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Transgenic Research

, Volume 17, Issue 2, pp 293–306 | Cite as

Transgene integration and organization in Cotton (Gossypium hirsutum L.) genome

  • Jun Zhang
  • Lin Cai
  • Jiaqin Cheng
  • Huizhu Mao
  • Xiaoping Fan
  • Zhaohong Meng
  • Ka Man Chan
  • Huijun Zhang
  • Jianfei Qi
  • Lianghui Ji
  • Yan HongEmail author
Original Paper
First Online:

Abstract

While genetically modified upland cotton (Gossypium hirsutum L.) varieties are ranked among the most successful genetically modified organisms (GMO), there is little knowledge on transgene integration in the cotton genome, partly because of the difficulty in obtaining large numbers of transgenic plants. In this study, we analyzed 139 independently derived T0 transgenic cotton plants transformed by Agrobacterium tumefaciens strain AGL1 carrying a binary plasmid pPZP-GFP. It was found by PCR that as many as 31% of the plants had integration of vector backbone sequences. Of the 110 plants with good genomic Southern blot results, 37% had integration of a single T-DNA, 24% had two T-DNA copies and 39% had three or more copies. Multiple copies of the T-DNA existed either as repeats in complex loci or unlinked loci. Our further analysis of two T1 populations showed that segregants with a single T-DNA and no vector sequence could be obtained from T0 plants having multiple T-DNA copies and vector sequence. Out of the 57 T-DNA/T-DNA junctions cloned from complex loci, 27 had canonical T-DNA tandem repeats, the rest (30) had deletions to T-DNAs or had inclusion of vector sequences. Overlapping micro-homology was present for most of the T-DNA/T-DNA junctions (38/57). Right border (RB) ends of the T-DNA were precise while most left border (LB) ends (64%) had truncations to internal border sequences. Sequencing of collinear vector integration outside LB in 33 plants gave evidence that collinear vector sequence was determined in agrobacterium culture. Among the 130 plants with characterized flanking sequences, 12% had the transgene integrated into coding sequences, 12% into repetitive sequences, 7% into rDNAs. Interestingly, 7% had the transgene integrated into chloroplast derived sequences. Nucleotide sequence comparison of target sites in cotton genome before and after T-DNA integration revealed overlapping microhomology between target sites and the T-DNA (8/8), deletions to cotton genome in most cases studied (7/8) and some also had filler sequences (3/8). This information on T-DNA integration in cotton will facilitate functional genomic studies and further crop improvement.

Keywords

Transgene Cotton (Gossypium hirsutum L.) Agrobacterium-mediated transformation Transgene/plant genome junctions Transgene repeats Vector backbone integration 
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Notes

Acknowledgements

This project was supported by an internal research grant of Temasek Life Sciences Laboratory, Singapore. We would like to thank Tan Jason and Ng Khar Meng for technical help.

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Jun Zhang
    • 1
    • 2
  • Lin Cai
    • 1
  • Jiaqin Cheng
    • 1
    • 3
  • Huizhu Mao
    • 1
  • Xiaoping Fan
    • 1
    • 4
  • Zhaohong Meng
    • 1
    • 4
  • Ka Man Chan
    • 1
  • Huijun Zhang
    • 1
    • 4
  • Jianfei Qi
    • 1
  • Lianghui Ji
    • 1
  • Yan Hong
    • 1
    Email author
  1. 1.Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
  2. 2.Shandong Cotton Research CenterJinanP. R. China
  3. 3.Institute of BotanyChinese Academy of SciencesBeijingP. R. China
  4. 4.Shanxi Cotton Research InstituteYunchengP. R. China

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