Variation and Distribution of the Oat Crown Rust-Fungus, Puccinia Coronata Avenae,in Britain in Relation to Breeding Resistant Oat Cultivars

1986 ◽  
pp. 81-82
Author(s):  
B. C. Clifford
Keyword(s):  
Rust Fungus ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Oat Crown Rust ◽  
Puccinia Coronata Avenae ◽  
Oat Cultivars

scholarly journals De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Marisa E. Miller ◽  
Ying Zhang ◽  
Vahid Omidvar ◽  
Jana Sperschneider ◽  
Benjamin Schwessinger ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Haplotype Diversity ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Oat Crown Rust

ABSTRACT Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae. IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae.

scholarly journals Crown rust pathotypes determined on oats in the Czech Republic from 2004 to 2006 and reaction to oat cultivars

2008 ◽  
Vol 44 (No. 2) ◽  
pp. 60-65 ◽  
Author(s):  
H. Jiráková ◽  
A. Hanzalová
Keyword(s):  
Czech Republic ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Resistance Breeding ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
The Czech Republic ◽  
Oat Crown Rust ◽  
Oat Cultivars ◽  
High Diversity

The incidence of oat crown rust (Puccinia coronata var. avenae Fraser et Ledingham) pathotypes was recorded in the Czech Republic in 2004–2006. The virulence of collected 79 monopustule oat crown rust isolates was assessed on 23 differentials. High diversity was observed; the isolates possessed from 0 to 8 virulence genes. More than 80% of pathotypes were recorded only once. Pathotypes BLBG and BLBC were the most frequent. None of the tested isolates was virulent to resistance genes Pc39, Pc50, Pc52, Pc59, Pc62 and Pc68. Registered cultivars Avenuda, Dalimil, Auron, Isak were susceptible to the majority of pathotypes, cvs. Abel, Ardo, Atego, Azur, Neklan, Radius and Saul to all used pathotypes. Only the Czech cultivar Vok was resistant to all but four used pathotypes. Acquired data are useful for resistance breeding.

scholarly journals De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

2017 ◽  
Author(s):  
Marisa E. Miller ◽  
Ying Zhang ◽  
Vahid Omidvar ◽  
Jana Sperschneider ◽  
Benjamin Schwessinger ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rust Fungus ◽  
Expression Patterns ◽  
Haplotype Diversity ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Oat Crown Rust

AbstractOat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle, Pca is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two Pca isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for a total assembly length of 99.16 Mbp for 12SD80 and 777 primary contigs with a total length of 105.25 Mbp for 12NC29, and approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of co-expressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in Pca.ImportanceDisease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae (Pca), which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding Pca, resources to study the molecular mechanisms underpinning pathogenicity and emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of Pca as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of Pca.

scholarly journals Virulence in Oat Crown Rust (Puccinia coronata f. sp. avenae) in the United States from 2006 through 2009

Plant Disease ◽  
2011 ◽  
Vol 95 (12) ◽  
pp. 1528-1534 ◽  
Author(s):  
M. L. Carson
Keyword(s):  
United States ◽  
Resistance Genes ◽  
The United States ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
The North ◽  
Oat Crown Rust ◽  
Primary Means ◽  
Oat Cultivars ◽  
The U.S

The use of race-specific seedling genes for resistance is the primary means of controlling crown rust of oat (Puccinia coronata f. sp. avenae) in the United States. To better utilize those resistance genes, knowledge of the occurrence and frequency of corresponding virulence in the population of P. coronata f. sp. avenae in the United States is essential. In total, 571 single-pustule isolates of oat crown rust were collected from cultivated and wild oat (Avena sativa and A. fatua, respectively) in the major oat production areas of the United States from 2006 through 2009. They were tested for virulence on seedlings of 31 differential oat lines in the greenhouse. In all, 201 races were found among the 357 isolates from the spring oat region of the north-central United States, and 140 races were found among 214 isolates from the southern winter oat region. The crown rust populations from the winter and spring oat regions were clearly differentiated from one another, differing in the frequency of virulence for 24 of the 31 differentials. Some virulence associations previously reported in the U.S. oat crown rust population were also found in both regions in this survey, even when the dataset was clone corrected. Associations between virulence to the Pc genes were predominately positive in both regions but both positive and negative associations occurred more frequently in the winter oat region, where sexual reproduction does not occur. Some of the virulence diversity in the oat crown rust population in the United States can be related to the deployment of resistance genes in commercial oat cultivars and virulence associations existing in the oat crown rust population. When data from a previous report covering 2001 through 2005 is combined with data reported in this article, the mean virulence of the U.S. populations of crown rust continued to increase from 2001 to 2009. Virulence to Pc38, Pc39, Pc45, Pc48, Pc52, Pc55, Pc56, Pc57, Pc59, Pc62, Pc63, Pc64, Pc68, and Pc96 significantly increased in one or both regions during this time period. No significant declines in virulence frequency were found in either region. Genes for crown rust resistance derived from A. sterilis appear to be as rapidly defeated as has happened to Pc genes from A. sativa. There is an urgent need to find additional sources of effective resistance to P. coronata f. sp. avenae and introgress it into adapted oat cultivars.

INHERITANCE OF RESISTANCE TO PUCCINIA CORONATA AVENAE AND ITS ASSOCIATION WITH SEED CHARACTERISTICS IN FOUR ACCESSIONS OF AVENA STERILIS

1976 ◽  
Vol 18 (4) ◽  
pp. 717-726 ◽  
Author(s):  
F. A. Kiehn ◽  
R. I. H. McKenzie ◽  
D. E. Harder
Keyword(s):  
Dominant Gene ◽  
Recessive Gene ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Seed Color ◽  
Inheritance Of Resistance ◽  
Avena Sterilis ◽  
Seedling Resistance ◽  
Oat Crown Rust ◽  
Puccinia Coronata Avenae

The inheritance of resistance to oat crown rust Puccinia coronata Cda. f. sp. avenae Eriks. was studied in four accessions of Avena sterilis L. Three of the accessions, CAV 4963, CAV 1358 and CAV 1376, originated from Israel, and one, CAV 1964, from Algeria. Seedling rust tests on F2 backcross families indicated that a single recessive gene, Pc-55, in CAV 4963 conditioned seedling resistance to 10 of 12 crown rust isolates tested. In CAV 1964, a single dominant gene Pc-56 conferred resistance in both the adult and seedling stages to all crown rust isolates tested except race 239, while a second dominant gene conditioned resistance to only two of the twelve cultures used. From adult and seedling tests it appeared that the resistance in CAV 1358 and CAV 1376 was conditioned by a number of recessive minor additive genes. The genes Pc-55 and Pc-56 are not allelic with the A. sterilis derived genes Pc-35, Pc-38, Pc-40, Pc-45, Pc-46, Pc-47, Pc-48, and Pc-50. Genes Pc-39 and Pc-55 are either very closely linked or allelic and Pc-56 is not closely linked to either Pc-39 or Pc-55. The usefulness of genes Pc-55 and Pc-56 was demonstrated in tests which showed that both genes were effective against 99.8 and 94.5%, respectively, of all crown rust cultures isolated in Canada in 1974 and 1975. The genes for seed color and awn character did not appear to be linked to the crown rust resistance genes. In CAV 4963, CAV 1358 and CAV 1376 the genes for grey color and wild type awns appeared to be linked with recombination values of about 2, 23 and 18%, respectively.

scholarly journals Diversity of oat crown rust (Puccinia coronata f.sp. avenae) isolates detected by virulence and AFLP analyses

2010 ◽  
Vol 46 (No. 3) ◽  
pp. 98-106 ◽  
Author(s):  
H. Klenová-Jiráková ◽  
L. Leišová-Svobodová ◽  
A. Hanzalová ◽  
L. Kučera
Keyword(s):  
Virulence Genes ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Aflp Analysis ◽  
Avirulence Genes ◽  
Correlation Relationship ◽  
Oat Crown Rust ◽  
Molecular Pattern ◽  
Oat Cultivars ◽  
Relationship Of

Forty Puccinia coronata f.sp. avenae isolates from several European countries and Israel were tested for virulence to 18 differential oat lines. Amplified Fragment Length Polymorphism (AFLP) analysis was used to evaluate diversity among the studied isolates. Twenty-nine different pathotypes were identified. The prevailing occurrence of pathotypes with a limited number of virulence genes may indicate that oat cultivars grown in Europe possess the limited number of resistance genes. A total of 501 AFLP polymorphic fragments were scored in the studied isolates using twelve primer combinations. All isolates had the unique AFLP molecular pattern. The genetic similarity of isolates from Serbia. Austria and from the Czech Republic indicates that oat crown rust urediniospores may often migrate to particular areas. The number of virulence genes in isolates also seems to play an important role in the clustering. Most isolates possessing a lower number of virulence genes (0–4) were grouped into two clusters, whereas another cluster was composed of a majority of isolates with 4–7 virulence genes. A significant correlation relationship of 0.187 (P = 0.007) was found between AFLP and virulence/avirulence genes based on distance matrices.

scholarly journals Virulence of Oat Crown Rust in Brazil and Uruguay

Plant Disease ◽  
2005 ◽  
Vol 89 (8) ◽  
pp. 802-808 ◽  
Author(s):  
K. J. Leonard ◽  
J. A. Martinelli
Keyword(s):  
Avena Sativa ◽  
Western Siberia ◽  
Specific Resistance ◽  
The United States ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
South American ◽  
Oat Crown Rust ◽  
High Virulence ◽  
Important Disease

Race-specific resistance to crown rust, the most important disease of oat (Avena sativa) in Bra-zil, often fails within a few years of use in Brazilian cultivars. Virulence of 144 isolates of Puccinia coronata from cultivated oat in Brazil in 1997 to 1999 and 36 isolates from Uruguay in 1994-95 and 1998 was tested on a set of 27 oat crown rust differentials lines, each with a different Pc gene for race-specific resistance. Frequencies of virulence and mean virulence complexity were compared among these five collections from Brazil and Uruguay as well as with mean virulence complexity for a collection of 17 isolates from cultivated oat in western Siberia in Russia. Virulence-avirulence for each of the 27 Pc genes was polymorphic in both Brazil and Uruguay. Virulence frequencies were similar for collections from Brazil in 1998 and 1999 and for the collection from Uruguay from 1998, but there were large differences between the 1997 collection and the 1998 and 1999 collections from Brazil. Mean virulence complexity in both Brazil and Uruguay was greater than reported in the United States and much greater than in the Russian collection of P. coronata. A large number of races of P. coronata were found, with no more than five isolates of any race found in a single year in Brazil or Uruguay. The high virulence complexity and great diversity of virulence polymorphisms in Brazil and Uruguay make it unlikely that race-specific resistance can be effective there even though the South American populations of P. coronata are apparently entirely asexual.

Assessment of virulence patterns in crown rust populations

1968 ◽  
Vol 46 (5) ◽  
pp. 613-617 ◽  
Author(s):  
George Fleischmann
Keyword(s):  
Crown Rust ◽  
Puccinia Coronata ◽  
Western Canada ◽  
Differential Host ◽  
Oat Crown Rust ◽  
Virulence Pattern ◽  
Continued Use ◽  
Race Identification

Two methods of determining the virulence pattern of oat crown rust, Puccinia coronata f. sp. avenae, populations collected in 1965, 1966, and 1967, in Eastern and Western Canada were compared. The results with a single-pustule isolate from each of 50 field collections were as accurate as those obtained with two single-pustule isolates from 100 or more field collections. The continued use of Bond and Ukraine as differential host varieties is of little value except for purposes of race identification, because they are attacked by most of the isolates.

INHERITANCE OF CROWN RUST RESISTANCE GENES IN AVENA STERILIS COLLECTIONS FROM ISRAEL, PORTUGAL, AND TUNISIA

1971 ◽  
Vol 13 (2) ◽  
pp. 251-255 ◽  
Author(s):  
G. Fleischmann ◽  
R. I. H. McKenzie ◽  
W. A. Shipton
Keyword(s):  
Resistance Genes ◽  
Rust Resistance ◽  
Dominant Gene ◽  
Crown Rust ◽  
Puccinia Coronata ◽  
Avena Sterilis ◽  
Wild Oats ◽  
Puccinia Coronata Avenae ◽  
Dominant Genes ◽  
Rust Resistance Genes

The inheritance of genes in three collections of Avena sterilis wild oats conferring resistance to races 216, 264, 295, 305, 326, 330, 332, and 446 of crown rust, Puccinia coronata avenae, was investigated. C. I. 8081 from Portugal contained a partially dominant gene, designated Pc47, which conferred resistance to all eight races. CW486 from Tunisia had a dominant gene, designated Pc50, which gave resistance to all races except 295, 326, and 446. F158 from Israel had two dominant genes; one, designated Pc48, conferred resistance to all the races but 305, while the second, designated Pc49, conferred resistance to races 216, 326, 330, 332, and 446. Genes Pc47, Pc48, Pc49, and Pc50 were inherited independently of each other and of those genes previously isolated from A. sterilis.

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