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Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm

Nature Genetics volume 55, pages 496–506 (2023)Cite this article

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Abstract

In the context of climate change, drought is one of the most limiting factors that influence crop production. Maize, as a major crop, is highly vulnerable to water deficit, which causes significant yield loss. Thus, identification and utilization of drought-resistant germplasm are crucial for the genetic improvement of the trait. Here we report on a high-quality genome assembly of a prominent drought-resistant genotype, CIMBL55. Genomic and genetic variation analyses revealed that 65 favorable alleles of 108 previously identified drought-resistant candidate genes were found in CIMBL55, which may constitute the genetic basis for its excellent drought resistance. Notably, ZmRtn16, encoding a reticulon-like protein, was found to contribute to drought resistance by facilitating the vacuole H+-ATPase activity, which highlights the role of vacuole proton pumps in maize drought resistance. The assembled CIMBL55 genome provided a basis for genetic dissection and improvement of plant drought resistance, in support of global food security.

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Fig. 1: The drought-resistant phenotypes and genome assembly of CIMBL55.
Fig. 2: Gene synteny analysis in CIMBL55 and B73.
Fig. 3: Identification of genetic variants and their associations with drought resistance.
Fig. 4: SV-related alterations in DNA methylation.
Fig. 5: ZmRtn16 positively contributes to drought resistance in maize.
Fig. 6: ZmRtn16 interacts with ZmVHA-A and E3 and facilitates ZmVHA functions.

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Data availability

All genomic data mentioned in this paper are available at NCBI under the project of PRJNA765111, including the CIMBL55 genome sequence (JAJHUH000000000) and the raw sequencing data used for the assembly (PacBio, illumina, Bionano, Hi-C) and DNA methylation analysis (BS-seq) of CIMBL55, B73, Mo17, wild type (LH244) and zmdrd1 mutants (SRP338635). Source data are provided with this paper. Supplementary figures and source data are available at Figshare (https://doi.org/10.6084/m9.figshare.21709943)72.

Code availability

We deposited customized scripts in the following GitHub repository (https://github.com/ttian627/CIMBL55_genome_assembly) and Zenodo (https://doi.org/10.5281/zenodo.7523457)73.

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Acknowledgements

We thank the great technical support of generating and propagating the transgenic maize provided by the staff in the Center of Crop Functional Genomics and Molecular Breeding at CAU. This research was supported by the Beijing Outstanding Young Scientist Program (BJJWZYJH01201910019026), the National Key Research and Development Program of China (2021YFD1200703), the National Natural Science Foundation of China (31625022, 32171940) and Chinese Postdoctoral Science Foundation (2019M660874, 2021T140714).

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Author notes

  1. Huajian Gao

    Present address: School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China

  2. These authors contributed equally: Tian Tian, Shuhui Wang.

Authors and Affiliations

  1. State Key Laboratory of Plant Environmental Resilience, College of Biological Science, China Agricultural University, Beijing, China

    Tian Tian, Shuhui Wang, Shiping Yang, Zhirui Yang, Shengxue Liu, Yijie Wang, Huajian Gao, Xiaohong Yang, Caifu Jiang & Feng Qin

  2. Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China

    Shuaisong Zhang, Xiaohong Yang, Caifu Jiang & Feng Qin

  3. National Maize Improvement Center of China, China Agricultural University, Beijing, China

    Xiaohong Yang

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Contributions

F.Q. designed and supervised the study and revised the manuscript. T.T. and S.W. analyzed the data, performed the experiments and drafted the manuscript. S.Y. identified the genetic variants in 30 maize accessions. Z.Y. generated the zmdrd1-ko plants. Y.W. and H.G. provided phenotypes for CIMBL55, B73 and Mo17 in fields. S.L. assisted in the candidate gene association analysis. S.Z. assisted in all the greenhouse experiments. X.Y. and C.J. provided maize materials and important suggestions for the work. All the author(s) read and approved the final manuscript.

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Correspondence to Feng Qin.

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Statistical supporting data of Supplementary Figs. 1, 6, 8, 10, 11.

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Unprocessed western blots.

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Tian, T., Wang, S., Yang, S. et al. Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm. Nat Genet 55, 496–506 (2023). https://doi.org/10.1038/s41588-023-01297-y

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