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Effective DNA extraction method for fragment analysis using capillary sequencer of the kelp, Saccharina

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Abstract

Deoxyribonucleic acid (DNA) fragment analysis can become an effective tool to study genetic differences between species and individuals on saccharinan kelp from which the little genetic diversity has been reported. Here, extraction methods of DNA suitable for use in analysis with a capillary sequencer is examined on Saccharina japonica var. diabolica which contains abundant polysaccharide. When amplified fragment length polymorphism was performed using genomic DNA extracted by seven different methods: (1) commercial kit, (2) original cetyl trimethylammonium bromide (CTAB) method, (3)–(5) three types of modified CTAB method, (6) modified sodium dodecyl sulfate (SDS) method, (7) combination of CTAB method and SDS method, a high reproducible peak that was suitable for analysis was noticeable in the electropherogram in the experiment with the last combination method (7). It is considered that the pretreatment washing of polysaccharide and the subsequent purification for protein and ribonucleic acid in SDS method and for polysaccharide in CTAB method are effective to obtain the high-purity DNA.

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Acknowledgment

The authors thank Prof S. J. Pang and Dr T. F. Shan (Institute of Oceanology, Chinese Academy of Sciences) for kind advice and useful comments. The authors also thank Mr S. Hamano and Mr H. Katsuragawa (Hokkaido University) for collecting materials. This research was supported by a research project, grant-in-aid for Scientific Research (21241055) from the Ministry of Education, Science, Sports and Culture, Japan and by the Environment Research and Technology Development Fund (S9) by the Ministry of the Environment, Japan.

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Authors and Affiliations

  1. Graduate School of Environmental Science, Hokkaido University, Hokkaido, 060-0810, Japan

    Takashi Maeda

  2. Wakkanai Fisheries Experimental Station, Hokkaido Research Organization, Hokkaido, 097-0001, Japan

    Tadashi Kawai

  3. Akkeshi Marine Station, Hokkaido University, Hokkaido, 088-1113, Japan

    Masahiro Nakaoka

  4. Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, 060-0809, Japan

    Norishige Yotsukura

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  1. Takashi Maeda
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  2. Tadashi Kawai
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  3. Masahiro Nakaoka
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  4. Norishige Yotsukura
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Correspondence to Norishige Yotsukura.

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Maeda, T., Kawai, T., Nakaoka, M. et al. Effective DNA extraction method for fragment analysis using capillary sequencer of the kelp, Saccharina . J Appl Phycol 25, 337–347 (2013). https://doi.org/10.1007/s10811-012-9868-3

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  • DOI: https://doi.org/10.1007/s10811-012-9868-3

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