Inheritance of Virulence, Construction of a Linkage Map, and Mapping Dominant Virulence Genes in Puccinia striiformis f. sp. tritici Through Characterization of a Sexual Population with Genotyping-by-Sequencing

Puccinia striiformis f. sp. tritici, the wheat stripe rust pathogen, is a dikaryotic, biotrophic, and macrocyclic fungus. Genetic study of P. striiformis f. sp. tritici virulence was not possible until the recent discovery of Berberis spp. and Mahonia spp. as alternate hosts. To determine inheritance of virulence and map virulence genes, a segregating population of 119 isolates was developed by self-fertilizing P. striiformis f. sp. tritici isolate 08-220 (race PSTv-11) on barberry leaves under controlled greenhouse conditions. The progeny isolates were phenotyped on a set of 29 wheat lines with single genes for race-specific resistance and genotyped with simple sequence repeat (SSR) markers, single nucleotide polymorphism (SNP) markers derived from secreted protein genes, and SNP markers from genotyping-by-sequencing (GBS). Using the GBS technique, 10,163 polymorphic GBS-SNP markers were identified. Clustering and principal component analysis grouped these markers into six genetic groups, and a genetic map, consisting of six linkage groups, was constructed with 805 markers. The six clusters or linkage groups resulting from these analyses indicated a haploid chromosome number of six in P. striiformis f. sp. tritici. Through virulence testing of the progeny isolates, the parental isolate was found to be homozygous for the avirulence loci corresponding to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrSP, YrTr1, Yr45, and Yr53 and homozygous for the virulence locus corresponding to resistance gene Yr41. Segregation was observed for virulence phenotypes in response to the remaining 19 single-gene lines. A single dominant gene or two dominant genes with different nonallelic gene interactions were identified for each of the segregating virulence phenotypes. Of 27 dominant virulence genes identified, 17 were mapped to two chromosomes. Markers tightly linked to some of the virulence loci may facilitate further studies to clone these genes. The virulence genes and their inheritance information are useful for understanding the host−pathogen interactions and for selecting effective resistance genes or gene combinations for developing stripe rust resistant wheat cultivars.

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

International Journal of Molecular Sciences ◽

10.3390/ijms21051685 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1685 ◽

Cited By ~ 2

Author(s):

Sajid Mehmood ◽

Marina Sajid ◽

Syed Kamil Husnain ◽

Jie Zhao ◽

Lili Huang ◽

...

Keyword(s):

Stripe Rust ◽

Puccinia Striiformis ◽

Single Gene ◽

Dominant Gene ◽

Wheat Varieties ◽

Parental Isolate ◽

The One ◽

Almost All ◽

Simple Sequence ◽

Dominant Genes

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.

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Races of Puccinia striiformis f. sp. tritici in the United States in 2011 and 2012 and Comparison with Races in 2010

Plant Disease ◽

10.1094/pdis-10-15-1122-re ◽

2016 ◽

Vol 100 (5) ◽

pp. 966-975 ◽

Cited By ~ 47

Author(s):

Anmin Wan ◽

Xianming Chen ◽

Jonathan Yuen

Keyword(s):

United States ◽

Stripe Rust ◽

Resistance Genes ◽

Puccinia Striiformis ◽

Single Gene ◽

Durable Resistance ◽

The United States ◽

Western United States ◽

Adult Plant ◽

Low Frequencies

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases on wheat in the United States. In 2011, severe wheat stripe rust caused extensive application of fungicides in the western United States, and the disease was more widespread and caused more yield loss in the eastern United States in 2012. In this study, we characterized virulences and identified races of P. striiformis f. sp. tritici by testing the stripe rust samples collected throughout the United States in 2011 and 2012 on a set of 18 Yr single-gene differentials. In 2011, 35 races were identified from 349 viable samples collected from 19 states of the United States and Ontario province of Canada, with PSTv-11 (35.5%), PSTv-37 (12.6%), PSTv-14 (11.8%), PSTv-4 (5.4%), and PSTv-34 (3.4%) as the top five predominant races. In 2012, 23 races were identified from 341 viable samples collected from 24 states of the United States and Ontario of Canada, with PSTv-37 (47.5%), PSTv-11 (11.7%), PSTv-14 (10.0%), PSTv-52 (9.4%), and PSTv-48 (4.4%) as the top five predominant races. Nationally, PSTv-37, PSTv-52, and PSTv-34 were most widely distributed, while PSTv-11, PSTv-14, PSTv-4, and PSTv-48 were mostly detected in the western United States. High frequencies (>80%) were detected for virulences to Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr44, and YrExp2; moderate frequencies (20 to 80%) for virulences to Yr1, Yr43, YrTr1, and YrTye; low frequencies (<10%) for virulences to Yr10, Yr24, Yr32, and YrSP; and virulences to Yr5 and Yr15 were not detected, indicating that these two genes are still effective against the P. striiformis f. sp. tritici population in the United States. Both positive and negative associations were identified between some of the virulences. In total, 55 races identified from 2010 to 2012 in the United States were clustered into two major virulence groups, and dynamics of predominant races and virulence frequencies for the 3 years were presented and discussed. This information is useful for making decisions when screening wheat germplasm for developing stripe-rust-resistant wheat cultivars and managing the disease by growing cultivars with adequate and durable resistance. The severe epidemics and the occurrence of the large number of races in the 3 years indicate that efforts should be made to use diverse resistance genes, especially to combine effective all-stage resistance genes with genes for high-temperature adult-plant resistance.

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Changes of Races and Virulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, in the United States from 1968 to 2009

Plant Disease ◽

10.1094/pdis-12-16-1786-re ◽

2017 ◽

Vol 101 (8) ◽

pp. 1522-1532 ◽

Cited By ~ 21

Author(s):

Tinglan Liu ◽

Anmin Wan ◽

Dengcai Liu ◽

Xianming Chen

Keyword(s):

United States ◽

Stripe Rust ◽

Virulence Genes ◽

Puccinia Striiformis ◽

Yellow Rust ◽

Single Gene ◽

The United States ◽

Wheat Cultivars ◽

New Races ◽

Serious Disease

Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici, is a serious disease of wheat in the world. The obligate biotrophic fungal pathogen changes its virulence rapidly, which can circumvent resistance in wheat cultivars and cause severe epidemics. Because P. striiformis f. sp. tritici races have been identified in the United States using different wheat genotypes in different time periods, it is difficult to make direct comparisons of the current population with historical populations. The objective of this study was to characterize historical populations with 18 Yr single-gene lines that are currently used to differentiate P. striiformis f. sp. tritici races in order to understand virulence and race changes of the pathogen over 40 years in the United States. From 908 P. striiformis f. sp. tritici isolates collected from 1968 to 2009 in the United States, 171 races were identified and their frequencies were determined. More races, more new races, and races with more virulence genes were detected since the year 2000 than prior to 2000. None of the races were virulent to Yr5 and Yr15, indicating that these genes have been effective since the late 1960s. Virulence genes to the remaining 16 Yr genes were detected in different periods, and most of them increased in frequency over time. Some virulence genes such as those to Yr17, Yr27, Yr32, Yr43, Yr44, YrTr1, and YrExp2 appeared 14 to 37 years earlier than previously reported, indicating the greater value of using Yr single-gene lines as differentials. Positive and negative associations were detected between virulence genes. The continual information on virulence and races in the P. striiformis f. sp. tritici populations is useful for understanding the evolution of the pathogen and for breeding wheat cultivars with effective resistance to stripe rust.

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Inheritance of Virulence and Linkages of Virulence Genes in an Ethiopian Isolate of the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Determined Through Sexual Recombination on Berberis holstii (Retracted)

Plant Disease ◽

10.1094/pdis-02-19-0269-re ◽

2019 ◽

Vol 103 (9) ◽

pp. 2451-2459 ◽

Cited By ~ 3

Author(s):

Gebreslasie Zeray Siyoum ◽

Qingdong Zeng ◽

Jie Zhao ◽

Xianming Chen ◽

Ayele Badebo ◽

...

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Resistance Genes ◽

Puccinia Striiformis ◽

Dominant Gene ◽

Wheat Diseases ◽

Rust Pathogen ◽

Parental Isolate ◽

Dominant Genes ◽

Yr Genes

The authors of Siyoum et al. 103:2451-2459 (2019) retracted this article because it proved to contain errors in statistical analyses of the data and subsequent data interpretations. This article was retracted on 14 November 2019. Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating wheat diseases in Ethiopia. To study virulence genetics of the pathogen, 117 progeny isolates were produced through sexual reproduction of an Ethiopian isolate of the stripe rust pathogen on Berberis holstii plants under controlled conditions. The parental and progeny isolates were characterized by phenotyping on wheat lines carrying single Yr genes for resistance and genotyped using 10 polymorphic simple sequence repeated (SSR) markers. The progeny isolates were classified into 37 virulence phenotypes and 75 multilocus genotypes. The parental isolate and progeny isolates were all avirulent to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrTr1, YrSP, and Yr76 but virulent to Yr1 and Yr2, indicating that the parental isolate was homozygous avirulent or homozygous virulent at these loci. The progeny isolates segregated for virulence to 12 Yr genes. Virulence phenotypes to Yr6, Yr28, Yr43, and Yr44 were controlled by a single dominant gene; those to Yr7, Yr9, Yr17, Yr27, Yr25, Yr31, and YrExp2 were each controlled by two dominant genes; and the virulence phenotype to Yr8 was controlled by two complementary dominant genes. A linkage map was constructed with seven SSR markers, and 16 virulence loci corresponding to 11 Yr resistance genes were mapped with some loci linked to each other. These results are useful in understanding host–pathogen interactions and selecting resistance genes to develop wheat cultivars with highly effective resistance to stripe rust.

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Molecular Mapping of Stripe Rust Resistance Gene Yr76 in Winter Club Wheat Cultivar Tyee

Phytopathology ◽

10.1094/phyto-01-16-0045-fi ◽

2016 ◽

Vol 106 (10) ◽

pp. 1186-1193 ◽

Cited By ~ 28

Author(s):

C. Xiang ◽

J. Y. Feng ◽

M. N. Wang ◽

X. M. Chen ◽

D. R. See ◽

...

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Molecular Mapping ◽

Mapping Population ◽

Puccinia Striiformis ◽

Single Gene ◽

Dominant Gene ◽

The United States ◽

Stripe Rust Resistance ◽

Isogenic Line

Tyee, one of the wheat cultivars used to differentiate races of Puccinia striiformis f. sp. tritici in the United States, was identified to have a single gene for all-stage resistance, tentatively named YrTye. To map the gene, Tyee was crossed with ‘Avocet Susceptible’ (AvS). Genetic analysis of the F1, F2, F2:3, and BC1 progenies confirmed a single dominant gene for resistance to race PSTv-37 that is avirulent to YrTye. A mapping population of 135 F2 plants was phenotyped with PSTv-37 and the derived F2:3 lines were tested with races PSTv-37, PSTv-40, and PSTv-79. The F2 mapping population was genotyped with simple sequence repeat (SSR) markers. A genetic map comprising 13 SSR markers located YrTye in chromosome 3AS flanked distally by SSR marker wmc11 and proximally by wmc532 at 2.6 and 3.4 cM, respectively. Amplification of Chinese Spring 3A deletion lines placed the gene in the distal bin 3AS4-0.45 to 1.00. Because YrTye is different from all formally named Yr genes in chromosomal location, we permanently name the gene Yr76. A near-isogenic line of spring common wheat was developed and selected by testing F3 lines derived from a AvS*4/Tyee cross with Tyee-avirulent and virulent races and the flanking markers. The specific SSR alleles flanking Yr76 were validated using cultivars and breeding lines with and without the gene, and showed high polymorphisms. The specificity of Yr76 is useful in differentiating P. striiformis f. sp. tritici races, and its tightly linked markers will be useful in developing resistant cultivars when combining the gene with other genes for resistance to stripe rust.

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Genetic Mapping of Powdery Mildew Resistance Genes in Wheat Landrace ‘Guizi 1’ Using Genotyping-By-Sequencing

10.21203/rs.3.rs-1031772/v1 ◽

2021 ◽

Author(s):

Luhua Li ◽

Xicui Yang ◽

Zhongni Wang ◽

Mingjian Ren ◽

Chang An ◽

...

Keyword(s):

Powdery Mildew ◽

Resistance Genes ◽

Quantitative Trait ◽

Powdery Mildew Resistance ◽

Dominant Gene ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Phenotypic Variance ◽

Nucleotide Polymorphisms ◽

Mildew Resistance

Abstract Wheat powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease of wheat (Triticum aestivum L.) worldwide that causes severe yield losses. Resistant wheat cultivars easily lose effective resistance against newly emerged Bgt strains; therefore, identifying new resistance genes is necessary for breeding resistant cultivars. ‘Guizi 1’ is a Chinese wheat cultivar with effective moderate and stable resistance against powdery mildew. A genetic analysis indicated that powdery mildew resistance in ‘Guizi 1’ was controlled by a single dominant gene, designated PmGZ1. In total, 110 F2 individual plants and the 2 parents were used for genotyping-by-sequencing, which produced 23,134 high-quality single-nucleotide polymorphisms (SNPs). The SNP distributions on the 21 chromosomes ranged from 134 on chromosome 6D to 6,288 on chromosome 3B. Chromosome 6A has 1,866 SNPs, among which 16 are located in a physical region between positions 307,802,221 and 309,885,836 in an approximate 2.3-cM region, which possessed the greatest SNP density. The average map distance between SNP markers was 0.1 cM. A quantitative trait locus with a significant epistatic effect on powdery mildew resistance was mapped to Chromosome 6A. The LOD value of PmGZ1 reached 34.8, and PmGZ1 was located within the confidence interval marked by chr6a-307802221 and chr6a-309885836. The phenotypic variance explained by PmGZ1 was 74.7%. Four candidate genes (two each encoding TaAP2-A and actin proteins) were annotated as resistance genes. The present results provide valuable information for wheat genetic improvement, quantitative trait loci fine mapping, and candidate gene validation.

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Identification and Mapping of QTL for Stripe Rust Resistance in the Chinese Wheat Cultivar Shumai126

Plant Disease ◽

10.1094/pdis-09-21-1946-re ◽

2021 ◽

Author(s):

Yufan Wang ◽

Yanling Hu ◽

Fangyi Gong ◽

Yarong Jin ◽

Yingjie Xia ◽

...

Keyword(s):

Stripe Rust ◽

Resistance Genes ◽

Rust Resistance ◽

Puccinia Striiformis ◽

Wheat Cultivar ◽

Single Nucleotide Polymorphism Array ◽

Recombinant Inbred Lines ◽

Snp Markers ◽

Growth Chamber ◽

Stripe Rust Resistance

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a damaging disease of wheat globally, and breeding resistant cultivars is the best control strategy. The Chinese winter wheat cultivar Shumai126 (SM126) exhibited strong resistance to P. striiformis f. sp. tritici in the field for more than ten years. The objective of this study was to identify and map quantitative trait loci (QTL) for resistance to stripe rust in a population of 154 recombinant inbred lines (RILs) derived from a cross between cultivars Taichang29 (TC29) and SM126. The RILs were tested in six field environments with a mixture of the Chinese prevalent races (CYR32, CYR33, CYR34, Zhong4, and HY46) of P. striiformis f. sp. tritici and in growth chamber with race CYR34 and genotyped using the Wheat55K SNP (single nucleotide polymorphism) array. Six QTL were mapped on chromosomes 1BL, 2AS, 2AL, 6AS, 6BS, and 7BL, respectively. All these QTL were contributed by SM126 except QYr.sicau-2AL. The QYr.sicau-1BL and QYr.sicau-2AS had major effects, explaining 27.00-39.91% and 11.89-17.11% of phenotypic variances, which may correspond to known resistance genes Yr29 and Yr69, respectively. The QYr.sicau-2AL, QYr.sicau-6AS, and QYr.sicau-6BS with minor effects are likely novel. QYr.sicau-7BL was only detected based on growth chamber seedling data. Additive effects were detected for the combination of QYr.sicau-1BL, QYr.sicau-2AS, and QYr.sicau-2AL. SNP markers linked to QYr.sicau-1BL (AX-111056129 and AX-108839316) and QYr.sicau-2AS (AX-111557864 and AX-110433540) were converted to breeder-friendly KASP (Kompetitive allele-specific PCR) markers that would facilitate the deployment of stripe rust resistance genes in wheat breeding.

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Rapid identification of a stripe rust resistance gene YrXK in Chinese wheat line Xike01015 using specific locus amplified fragment (SLAF) sequencing

Plant Disease ◽

10.1094/pdis-12-20-2648-re ◽

2021 ◽

Author(s):

Cai Sun ◽

Yike Liu ◽

Qiang Li ◽

Baotong Wang ◽

Shuhui Chen ◽

...

Keyword(s):

Stripe Rust ◽

Puccinia Striiformis ◽

Gene Annotation ◽

Dominant Gene ◽

Rapid Identification ◽

Wheat Breeding ◽

Stripe Rust Resistance ◽

Phenotypic Variance ◽

F2 Population ◽

Chinese Wheat

Wheat stripe rust, an airborne fungal disease and caused by Puccinia striiformis Westend. f. sp. tritici (Pst), is one of the most devastating diseases on wheat. It is the most effective and economical measure for the diseases control to identify high-level resistance genes and apply in wheat breeding. Chinese wheat cultivar Xike01015 presents high levels of all stage resistance (ASR) to the current predominant Pst race CYR33. In this study, a single dominant gene, designated as YrXk, was identified in Xike01015 conferring resistance to CYR33 with genetic analysis of F2 and BC1 population from cross of Mingxian169 (susceptible) and Xike01015. The specific length amplified fragment sequencing (SLAF-seq) strategy was used to construct linkage map in the F2 population. QTL analysis mapped YrXk to a 12.4 Mb segment on chromosome1BS, explaining over 86.96% phenotypic variance. Gene annotation in the QTL region identified three differential expressed candidate genes , TraesCS1B02G168600.1, TraesCS1B02G170200.1, and TraesCS1B02G172400.1. The qRT-PCR results displayed that TraesCS1B02G170200.1 and TraesCS1B02G168600.1 significantly up-regulated and down-regulated, respectively, and TraesCS1B02G170200.1 slightly up-regulated after changed with CYR33 in the seedling stage, which indicating these genes may function in wheat resistance to stripe rust. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

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Allelic analysis of stripe rust resistance genes on wheat chromosome 2BS

Genome ◽

10.1139/g08-079 ◽

2008 ◽

Vol 51 (11) ◽

pp. 922-927 ◽

Cited By ~ 35

Author(s):

P. G. Luo ◽

X. Y. Hu ◽

Z. L. Ren ◽

H. Y. Zhang ◽

K. Shu ◽

...

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Resistance Genes ◽

Rust Resistance ◽

Dominant Gene ◽

Wheat Chromosome ◽

Stripe Rust Resistance ◽

Resistance Response ◽

Rust Resistance Genes ◽

Yr Genes

Stripe rust, caused by Puccinia striiormis Westend f. sp. tritici, is one of the most important foliar diseases of wheat ( Triticum aestivum L.) worldwide. Stripe rust resistance genes Yr27, Yr31, YrSp, YrV23, and YrCN19 on chromosome 2BS confer resistance to some or all Chinese P. striiormis f. sp. tritici races CYR31, CYR32, SY11-4, and SY11-14 in the greenhouse. To screen microsatellite (SSR) markers linked with YrCN19, F1, F2, and F3 populations derived from cross Ch377/CN19 were screened with race CYR32 and 35 SSR primer pairs. Linkage analysis indicated that the single dominant gene YrCN19 in cultivar CN19 was linked with SSR markers Xgwm410, Xgwm374, Xwmc477, and Xgwm382 on chromosome 2BS with genetic distances of 0.3, 7.9, 12.3, and 21.2 cM, respectively. Crosses of CN19 with wheat lines carrying other genes on chromosome 2B showed that all were located at different loci. YrCN19 is thus different from the other reported Yr genes in chromosomal location and resistance response and was therefore named Yr41. Prospects and strategies of using Yr41 and other Yr genes in wheat improvement for stripe rust resistance are discussed.

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The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics

Nature Communications ◽

10.1038/s41467-021-27288-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jan Bettgenhaeuser ◽

Inmaculada Hernández-Pinzón ◽

Andrew M. Dawson ◽

Matthew Gardiner ◽

Phon Green ◽

...

Keyword(s):

Powdery Mildew ◽

Stripe Rust ◽

Resistance Genes ◽

Host Species ◽

Plant Pathogens ◽

Puccinia Striiformis ◽

Species Specificity ◽

Wheat Stripe Rust ◽

Barley Powdery Mildew ◽

Barley Stripe Rust

AbstractCrop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes, Rps6, Rps7, and Rps8, contribute to immunity in barley to wheat stripe rust. Rps7 cosegregates with barley powdery mildew resistance at the Mla locus. Using transgenic complementation of different Mla alleles, we confirm allele-specific recognition of wheat stripe rust by Mla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.

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