Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat

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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Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

Genes ◽

10.3390/genes11091107 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1107

Author(s):

Long Song ◽

Jing Qin Wu ◽

Chong Mei Dong ◽

Robert F. Park

Keyword(s):

Gene Expression ◽

Leaf Rust ◽

De Novo ◽

Puccinia Triticina ◽

Integrated Analysis ◽

Avirulence Genes ◽

Integrated Framework ◽

Rust Pathogen ◽

Avr Gene ◽

Avr Genes

The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.

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Identification of loci controlling non-host disease resistance in Arabidopsis against the leaf rust pathogen Puccinia triticina

Molecular Plant Pathology ◽

10.1111/j.1364-3703.2007.00431.x ◽

2007 ◽

Vol 8 (6) ◽

pp. 773-784 ◽

Cited By ~ 47

Author(s):

REZA SHAFIEI ◽

CUI HANG ◽

JEONG-GU KANG ◽

GARY J. LOAKE

Keyword(s):

Disease Resistance ◽

Leaf Rust ◽

Puccinia Triticina ◽

Host Disease ◽

Rust Pathogen

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PARTIAL RESISTANCE OF WHEAT (TRITICUM AESTIVUM) TO LEAF RUST (PUCCINIA TRITICINA) IN EGYPT. B. CHARACTERIZATION OF PARTIAL RESISTANCE TO LEAF RUST IN SOME EGYPTIAN WHEAT CULTIVARS.

Egyptian Journal of Agricultural Research ◽

10.21608/ejar.2014.156330 ◽

2014 ◽

Vol 92 (3) ◽

pp. 851-870

Author(s):

OSAMA A. BOULOT ◽

ALY A. ALY

Keyword(s):

Triticum Aestivum ◽

Leaf Rust ◽

Partial Resistance ◽

Puccinia Triticina ◽

Wheat Cultivars

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Wheat Apoplast-Localized Lipid Transfer Protein TaLTP3 Enhances Defense Responses Against Puccinia triticina

Frontiers in Plant Science ◽

10.3389/fpls.2021.771806 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jiaojie Zhao ◽

Weishuai Bi ◽

Shuqing Zhao ◽

Jun Su ◽

Mengyu Li ◽

...

Keyword(s):

Leaf Rust ◽

Lipid Transfer Protein ◽

Puccinia Triticina ◽

Defense Responses ◽

Transgenic Wheat ◽

Lipid Transfer ◽

Transfer Protein ◽

Pathogenesis Related ◽

Rust Pathogen ◽

Wheat Lines

Plant apoplast serves as the frontier battlefield of plant defense in response to different types of pathogens. Many pathogenesis-related (PR) proteins are accumulated in apoplastic space during the onset of plant–pathogen interaction, where they act to suppress pathogen infection. In this study, we found the expression of Triticum aestivum lipid transfer protein 3 (TaLTP3) gene was unregulated during incompatible interaction mediated by leaf rust resistance genes Lr39/41 at the early infection stage. Stable transgenic wheat lines overexpressing TaLTP3 exhibited enhanced resistance to leaf rust pathogen Puccinia triticina. Transcriptome analysis revealed that overexpression of TaLTP3 specifically activated the transcription of pathogenesis-related protein 1a (TaPR1a) and multiple plant hormone pathways, including salicylic acid (SA), jasmonic acid (JA), and auxin, in response to the infection of the model bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Further investigation indicated that TaLTP3 physically associated with wheat TaPR1a protein in the apoplast. Transgenic wheat lines overexpressing TaLTP3 and TaPR1a showed higher accumulations of reactive oxygen species (ROS) during plant defense responses. All these findings suggested that TaLTP3 is involved in wheat resistance against leaf rust pathogen infection and forming a TaLTP3-TaPR1a complex in apoplast against this pathogen, which provides new insights into the functional roles of PR proteins.

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