Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties

ABSTRACT

Genetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a potential approach to directly evaluate unintended effects caused by foreign genes. In this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons. The study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work offers empirical evidence to investigate the genomic-level disparities induced by genetic modification in soybeans, specifically focusing on seed tissues.

KEYWORDS:

• Differentially expressed genes
• GM soybean lines
• non-GM soybean lines
• soybean seed tissues
• transcriptomic analysis

Abbreviations

GM	=	genetic modified
GO	=	Gene Ontology
KEGG	=	Kyoto Encyclopedia of Genes and Genomes
DEG	=	differentially expressed gene

Acknowledgments

The authors appreciate Dr. Qingyu Wu (Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences) for suggestions and revisions of the paper.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contributions

M. Dong and C. Liu performed the experiments. Y. Long, W. Xu, W. Liu, and R. Chen performed the data analysis and prepared the figures. Y. Long and L. Li prepared the manuscript, X. Pei, R. Chen and W. Jin revised the manuscript. All authors read and approved the final manuscript.

Data availability statement

The sequence data was submitted to NCBI database and the number code is PRJNA668923.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21645698.2023.2233122

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This work was financially supported by National Major Special Project for the Development of Transgenic Organisms (2016ZX08012-003, 2016ZX08011-001), Agricultural Science and Technology Innovation Program of CAAS (CAAS-ZDRW202009), Central Public-interest Scientific Institution Basal Research Fund (1610392020001) and Agricultural Product Quality and Safety Supervision Project.