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Locci F, Parker JE. Plant NLR immunity activation and execution: a biochemical perspective. Open Biol 2024; 14:230387. [PMID: 38262605 PMCID: PMC10805603 DOI: 10.1098/rsob.230387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.
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Affiliation(s)
- Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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2
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Neto C, Hancock A. Genetic Architecture of Flowering Time Differs Between Populations With Contrasting Demographic and Selective Histories. Mol Biol Evol 2023; 40:msad185. [PMID: 37603463 PMCID: PMC10461413 DOI: 10.1093/molbev/msad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Understanding the evolutionary factors that impact the genetic architecture of traits is a central goal of evolutionary genetics. Here, we investigate how quantitative trait variation accumulated over time in populations that colonized a novel environment. We compare the genetic architecture of flowering time in Arabidopsis populations from the drought-prone Cape Verde Islands and their closest outgroup population from North Africa. We find that trait polygenicity is severely reduced in the island populations compared to the continental North African population. Further, trait architectures and reconstructed allelic histories best fit a model of strong directional selection in the islands in accord with a Fisher-Orr adaptive walk. Consistent with this, we find that large-effect variants that disrupt major flowering time genes (FRI and FLC) arose first, followed by smaller effect variants, including ATX2 L125F, which is associated with a 4-day reduction in flowering time. The most recently arising flowering time-associated loci are not known to be directly involved in flowering time, consistent with an omnigenic signature developing as the population approaches its trait optimum. Surprisingly, we find no effect in the natural population of EDI-Cvi-0 (CRY2 V367M), an allele for which an effect was previously validated by introgression into a Eurasian line. Instead, our results suggest the previously observed effect of the EDI-Cvi-0 allele on flowering time likely depends on genetic background, due to an epistatic interaction. Altogether, our results provide an empirical example of the effects demographic history and selection has on trait architecture.
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Affiliation(s)
- Célia Neto
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela Hancock
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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3
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Zhang C, Atanasov KE, Alcázar R. Spermine inhibits PAMP-induced ROS and Ca2+ burst and reshapes the transcriptional landscape of PAMP-triggered immunity in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:427-442. [PMID: 36264272 PMCID: PMC9786854 DOI: 10.1093/jxb/erac411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/18/2022] [Indexed: 05/31/2023]
Abstract
Polyamines are small polycationic amines whose levels increase during defense. Previous studies support the contribution of the polyamine spermine to defense responses. However, the potential contribution of spermine to pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) has not been completely established. Here, we compared the contribution of spermine and putrescine to early and late PTI responses in Arabidopsis. We found that putrescine and spermine have opposite effects on PAMP-elicited reactive oxygen species (ROS) production, with putrescine increasing and spermine lowering the flg22-stimulated ROS burst. Through genetic and pharmacological approaches, we found that the inhibitory effect of spermine on flg22-elicited ROS production is independent of polyamine oxidation, nitric oxide, and salicylic acid signaling but resembles chemical inhibition of RBOHD (RESPIRATORY BURST OXIDASE HOMOLOG D). Spermine can also suppress ROS elicited by FLS2-independent but RBOHD-dependent pathways, thus pointing to compromised RBOHD activity. Consistent with this, we found that spermine but not putrescine dampens flg22-stimulated cytosolic Ca2+ influx. Finally, we found that both polyamines differentially reshape transcriptional responses during PTI and disease resistance to Pseudomonas syringae. Overall, we provide evidence for the differential contributions of putrescine and spermine to PTI, with an impact on plant defense.
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Affiliation(s)
- Chi Zhang
- Department of Biology, Healthcare and Environment. Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Kostadin E Atanasov
- Department of Biology, Healthcare and Environment. Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
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4
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Atanasov KE, Díaz-Narváez LC, Alcázar R. Ammonium and nitric oxide condition the establishment of Arabidopsis Ler/Kas-2 immune-related hybrid incompatibility. PLANTA 2022; 256:76. [PMID: 36087170 PMCID: PMC9464153 DOI: 10.1007/s00425-022-03990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
High ammonium suppresses hybrid incompatibility between Ler and Kas-2 accessions through lowering nitric oxide levels and nitrate reductase activity required for autoimmunity. The immune-related hybrid incompatibility (HI) between Landsberg erecta (Ler) and Kashmir-2 (Kas-2) accessions is due to a deleterious genetic interaction between the RPP1 (RECOGNITION OF PERONOSPORA PARASITICA1)-like Ler locus and Kas-2 alleles of the receptor-like kinase SRF3 (STRUBBELIG RECEPTOR FAMILY 3). The genetic incompatibility is temperature-dependent and leads to constitutive activation of the salicylic acid (SA) pathway, dwarfism and cell death at 14-16 °C. Here we investigated the effect of nutrition on the occurrence of Ler/Kas-2 HI and found that high ammonium suppresses Ler/Kas-2 incompatible phenotypes independently of the ammonium/nitrate ratio. Ammonium feeding leads to compromised disease resistance to Pseudomonas syringae pv. tomato DC3000, lower total SA, nitric oxide and nitrate reductase activity in Ler/Kas-2 incompatible hybrids. In addition, we find that Ler/Kas-2 incompatibility is dependent on NPR1 (NONEXPRESSER OF PR GENES 1) and nitric oxide production. Overall, this work highlights the effect of nutrition on the expression of incompatible phenotypes independently of temperature.
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Lucía C Díaz-Narváez
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028, Barcelona, Spain.
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5
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Sikder MM, Vestergård M, Kyndt T, Topalović O, Kudjordjie EN, Nicolaisen M. Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion. THE ISME JOURNAL 2022; 16:2230-2241. [PMID: 35760884 PMCID: PMC9381567 DOI: 10.1038/s41396-022-01276-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 05/29/2023]
Abstract
In-depth understanding of metabolite-mediated plant-nematode interactions can guide us towards novel nematode management strategies. To improve our understanding of the effects of secondary metabolites on soil nematode communities, we grew Arabidopsis thaliana genetically altered in glucosinolate, camalexin, or flavonoid synthesis pathways, and analyzed their root-associated nematode communities using metabarcoding. To test for any modulating effects of the associated microbiota on the nematode responses, we characterized the bacterial and fungal communities. Finally, as a proxy of microbiome-modulating effects on nematode invasion, we isolated the root-associated microbiomes from the mutants and tested their effect on the ability of the plant parasitic nematode Meloidogyne incognita to penetrate tomato roots. Most mutants had altered relative abundances of several nematode taxa with stronger effects on the plant parasitic Meloidogyne hapla than on other root feeding taxa. This probably reflects that M. hapla invades and remains embedded within root tissues and is thus intimately associated with the host. When transferred to tomato, microbiomes from the flavonoid over-producing pap1-D enhanced M. incognita root-invasion, whereas microbiomes from flavonoid-deficient mutants reduced invasion. This suggests microbiome-mediated effect of flavonoids on Meloidogyne infectivity plausibly mediated by the alteration of the abundances of specific microbial taxa in the transferred microbiomes, although we could not conclusively pinpoint such causative microbial taxa.
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Affiliation(s)
- Md Maniruzzaman Sikder
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, 1342 Savar, Dhaka, Bangladesh
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark
| | - Tina Kyndt
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000, Gent, Belgium
| | - Olivera Topalović
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark
| | - Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark.
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6
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Pincot DDA, Feldmann MJ, Hardigan MA, Vachev MV, Henry PM, Gordon TR, Bjornson M, Rodriguez A, Cobo N, Famula RA, Cole GS, Coaker GL, Knapp SJ. Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2121-2145. [PMID: 35583656 PMCID: PMC9205853 DOI: 10.1007/s00122-022-04102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 05/05/2023]
Abstract
Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant to Fusarium oxysporum f. sp. fragariae, a devastating soil-borne pathogen of strawberry. Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria [Formula: see text] ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.
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Affiliation(s)
- Dominique D. A. Pincot
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Mitchell J. Feldmann
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Michael A. Hardigan
- Horticultural Crops Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR 97331 USA
| | - Mishi V. Vachev
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Peter M. Henry
- United States Department of Agriculture Agricultural Research Service, 1636 East Alisal Street, Salinas, CA 93905 USA
| | - Thomas R. Gordon
- Department of Plant Pathology, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Marta Bjornson
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Alan Rodriguez
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Nicolas Cobo
- Departamento de Producción, Agropecuaria Universidad de La Frontera, Temuco, Chile
| | - Randi A. Famula
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Glenn S. Cole
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Gitta L. Coaker
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Steven J. Knapp
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
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7
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Indirect recognition of pathogen effectors by NLRs. Essays Biochem 2022; 66:485-500. [PMID: 35535995 DOI: 10.1042/ebc20210097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
To perceive pathogen threats, plants utilize both plasma membrane-localized and intracellular receptors. Nucleotide-binding domain leucine-rich repeat containing (NLR) proteins are key receptors that can recognize pathogen-derived intracellularly delivered effectors and activate downstream defense. Exciting recent findings have propelled our understanding of the various recognition and activation mechanisms of plant NLRs. Some NLRs directly bind to effectors, but others can perceive effector-induced changes on targeted host proteins (guardees), or non-functional host protein mimics (decoys). Such guarding strategies are thought to afford the host more durable resistance to quick-evolving and diverse pathogens. Here, we review classic and recent examples of indirect effector recognition by NLRs and discuss strategies for the discovery and study of new NLR-decoy/guardee systems. We also provide a perspective on how executor NLRs and helper NLRs (hNLRs) provide recognition for a wider range of effectors through sensor NLRs and how this can be considered an expanded form of indirect recognition. Furthermore, we summarize recent structural findings on NLR activation and resistosome formation upon indirect recognition. Finally, we discuss existing and potential applications that harness NLR indirect recognition for plant disease resistance and crop resilience.
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8
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Freh M, Gao J, Petersen M, Panstruga R. Plant autoimmunity-fresh insights into an old phenomenon. PLANT PHYSIOLOGY 2022; 188:1419-1434. [PMID: 34958371 PMCID: PMC8896616 DOI: 10.1093/plphys/kiab590] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
The plant immune system is well equipped to ward off the attacks of different types of phytopathogens. It primarily relies on two types of immune sensors-plasma membrane-resident receptor-like kinases and intracellular nucleotide-binding domain leucine-rich repeat (NLRs) receptors that engage preferentially in pattern- and effector-triggered immunity, respectively. Delicate fine-tuning, in particular of the NLR-governed branch of immunity, is key to prevent inappropriate and deleterious activation of plant immune responses. Inadequate NLR allele constellations, such as in the case of hybrid incompatibility, and the mis-activation of NLRs or the absence or modification of proteins guarded by these NLRs can result in the spontaneous initiation of plant defense responses and cell death-a phenomenon referred to as plant autoimmunity. Here, we review recent insights augmenting our mechanistic comprehension of plant autoimmunity. The recent findings broaden our understanding regarding hybrid incompatibility, unravel candidates for proteins likely guarded by NLRs and underline the necessity for the fine-tuning of NLR expression at various levels to avoid autoimmunity. We further present recently emerged tools to study plant autoimmunity and draw a cross-kingdom comparison to the role of NLRs in animal autoimmune conditions.
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Affiliation(s)
- Matthias Freh
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen 52056, Germany
| | - Jinlan Gao
- Institute of Biology, Functional Genomics, Copenhagen University, Copenhagen 2200, Denmark
| | - Morten Petersen
- Institute of Biology, Functional Genomics, Copenhagen University, Copenhagen 2200, Denmark
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen 52056, Germany
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Langdon QK, Powell DL, Kim B, Banerjee SM, Payne C, Dodge TO, Moran B, Fascinetto-Zago P, Schumer M. Predictability and parallelism in the contemporary evolution of hybrid genomes. PLoS Genet 2022; 18:e1009914. [PMID: 35085234 PMCID: PMC8794199 DOI: 10.1371/journal.pgen.1009914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022] Open
Abstract
Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find unexpectedly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.
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Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Daniel L. Powell
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Shreya M. Banerjee
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Tristram O. Dodge
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Ben Moran
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Paola Fascinetto-Zago
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
- Hanna H. Gray Fellow, Howard Hughes Medical Institutes, Chevy Chase, Maryland, United States of America
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Sikder MM, Vestergård M, Kyndt T, Kudjordjie EN, Nicolaisen M. Phytohormones selectively affect plant parasitic nematodes associated with Arabidopsis roots. THE NEW PHYTOLOGIST 2021; 232:1272-1285. [PMID: 34115415 DOI: 10.1111/nph.17549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Phytohormones may affect plant-nematode interactions directly as chemo-attractants or -repellents, or indirectly through the root-associated microbiome or through host defense mechanisms. However, the exact roles of phytohormones in these complex plant-soil-nematode interactions are not well understood. We used Arabidopsis thaliana mutants impaired in phytohormone synthesis or sensitivity to elucidate their role in root-nematode interactions. As root-associated microorganisms may modulate these interactions, we explored correlations between the relative abundances of root-associated nematodes, and bacteria and fungi using amplicon sequencing. We found distinct shifts in relative abundances of a range of nematode taxa in the A. thaliana phytohormone mutants. The root knot nematode Meloidogyne hapla, a sedentary endoparasitic species that is in intimate contact with the host, was highly enriched in JA-, SA- and SL-impaired lines, and in an ET-insensitive line. Positive or negative correlations between specific microbial and nematode taxa were observed, but, as the inference of causal relationships between microbiome responses and effects on nematode communities is premature, this should be studied in detail in future studies. In conclusion, genetic derailment of hormonal balances generally rendered plants vulnerable to endoparasitic nematode attack. Furthermore, preliminary data suggest that this effect may be partially modulated by the associated microbiome.
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Affiliation(s)
- Md Maniruzzaman Sikder
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Tina Kyndt
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Gent, 9000, Belgium
| | - Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, 4200, Denmark
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11
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Li N, Tan Q, Ding J, Pan X, Ma Z. Fine mapping of Ne1, the hybrid necrosis gene complementary to Ne2 in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2813-2821. [PMID: 34023915 DOI: 10.1007/s00122-021-03860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Apart from confinement of Ne1 to a 4.45 Mb genomic segment, markers closely linked to Ne2 were identified and incomplete dominance of both genes in conditioning necrosis severity was shown. Hybrid necrosis in plants is characterized by premature death of leaves or plants in F1 hybrids. Interaction of two complementary dominant genes Ne1 and Ne2 in wheat (Triticum aestivum L.) is known to cause hybrid necrosis. However, the mechanism underlying this necrosis is still elusive. To obtain markers closely-linked to these two genes, Ne1-carrying cultivar Zheng891 was crossed with Ne2-carrying cultivar Pan555. Using BC1F1 plants derived from crosses of the F1 plants with the two parental lines, Ne1 and Ne2 were mapped to a 2.2 cM interval and a 2.3 cM interval with newly developed markers, respectively. Ne1 was further delimited to a 0.19 cM interval using 2015 Ne2-carrying F2 plants. Xwgrc3146, Xwgrc3147 and Xwgrc3150, three of the four markers co-segregating with Ne1, were all Zheng891-dominant, suggesting that, compared with Pan555, Ne1 is located in a region with substantial sequence diversity. The Ne1 interval is syntenic to chromosomes 5H, 4, 9 and 2 of barley, Brachypodium distachyon, rice and sorghum, respectively, and corresponds to a 4.45 Mb Chinese Spring sequence. Variations in necrosis severity of the F2 plants differing in Ne1 and Ne2 genotypes implied that these two genes are incompletely dominant in determining the timing and severity of necrosis.
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Affiliation(s)
- Na Li
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qiuyi Tan
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinhua Ding
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xinglai Pan
- Department of Food Crop Science, Cotton Research Institute, Shanxi Academy of Agriculture Sciences, Yuncheng, Shanxi, China
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China.
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12
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Li L, Weigel D. One Hundred Years of Hybrid Necrosis: Hybrid Autoimmunity as a Window into the Mechanisms and Evolution of Plant-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:213-237. [PMID: 33945695 DOI: 10.1146/annurev-phyto-020620-114826] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hybrid necrosis in plants refers to a genetic autoimmunity syndrome in the progeny of interspecific or intraspecific crosses. Although the phenomenon was first documented in 1920, it has been unequivocally linked to autoimmunity only recently, with the discovery of the underlying genetic and biochemical mechanisms. The most common causal loci encode immune receptors, which are known to differ within and between species. One mechanism can be explained by the guard hypothesis, in which a guard protein, often a nucleotide-binding site-leucine-rich repeat protein, is activated by interaction with a plant protein that mimics standard guardees modified by pathogen effector proteins. Another surprising mechanism is the formation of inappropriately active immune receptor complexes. In this review, we summarize our current knowledge of hybrid necrosis and discuss how its study is not only informing the understanding of immune gene evolution but also revealing new aspects of plant immune signaling.
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Affiliation(s)
- Lei Li
- 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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13
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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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14
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Ordon J, Martin P, Erickson JL, Ferik F, Balcke G, Bonas U, Stuttmann J. Disentangling cause and consequence: genetic dissection of the DANGEROUS MIX2 risk locus, and activation of the DM2h NLR in autoimmunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1008-1023. [PMID: 33629456 DOI: 10.1111/tpj.15215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding domain-leucine-rich repeat-type immune receptors (NLRs) protect plants against pathogenic microbes through intracellular detection of effector proteins. However, this comes at a cost, as NLRs can also induce detrimental autoimmunity in genetic interactions with foreign alleles. This may occur when independently evolved genomes are combined in inter- or intraspecific crosses, or when foreign alleles are introduced by mutagenesis or transgenesis. Most autoimmunity-inducing NLRs are encoded within highly variable NLR gene clusters with no known immune functions, which were termed autoimmune risk loci. Whether risk NLRs differ from sensor NLRs operating in natural pathogen resistance and how risk NLRs are activated in autoimmunity is unknown. Here, we analyzed the DANGEROUS MIX2 risk locus, a major autoimmunity hotspot in Arabidopsis thaliana. By gene editing and heterologous expression, we show that a single gene, DM2h, is necessary and sufficient for autoimmune induction in three independent cases of autoimmunity in accession Landsberg erecta. We focus on autoimmunity provoked by an EDS1-yellow fluorescent protein (YFP)NLS fusion protein to characterize DM2h functionally and determine features of EDS1-YFPNLS activating the immune receptor. Our data suggest that risk NLRs function in a manner reminiscent of sensor NLRs, while autoimmunity-inducing properties of EDS1-YFPNLS in this context are unrelated to the protein's functions as an immune regulator. We propose that autoimmunity, at least in some cases, may be caused by spurious, stochastic interactions of foreign alleles with coincidentally matching risk NLRs.
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Affiliation(s)
- Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Patrick Martin
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jessica Lee Erickson
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Filiz Ferik
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
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15
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Katsuyama Y, Doi M, Shioya S, Hane S, Yoshioka M, Date S, Miyahara C, Ogawa T, Takada R, Okumura H, Ikusawa R, Kitajima S, Oda K, Sato K, Tanaka Y, Tezuka T, Mino M. The role of chaperone complex HSP90-SGT1-RAR1 as the associated machinery for hybrid inviability between Nicotiana gossei Domin and N. tabacum L. Gene 2021; 776:145443. [PMID: 33484759 DOI: 10.1016/j.gene.2021.145443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 12/18/2022]
Abstract
Two cultured cell lines (GTH4 and GTH4S) of a Nicotiana interspecific F1 hybrid (N. gossei × N. tabacum) were comparatively analyzed to find genetic factors related to hybrid inviability. Both cell lines proliferated at 37 °C, but after shifting to 26 °C, GTH4 started to die similar to the F1 hybrid seedlings, whereas GTH4S survived. As cell death requires de novo expression of genes and proteins, we compared expressed protein profiles between the two cell lines, and found that NgSGT1, a cochaperone of the chaperone complex (HSP90-SGT1-RAR1), was expressed in GTH4 but not in GTH4S. Agrobacterium-mediated transient expression of NgSGT1, but not NtSGT1, induced cell death in leaves of N. tabacum, suggesting its possible role in hybrid inviability. Cell death in N. tabacum was also induced by transient expression of NgRAR1, but not NtRAR1. In contrast, transient expression of any parental combinations of three components revealed that NgRAR1 promoted cell death, whereas NtRAR1 suppressed it in N. tabacum. A specific inhibitor of HSP90, geldanamycin, inhibited the progression of hypersensitive response-like cell death in GTH4 and leaf tissue after agroinfiltration. The present study suggested that components of the chaperone complex are involved in the inviability of Nicotiana interspecific hybrid.
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Affiliation(s)
- Yushi Katsuyama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Mizuho Doi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sachi Shioya
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sanae Hane
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Momoko Yoshioka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shuichi Date
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Chika Miyahara
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Tomomichi Ogawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ryo Takada
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hanako Okumura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Rie Ikusawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sakihito Kitajima
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama, 7549-1 Yoshikawa, Kibi Chuou-chou, Kaga-gun, Okayama 716-1241, Japan
| | - Kenji Sato
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshikazu Tanaka
- Biotechnology Division Research & Development Department, The Wakasa Wan Energy Research Center, 64-52-1 Ngatani, Tsuruga, Fukui 914-0135, Japan
| | - Takahiro Tezuka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Masanobu Mino
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
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16
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Roudaire T, Héloir MC, Wendehenne D, Zadoroznyj A, Dubrez L, Poinssot B. Cross Kingdom Immunity: The Role of Immune Receptors and Downstream Signaling in Animal and Plant Cell Death. Front Immunol 2021; 11:612452. [PMID: 33763054 PMCID: PMC7982415 DOI: 10.3389/fimmu.2020.612452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Both plants and animals are endowed with sophisticated innate immune systems to combat microbial attack. In these multicellular eukaryotes, innate immunity implies the presence of cell surface receptors and intracellular receptors able to detect danger signal referred as damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs). Membrane-associated pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), C-type lectin receptors (CLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are employed by these organisms for sensing different invasion patterns before triggering antimicrobial defenses that can be associated with a form of regulated cell death. Intracellularly, animals nucleotide-binding and oligomerization domain (NOD)-like receptors or plants nucleotide-binding domain (NBD)-containing leucine rich repeats (NLRs) immune receptors likely detect effectors injected into the host cell by the pathogen to hijack the immune signaling cascade. Interestingly, during the co-evolution between the hosts and their invaders, key cross-kingdom cell death-signaling macromolecular NLR-complexes have been selected, such as the inflammasome in mammals and the recently discovered resistosome in plants. In both cases, a regulated cell death located at the site of infection constitutes a very effective mean for blocking the pathogen spread and protecting the whole organism from invasion. This review aims to describe the immune mechanisms in animals and plants, mainly focusing on cell death signaling pathways, in order to highlight recent advances that could be used on one side or the other to identify the missing signaling elements between the perception of the invasion pattern by immune receptors, the induction of defenses or the transmission of danger signals to other cells. Although knowledge of plant immunity is less advanced, these organisms have certain advantages allowing easier identification of signaling events, regulators and executors of cell death, which could then be exploited directly for crop protection purposes or by analogy for medical research.
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Affiliation(s)
- Thibault Roudaire
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Marie-Claire Héloir
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Aymeric Zadoroznyj
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurence Dubrez
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Benoit Poinssot
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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17
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Calvo-Baltanás V, Wang J, Chae E. Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances. FRONTIERS IN PLANT SCIENCE 2021; 11:576796. [PMID: 33717206 PMCID: PMC7953517 DOI: 10.3389/fpls.2020.576796] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.
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18
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Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. THE NEW PHYTOLOGIST 2021; 229:1215-1233. [PMID: 32970825 DOI: 10.1111/nph.16947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 05/14/2023]
Abstract
Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.
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Affiliation(s)
- Wei-Lin Wan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Sang-Tae Kim
- Department of Life Sciences, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662, South Korea
| | - Baptiste Castel
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Nuri Charoennit
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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19
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Vaid N, Ishihara H, Plötner B, Sageman-Furnas K, Wiszniewski A, Laitinen RAE. Leaf chlorosis in Arabidopsis thaliana hybrids is associated with transgenerational decline and imbalanced ribosome number. THE NEW PHYTOLOGIST 2020; 228:989-1000. [PMID: 32557724 DOI: 10.1111/nph.16752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 05/09/2023]
Abstract
The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD-box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this study, we use a sophisticated genetic approach to investigate genes underlying hybrid chlorosis. Sequence comparisons, DNA methylation inhibitor drug treatment and segregation analysis were used to investigate the epigenetic regulation of hybrid chlorosis. Relative rRNA numbers were quantified using real-time quantitative PCR. We confirmed the causality of AtRH18 and provided evidence for the involvement of the promoter region of AtRH18 in the hybrid chlorosis. Furthermore, AtMOM1 from the second parent was identified as the likely candidate gene on chromosome 1. Chlorotic hybrids displayed transgenerational decline in chlorosis, and DNA demethylation experiment restored chlorophyll levels in chlorotic hybrids. Quantification of rRNA indicated that hybrid chlorosis was associated with an imbalance in the ratio of cytosolic and plastid ribosomes. Our findings highlight that the epigenetic regulation of AtRH18 causes hybrid breakdown and provide novel information about the role of AtRH18 in plant development.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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20
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Powell DL, García-Olazábal M, Keegan M, Reilly P, Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal GG, Schartl M, Schumer M. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 2020; 368:731-736. [PMID: 32409469 DOI: 10.1126/science.aba5216] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
Abstract
The establishment of reproductive barriers between populations can fuel the evolution of new species. A genetic framework for this process posits that "incompatible" interactions between genes can evolve that result in reduced survival or reproduction in hybrids. However, progress has been slow in identifying individual genes that underlie hybrid incompatibilities. We used a combination of approaches to map the genes that drive the development of an incompatibility that causes melanoma in swordtail fish hybrids. One of the genes involved in this incompatibility also causes melanoma in hybrids between distantly related species. Moreover, this melanoma reduces survival in the wild, likely because of progressive degradation of the fin. This work identifies genes underlying a vertebrate hybrid incompatibility and provides a glimpse into the action of these genes in natural hybrid populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA. .,Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mateo García-Olazábal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Patrick Reilly
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany
| | - Alejandra P Díaz-Loyo
- Laboratorio de Ecología de la Conducta, Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Shreya Banerjee
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - Danielle Blakkan
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, and the Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA
| | - Manfred Schartl
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, Mexico.,Department of Biology, Texas A&M University, College Station, TX, USA.,Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bavaria, Germany.,Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA.,Xiphophorus Genetic Stock Center, Texas State University San Marcos, San Marcos, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.
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21
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Tamborski J, Krasileva KV. Evolution of Plant NLRs: From Natural History to Precise Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:355-378. [PMID: 32092278 DOI: 10.1146/annurev-arplant-081519-035901] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) monitor the plant intracellular environment for signs of pathogen infection. Several mechanisms of NLR-mediated immunity arose independently across multiple species. These include the functional specialization of NLRs into sensors and helpers, the independent emergence of direct and indirect recognition within NLR subfamilies, the regulation of NLRs by small RNAs, and the formation of NLR networks. Understanding the evolutionary history of NLRs can shed light on both the origin of pathogen recognition and the common constraints on the plant immune system. Attempts to engineer disease resistance have been sparse and rarely informed by evolutionary knowledge. In this review, we discuss the evolution of NLRs, give an overview of previous engineering attempts, and propose how to use evolutionary knowledge to advance future research in the generation of novel disease-recognition capabilities.
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Affiliation(s)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
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22
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Matsubara K. How Hybrid Breakdown Can Be Handled in Rice Crossbreeding? FRONTIERS IN PLANT SCIENCE 2020; 11:575412. [PMID: 33193514 PMCID: PMC7641626 DOI: 10.3389/fpls.2020.575412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 05/16/2023]
Abstract
In crosses between genetically divergent parents, traits such as weakness and sterility often segregate in later generations. This hybrid breakdown functions as a reproductive barrier and reduces selection efficiency in crossbreeding. Here, I provide an overview of hybrid breakdown in rice crosses and discuss ways to avoid and mitigate the effects of hybrid breakdown on rice crossbreeding, including genomics-assisted breeding.
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23
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Rowan BA, Heavens D, Feuerborn TR, Tock AJ, Henderson IR, Weigel D. An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics 2019; 213:771-787. [PMID: 31527048 PMCID: PMC6827372 DOI: 10.1534/genetics.119.302406] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022] Open
Abstract
Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of >17,000 COs between the Col-0 and Ler-0 accessions of Arabidopsis thaliana COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
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Affiliation(s)
- Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Tatiana R Feuerborn
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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24
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Deng J, Fang L, Zhu X, Zhou B, Zhang T. A CC-NBS-LRR gene induces hybrid lethality in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5145-5156. [PMID: 31270546 PMCID: PMC6793457 DOI: 10.1093/jxb/erz312] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/25/2019] [Indexed: 05/20/2023]
Abstract
Hybrid lethality forms a reproductive barrier that has been found in many eukaryotes. Most cases follow the Bateson-Dobzhansky-Muller genetic incompatibility model and involve two or more loci. In this study, we demonstrate that a coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) gene is the causal gene underlying the Le4 locus for interspecific hybrid lethality between Gossypium barbadense and G. hirsutum (cotton). Silencing this CC-NBS-LRR gene can restore F1 plants from a lethal to a normal phenotype. A total of 11 099 genes were differentially expressed between the leaves of normal and lethal F1 plants, of which genes related to autoimmune responses were highly enriched. Genes related to ATP-binding and ATPase were up-regulated before the lethal syndrome appeared; this may result in the conversion of Le4 into an active state and hence trigger immune signals in the absence of biotic/abiotic stress. We discuss our results in relation to the evolution and domestication of Sea Island cottons and the molecular mechanisms of hybrid lethality associated with autoimmune responses. Our findings provide new insights into reproductive isolation and may benefit cotton breeding.
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Affiliation(s)
- Jieqiong Deng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Lei Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
| | - Xiefei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Correspondence: or
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China
- Correspondence: or
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25
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van Wersch S, Li X. Stronger When Together: Clustering of Plant NLR Disease resistance Genes. TRENDS IN PLANT SCIENCE 2019; 24:688-699. [PMID: 31266697 DOI: 10.1016/j.tplants.2019.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/05/2019] [Accepted: 05/16/2019] [Indexed: 05/14/2023]
Abstract
Gene clustering is rare in eukaryotes. However, nucleotide-binding leucine-rich repeat (NLR)-encoding disease resistance (R) genes show consistent clustering in plant genomes. These arrangements are likely to provide coregulatory benefits, as suggested by growing evidence that the gene products of both paired and larger clusters of NLRs act together in triggering immunity. Head-to-head gene pairs where one of the encoded NLRs includes an integrated decoy domain appear to behave differently than clusters evolved from closely related typical NLRs. These patterns may help to explain the broad resistance that most plants have despite their finite number of R genes. By taking into consideration the relationship between genomic arrangement and function, we can improve our understanding of and ability to predict plant immune detection.
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Affiliation(s)
- Solveig van Wersch
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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26
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Ordon J, Bressan M, Kretschmer C, Dall'Osto L, Marillonnet S, Bassi R, Stuttmann J. Optimized Cas9 expression systems for highly efficient Arabidopsis genome editing facilitate isolation of complex alleles in a single generation. Funct Integr Genomics 2019; 20:151-162. [PMID: 30796544 DOI: 10.1007/s10142-019-00665-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 02/05/2019] [Indexed: 12/14/2022]
Abstract
Genetic resources for the model plant Arabidopsis comprise mutant lines defective in almost any single gene in reference accession Columbia. However, gene redundancy and/or close linkage often render it extremely laborious or even impossible to isolate a desired line lacking a specific function or set of genes from segregating populations. Therefore, we here evaluated strategies and efficiencies for the inactivation of multiple genes by Cas9-based nucleases and multiplexing. In first attempts, we succeeded in isolating a mutant line carrying a 70 kb deletion, which occurred at a frequency of ~ 1.6% in the T2 generation, through PCR-based screening of numerous individuals. However, we failed to isolate a line lacking Lhcb1 genes, which are present in five copies organized at two loci in the Arabidopsis genome. To improve efficiency of our Cas9-based nuclease system, regulatory sequences controlling Cas9 expression levels and timing were systematically compared. Indeed, use of DD45 and RPS5a promoters improved efficiency of our genome editing system by approximately 25-30-fold in comparison to the previous ubiquitin promoter. Using an optimized genome editing system with RPS5a promoter-driven Cas9, putatively quintuple mutant lines lacking detectable amounts of Lhcb1 protein represented approximately 30% of T1 transformants. These results show how improved genome editing systems facilitate the isolation of complex mutant alleles, previously considered impossible to generate, at high frequency even in a single (T1) generation.
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Affiliation(s)
- Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Mauro Bressan
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany.
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27
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Vaid N, Laitinen RAE. Diverse paths to hybrid incompatibility in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:199-213. [PMID: 30098060 DOI: 10.1111/tpj.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 05/28/2023]
Abstract
One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high-throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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28
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Ouyang Y, Zhang Q. The molecular and evolutionary basis of reproductive isolation in plants. J Genet Genomics 2018; 45:613-620. [PMID: 30459118 DOI: 10.1016/j.jgg.2018.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/19/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022]
Abstract
Reproductive isolation is defined as processes that prevent individuals of different populations from mating, survival or producing fertile offspring. Reproductive isolation is critical for driving speciation and maintaining species identity, which has been a fundamental concern in evolutionary biology. In plants, reproductive isolation can be divided into prezygotic and postzygotic reproductive barriers, according to its occurrence at different developmental stages. Postzygotic reproductive isolation caused by reduced fitness in hybrids is frequently observed in plants, which hinders gene flow between divergent populations and has substantial effects on genetic differentiation and speciation, and thus is a major obstacle for utilization of heterosis in hybrid crops. During the past decade, China has made tremendous progress in molecular and evolutionary basis of prezygotic and postzygotic reproductive barriers in plants. Present understandings in reproductive isolation especially with new data in the last several years well support three evolutionary genetic models, which represent a general mechanism underlying genomic differentiation and speciation. The updated understanding will offer new approaches for the development of wide-compatibility or neutral varieties, which facilitate breeding of hybrid rice as well as other hybrid crops.
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Affiliation(s)
- Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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29
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Atanasov KE, Liu C, Erban A, Kopka J, Parker JE, Alcázar R. NLR Mutations Suppressing Immune Hybrid Incompatibility and Their Effects on Disease Resistance. PLANT PHYSIOLOGY 2018; 177:1152-1169. [PMID: 29794019 PMCID: PMC6052992 DOI: 10.1104/pp.18.00462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Genetic divergence between populations can lead to reproductive isolation. Hybrid incompatibilities (HI) represent intermediate points along a continuum toward speciation. In plants, genetic variation in disease resistance (R) genes underlies several cases of HI. The progeny of a cross between Arabidopsis (Arabidopsis thaliana) accessions Landsberg erecta (Ler, Poland) and Kashmir2 (Kas2, central Asia) exhibits immune-related HI. This incompatibility is due to a genetic interaction between a cluster of eight TNL (TOLL/INTERLEUKIN1 RECEPTOR-NUCLEOTIDE BINDING-LEU RICH REPEAT) RPP1 (RECOGNITION OF PERONOSPORA PARASITICA1)-like genes (R1-R8) from Ler and central Asian alleles of a Strubbelig-family receptor-like kinase (SRF3) from Kas2. In characterizing mutants altered in Ler/Kas2 HI, we mapped multiple mutations to the RPP1-like Ler locus. Analysis of these suppressor of Ler/Kas2 incompatibility (sulki) mutants reveals complex, additive and epistatic interactions underlying RPP1-like Ler locus activity. The effects of these mutations were measured on basal defense, global gene expression, primary metabolism, and disease resistance to a local Hyaloperonospora arabidopsidis isolate (Hpa Gw) collected from Gorzów (Gw), where the Landsberg accession originated. Gene expression sectors and metabolic hallmarks identified for HI are both dependent and independent of RPP1-like Ler members. We establish that mutations suppressing immune-related Ler/Kas2 HI do not compromise resistance to Hpa Gw. QTL mapping analysis of Hpa Gw resistance point to RPP7 as the causal locus. This work provides insight into the complex genetic architecture of the RPP1-like Ler locus and immune-related HI in Arabidopsis and into the contributions of RPP1-like genes to HI and defense.
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Affiliation(s)
- Kostadin E Atanasov
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Changxin Liu
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Alexander Erban
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
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30
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Tennessen JA. Gene buddies: linked balanced polymorphisms reinforce each other even in the absence of epistasis. PeerJ 2018; 6:e5110. [PMID: 29967750 PMCID: PMC6026533 DOI: 10.7717/peerj.5110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/05/2018] [Indexed: 01/16/2023] Open
Abstract
The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. While these results may be intuitive, they have important implications for genetic architecture: clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations, and such genes cannot be assumed to be functionally associated. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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31
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Fishman L, Sweigart AL. When Two Rights Make a Wrong: The Evolutionary Genetics of Plant Hybrid Incompatibilities. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:707-731. [PMID: 29505737 DOI: 10.1146/annurev-arplant-042817-040113] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hybrids between flowering plant species often exhibit reduced fitness, including sterility and inviability. Such hybrid incompatibilities create barriers to genetic exchange that can promote reproductive isolation between diverging populations and, ultimately, speciation. Additionally, hybrid breakdown opens a window into hidden molecular and evolutionary processes occurring within species. Here, we review recent work on the mechanisms and origins of hybrid incompatibility in flowering plants, including both diverse genic interactions and chromosomal incompatibilities. Conflict and coevolution among and within plant genomes contributes to the evolution of some well-characterized genic incompatibilities, but duplication and drift also play important roles. Inversions, while contributing to speciation by suppressing recombination, rarely cause underdominant sterility. Translocations cause severe F1 sterility by disrupting meiosis in heterozygotes, making their fixation in outcrossing sister species a paradox. Evolutionary genomic analyses of both genic and chromosomal incompatibilities, in the context of population genetic theory, can explicitly test alternative scenarios for their origins.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
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32
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Alhajturki D, Muralidharan S, Nurmi M, Rowan BA, Lunn JE, Boldt H, Salem MA, Alseekh S, Jorzig C, Feil R, Giavalisco P, Fernie AR, Weigel D, Laitinen RAE. Dose-dependent interactions between two loci trigger altered shoot growth in BG-5 × Krotzenburg-0 (Kro-0) hybrids of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:392-406. [PMID: 28906562 DOI: 10.1111/nph.14781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/06/2017] [Indexed: 06/07/2023]
Abstract
Hybrids occasionally exhibit genetic interactions resulting in reduced fitness in comparison to their parents. Studies of Arabidopsis thaliana have highlighted the role of immune conflicts, but less is known about the role of other factors in hybrid incompatibility in plants. Here, we present a new hybrid incompatibility phenomenon in this species. We have characterized a new case of F1 hybrid incompatibility from a cross between the A. thaliana accessions Krotzenburg-0 (Kro-0) and BG-5, by conducting transcript, metabolite and hormone analyses, and identified the causal loci through genetic mapping. The F1 hybrids showed arrested growth of the main stem, altered shoot architecture, and altered concentrations of hormones in comparison to parents. The F1 phenotype could be rescued in a developmental-stage-dependent manner by shifting to a higher growth temperature. These F1 phenotypes were linked to two loci, one on chromosome 2 and one on chromosome 3. The F2 generation segregated plants with more severe phenotypes which were linked to the same loci as those in the F1 . This study provides novel insights into how previously unknown mechanisms controlling shoot branching and stem growth can result in hybrid incompatibility.
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Affiliation(s)
- Dema Alhajturki
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | | | - Markus Nurmi
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Beth A Rowan
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Helena Boldt
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Mohamed A Salem
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Christian Jorzig
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
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33
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Li G, Li X, Wang Y, Mi J, Xing F, Zhang D, Dong Q, Li X, Xiao J, Zhang Q, Ouyang Y. Three representative inter and intra-subspecific crosses reveal the genetic architecture of reproductive isolation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:349-362. [PMID: 28805257 DOI: 10.1111/tpj.13661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/25/2017] [Accepted: 08/07/2017] [Indexed: 05/28/2023]
Abstract
Systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra-high-density genetic maps, 43 single-locus quantitative trait loci (QTLs) and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice. Ten newly detected single-locus QTLs for inter- and intra-subspecific fertility are identified. Three loci for embryo-sac fertility are detected in both Nip × ZS97 and Nip × MH63 crosses, whereas QTLs for pollen fertility are not in common between the two crosses thus leading to fertility variation. Five loci responsible for fertility and segregation distortion are observed in the ZS97 × MH63 cross. The importance of two-locus interactions on fertility are quantified in the whole genome, which identify that three types of interaction contribute to fertility reduction in the hybrid. These results construct the genetic architecture with respect to various forms of reproductive barriers in rice, which have significant implications in utilization of inter-subspecific heterosis along with improvement in the fertility of indica-indica hybrids at single- and multi-locus level.
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Affiliation(s)
- Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoting Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Dahan Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiyan Dong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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34
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Samans B, Chalhoub B, Snowdon RJ. Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus. THE PLANT GENOME 2017; 10. [PMID: 29293818 DOI: 10.3835/plantgenome2017.02.0013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.
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Abstract
The first plant disease resistance (R) genes were identified and cloned more than two decades ago. Since then, many more R genes have been identified and characterized in numerous plant pathosystems. Most of these encode members of the large family of intracellular NLRs (NOD-like receptors), which also includes animal immune receptors. New discoveries in this expanding field of research provide new elements for our understanding of plant NLR function. But what do we know about plant NLR function today? Genetic, structural, and functional analyses have uncovered a number of commonalities and differences in pathogen recognition strategies as well as how NLRs are regulated and activate defense signaling, but many unknowns remain. This review gives an update on the latest discoveries and breakthroughs in this field, with an emphasis on structural findings and some comparison to animal NLRs, which can provide additional insights and paradigms in plant NLR function.
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Affiliation(s)
- Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
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Tran DTN, Chung EH, Habring-Müller A, Demar M, Schwab R, Dangl JL, Weigel D, Chae E. Activation of a Plant NLR Complex through Heteromeric Association with an Autoimmune Risk Variant of Another NLR. Curr Biol 2017; 27:1148-1160. [PMID: 28416116 PMCID: PMC5405217 DOI: 10.1016/j.cub.2017.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/09/2017] [Accepted: 03/09/2017] [Indexed: 12/18/2022]
Abstract
When independently evolved immune receptor variants meet in hybrid plants, they can activate immune signaling in the absence of non-self recognition. Such autoimmune risk alleles have recurrently evolved at the DANGEROUS MIX2 (DM2) nucleotide-binding domain and leucine-rich repeat (NLR)-encoding locus in A. thaliana. One of these activates signaling in the presence of a particular variant encoded at another NLR locus, DM1. We show that the risk variants of DM1 and DM2d NLRs signal through the same pathway that is activated when plant NLRs recognize non-self elicitors. This requires the P loops of each protein and Toll/interleukin-1 receptor (TIR)-domain-mediated heteromeric association of DM1 and DM2d. DM1 and DM2d each resides in a multimeric complex in the absence of signaling, with the DM1 complex shifting to higher molecular weight when heteromerizing DM2 variants are present. The activation of the DM1 complex appears to be sensitive to the conformation of the heteromerizing DM2 variant. Autoimmunity triggered by interaction of this NLR pair thus suggests that activity of heteromeric NLR signaling complexes depends on the sum of activation potentials of partner NLRs. Two unlinked plant NLRs physically interact to trigger autoimmunity The N-terminal TIR domains mediate heteromeric NLR association NLR multimerization is not sufficient for signaling
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Affiliation(s)
- Diep T N Tran
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anette Habring-Müller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Monika Demar
- 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
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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37
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Świadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, Laitinen RAE. Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2017; 213:900-915. [PMID: 27588563 DOI: 10.1111/nph.14155] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A. thaliana.
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Affiliation(s)
- Magdalena Świadek
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- University of Potsdam, Potsdam, 14476, Germany
| | - Daniela Sieh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Jing Yu
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Marco Todesco
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christian Jorzig
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | | | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Eunyoung Chae
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Florian Schröder
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
| | - Sang-Tae Kim
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
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Gu L, Wu Y, Jiang M, Si W, Zhang X, Tian D, Yang S. Dissimilar Manifestation of Heterosis in Superhybrid Rice at Early-Tillering Stage under Nutrient-Deficient and Nutrient-Sufficient Condition. PLANT PHYSIOLOGY 2016; 172:1142-1153. [PMID: 27540108 PMCID: PMC5047080 DOI: 10.1104/pp.16.00579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/14/2016] [Indexed: 05/13/2023]
Abstract
Heterosis has long been exploited for crop breeding; however, the genetic mechanisms, particularly the initial establishment of heterosis during the early vegetative growth phase, remain elusive. The biggest challenge for that is to exclude noise genes from the identified heterosis-related candidates. Herein, we use nutrient-deficient hybrid with no measurable growth heterosis as control. After filtering these irrelevant genes, only 336 differentially expressed genes (DEGs), which is significantly lower than in previous reports, were identified as heterosis-related genes in a superhybrid rice of Liang-You-Pei-Jiu (LYP9) at early-tillering stage. Among the DEGs that could be mapped to quantitative trait loci (QTL), approximately 72.8% could be covered by yield or growth vigor-related QTL, thereby suggesting that our DEGs were reliable and may have potential value to rice breeding. Among the 336 DEGs identified, a majority showed intermediate expression relative to that of its parental lines (i.e. additive effects), particularly, expression was frequently more similar to the paternal line rather than the maternal line (44.1% versus 32.7%); the remaining 27.1% were exclusively up- or down-regulated between the hybrid and either parent. Interestingly, up-regulated genes encoded various enzymes, whereas down-regulated genes were enriched in responses to stress, indicating that hybrids may benefit from both activating metabolism-related pathways and alleviating fitness cost through allelic interactions. Furthermore, a significantly larger proportion of divergent genes and higher nonsynonymous substitutions rates were detected in these DEGs, suggesting a potential contribution to the establishment of heterosis in superhybrid rice LYP9.
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Affiliation(s)
- Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Ying Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.)
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Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc Natl Acad Sci U S A 2016; 113:E4052-60. [PMID: 27354520 DOI: 10.1073/pnas.1607532113] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.
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Hou J, Fournier T, Schacherer J. Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast. FEMS Yeast Res 2016; 16:fow048. [PMID: 27288348 DOI: 10.1093/femsyr/fow048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/13/2022] Open
Abstract
Exploring the origin and extent of reproductive isolation within the same species is valuable to capture early events to the onset of speciation. In multiple genetic models, reproductive isolation was recently observed at the intraspecific scale, indicating that the raw potential for speciation segregates readily within populations, which could be a rule rather than an exception in a broad context. We briefly recapitulate the molecular evidence of intrinsic post-zygotic isolation in major model organisms including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and their close relatives. We then focus on recent advances in yeast and review the genetic basis of post-zygotic isolation within and between multiple members of the Saccharomyces genus, especially in Saccharomyces cerevisiae We discuss the role of various mechanisms involved in the onset of reproductive isolation including DNA sequence divergence, chromosomal rearrangement, cytonuclear as well as nuclear-nuclear genetic incompatibilities and provide a comparative view along a continuum of genetic differentiation, which encompasses intraspecific populations, recent delineating nascent species as well as closely related sister species in the same subphylum.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Téo Fournier
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
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41
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Goritschnig S, Steinbrenner AD, Grunwald DJ, Staskawicz BJ. Structurally distinct Arabidopsis thaliana NLR immune receptors recognize tandem WY domains of an oomycete effector. THE NEW PHYTOLOGIST 2016; 210:984-96. [PMID: 26725254 DOI: 10.1111/nph.13823] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/18/2015] [Indexed: 05/27/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NB-LRR, or NLR) receptors mediate pathogen recognition. The Arabidopsis thaliana NLR RPP1 recognizes the tandem WY-domain effector ATR1 from the oomycete Hyaloperonospora arabidopsidis through direct association with C-terminal LRRs. We isolated and characterized homologous NLR genes RPP1-EstA and RPP1-ZdrA from two Arabidopsis ecotypes, Estland (Est-1) and Zdarec (Zdr-1), responsible for recognizing a novel spectrum of ATR1 alleles. RPP1-EstA and -ZdrA encode nearly identical NLRs that are phylogenetically distinct from known immunity-activating RPP1 homologs and possess greatly expanded LRR domains. Site-directed mutagenesis and truncation analysis of ATR1 suggests that these homologs recognize a novel surface of the 2(nd) WY domain of ATR1, partially specified by a C-terminal region of the LRR domain. Synteny comparison with RPP1 loci involved in hybrid incompatibility suggests that these functions evolved independently. Closely related RPP1 homologs have diversified their recognition spectra through LRR expansion and sequence variation, allowing them to detect multiple surfaces of the same pathogen effector. Engineering NLR receptor specificity may require a similar combination of repeat expansion and tailored amino acid variation.
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Affiliation(s)
- Sandra Goritschnig
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Adam D Steinbrenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Derrick J Grunwald
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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42
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Stuttmann J, Peine N, Garcia AV, Wagner C, Choudhury SR, Wang Y, James GV, Griebel T, Alcázar R, Tsuda K, Schneeberger K, Parker JE. Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genet 2016; 12:e1005990. [PMID: 27082651 PMCID: PMC4833295 DOI: 10.1371/journal.pgen.1005990] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways. Plants tune their cellular and developmental programs to different environmental stimuli. Central players in the plant biotic stress response network are intracellular NLR receptors which intercept specific disease-inducing molecules (effectors) produced by pathogenic microbes. Variation in NLR gene repertoires between plant genetic lines is driven by pathogen selection pressure. One evolutionary question is how new, functional NLRs are assembled within a plant genome without mis-activating defense pathways, which can have strong negative effects on growth and fitness. This study focuses on a large, polymorphic sub-class of NLR receptors called TNLs present in dicotyledenous plant lineages. TNL receptors confer immunity to a broad range of pathogens. They also frequently underlie autoimmunity caused by their mis-regulation or deleterious allelic interactions with other genes in crosses between different genetic lines (hybrid incompatibility, HI). TNL pathogen-triggered and autoimmune responses require the conserved nucleocytoplasmic protein EDS1 to transcriptionally reprogram cells for defense. We discover in Arabidopsis thaliana that high levels of nuclear-enriched EDS1 induce transcriptional activation of defenses and growth inhibition without a pathogen effector stimulus. In a mutational screen, we identify one rapidly evolving TNL gene, DM2hLer, as a driver of nuclear EDS1 autoimmunity. DM2hLer also contributes to two separate cases of EDS1-dependent autoimmunity. Genetic cooperation between DM2hLer and EDS1 suggests a functional relationship in the transcriptional feed-forward regulation of defense pathways.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
- * E-mail: (JS); (JEP)
| | - Nora Peine
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana V. Garcia
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christine Wagner
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Sayan R. Choudhury
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yiming Wang
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Griebel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Alcázar
- Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (JS); (JEP)
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43
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Affiliation(s)
- Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Diep T. N. Tran
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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Agler MT, Ruhe J, Kroll S, Morhenn C, Kim ST, Weigel D, Kemen EM. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation. PLoS Biol 2016; 14:e1002352. [PMID: 26788878 PMCID: PMC4720289 DOI: 10.1371/journal.pbio.1002352] [Citation(s) in RCA: 619] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022] Open
Abstract
Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. Microbial interactions between kingdoms are responsible for significant microbiome variation on the surface of plants. Highly connected microbes are most important, amplifying abiotic and host factors to cause large perturbations in the structure of microbial communities. Under natural conditions, plant growth and behavior strongly depend on associated microbial communities called the microbiome. Much research has been performed to evaluate how the environment and plant genes help to determine the structure of the microbiome. Here, we show that interactions between microorganisms on plants can be responsible for large portions of observed microbial community structures on leaves. Importantly, particular microbes, termed “hub microbes” due to their central position in a microbial network, are disproportionally important in shaping microbial communities on plant hosts. We discovered fungal and oomycete hub microbes that act by suppressing the growth and diversity of other microbes—even across kingdoms—and several candidate bacterial hubs, which largely positively control the abundance of other bacteria. We also showed that factors impacting the microbial community—such as plant genotype—are strongest if they affect colonization of a hub microbe because the hub in turn affects colonization by many other microbes. Our results further suggest that hub microbes interact directly or via the microbial community. Hub microbes are thus promising targets for better understanding the effects of host genomic engineering and for future work in controlling disease-associated and beneficial host-associated microbial communities.
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Affiliation(s)
- Matthew T. Agler
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Ruhe
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Samuel Kroll
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eric M. Kemen
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
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Chen C, E Z, Lin HX. Evolution and Molecular Control of Hybrid Incompatibility in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1208. [PMID: 27563306 PMCID: PMC4980391 DOI: 10.3389/fpls.2016.01208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/29/2016] [Indexed: 05/09/2023]
Abstract
Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with "parasitic" selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
- *Correspondence: Chen Chen,
| | - Zhiguo E
- China National Rice Research InstituteHangzhou, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics and CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
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Cook DE, Mesarich CH, Thomma BPHJ. Understanding plant immunity as a surveillance system to detect invasion. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:541-63. [PMID: 26047564 DOI: 10.1146/annurev-phyto-080614-120114] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Various conceptual models to describe the plant immune system have been presented. The most recent paradigm to gain wide acceptance in the field is often referred to as the zigzag model, which reconciles the previously formulated gene-for-gene hypothesis with the recognition of general elicitors in a single model. This review focuses on the limitations of the current paradigm of molecular plant-microbe interactions and how it too narrowly defines the plant immune system. As such, we discuss an alternative view of plant innate immunity as a system that evolves to detect invasion. This view accommodates the range from mutualistic to parasitic symbioses that plants form with diverse organisms, as well as the spectrum of ligands that the plant immune system perceives. Finally, how this view can contribute to the current practice of resistance breeding is discussed.
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Affiliation(s)
- David E Cook
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands; ,
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