature. To study the function of TaRPM1 in wheat high-temperature seedling-plant (HTSP) resistance to Pst, the full length of TaRPM1 was cloned, with three copies each located on chromosomes 1A, 1B, and 1D. Transient expression of the TaRPM1-GFP fusion protein in Nicotiana benthamiana indicated that TaRPM1 localizes in the cytoplasm and nucleus. Profiling TaRPM1 expression indicated that TaRPM1 transcription was rapidly upregulated upon Pst inoculation under high temperature. In addition, TaRPM1 was induced by exogenous salicylic acid hormone application. Silencing TaRPM1 in wheat cultivar Xiaoyan 6 (XY 6) resulted in reduced HTSP resistance to Pst in terms of reduced number of necrotic cells and increased uredinial length, whereas no obvious phenotypic changes were observed in TaRPM1-silenced leaves under normal temperature. Related defense genes TaPR1 and TaPR2 were downregulated in TaRPM1-silenced plants under high temperature. We conclude that TaRPM1 is involved in HTSP resistance to Pst in XY 6.