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Awais M, Ali S, Ju M, Liu W, Zhang G, Zhang Z, Li Z, Ma X, Wang L, Du Z, Tian X, Zeng Q, Kang Z, Zhao J. Countrywide inter-epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China. Environ Microbiol 2022; 24:4684-4701. [PMID: 35859329 DOI: 10.1111/1462-2920.16096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
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 (FST = 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 (FST 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.
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Affiliation(s)
- Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Sajid Ali
- Department of Agriculture, Hazara University Mansehra, Mansehra, Pakistan
| | - Meng Ju
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zedong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zejian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Xinyao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Lin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Xiaxia Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
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An Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual Population. mSphere 2020; 5:5/3/e00128-20. [PMID: 32554716 PMCID: PMC7300351 DOI: 10.1128/msphere.00128-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe (yellow) rust, is an obligate, biotrophic fungus. It was difficult to study the genetics of the pathogen due to the lack of sexual reproduction. The recent discovery of alternate hosts for P. striiformis f. sp. tritici makes it possible to study inheritance and map genes involved in its interaction with plant hosts. To identify avirulence (Avr) genes in P. striiformis f. sp. tritici, we developed a segregating population by selfing isolate 12-368 on barberry (Berberis vulgaris) plants under controlled conditions. The dikaryotic sexual population segregated for avirulent/virulent phenotypes on nine Yr single-gene lines. The parental and progeny isolates were whole-genome sequenced at >30× coverage using Illumina HiSeq PE150 technology. A total of 2,637 high-quality markers were discovered by mapping the whole-genome sequencing (WGS) reads to the reference genome of strain 93-210 and used to construct a genetic map, consisting of 41 linkage groups, spanning 7,715.0 centimorgans (cM) and covering 68 Mb of the reference genome. The recombination rate was estimated to be 1.81 ± 2.32 cM/10 kb. Quantitative trait locus analysis mapped six Avr gene loci to the genetic map, including an Avr cluster harboring four Avr genes, AvYr7, AvYr43, AvYr44, and AvYrExp2 Aligning the genetic map to the reference genome identified Avr candidates and narrowed them to a small genomic region (<200 kb). The discovery of the Avr gene cluster is useful for understanding pathogen evolution, and the identification of candidate genes is an important step toward cloning Avr genes for studying molecular mechanisms of pathogen-host interactions.IMPORTANCE Stripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis of the interactions between wheat genes for resistance and P. striiformis f. sp. tritici genes for avirulence is useful for improving cultivar resistance for more effective control of the disease. This study developed a high-quality map that facilitates genomic and genetic studies of important traits related to pathogen pathogenicity and adaptation to different environments and crop cultivars carrying different resistance genes. The information on avirulence/virulence genes identified in this study can be used for guiding breeding programs to select combinations of genes for developing new cultivars with effective resistance to mitigate this devastating disease.
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Kerr ED, Phung TK, Caboche CH, Fox GP, Platz GJ, Schulz BL. The intrinsic and regulated proteomes of barley seeds in response to fungal infection. Anal Biochem 2019; 580:30-35. [PMID: 31181183 DOI: 10.1016/j.ab.2019.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 01/14/2023]
Abstract
Barley is an important cereal grain used for beer brewing, animal feed, and human food consumption. Fungal disease can impact barley production, as it causes substantial yield loss and lowers seed quality. We used sequential window acquisition of all theoretical ions mass spectrometry (SWATH-MS) to measure and quantify the relative abundance of proteins within seeds of different barley varieties under various fungal pathogen burdens (ProteomeXchange Datasets PXD011303 and PXD014093). Fungal burden in the leaves and stems of barley resulted in changes to the seed proteome. However, these changes were minimal and showed substantial variation among barley samples infected with different pathogens. The limited effect of intrinsic disease resistance on the seed proteome is consistent with the main mediators of disease resistance being present in the leaves and stems of the plant. The seeds of barley varieties accredited for use as malt had higher levels of proteins associated with starch synthesis and beer quality. The proteomic workflows developed and implemented here have potential application in quality control, breeding and processing of barley, and other agricultural products.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Christopher H Caboche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Glen P Fox
- Centre for Nutrition and Food Sciences, Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, 4072, Queensland, Australia
| | - Greg J Platz
- Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, 4370, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4072, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, Australia; Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia, 4072, Queensland, Australia.
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Panwar V, Jordan M, McCallum B, Bakkeren G. Host-induced silencing of essential genes in Puccinia triticina through transgenic expression of RNAi sequences reduces severity of leaf rust infection in wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1013-1023. [PMID: 28941315 PMCID: PMC5902777 DOI: 10.1111/pbi.12845] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/18/2017] [Accepted: 09/20/2017] [Indexed: 05/05/2023]
Abstract
Leaf rust, caused by the pathogenic fungus Puccinia triticina (Pt), is one of the most serious biotic threats to sustainable wheat production worldwide. This obligate biotrophic pathogen is prevalent worldwide and is known for rapid adaptive evolution to overcome resistant wheat varieties. Novel disease control approaches are therefore required to minimize the yield losses caused by Pt. Having shown previously the potential of host-delivered RNA interference (HD-RNAi) in functional screening of Pt genes involved in pathogenesis, we here evaluated the use of this technology in transgenic wheat plants as a method to achieve protection against wheat leaf rust (WLR) infection. Stable expression of hairpin RNAi constructs with sequence homology to Pt MAP-kinase (PtMAPK1) or a cyclophilin (PtCYC1) encoding gene in susceptible wheat plants showed efficient silencing of the corresponding genes in the interacting fungus resulting in disease resistance throughout the T2 generation. Inhibition of Pt proliferation in transgenic lines by in planta-induced RNAi was associated with significant reduction in target fungal transcript abundance and reduced fungal biomass accumulation in highly resistant plants. Disease protection was correlated with the presence of siRNA molecules specific to targeted fungal genes in the transgenic lines harbouring the complementary HD-RNAi construct. This work demonstrates that generating transgenic wheat plants expressing RNAi-inducing transgenes to silence essential genes in rust fungi can provide effective disease resistance, thus opening an alternative way for developing rust-resistant crops.
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Affiliation(s)
- Vinay Panwar
- Agriculture and Agri‐Food CanadaMorden Research and Development CentreMordenMBCanada
- Agriculture and Agri‐Food CanadaSummerland Research and Development CentreSummerlandBCCanada
| | - Mark Jordan
- Agriculture and Agri‐Food CanadaMorden Research and Development CentreMordenMBCanada
| | - Brent McCallum
- Agriculture and Agri‐Food CanadaMorden Research and Development CentreMordenMBCanada
| | - Guus Bakkeren
- Agriculture and Agri‐Food CanadaSummerland Research and Development CentreSummerlandBCCanada
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Rutter WB, Salcedo A, Akhunova A, He F, Wang S, Liang H, Bowden RL, Akhunov E. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses. BMC Genomics 2017; 18:291. [PMID: 28403814 PMCID: PMC5389088 DOI: 10.1186/s12864-017-3678-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). RESULTS The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. CONCLUSIONS Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.
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Affiliation(s)
- William B. Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414 USA
| | - Andres Salcedo
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Alina Akhunova
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 101 Gateway, Suite A, College Station, TX 77845 USA
| | - Hanquan Liang
- Integrated Genomics Facility, Kansas State University, Manhattan, KS 66506 USA
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006 China
| | - Robert L. Bowden
- USDA ARS, Hard Winter Wheat Genetics Research Unit, Throckmorton Plant Sciences Center, Manhattan, KS 66506 USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
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Wu JQ, Sakthikumar S, Dong C, Zhang P, Cuomo CA, Park RF. Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia. FRONTIERS IN PLANT SCIENCE 2017; 8:148. [PMID: 28232843 PMCID: PMC5298990 DOI: 10.3389/fpls.2017.00148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/24/2017] [Indexed: 05/05/2023]
Abstract
Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.
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Affiliation(s)
- Jing Qin Wu
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Sharadha Sakthikumar
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Chongmei Dong
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Peng Zhang
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Christina A. Cuomo
- Genome Sequencing and Analysis Program, Broad Institute of Massachusetts Institute of Technology (MIT) and HarvardCambridge, MA, USA
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
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Rautenbach M, Troskie AM, Vosloo JA. Antifungal peptides: To be or not to be membrane active. Biochimie 2016; 130:132-145. [PMID: 27234616 DOI: 10.1016/j.biochi.2016.05.013] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/20/2016] [Indexed: 02/06/2023]
Abstract
Most antifungal peptides (AFPs), if not all, have membrane activity, while some also have alternative targets. Fungal membranes share many characteristics with mammalian membranes with only a few differences, such as differences in sphingolipids, phosphatidylinositol (PI) content and the main sterol is ergosterol. Fungal membranes are also more negative and a better target for cationic AFPs. Targeting just the fungal membrane lipids such as phosphatidylinositol and/or ergosterol by AFPs often translates into mammalian cell toxicity. Conversely, a specific AFP target in the fungal pathogen, such as glucosylceramide, mannosyldiinositol phosphorylceramide or a fungal protein target translates into high pathogen selectivity. However, a lower target concentration, absence or change in the specific fungal target can naturally lead to resistance, although such resistance in turn could result in reduced pathogen virulence. The question is then to be or not to be membrane active - what is the best choice for a successful AFP? In this review we deliberate on this question by focusing on the recent advances in our knowledge on how natural AFPs target fungi.
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Affiliation(s)
- Marina Rautenbach
- BIOPEP Peptide Group, Department of Biochemistry, University of Stellenbosch, South Africa.
| | - Anscha M Troskie
- BIOPEP Peptide Group, Department of Biochemistry, University of Stellenbosch, South Africa
| | - J Arnold Vosloo
- BIOPEP Peptide Group, Department of Biochemistry, University of Stellenbosch, South Africa
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Zheng W, Huang L, Huang J, Wang X, Chen X, Zhao J, Guo J, Zhuang H, Qiu C, Liu J, Liu H, Huang X, Pei G, Zhan G, Tang C, Cheng Y, Liu M, Zhang J, Zhao Z, Zhang S, Han Q, Han D, Zhang H, Zhao J, Gao X, Wang J, Ni P, Dong W, Yang L, Yang H, Xu JR, Zhang G, Kang Z. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. Nat Commun 2013; 4:2673. [PMID: 24150273 PMCID: PMC3826619 DOI: 10.1038/ncomms3673] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/26/2013] [Indexed: 11/08/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a 'fosmid-to-fosmid' strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the 'fosmid-to-fosmid' strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.
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Affiliation(s)
- Wenming Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crop in Henan Province and College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province 450002, China
- These authors contributed equally to this work
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- These authors contributed equally to this work
| | - Jinqun Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- These authors contributed equally to this work
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- USDA-ARS and Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, USA
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Zhuang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuangzhao Qiu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueling Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guoliang Pei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Minjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinshan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhongtao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoning Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peixiang Ni
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Dong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linfeng Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Gengyun Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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Bernardo L, Prinsi B, Negri AS, Cattivelli L, Espen L, Valè G. Proteomic characterization of the Rph15 barley resistance gene-mediated defence responses to leaf rust. BMC Genomics 2012; 13:642. [PMID: 23167439 PMCID: PMC3541957 DOI: 10.1186/1471-2164-13-642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Background Leaf rust, caused by the biotrophic fungal pathogen Puccinia hordei, is one of the most important foliar disease of barley (Hordeum vulgare) and represents a serious threat in many production regions of the world. The leaf rust resistance gene Rph15 is of outstanding interest for resistance breeding because it confers resistance to over 350 Puccinia hordei isolates collected from around the world. Molecular and biochemical mechanisms responsible for the Rph15 effectiveness are currently not investigated. The aim of the present work was to study the Rph15-based defence responses using a proteomic approach. Results Protein pattern changes in response to the leaf rust pathogen infection were investigated in two barley near isogenic lines (NILs), Bowman (leaf rust susceptible) and Bowman-Rph15 (leaf rust resistant), differing for the introgression of the leaf rust resistance gene Rph15. Two infection time points, 24 hours and four days post inoculation (dpi), were analysed. No statistically significant differences were identified at the early time point, while at 4 dpi eighteen protein spots were significantly up or down regulated with a fold-change equal or higher than two in response to pathogen infection. Almost all the pathogen-responsive proteins were identified in the Bowman-Rph15 resistant NIL. Protein spots were characterized by LC-MS/MS analysis and found to be involved in photosynthesis and energy metabolism, carbohydrate metabolism, protein degradation and defence. Proteomic data were complemented by transcriptional analysis of the respective genes. The identified proteins can be related to modulation of the photosynthetic apparatus components, re-direction of the metabolism to sustain defence responses and deployment of defence proteins. Conclusions The identification of leaf rust infection-modulated defence responses restricted to the resistant NIL support the hypothesis that basal defence responses of Bowman, but not the Rph15 resistance gene-based ones, are suppressed or delayed by pathogen effectors to levels below the detection power of the adopted proteomic approach. Additionally, Rph15-mediated resistance processes identified mainly resides on a modulation of primary metabolism, affecting photosyntesis and carbohydrate pool.
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Affiliation(s)
- Letizia Bernardo
- CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda, PC I-29017, Italy
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Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms. Anal Bioanal Chem 2012; 404:1247-55. [DOI: 10.1007/s00216-012-6091-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 11/26/2022]
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Bolton MD, Kolmer JA, Xu WW, Garvin DF. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1515-27. [PMID: 18986248 DOI: 10.1094/mpmi-21-12-1515] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. We used the Affymetrix GeneChip Wheat Genome Array to compare transcriptional changes of near-isogenic lines of Thatcher wheat in a compatible interaction, an incompatible interaction conferred by the resistance gene Lr1, and the race-nonspecific response conditioned by Lr34 3 and 7 days postinoculation (dpi) with P. triticina. No differentially expressed genes were detected in Lr1 plants at either timepoint whereas, in the compatible Thatcher interaction, differentially expressed genes were detected only at 7 dpi. In contrast, differentially expressed genes were identified at both timepoints in P. triticina-inoculated Lr34 plants. At 3 dpi, upregulated genes associated with Lr34-mediated resistance encoded various defense and stress-related proteins, secondary metabolism enzymes, and transcriptional regulation and cellular-signaling proteins. Further, coordinated upregulation of key genes in several metabolic pathways that can contribute to increased carbon flux through the tricarboxylic cycle was detected. This indicates that Lr34-mediated resistance imposes a high energetic demand that leads to the induction of multiple metabolic responses to support cellular energy requirements. These metabolic responses were not sustained through 7 dpi, and may explain why Lr34 fails to inhibit the pathogen fully but does increase the latent period.
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Affiliation(s)
- Melvin D Bolton
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Plant Science Research Unit, 411 Borlaug Hall, University of Minnesota, 1991 Upper Buford Circle, St. Paul 55108, USA
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Mehta A, Brasileiro ACM, Souza DSL, Romano E, Campos MA, Grossi-de-Sá MF, Silva MS, Franco OL, Fragoso RR, Bevitori R, Rocha TL. Plant-pathogen interactions: what is proteomics telling us? FEBS J 2008; 275:3731-46. [PMID: 18616468 DOI: 10.1111/j.1742-4658.2008.06528.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the years, several studies have been performed to analyse plant-pathogen interactions. Recently, functional genomic strategies, including proteomics and transcriptomics, have contributed to the effort of defining gene and protein function and expression profiles. Using these 'omic' approaches, pathogenicity- and defence-related genes and proteins expressed during phytopathogen infections have been identified and enormous datasets have been accumulated. However, the understanding of molecular plant-pathogen interactions is still an intriguing area of investigation. Proteomics has dramatically evolved in the pursuit of large-scale functional assignment of candidate proteins and, by using this approach, several proteins expressed during phytopathogenic interactions have been identified. In this review, we highlight the proteins expressed during plant-virus, plant-bacterium, plant-fungus and plant-nematode interactions reported in proteomic studies, and discuss these findings considering the advantages and limitations of current proteomic tools.
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Affiliation(s)
- Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.
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Cloutier S, McCallum BD, Loutre C, Banks TW, Wicker T, Feuillet C, Keller B, Jordan MC. Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. PLANT MOLECULAR BIOLOGY 2007; 65:93-106. [PMID: 17611798 DOI: 10.1007/s11103-007-9201-8] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 06/08/2007] [Indexed: 05/16/2023]
Abstract
In hexaploid wheat, leaf rust resistance gene Lr1 is located at the distal end of the long arm of chromosome 5D. To clone this gene, an F(1)-derived doubled haploid population and a recombinant inbred line population from a cross between the susceptible cultivar AC Karma and the resistant line 87E03-S2B1 were phenotyped for resistance to Puccinia triticina race 1-1 BBB that carries the avirulence gene Avr1. A high-resolution genetic map of the Lr1 locus was constructed using microsatellite, resistance gene analog (RGA), BAC end (BE), and low pass (LP) markers. A physical map of the locus was constructed by screening a hexaploid wheat BAC library from cultivar Glenlea that is known to have Lr1. The locus comprised three RGAs from a gene family related to RFLP marker Xpsr567. Markers specific to each paralog were developed. Lr1 segregated with RGA567-5 while recombinants were observed for the other two RGAs. Transformation of the susceptible cultivar Fielder with RGA567-5 demonstrated that it corresponds to the Lr1 resistance gene. In addition, the candidate gene was also confirmed by virus-induced gene silencing. Twenty T (1) lines from resistant transgenic line T (0)-938 segregated for resistance, partial resistance and susceptibility to Avr1 corresponding to a 1:2:1 ratio for a single hemizygous insertion. Transgene presence and expression correlated with the phenotype. The resistance phenotype expressed by Lr1 seemed therefore to be dependant on the zygosity status. T (3)-938 sister lines with and without the transgene were further tested with 16 virulent and avirulent rust isolates. Rust reactions were all as expected for Lr1 thereby providing additional evidence toward the Lr1 identity of RGA567-5. Sequence analysis of Lr1 indicated that it is not related to the previously isolated Lr10 and Lr21 genes and unlike these genes, it is part of a large gene family.
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Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, R3T 2M9, Winnipeg, MB, Canada.
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