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NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population

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Abstract

Background

As the transformation process can induce mutations in host plants, molecular characterization of the associated genomic changes is important not only for practical food safety but also for understanding the fundamental theories of genome evolution.

Objectives

To investigate a population-scale comparative study of the genome-wide spectrum of sequence variants in the transgenic genome with the variations present in 3000 rice varieties.

Results

On average, we identified 19,273 SNPs (including Indels) per transgenic line in which 10,729 SNPs were at the identical locations in the three transgenic rice plants. We found that these variations were predominantly present in specific regions in chromosomes 8 and 10. Majority (88%) of the identified variations were detected at the same genomic locations as those in natural rice population, implying that the transgenic induced mutations had a tendency to be common alleles.

Conclusion

Genomic variations in transgenic rice plants frequently occurred at the same sites as the major alleles found in the natural rice population, which implies that the sequence variations occur within the limits of a biological system to ensure survival.

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Data availability

The datasets supporting the results of this article are available in the NCBI Sequence Read Archive repository [SRX2762614, SRX2762615, SRX2762616, SRX2762617, SRX2762618, and SRX2762619]. The SNP and Indel datasets of the 3K rice genomes are available in a public repository under the link: http://snp-seek.irri.org/_download.zul (Mansueto et al. 2017).

Abbreviations

SNP:

Single nucleotide polymorphism

Indel:

Insertion and deletion

Mb:

Mega base pair

3K RGP:

3000 rice genomes project

GM:

Genetically modified

T-DNA:

Transfer DNA

Kb:

Kilo base pair

2, 4-D:

2, 4-Dichlorophenoxyacetic acid

DSB:

Double strand breaks

BWA:

Burrow Wheeler Aligner

GATK:

Genome analysis toolkit

SEA:

Singular enrichment analysis.

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Funding

This work was supported by a grant from the Next-Generation BioGreen21 Program (PJ013658022018 to YSK), Rural Development Administration, Republic of Korea.

Author information

Author notes

  1. Su-Hyun Park

    Present address: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA

Authors and Affiliations

  1. Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea

    Doori Park & Nam-Soo Kim

  2. Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea

    Su-Hyun Park, Youn Shic Kim & Ju-Kon Kim

  3. Phyzen Genomics Institute, Seongnam, South Korea

    Beom-Soon Choi

  4. Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, South Korea

    Nam-Soo Kim

  5. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea

    Ik-Young Choi

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  1. Doori Park
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Contributions

JKK and IYC conceived and designed the project. DP was a major contributor to the data analysis and drafted the manuscript. SHP and YSK constructed the transgenic plants and prepared sample materials. BSC analyzed the data. NSK analyzed the data and wrote the paper. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Ju-Kon Kim, Nam-Soo Kim or Ik-Young Choi.

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All authors declare that they have no conflict of interests.

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Park, D., Park, SH., Kim, Y.S. et al. NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population. Genes Genom 41, 213–222 (2019). https://doi.org/10.1007/s13258-018-0754-5

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  • DOI: https://doi.org/10.1007/s13258-018-0754-5

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