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Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon

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Abstract

The rice low phytic acid (lpa) mutant Os-lpa-XS110-1(XS-lpa) has ~45 % reduction in seed phytic acid (PA) compared with the wild-type cultivar Xiushui 110. Previously, a single recessive gene mutation was shown to be responsible for the lpa phenotype and was mapped to a region of chromosome 3 near OsMIK (LOC_Os03g52760) and OsIPK1 (LOC_Os03g51610), two genes involved in PA biosynthesis. Here, we report the identification of a large insert in the intron of OsMIK in the XS-lpa mutant. Sequencing of fragments amplified through TAIL-PCRs revealed that the insert was a derivative of the LINE retrotransposon gene LOC_Os03g56910. Further analyses revealed the following characteristics of the insert and its impacts: (1) the inserted sequence of LOC_Os03g56910 was split at its third exon and rejoined inversely, with its 5′ and 3′ flanking sequences inward and the split third exon segments outward; (2) the LOC_Os03g56910 remained in its original locus in XS-lpa, and the insertion probably resulted from homologous recombination repair of a DNA double strand break; (3) while the OsMIK transcripts of XS-lpa and Xiushui 110 were identical, substantial reductions of the transcript abundance (~87 %) and the protein level (~60 %) were observed in XS-lpa, probably due to increased methylation in its promoter region. The above findings are discussed in the context of plant mutagenesis, epigenetics and lpa breeding.

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Acknowledgments

The research was financially supported by the Sino-Swiss Joint Research Project (2009 DFA32040 and IZLCZ3 123946I) and Natural Science Foundation of China through research contracts No. 30900887, and in part supported by Zhejiang Provincial Innovation Team of Nuclear Agricultural Science and Technology (2010R50033) and Natural Science Foundation (LY13C130002), the Special Fund for Agro-scientific Research in the Public Interest (201103007). We are grateful to Dr. Chao-Yang Cheng and the anonymous reviewers for their critical comments on early versions of the manuscript.

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Authors and Affiliations

  1. State Key Laboratory of Rice Biology and Key Laboratory of Nuclear-Agricultural Sciences of the Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China

    Hai-Jun Zhao, Hai-Rui Cui, Yuan-Yuan Tan, Jun-Jie Fu & Qing-Yao Shu

  2. Dongyang Maize Research Institute of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Zhejiang, China

    Xiu-Hong Xu

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

    Guo-Zhen Liu

  4. Department of Plant Molecular Biology, Biophore, University of Lausanne, 1015, Lausanne, Switzerland

    Yves Poirier

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  1. Hai-Jun Zhao
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Correspondence to Qing-Yao Shu.

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Communicated by T. Tai.

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Zhao, HJ., Cui, HR., Xu, XH. et al. Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon. Theor Appl Genet 126, 3009–3020 (2013). https://doi.org/10.1007/s00122-013-2189-3

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