Resistance of transgenic papaya trees to papaya ringspot in Brazil

The objective of this work was to evaluate the resistance of transgenic papaya populations (PTPs) to Papaya ringspot virus-P (PRSV-P). 'Sunrise Solo' transgenic papaya plants were produced with the gene of the PRSV-P protein coat, and PRSV was mechanically inoculated in plants in greenhouse conditions. The presence of the CP/PRSV gene and homozygosis were evaluated by polymerase chain reaction (PCR). Selected plants and the 'Sunrise Solo' control were transplanted to the field for agronomic evaluations. The plants evaluated in greenhouse conditions showed resistance between 96.3 and 5.8%, without variation of symptoms. The PTPs 1/6, 1/7, 1/9, 1/10, 1/15, 2/38, 2/41, 2/56, 2/65, 3/27, 3/46, 3/48, 4/9, 4/27, 8/4, 8/23, 8/33, 18/3, 18/4, 18/8, 18/22, 18/27, 28/97, 28/104, and 28/110 showed no symptoms, they were ELISA negative, and most of them contained the CP and NPT II genes. PTPs 1/6 and 3/46 had the CP gene in homozygosis and in double insertion. PTPs 1/6/20, 1/6/59, 1/6/64, 1/6/90, 3/46/44, 3/46/52, and 18/27/97 had a well-formed fruit cluster, piriform fruit weighing approximately 500 grams, orange pulp, and less than 10% carpelloidy. PTPs 1/6/59 and 3/46/52 show resistance to PRSV, good agronomic characteristics, and the CP gene in homozygosis.

Genomic Variation between PRSV Resistant Transgenic SunUp and Its Progenitor Cultivar Sunset

Background: The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. Results: In this study, a total of more than 74 million Illumina reads for progenitor ‘Sunset’ were mapped onto transgenic papaya ‘SunUp’ reference genome. 310,364 single nucleotide polymorphisms (SNPs), 34,071 small Inserts/deletions (InDels) and 1,200 large structural variations (SVs) were detected between ‘Sunset’ and ‘SunUp’. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4×10-4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. Spontaneous mutations were the leading cause of SNPs in transgenic papaya ‘SunUp’. A total of 3,430 nuclear plastid DNA (NUPT) and 2,764 nuclear mitochondrial DNA (NUMT) junction sites have been found in ‘SunUp’, which is proportionally higher than the predicted total NUPT and NUMT junction sites in ‘Sunset’ (3,346 and 2,745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘SunUp’ and ‘Sunset’. The average identity between ‘SunUp’ specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by ‘SunUp’ and ‘Sunset’. Six ‘SunUp’ organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18~100%). None of the paired-end spans of mapped ‘Sunset’ reads were elongated by any ‘SunUp’ transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions.Conclusions: Comparative whole-genome analyses between ‘SunUp’ and ‘Sunset’ provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.

Genomic Variation between PRSV Resistant Transgenic SunUp and Its Progenitor Cultivar Sunset Induced by Particle Bombardment Transformation

The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. In this study, a total of more than 74 million Illumina reads for progenitor ‘Sunset’ were mapped onto transgenic papaya ‘SunUp’ reference genome. 310,364 single nucleotide polymorphisms (SNPs), 34,071 Small Inserts/deletions (InDels) and 1,200 large structural variations (SVs) were detected between ‘Sunset’ and ‘SunUp’. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4×10 -4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. Spontaneous mutations were the leading cause of SNPs in transgenic papaya ‘SunUp’. A total of 3,430 nuclear plastid DNA (NUPT) and 2,764 nuclear mitochondrial DNA (NUMT) junction sites have been found in ‘SunUp’, which is proportionally higher than the predicted total NUPT and NUMT junction sites in ‘Sunset’ (3,346 and 2,745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘SunUp’ and ‘Sunset’. The average identity between ‘SunUp’ specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by ‘SunUp’ and ‘Sunset’. Six ‘SunUp’ organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18~100%). None of the paired-end spans of mapped ‘Sunset’ reads were elongated by any ‘SunUp’ transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. Comparative whole-genome analyses between ‘SunUp’ and ‘Sunset’ provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.