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A down-regulated epi-allele of the genomes uncoupled 4 gene generates a xantha marker trait in rice

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Abstract

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A γ-ray-induced xantha trait is epigenetically controlled by the genomes uncoupled 4 gene with enhanced promoter segment methylation and down-regulated expression in rice.

Abstract

For easy testing and to increase varietal purity, a xantha mutation (xnt), which turns plants yellow and makes them visually distinguishable from normal green rice, has been generated and bred into male sterile lines for hybrid rice production. The xnt locus was previously fine mapped to a ~100-kb interval on chromosome 11, but its identity was unknown. In this study, xnt was further narrowed down to a 57-kb fragment carrying eight opening reading frames (ORFs). All eight ORFs had identical genomic sequences and all but ORF2 (g enomes uncoupled 4, OsGUN4) had similar transcript abundance in the xantha mutant Huangyu B (HYB) and its parental variety Longtefu B (LTB). The expression of OsGUN4, however, was significantly reduced in HYB compared with LTB in terms of both transcript abundance (0.2 % that of LTB) and expressed protein level (barely detectable in HYB but greater than the heat shock protein reference in LTB). Therefore, OsGUN4 was identified as the candidate gene underlying the xantha trait. The function of OsGUN4 in the xantha phenotype was confirmed by identification and characterization of new allelic OsGUN4 mutations. Comparative bisulfite genomic sequencing of OsGUN4 revealed increased methylation in a promoter region in the mutant, and the correlation between increased methylation and the xantha phenotype was further verified by demethylation treatment. In summary, we have identified an epi-allele of OsGUN4 as the causal gene of the xantha marker trait and revealed that enhanced methylation in its promoter down-regulated its expression in rice.

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Acknowledgments

The research was supported by a Grant (No: 11275171) from the National Natural Science Foundation of China and in part by the Special Funds for Agro-scientific Research in the Public Interest (201103007), and the Zhejiang 8812 Program. We are grateful to Dr. David W. Bollivar of Illinois Wesleyan University, USA, for suggesting OsGUN4 as the candidate gene of XNT based on our fine mapping paper.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The authors declare that the experiments comply with the current laws of China.

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Authors and Affiliations

  1. National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, 310029, Hangzhou, China

    Rui-Qing Li, Jian-Zhong Huang, Hai-Jun Zhao & Qing-Yao Shu

  2. Jiaxing Academy of Agricultural Sciences, 314016, Jiaxing, Zhejiang, China

    Hao-Wei Fu & You-Fa Li

  3. College of Life Science, Hebei Agricultural University, 071001, Baoding, China

    Guo-Zhen Liu

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  1. Rui-Qing Li
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Correspondence to Qing-Yao Shu.

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Communicated by Thomas H.Tai.

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Li, RQ., Huang, JZ., Zhao, HJ. et al. A down-regulated epi-allele of the genomes uncoupled 4 gene generates a xantha marker trait in rice. Theor Appl Genet 127, 2491–2501 (2014). https://doi.org/10.1007/s00122-014-2393-9

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  • DOI: https://doi.org/10.1007/s00122-014-2393-9

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