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RETRACTED ARTICLE: An assessment of transgenomics as a tool for gene discovery in Populus euphratica Oliv.

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This article was retracted on 26 November 2018

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Abstract

Key message

Transgenomics for gene discovery in Populus euphratica.

Abstract

Transgenomics, a member of the omics family of methodologies, is characterized as the introduction of DNA from one organism into another on a genome-wide scale followed by the identification of recipients with altered phenotypes. This strategy allows investigators to identify the gene(s) involved in these phenotypic changes. It is particularly promising for woody plants that have a long life cycle and for which molecular tools are limited. In this study, we constructed a large-insert binary bacterial artificial chromosome library of Populus euphratica, a stress-tolerant poplar species, which included 55,296 clones with average insert sizes of about 127 kb. To date, 1077 of the clones have been transformed into Arabidopsis thaliana via Agrobacterium by the floral dip method. Of these, 69 transgenic lines showed phenotypic changes represented by diverse aspects of plant form and development, 22 of which were reproducibly associated with the same phenotypic change. One of the clones conferring transgenic plants with increased salt tolerance, 002A1F06, was further analyzed and the 127,284 bp insert in this clone harbored eight genes that have been previously reported to be involved in stress resistance. This study demonstrates that transgenomics is useful in the study of functional genomics of woody plants and in the identification of novel gene(s) responsible for economically important traits. Thus, transgenomics can also be used for validation of quantitative trait loci mapped by molecular markers.

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Change history

  • 26 November 2018

    This article (Zhou et al. 2018) has been retracted by the authors because the sequence BIBAC 002A111F06 was incorrectly assigned to the wrong bacterial species. The BIBAC 002A111F06 sequence (GenBank Accession KC129717) reported in the paper was attributed to Populus euphratica Oliv. The BLAST search of this KC129717 sequence against the nr database at NCBI showed that it has very high similarity to a genomic sequence from the gram-negative bacteria Stenotrophomonas maltophilia. The bacterium associates with Populus euphratica Oliv. and DNA isolated from Populus euphratica Oliv. for the construction of the BIBAC clone library inlcuded DNA from Stenotrophomonas maltophilia. Therefore, the phenotype of the transgenic Arabidopsis line carrying the KC129717 sequence cannot be attributed to genes from Populus euphratica Oliv. The authors apologize for the confusion and misinterpretation of our data resulting from the incorrect sequence assignment. All authors agree to this retraction.

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Acknowledgements

We would like to thank Dr. Hong-Bin Zhang of A&M University for guidance in BIBAC library construction. We would also like to thank Drs. Ren-Ying Zhuo (The Research Institute of Subtropical Forestry, Chinese Academy of Forestry), Zhou Zhou (Henan University), Hai-Feng Yang (Inner Mongolia Agricultural University), Min-Sheng Yang (Hebei Agricultural University), Xin-Ye Zhang (Hubei Forestry Academy), Xiao-Ping Ao (Central South University), and Xiao-Yu Li (Huangshan University) for their collaboration on the transformation work. This work was supported by the Special Fund on Essential Research for National Non-profit Institutions to the Chinese Academy of Forestry (CAFYBB2011001).

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  1. Jing Zhou: First author.

Authors and Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Jing Zhou, Xin Liu, Shu-Tang Zhao, Jian-Jun Hu, Xiao-Peng Peng, Xiao-Li Qi, Tie-Long Cheng & Meng-Zhu Lu

  2. Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China

    Jie-Wei Zhang

  3. School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China

    Jie-Hua Wang

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  1. Jing Zhou
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Additional information

This article has been retracted by the authors because the sequence BIBAC 002A111F06 was incorrectly assigned to the wrong bacterial species. The BIBAC 002A111F06 sequence (GenBank Accession KC129717) reported in the paper was attributed to Populus euphratica Oliv. The BLAST search of this KC129717 sequence against the nr database at NCBI showed that it has very high similarity to a genomic sequence from the gram-negative bacteria Stenotrophomonas maltophilia. The bacterium associates with Populus euphratica Oliv. and DNA isolated from Populus euphratica Oliv. for the construction of the BIBAC clone library inlcuded DNA from Stenotrophomonas maltophilia. Therefore, the phenotype of the transgenic Arabidopsis line carrying the KC129717 sequence cannot be attributed to genes from Populus euphratica Oliv. The authors apologize for the confusion and misinterpretation of our data resulting from the incorrect sequence assignment. All authors agree to this retraction.

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11103_2018_755_MOESM5_ESM.tiff

Figure S1. The repeatable phenotypic changes of the additional T1 transgenic A. thaliana plants with BIBAC clones listed in Figure 2. The reproducible phenotypic changes of transgenic T1 A. thaliana plants with BIBAC clones in Figure 2. (a) 007A2D05, 135A1H05, and 007A1E12, early flowering. (b) 007A2G09, increased number of rosette leaves. (c) 007A2D06 and 007A1D01, abortion. (d) 002A1D09, 002A1B06, and 017A1H12, dwarfism and late flowering. Seedlings were grown for 5 (a, b) or 7 (c, d) weeks. WT: wild-type plants. (TIFF 4606 KB)

11103_2018_755_MOESM6_ESM.tiff

Figure S2. Additional repeatable phenotypic changes of T1 transgenic A. thaliana plants with BIBAC clones. (a) 007B1C08, early bolting and small rosette leaves. (b) 007A2B03, early bolting. (c) 007A1D10, early bolting. (d) 007A2B05, dwarfism. (e) 007A2F04, dwarfism. Seedlings were grown for 5 (a–d) or 7 (e) weeks. WT: wild-type plants. (TIFF 4706 KB)

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Zhou, J., Liu, X., Zhao, ST. et al. RETRACTED ARTICLE: An assessment of transgenomics as a tool for gene discovery in Populus euphratica Oliv.. Plant Mol Biol 97, 525–535 (2018). https://doi.org/10.1007/s11103-018-0755-4

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