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Wang B, Meng T, Xiao B, Yu T, Yue T, Jin Y, Ma P. Fighting wheat powdery mildew: from genes to fields. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:196. [PMID: 37606731 DOI: 10.1007/s00122-023-04445-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.
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Affiliation(s)
- Bo Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ting Meng
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tianying Yu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tingyan Yue
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resource Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China.
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2
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Martin EC, Ion CF, Ifrimescu F, Spiridon L, Bakker J, Goverse A, Petrescu AJ. NLRscape: an atlas of plant NLR proteins. Nucleic Acids Res 2022; 51:D1470-D1482. [PMID: 36350627 PMCID: PMC9825502 DOI: 10.1093/nar/gkac1014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
NLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread-in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.
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Affiliation(s)
- Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Catalin F Ion
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Florin Ifrimescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Jaap Bakker
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
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Martin EC, Spiridon L, Goverse A, Petrescu AJ. NLRexpress-A bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity. FRONTIERS IN PLANT SCIENCE 2022; 13:975888. [PMID: 36186050 PMCID: PMC9519389 DOI: 10.3389/fpls.2022.975888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 05/13/2023]
Abstract
Examination of a collection of over 80,000 Plant Nod-like receptors (NLRs) revealed an overwhelming sequence diversity underlying functional specificity of pathogen detection, signaling and cooperativity. The NLR canonical building blocks-CC/TIR/RPW8, NBS and LRR-contain, however, a number of conserved sequence motifs showing a significant degree of invariance amongst different NLR groups. To identify these motifs we developed NLRexpress-a bundle of 17 machine learning (ML)-based predictors, able to swiftly and precisely detect CC, TIR, NBS, and LRR motifs while minimizing computing time without accuracy losses-aimed as an instrument scalable for screening overall proteomes, transcriptomes or genomes for identifying integral NLRs and discriminating them against incomplete sequences lacking key motifs. These predictors were further used to screen a subset of ∼34,000 regular plant NLR sequences. Motifs were analyzed using unsupervised ML techniques to assess the structural correlations hidden underneath pattern variabilities. Both the NB-ARC switch domain which admittedly is the most conserved region of NLRs and the highly diverse LRR domain with its vastly variable lengths and repeat irregularities-show well-defined relations between motif subclasses, highlighting the importance of structural invariance in shaping NLR sequence diversity. The online NLRexpress webserver can be accessed at https://nlrexpress.biochim.ro.
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Affiliation(s)
- Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrei-José Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- *Correspondence: Andrei-José Petrescu,
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4
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Lindner S, Keller B, Singh SP, Hasenkamp Z, Jung E, Müller MC, Bourras S, Keller B. Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:200-214. [PMID: 32645755 DOI: 10.1111/tpj.14917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The development of improved plant nucleotide-binding, leucine-rich repeat (LRR) immune receptors (NLRs) has mostly been based on random mutagenesis or on structural information available for specific receptors complexed with the recognized pathogen effector. Here, we use a targeted mutagenesis approach based on the natural diversity of the Pm3 powdery mildew resistance alleles present in different wheat (Triticum aestivum) genotypes. In order to understand the functional importance of the amino acid polymorphisms between the active immune receptor PM3A and the inactive ancestral variant PM3CS, we exchanged polymorphic regions and residues in the LRR domain of PM3A with the corresponding segments of PM3CS. These novel variants were functionally tested for recognition of the corresponding AVRPM3A2/F2 avirulence protein in Nicotiana benthamiana. We identified polymorphic residues in four regions of PM3A that enhance the immune response, but also residues that reduce it or result in complete loss of function. We found that the identified critical residues in PM3A modify its activation threshold towards different protein variants of AVRPM3A2/F2 . PM3A variants with a lowered threshold gave a stronger overall response and gained an extended recognition spectrum. One of these variant proteins with a single amino acid change was stably transformed into wheat, where it conferred race-specific resistance to mildew. This is a proof of concept that improved PM3A variants with an enlarged recognition spectrum can be engineered based on natural diversity by exchanging single or multiple residues that modulate resistance function.
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Affiliation(s)
- Stefan Lindner
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Bettina Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Simrat P Singh
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Zsuzsanna Hasenkamp
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Marion C Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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5
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Karasov TL, Shirsekar G, Schwab R, Weigel D. What natural variation can teach us about resistance durability. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:89-98. [PMID: 32535454 DOI: 10.1016/j.pbi.2020.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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6
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Distribution and Nucleotide Diversity of Yr15 in Wild Emmer Populations and Chinese Wheat Germplasm. Pathogens 2020; 9:pathogens9030212. [PMID: 32183066 PMCID: PMC7157507 DOI: 10.3390/pathogens9030212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/27/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat. The wild emmer gene, Yr15 (Wtk1), which confers a strong broad-spectrum resistance to Pst isolates, is composed of kinase and pseudokinase domains. The analysis of 361 wild emmer accessions from a wide range of natural habitats confirms that functional Wtk1 is distributed mainly along a narrow axis from Mt. Carmel to Mt. Hermon regions, in the northern part of Israel, where environmental conditions are favorable to the onset of stripe rust. An analysis of full-length Wtk1 DNA sequences from 49 wild emmer accessions identified three haplotypes and extremely low nucleotide diversity (π = 0.00002). The sequence diversity of Wtk1 is 9.5 times lower than that of broad-spectrum partial resistance gene Yr36 (π = 0.00019), and both are in sharp contrast to the high level of nucleotide diversity previously reported for race-specific resistance genes (e.g., Lr10 and Pm3). However, the nonfunctional wtk1 sequences possess high level of nucleotide diversity (π = 0.07). These results may reflect the different resistance mechanisms and the different evolutionary processes that shaped these resistance genes. Yr15 was absent in 189 Chinese wheat landraces and was present in only 1.02% of the 583 tested modern Chinese wheat cultivars. These results corroborate our previous results showing that Yr15 was absent in 94% of a worldwide collection of 513 wheat cultivars, therefore indicating the importance of Yr15 in wheat stripe rust resistance breeding programs in China and elsewhere around the globe.
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LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. Genes (Basel) 2020; 11:genes11030286. [PMID: 32182725 PMCID: PMC7140858 DOI: 10.3390/genes11030286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein-protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.
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8
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Baudin M, Schreiber KJ, Martin EC, Petrescu AJ, Lewis JD. Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:352-370. [PMID: 31557357 DOI: 10.1111/tpj.14547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 05/26/2023]
Abstract
NLR (nucleotide-binding [NB] leucine-rich repeat [LRR] receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly modulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor-like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana that allowed us to demonstrate that ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modelling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions modulate ZAR1 activity. We identified determinants required for the formation of the ZARCC oligomer and its activity. Lastly, we characterized intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Karl J Schreiber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, USA
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Maekawa T, Kracher B, Saur IML, Yoshikawa-Maekawa M, Kellner R, Pankin A, von Korff M, Schulze-Lefert P. Subfamily-Specific Specialization of RGH1/MLA Immune Receptors in Wild Barley. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:107-119. [PMID: 30295580 DOI: 10.1094/mpmi-07-18-0186-fi] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The barley disease resistance (R) gene locus mildew locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis hordei and has been introgressed into modern cultivars from diverse germplasms, including the wild relative Hordeum spontaneum. Known Mla disease resistance specificities to B. graminis hordei appear to encode allelic variants of the R gene homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Here, we sequenced and assembled the transcriptomes of 50 H. spontaneum accessions representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, linked neither to geographic origin nor population structure, and could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil (CC) signaling domains that are both capable of eliciting cell death. The presence of positively selected sites located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both CC signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the population. Unexpectedly, known MLA receptor variants that confer B. graminis hordei resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially as adaptation to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Takaki Maekawa
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Barbara Kracher
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Isabel M L Saur
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | | | - Ronny Kellner
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Artem Pankin
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Maria von Korff
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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Field grown transgenic Pm3e wheat lines show powdery mildew resistance and no fitness costs associated with high transgene expression. Transgenic Res 2018; 28:9-20. [PMID: 30302615 DOI: 10.1007/s11248-018-0099-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 10/03/2018] [Indexed: 10/28/2022]
Abstract
Pm3 from wheat encodes a nucleotide-binding leucine-rich repeat type of receptor and confers resistance to powdery mildew caused by the fungal pathogen Blumeria graminis f.sp. tritici (Bgt). Each of the 17 functional Pm3 alleles identified so far confers resistance to a distinct spectrum of Bgt isolates. Variant Pm3e has been found in wheat donor line W150 and differs only by two amino acids from the non-functional variant Pm3CS. In order to evaluate the capability of Pm3e to provide powdery mildew field resistance, we generated transgenic Pm3e lines by biolistic transformation of the powdery mildew susceptible spring wheat cultivar Bobwhite. Field trials conducted during four field seasons in Switzerland showed significant and strong powdery mildew resistance of the Pm3e transgenic lines, whereas the corresponding biological sister lines, not containing the transgene, were severely powdery mildew infected. Thus Pm3e alone is responsible for the strong resistance phenotype. The field grown transgenic lines showed high transgene expression and Pm3e protein accumulation with no fitness costs on plant development and yield associated with Pm3e abundance. Line E#1 as well as sister line E#1 showed delayed flowering due to somaclonal variation. The study shows the capability of Pm3e in providing strong powdery mildew field resistance, making its use in wheat breeding programs very promising.
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Krattinger SG, Keller B. Molecular genetics and evolution of disease resistance in cereals. THE NEW PHYTOLOGIST 2016; 212:320-32. [PMID: 27427289 DOI: 10.1111/nph.14097] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 05/02/2023]
Abstract
Contents 320 I. 320 II. 321 III. 321 IV. 322 V. 324 VI. 328 VII. 329 330 References 330 SUMMARY: Cereal crops produce a large part of the globally consumed food and feed. Because of the constant presence of devastating pathogens, the molecular characterization of disease resistance is a major research area and highly relevant for breeding. There has been recent and accelerating progress in the understanding of three distinct resistance mechanisms in cereals: resistance conferred by plasma membrane-localized receptor proteins; race-specific resistance conferred by intracellular immune receptors; and quantitative disease resistance. Intracellular immune receptors provide a particularly rich source for evolutionary studies, and have, for example, resulted in the recent discovery of a novel detection mechanism based on integrated decoy domains. Evolutionary studies have also revealed the origins of active resistance genes in both wild progenitors of today's cereals as well as in cultivated forms. In addition, independent evolution of orthologous genes in related cereals has resulted in resistance to different pathogen species. Quantitative resistance genes have been best characterized in wheat. The quantitative resistance genes identified so far in wheat encode transporter proteins or unusual kinase proteins. The recent discoveries in these three different resistance mechanisms have contributed to the basic molecular understanding of cereal immunity against pathogens and have suggested novel applications for resistance breeding.
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Affiliation(s)
- Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
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Huang L, Raats D, Sela H, Klymiuk V, Lidzbarsky G, Feng L, Krugman T, Fahima T. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:279-301. [PMID: 27296141 DOI: 10.1146/annurev-phyto-080614-120254] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.
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Affiliation(s)
- Lin Huang
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Dina Raats
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Valentina Klymiuk
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Gabriel Lidzbarsky
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Lihua Feng
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
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Sukarta OCA, Slootweg EJ, Goverse A. Structure-informed insights for NLR functioning in plant immunity. Semin Cell Dev Biol 2016; 56:134-149. [PMID: 27208725 DOI: 10.1016/j.semcdb.2016.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.
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Affiliation(s)
- Octavina C A Sukarta
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik J Slootweg
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Aska Goverse
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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15
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Huang L, Sela H, Feng L, Chen Q, Krugman T, Yan J, Dubcovsky J, Fahima T. Distribution and haplotype diversity of WKS resistance genes in wild emmer wheat natural populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:921-34. [PMID: 26847646 DOI: 10.1007/s00122-016-2672-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/09/2016] [Indexed: 05/18/2023]
Abstract
The wheat stripe rust resistance gene Yr36 ( WKS1 ) with a unique kinase-START domain architecture is highly conserved in wild emmer wheat natural populations. Wild emmer wheat (Triticum dicoccoides) populations have developed various resistance strategies against the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). The wild emmer gene, Yr36 (WKS1), which confers partial resistance to a broad spectrum of Pst races, is composed of a kinase and a START lipid-binding domain, a unique gene architecture found only in the Triticeae tribe. The analysis of 435 wild emmer accessions from a broad range of natural habitats revealed that WKS1 and its paralogue WKS2 are present only in the southern distribution range of wild emmer in the Fertile Crescent, supporting the idea that wheat domestication occurred in the northern populations. An analysis of full-length WKS1 sequence from 54 accessions identified 15 different haplotypes and very low-nucleotide diversity (π = 0.00019). The high level of WKS1 sequence conservation among wild emmer populations is in contrast to the high level of diversity previously observed in NB-LRR genes (e.g., Lr10 and Pm3). This phenomenon may reflect the different resistance mechanisms and different evolutionary pathways that shaped these genes, and may shed light on the evolution of genes that confer partial resistance to stripe rust. Only five WKS1 coding sequence haplotypes were revealed among all tested accessions, encoding four different putative WKS1 proteins (designated P0, P1, P2, and P3). Infection tests showed that P0, P1, and P3 haplotypes display a resistance response, while P2 displayed a susceptible response. These results show that the WKS1 proteins (P0, P1, and P3) can be useful to improve wheat resistance to stripe rust.
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Affiliation(s)
- Lin Huang
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
| | - Hanan Sela
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
- The Institute for Cereal Crops Improvement, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Lihua Feng
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
| | - Qijiao Chen
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Tamar Krugman
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
| | - Jun Yan
- Faculty of Industrial Biotechnology, Chengdu University, Chengdu, 610106, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tzion Fahima
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel.
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