Comparing Genetic Engineering with Selective Breeding

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Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21 (2013)


Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding.


These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study.

A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments (2014)


During genetic engineering, DNA is inserted into a plant’s genome, and such insertions are often accompanied by the insertion of additional DNA, deletions and/or rearrangements. These genetic changes are collectively known as insertional effects, and they have the potential to give rise to unintended traits in plants. In addition, there are many other genetic changes that occur in plants both spontaneously and as a result of conventional breeding practices.
Genetic changes similar to insertional effects occur in plants, namely as a result of the movement of transposable elements, the repair of double-strand breaks by non-homologous end-joining, and the intracellular transfer of organelle DNA. Based on this similarity, insertional effects should present a similar level of risk as these other genetic changes in plants, and it is within the context of these genetic changes that insertional effects must be considered.

Increased familiarity with genetic engineering techniques and advances in molecular analysis techniques have provided us with a greater understanding of the nature and impact of genetic changes in plants, and this can be used to refine pre-market assessments of genetically engineered plants and food and feeds derived from genetically engineered plants.

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content (2009)


Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes.
A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.


There is a growing appreciation for the role of genome structural variation in creating phenotypic variation within a species. Comparative genomic hybridization was used to compare the genome structures of two maize inbred lines, B73 and Mo17. The data reinforce the view that maize is a highly polymorphic species, but also show that there are often large genomic regions that have little or no variation.
We identify several hundred sequences that, while present in both B73 and Mo17, have copy number differences in the two genomes. In addition, there are several thousand sequences, including at least 180 sequences annotated as single-copy genes, that are present in one genome but entirely missing in the other genome. This genome content variation leads to differences in transcript content between inbred lines and likely contributes to phenotypic diversity and heterosis in maize.

Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion (2008)


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.

Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait. (2016)


OBJECTIVES: Here we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible.
CONCLUSION: The effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation.

Evaluation of Genetically Engineered Crops Using Transcriptomic, Proteomic, and Metabolomic Profiling Techniques (2013)

The question addressed is: may the improvement of a plant variety through the acquisition of a new desired GE trait lead to unintended effects (i.e. going beyond that of the original genetic modification) and, if so, does this have an impact on health? Possible mediators of such pleiotropic effects could be altered expression of untargeted genes or metabolic effects of a novel gene product. Current tools to assess the food safety of GE crops include extensive multisite and multiyear agronomic evaluations, compositional analyses, animal nutrition, and classical toxicology evaluations.
In the 2000s, new methodologies were developed to allow, in theory, a holistic search for alterations in GE crops at different biological levels (transcripts, proteins, metabolites). These methodologies include cDNA microarrays, microRNA fingerprinting, proteome, metabolome, and toxicological profiling. The term “omics” in relation to food and feed safety appeared for the first time in 2005 (Li et al., 2005). This review highlights the knowledge generated by recently published profiling studies regarding the effect of genetic modification itself, compared with environmental and intervariety variation, for major crops (44 studies) and for Arabidopsis (Arabidopsis thaliana) as a reference plant.

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes (2017) ABSTRACT

Commercial-scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders.
During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial-scale breeders have implemented extensive plant selection practices to identify the top-performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years.
Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy

of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes. [PDF]

Stacking transgenic event DAS-Ø15Ø7-1 alters maize composition less than traditional breeding (2017) SUMMARY

The impact of crossing (‘stacking’) genetically modified (GM) events on maize-grain biochemical composition was compared with the impact of generating nonGM hybrids. The compositional similarity of seven GM stacks containing event DAS-Ø15Ø7-1, and their matched nonGM near-isogenic hybrids (iso-hybrids) was compared with the compositional similarity of concurrently grown nonGM hybrids and these same iso-hybrids. Scatter plots were used to visualize comparisons among hybrids and a coefficient of identity (per cent of variation explained by line of identity) was calculated to quantify the relationships within analyte profiles.
The composition of GM breeding stacks was more similar to the composition of iso-hybrids than was the composition of nonGM hybrids. NonGM breeding more strongly influenced crop composition than did transgenesis or stacking of GM events. These findings call into question the value of uniquely requiring composition studies for GM crops, especially for breeding stacks composed of GM events previously found to be compositionally normal.