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Fuentes RR, Nieuwenhuis R, Chouaref J, Hesselink T, van Dooijeweert W, van den Broeck HC, Schijlen E, Schouten HJ, Bai Y, Fransz P, Stam M, de Jong H, Trivino SD, de Ridder D, van Dijk ADJ, Peters SA. A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS Genet 2024; 20:e1011336. [PMID: 38950081 PMCID: PMC11244794 DOI: 10.1371/journal.pgen.1011336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 07/12/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024] Open
Abstract
Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Jihed Chouaref
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem van Dooijeweert
- Centre for Genetic Resources, Wageningen University and Research, Wageningen, The Netherlands
| | - Hetty C van den Broeck
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk J Schouten
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
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2
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H. El-Sappah A, Qi S, A. Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus. FRONTIERS IN PLANT SCIENCE 2022; 13:1081549. [PMID: 36600922 PMCID: PMC9807178 DOI: 10.3389/fpls.2022.1081549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.
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Affiliation(s)
- Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Shiming Qi
- College of Agriculture and Ecological Engineering, Hexi University, Zhangye, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Alaa M. Saleh
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Lingyun Wan
- Key Laboratory of Guangxi for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guo-ting Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Muhammad Ihtisham
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zarqa Noor
- School of Chemical Engineering Beijing Institute of Technology, Beijing, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST–Kashmir, Sopore, India
| | - Xin Zhao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Kuan Yan
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
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3
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Boideau F, Richard G, Coriton O, Huteau V, Belser C, Deniot G, Eber F, Falentin C, Ferreira de Carvalho J, Gilet M, Lodé-Taburel M, Maillet L, Morice J, Trotoux G, Aury JM, Chèvre AM, Rousseau-Gueutin M. Epigenomic and structural events preclude recombination in Brassica napus. THE NEW PHYTOLOGIST 2022; 234:545-559. [PMID: 35092024 DOI: 10.1111/nph.18004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Meiotic recombination is a major evolutionary process generating genetic diversity at each generation in sexual organisms. However, this process is highly regulated, with the majority of crossovers lying in the distal chromosomal regions that harbor low DNA methylation levels. Even in these regions, some islands without recombination remain, for which we investigated the underlying causes. Genetic maps were established in two Brassica napus hybrids to detect the presence of such large nonrecombinant islands. The role played by DNA methylation and structural variations in this local absence of recombination was determined by performing bisulfite sequencing and whole genome comparisons. Inferred structural variations were validated using either optical mapping or oligo fluorescence in situ hybridization. Hypermethylated or inverted regions between Brassica genomes were associated with the absence of recombination. Pairwise comparisons of nine B. napus genome assemblies revealed that such inversions occur frequently and may contain key agronomic genes such as resistance to biotic stresses. We conclude that such islands without recombination can have different origins, such as DNA methylation or structural variations in B. napus. It is thus essential to take into account these features in breeding programs as they may hamper the efficient combination of favorable alleles in elite varieties.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Gwenaelle Deniot
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | | | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | | | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
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4
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Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Eerolla P, Spindlow DJ, Kashyap SP, Singh B, Prasanna HC, Thompson AJ, Mohareb FR. De Novo Genome Assembly Of Solanum Sitiens Reveals Structural Variation Associated With Drought And Salinity Tolerance. Bioinformatics 2021; 37:1941–1945. [PMID: 33515237 PMCID: PMC8496510 DOI: 10.1093/bioinformatics/btab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 11/23/2022] Open
Abstract
MOTIVATION Solanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. RESULTS A high-quality de novo genome and transcriptome assembly for S. sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (∼159X coverage) and PacBio long reads (∼44X coverage), generating a total of ∼262 Gbp of DNA sequence. A reference genome of 1,245 Mbp, arranged in 1,483 scaffolds with a N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7. AVAILABILITY S. sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI's Sequence Read Archive, under the BioProject number "PRJNA633104".All the commands and scripts necessary to generate the assembly are available at the following github repository: https://github.com/MCorentin/Solanum_sitiens_assembly. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Corentin Molitor
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Tomasz J Kurowski
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Pedro M Fidalgo de Almeida
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Pramod Eerolla
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Daniel J Spindlow
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Sarvesh P Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Bijendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - H C Prasanna
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India
| | - Andrew J Thompson
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
| | - Fady R Mohareb
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK
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5
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Yan Z, Wolters AMA, Navas-Castillo J, Bai Y. The Global Dimension of Tomato Yellow Leaf Curl Disease: Current Status and Breeding Perspectives. Microorganisms 2021; 9:740. [PMID: 33916319 PMCID: PMC8066563 DOI: 10.3390/microorganisms9040740] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of the vectors, whiteflies of the Bemisia tabaci complex, has been responsible for many TYLCD outbreaks. In this review, we summarize the current knowledge of TYLCV and TYLV-like begomoviruses and the driving forces of the increasing global significance through rapid evolution of begomovirus variants, mixed infection in the field, association with betasatellites and host range expansion. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in controlling TYLCD. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Currently, Ty-1 and Ty-3 are the primary resistance genes widely used in tomato breeding programs. Ty-2 is also exploited commercially either alone or in combination with other Ty-genes (i.e., Ty-1, Ty-3 or ty-5). Additionally, screening of a large collection of wild tomato species has resulted in the identification of novel TYLCD resistance sources. In this review, we focus on genetic resources used to date in breeding for TYLCVD resistance. For future breeding strategies, we discuss several leads in order to make full use of the naturally occurring and engineered resistance to mount a broad-spectrum and sustainable begomovirus resistance.
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Affiliation(s)
- Zhe Yan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Anne-Marie A. Wolters
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Weinberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
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6
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Shen X, Yan Z, Wang X, Wang Y, Arens M, Du Y, Visser RGF, Kormelink R, Bai Y, Wolters AMA. The NLR Protein Encoded by the Resistance Gene Ty-2 Is Triggered by the Replication-Associated Protein Rep/C1 of Tomato Yellow Leaf Curl Virus. FRONTIERS IN PLANT SCIENCE 2020; 11:545306. [PMID: 33013967 PMCID: PMC7511541 DOI: 10.3389/fpls.2020.545306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/20/2020] [Indexed: 05/03/2023]
Abstract
The whitefly-transmitted tomato yellow leaf curl virus (TYLCV) is one of the most destructive viral pathogens of cultivated tomato. To combat TYLCV, resistance gene Ty-2 has been introduced into cultivated tomato (Solanum lycopersicum) from wild tomato species Solanum habrochaites by interspecific crossing. Introgression lines with Ty-2 contain a large inversion compared with S. lycopersicum, which causes severe suppression of recombination and has hampered the cloning of Ty-2 so far. Here, we report the fine-mapping and cloning of Ty-2 using crosses between a Ty-2 introgression line and several susceptible S. habrochaites accessions. Ty-2 was shown to encode a nucleotide-binding leucine-rich repeat (NLR) protein. For breeding purposes, a highly specific DNA marker tightly linked to the Ty-2 gene was developed permitting marker-assisted selection. The resistance mediated by Ty-2 was effective against the Israel strain of TYLCV (TYLCV-IL) and tomato yellow leaf curl virus-[China : Shanghai2] (TYLCV-[CN : SH2]), but not against tomato yellow leaf curl Sardinia virus (TYLCSV) and leafhopper-transmitted beet curly top virus (BCTV). By co-infiltration experiments we showed that transient expression of the Rep/C1 protein of TYLCV, but not of TYLCSV triggered a hypersensitive response (HR) in Nicotiana benthamiana plants co-expressing the Ty-2 gene. Our results indicate that the Rep/C1 gene of TYLCV-IL presents the avirulence determinant of Ty-2-mediated resistance.
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Affiliation(s)
- Xuexue Shen
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Zhe Yan
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Xiaoxuan Wang
- Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yinlei Wang
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Marjon Arens
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Yongchen Du
- Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Richard Kormelink
- Laboratory of Virology, Wageningen University & Research, Wageningen, Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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7
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Yan Z, Pérez-de-Castro A, Díez MJ, Hutton SF, Visser RGF, Wolters AMA, Bai Y, Li J. Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm. FRONTIERS IN PLANT SCIENCE 2018; 9:1198. [PMID: 30177938 PMCID: PMC6110163 DOI: 10.3389/fpls.2018.01198] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/26/2018] [Indexed: 05/19/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato (Solanum lycopersicum) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from S. arcanum, 43 from S. chilense, 1 from S. chmielewskii, 28 from S. corneliomulleri, 5 from S. habrochaites, 4 from S. huaylasense, 2 from S. neorickii, 1 from S. pennellii, 39 from S. peruvianum, and 1 from S. pimpinellifolium. Most of the screened S. chilense accessions remained symptomless. Many symptomless accessions were also identified in S. arcanum, S. corneliomulleri, and S. peruvianum. A large number of S. pimpinellifolium accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the Ty-1/Ty-3 gene in few S. chilense accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned Ty-genes in TYLCV-resistant accessions.
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Affiliation(s)
- Zhe Yan
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Ana Pérez-de-Castro
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Ciudad Politécnica de la Innovación, Universitat Politècnica de València, Valencia, Spain
| | - Maria J. Díez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Ciudad Politécnica de la Innovación, Universitat Politècnica de València, Valencia, Spain
| | - Samuel F. Hutton
- Gulf Coast Research and Education Center, University of Florida, Gainesville, FL, United States
| | - Richard G. F. Visser
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Anne-Marie A. Wolters
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Yuling Bai
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Junming Li
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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8
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Yamaguchi H, Ohnishi J, Saito A, Ohyama A, Nunome T, Miyatake K, Fukuoka H. An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018. [PMID: 29532116 DOI: 10.1007/s00122-018-3082-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
An NB-LRR gene, TYNBS1, was isolated from Begomovirus-resistance locus Ty-2. Transgenic plant analysis revealed that TYNBS1 is a functional resistance gene. TYNBS1 is considered to be synonymous with Ty-2. Tomato yellow leaf curl disease caused by Tomato yellow leaf curl virus (TYLCV) is a serious threat to tomato (Solanum lycopersicum L.) production worldwide. A Begomovirus resistance gene, Ty-2, was introduced into cultivated tomato from Solanum habrochaites by interspecific crossing. To identify the Ty-2 gene, we performed genetic analysis. Identification of recombinant line 3701 confirmed the occurrence of a chromosome inversion in the Ty-2 region of the resistant haplotype. Genetic analysis revealed that the Ty-2 gene is linked to an introgression encompassing two markers, SL11_25_54277 and repeat A (approximately 200 kb). Genomic sequences of the upper and lower border of the inversion section of susceptible and resistant haplotypes were determined. Two nucleotide-binding domain and leucine-rich repeat-containing (NB-LRR) genes, TYNBS1 and TYNBS2, were identified around the upper and lower ends of the inversion section, respectively. TYNBS1 strictly co-segregated with TYLCV resistance, whereas TYNBS2 did not. Genetic introduction of genomic fragments containing the TYNBS1 gene into susceptible tomato plants conferred TYLCV resistance. These results demonstrate that TYNBS1 is a functional resistance gene for TYLCV, and is synonymous with the Ty-2 gene.
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Affiliation(s)
- Hirotaka Yamaguchi
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan.
| | - Jun Ohnishi
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
| | - Atsushi Saito
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
| | - Akio Ohyama
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
| | - Hiroyuki Fukuoka
- Institute of Vegetable and Floriculture Science, NARO, 360 Kusawa, Ano-cho, Tsu, Mie, 514-2392, Japan
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9
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Bennewitz S, Bergau N, Tissier A. QTL Mapping of the Shape of Type VI Glandular Trichomes in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:1421. [PMID: 30319679 PMCID: PMC6168718 DOI: 10.3389/fpls.2018.01421] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/06/2018] [Indexed: 05/17/2023]
Abstract
Glandular trichomes contribute to the high resistance of wild tomato species against insect pests not only thanks to the metabolites they produce but also because of morphological and developmental features which support the high production of these defense compounds. In Solanum habrochaites, type VI trichomes have a distinct spherical shape and a large intercellular storage cavity where metabolites can accumulate and are released upon breaking off of the glandular cells. In contrast, the type VI trichomes of S. lycopersicum have a four-leaf clover shape corresponding to the four glandular cells and a small internal cavity with limited capacity for storage of compounds. To better characterize the genetic factors underlying these trichome morphological differences we created a back-cross population of 116 individuals between S. habrochaites LA1777 and S. lycopersicum var. cerasiforme WVa106. A trichome score that reflects the shape of the type VI trichomes allowing the quantification of this trait was designed. The scores were distributed normally across the population, which was mapped with a total of 192 markers. This resulted in the identification of six quantitative trait locus (QTLs) on chromosomes I, VII, VII, and XI. The QTL on chromosome I with the highest LOD score was confirmed and narrowed down to a 500 gene interval in an advanced population derived from one of the back-cross lines. Our results provide the foundation for the genetic dissection of type VI trichome morphology and the introgression of these trichome traits into cultivated tomato lines for increased insect resistance. Key Message: This work shows that the shape of type VI glandular trichomes in tomato is a genetically defined trait controlled by multiple QTLs with one on chromosome I being the major contributor.
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Affiliation(s)
| | | | - Alain Tissier
- *Correspondence: Alain Tissier, orcid.org/0000-0002-9406-4245
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Puchta H. Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:5-15. [PMID: 26677816 DOI: 10.1111/tpj.13100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/21/2023]
Abstract
It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system was discovered, a tool became available allowing the extension of this approach from one to three dimensions and to construct at least partly synthetic entities on the genome, epigenome and transcriptome levels. The second dimension can be obtained by targeting the Cas9 protein to multiple unique genomic sites by applying multiple different single guiding (sg) RNAs, each defining a different DNA-binding site. Finally, the simultaneous use of phylogenetically different Cas9 proteins or sgRNAs that harbour different types of protein binding motives, allows for a third dimension of control. Thus, different types of enzyme activities - fused either to one type of Cas9 orthologue or to one type of RNA-binding domain specific to one type of sgRNA - can be targeted to multiple different genomic sites simultaneously. Thus, it should be possible to induce quantitatively different levels of expression of certain sets of genes and at the same time to repress other genes, redefining the nuclear transcriptome. Likewise, by the use of different types of histone-modifying and/or DNA (de)methylating activities, the epigenome of plants should be reprogrammable. On our way to synthetic plant genomes, the next steps will be to use complex genome engineering approaches within or between species borders to restructure and recombine natural or artificial chromosomes.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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