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A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles

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Abstract

Key message

The novel ZmR1CQ01 allele for maize anthocyanin synthesis was identified, and the biological function and regulatory molecular mechanisms of three ZmR1 alleles were unveiled.

Abstract

Anthocyanins in maize are valuable to human health. The R1 gene family is one of the important regulatory genes for the tissue-specific distribution of anthocyanins. R1 gene allelic variations are abundant and its biological function and regulatory molecular mechanisms are not fully understood. By exploiting genetic mapping and transgenic verification, we found that anthocyanin pigmentation in maize leaf midrib was controlled by ZmR1 on chromosome 10. Allelism test of maize zmr1 EMS mutants confirmed that anthocyanin pigmentation in leaf sheath was also controlled by ZmR1. ZmR1CQ01 was a novel ZmR1 allelic variation obtained from purple maize. Its overexpression caused the whole maize plant to turn purple. ZmR1B73 allele confers anthocyanin accumulation in near ground leaf sheath rather than in leaf midribs. The mRNA expression level of ZmR1B73 was low in leaf midribs, resulting in no anthocyanin accumulation. ZmR1B73 overexpression promoted anthocyanin accumulation in leaf midribs. Loss of exon 5 resulted in ZmR1ZN3 allele function destruction and no anthocyanin accumulation in leaf midrib and leaf sheath. DNA affinity purification sequencing revealed 1010 genes targeted by ZmR1CQ01, including the bz2 in anthocyanin synthesis pathway. RNA-seq analysis showed 55 genes targeted by ZmR1CQ01 changed the expression level significantly, and the expression of genes encoding key enzymes in flavonoid and phenylpropanoid biosynthesis pathways were significantly up-regulated. ZmR1 functional molecular marker was developed. These results revealed the effects of transcriptional regulation and sequence variation on ZmR1 function and identified the genes targeted by ZmR1CQ01 at the genome-wide level.

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Data availability

The BSR-seq raw data were deposited in the NCBI Sequence Read Archive (SRA) database (accession number: PRJNA657510). The RNA-seq raw data of leaf midribs of CQ01 and B73 were deposited in the NCBI SRA database (accession number: PRJNA657510). The RNA-seq raw data of leaves of wild-type and ZmR1CQ01-overexpressing transgenic Jing724 were deposited in the NCBI SRA database (accession number: PRJNA792089). The DAP-seq raw data were deposited in the NCBI SRA database [accession number: PRJNA792070 (SAMN26185953)]. The DNA and transcript sequences of ZmR1 in different maize accessions have been deposited in the NCBI GenBank database under the following accession numbers: ON256208 (ZmR1B73), ON256209 (ZmR1CQ01), ON256210 (ZmR1ZN3).

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Funding

This work was supported by the Special Program for Innovation of Beijing Academy of Agriculture and Forestry Sciences (KJCX201907-2), the Youth Research Fund of Beijing Academy of Agriculture and Forestry Sciences (QNJJ202028), the Construction of Collaborative Innovation Center of Beijing Academy of Agricultural and Forestry Sciences (Collaborative Innovation Center of Crop Phenomics, KJCX201917), the Major Scientific and Technological Achievements Cultivation Project of Beijing Academy of Agriculture and Forestry Sciences (MSTA202101), and the Post Expert of Crop Innovation Team of Beijing Industrial Technology System (PECI202201).

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  1. Meijie Luo, Baishan Lu and Yaxing Shi have equally contributed to this work.

Authors and Affiliations

  1. Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China

    Meijie Luo, Baishan Lu, Yaxing Shi, Yanxin Zhao, Zhiyuan Wei, Chunyuan Zhang, Yuandong Wang, Hui Liu, Yamin Shi, Jinxiao Yang, Wei Song, Yanli Fan, Li Xu, Ronghuan Wang & Jiuran Zhao

  2. Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China

    Xiaoduo Lu

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  1. Meijie Luo
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  2. Baishan Lu
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Contributions

LM, ZJ and WR designed the experiments. LM, LB, SY (Yaxing Shi), WZ, LH, SY (Yamin Shi) and YJ performed the experiments and collected data. LM, SW, ZY, LB, SY (Yaxing Shi), ZC, WY, LX, FY and XL analyzed the data. LM wrote the manuscript. All authors reviewed the manuscript.

Corresponding authors

Correspondence to Meijie Luo, Ronghuan Wang or Jiuran Zhao.

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Communicated by Thomas Lubberstedt.

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Luo, M., Lu, B., Shi, Y. et al. A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles. Theor Appl Genet 135, 3039–3055 (2022). https://doi.org/10.1007/s00122-022-04166-0

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