The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop

Edited by Eugene W. Nester, University of Washington, Seattle, WA, and approved March 16, 2015 (received for review October 13, 2014)
April 20, 2015
112 (18) 5844-5849

Significance

We communicate the rather remarkable observation that among 291 tested accessions of cultivated sweet potato, all contain one or more transfer DNA (T-DNA) sequences. These sequences, which are shown to be expressed in a cultivated sweet potato clone (“Huachano”) that was analyzed in detail, suggest that an Agrobacterium infection occurred in evolutionary times. One of the T-DNAs is apparently present in all cultivated sweet potato clones, but not in the crop’s closely related wild relatives, suggesting the T-DNA provided a trait or traits that were selected for during domestication. This finding draws attention to the importance of plant–microbe interactions, and given that this crop has been eaten for millennia, it may change the paradigm governing the “unnatural” status of transgenic crops.

Abstract

Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world’s arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.

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Data Availability

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo [accession nos. KM052616 (IbT-DNA1 “Huachano”), KM052617 (IbT-DNA2 “Huachano”), KM113766 (IbT-DNA1 BAC clone “Xu781”), KM658948 (ORF13 CIP_420065), KM658949 (ORF13 CIP_440031), KM658950 (ORF13 CIP_440166), KM658951 (ORF13 PI_561255), KM658952 (ORF13 CIP_403552), KM658953 (ORF13 CIP107665.9), KM658954 (iaaM CIP_440132), KM658955 (iaaM CIP_440166), KM658956 (iaaM CIP_440274), KM658957 (iaaM: CIP_440398), KM658958 (iaaM CIP_400450), KM658959 (iaaM CIP_441724), KM658960 (iaaM CIP_440116), KM658961 (iaaM CIP_440146), and KM658962 (iaaM CIP_440031)].

Acknowledgments

We thank Lien De Smet, Isabelle Tilmant, Milton Untiveros, Bruno Lertora, Roland Robles, and Clauvis Taning for technical assistance; Martine De Cock and Ivonne Valdizan for help with layout and formatting; Wolfgang Gruneberg for sharing phenotypic and yield data for the BxT (Beauregard by Tanzania) population; Felipe de Mendiburo and Hannele Lindqvist Kreuze for advice on statistical analysis; Genoveva Rossel and David Tay for sharing ploidy information and DNA from germplasm accessions; Zengzhi Si for helping to screen the BAC library; and Jason McKinney (Fluidigm), Cameron Gundry, and Matt Poulson (BioFire Diagnostics) for high resolution melting primer design using sequence data provided by R.J. and screening of the sweet potato collection of the US Department of Agriculture. This work was supported by grants from the Special Research Fund of Ghent University (BOF 01SB0710 and 01W02112) and the Consultative Group on International Agricultural Research (CGIAR) consortium research program on roots, tubers, and bananas. T.K. is a postdoctoral fellow of the Research Foundation-Flanders.

Supporting Information

Supporting Information (PDF)
Supporting Information
pnas.1419685112.sd01.xlsx
pnas.1419685112.sd02.xlsx
pnas.1419685112.sd03.xlsx
pnas.1419685112.sd04.xlsx
pnas.1419685112.sd05.docx

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 112 | No. 18
May 5, 2015
PubMed: 25902487

Classifications

Data Availability

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo [accession nos. KM052616 (IbT-DNA1 “Huachano”), KM052617 (IbT-DNA2 “Huachano”), KM113766 (IbT-DNA1 BAC clone “Xu781”), KM658948 (ORF13 CIP_420065), KM658949 (ORF13 CIP_440031), KM658950 (ORF13 CIP_440166), KM658951 (ORF13 PI_561255), KM658952 (ORF13 CIP_403552), KM658953 (ORF13 CIP107665.9), KM658954 (iaaM CIP_440132), KM658955 (iaaM CIP_440166), KM658956 (iaaM CIP_440274), KM658957 (iaaM: CIP_440398), KM658958 (iaaM CIP_400450), KM658959 (iaaM CIP_441724), KM658960 (iaaM CIP_440116), KM658961 (iaaM CIP_440146), and KM658962 (iaaM CIP_440031)].

Submission history

Published online: April 20, 2015
Published in issue: May 5, 2015

Keywords

  1. horizontal gene transfer
  2. Agrobacterium spp.
  3. food safety
  4. sweet potato
  5. transgenic crops

Acknowledgments

We thank Lien De Smet, Isabelle Tilmant, Milton Untiveros, Bruno Lertora, Roland Robles, and Clauvis Taning for technical assistance; Martine De Cock and Ivonne Valdizan for help with layout and formatting; Wolfgang Gruneberg for sharing phenotypic and yield data for the BxT (Beauregard by Tanzania) population; Felipe de Mendiburo and Hannele Lindqvist Kreuze for advice on statistical analysis; Genoveva Rossel and David Tay for sharing ploidy information and DNA from germplasm accessions; Zengzhi Si for helping to screen the BAC library; and Jason McKinney (Fluidigm), Cameron Gundry, and Matt Poulson (BioFire Diagnostics) for high resolution melting primer design using sequence data provided by R.J. and screening of the sweet potato collection of the US Department of Agriculture. This work was supported by grants from the Special Research Fund of Ghent University (BOF 01SB0710 and 01W02112) and the Consultative Group on International Agricultural Research (CGIAR) consortium research program on roots, tubers, and bananas. T.K. is a postdoctoral fellow of the Research Foundation-Flanders.

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Tina Kyndt1
Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium;
Dora Quispe1
Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium;
International Potato Center, Lima 12, Peru;
Hong Zhai
Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China, 100193; and
Robert Jarret
Plant Genetic Resources Unit, US Department of Agriculture, Agricultural Research Service, Griffin, GA 30223
Marc Ghislain
International Potato Center, Lima 12, Peru;
Qingchang Liu
Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China, 100193; and
Godelieve Gheysen
Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium;

Notes

2
To whom correspondence should be addressed. Email: [email protected].
Author contributions: J.F.K. designed research; Q.L. and G.G. supervised research; T.K., D.Q., H.Z., R.J., Q.L., and J.F.K. performed research; T.K., D.Q., H.Z., R.J., M.G., G.G., and J.F.K. analyzed data; and T.K., D.Q., R.J., M.G., G.G., and J.F.K. wrote the paper.
1
T.K. and D.Q. contributed equally to this work.

Competing Interests

The authors declare no conflict of interest.

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    The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop
    Proceedings of the National Academy of Sciences
    • Vol. 112
    • No. 18
    • pp. 5545-E2413

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