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Effects of stacking breeding on the methylome and transcriptome profile of transgenic rice with glyphosate tolerance

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Abstract

Main conclusion

Transcriptomics and methylomics were used to identify the potential effects resulting from GM rice breeding stacks, which provided scientific data for the safety assessment strategy of stacked GM crops in China.

Abstract

Gene interaction is one of the main concerns for stacked genetically modified crop safety. With the development of technology, the combination of omics and bioinformatics has become a useful tool to evaluate the unintended effects of genetically modified crops. In this study, transcriptomics and methylomics were used as molecular profiling techniques to identify the potential effects of stack through breeding. Stacked transgenic rice En-12 × Ec-26 was used as material, which was obtained through hybridization using parents En-12 and Ec-26, in which the foreign protein can form functional EPSPS protein by intein-mediated trans-splitting. Differentially methylated region (DMR) analysis showed that the effect of stacking breeding on methylation was less than that of genetic transformation at the methylome level. Differentially expressed gene (DEG) analysis showed that the DEGs between En-12 × Ec-26 and its parents were far fewer than those between transgenic rice and Zhonghua 11 (ZH11), and no unintended new genes were found in En-12 × Ec-26. Statistical analysis of gene expression and methylation involved in shikimic acid metabolism showed that there was no difference in gene expression, although there were 16 and 10 DMR genes between En-12 × Ec-26 and its parents (En and Ec) in methylation, respectively. The results indicated that the effect of stacking breeding on gene expression and DNA methylation was less than the effect of genetic transformation. This study provides scientific data supporting safety assessments of stacked GM crops in China.

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Data availability

The raw sequence data from this study have been deposited at the NCBI Sequence Read Archive (BioProject accession ID: PRJNA938183).

Abbreviations

DEG:

Differentially expressed gene

DMC:

Differentially methylated region

GM:

Genetically modified

GMC:

Genetically modified crop

ZH11:

Rice variety Zhonghua 11

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Acknowledgements

This work was supported by grants from the evaluation techniques for unexpected effects of biotechnology products in the major project of agricultural biological breeding (2022ZD0402003) and the innovation engineering innovation team of the Chinese Academy of Agricultural Sciences in 2022 (110239210012052).

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Author notes

  1. Xujing Wang, Shance Niu and Jiangtao Yang have equally contributed to this work.

Authors and Affiliations

  1. Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Xujing Wang, Jiangtao Yang, Yufeng Dong, Xiaojing Liu & Zhixing Wang

  2. Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China

    Xujing Wang, Jiangtao Yang, Xiaojing Liu & Zhixing Wang

  3. Development Center for Science and Technology, MARA, Beijing, 100122, China

    Yue Jiao

  4. College of Horticulture, Hebei Agricultural University, Baoding, 071001, China

    Shance Niu

  5. State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China

    Shance Niu

  6. Cropedit Biotechnology Co., Ltd, Beijing, 102206, China

    Yufeng Dong

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  1. Xujing Wang
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Wang, X., Niu, S., Yang, J. et al. Effects of stacking breeding on the methylome and transcriptome profile of transgenic rice with glyphosate tolerance. Planta 258, 34 (2023). https://doi.org/10.1007/s00425-023-04181-5

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