Open AccessTranscriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation
Author(s) -
Dae Kwan Ko,
Satya Swathi Nadakuduti,
David S. Douches,
C. Robin Buell
Publication year - 2018
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0206055
Subject(s) - transcriptome , transformation (genetics) , biology , genetically modified crops , profiling (computer programming) , transgene , computational biology , gene expression profiling , microbiology and biotechnology , genetics , gene expression , gene , computer science , operating system
Crop genetic engineering involves transformation in which transgenic plants are regenerated through tissue culture manipulations that can elicit somaclonal variation due to mutations, translocations, and/or epigenetic alterations. Here, we report on alterations in the transcriptome in a panel of transgenic potato plants engineered to be herbicide resistant. Using an inbred diploid potato clone (DMRH S5 28–5), ten single-insert transgenic lines derived from independent Agrobacterium -mediated transformation events were selected for herbicide resistance using an allelic variant of acetolactate synthase ( mALS1 ). Expression abundances of the single-copy mALS1 transgene varied in individual transgenic lines was correlated with the level of phenotypic herbicide resistance, suggesting the importance of transgene expression in transgenic performance. Using RNA-sequencing, differentially expressed genes were identified with the proportion of genes up-regulated significantly higher than down-regulated genes in the panel, suggesting a differential impact of the plant transformation on gene expression activation compared to repression. Not only were transcription factors among the differentially expressed genes but specific transcription factor binding sites were also enriched in promoter regions of differentially expressed genes in transgenic lines, linking transcriptomic variation with specific transcription factor activity. Collectively, these results provide an improved understanding of transcriptomic variability caused by plant transformation.