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Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in radish (Raphanus sativus L.) containing DCGMS cytoplasm

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Abstract

A novel cytoplasmic male sterility (CMS) conferred by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its restorer-of-fertility gene (Rfd1) was previously reported in radish (Raphanus sativus L.). Its inheritance of fertility restoration and profiles of mitochondrial DNA (mtDNA)-based molecular markers were reported to be different from those of Ogura CMS, the first reported CMS in radish. The complete mitochondrial genome sequence (239,186 bp; GenBank accession No. KC193578) of DCGMS mitotype is reported in this study. Thirty-four protein-coding genes and three ribosomal RNA genes were identified. Comparative analysis of a mitochondrial genome sequence of DCGMS and previously reported complete sequences of normal and Ogura CMS mitotypes revealed various recombined structures of seventeen syntenic sequence blocks. Short-repeat sequences were identified in almost all junctions between syntenic sequence blocks. Phylogenetic analysis of three radish mitotypes showed that DCGMS was more closely related to the normal mitotype than to the Ogura mitotype. A single 1,551-bp unique region was identified in DCGMS mtDNA sequences and a novel chimeric gene, designated orf463, consisting of 128-bp partial sequences of cox1 gene and 1,261-bp unidentified sequences were found in the unique region. No other genes with a chimeric structure, a major feature of most characterized CMS-associated genes in other plant species, were found in rearranged junctions of syntenic sequence blocks. Like other known CMS-associated mitochondrial genes, the predicted gene product of orf463 contained 12 transmembrane domains. Thus, this gene product might be integrated into the mitochondrial membrane. In total, the results indicate that orf463 is likely to be a casual factor for CMS induction in radish containing the DCGMS cytoplasm.

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Acknowledgments

This work was supported by a Grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ007992), Rural Development Administration and a grant (108169-05-01-SB010) from the Technology Development Program for Agriculture and Forestry, Ministry of Agriculture and Forestry, Republic of Korea.

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  1. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Jee Young Park, Jonghoon Lee & Tae-Jin Yang

  2. Dongbu Vegetable Breeding Institute, Dongbu Farm Hannong Co. Ltd., Ansung, 305-708, Republic of Korea

    Young-Pyo Lee

  3. National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Beom-Soon Choi

  4. Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea

    Sunggil Kim

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  1. Jee Young Park
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Correspondence to Sunggil Kim or Tae-Jin Yang.

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Communicated by M. Xu.

J. Y. Park and Y. -P. Lee equally contributed to this work.

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122_2013_2090_MOESM1_ESM.tif

Supplementary Fig. 1. The position of sequenced BAC clones and sequencing depths. The colored lines above the gray-colored circle indicate the BAC clones selected for sequencing. Sequencing depths are shown inside the gray-colored circle. The numbers outside the circles indicate nucleotide position of the complete mitochondrial genome sequence deposited to GenBank under accession number of KC193578 (TIFF 304 kb)

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Park, J.Y., Lee, YP., Lee, J. et al. Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in radish (Raphanus sativus L.) containing DCGMS cytoplasm. Theor Appl Genet 126, 1763–1774 (2013). https://doi.org/10.1007/s00122-013-2090-0

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