A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution

Despite the global economic importance of the wheat leaf rust pathogen Puccinia triticina (Pt), genomic resources for Pt are limited and chromosome-level assemblies of Pt are lacking. Here, we present a complete haplotype-resolved genome assembly at a chromosome-scale for Pt using the Australian pathotype 64-(6),(7),(10),11 (Pt64; North American race LBBQB) built upon the newly developed technologies of PacBio and Hi-C sequencing. PacBio reads with ∼200-fold coverage (29.8 Gb data) were assembled by Falcon and Falcon-unzip and subsequently scaffolded with Hi-C data using Falcon-phase and Proximo. This approach allowed us to construct 18 chromosome pseudomolecules ranging from 3.5 to 12.3 Mb in size for each haplotype of the dikaryotic genome of Pt64. Each haplotype had a total length of ∼147 Mb, scaffold N50 of ∼9.4 Mb, and was ∼93% complete for BUSCOs. Each haplotype had ∼29,800 predicted genes, of which ∼2,000 were predicted as secreted proteins (SPs). The investigation of structural variants (SVs) between haplotypes A and B revealed that 10% of the total genome was spanned by SVs, highlighting variations previously undetected by short-read based assemblies. For the first time, the mating type (MAT) genes on each haplotype of Pt64 were identified, which showed that MAT loci a and b are located on two chromosomes (chromosomes 7 and 14), representing a tetrapolar type. Furthermore, the Pt64 assembly enabled haplotype-based evolutionary analyses for 21 Australian Pt isolates, which highlighted the importance of a haplotype resolved reference when inferring genetic relationships using whole genome SNPs. This Pt64 assembly at chromosome-scale with full phase information provides an invaluable resource for genomic and evolutionary research, which will accelerate the understanding of molecular mechanisms underlying Pt-wheat interactions and facilitate the development of durable resistance to leaf rust in wheat and sustainable control of rust disease.

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Efficacy of plant extracts in controlling wheat leaf rust disease caused by Puccinia triticina

Egyptian Journal of Basic and Applied Sciences ◽

10.1016/j.ejbas.2016.09.002 ◽

2017 ◽

Vol 4 (1) ◽

pp. 67-73 ◽

Cited By ~ 11

Author(s):

Yasser M. Shabana ◽

Mohamed E. Abdalla ◽

Atef A. Shahin ◽

Mohammed M. El-Sawy ◽

Ibrahim S. Draz ◽

...

Keyword(s):

Leaf Rust ◽

Plant Extracts ◽

Puccinia Triticina ◽

Wheat Leaf Rust ◽

Rust Disease ◽

Wheat Leaf

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Dissecting the first phased dikaryotic genomes of the wheat rust pathogen Puccinia triticina reveals the mechanisms of somatic exchange in nature

10.1101/705475 ◽

2019 ◽

Cited By ~ 2

Author(s):

Jing Qin Wu ◽

Chongmei Dong ◽

Long Song ◽

Christina A. Cuomo ◽

Robert F. Park

Keyword(s):

Leaf Rust ◽

Somatic Hybridization ◽

Puccinia Triticina ◽

Genomic Variation ◽

Hybrid Wheat ◽

Wheat Cultivars ◽

Wheat Leaf Rust ◽

Virulence Evolution ◽

Rust Pathogen ◽

Wheat Leaf

AbstractAlthough somatic hybridization (SH) has been proposed as a means of accelerating rust pathogen virulence evolution in the absence of sexual recombination, previous studies are limited to the laboratory and none have revealed how this process happens. Using long-read sequencing, we generated dikaryotic phased genomes and annotations for three Australian field-collected isolates of the wheat leaf rust pathogen (Puccinia triticina; Pt), including a putative asexual hybrid (Pt64) and two putative parental isolates (Pt104 and Pt53; 132-141 Mb,155-176 contigs, N50 of 1.9-2.1 Mb). The genetic dissection based on the high-quality phased genomes including whole-genome alignments, phylogenetic and syntenic analyses along with short-read sequencing of 27 additional Pt isolates convergently demonstrated that Pt64, which rendered several commercial hybrid wheat cultivars susceptible to leaf rust, arose from SH between isolates within the Pt53 and Pt104 lineages. Parentage analysis demonstrated the role of mitotic crossover in the derivation of both nuclei of Pt64. Within HD mating type genes, the distinct specificity regions in Pt64 and the distinct phylogenetic pattern of the remaining admixed isolates suggested high genetic variation in specificity-related regions on the b locus intrinsically associated with the SH. This study not only provided a fundamental platform for investigating genomic variation underlying virulence evolution in one of the most devastating wheat pathogens, but also offered an in-depth understanding of the mechanisms of naturally occurring SH. This asexual mechanism can be broadly exploited by any dikaryotic pathogen to accelerate virulence evolution, and understanding this process is both urgent and crucial for sustainable pathogen control.ImportanceStrategies to manage plant rust pathogens are challenged by the constant emergence of new virulence. Although somatic hybridization has been proposed as a means by which rusts could overcome host resistance rapidly and cause crop loss, there is very little evidence of this process in nature and the mechanisms underlying it are not known. This study generated and analysed the first dikaryotic phased genomes of the wheat leaf rust pathogen, identifying an isolate as a hybrid and for the first time unveiling parasexuality via mitotic crossover in a rust pathogen. The erosion of the resistance of several hybrid wheat cultivars in agriculture by the hybrid rust has important implications for breeding efforts targeting durable resistance and sustained rust control.

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Virulence and molecular polymorphisms of the wheat leaf rust fungus Puccinia triticina in Canada from 1997 to 2007

Botany ◽

10.1139/b10-034 ◽

2010 ◽

Vol 88 (6) ◽

pp. 575-589 ◽

Cited By ~ 16

Author(s):

Xiben Wang ◽

Guus Bakkeren ◽

Brent McCallum

Keyword(s):

Leaf Rust ◽

Expressed Sequence Tag ◽

Rust Fungus ◽

Puccinia Triticina ◽

Leaf Rust Resistance ◽

Significant Shift ◽

Wheat Leaf Rust ◽

Rust Disease ◽

The Pacific ◽

Wheat Leaf

Populations of Puccinia triticina , one of the casual agents of wheat leaf rust disease, in the pacific (British Columbia and Alberta), prairie (Manitoba and Saskatchewan), and eastern regions (Quebec and Ontario) of Canada from 1997 to 2007 were analyzed for virulence and genetic diversity by revealing expressed sequence tag derived simple sequence repeat (EST-SSR) polymorphisms. Since 1997, a significant shift in the virulence of P. triticina occurred across Canada. The diversity of P. triticina virulence phenotypes in Manitoba and Saskatchewan, as measured by Shannon and Simpson indexes, decreased due to the directional selection toward predominant virulence phenotypes, whereas it remained relatively constant in Quebec and Ontario. The clustering of P. triticina virulence phenotypes from 1997 to 2007 was similar to that found in previous years, and was correlated with virulence to leaf rust resistance genes Lr2a, Lr2c, and Lr17a. Distinct EST-SSR profiles were found in different groups of P. triticina virulence phenotypes based on virulence to Lr2a, Lr2c, and Lr17a. In addition, the population of P. triticina in Manitoba and Saskatchewan was different from that in Quebec and Ontario from 1997 to 2007, based on both virulence characteristics and EST-SSR genotypes.

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Durable resistance to Puccinia triticina by accumulation of resistance genes

Genetika ◽

10.2298/gensr0903355b ◽

2009 ◽

Vol 41 (3) ◽

pp. 353-378 ◽

Cited By ~ 2

Author(s):

Jelena Boskovic ◽

Momcilo Boskovic

Keyword(s):

Leaf Rust ◽

Resistance Genes ◽

Durable Resistance ◽

Puccinia Triticina ◽

Recurrent Parent ◽

Considerable Influence ◽

Wheat Leaf Rust ◽

Resistant Genes ◽

Wheat Leaf ◽

Hybrid Lines

The individual use of single race-specific resistance genes with major phenotypic effects has rarely provided lasting resistance. However, breeding and combining or pyramiding of resistance genes into individual cultivars has had considerable success, particularly in situations in which the pathogen does not reproduce sexually, as in the case of wheat leaf rust pathogen. In European-Mediterranean region perfomed international investigations of wheat leaf rust proved that breeding of new lines of wheat resistant to Puccinia triticina Eriks. for differentiation of pathogen population, as well as for sources of durable resistance is necessary. Breeding of such resistant lines has proved necessary due to the unsatisfatory survey results of these regions on standard isogenic Lr lines. It has become clear that these regions needed new, more efficient differential resistance genes, as well as sources of resistance. In the beginning, after extensive screening tests of several International Rust Nurseries, 18 donors of resistance had been selected as crosses with recurrent parents' varieties Princ and Starke. These hybrid lines had been comparatively tested with twenty six Lr single gene lines using twenty especially virulent cultures of P. triticina in order to check the presence of these known Lr genes in our hybrid lines. Considerable influence of recurrent parent to the number of resistant genes in used donors was demonstrated. On the other hand, considerable influence of the pathogen culture was established to the number of resistance genes in used donors. In order to enhance resistance and pyramiding genes in these hybrids, the most interesting selected eight lines have been crossed with only effective isogenic ones, containing the strong genes Lr9, Lr19 and Lr24. On the basis of different segregation rations of all crossing combinations it was proved that no one of resistant donors contained the applied strong resistant genes. It means that our hybrid lines contained resistant genes from the donors, as well as three strong resistant genes Lr9, Lr19 and Lr24.

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Virulence in Puccinia triticina for Durum Wheat Cultivar Creso and Other Durum Wheat Cultivars Carrying Resistance Gene Lr14a in France

Plant Disease ◽

10.1094/pdis-94-8-1068a ◽

2010 ◽

Vol 94 (8) ◽

pp. 1068-1068 ◽

Cited By ~ 7

Author(s):

H. Goyeau ◽

K. Ammar ◽

J. Berder

Keyword(s):

Durum Wheat ◽

Leaf Rust ◽

Resistance Gene ◽

Genetic Basis ◽

Durable Resistance ◽

Puccinia Triticina ◽

Field Trials ◽

Minor Effect ◽

Wheat Leaf Rust ◽

Wheat Leaf

Durum wheat cv. Creso has been mentioned as having durable resistance to leaf rust (2–4). However, an average final disease level of 70S on the modified Cobb scale was scored on Creso across three locations in inoculated field trials in France during 2009. A mixture of two durum wheat leaf rust isolates commonly found in France was used for the inoculation, one was virulent on Lr23 and the other was avirulent on this gene, their identical avirulence/virulence formula for other genes was Lr1, 2a, 2b, 3, 3bg, 3ka, 9, 11, 13, 15, 16, 17, 19, 24, 25, 26, 27+31/Lr2c, 10, 14a, 14b, 20, 21, 33, and 44. On cv. Llareta Inia and breeding line Somateria, both of which carry the resistance gene Lr14a, the average final disease level was, respectively, 95S and 80S. Creso, Llareta Inia, and Somateria displayed average final disease levels of, respectively, 0, 10S, and 1 in field trials inoculated with race CBG/BP in 2009 at two locations in Mexico (Ciudad Obregon and El Batan). Race CBG/BP, virulent on Lr3, 10, 11, 14b, 20, 23, 27 + 31, and 33, is the most widely virulent race identified so far in Mexico where Lr14a remains effective for durum wheat. Virulence for Lr14a in durum wheat leaf rust populations was already mentioned to be present in France since 2000 (1). It has been suggested that the resistance of Creso, which has remained durable in Italy since 1975 (4), could be due to a gene close to but different from Lr14a. Alternatively, the fact that Creso's reaction was significantly lower than those of Llareta Inia or Somateria could indicate the presence of another gene, of minor effect, in addition to Lr14a. Whatever the genetic basis of the Creso resistance may be, it has been overcome by common French pathotypes and its usefulness in breeding, at a regional if not global level, has become questionable. References: (1) H. Goyeau et al. Phytopathology 96:264, 2006. (2) S. A. Herrera-Foessel et al. Plant Dis. 92:469, 2008. (3) M. Maccaferri et al. Theor. Appl. Genet. 117:1225, 2008. (4) D. Marone et al. Mol. Breed. 24:25, 2009.

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Geographical Distribution of Physiologic Races of Puccinia triticina and Postulation of Resistance Genes in New Wheat Cultivars in Egypt

International Journal of Phytopathology ◽

10.33687/phytopath.001.01.0018 ◽

2012 ◽

Vol 1 (1) ◽

pp. 73-80 ◽

Cited By ~ 1

Author(s):

Nour E. K. Soliman ◽

Ashraf M. M. Abdelbacki ◽

Mohammad A.A. Najeeb ◽

Reda I. Omara

Keyword(s):

Leaf Rust ◽

Geographical Distribution ◽

Resistance Genes ◽

Puccinia Triticina ◽

Wheat Cultivars ◽

Wheat Leaf Rust ◽

Rust Disease ◽

Lr Genes ◽

Wheat Leaf ◽

Physiologic Races

Knowledge of the geographical distribution for physiologic races of Puccinia triticina and identification of leaf rust resistance genes (Lr ,s) in the recent Egyptian wheat cultivars are essential for maximizing resistance in future-bred cultivars. The aim of this study was to know the status of resistance in Egyptian wheat cultivars against wheat leaf rust and the most frequent race distributed. Infected samples were collected from five Governorates, i.e., Dakahlia, Kafr el-Sheikh, Beheira, Sharqia and Sohag comprised the wheat growing area in Egypt. These samples were isolated, purified and identified on the differential stes. Gene postulation was done using fifteen identified races on Egyptian wheat cultivars correlated with Lr genes. Thirty three races identified during three seasons 2009/2010, 2010/2011 and 2011/2012. The most frequent race was TK (10%) followed by race BB (7.58%), PK (6.55%), TT (4.82%), PT (3.79%) and MT (3.44%). Moreover, races; BB, TT and PT were present during three seasons while these races appeared in some Governorates and disappeared in other Governorates. On the other hand, the most frequently occurring gene in ten Egyptian wheat cultivars was Lr35 (70%), followed by Lr22 (60%), Lr27 (40%), Lr34 (30%), Lr19 (30%),Lr18 (10%),Lr36 (10%) and Lr46 (10%), eight out of sixteen Lr genes were not present in the tested cultivars. It is concluded that there was a good variation in Lr genes carried by wheat cultivars commercially grown in Egypt. Therefore, strategies for deploying resistance genes to prolong effective disease resistance are suggested to control wheat leaf rust disease.

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