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Gurina AA, Gancheva MS, Alpatieva NV, Rogozina EV. In silico search for and analysis of R gene variation in primitive cultivated potato species. Vavilovskii Zhurnal Genet Selektsii 2024; 28:175-184. [PMID: 38680181 PMCID: PMC11043503 DOI: 10.18699/vjgb-24-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 05/01/2024] Open
Abstract
Pathogen recognition receptors encoded by R genes play a key role in plant protection. Nowadays, R genes are a basis for breeding many crops, including potato. Many potato R genes have been discovered and found suitable for breeding thanks to the studies of a wide variety of wild potato species. The use of primitive cultivated potato species (PCPS) as representatives of the primary gene pool can also be promising in this respect. PCPS are the closest to the early domesticated forms of potato; therefore, their investigation could help understand the evolution of R genes. The present study was aimed at identifying and analyzing R genes in PCPS listed in the open database of NCBI and Solomics DB. In total, the study involved 27 accessions belonging to three species: Solanum phureja Juz. & Bukasov, S. stenotomum Juz. & Bukasov and S. goniocalyx Juz. & Bukasov Materials for the analysis were the sequencing data for the said three species from the PRJNA394943 and PRJCA006011 projects. An in silico search was carried out for sequences homologous to 26 R genes identified in potato species differing in phylogenetic distance from PCPS, namely nightshade (S. americanum), North- (S. bulbocastanum, S. demissum) and South-American (S. venturii, S. berthaultii) wild potato species, as well as the cultivated potato species S. tuberosum and S. andigenum. Homologs of all investigated protein-coding sequences were discovered in PCPS with a relatively high degree of similarity (85-100 %). Homologs of the Rpi-R3b, Rpi-amr3 and Rpi-ber1 genes have been identified in PCPS for the first time. An analysis of polymorphism of nucleotide and amino acid sequences has been carried out for 15 R genes. The differences in frequencies of substitutions in PCPS have been demonstrated by analysis of R genes, the reference sequences of which have been identified in different species. For all the studied NBS-LRR genes, the proportion of substituted amino acids in the LRR domain exceeds this figure for the NBS domain. The potential prospects of using PCPS as sources of resistance to Verticillium wilt have been shown.
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Affiliation(s)
- A A Gurina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - M S Gancheva
- St. Petersburg State University, St. Petersburg, Russia
| | - N V Alpatieva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - E V Rogozina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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Bali S, Gleason C. Unveiling the Diversity: Plant Parasitic Nematode Effectors and Their Plant Interaction Partners. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:179-189. [PMID: 37870371 DOI: 10.1094/mpmi-09-23-0124-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Root-knot and cyst nematodes are two groups of plant parasitic nematodes that cause the majority of crop losses in agriculture. As a result, these nematodes are the focus of most nematode effector research. Root-knot and cyst nematode effectors are defined as secreted molecules, typically proteins, with crucial roles in nematode parasitism. There are likely hundreds of secreted effector molecules exuded through the nematode stylet into the plant. The current research has shown that nematode effectors can target a variety of host proteins and have impacts that include the suppression of plant immune responses and the manipulation of host hormone signaling. The discovery of effectors that localize to the nucleus indicates that the nematodes can directly modulate host gene expression for cellular reprogramming during feeding site formation. In addition, plant peptide mimicry by some nematode effectors highlights the sophisticated strategies the nematodes employ to manipulate host processes. Here we describe research on the interactions between nematode effectors and host proteins that will provide insights into the molecular mechanisms underpinning plant-nematode interactions. By identifying the host proteins and pathways that are targeted by root-knot and cyst nematode effectors, scientists can gain a better understanding of how nematodes establish feeding sites and subvert plant immune responses. Such information will be invaluable for future engineering of nematode-resistant crops, ultimately fostering advancements in agricultural practices and crop protection. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.
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Affiliation(s)
- Sapinder Bali
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
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Pidon H, Ruge-Wehling B, Will T, Habekuß A, Wendler N, Oldach K, Maasberg-Prelle A, Korzun V, Stein N. High-resolution mapping of Ryd4 Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:60. [PMID: 38409375 PMCID: PMC10896957 DOI: 10.1007/s00122-024-04542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
KEY MESSAGE We mapped Ryd4Hb in a 66.5 kbp interval in barley and dissociated it from a sublethality factor. These results will enable a targeted selection of the resistance in barley breeding. Virus diseases are causing high yield losses in crops worldwide. The Barley yellow dwarf virus (BYDV) complex is responsible for one of the most widespread and economically important viral diseases of cereals. While no gene conferring complete resistance (immunity) has been uncovered in the primary gene pool of barley, sources of resistance were searched and identified in the wild relative Hordeum bulbosum, representing the secondary gene pool of barley. One such locus, Ryd4Hb, has been previously introgressed into barley, and was allocated to chromosome 3H, but is tightly linked to a sublethality factor that prevents the incorporation and utilization of Ryd4Hb in barley varieties. To solve this problem, we fine-mapped Ryd4Hb and separated it from this negative factor. We narrowed the Ryd4Hb locus to a corresponding 66.5 kbp physical interval in the barley 'Morex' reference genome. The region comprises a gene from the nucleotide-binding and leucine-rich repeat immune receptor family, typical of dominant virus resistance genes. The closest homolog to this Ryd4Hb candidate gene is the wheat Sr35 stem rust resistance gene. In addition to the fine mapping, we reduced the interval bearing the sublethality factor to 600 kbp in barley. Aphid feeding experiments demonstrated that Ryd4Hb provides a resistance to BYDV rather than to its vector. The presented results, including the high-throughput molecular markers, will permit a more targeted selection of the resistance in breeding, enabling the use of Ryd4Hb in barley varieties.
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Affiliation(s)
- Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
| | - Brigitte Ruge-Wehling
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
| | - Torsten Will
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Antje Habekuß
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | | | | | | | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Göttingen, Germany.
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Wang Y, Brown LH, Adams TM, Cheung YW, Li J, Young V, Todd DT, Armstrong MR, Neugebauer K, Kaur A, Harrower B, Oome S, Wang X, Bayer M, Hein I. SMRT-AgRenSeq-d in potato ( Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5. HORTICULTURE RESEARCH 2023; 10:uhad211. [PMID: 38023472 PMCID: PMC10681002 DOI: 10.1093/hr/uhad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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Affiliation(s)
- Yuhan Wang
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Lynn H Brown
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas M Adams
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuk Woon Cheung
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Jie Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Vanessa Young
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Drummond T Todd
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles R Armstrong
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Konrad Neugebauer
- Biomathematics and Statistics Scotland, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Crop Research Centre, Teagasc, Oak Park, Carlow R93 XE12, Ireland
| | - Brian Harrower
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Stan Oome
- HZPC Research B.V. HZPC, Edisonweg 5, 8501 XG Joure, Netherlands
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Micha Bayer
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
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Dutta TK, Ray S, Phani V. The status of the CRISPR/Cas9 research in plant-nematode interactions. PLANTA 2023; 258:103. [PMID: 37874380 DOI: 10.1007/s00425-023-04259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/01/2023] [Indexed: 10/25/2023]
Abstract
MAIN CONCLUSION As an important biotic stressor, plant-parasitic nematodes afflict global crop productivity. Deployment of CRISPR/Cas9 system that selectively knock out host susceptibility genes conferred improved nematode tolerance in crop plants. As an important biotic stressor, plant-parasitic nematodes cause a considerable yield decline in crop plants that eventually contributes to a negative impact on global food security. Being obligate plant parasites, the root-knot and cyst nematodes maintain an intricate and sophisticated relationship with their host plants by hijacking the host's physiological and metabolic pathways for their own benefit. Significant progress has been made toward developing RNAi-based transgenic crops that confer nematode resistance. However, the strategy of host-induced gene silencing that targets nematode effectors is likely to fail because the induced silencing of effectors (which interact with plant R genes) may lead to the development of nematode phenotypes that break resistance. Lately, the CRISPR/Cas9-based genome editing system has been deployed to achieve host resistance against bacteria, fungi, and viruses. In these studies, host susceptibility (S) genes were knocked out to achieve resistance via loss of susceptibility. As the S genes are recessively inherited in plants, induced mutations of the S genes are likely to be long-lasting and confer broad-spectrum resistance. A number of S genes contributing to plant susceptibility to nematodes have been identified in Arabidopsis thaliana, rice, tomato, cucumber, and soybean. A few of these S genes were targeted for CRISPR/Cas9-based knockout experiments to improve nematode tolerance in crop plants. Nevertheless, the CRISPR/Cas9 system was mostly utilized to interrogate the molecular basis of plant-nematode interactions rather than direct research toward achieving tolerance in crop plants. The current standalone article summarizes the progress made so far on CRISPR/Cas9 research in plant-nematode interactions.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Soham Ray
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya, Dakshin Dinajpur, West Bengal, 733133, India
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Xu S, Tian P, Jiang Z, Chen X, Li B, Sun J, Zhang Z. Transcriptome analysis of two tobacco varieties with contrast resistance to Meloidogyne incognita in response to PVY M SN R infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1213494. [PMID: 37701805 PMCID: PMC10493397 DOI: 10.3389/fpls.2023.1213494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023]
Abstract
Root-knot nematode (RKN) disease is a major disease of tobacco worldwide, which seriously hinders the improvement of tobacco yield and quality. Obvious veinal necrosis-hypersensitive responses are observed only in RKN-resistant lines infected by Potyvirus Y (PVY) MSNR, making this an effective approach to screen for RKN-resistant tobacco. RNA-seq analysis, real-time quantitative PCR (qRT-PCR) and functional enrichment analysis were conducted to gain insight into the transcription dynamics difference between G28 (RKN-resistant) and CBH (RKN-susceptible) varieties infected with PVY MSNR. Results showed that a total of 7900, 10576, 9921, 11530 and 12531 differentially expressed genes (DEGs) were identified between the two varieties at 0, 1, 3, 5, and 7 d after infection, respectively. DEGs were associated with plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and photosynthesis-related metabolic pathways. Additional DEGs related to starch and sucrose metabolism, energy production, and the indole-3-acetic acid signaling pathway were induced in CBH plants after infection. DEGs related to phenylpropanoid biosynthesis, abscisic acid, salicylic acid, brassinosteroids, and jasmonic acid signaling pathway were induced in G28 after infection. Our findings reveal DEGs that may contribute to differences in PVY MSNR resistance among tobacco varieties. These results help us to understand the differences in transcriptional dynamics and metabolic processes between RKN-resistant and RKN-susceptible varieties involved in tobacco-PVY MSNR interaction.
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Affiliation(s)
- Shixiao Xu
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
| | - Pei Tian
- China Tobacco Jiangsu Industry Co, Ltd. Xuzhou Cigarette Factory, Xuzhou, China
| | - Zhimin Jiang
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Xiaoxiang Chen
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Bo Li
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Jutao Sun
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
| | - Zhiqiang Zhang
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
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Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
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Bairwa A, Sood S, Bhardwaj V, Rawat S, Tamanna T, Siddappa S, Venkatasalam EP, Dipta B, Sharma AK, Kumar A, Singh B, Mhatre PH, Sharma S, Kumar V. Identification of genes governing resistance to PCN (Globodera rostochiensis) through transcriptome analysis in Solanum tuberosum. Funct Integr Genomics 2023; 23:242. [PMID: 37453957 DOI: 10.1007/s10142-023-01164-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Potato cyst nematodes (PCNs) are major pests worldwide that affect potato production. The molecular changes happening in the roots upon PCN infection are still unknown. Identification of transcripts and genes governing PCN resistance will help in the development of resistant varieties. Hence, differential gene expression of compatible (Kufri Jyoti) and incompatible (JEX/A-267) potato genotypes was studied before (0 DAI) and after (10 DAI) inoculation of Globodera rostochiensis J2s through RNA sequencing (RNA-Seq). Total sequencing reads generated ranged between 33 and 37 million per sample, with a read mapping of 48-84% to the potato reference genome. In the infected roots of the resistant genotype JEX/A-267, 516 genes were downregulated, and 566 were upregulated. In comparison, in the susceptible genotype Kufri Jyoti, 316 and 554 genes were downregulated and upregulated, respectively. Genes encoding cell wall proteins, zinc finger protein, WRKY transcription factors, MYB transcription factors, disease resistance proteins, and pathogenesis-related proteins were found to be majorly involved in the incompatible reaction after PCN infection in the resistant genotype, JEX/A-267. Furthermore, RNA-Seq results were validated through quantitative real-time PCR (qRT-PCR), and it was observed that ATP, FLAVO, CYTO, and GP genes were upregulated at 5 DAI, which was subsequently downregulated at 10 DAI. The genes encoding ATP, FLAVO, LBR, and GP were present in > 1.5 fold before infection in JEX-A/267 and upregulated 7.9- to 27.6-fold after 5 DAI; subsequently, most of these genes were downregulated to 0.9- to 2.8-fold, except LBR, which was again upregulated to 44.4-fold at 10 DAI.
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Affiliation(s)
- Aarti Bairwa
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India.
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India.
| | - Shashi Rawat
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Tamanna Tamanna
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Sundaresha Siddappa
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - E P Venkatasalam
- ICAR-Central Potato Research Station, Muthorai, 643004, The Nilgiris, Udhagamandalam, Tamil Nadu, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Ashwani K Sharma
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Priyank H Mhatre
- ICAR-Central Potato Research Station, Muthorai, 643004, The Nilgiris, Udhagamandalam, Tamil Nadu, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, 171001, Shimla, Himachal Pradesh, India
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Akai K, Asano K, Suzuki C, Shimosaka E, Tamiya S, Suzuki T, Takeuchi T, Ohki T. De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene ( Rychc) derived from Solanum chacoense. BREEDING SCIENCE 2023; 73:168-179. [PMID: 37404346 PMCID: PMC10316315 DOI: 10.1270/jsbbs.22078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/11/2022] [Indexed: 07/06/2023]
Abstract
The isolation of disease resistance genes introduced from wild or related cultivated species is essential for understanding their mechanisms, spectrum and risk of breakdown. To identify target genes not included in reference genomes, genomic sequences with the target locus must be reconstructed. However, de novo assembly approaches of the entire genome, such as those used for constructing reference genomes, are complicated in higher plants. Moreover, in the autotetraploid potato, the heterozygous regions and repetitive structures located around disease resistance gene clusters fragment the genomes into short contigs, making it challenging to identify resistance genes. In this study, we report that a de novo assembly approach of a target gene-specific homozygous dihaploid developed through haploid induction was suitable for gene isolation in potatoes using the potato virus Y resistance gene Rychc as a model. The assembled contig containing Rychc-linked markers was 3.3 Mb in length and could be joined with gene location information from the fine mapping analysis. Rychc was successfully identified in a repeated island located on the distal end of the long arm of chromosome 9 as a Toll/interleukin-1 receptor-nucleotide-binding site-leucine rich repeat (TIR-NBS-LRR) type resistance gene. This approach will be practical for other gene isolation projects in potatoes.
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Affiliation(s)
- Kotaro Akai
- Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization, Memuro, Hokkaido 082-0081, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kenji Asano
- Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Chika Suzuki
- Hokkaido Research Organization, Central Agricultural Experiment Station, Naganuma, Hokkaido 069-1395, Japan
| | - Etsuo Shimosaka
- Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Seiji Tamiya
- Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Takako Suzuki
- Hokkaido Research Organization, Central Agricultural Experiment Station, Naganuma, Hokkaido 069-1395, Japan
| | - Toru Takeuchi
- Hokkaido Research Organization, Central Agricultural Experiment Station, Naganuma, Hokkaido 069-1395, Japan
| | - Takehiro Ohki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
- National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center, Sapporo, Hokkaido 062-8555, Japan
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Systematic mutagenesis of Polerovirus protein P0 reveals distinct and overlapping amino acid functions in Nicotiana glutinosa. Virology 2023; 578:24-34. [PMID: 36462495 DOI: 10.1016/j.virol.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022]
Abstract
The protein P0 serves as the viral suppressor of RNA silencing (VSR) for poleroviruses, but elicits the hypersensitive response (HR) in specific Nicotiana species. We subjected P0 proteins from turnip yellows virus (P0Tu) and potato leafroll virus (P0PL) to serial deletion and performed extensive site-directed mutagenesis of P0Tu. Most deletions of the N-terminus and many substitution mutations disrupted both HR elicitation and VSR activity. Two conserved blocks of amino acid residues were found to be associated with HR. A double lysine to arginine substitution in HR-specific block 1 caused P0Tu to elicit a more robust HR. Conversely, deletion or mutation of block 2 in the C-terminus preserved VSR activity, but impaired HR elicitation, allowing virus escape from Nicotiana glutinosa resistance when expressed in the heterologous potato virus X vector. Our observations suggest that P0 residues responsible for suppressing RNA silencing and eliciting HR have overlapping, but distinct functions.
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Zheng Q, Bertran A, Brand A, van Schaik CC, van de Ruitenbeek SJS, Smant G, Goverse A, Sterken MG. Comparative Transcriptome Analysis Reveals the Specific Activation of Defense Pathways Against Globodera pallida in Gpa2 Resistant Potato Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:909593. [PMID: 35783958 PMCID: PMC9248836 DOI: 10.3389/fpls.2022.909593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Cyst nematodes are considered a dominant threat to yield for a wide range of major food crops. Current control strategies are mainly dependent on crop rotation and the use of resistant cultivars. Various crops exhibit single dominant resistance (R) genes that are able to activate effective host-specific resistance to certain cyst nematode species and/or populations. An example is the potato R gene Gpa2, which confers resistance against the potato cyst nematode (PCN), Globodera pallida population D383. Activation of Gpa2 results in a delayed resistance response, which is characterized by a layer of necrotic cells formed around the developing nematode feeding structure. However, knowledge about the Gpa2-induced defense pathways is still lacking. Here, we uncover the transcriptional changes and gene expression network induced upon Gpa2 activation in potato roots infected with G. pallida. To this end, in vitro-grown Gpa2-resistant potato roots were infected with the avirulent population D383 and virulent population Rookmaker. Infected root segments were harvested at 3 and 6 dpi and sent for RNA sequencing. Comparative transcriptomics revealed a total of 1,743 differentially expressed genes (DEGs) upon nematode infection, of which 559 DEGs were specifically regulated in response to D383 infection. D383-specific DEGs associated with Gpa2-mediated defense mainly relates to calcium-binding activity, salicylic acid (SA) biosynthesis, and systemic acquired resistance (SAR). These data reveal that cyst nematode resistance in potato roots depends on conserved downstream signaling pathways involved in plant immunity, which are also known to contribute to R genes-mediated resistance against other pathogens with different lifestyles.
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12
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Kaur G, Yadav IS, Bhatia D, Vikal Y, Neelam K, Dhillon NK, Praba UP, Mangat GS, Singh K. BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima. Front Genet 2022; 13:871833. [PMID: 35774507 PMCID: PMC9237506 DOI: 10.3389/fgene.2022.871833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC1F1 population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.
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Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Yogesh Vikal,
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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13
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Sukarta OCA, Zheng Q, Slootweg EJ, Mekken M, Mendel M, Putker V, Bertran A, Brand A, Overmars H, Pomp R, Roosien J, Boeren S, Smant G, Goverse A. GLYCINE-RICH RNA-BINDING PROTEIN 7 potentiates effector-triggered immunity through an RNA recognition motif. PLANT PHYSIOLOGY 2022; 189:972-987. [PMID: 35218353 PMCID: PMC9157115 DOI: 10.1093/plphys/kiac081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The activity of intracellular plant nucleotide-binding leucine-rich repeat (NB-LRR) immune receptors is fine-tuned by interactions between the receptors and their partners. Identifying NB-LRR interacting proteins is therefore crucial to advance our understanding of how these receptors function. A co-immunoprecipitation/mass spectrometry screening was performed in Nicotiana benthamiana to identify host proteins associated with the resistance protein Gpa2, a CC-NB-LRR immune receptor conferring resistance against the potato cyst nematode Globodera pallida. A combination of biochemical, cellular, and functional assays was used to assess the role of a candidate interactor in defense. A N. benthamiana homolog of the GLYCINE-RICH RNA-BINDING PROTEIN7 (NbGRP7) protein was prioritized as a Gpa2-interacting protein for further investigations. NbGRP7 also associates in planta with the homologous Rx1 receptor, which confers immunity to Potato Virus X. We show that NbGRP7 positively regulates extreme resistance by Rx1 and cell death by Gpa2. Mutating the NbGRP7 RNA recognition motif (RRM) compromises its role in Rx1-mediated defense. Strikingly, ectopic NbGRP7 expression is likely to impact the steady-state levels of Rx1, which relies on an intact RRM. Our findings illustrate that NbGRP7 is a pro-immune component in effector-triggered immunity by regulating Gpa2/Rx1 function at a posttranscriptional level.
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Affiliation(s)
- Octavina C A Sukarta
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Qi Zheng
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erik J Slootweg
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Mark Mekken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Melanie Mendel
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Vera Putker
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - André Bertran
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Anouk Brand
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rikus Pomp
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jan Roosien
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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14
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Goverse A, Mitchum MG. At the molecular plant-nematode interface: New players and emerging paradigms. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102225. [PMID: 35537283 DOI: 10.1016/j.pbi.2022.102225] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Plant-parasitic nematodes (PPNs) secrete an array of molecules that can lead to their detection by or promote infection of their hosts. However, the function of these molecules in plant cells is often unknown or limited to phenotypic observations. Similarly, how plant cells detect and/or respond to these molecules is still poorly understood. Here, we highlight recent advances in mechanistic insights into the molecular dialogue between PPNs and plants at the cellular level. New discoveries reveal a) the essential roles of extra- and intracellular plant receptors in PPN perception and the manipulation of host immune- or developmental pathways during infection and b) how PPNs target such receptors to manipulate their hosts. Finally, the plant secretory pathway has emerged as a critical player in PPN peptide delivery, feeding site formation and non-canonical resistance.
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Affiliation(s)
- Aska Goverse
- Laboratory of Nematology, Dept of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
| | - Melissa G Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
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15
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Meng G, Xiao Y, Li A, Qian Z, Xie Y, Yang L, Lin H, Yang W. Mapping and characterization of the Rx3 gene for resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1637-1656. [PMID: 35217878 DOI: 10.1007/s00122-022-04059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Rx3 encodes a typical CC-NBS-LRR resistance protein and confers the resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 causing bacterial spot in tomato. Bacterial spot caused by at least four species of Xanthomonas is an epidemic disease severely affecting tomato production worldwide. The use of resistant cultivars is an economical and effective approach to control the disease. An unimproved tomato breeding line Hawaii 7988 has been considered as the most reliable source for resistance to X. euvesicatoria pv. euvesicatoria race T1, and the Rx3 locus located at a 4.53-Mb region on chromosome 5 (SL4.0) is the major locus for resistance to race T1 in this line. In the current study, the Rx3 locus was firstly located to a 1.05-Mb region based on comparisons of marker polymorphisms between the susceptible line Ohio 88119 and resistant lines Hawaii 7998, Ohio 9834 and FG02-7530. Using recombinant inbred lines (F5:6, F6:7, and F7:8) derived from a cross between Ohio 88119 and Ohio 9834, the Rx3 locus was finally mapped to a 64.3-kb interval between markers MG-Rx3-4 and MG-Rx3-A6. The Solyc05g053980 gene, designated as Rx3, encoding a coiled-coil nucleotide-binding leucine-rich repeat protein was considered as the candidate for the Rx3 locus. Expression of the gene could be induced by the infection of race T1 strain. Knockout of the Solyc05g053980 gene through CRISPR/Cas9 editing system in the resistant line FG02-7530 decreased resistance to race T1 strain. These results provide a close step for understanding the resistance mechanism to race T1 in Hawaii 7998 and guide tomato breeders accordingly to improve bacterial spot disease resistance in tomato.
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Affiliation(s)
- Ge Meng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Yao Xiao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
- Jiangxi Province Key Laboratory of Tuberous Plant Biology, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Aitong Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Zilin Qian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Yinge Xie
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Luyao Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Huabing Lin
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China
| | - Wencai Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, Beijing, 100193, China.
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing, 100193, China.
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16
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Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview. BIOLOGY 2022; 11:biology11040604. [PMID: 35453803 PMCID: PMC9026384 DOI: 10.3390/biology11040604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022]
Abstract
Simple Summary Monitoring the change in genetic diversity over time and space in crop species is essential to facilitating further improvement. As the world’s most important tuber crop for human consumption, and an ideal candidate to help address global food security, the cultivated potato deserves in-depth study in this regard. In this overview, some aspects of spatiotemporal diversity assessment in the cultivated potato are examined with the aim of promoting appropriate strategies for breeding programs in line with challenges relating to sustainable crop production. Abstract We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of 35 microsatellite markers (SSR). Genotypic data covering a total of 407 alleles was analyzed using both self-organizing map (SOM) and discriminant analysis of principal components (DAPC) de novo and a priori clustering methods, respectively. Data analysis based on different models of genetic structuring provided evidence of (1) at least two early lineages that have been maintained since their initial introduction from the Andes into Europe in the 16th century, followed by later ones coming from reintroduction events from the US in the mid-1800s; (2) a level of diversity that has gradually evolved throughout the studied time periods and areas, with the most modern variety groups encompassing most of the diversity found in earlier decades; (3) the emergence of new genetic groups within the current population due to increases in the use of germplasm enhancement practices using exotic germplasms. In addition, analysis revealed significant genetic differentiation both among and within the spatiotemporal groups of germplasm studied. Our results therefore highlight that no major genetic narrowing events have occurred within the cultivated potato over the past three centuries. On the contrary, the genetic base shows promising signs of improvement, thanks to extensive breeding work that is gaining momentum. This overview could be drawn on not only to understand better how past decisions have impacted the current genetic cultivated potato resources, but also to develop appropriate new strategies for breeding programs consistent with the socio-economic and sustainability challenges faced by agrifood systems.
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Transcription Factor Pso9TF Assists Xinjiang Wild Myrobalan Plum ( Prunus sogdiana) PsoRPM3 Disease Resistance Protein to Resist Meloidogyne incognita. PLANTS 2021; 10:plants10081561. [PMID: 34451606 PMCID: PMC8402125 DOI: 10.3390/plants10081561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 11/26/2022]
Abstract
The root-knot nematode (Meloidogyne incognita) causes huge economic losses in the agricultural industry throughout the world. Control methods against these polyphagous plant endoparasites are sparse, the preferred one being the deployment of plant cultivars or rootstocks bearing resistance genes against Meloidogyne species. Our previous study has cloned one resistance gene, PsoRPM3, from Xinjiang wild myrobalan plum (Prunus sogdiana). However, the function of PsoRPM3 remains elusive. In the present study, we have investigated the regulatory mechanism of PsoRPM3 in plant defense responses to M. incognita. Our results indicate that fewer giant cells were detected in the roots of the PsoRPM3 transgenic tobacco than wild tobacco lines after incubation with M. incognita. Transient transformations of full-length and TN structural domains of PsoRPM3 have induced significant hypersensitive responses (HR), suggesting that TIR domain might be the one which caused HR. Further, yeast two-hybrid results revealed that the full-length and LRR domain of PsoRPM3 could interact with the transcription factor Pso9TF. The addition of Pso9TF increased the ROS levels and induced HR. Thus, our data revealed that the LRR structural domain of PsoRPM3 may be associated with signal transduction. Moreover, we did not find any relative inductions of defense-related genes PsoEDS1, PsoPAD4 and PsoSAG101 in P. sogdiana, which has been incubated with M. incognita. In summary, our work has shown the key functional domain of PsoRPM3 in the regulation of defense responses to M. incognita in P. sogdiana.
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18
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Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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19
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Sato K, Uehara T, Holbein J, Sasaki-Sekimoto Y, Gan P, Bino T, Yamaguchi K, Ichihashi Y, Maki N, Shigenobu S, Ohta H, Franke RB, Siddique S, Grundler FMW, Suzuki T, Kadota Y, Shirasu K. Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria. FRONTIERS IN PLANT SCIENCE 2021; 12:680151. [PMID: 34122492 PMCID: PMC8194700 DOI: 10.3389/fpls.2021.680151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Root-knot nematodes (RKNs) are among the most devastating pests in agriculture. Solanum torvum Sw. (Turkey berry) has been used as a rootstock for eggplant (aubergine) cultivation because of its resistance to RKNs, including Meloidogyne incognita and M. arenaria. We previously found that a pathotype of M. arenaria, A2-J, is able to infect and propagate in S. torvum. In vitro infection assays showed that S. torvum induced the accumulation of brown pigments during avirulent pathotype A2-O infection, but not during virulent A2-J infection. This experimental system is advantageous because resistant and susceptible responses can be distinguished within a few days, and because a single plant genome can yield information about both resistant and susceptible responses. Comparative RNA-sequencing analysis of S. torvum inoculated with A2-J and A2-O at early stages of infection was used to parse the specific resistance and susceptible responses. Infection with A2-J did not induce statistically significant changes in gene expression within one day post-inoculation (DPI), but afterward, A2-J specifically induced the expression of chalcone synthase, spermidine synthase, and genes related to cell wall modification and transmembrane transport. Infection with A2-O rapidly induced the expression of genes encoding class III peroxidases, sesquiterpene synthases, and fatty acid desaturases at 1 DPI, followed by genes involved in defense, hormone signaling, and the biosynthesis of lignin at 3 DPI. Both isolates induced the expression of suberin biosynthetic genes, which may be triggered by wounding during nematode infection. Histochemical analysis revealed that A2-O, but not A2-J, induced lignin accumulation at the root tip, suggesting that physical reinforcement of cell walls with lignin is an important defense response against nematodes. The S. torvum-RKN system can provide a molecular basis for understanding plant-nematode interactions.
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Affiliation(s)
- Kazuki Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Taketo Uehara
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Julia Holbein
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Yuko Sasaki-Sekimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takahiro Bino
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | | | - Noriko Maki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Rochus B. Franke
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Shahid Siddique
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Florian M. W. Grundler
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Yasuhiro Kadota
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
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20
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Price JA, Coyne D, Blok VC, Jones JT. Potato cyst nematodes Globodera rostochiensis and G. pallida. MOLECULAR PLANT PATHOLOGY 2021; 22:495-507. [PMID: 33709540 PMCID: PMC8035638 DOI: 10.1111/mpp.13047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 05/12/2023]
Abstract
TAXONOMY Phylum Nematoda; class Chromadorea; order Rhabditida; suborder Tylenchina; infraorder Tylenchomorpha; superfamily Tylenchoidea; family Heteroderidae; subfamily Heteroderinae; Genus Globodera. BIOLOGY Potato cyst nematodes (PCN) are biotrophic, sedentary endoparasitic nematodes. Invasive (second) stage juveniles (J2) hatch from eggs in response to the presence of host root exudates and subsequently locate and invade the host. The nematodes induce the formation of a large, multinucleate syncytium in host roots, formed by fusion of up to 300 root cell protoplasts. The nematodes rely on this single syncytium for the nutrients required to develop through a further three moults to the adult male or female stage. This extended period of biotrophy-between 4 and 6 weeks in total-is almost unparalleled in plant-pathogen interactions. Females remain at the root while adult males revert to the vermiform body plan of the J2 and leave the root to locate and fertilize the female nematodes. The female body forms a cyst that contains the next generation of eggs. HOST RANGE The host range of PCN is limited to plants of the Solanaceae family. While the most economically important hosts are potato (Solanum tuberosum), tomato (Solanum lycopersicum), and aubergine (Solanum melongena), over 170 species of Solanaceae are thought to be potential hosts for PCN (Sullivan et al., 2007). DISEASE SYMPTOMS Symptoms are similar to those associated with nutrient deficiency, such as stunted growth, yellowing of leaves and reduced yields. This absence of specific symptoms reduces awareness of the disease among growers. DISEASE CONTROL Resistance genes (where available in suitable cultivars), application of nematicides, crop rotation. Great effort is put into reducing the spread of PCN through quarantine measures and use of certified seed stocks. USEFUL WEBSITES Genomic information for PCN is accessible through WormBase ParaSite.
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Affiliation(s)
- James A. Price
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA)NairobiKenya
| | - Vivian C. Blok
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - John T. Jones
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
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21
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Ramos RN, Martin GB, Pombo MA, Rosli HG. WRKY22 and WRKY25 transcription factors are positive regulators of defense responses in Nicotiana benthamiana. PLANT MOLECULAR BIOLOGY 2021; 105:65-82. [PMID: 32909182 DOI: 10.1007/s11103-020-01069-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE NbWRKY22 and NbWRKY25 are required for full activation of bacteria-associated pattern- and effector-triggered immunity as well as for the response to other non-bacterial defense elicitors. Plants defend themselves against pathogens using a two-layered immune system. Pattern-triggered immunity (PTI) can be activated upon recognition of epitopes from flagellin including flg22. Pseudomonas syringae pv. tomato (Pst) delivers effector proteins into the plant cell to promote host susceptibility. However, some plants express resistance (R) proteins that recognize specific effectors leading to the activation of effector-triggered immunity (ETI). Resistant tomato lines such as Rio Grande-PtoR (RG-PtoR) recognize two Pst effectors, AvrPto and AvrPtoB, and activate ETI through the Pto/Prf protein complex. Using RNA-seq, we identified two tomato WRKY transcription factor genes, SlWRKY22 and SlWRKY25, whose expression is increased during Pst-induced ETI. Silencing of the WRKY25/22 orthologous genes in Nicotiana benthamiana led to a delay in programmed cell death normally associated with AvrPto recognition or several non-bacterial effector/R protein pairs. An increase in disease symptoms was observed in silenced plants infiltrated with Pseudomonas syringae pv. tabaci expressing AvrPto or HopQ1-1. Expression of both tomato WRKY genes is also induced upon treatment with flg22 and callose deposition and cell death suppression assays in WRKY25/22-silenced N. benthamiana plants supported their involvement in PTI. Our results reveal an important role for two WRKYs as positive regulators of plant immunity against bacterial and potentially non-bacterial pathogens.
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Affiliation(s)
- Romina N Ramos
- INFIVE, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Marina A Pombo
- INFIVE, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina.
| | - Hernan G Rosli
- INFIVE, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
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22
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Gartner U, Hein I, Brown LH, Chen X, Mantelin S, Sharma SK, Dandurand LM, Kuhl JC, Jones JT, Bryan GJ, Blok VC. Resisting Potato Cyst Nematodes With Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:661194. [PMID: 33841485 PMCID: PMC8027921 DOI: 10.3389/fpls.2021.661194] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2021] [Indexed: 05/17/2023]
Abstract
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lynn H. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sophie Mantelin
- INRAE UMR Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Sanjeev K. Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Louise-Marie Dandurand
- Entomology, Plant Pathology and Nematology Department, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Vivian C. Blok
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Vivian C. Blok,
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23
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Zheng Q, Putker V, Goverse A. Molecular and Cellular Mechanisms Involved in Host-Specific Resistance to Cyst Nematodes in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:641582. [PMID: 33767723 PMCID: PMC7986850 DOI: 10.3389/fpls.2021.641582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/16/2021] [Indexed: 05/17/2023]
Abstract
Cyst nematodes are able to infect a wide range of crop species and are regarded as a major threat in crop production. In response to invasion of cyst nematodes, plants activate their innate immune system to defend themselves by conferring basal and host-specific defense responses depending on the plant genotype. Basal defense is dependent on the detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), while host-specific defense mainly relies on the activation of canonical and non-canonical resistance (R) genes or quantitative trait loci (QTL). Currently, application of R genes and QTLs in crop species is a major approach to control cyst nematode in crop cultivation. However, emerging virulent cyst nematode field populations are threatening crop production due to host genetic selection by the application of a limited set of resistance genes in current crop cultivars. To counteract this problem, increased knowledge about the mechanisms involved in host-specific resistance mediated by R genes and QTLs to cyst nematodes is indispensable to improve their efficient and sustainable use in field crops. Despite the identification of an increasing number of resistance traits to cyst nematodes in various crops, the underlying genes and defense mechanisms are often unknown. In the last decade, indebt studies on the functioning of a number of cyst nematode R genes and QTLs have revealed novel insights in how plants respond to cyst nematode infection by the activation of host-specific defense responses. This review presents current knowledge of molecular and cellular mechanisms involved in the recognition of cyst nematodes, the activation of defense signaling and resistance response types mediated by R genes or QTLs. Finally, future directions for research are proposed to develop management strategies to better control cyst nematodes in crop cultivation.
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Affiliation(s)
- Qi Zheng
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Vera Putker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
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24
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Mironenko NV, Gavrilenko TA, Khiutti AV, Afanasenko OS. [Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance]. Vavilovskii Zhurnal Genet Selektsii 2020; 24:705-721. [PMID: 33738388 PMCID: PMC7960448 DOI: 10.18699/vj20.665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран-
тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в
статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред-
ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и
молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости
популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не-
матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу
образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости
нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля-
ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со-
временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera
pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды.
К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических
нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и
возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с
длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически
наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до-
стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую-
щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде-
ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и
QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов
и подходов. Представлены результаты изучения структурной и функциональной
организации генов устойчиво-
сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле-
кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых
сортов, в том числе с групповой устойчивостью.
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Affiliation(s)
- N V Mironenko
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T A Gavrilenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - A V Khiutti
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O S Afanasenko
- All-Russian Research Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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25
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Mathew R, Opperman CH. Current Insights into Migratory Endoparasitism: Deciphering the Biology, Parasitism Mechanisms, and Management Strategies of Key Migratory Endoparasitic Phytonematodes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E671. [PMID: 32466416 PMCID: PMC7356796 DOI: 10.3390/plants9060671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 01/12/2023]
Abstract
Despite their physiological differences, sedentary and migratory plant-parasitic nematodes (PPNs) share several commonalities. Functional characterization studies of key effectors and their targets identified in sedentary phytonematodes are broadly applied to migratory PPNs, generalizing parasitism mechanisms existing in distinct lifestyles. Despite their economic significance, host-pathogen interaction studies of migratory endoparasitic nematodes are limited; they have received little attention when compared to their sedentary counterparts. Because several migratory PPNs form disease complexes with other plant-pathogens, it is important to understand multiple factors regulating their feeding behavior and lifecycle. Here, we provide current insights into the biology, parasitism mechanism, and management strategies of the four-key migratory endoparasitic PPN genera, namely Pratylenchus, Radopholus, Ditylenchus, and Bursaphelenchus. Although this review focuses on these four genera, many facets of feeding mechanisms and management are common across all migratory PPNs and hence can be applied across a broad genera of migratory phytonematodes.
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Affiliation(s)
| | - Charles H. Opperman
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA;
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26
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Kondrák M, Kopp A, Uri C, Sós-Hegedűs A, Csákvári E, Schiller M, Barta E, Cernák I, Polgár Z, Taller J, Bánfalvi Z. Mapping and DNA sequence characterisation of the Rysto locus conferring extreme virus resistance to potato cultivar 'White Lady'. PLoS One 2020; 15:e0224534. [PMID: 32231371 PMCID: PMC7108733 DOI: 10.1371/journal.pone.0224534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/01/2020] [Indexed: 11/29/2022] Open
Abstract
Virus resistance genes carried by wild plant species are valuable resources for plant breeding. The Rysto gene, conferring a broad spectrum of durable resistance, originated from Solanum stoloniferum and was introgressed into several commercial potato cultivars, including ‘White Lady’, by classical breeding. Rysto was mapped to chromosome XII in potato, and markers used for marker-assisted selection in breeding programmes were identified. Nevertheless, there was no information on the identity of the Rysto gene. To begin to reveal the identification of Rysto, fine-scale genetic mapping was performed which, in combination with chromosome walking, narrowed down the locus of the gene to approximately 1 Mb. DNA sequence analysis of the locus identified six full-length NBS-LRR-type (short NLR-type) putative resistance genes. Two of them, designated TMV2 and TMV3, were similar to a TMV resistance gene isolated from tobacco and to Y-1, which co-segregates with Ryadg, the extreme virus resistance gene originated from Solanum andigena and localised to chromosome XI. Furthermore, TMV2 of ‘White Lady’ was found to be 95% identical at the genomic sequence level with the recently isolated Rysto gene of the potato cultivar ‘Alicja’. In addition to the markers identified earlier, this work generated five tightly linked new markers which can serve potato breeding efforts for extreme virus resistance.
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Affiliation(s)
- Mihály Kondrák
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Andrea Kopp
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Csilla Uri
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | | | - Edina Csákvári
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mátyás Schiller
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Endre Barta
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - István Cernák
- Potato Research Centre, University of Pannonia, Keszthely, Hungary
| | - Zsolt Polgár
- Potato Research Centre, University of Pannonia, Keszthely, Hungary
| | - János Taller
- Department of Plant Sciences and Biotechnology, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Zsófia Bánfalvi
- NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
- * E-mail:
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27
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Dolatabadian A, Bayer PE, Tirnaz S, Hurgobin B, Edwards D, Batley J. Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:969-982. [PMID: 31553100 PMCID: PMC7061875 DOI: 10.1111/pbi.13262] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 05/18/2023]
Abstract
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
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Affiliation(s)
- Aria Dolatabadian
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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Kim JH, Castroverde CDM. Diversity, Function and Regulation of Cell Surface and Intracellular Immune Receptors in Solanaceae. PLANTS 2020; 9:plants9040434. [PMID: 32244634 PMCID: PMC7238418 DOI: 10.3390/plants9040434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 12/29/2022]
Abstract
The first layer of the plant immune system comprises plasma membrane-localized receptor proteins and intracellular receptors of the nucleotide-binding leucine-rich repeat protein superfamily. Together, these immune receptors act as a network of surveillance machines in recognizing extracellular and intracellular pathogen invasion-derived molecules, ranging from conserved structural epitopes to virulence-promoting effectors. Successful pathogen recognition leads to physiological and molecular changes in the host plants, which are critical for counteracting and defending against biotic attack. A breadth of significant insights and conceptual advances have been derived from decades of research in various model plant species regarding the structural complexity, functional diversity, and regulatory mechanisms of these plant immune receptors. In this article, we review the current state-of-the-art of how these host surveillance proteins function and how they are regulated. We will focus on the latest progress made in plant species belonging to the Solanaceae family, because of their tremendous importance as model organisms and agriculturally valuable crops.
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Affiliation(s)
- Jong Hum Kim
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Howard Hughes Medical Institute, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (J.H.K.); (C.D.M.C.)
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29
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Tomato Natural Resistance Genes in Controlling the Root-Knot Nematode. Genes (Basel) 2019; 10:genes10110925. [PMID: 31739481 PMCID: PMC6896013 DOI: 10.3390/genes10110925] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 02/01/2023] Open
Abstract
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to the RKN have already been identified as Mi-1, Mi-2, Mi-3, Mi-4, Mi-5, Mi-6, Mi-7, Mi-8, Mi-9, and Mi-HT. Only five of these genes have been mapped. The major problem is that their resistance breaks down at high temperatures. Some of these genes still work at high temperatures. In this paper, the mechanism and characteristics of these natural resistance genes are summarized. Other difficulties in using these genes in the resistance and how to improve them are also mentioned.
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30
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Bagga S, Lucero Y, Apodaca K, Rajapakse W, Lujan P, Ortega JL, Sengupta-Gopalan C. Chile (Capsicum annuum) plants transformed with the RB gene from Solanum bulbocastanum are resistant to Phytophthora capsici. PLoS One 2019; 14:e0223213. [PMID: 31589629 PMCID: PMC6779293 DOI: 10.1371/journal.pone.0223213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/15/2019] [Indexed: 01/04/2023] Open
Abstract
Phytophthora capsici is a soil borne pathogen, and is among the most destructive pathogens for Capsicum annuum (chile). P. capsici is known to cause diseases on all parts of the chile plants. Therefore, it requires independent resistance genes to control disease symptoms that are induced by each of the P. capsici strains. This requirement of multiple resistance genes to confer resistance to P. capsici, in chile makes breeding for resistance a daunting pursuit. Against this backdrop, a genetic engineering approach would be to introduce a broad host resistance gene into chile in order to protect it from different races of P. capsici. Notably, a broad host resistance gene RB from Solanum bulbocastanum has been shown to confer resistance to P. infestans in both S. tuberosum and S. lycopersicum. We agroinfiltrated the RB gene into the leaves of susceptible chile plants, demonstrating that the gene is also capable of lending resistance to P. capsici in chile. We introduced the RB gene into chile by developing an Agrobacterium tumefaciens mediated transformation system. The integration of the RB gene into the genome of the primary transformants and its subsequent transfer to the F1 generation was confirmed by genomic PCR using primers specific for the RB gene. A 3:1 ratio for the presence and absence of the RB gene was observed in the F1 progeny. In addition to showing resistance to P. capsici in a leaf inoculation experiment, about 30% of the F1 progeny also exhibited resistance to root inoculation. Our data, when taken together, suggests that the RB gene from S. bulbocastanum confers resistance against P. capsici in C. annuum, thereby demonstrating that the RB gene has an even broader host range than reported in the literature–both in terms of the host and the pathogen.
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Affiliation(s)
- Suman Bagga
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
| | - Yvonne Lucero
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
| | - Kimberly Apodaca
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
| | - Wathsala Rajapakse
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
| | - Phillip Lujan
- Department of Entomology, Plant Pathology, Weed Science, New Mexico State University, Las Cruces, NM, United States of America
| | - Jose Luis Ortega
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
| | - Champa Sengupta-Gopalan
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States of America
- * E-mail:
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31
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Zhu M, van Grinsven IL, Kormelink R, Tao X. Paving the Way to Tospovirus Infection: Multilined Interplays with Plant Innate Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:41-62. [PMID: 30893008 DOI: 10.1146/annurev-phyto-082718-100309] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tospoviruses are among the most important plant pathogens and cause serious crop losses worldwide. Tospoviruses have evolved to smartly utilize the host cellular machinery to accomplish their life cycle. Plants mount two layers of defense to combat their invasion. The first one involves the activation of an antiviral RNA interference (RNAi) defense response. However, tospoviruses encode an RNA silencing suppressor that enables them to counteract antiviral RNAi. To further combat viral invasion, plants also employ intracellular innate immune receptors (e.g., Sw-5b and Tsw) to recognize different viral effectors (e.g., NSm and NSs). This leads to the triggering of a much more robust defense against tospoviruses called effector-triggered immunity (ETI). Tospoviruses have further evolved their effectors and can break Sw-5b-/Tsw-mediated resistance. The arms race between tospoviruses and both layers of innate immunity drives the coevolution of host defense and viral genes involved in counter defense. In this review, a state-of-the-art overview is presented on the tospoviral life cycle and the multilined interplays between tospoviruses and the distinct layers of defense.
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Affiliation(s)
- Min Zhu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Irene Louise van Grinsven
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
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Lahari Z, Ribeiro A, Talukdar P, Martin B, Heidari Z, Gheysen G, Price AH, Shrestha R. QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice ( Oryza sativa L.). EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2019; 215:117. [PMID: 31274875 PMCID: PMC6570777 DOI: 10.1007/s10681-019-2427-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/27/2019] [Indexed: 05/31/2023]
Abstract
The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite's life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F2 progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20 and 23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification.
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Affiliation(s)
- Zobaida Lahari
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Antonio Ribeiro
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Partha Talukdar
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Brennan Martin
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Zeynab Heidari
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | - Godelieve Gheysen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Adam H. Price
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Roshi Shrestha
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
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Van Gansbeke B, Khoo KHP, Lewis JG, Chalmers KJ, Mather DE. Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1309-1320. [PMID: 30656354 PMCID: PMC6476833 DOI: 10.1007/s00122-019-03279-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/07/2019] [Indexed: 05/29/2023]
Abstract
The cereal cyst nematode resistance locus Rha2 was mapped to a 978 kbp region on the long arm of barley chromosome 2H. Three candidate genes are discussed. The cereal cyst nematode (CCN) Heterodera avenae is a soil-borne obligate parasite that can cause severe damage to cereals. This research involved fine mapping of Rha2, a CCN resistance locus on chromosome 2H of barley. Rha2 was previously mapped relative to restriction fragment length polymorphisms (RFLPs) in two mapping populations. Anchoring of flanking RFLP clone sequences to the barley genome assembly defined an interval of 5077 kbp. Genotyping-by-sequencing of resistant and susceptible materials led to the discovery of potentially useful single nucleotide polymorphisms (SNPs). Assays were designed for these SNPs and applied to mapping populations. This narrowed the region of interest to 3966 kbp. Further fine mapping was pursued by crossing and backcrossing the resistant cultivar Sloop SA to its susceptible ancestor Sloop. Evaluation of F2 progeny confirmed that the resistance segregates as a single dominant gene. Genotyping of 9003 BC2F2 progeny identified recombinants. Evaluation of recombinant BC2F3 progeny narrowed the region of interest to 978 kbp. Two of the SNPs within this region proved to be diagnostic of CCN resistance across a wide range of barley germplasm. Fluorescence-based and gel-based assays were developed for these SNPs for use in marker-assisted selection. Within the candidate region of the reference genome, there are nine high-confidence predicted genes. Three of these, one that encodes RAR1 (a cysteine- and histidine-rich domain-containing protein), one that is predicted to encode an acetylglutamate kinase and one that is predicted to encode a tonoplast intrinsic protein, are discussed as candidate genes for CCN resistance.
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Affiliation(s)
- Bart Van Gansbeke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Kelvin H P Khoo
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - John G Lewis
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA, 5001, Australia
| | - Kenneth J Chalmers
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Diane E Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
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Zhong X, Zhou Q, Cui N, Cai D, Tang G. BvcZR3 and BvHs1pro-1 Genes Pyramiding Enhanced Beet Cyst Nematode ( Heterodera schachtii Schm.) Resistance in Oilseed Rape ( Brassica napus L.). Int J Mol Sci 2019; 20:ijms20071740. [PMID: 30965683 PMCID: PMC6479909 DOI: 10.3390/ijms20071740] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/03/2019] [Accepted: 04/06/2019] [Indexed: 11/16/2022] Open
Abstract
Beet cyst nematode (Heterodera schachtii Schm.) is one of the most damaging pests in sugar beet growing areas around the world. The Hs1pro-1 and cZR3 genes confer resistance to the beet cyst nematode, and both were cloned from sugar beet translocation line (A906001). The translocation line carried the locus from B. procumbens chromosome 1 including Hs1pro-1 gene and resistance gene analogs (RGA), which confer resistance to Heterodera schachtii. In this research, BvHs1pro-1 and BvcZR3 genes were transferred into oilseed rape to obtain different transgenic lines by A. tumefaciens mediated transformation method. The cZR3Hs1pro-1 gene was pyramided into the same plants by crossing homozygous cZR3 and Hs1pro-1 plants to identify the function and interaction of cZR3 and Hs1pro-1 genes. In vitro and in vivo cyst nematode resistance tests showed that cZR3 and Hs1pro-1 plants could be infested by beet cyst nematode (BCN) juveniles, however a large fraction of penetrated nematode juveniles was not able to develop normally and stagnated in roots of transgenic plants, consequently resulting in a significant reduction in the number of developed nematode females. A higher efficiency in inhibition of nematode females was observed in plants expressing pyramiding genes than in those only expressing a single gene. Molecular analysis demonstrated that BvHs1pro-1 and BvcZR3 gene expressions in oilseed rape constitutively activated transcription of plant-defense related genes such as NPR1 (non-expresser of PR1), SGT1b (enhanced disease resistance 1) and RAR1 (suppressor of the G2 allele of skp1). Transcript of NPR1 gene in transgenic cZR3 and Hs1pro-1 plants were slightly up-regulated, while its expression was considerably enhanced in cZR3Hs1pro-1 gene pyramiding plants. The expression of EDS1 gene did not change significantly among transgenic cZR3, Hs1pro-1 and cZR3Hs1pro-1 gene pyramiding plants and wild type. The expression of SGT1b gene was slightly up-regulated in transgenic cZR3 and Hs1pro-1 plants compared with the wild type, however, its expression was not changed in cZR3Hs1pro-1 gene pyramiding plant and had no interaction effect. RAR1 gene expression was significantly up-regulated in transgenic cZR3 and cZR3Hs1pro-1 genes pyramiding plants, but almost no expression was found in Hs1pro-1 transgenic plants. These results show that nematode resistance genes from sugar beet were functional in oilseed rape and conferred BCN resistance by activation of a CC-NBS-LRR R gene mediated resistance response. The gene pyramiding had enhanced resistance, thus offering a novel approach for the BCN control by preventing the propagation of BCN in oilseed rape. The transgenic oilseed rape could be used as a trap crop to offer an alternative method for beet cyst nematode control.
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Affiliation(s)
- Xuanbo Zhong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Qizheng Zhou
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Nan Cui
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Daguang Cai
- Department of Molecular Phytopathology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, D-24118 Kiel, Germany.
| | - Guixiang Tang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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Armstrong MR, Vossen J, Lim TY, Hutten RCB, Xu J, Strachan SM, Harrower B, Champouret N, Gilroy EM, Hein I. Tracking disease resistance deployment in potato breeding by enrichment sequencing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:540-549. [PMID: 30107090 DOI: 10.1101/360644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/26/2018] [Accepted: 08/12/2018] [Indexed: 05/26/2023]
Abstract
Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans) gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.
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Affiliation(s)
- Miles R Armstrong
- CMS, The James Hutton Institute, Dundee, UK
- School of Life Sciences, Division of Plant Sciences at the James Hutton Institute, University of Dundee, Dundee, UK
| | - Jack Vossen
- Wageningen University, Wageningen, The Netherlands
| | | | | | - Jianfei Xu
- Chinese Academy of Agricultural Science (CAAS), Beijing, China
| | | | | | | | | | - Ingo Hein
- CMS, The James Hutton Institute, Dundee, UK
- School of Life Sciences, Division of Plant Sciences at the James Hutton Institute, University of Dundee, Dundee, UK
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Armstrong MR, Vossen J, Lim TY, Hutten RCB, Xu J, Strachan SM, Harrower B, Champouret N, Gilroy EM, Hein I. Tracking disease resistance deployment in potato breeding by enrichment sequencing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:540-549. [PMID: 30107090 PMCID: PMC6335062 DOI: 10.1111/pbi.12997] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/26/2018] [Accepted: 08/12/2018] [Indexed: 05/09/2023]
Abstract
Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans) gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.
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Affiliation(s)
- Miles R. Armstrong
- CMSThe James Hutton InstituteDundeeUK
- School of Life SciencesDivision of Plant Sciences at the James Hutton InstituteUniversity of DundeeDundeeUK
| | - Jack Vossen
- Wageningen UniversityWageningenThe Netherlands
| | - Tze Yin Lim
- CMSThe James Hutton InstituteDundeeUK
- Present address:
Department of MedicineColumbia UniversityNew YorkNYUSA
| | | | - Jianfei Xu
- Chinese Academy of Agricultural Science (CAAS)BeijingChina
| | | | | | | | | | - Ingo Hein
- CMSThe James Hutton InstituteDundeeUK
- School of Life SciencesDivision of Plant Sciences at the James Hutton InstituteUniversity of DundeeDundeeUK
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Araújo ACD, Fonseca FCDA, Cotta MG, Alves GSC, Miller RNG. Plant NLR receptor proteins and their potential in the development of durable genetic resistance to biotic stresses. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Sato K, Kadota Y, Shirasu K. Plant Immune Responses to Parasitic Nematodes. FRONTIERS IN PLANT SCIENCE 2019; 10:1165. [PMID: 31616453 PMCID: PMC6775239 DOI: 10.3389/fpls.2019.01165] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/26/2019] [Indexed: 05/19/2023]
Abstract
Plant-parasitic nematodes (PPNs), such as root-knot nematodes (RKNs) and cyst nematodes (CNs), are among the most devastating pests in agriculture. RKNs and CNs induce redifferentiation of root cells into feeding cells, which provide water and nutrients to these nematodes. Plants trigger immune responses to PPN infection by recognizing PPN invasion through several different but complementary systems. Plants recognize pathogen-associated molecular patterns (PAMPs) sderived from PPNs by cell surface-localized pattern recognition receptors (PRRs), leading to pattern-triggered immunity (PTI). Plants can also recognize tissue and cellular damage caused by invasion or migration of PPNs through PRR-based recognition of damage-associated molecular patterns (DAMPs). Resistant plants have the added ability to recognize PPN effectors via intracellular nucleotide-binding domain leucine-rich repeat (NLR)-type immune receptors, leading to NLR-triggered immunity. Some PRRs may also recognize apoplastic PPN effectors and induce PTI. Plant immune responses against PPNs include the secretion of anti-nematode enzymes, the production of anti-nematode compounds, cell wall reinforcement, production of reactive oxygen species and nitric oxide, and hypersensitive response-mediated cell death. In this review, we summarize the recognition mechanisms for PPN infection and what is known about PPN-induced immune responses in plants.
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Affiliation(s)
- Kazuki Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yasuhiro Kadota
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- *Correspondence: Yasuhiro Kadota, ; Ken Shirasu,
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Science, University of Tokyo, Bunkyo, Japan
- *Correspondence: Yasuhiro Kadota, ; Ken Shirasu,
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Changkwian A, Venkatesh J, Lee JH, Han JW, Kwon JK, Siddique MI, Solomon AM, Choi GJ, Kim E, Seo Y, Kim YH, Kang BC. Physical Localization of the Root-Knot Nematode ( Meloidogyne incognita) Resistance Locus Me7 in Pepper ( Capsicum annuum). FRONTIERS IN PLANT SCIENCE 2019; 10:886. [PMID: 31354762 PMCID: PMC6629957 DOI: 10.3389/fpls.2019.00886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/21/2019] [Indexed: 05/09/2023]
Abstract
The root-knot nematode (RKN) Meloidogyne incognita severely reduces yields of pepper (Capsicum annuum) worldwide. A single dominant locus, Me7, conferring RKN resistance was previously mapped on the long arm of pepper chromosome P9. In the present study, the Me7 locus was fine mapped using an F2 population of 714 plants derived from a cross between the RKN-susceptible parent C. annuum ECW30R and the RKN-resistant parent C. annuum CM334. CM334 exhibits suppressed RKN juvenile movement, suppressed feeding site enlargement and significant reduction in gall formation compared with ECW30R. RKN resistance screening in the F2 population identified 558 resistant and 156 susceptible plants, which fit a 3:1 ratio confirming that this RKN resistance was controlled by a single dominant gene. Using the C. annuum CM334 reference genome and BAC library sequencing, fine mapping of Me7 markers was performed. The Me7 locus was delimited between two markers G21U3 and G43U3 covering a physical interval of approximately 394.7 kb on the CM334 chromosome P9. Nine markers co-segregated with the Me7 gene. A cluster of 25 putative nucleotide-binding site and leucine-rich repeat (NBS-LRR)-type disease resistance genes were predicted in the delimited Me7 region. We propose that RKN resistance in CM334 is mediated by one or more of these NBS-LRR class R genes. The Me7-linked markers identified here will facilitate marker-assisted selection (MAS) for RKN resistance in pepper breeding programs, as well as functional analysis of Me7 candidate genes in C. annuum.
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Affiliation(s)
- Amornrat Changkwian
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jelli Venkatesh
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Woong Han
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Muhammad Irfan Siddique
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Abate Mekonnen Solomon
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Gyung-Ja Choi
- Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejoen, South Korea
| | - Eunji Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yunhee Seo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Young-Ho Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang,
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Zhou X, Liu J, Bao S, Yang Y, Zhuang Y. Molecular Cloning and Characterization of a Wild Eggplant Solanum aculeatissimum NBS-LRR Gene, Involved in Plant Resistance to Meloidogyne incognita. Int J Mol Sci 2018; 19:E583. [PMID: 29462897 PMCID: PMC5855805 DOI: 10.3390/ijms19020583] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/03/2018] [Accepted: 02/14/2018] [Indexed: 11/23/2022] Open
Abstract
Root-knot nematodes, Meloidogyne spp., cause considerable damage in eggplant production. Transferring of resistance genes from wild relatives would be valuable for the continued improvement of eggplant. Solanum aculeatissimum, a wild relative of eggplant possessing resistance to Meloidogyne incognita, is potentially useful for genetically enhancing eggplant. In the present study, we have isolated and characterized a nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance gene, designated as SacMi. The full-length cDNA of the SacMi gene was obtained using the technique of rapid-amplification of cDNA ends (RACE). The open reading frame of the SacMi gene was 4014 bp and encoded a protein of 1338 amino acids. Sequence analysis indicated that SacMi belong to the non- Toll/Interleukin-1 receptor (TIR)-NBS-LRR type disease-resistance genes. Interestingly, quantitative RT-PCR showed that SacMi is expressed at low levels in uninfected roots, but was up-regulated by infection with M. incognita. To investigate the role of SacMi in S. aculeatissimum resistance against M. incognica, the tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) system was used. Silencing of SacMi enhanced susceptibility of S. aculeatissimum plants to M. incognita, suggesting the possible involvement of SacMi in resistance against M. incognita infection.
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Affiliation(s)
- Xiaohui Zhou
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Jun Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Shengyou Bao
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Yan Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Yong Zhuang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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Santos JRP, Ndeve AD, Huynh BL, Matthews WC, Roberts PA. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance. PLoS One 2018; 13:e0189185. [PMID: 29300744 PMCID: PMC5754085 DOI: 10.1371/journal.pone.0189185] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.
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Affiliation(s)
- Jansen Rodrigo Pereira Santos
- Department of Nematology, University of California, Riverside, California, United States of America
- * E-mail: (JRPS); (PAR)
| | - Arsenio Daniel Ndeve
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, California, United States of America
| | - William Charles Matthews
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Philip Alan Roberts
- Department of Nematology, University of California, Riverside, California, United States of America
- * E-mail: (JRPS); (PAR)
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de Oliveira AS, Boiteux LS, Kormelink R, Resende RO. The Sw-5 Gene Cluster: Tomato Breeding and Research Toward Orthotospovirus Disease Control. FRONTIERS IN PLANT SCIENCE 2018; 9:1055. [PMID: 30073012 PMCID: PMC6060272 DOI: 10.3389/fpls.2018.01055] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/28/2018] [Indexed: 05/19/2023]
Abstract
The Sw-5 gene cluster encodes protein receptors that are potentially able to recognize microbial products and activate signaling pathways that lead to plant cell immunity. Although there are several Sw-5 homologs in the tomato genome, only one of them, named Sw-5b, has been extensively studied due to its functionality against a wide range of (thrips-transmitted) orthotospoviruses. The Sw-5b gene is a dominant resistance gene originally from a wild Peruvian tomato that has been used in tomato breeding programs aiming to develop cultivars with resistance to these viruses. Here, we provide an overview starting from the first reports of Sw-5 resistance, positional cloning and the sequencing of the Sw-5 gene cluster from resistant tomatoes and the validation of Sw-5b as the functional protein that triggers resistance against orthotospoviruses. Moreover, molecular details of this plant-virus interaction are also described, especially concerning the roles of Sw-5b domains in the sensing of orthotospoviruses and in the signaling cascade leading to resistance and hypersensitive response.
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Affiliation(s)
- Athos S. de Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
- *Correspondence: Athos S. de Oliveira,
| | - Leonardo S. Boiteux
- National Center for Vegetable Crops Research (CNPH), Embrapa Vegetables, Brasília, Brazil
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University and Research Center, Wageningen, Netherlands
| | - Renato O. Resende
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
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Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC PLANT BIOLOGY 2017; 17:251. [PMID: 29297325 PMCID: PMC5751396 DOI: 10.1186/s12870-017-1193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode. CONCLUSION Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.
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Affiliation(s)
- Alex V Kochetov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Novosibirsk State Agrarian University, Novosibirsk, 630039, Russia.
| | - Anastasiya Y Glagoleva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Elena K Khlestkina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | | | | | | | | | - Nikolay A Shmakov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
| | - Olga Y Antonova
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Tatyana A Gavrilenko
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
- St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Natalia V Alpatyeva
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Alexander Khiutti
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| | - Olga S Afanasenko
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
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Wu CH, Abd-El-Haliem A, Bozkurt TO, Belhaj K, Terauchi R, Vossen JH, Kamoun S. NLR network mediates immunity to diverse plant pathogens. Proc Natl Acad Sci U S A 2017; 114:8113-8118. [PMID: 28698366 PMCID: PMC5544293 DOI: 10.1073/pnas.1702041114] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Both plants and animals rely on nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to respond to invading pathogens and activate immune responses. An emerging concept of NLR function is that "sensor" NLR proteins are paired with "helper" NLRs to mediate immune signaling. However, our fundamental knowledge of sensor/helper NLRs in plants remains limited. In this study, we discovered a complex NLR immune network in which helper NLRs in the NRC (NLR required for cell death) family are functionally redundant but display distinct specificities toward different sensor NLRs that confer immunity to oomycetes, bacteria, viruses, nematodes, and insects. The helper NLR NRC4 is required for the function of several sensor NLRs, including Rpi-blb2, Mi-1.2, and R1, whereas NRC2 and NRC3 are required for the function of the sensor NLR Prf. Interestingly, NRC2, NRC3, and NRC4 redundantly contribute to the immunity mediated by other sensor NLRs, including Rx, Bs2, R8, and Sw5. NRC family and NRC-dependent NLRs are phylogenetically related and cluster into a well-supported superclade. Using extensive phylogenetic analysis, we discovered that the NRC superclade probably emerged over 100 Mya from an NLR pair that diversified to constitute up to one-half of the NLRs of asterids. These findings reveal a complex genetic network of NLRs and point to a link between evolutionary history and the mechanism of immune signaling. We propose that this NLR network increases the robustness of immune signaling to counteract rapidly evolving plant pathogens.
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Affiliation(s)
- Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Ahmed Abd-El-Haliem
- Plant Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 606-8501, Japan
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
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Ali MA, Azeem F, Abbas A, Joyia FA, Li H, Dababat AA. Transgenic Strategies for Enhancement of Nematode Resistance in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:750. [PMID: 28536595 PMCID: PMC5422515 DOI: 10.3389/fpls.2017.00750] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
Plant parasitic nematodes (PPNs) are obligate biotrophic parasites causing serious damage and reduction in crop yields. Several economically important genera parasitize various crop plants. The root-knot, root lesion, and cyst nematodes are the three most economically damaging genera of PPNs on crops within the family Heteroderidae. It is very important to devise various management strategies against PPNs in economically important crop plants. Genetic engineering has proven a promising tool for the development of biotic and abiotic stress tolerance in crop plants. Additionally, the genetic engineering leading to transgenic plants harboring nematode resistance genes has demonstrated its significance in the field of plant nematology. Here, we have discussed the use of genetic engineering for the development of nematode resistance in plants. This review article also provides a detailed account of transgenic strategies for the resistance against PPNs. The strategies include natural resistance genes, cloning of proteinase inhibitor coding genes, anti-nematodal proteins and use of RNA interference to suppress nematode effectors. Furthermore, the manipulation of expression levels of genes induced and suppressed by nematodes has also been suggested as an innovative approach for inducing nematode resistance in plants. The information in this article will provide an array of possibilities to engineer resistance against PPNs in different crop plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Amjad Abbas
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
| | - Faiz A. Joyia
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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De Oliveira AS, Koolhaas I, Boiteux LS, Caldararu OF, Petrescu A, Oliveira Resende R, Kormelink R. Cell death triggering and effector recognition by Sw-5 SD-CNL proteins from resistant and susceptible tomato isolines to Tomato spotted wilt virus. MOLECULAR PLANT PATHOLOGY 2016; 17:1442-1454. [PMID: 27271212 PMCID: PMC6638320 DOI: 10.1111/mpp.12439] [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: 03/08/2016] [Revised: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 05/16/2023]
Abstract
Only a limited number of dominant resistance genes acting against plant viruses have been cloned, and further functional studies of these have been almost entirely limited to the resistance genes Rx against Potato virus X (PVX) and N against Tobacco mosaic virus (TMV). Recently, the cell-to-cell movement protein (NSM ) of Tomato spotted wilt virus (TSWV) has been identified as the avirulence determinant (Avr) of Sw-5b-mediated resistance, a dominant resistance gene which belongs to the class of SD-CC-NB-LRR (Solanaceae domain-coiled coil-nucleotide-binding-leucine-rich repeat, SD-CNL) resistance genes. On transient expression of the NSM protein in tomato and transgenic Nicotiana benthamiana harbouring the Sw-5b gene, a hypersensitive cell death response (HR) is triggered. Here, it is shown that high accumulation of the Sw-5b protein in N. benthamiana leaves, achieved by co-expression of the Sw-5b protein with RNA silencing suppressors (RSSs), leads to auto-activity in the absence of NSM . In a similar approach, Sw-5a, the highest conserved paralogue of Sw-5b from Solanum peruvianum, also triggered HR by auto-activation, whereas the highest conserved orthologue from susceptible S. lycopersicum, named Sw-5aS , did not. However, neither of the last two homologues was able to trigger an NSM -dependent HR. Truncated and mutated versions of these Sw-5 proteins revealed that the NB-ARC [nucleotide-binding adaptor shared by Apaf-1 (from humans), R proteins and CED-4 (from nematodes)] domain is sufficient for the triggering of HR and seems to be suppressed by the SD-CC domain. Furthermore, a single mutation was sufficient to restore auto-activity within the NB-ARC domain of Sw-5aS . When the latter domain was fused to the Sw-5b LRR domain, NSM -dependent HR triggering was regained, but not in the presence of its own Sw-5aS LRR domain. Expression analysis in planta revealed a nucleocytoplasmic localization pattern of Sw-5b, in which the SD-CC domain seems to be required for nuclear translocation. Although the Sw-5 N-terminal CC domain, in contrast with Rx, contains an additional SD, most findings from this study support a conserved role of domains within NB-LRR (NLR) proteins against plant viruses.
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Affiliation(s)
- Athos Silva De Oliveira
- Laboratory of Virology, Department of Plant SciencesWageningen UniversityDroevendaalsesteeg 1WageningenPB6708the Netherlands
- Department of Cell Biology, Institute of Biological SciencesUniversity of Brasília (UnB)Asa Norte 70910‐900BrasíliaDFBrazil
| | - Ivo Koolhaas
- Laboratory of Virology, Department of Plant SciencesWageningen UniversityDroevendaalsesteeg 1WageningenPB6708the Netherlands
| | | | - Octav F. Caldararu
- Department of Bioinformatics and Structural BiochemistryInstitute of Biochemistry of the Romanian AcademySplaiul Independentei 296Bucharest060036Romania
| | - Andrei‐Jose Petrescu
- Department of Bioinformatics and Structural BiochemistryInstitute of Biochemistry of the Romanian AcademySplaiul Independentei 296Bucharest060036Romania
| | - Renato Oliveira Resende
- Department of Cell Biology, Institute of Biological SciencesUniversity of Brasília (UnB)Asa Norte 70910‐900BrasíliaDFBrazil
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant SciencesWageningen UniversityDroevendaalsesteeg 1WageningenPB6708the Netherlands
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Vossen JH, van Arkel G, Bergervoet M, Jo KR, Jacobsen E, Visser RGF. The Solanum demissum R8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1785-96. [PMID: 27314264 PMCID: PMC4983296 DOI: 10.1007/s00122-016-2740-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/04/2016] [Indexed: 05/22/2023]
Abstract
The potato late blight resistance gene R8 has been cloned. R8 is found in five late blight resistant varieties deployed in three different continents. R8 recognises Avr8 and is homologous to the NB-LRR protein Sw-5 from tomato. The broad spectrum late blight resistance gene R8 from Solanum demissum was cloned based on a previously published coarse map position on the lower arm of chromosome IX. Fine mapping in a recombinant population and bacterial artificial chromosome (BAC) library screening resulted in a BAC contig spanning 170 kb of the R8 haplotype. Sequencing revealed a cluster of at least ten R gene analogues (RGAs). The seven RGAs in the genetic window were subcloned for complementation analysis. Only one RGA provided late blight resistance and caused recognition of Avr8. From these results, it was concluded that the newly cloned resistance gene was indeed R8. R8 encodes a typical intracellular immune receptor with an N-terminal coiled coil, a central nucleotide binding site and 13 C-terminal leucine rich repeats. Phylogenetic analysis of a set of representative Solanaceae R proteins shows that R8 resides in a clearly distinct clade together with the Sw-5 tospovirus R protein from tomato. It was found that the R8 gene is present in late blight resistant potato varieties from Europe (Sarpo Mira), USA (Jacqueline Lee, Missaukee) and China (PB-06, S-60). Indeed, when tested under field conditions, R8 transgenic potato plants showed broad spectrum resistance to the current late blight population in the Netherlands, similar to Sarpo Mira.
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Affiliation(s)
- Jack H Vossen
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
| | - Gert van Arkel
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Marjan Bergervoet
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Kwang-Ryong Jo
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Evert Jacobsen
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
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50
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Abstract
Many plants, both in nature and in agriculture, are resistant to multiple diseases. Although much of the plant innate immunity system provides highly specific resistance, there is emerging evidence to support the hypothesis that some components of plant defense are relatively nonspecific, providing multiple disease resistance (MDR). Understanding MDR is of fundamental and practical interest to plant biologists, pathologists, and breeders. This review takes stock of the available evidence related to the MDR hypothesis. Questions about MDR are considered primarily through the lens of forward genetics, starting at the organismal level and proceeding to the locus level and, finally, to the gene level. At the organismal level, MDR may be controlled by clusters of R genes that evolve under diversifying selection, by dispersed, pathogen-specific genes, and/or by individual genes providing MDR. Based on the few MDR loci that are well-understood, MDR is conditioned by diverse mechanisms at the locus and gene levels.
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Affiliation(s)
- Tyr Wiesner-Hanks
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853; ,
| | - Rebecca Nelson
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853; ,
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