Article

Tropical Plant Biology

, Volume 1, Issue 3, pp 293-309

First online:

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

  • Jon Y. SuzukiAffiliated withUSDA-ARS Pacific Basin Agricultural Research Center
  • , Savarni TripathiAffiliated withUSDA-ARS Pacific Basin Agricultural Research CenterPlant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii
  • , Gustavo A. FermínAffiliated withCentro Jardín Botánico, Universidad de los Andes
  • , Fuh-Jyh JanAffiliated withDepartment of Plant Pathology, National Chung Hsing University
  • , Shaobin HouAffiliated withAdvanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii
  • , Jimmy H. SawAffiliated withAdvanced Studies in Genomics, Proteomics and Bioinformatics, University of HawaiiDepartment of Microbiology, University of Hawaii
  • , Christine M. AckermanAffiliated withHawaii Agricultural Research Center
  • , Qingyi YuAffiliated withHawaii Agricultural Research Center
  • , Michael C. SchatzAffiliated withCenter for Bioinformatics and Computational Biology, University of Maryland
    • , Karen Y. PitzAffiliated withPlant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii
    • , Marcela YépesAffiliated withDepartment of Plant Pathology, Cornell University
    • , Maureen M. M. FitchAffiliated withUSDA-ARS Pacific Basin Agricultural Research Center
    • , Richard M. ManshardtAffiliated withDepartment of Tropical Plant and Soil Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii
    • , Jerry L. SlightomAffiliated withAureoGen Biosciences
    • , Stephen A. FerreiraAffiliated withPlant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii
    • , Steven L. SalzbergAffiliated withCenter for Bioinformatics and Computational Biology, University of Maryland
    • , Maqsudul AlamAffiliated withAdvanced Studies in Genomics, Proteomics and Bioinformatics, University of HawaiiDepartment of Microbiology, University of Hawaii
    • , Ray MingAffiliated withHawaii Agricultural Research CenterDepartment of Plant Biology, University of Illinois at Urbana-Champaign
    • , Paul H. MooreAffiliated withUSDA-ARS Pacific Basin Agricultural Research Center
    • , Dennis GonsalvesAffiliated withUSDA-ARS Pacific Basin Agricultural Research Center Email author 

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Abstract

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.

Keywords

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