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A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica

Abstract

Key message

we identified a functional chromogen gene C from wild rice, providing a new insight of anthocyanin biosynthesis pathway in indica and japonica.

Abstract

Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C, OrC1, from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica. Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica. Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI, OsF3H and OsANS and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1, provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice.

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Acknowledgements

We especially thank Dr. Peng Zhang (The University of Sydney, Australia) and Dr. Hao Chen (Huazhong Agricultural University, China) for critical reading of the manuscript. This work was supported by the National Key R&D Program of China (2016YFD0100101) and the National Natural Science Foundation of China (31471471).

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Authors

Contributions

WH Qiao, JH Lan and QW Yang conceived and designed the experiments. WH Qiao and YY Wang performed the experiments and wrote the paper. R Xu, ZY Yang, JR Wang and JF Huang analyzed the data. Y Sun, L Su and LZ Zhang performed fine mapping. SJ Liu, YL Tian, LM Chen and X Liu contributed to field investigation. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Weihua Qiao, Jinhao Lan or Qingwen Yang.

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Communicated by Jessica Rutkoski.

Supplementary Information

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Supplementary file 1 (DOCX 38 kb)

Supplementary file 2 (TIF 3965 kb)

Supplementary file 3 (DOCX 38 kb)

Supplementary file 4 (TIF 12681 kb)

Supplementary file 5 (DOC 38 kb)

Supplementary file 6 (DOCX 16 kb)

Supplementary file 7 (TIF 2336 kb)

Supplementary file 8 (DOC 18 kb)

122_2021_3787_MOESM9_ESM.tif

Genotype analysis of promoter region of C1. (a) Sequence polymorphism of different haplotypes of C1 promoter from 180 accessions. No. of Acc.: number of accessions, I: O. sativa. indica, J: O. sativa. japonica, R: O. rufipongon, N: O. nivara. (b) Haplotype network of C1 promoter.

Supplementary file 8 (TIF 8402 kb)

122_2021_3787_MOESM10_ESM.tif

Genotype analysis of promoter region of C1. (a) Sequence polymorphism of different haplotypes of C1 promoter from 180 accessions. No. of Acc.: number of accessions, I: O. sativa. indica, J: O. sativa. japonica, R: O. rufipongon, N: O. nivara. (b) Haplotype network of C1 promoter.

Supplementary file 8 (TIF 2267 kb)

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Qiao, W., Wang, Y., Xu, R. et al. A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica. Theor Appl Genet 134, 1531–1543 (2021). https://doi.org/10.1007/s00122-021-03787-1

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