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Enhancing grain-yield-related traits by CRISPR–Cas9 promoter editing of maize CLE genes


Several yield-related traits selected during crop domestication and improvement1,2 are associated with increases in meristem size3, which is controlled by CLE peptide signals in the CLAVATA–WUSCHEL pathway4,5,6,7,8,9,10,11,12,13. Here, we engineered quantitative variation for yield-related traits in maize by making weak promoter alleles of CLE genes, and a null allele of a newly identified partially redundant compensating CLE gene, using CRISPR–Cas9 genome editing. These strategies increased multiple maize grain-yield-related traits, supporting the enormous potential for genomic editing in crop enhancement.

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Fig. 1: Mutation of ZmCLE7 and ZmFCP1 promoters by CRISPR–Cas9.
Fig. 2: ZmCLE7 promoter-edited alleles as heterozygotes with a null allele increase IM size.
Fig. 3: ZmCLE7 and ZmFCP1 promoter-edited alleles as heterozygotes with a null allele increase grain-yield-related traits by producing enlarged, non-fasciated ears.
Fig. 4: ZmCLE1E5 CRISPR null alleles enhance meristem size and grain-yield-related traits.

Data availability

The sequences of ZmFCP1 and ZmCLE7 promoter-edited alleles are listed in Supplementary Table 4. The RNA-seq datasets are available from the National Center for Biotechnology Information; the BioProject and SRA accession numbers are PRJNA494874 and SRR12616467SRR12616470. Source data are provided with this paper.


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We thank T. Mulligan and K. Schlecht for plant care, Z. Lippman and T. Tran for comments and discussion, and C. Fugina, B. Siegel and M. Kallman for their enthusiastic involvement in some of this work. This work was supported by funding from the National Science Foundation (grant no. IOS-1546837) and from Inari Agricuture, Inc., and from the Next-Generation BioGreen 21 Program System and Synthetic Agro-biotech Center (grant no. PJ01322602) from the Rural Development Administration, Republic of Korea, Office of China Postdoctoral Affairs Fellowship (Fellowship to L.L.), and USDA NIFA Postdoctoral Fellowship (award no. 2019-67012-29654 to J.G.).

Author information




L.L. performed all experimental procedures except as described below, and prepared figures and co-wrote the manuscript. E.D.A., T.S. and Q.W. designed the promoter CRISPR sgRNAs and prepared the constructs for maize transformation. R.C. performed IM size measurements of the promoter CRISPR alleles. J.G. and M.B. performed the evolution analysis and co-wrote the manuscript. D.J. supervised the research and co-wrote the manuscript.

Corresponding author

Correspondence to David Jackson.

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Competing interests

D.J. is a consultant with Inari, who have licensed promoter fine-tuning technology from Cold Spring Harbor Laboratory. The other authors declare no conflicts of interest.

Additional information

Peer review information Nature Plants thanks Scott Boden, Feng Tian, Thorsten Schnurbusch and Cristobal Uauy for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Liu, L., Gallagher, J., Arevalo, E.D. et al. Enhancing grain-yield-related traits by CRISPR–Cas9 promoter editing of maize CLE genes. Nat. Plants 7, 287–294 (2021).

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