Tropical Plant Biology

, Volume 1, Issue 3–4, pp 293–309 | Cite as

Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop

  • Jon Y. Suzuki
  • Savarni Tripathi
  • Gustavo A. Fermín
  • Fuh-Jyh Jan
  • Shaobin Hou
  • Jimmy H. Saw
  • Christine M. Ackerman
  • Qingyi Yu
  • Michael C. Schatz
  • Karen Y. Pitz
  • Marcela Yépes
  • Maureen M. M. Fitch
  • Richard M. Manshardt
  • Jerry L. Slightom
  • Stephen A. Ferreira
  • Steven L. Salzberg
  • Maqsudul Alam
  • Ray Ming
  • Paul H. Moore
  • Dennis GonsalvesEmail author


Inserts and insert sites in transgenic, papaya ringspot virus (PRSV)-resistant commercial papaya Rainbow and SunUp, were characterized as part of a petition to Japan to allow import of fresh fruit of these cultivars from the U.S. and to provide data for a larger study aimed at understanding the global impact of DNA transformation on whole genome structure. The number and types of inserts were determined by Southern analysis using probes spanning the entire transformation plasmid and their sequences determined from corresponding clones or sequence reads from the whole-genome shotgun (WGS) sequence of SunUp papaya. All the functional transgenes, coding for the PRSV coat protein (CP), neophosphotransferase (nptII) and β-glucuronidase (uidA) were found in a single 9,789 basepair (bp) insert. Only two other inserts, one consisting of a 290 bp nonfunctional fragment of the nptII gene and a 1,533 bp plasmid-derived fragment containing a nonfunctional 222 bp segment of the tetA gene were detected in Rainbow and SunUp. Detection of the same three inserts in samples representing transgenic generations five to eight (R5 to R8) suggests that the three inserts are stably inherited. Five out of the six genomic DNA segments flanking the three inserts were nuclear plastid sequences (nupts). From the biosafety standpoint, no changes to endogenous gene function based on sequence structure of the transformation plasmid DNA insertion sites could be determined and no allergenic or toxic proteins were predicted from analysis of the insertion site and flanking genomic DNA.


Biosafety Genetically engineered Papaya ringspot virus Particle bombardment Rainbow papaya SunUp papaya Transgene 



base pair


coat protein


double-stranded break


enzyme-linked immunosorbent assay


Food and Agriculture Organization (of the United Nations)


genetically engineered




International Union of Immunological Societies


kilobase pair


matrix attachment regions


nonhomologous end joining


nuclear plastid DNA


nuclear plastid sequence


nuclear mitochondrial sequence


open reading frame


polymerase chain reaction


pathogen-derived resistance


post-transcriptional gene silencing


Papaya ringspot virus


Structural Database for Allergenic Proteins


transferred DNA

Topo I

Topoisomerase I

Topo II

Topoisomerase II


whole-genome shotgun


World Health Organization


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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Jon Y. Suzuki
    • 1
  • Savarni Tripathi
    • 1
    • 7
  • Gustavo A. Fermín
    • 2
  • Fuh-Jyh Jan
    • 3
  • Shaobin Hou
    • 4
  • Jimmy H. Saw
    • 4
    • 11
  • Christine M. Ackerman
    • 5
  • Qingyi Yu
    • 5
  • Michael C. Schatz
    • 6
  • Karen Y. Pitz
    • 7
  • Marcela Yépes
    • 8
  • Maureen M. M. Fitch
    • 1
  • Richard M. Manshardt
    • 9
  • Jerry L. Slightom
    • 10
  • Stephen A. Ferreira
    • 7
  • Steven L. Salzberg
    • 6
  • Maqsudul Alam
    • 4
    • 11
  • Ray Ming
    • 5
    • 12
  • Paul H. Moore
    • 1
  • Dennis Gonsalves
    • 1
    Email author
  1. 1.USDA-ARS Pacific Basin Agricultural Research CenterHiloUSA
  2. 2.Centro Jardín BotánicoUniversidad de los AndesMéridaVenezuela
  3. 3.Department of Plant PathologyNational Chung Hsing UniversityTaichung, TaiwanRepublic of China
  4. 4.Advanced Studies in Genomics, Proteomics and BioinformaticsUniversity of HawaiiHonoluluUSA
  5. 5.Hawaii Agricultural Research CenterHonoluluUSA
  6. 6.Center for Bioinformatics and Computational BiologyUniversity of MarylandCollege ParkUSA
  7. 7.Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human ResourcesUniversity of HawaiiHonoluluUSA
  8. 8.Department of Plant PathologyCornell UniversityGenevaUSA
  9. 9.Department of Tropical Plant and Soil Sciences, College of Tropical Agriculture and Human ResourcesUniversity of HawaiiHonoluluUSA
  10. 10.AureoGen BiosciencesKalamazooUSA
  11. 11.Department of MicrobiologyUniversity of HawaiiHonoluluUSA
  12. 12.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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