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Xu L, Wang S, Wang W, Wang H, Welsh L, Boevink PC, Whisson SC, Birch PRJ. Proteolytic processing of both RXLR and EER motifs in oomycete effectors. THE NEW PHYTOLOGIST 2025; 245:1640-1654. [PMID: 39327921 PMCID: PMC11754927 DOI: 10.1111/nph.20130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/20/2024] [Indexed: 09/28/2024]
Abstract
Arg-any amino acid-Leu-Arg (RXLR) effectors are central oomycete virulence factors that suppress plant immunity. Relatively little is known about how they are processed post-translationally before delivery into host cells. A range of molecular, cell and biochemical processes were used to investigate proteolytic processing of RXLR and Glu-Glu-Arg (EER) motifs in Phytophthora infestans effectors. Proteolytic cleavage at the RXLR motif occurred before secretion in all effectors tested, suggesting it is a general rule. Cleavage occurred between the leucine and the second arginine. There was no cleavage of a naturally occurring second RXLR motif in a structured region of Pi21388/AvrBlb1, or one introduced at a similar position in effector Pi04314, in keeping with the motif being positionally constrained, potentially to disordered regions closely following the signal peptide. Remarkably, independent proteolytic cleavage of the EER motif, often found immediately after the RXLR, was also observed, occurring immediately after the arginine. Full-length effectors expressed in host plant Nicotiana benthamiana revealed that, although secreted, they were poorly processed, suggesting that RXLR and EER cleavage does not occur in all eukaryotic cells. We conclude that, whether possessing both RXLR and EER, or either motif alone, these effectors are likely generally proteolytically processed before secretion.
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Affiliation(s)
- Lin Xu
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee, at James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Shumei Wang
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee, at James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Wei Wang
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee, at James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Haixia Wang
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee, at James Hutton InstituteInvergowrieDundeeDD2 5DAUK
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest Agriculture & Forestry UniversityYanglingShanxi712100China
| | - Lydia Welsh
- Cell and Molecular Sciences, James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Petra C. Boevink
- Cell and Molecular Sciences, James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Stephen C. Whisson
- Cell and Molecular Sciences, James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee, at James Hutton InstituteInvergowrieDundeeDD2 5DAUK
- Cell and Molecular Sciences, James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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Hosaka AJ, Sanetomo R, Hosaka K. Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole-genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39585203 DOI: 10.1111/tpj.17158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 11/06/2024] [Accepted: 11/09/2024] [Indexed: 11/26/2024]
Abstract
Mexican wild diploid potato species are reproductively isolated from A-genome species, including cultivated potatoes; thus, their genomic relationships remain unknown. Solanum stoloniferum Schlechtd. et Bché. (2n = 4x = 48, AABB) is a Mexican allotetraploid species frequently used in potato breeding. We constructed a chromosome-scale assembly of the S. stoloniferum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. The final assembly consisted of 1742 Mb, among which 745 Mb and 713 Mb were anchored to the 12 A-genome and 12 B-genome chromosomes, respectively. Using the RNA-seq datasets, we detected 20 994 and 19 450 genes in the A and B genomes, respectively. Among these genes, 5138 and 3594 were specific to the A and B genomes, respectively, and 15 856 were homoeologous, of which 18.6-25.4% were biasedly expressed. Structural variations such as large pericentromeric inversions were frequently found between the A- and B-genome chromosomes. A comparison of the gene sequences from 38 diverse genomes of the related Solanum species revealed that the S. stoloniferum B genome and Mexican diploid species, with the exception of S. verrucosum, were monophyletically distinct from the S. stoloniferum A genome and the other A-genome species, indicating that the Mexican diploid species share the B genome. The content and divergence of transposable elements (TEs) revealed recent bursts and transpositions of TEs after polyploidization. Thus, the S. stoloniferum genome has undergone dynamic structural differentiation and TE mobilization and reorganization to stabilize the genomic imbalance. This study provides new insights into polyploid evolution and the efficient use of allotetraploid species in potato breeding.
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Affiliation(s)
- Awie J Hosaka
- Nihon BioData Corporation, Takatsu, Kawasaki, Kanagawa, 213-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
| | - Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kazuyoshi Hosaka
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
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Liu H, Zhang W, He Q, Aikemu R, Xu H, Guo Z, Wang L, Li W, Wang G, Wang X, Guo W. Re-localization of a repeat-containing fungal effector by apoplastic protein Chitinase-like 1 blocks its toxicity. Nat Commun 2024; 15:10122. [PMID: 39578470 PMCID: PMC11584738 DOI: 10.1038/s41467-024-54470-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/08/2024] [Indexed: 11/24/2024] Open
Abstract
A fungal effector that is toxic to plant cells was identified in Verticillium dahliae. The effector contains a non-canonical Common in several Fungal Extracellular Membrane proteins (CFEM) domain, a tandem repeat region consisting of four 14-amino acid repeats rich in proline, and a C-terminal region, thus is designated V. dahliae tetrapeptide repeat protein (VdTRP). The membrane targeting of VdTRP is vital for its cell toxicity. CFEM mediates the membrane targeting and the tandem repeat region exerts the toxic function upon cell membrane. The chitinase-like 1 (CTL1), an essential apoplastic protein of cotton, can redirect VdTRP from cell membrane to apoplast. Transgenic cotton overexpressing CTL1 greatly enhances cotton resistance to V. dahliae without affecting cotton growth and development, implicating its potential application in breeding cotton with high wilt resistance. Our data demonstrates that genetic manipulation of effector target constitutes potential strategy for improving crop resistance to fungal pathogens.
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Affiliation(s)
- Hanqiao Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenshu Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qinqfei He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Reyila Aikemu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huijuan Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhan Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lu Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weixi Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guilin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Wang
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China.
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing, 210095, China.
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Oh S, Kim MS, Kang HJ, Kim T, Kong J, Choi D. Conserved effector families render Phytophthora species vulnerable to recognition by NLR receptors in nonhost plants. Nat Commun 2024; 15:10070. [PMID: 39567537 PMCID: PMC11579510 DOI: 10.1038/s41467-024-54452-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 11/04/2024] [Indexed: 11/22/2024] Open
Abstract
NLR receptor is suggested as a component of plant nonhost resistance (NHR). However, the evolutionary process of how plants develop receptors for recognizing broad-spectrum pathogens is still elusive. Here, we observe that multiple RxLR effector families including 12 reported avirulence effectors of Phytophthora infestans are broadly conserved across the Phytophthora species. We select 69 effectors distributed into 8 families from 6 Phytophthora species, and confirm that 60.87% of the tested effectors are recognized by Solanum NLRs according to their defined families. Furthermore, we confirm that expression of R1, R8, and Rpi-amr1 confer broad-spectrum resistance against multiple Phytophthora species. Combined results suggest that conserved effector families of Phytophthora species allow solanaceous plants to recognize broad-spectrum pathogens via NLRs that originally reported to recognize P. infestans. Thus, NLR-mediated recognition would contribute to NHR against pathogens that possess similar repertoires of effectors. Moreover, this homology-based approach would be applicable to other plant-pathogen systems and provide an alternative strategy of genetic mapping to identify functional NLRs against various crop-threatening pathogens.
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Affiliation(s)
- Soohyun Oh
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung-Shin Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin, 17058, Republic of Korea
| | - Hui Jeong Kang
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taewon Kim
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junhyeong Kong
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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5
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Wen Q, Wang S, Zhang X, Zhou Z. Recent advances of NLR receptors in vegetable disease resistance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112224. [PMID: 39142606 DOI: 10.1016/j.plantsci.2024.112224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024]
Abstract
Plants mainly depend on both cell-surface and intracellular receptors to defend against various pathogens. The nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular receptors that recognize pathogen effectors. The first NLR was cloned thirty years ago. Genomic sequencing and biotechnologies accelerated NLR gene isolation. NLR genes have been proven useful in breeding disease resistant crops. Here, we summarized the current knowledge of strategies for NLR gene isolation and provided a list of NLRs cloned in vegetables. We also discussed the mechanisms underlying NLR gene function, the challenges of NLRs in vegetable breeding and directions for future studies.
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Affiliation(s)
- Qing Wen
- Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Shaoyun Wang
- Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China
| | - Zhaoyang Zhou
- Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China.
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Sun B, Huang J, Kong L, Gao C, Zhao F, Shen J, Wang T, Li K, Wang L, Wang Y, Halterman DA, Dong S. Alternative splicing of a potato disease resistance gene maintains homeostasis between growth and immunity. THE PLANT CELL 2024; 36:3729-3750. [PMID: 38941447 PMCID: PMC11371151 DOI: 10.1093/plcell/koae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Plants possess a robust and sophisticated innate immune system against pathogens and must balance growth with rapid pathogen detection and defense. The intracellular receptors with nucleotide-binding leucine-rich repeat (NLR) motifs recognize pathogen-derived effector proteins and thereby trigger the immune response. The expression of genes encoding NLR receptors is precisely controlled in multifaceted ways. The alternative splicing (AS) of introns in response to infection is recurrently observed but poorly understood. Here we report that the potato (Solanum tuberosum) NLR gene RB undergoes AS of its intron, resulting in 2 transcriptional isoforms, which coordinately regulate plant immunity and growth homeostasis. During normal growth, RB predominantly exists as an intron-retained isoform RB_IR, encoding a truncated protein containing only the N-terminus of the NLR. Upon late blight infection, the pathogen induces intron splicing of RB, increasing the abundance of RB_CDS, which encodes a full-length and active R protein. By deploying the RB splicing isoforms fused with a luciferase reporter system, we identified IPI-O1 (also known as Avrblb1), the RB cognate effector, as a facilitator of RB AS. IPI-O1 directly interacts with potato splicing factor StCWC15, resulting in altered localization of StCWC15 from the nucleoplasm to the nucleolus and nuclear speckles. Mutations in IPI-O1 that eliminate StCWC15 binding also disrupt StCWC15 re-localization and RB intron splicing. Thus, our study reveals that StCWC15 serves as a surveillance facilitator that senses the pathogen-secreted effector and regulates the trade-off between RB-mediated plant immunity and growth, expanding our understanding of molecular plant-microbe interactions.
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Affiliation(s)
- Biying Sun
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Huang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Liang Kong
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuyun Gao
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Zhao
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayong Shen
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Kangping Li
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Luyao Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen Branch, Shenzhen, Guangdong 518120, China
| | - Yuanchao Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Dennis A Halterman
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
- US Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706-1514, USA
| | - Suomeng Dong
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
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Yadav V, Pal D, Poonia AK. A Study on Genetically Engineered Foods: Need, Benefits, Risk, and Current Knowledge. Cell Biochem Biophys 2024; 82:1931-1946. [PMID: 39020085 DOI: 10.1007/s12013-024-01390-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Food requirements have always been a top priority, and with the exponential growth of the human population, there is an increasing need for large quantities of food. Traditional cultivation methods are not able to meet the current demand for food products. One significant challenge is the shortened shelf-life of naturally occurring food items, which directly contributes to food scarcity. Contaminating substances such as weeds and pests play a crucial role in this issue. In response, researchers have introduced genetically engineered (GE) food as a potential solution. These food products are typically created by adding or replacing genes in the DNA of naturally occurring foods. GE foods offer various advantages, including increased quality and quantity of food production, adaptability to various climatic conditions, modification of vitamin and mineral levels, and prolonged shelf life. They address the major concerns of global food scarcity and food security. However, the techniques used in the production of GE foods may not be universally acceptable due to the genetic alteration of animal genes into plants or vice versa. Additionally, their unique nature necessitates further long-term studies. This study delves into the procedures and growth stages of DNA sequencing, covering the benefits, risks, industrial relevance, current knowledge, and future challenges of GE foods. GE foods have the potential to extend the shelf life of food items, alleviate food shortages, and fulfill the current nutritional food demand.
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Affiliation(s)
- Venkteshwar Yadav
- Department of Chemical Engineering, National Institute of Technology Raipur, Raipur, Chhattisgarh, 492010, India
| | - Dharm Pal
- Department of Chemical Engineering, National Institute of Technology Raipur, Raipur, Chhattisgarh, 492010, India.
| | - Anil Kumar Poonia
- Department of Chemical Engineering, National Institute of Technology Raipur, Raipur, Chhattisgarh, 492010, India
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Coomber A, Saville A, Ristaino JB. Evolution of Phytophthora infestans on its potato host since the Irish potato famine. Nat Commun 2024; 15:6488. [PMID: 39103347 DOI: 10.1038/s41467-024-50749-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845-1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845-1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection.
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Affiliation(s)
- Allison Coomber
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
- Functional Genomics Program, NC State University, Raleigh, NC, USA
| | - Amanda Saville
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA.
- Emerging Plant Disease and Global Food Security Cluster, NC State University, Raleigh, NC, USA.
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Berindean IV, Taoutaou A, Rida S, Ona AD, Stefan MF, Costin A, Racz I, Muntean L. Modern Breeding Strategies and Tools for Durable Late Blight Resistance in Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:1711. [PMID: 38931143 PMCID: PMC11207681 DOI: 10.3390/plants13121711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/08/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024]
Abstract
Cultivated potato (Solanum tuberosum) is a major crop worldwide. It occupies the second place after cereals (corn, rice, and wheat). This important crop is threatened by the Oomycete Phytophthora infestans, the agent of late blight disease. This pathogen was first encountered during the Irish famine during the 1840s and is a reemerging threat to potatoes. It is mainly controlled chemically by using fungicides, but due to health and environmental concerns, the best alternative is resistance. When there is no disease, no treatment is required. In this study, we present a summary of the ongoing efforts concerning resistance breeding of potato against this devastating pathogen, P. infestans. This work begins with the search for and selection of resistance genes, whether they are from within or from outside the species. The genetic methods developed to date for gene mining, such as effectoromics and GWAS, provide researchers with the ability to identify genes of interest more efficiently. Once identified, these genes are cloned using molecular markers (MAS or QRL) and can then be introduced into different cultivars using somatic hybridization or recombinant DNA technology. More innovative technologies have been developed lately, such as gene editing using the CRISPR system or gene silencing, by exploiting iRNA strategies that have emerged as promising tools for managing Phytophthora infestans, which can be employed. Also, gene pyramiding or gene stacking, which involves the accumulation of two or more R genes on the same individual plant, is an innovative method that has yielded many promising results. All these advances related to the development of molecular techniques for obtaining new potato cultivars resistant to P. infestans can contribute not only to reducing losses in agriculture but especially to ensuring food security and safety.
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Affiliation(s)
- Ioana Virginia Berindean
- Department of Crops Sciences: Genetics, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (I.V.B.)
| | - Abdelmoumen Taoutaou
- Laboratoire de Phytopathologie et Biologie Moléculaire, Département de Botanique, École Nationale, Supérieure Agronomique, Avenue Pasteur (ENSA-ES 1603), Hassan Badi, El-Harrach, Algiers 16200, Algeria
| | - Soumeya Rida
- Département d’Agronomie, Faculté des Sciences de la Nature et de la Vie (SNV), Université Chadli Bendjedid, BP N°73, El Tarf 36000, Algeria
| | - Andreea Daniela Ona
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
| | - Maria Floriana Stefan
- National Institute of Research and Development for Potato and Sugar Beet Braşov, Fundaturii Street 2, 500470 Braşov, Romania
| | - Alexandru Costin
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
| | - Ionut Racz
- Department of Crops Sciences: Genetics, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (I.V.B.)
| | - Leon Muntean
- Department of Crops Sciences: Plant Breeding, Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, 400372 Cluj-Napoca, Romania; (A.D.O.)
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van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, Chavarro-Carrero E, Meijer HJG, Feurtey A, Maryani N, Ordóñez N, Schneiders H, Nijbroek K, Wittenberg AHJ, Hofstede R, García-Bastidas F, Sørensen A, Swennen R, Drenth A, Stukenbrock EH, Kema GHJ, Seidl MF. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. THE NEW PHYTOLOGIST 2024; 242:610-625. [PMID: 38402521 DOI: 10.1111/nph.19604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.
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Affiliation(s)
- Anouk C van Westerhoven
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Carolina Aguilera-Galvez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Giuliana Nakasato-Tagami
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Einar Martinez de la Parte
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Edgar Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department Biointeractions and Plant Health, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alice Feurtey
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
- Plant Pathology, Eidgenössische Technische Hochschule Zürich, Rämistrasse 101, 8092, Zürich, Switzerland
| | - Nani Maryani
- Biology Education, Universitas Sultan Ageng Tirtayasa, Jalan Raya Palka No.Km 3, 42163, Banten, Indonesia
| | - Nadia Ordóñez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harrie Schneiders
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Rene Hofstede
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Anker Sørensen
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Ronny Swennen
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Catholic University of Leuven, Oude Markt 13, 3000, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15 Naguru E Rd, Kampala, PO Box 7878, Uganda
| | - Andre Drenth
- The University of Queensland, St Lucia, 4072, Brisbane, Queensland, Australia
| | - Eva H Stukenbrock
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michael F Seidl
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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11
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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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12
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Christian N, Perlin MH. Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes. Mycologia 2024; 116:227-250. [PMID: 38380970 DOI: 10.1080/00275514.2023.2299658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/22/2023] [Indexed: 02/22/2024]
Abstract
Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
| | - Michael H Perlin
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
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13
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Peng J, Wang X, Wang H, Li X, Zhang Q, Wang M, Yan J. Advances in understanding grapevine downy mildew: From pathogen infection to disease management. MOLECULAR PLANT PATHOLOGY 2024; 25:e13401. [PMID: 37991155 PMCID: PMC10788597 DOI: 10.1111/mpp.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023]
Abstract
Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.
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Affiliation(s)
- Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hui Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qi Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Meng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
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14
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Tomar V, Rikkerink EHA, Song J, Sofkova-Bobcheva S, Bus VGM. Structure-Function Characterisation of Eop1 Effectors from the Erwinia-Pantoea Clade Reveals They May Acetylate Their Defence Target through a Catalytic Dyad. Int J Mol Sci 2023; 24:14664. [PMID: 37834112 PMCID: PMC10572645 DOI: 10.3390/ijms241914664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The YopJ group of acetylating effectors from phytopathogens of the genera Pseudomonas and Ralstonia have been widely studied to understand how they modify and suppress their host defence targets. In contrast, studies on a related group of effectors, the Eop1 group, lag far behind. Members of the Eop1 group are widely present in the Erwinia-Pantoea clade of Gram-negative bacteria, which contains phytopathogens, non-pathogens and potential biocontrol agents, implying that they may play an important role in agroecological or pathological adaptations. The lack of research in this group of YopJ effectors has left a significant knowledge gap in their functioning and role. For the first time, we perform a comparative analysis combining AlphaFold modelling, in planta transient expressions and targeted mutational analyses of the Eop1 group effectors from the Erwinia-Pantoea clade, to help elucidate their likely activity and mechanism(s). This integrated study revealed several new findings, including putative binding sites for inositol hexakisphosphate and acetyl coenzyme A and newly postulated target-binding domains, and raises questions about whether these effectors function through a catalytic triad mechanism. The results imply that some Eop1s may use a catalytic dyad acetylation mechanism that we found could be promoted by the electronegative environment around the active site.
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Affiliation(s)
- Vishant Tomar
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Erik H. A. Rikkerink
- Mt Albert Research Centre, The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Janghoon Song
- Pear Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Naju 58216, Republic of Korea
| | - Svetla Sofkova-Bobcheva
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand;
| | - Vincent G. M. Bus
- Hawkes Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4130, New Zealand;
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De la Cruz G, Blas R, Pérez W, Neyra E, Ortiz R. Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group. FRONTIERS IN PLANT SCIENCE 2023; 14:1210046. [PMID: 37780511 PMCID: PMC10535101 DOI: 10.3389/fpls.2023.1210046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/10/2023] [Indexed: 10/03/2023]
Abstract
Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.
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Affiliation(s)
- Germán De la Cruz
- Laboratorio de Genética y Biotecnología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de San Cristóbal de Huamanga (UNSCH), Ayacucho, Peru
| | - Raúl Blas
- Instituto de Biotecnologia (IBT), Facultad de Agronomia, Universidad Nacional Agraria La Molina (UNALM), Lima, Peru
| | - Willmer Pérez
- Plant Pathology Laboratory, Crop and Systems Sciences Division, International Potato Center, Lima, Peru
| | - Edgar Neyra
- Unidad de Genómica, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento Académico de Tecnología Médica, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Oh S, Kim S, Park HJ, Kim MS, Seo MK, Wu CH, Lee HA, Kim HS, Kamoun S, Choi D. Nucleotide-binding leucine-rich repeat network underlies nonhost resistance of pepper against the Irish potato famine pathogen Phytophthora infestans. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36912620 DOI: 10.1111/pbi.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Nonhost resistance (NHR) is a robust plant immune response against non-adapted pathogens. A number of nucleotide-binding leucine-rich repeat (NLR) proteins that recognize non-adapted pathogens have been identified, although the underlying molecular mechanisms driving robustness of NHR are still unknown. Here, we screened 57 effectors of the potato late blight pathogen Phytophthora infestans in nonhost pepper (Capsicum annuum) to identify avirulence effector candidates. Selected effectors were tested against 436 genome-wide cloned pepper NLRs, and we identified multiple functional NLRs that recognize P. infestans effectors and confer disease resistance in the Nicotiana benthamiana as a surrogate system. The identified NLRs were homologous to known NLRs derived from wild potatoes that recognize P. infestans effectors such as Avr2, Avrblb1, Avrblb2, and Avrvnt1. The identified CaRpi-blb2 is a homologue of Rpi-blb2, recognizes Avrblb2 family effectors, exhibits feature of lineage-specifically evolved gene in microsynteny and phylogenetic analyses, and requires pepper-specific NRC (NLR required for cell death)-type helper NLR for proper function. Moreover, CaRpi-blb2-mediated hypersensitive response and blight resistance were more tolerant to suppression by the PITG_15 278 than those mediated by Rpi-blb2. Combined results indicate that pepper has stacked multiple NLRs recognizing effectors of non-adapted P. infestans, and these NLRs could be more tolerant to pathogen-mediated immune suppression than NLRs derived from the host plants. Our study suggests that NLRs derived from nonhost plants have potential as untapped resources to develop crops with durable resistance against fast-evolving pathogens by stacking the network of nonhost NLRs into susceptible host plants.
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Affiliation(s)
- Soohyun Oh
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sejun Kim
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyo-Jeong Park
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Myung-Shin Kim
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Min-Ki Seo
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hyun-Ah Lee
- Department of Horticulture, Division of Smart Horticulture, Yonam University, Cheonan, South Korea
| | - Hyun-Soon Kim
- Korean Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, South Korea
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Doil Choi
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Population Dynamics of Phytophthora infestans in Egypt Reveals Clonal Dominance of 23_A1 and Displacement of 13_A2 Clonal Lineage. J Fungi (Basel) 2023; 9:jof9030349. [PMID: 36983517 PMCID: PMC10054562 DOI: 10.3390/jof9030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023] Open
Abstract
Potato (Solanum tuberosum L.) and tomato (S. lycopersicum L.) are the most economically important vegetable crops in Egypt and worldwide. The winter crop in Egypt is particularly prone to late blight caused by Phytophthora infestans. A total of 152 P. infestans isolates were isolated from the 2013, 2014, 2016 and 2018 winter crops with 82 isolates from potato, 69 from tomato and one isolate from eggplant (S. melongena L.). All isolates belonged to the A1 mating type with no evidence of A2 or self-fertile strains. The majority of isolates (53%) were sensitive to metalaxyl, 32% were intermediate and 15% were resistant. Variation in aggressiveness between three P. infestans isolates EG-005 (13_A2) and EG-276 (23_A1) from potato, and EG-237 (23_A1) from eggplant was determined on tuber slices and leaflets of 10 potato cultivars. The eggplant isolate EG-237 showed higher sporulation capacity compared with the other tested isolates and was able to infect potato (Lady Rosetta cv) and tomato (Super Strain B cv). The simple sequence repeat (SSR) genotyping data showed that in contrast to our previous work (3-year period 2010–12) in which the proportion of 13_A2 lineage was 35%, all isolates belonged to the 23_A1 lineage. There was no evidence for the existence of the A2 mating type or 13_A2 lineage even in the destroyed field crops of some cultivars (Cara, Bellini and Valor) that had been reported as resistant to 23_A1. The data have been submitted into the Euroblight database to allow temporal and spatial genetic diversity to be examined in comparison with other regional P. infestans populations. The AVR2 and AVR2-like RXLR effector genes were amplified and sequenced. In the avirulent AVR2 gene, only one heterozygous SNP was detected at position 31 in the N terminus in six isolates out of eleven, whereas two heterozygous SNPs were detected at position 29 in the N-terminus and ninety-two in the C- terminus of the AVR2-like gene. This suggests that changes in the previously reported virulence profile of 23_A1 are not related to commercial cultivars carrying the R2 gene. In addition, this is the first report of P. infestans on eggplant in Egypt.
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Tu Q, Wang L, An Q, Shuai J, Xia X, Dong Y, Zhang X, Li G, He Y. Comparative transcriptomics identifies the key in planta-expressed genes of Fusarium graminearum during infection of wheat varieties. Front Genet 2023; 14:1166832. [PMID: 37144121 PMCID: PMC10151574 DOI: 10.3389/fgene.2023.1166832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Fusarium head blight (FHB), caused mainly by the fungus Fusarium graminearum, is one of the most devastating diseases in wheat, which reduces the yield and quality of grain. Fusarium graminearum infection of wheat cells triggers dynamic changes of gene expression in both F. graminearum and wheat, leading to molecular interactions between pathogen and host. The wheat plant in turn activates immune signaling or host defense pathways against FHB. However, the mechanisms by which F. graminearum infects wheat varieties with different levels of host resistance are largely limited. In this study, we conducted a comparative analysis of the F. graminearum transcriptome in planta during the infection of susceptible and resistant wheat varieties at three timepoints. A total of 6,106 F. graminearum genes including those functioning in cell wall degradation, synthesis of secondary metabolites, virulence, and pathogenicity were identified during the infection of different hosts, which were regulated by hosts with different genetic backgrounds. Genes enriched with metabolism of host cell wall components and defense response processes were specifically dynamic during the infection with different hosts. Our study also identified F. graminearum genes that were specifically suppressed by signals derived from the resistant plant host. These genes may represent direct targets of the plant defense against infection by this fungus. Briefly, we generated databases of in planta-expressed genes of F. graminearum during infection of two different FHB resistance level wheat varieties, highlighted their dynamic expression patterns and functions of virulence, invasion, defense response, metabolism, and effector signaling, providing valuable insight into the interactions between F. graminearum and susceptible/resistant wheat varieties.
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Affiliation(s)
- Qiang Tu
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Lirong Wang
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Qi An
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jie Shuai
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Life Sciences and Engineering, Wheat Research Institute, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiaobo Xia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yifan Dong
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xu Zhang
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Gang Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Gang Li, ; Yi He,
| | - Yi He
- CIMMYT-JAAS Joint Center for Wheat Diseases, The Research Center of Wheat Scab, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- *Correspondence: Gang Li, ; Yi He,
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Redkar A, Cevik V, Bailey K, Zhao H, Kim DS, Zou Z, Furzer OJ, Fairhead S, Borhan MH, Holub EB, Jones JDG. The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors. THE NEW PHYTOLOGIST 2023; 237:532-547. [PMID: 35838065 PMCID: PMC10087428 DOI: 10.1111/nph.18378] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 05/26/2023]
Abstract
The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their capacity to infect different host plant species. Each A. candida race encodes secreted proteins with a CX2 CX5 G ('CCG') motif that are polymorphic and show presence/absence variation, and are therefore candidate effectors. The White Rust Resistance 4 (WRR4) locus in Arabidopsis thaliana accession Col-0 contains three genes that encode intracellular nucleotide-binding domain leucine-rich repeat immune receptors. The Col-0 alleles of WRR4A and WRR4B confer resistance to multiple A. candida races, although both WRR4A and WRR4B can be overcome by the Col-0-virulent race 4 isolate AcEx1. Comparison of CCG candidate effectors in avirulent and virulent races, and transient co-expression of CCG effectors from four A. candida races in Nicotiana sp. or A. thaliana, revealed CCG effectors that trigger WRR4A- or WRR4B-dependent hypersensitive responses. We found eight WRR4A-recognised CCGs and four WRR4B-recognised CCGs, the first recognised proteins from A. candida for which the cognate immune receptors in A. thaliana are known. This multiple recognition capacity potentially explains the broad-spectrum resistance to several A. candida races conferred by WRR4 paralogues. We further show that of five tested CCGs, three confer enhanced disease susceptibility when expressed in planta, consistent with A. candida CCG proteins being effectors.
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Affiliation(s)
- Amey Redkar
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BotanySavitribai Phule Pune UniversityGaneshkhindPune411007India
| | - Volkan Cevik
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Kate Bailey
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - He Zhao
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - Dae Sung Kim
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Present address:
State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei UniversityWuhan430062China
| | - Zhou Zou
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Oliver J. Furzer
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BiologyUniversity of North CarolinaChapel HillNC27599USA
| | - Sebastian Fairhead
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
| | - M. Hossein Borhan
- Agriculture and Agri‐Food Canada107 Science PlaceSaskatoonSKS7N 0X2Canada
| | - Eric B. Holub
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
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20
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Combier M, Evangelisti E, Piron MC, Schornack S, Mestre P. Candidate effector proteins from the oomycetes Plasmopara viticola and Phytophthora parasitica share similar predicted structures and induce cell death in Nicotiana species. PLoS One 2022; 17:e0278778. [PMID: 36459530 PMCID: PMC9718384 DOI: 10.1371/journal.pone.0278778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Effector proteins secreted by plant pathogens are essential for infection. Cytoplasmic RXLR effectors from oomycetes are characterized by the presence of RXLR and EER motifs that are frequently linked to WY- and/or LWY-domains, folds that are exclusive to this effector family. A related family of secreted candidate effector proteins, carrying WY-domains and the EER motif but lacking the canonical RXLR motif, has recently been described in oomycetes and is mainly found in downy mildew pathogens. Plasmopara viticola is an obligate biotrophic oomycete causing grapevine downy mildew. Here we describe a conserved Pl. viticola secreted candidate non-RXLR effector protein with cell death-inducing activity in Nicotiana species. A similar RXLR effector candidate from the broad host range oomycete pathogen Phytophthora parasitica also induces cell death in Nicotiana. Through comparative tertiary structure modelling, we reveal that both proteins are predicted to carry WY- and LWY-domains. Our work supports the presence of LWY-domains in non-RXLR effectors and suggests that effector candidates with similar domain architecture may exert similar activities.
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Affiliation(s)
- Maud Combier
- SVQV, UMR-A 1131, Université de Strasbourg, INRAE, Colmar, France
| | - Edouard Evangelisti
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | | | - Sebastian Schornack
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Pere Mestre
- SVQV, UMR-A 1131, Université de Strasbourg, INRAE, Colmar, France
- * E-mail:
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21
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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Microbial Effectors: Key Determinants in Plant Health and Disease. Microorganisms 2022; 10:1980. [PMID: 36296254 PMCID: PMC9610748 DOI: 10.3390/microorganisms10101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Effectors are small, secreted molecules that alter host cell structure and function, thereby facilitating infection or triggering a defense response. Effectoromics studies have focused on effectors in plant-pathogen interactions, where their contributions to virulence are determined in the plant host, i.e., whether the effector induces resistance or susceptibility to plant disease. Effector molecules from plant pathogenic microorganisms such as fungi, oomycetes and bacteria are major disease determinants. Interestingly, the effectors of non-pathogenic plant organisms such as endophytes display similar functions but have different outcomes for plant health. Endophyte effectors commonly aid in the establishment of mutualistic interactions with the plant and contribute to plant health through the induction of systemic resistance against pathogens, while pathogenic effectors mainly debilitate the plant's immune response, resulting in the establishment of disease. Effectors of plant pathogens as well as plant endophytes are tools to be considered in effectoromics for the development of novel strategies for disease management. This review aims to present effectors in their roles as promotors of health or disease for the plant host.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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22
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Paluchowska P, Śliwka J, Yin Z. Late blight resistance genes in potato breeding. PLANTA 2022; 255:127. [PMID: 35576021 PMCID: PMC9110483 DOI: 10.1007/s00425-022-03910-6] [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: 01/28/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
Using late blight resistance genes targeting conservative effectors of Phytophthora infestans and the constructing gene pyramids may lead to durable, broad-spectrum resistance, which could be accelerated through genetic engineering. Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. In 2020, potato production was estimated to be more than 359 million tons according to the Food and Agriculture Organization (FAO). Potato is affected by many pathogens, among which Phytophthora infestans, causing late blight, is of the most economic importance. Crop protection against late blight requires intensive use of fungicides, which has an impact on the environment and humans. Therefore, new potato cultivars have been bred using resistance genes against P. infestans (Rpi genes) that originate from wild relatives of potato. Such programmes were initiated 100 years ago, but the process is complex and long. The development of genetic engineering techniques has enabled the direct transfer of resistance genes from potato wild species to cultivars and easier pyramiding of multiple Rpi genes, which potentially increases the durability and spectrum of potato resistance to rapidly evolving P. infestans strains. In this review, we summarize the current knowledge concerning Rpi genes. We also discuss the use of Rpi genes in breeding as well as their detection in existing potato cultivars. Last, we review new sources of Rpi genes and new methods used to identify them and discuss interactions between P. infestans and host.
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Affiliation(s)
- Paulina Paluchowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Zhimin Yin
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
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23
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El-Ganainy SM, Iqbal Z, Awad HM, Sattar MN, Tohamy AM, Abbas AO, Squires J, Cooke DEL. Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes. J Fungi (Basel) 2022; 8:jof8050468. [PMID: 35628724 PMCID: PMC9147654 DOI: 10.3390/jof8050468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/10/2022] Open
Abstract
Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management.
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Affiliation(s)
- Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Hossam Mohamed Awad
- Agriculture Botany Department, Menofia University, Shibin El-Kom 32415, Egypt;
| | - Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Abdel Mohsen Tohamy
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
| | - Ahmed O. Abbas
- Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | | | - David E. L. Cooke
- The James Hutton Institute, Dundee DD2 5DA, UK;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
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24
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. THE PLANT CELL 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 360] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
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25
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Dagvadorj B, Outram MA, Williams SJ, Solomon PS. The necrotrophic effector ToxA from Parastagonospora nodorum interacts with wheat NHL proteins to facilitate Tsn1-mediated necrosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:407-418. [PMID: 35061310 DOI: 10.1111/tpj.15677] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The plant pathogen Parastagonospora nodorum secretes necrotrophic effectors to promote disease. These effectors induce cell death on wheat cultivars carrying dominant susceptibility genes in an inverse gene-for-gene manner. However, the molecular mechanisms underpinning these interactions and resulting cell death remain unclear. Here, we used a yeast two-hybrid library approach to identify wheat proteins that interact with the necrotrophic effector ToxA. Using this strategy, we identified an interaction between ToxA and a wheat transmembrane NDR/HIN1-like protein (TaNHL10) and confirmed the interaction using in planta co-immunoprecipitation and confocal microscopy co-localization analysis. We showed that the C-terminus of TaNHL10 is extracellular whilst the N-terminus is localized in the cytoplasm. Further analyses using yeast two-hybrid and confocal microscopy co-localization showed that ToxA interacts with the C-terminal LEA2 extracellular domain of TaNHL10. Random mutagenesis was then used to identify a ToxA mutant, ToxAN109D , which was unable to interact with TaNHL10 in yeast two-hybrid assays. Subsequent heterologous expression and purification of ToxAN109D in Nicotiania benthamiana revealed that the mutated protein was unable to induce necrosis on Tsn1-dominant wheat cultivars, confirming that the interaction of ToxA with TaNHL10 is required to induce cell death. Collectively, these data advance our understanding on how ToxA induces cell death during infection and further highlight the importance of host cell surface interactions in necrotrophic pathosystems.
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Affiliation(s)
- Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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26
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Li H, Hu R, Fan Z, Chen Q, Jiang Y, Huang W, Tao X. Dual RNA Sequencing Reveals the Genome-Wide Expression Profiles During the Compatible and Incompatible Interactions Between Solanum tuberosum and Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2022; 13:817199. [PMID: 35401650 PMCID: PMC8993506 DOI: 10.3389/fpls.2022.817199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating plant disease. P. infestans genome encodes hundreds of effectors, complicating the interaction between the pathogen and its host and making it difficult to understand the interaction mechanisms. In this study, the late blight-resistant potato cultivar Ziyun No.1 and the susceptible potato cultivar Favorita were infected with P. infestans isolate SCPZ16-3-1 to investigate the global expression profiles during the compatible and incompatible interactions using dual RNA sequencing (RNA-seq). Most of the expressed Arg-X-Leu-Arg (RXLR) effector genes were suppressed during the first 24 h of infection, but upregulated after 24 h. Moreover, P. infestans induced more specifically expressed genes (SEGs), including RXLR effectors and cell wall-degrading enzymes (CWDEs)-encoding genes, in the compatible interaction. The resistant potato activated a set of biotic stimulus responses and phenylpropanoid biosynthesis SEGs, including kirola-like protein, nucleotide-binding site-leucine-rich repeat (NBS-LRR), disease resistance, and kinase genes. Conversely, the susceptible potato cultivar upregulated more kinase, pathogenesis-related genes than the resistant cultivar. This study is the first study to characterize the compatible and incompatible interactions between P. infestans and different potato cultivars and provides the genome-wide expression profiles for RXLR effector, CWDEs, NBS-LRR protein, and kinase-encoding genes.
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Affiliation(s)
- Honghao Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Rongping Hu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Zhonghan Fan
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Qinghua Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Yusong Jiang
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Weizao Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiang Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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27
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Luo M, Sun X, Qi Y, Zhou J, Wu X, Tian Z. Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity. BMC PLANT BIOLOGY 2021; 21:582. [PMID: 34886813 PMCID: PMC8656059 DOI: 10.1186/s12870-021-03364-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The oomycete pathogen secretes many effectors into host cells to manipulate host defenses. For the majority of effectors, the mechanisms related to how they alter the expression of host genes and reprogram defenses are not well understood. In order to investigate the molecular mechanisms governing the influence that the Phytophthora infestans RXLR effector Pi04089 has on host immunity, a comparative transcriptome analysis was conducted on Pi04089 stable transgenic and wild-type potato plants. RESULTS Potato plants stably expressing Pi04089 were more susceptible to P. infestans. RNA-seq analysis revealed that 658 upregulated genes and 722 downregulated genes were characterized in Pi04089 transgenic lines. A large number of genes involved in the biological process, including many defense-related genes and certain genes that respond to salicylic acid, were suppressed. Moreover, the comparative transcriptome analysis revealed that Pi04089 significantly inhibited the expression of many flg22 (a microbe-associated molecular pattern, PAMP)-inducible genes, including various Avr9/Cf-9 rapidly elicited (ACRE) genes. Four selected differentially expressed genes (StWAT1, StCEVI57, StKTI1, and StP450) were confirmed to be involved in host resistance against P. infestans when they were transiently expressed in Nicotiana benthamiana. CONCLUSION The P. infestans effector Pi04089 was shown to suppress the expression of many resistance-related genes in potato plants. Moreover, Pi04089 was found to significantly suppress flg22-triggered defense signaling in potato plants. This research provides new insights into how an oomycete effector perturbs host immune responses at the transcriptome level.
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Affiliation(s)
- Ming Luo
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Xinyuan Sun
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Yetong Qi
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Jing Zhou
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Xintong Wu
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China.
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China.
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China.
- Hubei Hongshan laboratory. Huazhong Agricultural University (HZAU), No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
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28
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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29
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Zhao J, Song J. NLR immune receptor RB is differentially targeted by two homologous but functionally distinct effector proteins. PLANT COMMUNICATIONS 2021; 2:100236. [PMID: 34778749 PMCID: PMC8577132 DOI: 10.1016/j.xplc.2021.100236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/05/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) receptors mediate immune responses by directly or indirectly sensing pathogen-derived effectors. Despite significant advances in the understanding of NLR-mediated immunity, the mechanisms by which pathogens evolve to suppress NLR activation triggered by cognate effectors and gain virulence remain largely unknown. The agronomically important immune receptor RB recognizes the ubiquitous and highly conserved IPI-O RXLR family members (e.g., IPI-O1) from Phytophthora infestans, and this process is suppressed by the rarely present and homologous effector IPI-O4. Here, we report that self-association of RB via the coiled-coil (CC) domain is required for RB activation and is differentially affected by avirulence and virulence effectors. IPI-O1 moderately reduces the self-association of RB CC, potentially leading to changes in the conformation and equilibrium of RB, whereas IPI-O4 dramatically impairs CC self-association to prevent RB activation. We also found that IPI-O1 associates with itself, whereas IPI-O4 does not. Notably, IPI-O4 interacts with IPI-O1 and disrupts its self-association, therefore probably blocking its avirulence function. Furthermore, IPI-O4 enhances the interaction between RB CC and IPI-O1, possibly sequestering RB and IPI-O1 and subsequently blocking their interactions with signaling components. Taken together, these findings considerably extend our understanding of the underlying mechanisms by which emerging virulent pathogens suppress the NLR-mediated recognition of cognate effectors.
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Affiliation(s)
- Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Dallas, TX 75252, USA
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Dallas, TX 75252, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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30
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Dagvadorj B, Solomon PS. Simple and efficient heterologous expression of necrosis-inducing effectors using the model plant Nicotiana benthamiana. PLANT DIRECT 2021; 5:e341. [PMID: 34466773 PMCID: PMC8381856 DOI: 10.1002/pld3.341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
Plant fungal pathogens cause devastating diseases on cereal plants and threaten global food security. During infection, these pathogens secrete proteinaceous effectors that promote disease. Some of these effectors from necrotrophic plant pathogens induce a cell death response (necrosis), which facilitates pathogen growth in planta. Characterization of these effectors typically requires heterologous expression, and microbial expression systems such as bacteria and yeast are the predominantly used. However, microbial expression systems often require optimization for any given effector and are, in general, not suitable for effectors involving cysteine bridges and posttranslational modifications for activity. Here, we describe a simple and efficient method for expressing such effectors in the model plant Nicotiana benthamiana. Briefly, an effector protein is transiently expressed and secreted into the apoplast of N. benthamiana by Agrobacterium-mediated infiltration. Two to three days subsequent to agroinfiltration, the apoplast from the infiltrated leaves is extracted and can be directly used for phenotyping on host plants. The efficacy of this approach was demonstrated by expressing the ToxA, Tox3, and Tox1 necrosis-inducing effectors from Parastagonospora nodorum. All three effectors produced in N. benthamiana were capable of inducing necrosis in wheat lines, and two of three showed visible bands on Coomassie-stained gel. These data suggest that N. benthamiana-agroinfiltration system is a feasible tool to obtain fungal effectors, especially those that require disulfide bonds and posttranslational modifications. Furthermore, due to the low number of proteins typically observed in the apoplast (compared with intracellular), this simple and high-throughput approach circumvents the requirement to lyse cells and further purifies the target proteins that are required in other heterologous systems. Because of its simplicity and potential for high-throughput, this method is highly amenable to the phenotyping of candidate protein effectors on host plants.
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Affiliation(s)
- Bayantes Dagvadorj
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Peter S. Solomon
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
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Jayaraman J, Chatterjee A, Hunter S, Chen R, Stroud EA, Saei H, Hoyte S, Deroles S, Tahir J, Templeton MD, Brendolise C. Rapid Methodologies for Assessing Pseudomonas syringae pv. actinidiae Colonization and Effector-Mediated Hypersensitive Response in Kiwifruit. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:880-890. [PMID: 33834857 DOI: 10.1094/mpmi-02-21-0043-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The infection of Pseudomonas syringae pv. actinidiae in kiwifruit is currently assessed by numerous methodologies, each with their own limitations. Most studies are based on either a laborious method of growth quantification of the pathogen or qualitative assessments by visual scoring following stem or cutting inoculation. Additionally, when assessing for resistance against specific pathogen effectors, confounding interactions between multiple genes in the pathogen can make mapping resistance phenotypes nearly impossible. Here, we present robust alternative methods to quantify pathogen load based on rapid bacterial DNA quantification by PCR, the use of Pseudomonas fluorescens, and a transient reporter eclipse assay for assessing resistance conferred by isolated bacterial avirulence genes. These assays compare well with bacterial plate counts to assess bacterial colonization as a result of plant resistance activation. The DNA-based quantification, when coupled with the P. fluorescens and reporter eclipse assays to independently identify bacterial avirulence genes, is rapid, highly reproducible, and scalable for high-throughput screens of multiple cultivars or genotypes. Application of these methodologies will allow rapid and high-throughput identification of resistant cultivars and the bacterial avirulence genes they recognize, facilitating resistance gene discovery for plant breeding programs.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, Lincoln, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Shannon Hunter
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Ronan Chen
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Erin A Stroud
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hassan Saei
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Stephen Hoyte
- The New Zealand Institute for Plant and Food Research Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Simon Deroles
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, Lincoln, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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32
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021. [PMID: 33677602 DOI: 10.1101/2020.09.24.308585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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33
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021; 33:1447-1471. [PMID: 33677602 PMCID: PMC8254500 DOI: 10.1093/plcell/koab069] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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Monino‐Lopez D, Nijenhuis M, Kodde L, Kamoun S, Salehian H, Schentsnyi K, Stam R, Lokossou A, Abd‐El‐Haliem A, Visser RG, Vossen JH. Allelic variants of the NLR protein Rpi-chc1 differentially recognize members of the Phytophthora infestans PexRD12/31 effector superfamily through the leucine-rich repeat domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:182-197. [PMID: 33882622 PMCID: PMC8362081 DOI: 10.1111/tpj.15284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 05/22/2023]
Abstract
Phytophthora infestans is a pathogenic oomycete that causes the infamous potato late blight disease. Resistance (R) genes from diverse Solanum species encode intracellular receptors that trigger effective defense responses upon the recognition of cognate RXLR avirulence (Avr) effector proteins. To deploy these R genes in a durable fashion in agriculture, we need to understand the mechanism of effector recognition and the way the pathogen evades recognition. In this study, we cloned 16 allelic variants of the Rpi-chc1 gene from Solanum chacoense and other Solanum species, and identified the cognate P. infestans RXLR effectors. These tools were used to study effector recognition and co-evolution. Functional and non-functional alleles of Rpi-chc1 encode coiled-coil nucleotide-binding leucine-rich repeat (CNL) proteins, being the first described representatives of the CNL16 family. These alleles have distinct patterns of RXLR effector recognition. While Rpi-chc1.1 recognized multiple PexRD12 (Avrchc1.1) proteins, Rpi-chc1.2 recognized multiple PexRD31 (Avrchc1.2) proteins, both belonging to the PexRD12/31 effector superfamily. Domain swaps between Rpi-chc1.1 and Rpi-chc1.2 revealed that overlapping subdomains in the leucine-rich repeat (LRR) domain are responsible for the difference in effector recognition. This study showed that Rpi-chc1.1 and Rpi-chc1.2 evolved to recognize distinct members of the same PexRD12/31 effector family via the LRR domain. The biased distribution of polymorphisms suggests that exchange of LRRs during host-pathogen co-evolution can lead to novel recognition specificities. These insights will guide future strategies to breed durable resistant varieties.
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Affiliation(s)
- Daniel Monino‐Lopez
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Maarten Nijenhuis
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Agrico ResearchBurchtweg 17Bant8314PPThe Netherlands
| | - Linda Kodde
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research Park, NorwichUK
| | - Hamed Salehian
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Kyrylo Schentsnyi
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Center for Plant Molecular BiologyAuf der Morgenstelle 32Tübingen2076Germany
| | - Remco Stam
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Technical University MunichMunichGermany
| | - Anoma Lokossou
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Ahmed Abd‐El‐Haliem
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Rijk Zwaan Breeding B.VBurgemeester Crezéelaan 40De Lier2678KXThe Netherlands
| | - Richard G.F. Visser
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Jack H. Vossen
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
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35
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Sharma S, Sundaresha S, Bhardwaj V. Biotechnological approaches in management of oomycetes diseases. 3 Biotech 2021; 11:274. [PMID: 34040923 DOI: 10.1007/s13205-021-02810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/24/2021] [Indexed: 11/26/2022] Open
Abstract
Plant pathogenic oomycetes cause significant impact on agriculture and, therefore, their management is utmost important. Though conventional methods to combat these pathogens (resistance breeding and use of fungicides) are available but these are limited by the availability of resistant cultivars due to evolution of new pathogenic races, development of resistance in the pathogens against agrochemicals and their potential hazardous effects on the environment and human health. This has fuelled a continual search for novel and alternate strategies for management of phytopathogens. The recent advances in oomycetes genome (Phytophthora infestans, P. ramorum, P. sojae, Pythium ultimum, Albugo candida etc.) would further help in understanding host-pathogen interactions essentially needed for designing effective management strategies. In the present communication the novel and alternate strategies for the management of oomycetes diseases are discussed.
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Affiliation(s)
- Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - S Sundaresha
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
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36
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Martynov VV, Chizhik VK. The Study of Polymorphism of the ipiO Gene Family in Oomycete Phytophthora infestans (Mont.) De Bary in the Moscow Region Population Using SSCP Analysis. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep 2021; 41:227917. [PMID: 33619567 PMCID: PMC7937907 DOI: 10.1042/bsr20203544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 01/25/2023] Open
Abstract
Calonectria henricotiae (Che) and C. pseudonaviculata (Cps) are destructive fungal pathogens causing boxwood blight, a persistent threat to horticultural production, landscape industries, established gardens, and native ecosystems. Although extracellular proteins including effectors produced by fungal pathogens are known to play a fundamental role in pathogenesis, the composition of Che and Cps extracellular proteins has not been examined. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics prediction tools, 630 extracellular proteins and 251 cell membrane proteins of Che and Cps were identified in the classical secretion pathway in the present study. In the non-classical secretion pathway, 79 extracellular proteins were identified. The cohort of proteins belonged to 364 OrthoMCL clusters, with the majority (62%) present in both species, and a subset unique to Che (19%) and Cps (20%). These extracellular proteins were predicted to play important roles in cell structure, regulation, metabolism, and pathogenesis. A total of 124 proteins were identified as putative effectors. Many of them are orthologs of proteins with documented roles in suppressing host defense and facilitating infection processes in other pathosystems, such as SnodProt1-like proteins in the OrthoMCL cluster OG5_152723 and PhiA-like cell wall proteins in the cluster OG5_155754. This exploratory study provides a repository of secreted proteins and putative effectors that can provide insights into the virulence mechanisms of the boxwood blight pathogens.
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Li Q, Wang B, Yu J, Dou D. Pathogen-informed breeding for crop disease resistance. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:305-311. [PMID: 33095498 DOI: 10.1111/jipb.13029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
The development of durable and broad-spectrum resistance is an economical and eco-friendly approach to control crop diseases for sustainable agricultural production. Emerging knowledge of the molecular basis of pathogenesis and plant-pathogen interactions has contributed to the development of novel pathogen-informed breeding strategies beyond the limits imposed by conventional breeding. Here, we review the current status of pathogen-assisted resistance-related gene cloning. We also describe how pathogen effector proteins can be used to identify resistance resources and to inform cultivar deployment. Finally, we summarize the main approaches for pathogen-directed plant improvement, including transgenesis and genome editing. Thus, we describe the emerging role of pathogen-related studies in the breeding of disease-resistant varieties, and propose innovative pathogen-informed strategies for future applications.
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Affiliation(s)
- Qi Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jinping Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
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39
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Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, Stam R, van Oosterhout C, Fairhead S, Heal R, Cocker JM, Bhanvadia S, Barrett W, Wu CH, Adachi H, Song T, Kamoun S, Vleeshouwers VGAA, Tomlinson L, Wulff BBH, Jones JDG. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. NATURE PLANTS 2021; 7:198-208. [PMID: 33574576 PMCID: PMC7116783 DOI: 10.1038/s41477-021-00854-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Affiliation(s)
- Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- US Department of Agriculture-Agricultural Research Service, Madison, WI, USA
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Bayer Crop Science, Chesterfield, MO, USA
| | - Agnieszka I Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Remco Stam
- Phytopathology, Technical University Munich, Freising, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan M Cocker
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- University of Hull, Hull, UK
| | - Shivani Bhanvadia
- Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
| | - William Barrett
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Karki HS, Jansky SH, Halterman DA. Screening of Wild Potatoes Identifies New Sources of Late Blight Resistance. PLANT DISEASE 2021; 105:368-376. [PMID: 32755364 DOI: 10.1094/pdis-06-20-1367-re] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Late blight (LB) of potato is considered one of the most devastating plant diseases in the world. Most cultivated potatoes are susceptible to this disease. However, wild relatives of potatoes are an excellent source of LB resistance. We screened 384 accessions of 72 different wild potato species available from the U.S. Potato GeneBank against the LB pathogen Phytophthora infestans in a detached leaf assay (DLA). P. infestans isolates US-23 and NL13316 were used in the DLA to screen the accessions. Although all plants in 273 accessions were susceptible, all screened plants in 39 accessions were resistant. Resistant and susceptible plants were found in 33 accessions. All tested plants showed a partial resistance phenotype in two accessions, segregation of resistant and partial resistant plants in nine accessions, segregation of partially resistant and susceptible plants in four accessions, and segregation of resistant, partially resistant, and susceptible individuals in 24 accessions. We found several species that were never before reported to be resistant to LB: Solanum albornozii, S. agrimoniifolium, S. chomatophilum, S. ehrenbergii, S. hypacrarthrum, S. iopetalum, S. palustre, S. piurae, S. morelliforme, S. neocardenasii, S. trifidum, and S. stipuloideum. These new species could provide novel sources of LB resistance. P. infestans clonal lineage-specific screening of selected species was conducted to identify the presence of RB resistance. We found LB resistant accessions in Solanum verrucosum, Solanum stoloniferum, and S. morelliforme that were susceptible to the RB overcoming isolate NL13316, indicating the presence of RB-like resistance in these species.
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Affiliation(s)
- Hari S Karki
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706
| | - Shelly H Jansky
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706
| | - Dennis A Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706
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Duan Y, Duan S, Xu J, Zheng J, Hu J, Li X, Li B, Li G, Jin L. Late Blight Resistance Evaluation and Genome-Wide Assessment of Genetic Diversity in Wild and Cultivated Potato Species. FRONTIERS IN PLANT SCIENCE 2021; 12:710468. [PMID: 34659284 PMCID: PMC8514749 DOI: 10.3389/fpls.2021.710468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/07/2021] [Indexed: 05/13/2023]
Abstract
Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato-producing regions of the world. Cultivation of resistant varieties is the most effective and environmentally friendly way to control potato late blight disease, and identification of germplasms with late blight resistance and clarification their genetic relationship would promote the development of the resistant varieties. In this study, a diverse population of 189 genotypes with potential late blight resistance, consisting of 20 wild species and cultivated Solanum tuberosum Andigenum group and Chilotanum group, was screened for the presence of late blight resistance by performing challenge inoculation with four Phytophthora infestans isolates including one 13_A2 isolate, CN152. Ten elite resources with broad-spectrum resistance and 127 with isolate-specific resistance against P. infestans were identified. To improve the available gene pool for future potato breeding programs, the population was genotyped using 30 simple sequence repeat (SSR) markers covering the entire potato genome. A total of 173 alleles were detected with an average of 5.77 alleles per locus. Structure analysis discriminated the 189 potato genotypes into five populations based on taxonomic classification and genetic origin with some deviations. There was no obvious clustering by country of origin, ploidy level, EBN (endosperm balance number) value, or nuclear clade. Analysis of molecular variance showed 10.08% genetic variation existed among populations. The genetic differentiation (Fst) ranged from 0.0937 to 0.1764, and the nucleotide diversity (π) was 0.2269 across populations with the range from 0.1942 to 0.2489. Further genotyping of 20K SNP array confirmed the classification of SSRs and could uncover the genetic relationships of Solanum germplasms. Our results indicate that there exits abundant genetic variation in wild and cultivated potato germplasms, while the cultivated S. tuberosum Chilotanum group has lower genetic diversity. The phenotypic and genetic information obtained in this study provide a useful guide for hybrid combination and resistance introgression from wild gene pool into cultivated species for cultivar improvement, as well as for germplasm conservation efforts and resistance gene mining.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Liping Jin
- *Correspondence: Guangcun Li, , Liping Jin,
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42
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Singh A, Rajput V, Singh AK, Sengar RS, Singh RK, Minkina T. Transformation Techniques and Their Role in Crop Improvements: A Global Scenario of GM Crops. POLICY ISSUES IN GENETICALLY MODIFIED CROPS 2021:515-542. [DOI: 10.1016/b978-0-12-820780-2.00023-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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Torres Ascurra Y, Lin X, Wolters PJ, Vleeshouwers VGAA. Identification of Solanum Immune Receptors by Bulked Segregant RNA-Seq and High-Throughput Recombinant Screening. Methods Mol Biol 2021; 2354:315-330. [PMID: 34448167 DOI: 10.1007/978-1-0716-1609-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The identification, understanding, and deployment of immune receptors are crucial to achieve high-level and durable resistance for crops against pathogens. In potato, many R genes have been identified using map-based cloning strategies. However, this is a challenging and laborious task that involves the development of a high number of molecular markers for the initial mapping, and the screening of thousands of plants for fine mapping. Bulked segregant RNA-Seq (BSR-Seq) has proven to be an efficient technique for the mapping of resistance genes. The RNA from two bulks of plants with contrasting phenotypes is sequenced and analyzed to identify single-nucleotide polymorphism (SNPs) markers linked to the target gene. Subsequently, the SNP markers that are identified can be used to delimit the mapping interval. Additionally, we designed an in vitro recombinant screening strategy that is advantageous for analyzing a large number of plants, in terms of time, space, and cost. Tips and detailed protocols, including BSR-Seq, bioinformatic analysis, and recombinant screening, are provided in this chapter.
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Affiliation(s)
- Yerisf Torres Ascurra
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiao Lin
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Pieter J Wolters
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
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44
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Singh KP, Kumari P, Rai PK. Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2021; 12:617405. [PMID: 33747001 PMCID: PMC7965955 DOI: 10.3389/fpls.2021.617405] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/08/2021] [Indexed: 05/15/2023]
Abstract
Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.
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Affiliation(s)
- Kaushal Pratap Singh
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, India
- *Correspondence: Kaushal Pratap Singh,
| | - Preetesh Kumari
- Genetics Division, ICAR-Indian Agricultural Research Institute, New Delhi, India
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45
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Yang Y, Fan G, Zhao Y, Wen Q, Wu P, Meng Y, Shan W. Cytidine-to-Uridine RNA Editing Factor NbMORF8 Negatively Regulates Plant Immunity to Phytophthora Pathogens. PLANT PHYSIOLOGY 2020; 184:2182-2198. [PMID: 32972981 PMCID: PMC7723075 DOI: 10.1104/pp.20.00458] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/15/2020] [Indexed: 05/10/2023]
Abstract
Mitochondria and chloroplasts play key roles in plant-pathogen interactions. Cytidine-to-uridine (C-to-U) RNA editing is a critical posttranscriptional modification in mitochondria and chloroplasts that is specific to flowering plants. Multiple organellar RNA-editing factors (MORFs) form a protein family that participates in C-to-U RNA editing, but little is known regarding their immune functions. Here, we report the identification of NbMORF8, a negative regulator of plant immunity to Phytophthora pathogens. Using virus-induced gene silencing and transient expression in Nicotiana benthamiana, we show that NbMORF8 functions through the regulation of reactive oxygen species production, salicylic acid signaling, and accumulation of multiple Arg-X-Leu-Arg effectors of Phytophthora pathogens. NbMORF8 is localized to mitochondria and chloroplasts, and its immune function requires mitochondrial targeting. The conserved MORF box domain is not required for its immune function. Furthermore, we show that the preferentially mitochondrion-localized NbMORF proteins negatively regulate plant resistance against Phytophthora, whereas the preferentially chloroplast-localized ones are positive immune regulators. Our study reveals that the C-to-U RNA-editing factor NbMORF8 negatively regulates plant immunity to the oomycete pathogen Phytophthora and that mitochondrion- and chloroplast-localized NbMORF family members exert opposing effects on immune regulation.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guangjin Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qujiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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46
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Pradhan A, Ghosh S, Sahoo D, Jha G. Fungal effectors, the double edge sword of phytopathogens. Curr Genet 2020; 67:27-40. [PMID: 33146780 DOI: 10.1007/s00294-020-01118-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 12/17/2022]
Abstract
Phyto-pathogenic fungi can cause huge damage to crop production. During millions of years of coexistence, fungi have evolved diverse life-style to obtain nutrients from the host and to colonize upon them. They deploy various proteinaceous as well as non-proteinaceous secreted molecules commonly referred as effectors to sabotage host machinery during the infection process. The effectors are important virulence determinants of pathogenic fungi and play important role in successful pathogenesis, predominantly by avoiding host-surveillance system. However, besides being important for pathogenesis, the fungal effectors end-up being recognized by the resistant cultivars of the host, which mount a strong immune response to ward-off pathogens. Various recent studies involving different pathosystem have revealed the virulence/avirulence functions of fungal effectors and their involvement in governing the outcome of host-pathogen interactions. However, the effectors and their cognate resistance gene in the host remain elusive for several economically important fungal pathogens. In this review, using examples from some of the biotrophic, hemi-biotrophic and necrotrophic pathogens, we elaborate the double-edged functions of fungal effectors. We emphasize that knowledge of effector functions can be helpful in effective management of fungal diseases in crop plants.
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Affiliation(s)
- Amrita Pradhan
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Debashis Sahoo
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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47
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Lin X, Song T, Fairhead S, Witek K, Jouet A, Jupe F, Witek AI, Karki HS, Vleeshouwers VGAA, Hein I, Jones JDG. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq). MOLECULAR PLANT PATHOLOGY 2020; 21:1502-1512. [PMID: 32935441 DOI: 10.1101/2020.05.14.095158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 05/23/2023]
Abstract
Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Ingo Hein
- School of Life Sciences, Division of Plant Sciences, University of Dundee, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
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48
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Panstruga R, Moscou MJ. What is the Molecular Basis of Nonhost Resistance? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1253-1264. [PMID: 32808862 DOI: 10.1094/mpmi-06-20-0161-cr] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringer Weg 1, 52056 Aachen, Germany
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, United Kingdom
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49
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Lin X, Song T, Fairhead S, Witek K, Jouet A, Jupe F, Witek AI, Karki HS, Vleeshouwers VGAA, Hein I, Jones JDG. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq). MOLECULAR PLANT PATHOLOGY 2020; 21:1502-1512. [PMID: 32935441 PMCID: PMC7548994 DOI: 10.1111/mpp.12987] [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: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 05/22/2023]
Abstract
Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | | | - Kamil Witek
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Florian Jupe
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
Bayer Crop ScienceChesterfieldMissouriUSA
| | | | - Hari S. Karki
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
U.S. Department of Agriculture–Agricultural Research ServiceMadisonWisconsinUSA
| | | | - Ingo Hein
- School of Life SciencesDivision of Plant SciencesUniversity of DundeeDundeeUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrie, DundeeUK
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50
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Karasov TL, Shirsekar G, Schwab R, Weigel D. What natural variation can teach us about resistance durability. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:89-98. [PMID: 32535454 DOI: 10.1016/j.pbi.2020.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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