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Nicolia A, Proux-Wéra E, Åhman I, Onkokesung N, Andersson M, Andreasson E, Zhu LH. Targeted gene mutation in tetraploid potato through transient TALEN expression in protoplasts. J Biotechnol 2015; 204:17-24. [PMID: 25848989 DOI: 10.1016/j.jbiotec.2015.03.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/24/2015] [Accepted: 03/27/2015] [Indexed: 12/25/2022]
Abstract
Potato is the third largest food crop in the world, however, the high degree of heterozygosity, the tetrasomic inheritance and severe inbreeding depression are major difficulties for conventional potato breeding. The rapid development of modern breeding methods offers new possibilities to enhance breeding efficiency and precise improvement of desirable traits. New site-directed mutagenesis techniques that can directly edit the target genes without any integration of recombinant DNA are especially favorable. Here we present a successful pipeline for site-directed mutagenesis in tetraploid potato through transient TALEN expression in protoplasts. The transfection efficiency of protoplasts was 38-39% and the site-directed mutation frequency was 7-8% with a few base deletions as the predominant type of mutation. Among the protoplast-derived calli, 11-13% showed mutations and a similar frequency (10%) was observed in the regenerated shoots. Our results indicate that the site-directed mutagenesis technology could be used as a new breeding method in potato as well as for functional analysis of important genes to promote sustainable potato production.
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Affiliation(s)
- Alessandro Nicolia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden; Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Estelle Proux-Wéra
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Inger Åhman
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Nawaporn Onkokesung
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mariette Andersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Li-Hua Zhu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Amar D, Frades I, Danek A, Goldberg T, Sharma SK, Hedley PE, Proux-Wera E, Andreasson E, Shamir R, Tzfadia O, Alexandersson E. Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. BMC PLANT BIOLOGY 2014; 14:329. [PMID: 25476999 PMCID: PMC4274702 DOI: 10.1186/s12870-014-0329-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/10/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. RESULTS We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. CONCLUSIONS We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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Affiliation(s)
- David Amar
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Itziar Frades
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Agnieszka Danek
- Institute of Informatics, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland.
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University of Munich, Arcisstraße 21, 80333, Munich, Germany.
| | - Sanjeev K Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Estelle Proux-Wera
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
- Current affiliation: SciLifeLab, Stockholm University, Universitetsvägen 10, 114 18, Stockholm, Sweden.
| | - Erik Andreasson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Oren Tzfadia
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
| | - Erik Alexandersson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Burra DD, Berkowitz O, Hedley PE, Morris J, Resjö S, Levander F, Liljeroth E, Andreasson E, Alexandersson E. Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans. BMC PLANT BIOLOGY 2014; 14:254. [PMID: 25270759 PMCID: PMC4192290 DOI: 10.1186/s12870-014-0254-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/20/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling. RESULTS Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with β-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid. CONCLUSIONS Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.
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Affiliation(s)
- Dharani Dhar Burra
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Oliver Berkowitz
- />Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
- />School of Plant Biology, The University of Western Australia, Crawley, WA 6009 Australia
- />Present address: Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Pete E Hedley
- />Genome Technology, James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Jenny Morris
- />Genome Technology, James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Svante Resjö
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Erland Liljeroth
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Alexandersson
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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