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Farrall T, Brawner J, Dinsdale A, Kehoe M. A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics. Int J Mol Sci 2024; 25:8348. [PMID: 39125919 PMCID: PMC11312432 DOI: 10.3390/ijms25158348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/20/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation.
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Affiliation(s)
- Thomas Farrall
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Jeremy Brawner
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Adrian Dinsdale
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
| | - Monica Kehoe
- Diagnostic Laboratory Services, Biosecurity and Sustainability, Department of Primary Industries and Regional Development (DPIRD), Perth, WA 6151, Australia
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [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: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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3
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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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4
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Wang Y, Brown LH, Adams TM, Cheung YW, Li J, Young V, Todd DT, Armstrong MR, Neugebauer K, Kaur A, Harrower B, Oome S, Wang X, Bayer M, Hein I. SMRT-AgRenSeq-d in potato ( Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5. HORTICULTURE RESEARCH 2023; 10:uhad211. [PMID: 38023472 PMCID: PMC10681002 DOI: 10.1093/hr/uhad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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Affiliation(s)
- Yuhan Wang
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Lynn H Brown
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas M Adams
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuk Woon Cheung
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Jie Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Vanessa Young
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Drummond T Todd
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles R Armstrong
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Konrad Neugebauer
- Biomathematics and Statistics Scotland, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Crop Research Centre, Teagasc, Oak Park, Carlow R93 XE12, Ireland
| | - Brian Harrower
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Stan Oome
- HZPC Research B.V. HZPC, Edisonweg 5, 8501 XG Joure, Netherlands
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Micha Bayer
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
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5
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Yu PL, Fulton JC, Hudson OH, Huguet-Tapia JC, Brawner JT. Next-generation fungal identification using target enrichment and Nanopore sequencing. BMC Genomics 2023; 24:581. [PMID: 37784013 PMCID: PMC10544392 DOI: 10.1186/s12864-023-09691-w] [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: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. RESULTS Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. CONCLUSIONS Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.
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Affiliation(s)
- Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Owen H Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
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Hebelstrup KH, Azariadis A, Cordes A, Henriksen PS, Brinch-Pedersen H. Prehistoric Plant Exploitation and Domestication: An Inspiration for the Science of De Novo Domestication in Present Times. PLANTS (BASEL, SWITZERLAND) 2023; 12:2310. [PMID: 37375935 DOI: 10.3390/plants12122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture.
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Affiliation(s)
- Kim Henrik Hebelstrup
- Department of Agroecology, Section for Crop Genetics and Biotechnology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Aristotelis Azariadis
- Department of Agroecology, Section for Crop Genetics and Biotechnology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Adam Cordes
- Department of Agroecology, Section for Crop Genetics and Biotechnology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
- Department of Environmental Archaeology and Materials Science, National Museum of Denmark, I.C. Modewegsvej 9, 2800 Brede, Denmark
| | - Peter Steen Henriksen
- Department of Environmental Archaeology and Materials Science, National Museum of Denmark, I.C. Modewegsvej 9, 2800 Brede, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Section for Crop Genetics and Biotechnology, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
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Adams TM, Smith M, Wang Y, Brown LH, Bayer MM, Hein I. HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. BMC Bioinformatics 2023; 24:204. [PMID: 37198529 DOI: 10.1186/s12859-023-05335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 05/11/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise. RESULTS Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license. CONCLUSIONS HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses.
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Affiliation(s)
- Thomas M Adams
- Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK.
| | - Moray Smith
- Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK
- School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Yuhan Wang
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Lynn H Brown
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Micha M Bayer
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Ingo Hein
- Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK.
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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Rogozina EV, Gurina AA, Chalaya NA, Zoteyeva NM, Kuznetsova MA, Beketova MP, Muratova OA, Sokolova EA, Drobyazina PE, Khavkin EE. Diversity of Late Blight Resistance Genes in the VIR Potato Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:273. [PMID: 36678985 PMCID: PMC9862067 DOI: 10.3390/plants12020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Late blight (LB) caused by the oomycete Phytophthora infestans (Mont.) de Bary is the greatest threat to potato production worldwide. Current potato breeding for LB resistance heavily depends on the introduction of new genes for resistance to P. infestans (Rpi genes). Such genes have been discovered in highly diverse wild, primitive, and cultivated species of tuber-bearing potatoes (Solanum L. section Petota Dumort.) and introgressed into the elite potato cultivars by hybridization and transgenic complementation. Unfortunately, even the most resistant potato varieties have been overcome by LB due to the arrival of new pathogen strains and their rapid evolution. Therefore, novel sources for germplasm enhancement comprising the broad-spectrum Rpi genes are in high demand with breeders who aim to provide durable LB resistance. The Genbank of the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg harbors one of the world's largest collections of potato and potato relatives. In this study, LB resistance was evaluated in a core selection representing 20 species of seven Petota series according to the Hawkes (1990) classification: Bulbocastana (Rydb.) Hawkes, Demissa Buk., Longipedicellata Buk., Maglia Bitt., Pinnatisecta (Rydb.) Hawkes, Tuberosa (Rydb.) Hawkes (wild and cultivated species), and Yungasensa Corr. LB resistance was assessed in 96 accessions representing 18 species in the laboratory test with detached leaves using a highly virulent and aggressive isolate of P. infestans. The Petota species notably differed in their LB resistance: S. bulbocastanum Dun., S. demissum Lindl., S. cardiophyllum Lindl., and S. berthaultii Hawkes stood out at a high frequency of resistant accessions (7-9 points on a 9-point scale). Well-established specific SCAR markers of ten Rpi genes-Rpi-R1, Rpi-R2/Rpi-blb3, Rpi-R3a, Rpi-R3b, Rpi-R8, Rpi-blb1/Rpi-sto1, Rpi-blb2, and Rpi-vnt1-were used to mine 117 accessions representing 20 species from seven Petota series. In particular, our evidence confirmed the diverse Rpi gene location in two American continents. The structural homologs of the Rpi-R2, Rpi-R3a, Rpi-R3b, and Rpi-R8 genes were found in the North American species other than S. demissum, the species that was the original source of these genes for early potato breeding, and in some cases, in the South American Tuberosa species. The Rpi-blb1/Rpi-sto1 orthologs from S. bulbocastanum and S. stoloniferum Schlechtd et Bché were restricted to genome B in the Mesoamerican series Bulbocastana, Pinnatisecta, and Longipedicellata. The structural homologs of the Rpi-vnt1 gene that were initially identified in the South American species S. venturii Hawkes and Hjert. were reported, for the first time, in the North American series of Petota species.
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Affiliation(s)
- Elena V. Rogozina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Alyona A. Gurina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda A. Chalaya
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda M. Zoteyeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | | | | | | | | | | | - Emil E. Khavkin
- Institute of Agricultural Biotechnology, Moscow 127550, Russia
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9
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Runno-Paurson E, Nassar H, Tähtjärv T, Eremeev V, Hansen M, Niinemets Ü. High Temporal Variability in Late Blight Pathogen Diversity, Virulence, and Fungicide Resistance in Potato Breeding Fields: Results from a Long-Term Monitoring Study. PLANTS 2022; 11:plants11182426. [PMID: 36145827 PMCID: PMC9502785 DOI: 10.3390/plants11182426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022]
Abstract
Long-term site-specific studies describing changes in the phenotypic variability of Phytophthora infestans populations allow quantitative predictions of pathogen spread and possible outbreaks of epidemics, and provide key input for regional resistance breeding programs. Late blight samples were collected from potato (Solanum tuberosum) breeding fields in Estonia during a twelve-year study period between 2001 and 2014. In total, 207 isolates were assessed for mating type and 235 isolates for metalaxyl resistance and 251 isolates for virulence factors. The frequency of mating types strongly fluctuated across the years, whereas the later period of 2010–2014 was dominated by the A2 mating. Despite fluctuations, both mating types were recorded in the same fields in most years, indicating sustained sexual reproduction of P. infestans with oospore production. Metalaxyl-resistant and intermediately resistant strains dominated in the first years of study, but with the progression of the study, metalaxyl-sensitive isolates became dominant, reaching up to 88%. Racial diversity, characterized by normalized Shannon diversity index decreased in time, varying from 1.00 in 2003 to 0.43 in 2013. The frequency of several virulence factors changed in a time-dependent manner, with R2 increasing and R6, R8, and R9 decreasing in time. Potato cultivar resistance background did not influence the frequency of P. infestans mating type, response to metalaxyl, and racial diversity. However, the diversity index decreased in time among isolates collected from resistant and susceptible cultivars, and remained at a high level in moderately resistant cultivars. These data demonstrate major time-dependent changes in racial diversity, fungicide resistance, and virulence factors in P. infestans, consistent with alterations in the control strategies and popularity of potato cultivars with different resistance.
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Affiliation(s)
- Eve Runno-Paurson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
- Correspondence:
| | - Helina Nassar
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Terje Tähtjärv
- Estonian Crop Research Institute, J. Aamisepa 1, 48309 Jõgeva, Estonia
| | - Viacheslav Eremeev
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Merili Hansen
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia
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10
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Abuley IK, Hansen JG. Characterization of the Level and Type of Resistance of Potato Varieties to Late Blight ( Phytophthora infestans). PHYTOPATHOLOGY 2022; 112:1917-1927. [PMID: 35357158 DOI: 10.1094/phyto-07-21-0309-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the level and type of resistance in potato varieties is relevant for integrating varietal resistance into the management of potato late blight. Accordingly, 54 potato varieties were tested for their level and type of resistance to late blight in 2019 and 2020 in Denmark. Spreader rows were artificially inoculated to ensure an even inoculum distribution in the trial. Disease severity was assessed once or twice per week. Cluster analysis (CA) was done based on the weighted mean absolute rate (WMAR), the relative area under the disease progress curve, the onset of disease (Xo), the severity of disease in the middle of the season, the time to reach 1% disease severity, the time to reach final disease severity, and the maximum disease severity. The resistance types were determined by comparing the tested varieties to Bintje (susceptible reference) for Xo and WMAR. The CA ranked the varieties as susceptible, moderately resistant, resistant, and very resistant based on their level of resistance. Except for a few varieties, the expressed resistance levels varied between the years. Several varieties that were susceptible in 2019 were moderately resistant in 2020. Also, the types of resistance that the varieties exhibited varied from year to year. In 2020, most varieties exhibited race-specific resistance, while in 2019 they mostly showed susceptible characteristics. The variation between years for the level and types of resistance of the varieties highlights the importance of regularly monitoring varietal resistance across time and space.
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Affiliation(s)
- I K Abuley
- Department of Agroecology, Aarhus University Flakkebjerg, Forsøgsvej 1, Slagelse 4200
| | - J G Hansen
- Department of Agroecology, Aarhus University Flakkebjerg, Forsøgsvej 1, Slagelse 4200
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11
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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12
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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: 8] [Impact Index Per Article: 4.0] [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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13
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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14
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Sun K, Schipper D, Jacobsen E, Visser RGF, Govers F, Bouwmeester K, Bai Y. Silencing susceptibility genes in potato hinders primary infection of Phytophthora infestans at different stages. HORTICULTURE RESEARCH 2022; 9:uhab058. [PMID: 35043191 PMCID: PMC8968627 DOI: 10.1093/hr/uhab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 11/12/2021] [Indexed: 06/01/2023]
Abstract
Most potato cultivars are susceptible to late blight disease caused by the oomycete pathogen Phytophthora infestans. A new source of resistance to prevent or diminish pathogen infection is found in the genetic loss of host susceptibility. Previously, we showed that RNAi-mediated silencing of the potato susceptibility (S) genes StDND1, StDMR1 and StDMR6 leads to increased late blight resistance. The mechanisms underlying this S-gene mediated resistance have thus far not been identified. In this study, we examined the infection process of P. infestans on StDND1-, StDMR1- and StDMR6-silenced potato lines. Microscopic analysis showed that penetration of P. infestans spores was hampered on StDND1-silenced plants. On StDMR1- and StDMR6-silenced plants, P. infestans infection was arrested at a primary infection stage by enhanced cell death responses. Histochemical staining revealed that StDMR1- and StDMR6-silenced plants display elevated ROS levels in cells at the infection sites. Resistance in StDND1-silenced plants, however, seems not to rely on a cell death response as ROS accumulation was found to be absent at most inoculated sites. Quantitative analysis of marker gene expression suggests that the increased resistance observed in StDND1- and StDMR6-silenced plants relies on an early onset of SA- and ET-mediated signalling pathways. Resistance mediated by silencing StDMR1 was found to be correlated with the early induction of SA-mediated signalling. These data provide evidence that different defense mechanisms are involved in late blight resistance mediated by functional impairment of different potato S-genes.
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Affiliation(s)
- Kaile Sun
- College of Horticulture, Henan Agricultural University, Nongye Road 63, 450002 Zhengzhou, Henan, China
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Danny Schipper
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Evert Jacobsen
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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15
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Singh D, Kaur A, Kaur M, Kumar A. In vitro screening of Indian potato cultivars for the salt stress and associated physio-biochemical changes. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00949-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Frailie TB, Innes RW. Engineering healthy crops: molecular strategies for enhancing the plant immune system. Curr Opin Biotechnol 2021; 70:151-157. [PMID: 34030033 DOI: 10.1016/j.copbio.2021.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Crop diseases caused by viruses, bacteria, fungi, oomycetes and nematodes constitute major costs for farmers in terms of control measures and yield losses. Enhancing resistance to these pathogens via genetic modification or genome editing represents an economically and environmentally attractive path forward. Recent advances in our understanding of how plants detect pathogens and activate immune responses is now enabling enhancement of disease resistance traits. In particular, the recent determination of structures of both cell surface and intracellular immune receptors in plants in their activated states is providing new insights into how recognition complexes can be modified to expand recognition specificities to confer resistance to otherwise virulent pathogens. By expanding the repertoire of both cell surface and intracellular recognition systems, and combining them, it is expected that resistance to numerous diseases will be enhanced and will be more durable.
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Affiliation(s)
- Tyler B Frailie
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Khiutti AV, Rybakov DA, Gavrilenko TA, Afanasenko OS. [Resistance to causal agents of late blight and golden potato nematode of the modern cultivars of seed potatoes and their phytosanitary status in various agroclimatic zones of the European part of Russia]. Vavilovskii Zhurnal Genet Selektsii 2021; 24:363-375. [PMID: 33659819 PMCID: PMC7893150 DOI: 10.18699/vj20.629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Активная экспансия зарубежных сортов картофеля на территорию Российской Федерации привела
к смене доминирующих видов патогенов этой культуры и появлению новых патотипов возбудителей вредоносных болезней. Целью работы была оценка устойчивости к возбудителям фитофтороза и глободероза современного сортимента картофеля и определение поражаемости возделываемых сортов картофеля грибными и оомицетными болезнями в различных агроклиматических зонах России. Проведена оценка устойчивости 41 сорта
зарубежной селекции, разрешенного к использованию на территории РФ, к патотипу Ro1 Globodera rostochiensis
и к изоляту VZR17 Phytophthora infestans, включающего гены вирулентности 1.2.3.4.5.6.7.8.9.10.11. Устойчивыми
к золотистой картофельной нематоде оказались 38 сортов. У 96.6 % изученных нематодоустойчивых сортов
выявлен маркер гена Н1 устойчивости к патотипу Ro1 G. rostochiensis, восприимчивые сорта этим маркером
не обладали. Абсолютной устойчивостью к возбудителю фитофтороза отличались сорта Alouette и Sarpo Mira
(балл 9); высоким уровнем устойчивости (баллы 6 и 7) характеризовались сорта Evolution, Red Fantasy и Ricarda.
Сорта Baltic Rose, Damaris, Desiree, Gala, Labella, Laperla, Mia, Sanibel, Zekura, Queen Anne, Red Lady и 7 for 7 были
отнесены к восприимчивым, хотя в характеристиках оригинаторов указана средняя устойчивость к фитофторозу. Фитопатологическая экспертиза проведена для 92 образцов 39 сортов семенного картофеля из четырех
федеральных округов РФ: Приволжского, Северо-Западного, Центрального и Северо-Кавказского. Наибольшее
распространение на всех сортах получили ризоктониоз, сухая фузариозная гниль и серебристая парша. Стопроцентное поражение клубней серебристой паршой отмечено в различных регионах на сортах элитных репродукций Red Scarlett, Evolution, Labella, Colombo, Gala, Невский. Широко распространен антракноз картофеля;
сильнее всего были поражены клубни элитной и второй репродукции сорта Red Scarlett – от 50.0 до 71.4 % в
Центральном федеральном округе.
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Affiliation(s)
- A V Khiutti
- All-Russian Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D A Rybakov
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - T A Gavrilenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O S Afanasenko
- All-Russian Institute of Plant Protection, Pushkin, St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Gartner U, Hein I, Brown LH, Chen X, Mantelin S, Sharma SK, Dandurand LM, Kuhl JC, Jones JT, Bryan GJ, Blok VC. Resisting Potato Cyst Nematodes With Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:661194. [PMID: 33841485 PMCID: PMC8027921 DOI: 10.3389/fpls.2021.661194] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2021] [Indexed: 05/17/2023]
Abstract
Potato cyst nematodes (PCN) are economically important pests with a worldwide distribution in all temperate regions where potatoes are grown. Because above ground symptoms are non-specific, and detection of cysts in the soil is determined by the intensity of sampling, infestations are frequently spread before they are recognised. PCN cysts are resilient and persistent; their cargo of eggs can remain viable for over two decades, and thus once introduced PCN are very difficult to eradicate. Various control methods have been proposed, with resistant varieties being a key environmentally friendly and effective component of an integrated management programme. Wild and landrace relatives of cultivated potato have provided a source of PCN resistance genes that have been used in breeding programmes with varying levels of success. Producing a PCN resistant variety requires concerted effort over many years before it reaches what can be the biggest hurdle-commercial acceptance. Recent advances in potato genomics have provided tools to rapidly map resistance genes and to develop molecular markers to aid selection during breeding. This review will focus on the translation of these opportunities into durably PCN resistant varieties.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lynn H. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sophie Mantelin
- INRAE UMR Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Sanjeev K. Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Louise-Marie Dandurand
- Entomology, Plant Pathology and Nematology Department, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Vivian C. Blok
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Vivian C. Blok,
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19
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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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20
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Lin X, Armstrong M, Baker K, Wouters D, Visser RGF, Wolters PJ, Hein I, Vleeshouwers VGAA. RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes. THE NEW PHYTOLOGIST 2020; 227:1264-1276. [PMID: 32285454 PMCID: PMC7383770 DOI: 10.1111/nph.16608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/27/2020] [Indexed: 05/29/2023]
Abstract
The identification of immune receptors in crop plants is time-consuming but important for disease control. Previously, resistance gene enrichment sequencing (RenSeq) was developed to accelerate mapping of nucleotide-binding domain and leucine-rich repeat containing (NLR) genes. However, resistances mediated by pattern recognition receptors (PRRs) remain less utilized. Here, our pipeline shows accelerated mapping of PRRs. Effectoromics leads to precise identification of plants with target PRRs, and subsequent RLP/K enrichment sequencing (RLP/KSeq) leads to detection of informative single nucleotide polymorphisms that are linked to the trait. Using Phytophthora infestans as a model, we identified Solanum microdontum plants that recognize the apoplastic effectors INF1 or SCR74. RLP/KSeq in a segregating Solanum population confirmed the localization of the INF1 receptor on chromosome 12, and led to the rapid mapping of the response to SCR74 to chromosome 9. By using markers obtained from RLP/KSeq in conjunction with additional markers, we fine-mapped the SCR74 receptor to a 43-kbp G-LecRK locus. Our findings show that RLP/KSeq enables rapid mapping of PRRs and is especially beneficial for crop plants with large and complex genomes. This work will enable the elucidation and characterization of the nonNLR plant immune receptors and ultimately facilitate informed resistance breeding.
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Affiliation(s)
- Xiao Lin
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Miles Armstrong
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Katie Baker
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Doret Wouters
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Richard G. F. Visser
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Pieter J. Wolters
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Ingo Hein
- Cell and Molecular SciencesThe James Hutton InstituteDundeeDD2 5DAUK
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeDD2 5DAUK
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21
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Safety evaluation of E12, W8, X17, and Y9 potatoes: Nutritional evaluation and 90-day subchronic feeding study in rats. Regul Toxicol Pharmacol 2020; 115:104712. [PMID: 32540328 DOI: 10.1016/j.yrtph.2020.104712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 11/22/2022]
Abstract
The nutritional and health effects of four biotech potato events, E12, W8, X17, and Y9, were evaluated in a subchronic rodent feeding study. E12 contains pSIM1278 insert DNA derived from potato and designed to down regulate potato genes through RNAi. These changes result in reduced black spot and reduced acrylamide. W8, X17, and Y9 contain the DNA inserts from pSIM1278 and pSIM1678 to further reduce acrylamide and express a gene from wild potato that protects against late blight. Rats were fed diets containing 20% cooked, dried potatoes from these four events and three conventional potato varieties. Compositional analyses of the processed potatoes and the rodent diets demonstrated comparability between the four events and their respective conventional varieties. Rats consumed the diets for 90 days and were evaluated for body weight, dietary intake, clinical signs, ophthalmology, neurobehavioral parameters, clinical pathology, organ weights, gross pathology, and histopathology. No adverse effects were observed as a result of test diet consumption. These results support the conclusion that foods containing E12, W8, X17, or Y9 potatoes are as safe, wholesome and nutritious as foods from conventional potato varieties.
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Yang X, Guo X, Chen G, Dong D, Liu F, Yang Y, Yang Y, Li G. Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling. PeerJ 2020; 8:e9096. [PMID: 32411536 PMCID: PMC7207217 DOI: 10.7717/peerj.9096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao Guo
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Daofeng Dong
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Fang Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yu Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing, China
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Muratova (Fadina) OA, Beketova MP, Kuznetsova MA, Rogozina EV, Khavkin EE. South American species <i>Solanum alandiae</i> Card. and <i>S. okadae</i> Hawkes et Hjerting as potential sources of genes for potato late blight resistance. PROCEEDINGS ON APPLIED BOTANY, GENETICS AND BREEDING 2020. [DOI: 10.30901/2227-8834-2020-1-73-83] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
For several decades, wild species of Solanum L. section Petota Dumort. have been involved in potato cultivar breeding for robust resistance to pests and diseases. Potato late blight (LB) is caused by oomycete Phytophthora infestans (Mont.) de Bary, and the genes for race-specific resistance to P. infestans (Rpi genes) have been introgressed into cultivated potatoes by remote crosses and trans- or cisgenesis, first from S. demissum Buk. and, more recently, from other wild species, such as S. bulbocastanum Dun., S. stoloniferum Schlechtd. et Bché, and S. venturii Hawkes et Hjerting (according to the nomenclature by Hawkes, 1990). Most wild species already involved in breeding for LB resistance came from North and Central Americas: series Bulbocastana (Rydb.) Hawkes, Demissa Buk. and Longipedicellata Buk., and some Rpi genes of these species have been already characterized in much detail. Rpi genes of South American species, including the series Tuberosa (Rydb.) Hawkes, have not been sufficiently investigated. Among the latter, this study focuses on the Rpi genes of S. alandiae Card. and S. okadae Hawkes et Hjerting. Four accessions of S. alandiae, one accession of S. okadae and 11 clones of interspecific potato hybrids comprising S. alandiae germplasm from the VIR collection were PCR-screened using specific SCAR (Sequence Characterized Amplified Region) markers for eight Rpi genes. SCAR amplicons of five Rpi genes registered in this study were validated by comparing their sequences with those of prototype genes deposited in the NCBI Genbank. Among the structural homologues of Rpi genes found in S. alandiae and S. okadae, of special interest are homologues of CC-NB-LRR resistance genes with broad specificity towards P. infestans races, in particular R2=Rpi-blb3, R8, R9a, Rpi-vnt1 and Rpi-blb2 (94–99, 94–99, 86–89, 92–98 and 91% identity with the prototype genes, respectively). Our data may help to better understand the process of Rpi gene divergence along with the evolution of tuberbearing Solanum species, particularly in the series Tuberosa.
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Affiliation(s)
| | - M. P. Beketova
- All-Russian Research Institute of Agricultural Biotechnology
| | | | - E. V. Rogozina
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources
| | - E. E. Khavkin
- All-Russian Research Institute of Agricultural Biotechnology
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24
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Grech‐Baran M, Witek K, Szajko K, Witek AI, Morgiewicz K, Wasilewicz‐Flis I, Jakuczun H, Marczewski W, Jones JDG, Hennig J. Extreme resistance to Potato virus Y in potato carrying the Ry sto gene is mediated by a TIR-NLR immune receptor. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:655-667. [PMID: 31397954 PMCID: PMC7004898 DOI: 10.1111/pbi.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Rysto was found to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.
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Affiliation(s)
- Marta Grech‐Baran
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Karolina Morgiewicz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
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Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans. G3-GENES GENOMES GENETICS 2020; 10:623-634. [PMID: 31818876 PMCID: PMC7003068 DOI: 10.1534/g3.119.400818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.
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Jouanin A, Borm T, Boyd LA, Cockram J, Leigh F, Santos BA, Visser RG, Smulders MJ. Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Strachan SM, Armstrong MR, Kaur A, Wright KM, Lim TY, Baker K, Jones J, Bryan G, Blok V, Hein I. Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1283-1294. [PMID: 30666393 PMCID: PMC6449323 DOI: 10.1007/s00122-019-03278-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/07/2019] [Indexed: 05/26/2023]
Abstract
The nematode resistance gene H2 was mapped to the distal end of chromosome 5 in tetraploid potato. The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum, confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida. A cross between tetraploid H2-containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi-R1, Rpi-R3a, Rpi-R3b variant, Gpa2 and Rx, which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele-specific KASP markers further defined the locus containing the H2 gene to a 4.7 Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4 MB and 6.1 MB in the potato reference genome.
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Affiliation(s)
- Shona M Strachan
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Miles R Armstrong
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- School of Life Sciences, Division of Plant Sciences at the JHI, University of Dundee, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- Thapar Institute of Engineering and Technology, Patiala, Punjab, 147001, India
| | - Kathryn M Wright
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
| | - Tze Yin Lim
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- Columbia University, New York, NY, 10027, USA
| | - Katie Baker
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- Synpromics, Edinburgh, EH25 9RG, UK
| | - John Jones
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Glenn Bryan
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Vivian Blok
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK
| | - Ingo Hein
- The James Hutton Institute, CMS, Errol Road, Dundee, DD2 5DA, UK.
- School of Life Sciences, Division of Plant Sciences at the JHI, University of Dundee, Dundee, DD2 5DA, UK.
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28
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Smulders MJM, Arens P, Bourke PM, Debener T, Linde M, Riek JD, Leus L, Ruttink T, Baudino S, Hibrant Saint-Oyant L, Clotault J, Foucher F. In the name of the rose: a roadmap for rose research in the genome era. HORTICULTURE RESEARCH 2019; 6:65. [PMID: 31069087 PMCID: PMC6499834 DOI: 10.1038/s41438-019-0156-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/18/2019] [Indexed: 05/07/2023]
Abstract
The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.
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Affiliation(s)
- Marinus J. M. Smulders
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Peter M. Bourke
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Thomas Debener
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marcus Linde
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Jan De Riek
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Leen Leus
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Tom Ruttink
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Sylvie Baudino
- BVpam CNRS, FRE 3727, UJM-Saint-Étienne, Univ. Lyon, Saint-Etienne, France
| | - Laurence Hibrant Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Jeremy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
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