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Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants

Author

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  • Jiuer Liu

    (School of Life Sciences, Sun Yat-sen University)

  • Feng-Zhu Wang

    (School of Life Sciences, Sun Yat-sen University)

  • Chong Li

    (School of Life Sciences, Sun Yat-sen University)

  • Yujia Li

    (School of Life Sciences, Sun Yat-sen University)

  • Jian-Feng Li

    (School of Life Sciences, Sun Yat-sen University)

Abstract

Tandemly arrayed genes (TAGs) with functional redundancy and chromosomal linkage constitute 14 ~ 35% in sequenced plant genomes. The multiplex CRISPR system is the tool of choice for creating targeted TAG deletions. Here, we show that up to ~80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion (delinver) bi-alleles, which are easily misidentified as homozygous deletion alleles by routine PCR-based genotyping. This can lead to misinterpretation of experimental data and production of progenies with genetic heterogeneity in an unnoticed manner. In ~2,650 transgenic events, delinver mutation frequencies are predominantly correlated with deletion frequencies but unrelated to chromosomal locations or deletion sizes. Delinver mutations also occur frequently at genomic non-TAG loci during multiplexed CRISPR editing. Our work raises the alarm about delinver mutations as common unwanted products of targeted TAG deletions in plants and helps prevent false interpretation of plant TAG functions due to this hidden genotype issue.

Suggested Citation

  • Jiuer Liu & Feng-Zhu Wang & Chong Li & Yujia Li & Jian-Feng Li, 2023. "Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42490-1
    DOI: 10.1038/s41467-023-42490-1
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    References listed on IDEAS

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    1. Tao Zhang & Michael Mudgett & Ratnala Rambabu & Bradley Abramson & Xinhua Dai & Todd P. Michael & Yunde Zhao, 2022. "Retraction Note: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
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