Effect of Transgenesis on mRNA and miRNA Profiles in Cucumber Fruits Expressing Thaumatin II

Abstract

Transgenic plants are commonly used in breeding programs because of the various features that can be introduced. However, unintended effects caused by genetic transformation are still a topic of concern. This makes research on the nutritional safety of transgenic crop plants extremely interesting. Cucumber (Cucumis sativus L.) is a crop that is grown worldwide. The aim of this study was to identify and characterize differentially expressed genes and regulatory miRNAs in transgenic cucumber fruits that contain the thaumatin II gene, which encodes the sweet-tasting protein thaumatin II, by NGS sequencing. We compared the fruit transcriptomes and miRNomes of three transgenic cucumber lines with wild-type cucumber. In total, we found 47 differentially expressed genes between control and all three transgenic lines. We performed the bioinformatic functional analysis and gene ontology classification. We also identified 12 differentially regulated miRNAs, from which three can influence the two targets (assigned as DEGs) in one of the studied transgenic lines (line 224). We found that the transformation of cucumber with thaumatin II and expression of the transgene had minimal impact on gene expression and epigenetic regulation by miRNA, in the cucumber fruits.

Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

“…Overexpression of PdNF-YB21 increased the drought resistance of transgenic poplars by positively regulating root growth and enlarging xylem vessels [ 30 ]. Recently, some studies have demonstrated that miRNA responded to abiotic stresses by regulating the expression of their target gene NF-Y [ 31 ]. The overexpression of soybean miR169c in transgenic Arabidopsis conferred increased drought stress sensitivity via inhibiting the expression of its target AtNF - YA gene [ 32 ].…”

Influence of transgenesis on genome variability in cucumber lines with a thaumatin II gene

“…Analysis of the expression level of the thaumatin II gene in cucumber transgenic lines showed that transgene expression occurs in all three thaumatin lines, but the level of expression varies (Pawełkowicz et al 2020 ). The lowest expression level was obtained for 225 line, despite it having a double copy of T-DNA.…”

“…Regarding RNA-seq and miRNA-seq analyses in the fruits of three transgenic lines (212, 224, and 225), it was concluded that transformation of the cucumber genome with thaumatin II and expression of the transgene had minimal impact on gene expression and epigenetic regulation by miRNA in the cucumber fruits (Pawełkowicz et al 2020 ). The next important step was a comparative genome analysis, which aimed to check if and how transgene insertion affects gene expression.…”

“…Earlier analysis carried out on these lines determined the gene copy number and chromosomal location (Szwacka et al 2000(Szwacka et al , 2002Tagashira et al 2005) but did not show its position in the cucumber genome. Metabolic and organoleptic analyses (Szwacka et al 2002(Szwacka et al , 2012Tagashira et al 2005), and lastly profiles of mRNA and miRNA (Pawełkowicz et al 2020), were also performed, but no comparative genomic analysis was made to evaluate changes throughout the genome. Therefore, in this study, we performed re-sequencing and comparative genomic analyses to determine changes in the genomes of transgenic lines relative to the B10 cucumber reference line used for transformation.…”

Molecular insight into somaclonal variation phenomena from transcriptome profiling of cucumber (Cucumis sativus L.) lines

“…Previously, we also examined three independent transgenic cucumber lines (Pawełkowicz et al 2020) that were derived from the same B10 line and, after transformation, were regenerated in in vitro cultures. The changes in gene expression between transgenic lines compared with the control line (plants were grown in the same field experiment as the somaclones) were as follows: three, six, and 38 DEGs in the respective analyzed transgenic lines (Pawełkowicz et al 2020). The number of DEGs detected in the somaclonal lines was significantly higher than those observed among the transgenic lines.…”