Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

Abstract

Controversy regarding genetically modified (GM) plants and their potential impact on human health contrasts with the tacit acceptance of other plants that were also modified, but not considered as GM products (e.g., varieties raised through conventional breeding such as mutagenesis). What is beyond the phenotype of these improved plants? Should mutagenized plants be treated differently from transgenics? We have evaluated the extent of transcriptome modification occurring during rice improvement through transgenesis versus mutation breeding. We used oligonucleotide microarrays to analyze gene expression in four different pools of four types of rice plants and respective controls: (i) a gamma-irradiated stable mutant, (ii) the M1 generation of a 100-Gy gamma-irradiated plant, (iii) a stable transgenic plant obtained for production of an anticancer antibody, and (iv) the T1 generation of a transgenic plant produced aiming for abiotic stress improvement, and all of the unmodified original genotypes as controls. We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants. We propose that the safety assessment of improved plant varieties should be carried out on a case-by-case basis and not simply restricted to foods obtained through genetic engineering.

Fig. 1.

Plant material used and hierarchical clustering dendrogram of the different samples.

Fig. 2.

Volcano plots for differentially expressed genes. Differentially expressed genes appear above the thick horizontal lines. Genes induced >2-fold are on the right of the right vertical lines, and the ones repressed >2-fold are on the left of the left vertical line. The numbers corresponding to the differentially expressed genes induced >2-fold for each experiment (red-shadowed area) are red, and those corresponding to the genes repressed >2-fold (blue-shadowed area) are blue. The green-shadowed area corresponds to differentially expressed genes that were up- or down-regulated <2-fold (green-colored numbers). Blue-colored genes are those with P between 0 and 0.5, and red-colored genes are those with P between 0.5 and 1.