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Fine mapping qKRN5.04 provides a functional gene negatively regulating maize kernel row number

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Abstract

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Zm00001d016075 was identified by fine mapping qKRN5.04. The function of Zm00001d016075, negatively modulating maize (Zea Mays L.) kernel row number (KRN), was verified by CRISPR-Cas9. InDel308 located in the promoter of Zm00001d016075 has potential for use as a molecular marker to identify KRN in maize breeding.

Abstract

Kernel row number (KRN), controlled by multiple quantitative trait loci (QTLs), is one of the most important traits that relate to maize production and domestication. Here, fine mapping was conducted to study a major QTL, qKRN5.04, to a 65-kb genomic region using a progeny test strategy in an advanced backcross population, in which Nong531 (N531) and the inbred line of Silunuo (SLN) were employed as the recurrent and the donor parent, respectively. Within this region, there was only one gene (Zm00001d016075) based on the B73 reference genome. Furthermore, we performed regional association mapping using a panel of 236 diverse inbred lines and observed that all significant SNPs were located within Zm00001d016075. The expression of Zm00001d016075 was significantly higher in N531 and qKRN5.04N531 than qKRN5.04SLN, resulting from the different promoter activity of Zm00001d016075. Sequence analysis revealed that InDel308, located in the promoter of Zm00001d016075, was related to the KRN variation in different maize inbred lines. Using the CRISPR-Cas9 strategy, we determined Zm00001d016075 played a role in negatively regulating KRN and had a moderate effect on 10-kernel width, 100-kernel weight, kernels per ear, and grain yield per ear. These results provide critical insights on the genetic basis and quantitative variation for KRN.

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Acknowledgements

We thank Professor Jianmin Wan, Chuanxiao Xie, and Meiliang Zhou for kindly supplying vectors and for helping with subcellular localization, genomic editing, and promoter activity analysis, respectively. We thank the Core Facility Platform, Institute of Crop Sciences at the Chinese Academy of Agricultural Sciences (CAAS) for their assistance with confocal analyses. None of these funding agencies have any relationship with the publication of this manuscript.

Funding

This work was financially supported by the Ministry of Science and Technology of China (2021YFD1200701, 2020YFE0202300), the National Natural Science Foundation (31801373), the China Postdoctoral Science Foundation (2021M700452) and the Agricultural Science and Technology Innovation Program (ASTIP) for CAAS.

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Authors and Affiliations

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

    Yixin An, Lin Chen, Yong-Xiang Li, Chunhui Li, Yunsu Shi, Dengfeng Zhang, Yu Li & Tianyu Wang

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  1. Yixin An
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  2. Lin Chen
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  3. Yong-Xiang Li
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  4. Chunhui Li
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  5. Yunsu Shi
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  6. Dengfeng Zhang
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  7. Yu Li
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  8. Tianyu Wang
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Contributions

TW and YL designed research, YA, LC, YXL, CL, YS, and DZ performed research, YA, LC, and YXL analyzed data, and YA and TW wrote the manuscript.

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Correspondence to Yu Li or Tianyu Wang.

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All reference data that are not presented in this manuscript are available in the supplemental tables. All materials are available to the public upon request and under material transfer agreement.

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Communicated by Thomas Lubberstedt.

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An, Y., Chen, L., Li, YX. et al. Fine mapping qKRN5.04 provides a functional gene negatively regulating maize kernel row number. Theor Appl Genet 135, 1997–2007 (2022). https://doi.org/10.1007/s00122-022-04089-w

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