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Development and validation of genomic simple sequence repeat markers in Erianthus arundinaceus

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Abstract

Erianthus arundinaceus, a member of the Saccharum complex, is of interest as a potential resource for sugarcane improvement and as a bioenergy crop. Genetic analyses of germplasm collections of E. arundinaceus are being used increasingly. To expand the genomic resources in E. arundinaceus, we aimed at developing simple sequence repeat markers. Using pyrosequencing on the 454 GS FLX system, we sequenced genomic DNA from “JW630” collected in Japan. A total of 1682 candidate loci were used to design the primers, and 1234 primer pairs amplified fragments of the expected size in the primer screening with three wild E. arundinaceus accessions (JW630, “JW4,” and “IJ76-349”). The efficiency of genotyping was validated with a subset of 174 primer pairs and 8 E. arundinaceus accessions. Of these primer pairs, 171 amplified fragments in all accessions tested and 162 detected polymorphic loci. The average values of genetic parameters were estimated as 0.30 (range, 0.09–0.49) for polymorphic information content, 1.65 (0.00–5.87) for marker index, and 2.78 (0.00–8.75) for resolving power. Using these parameters, we selected 61 primer pairs with large discriminatory power for the analyzed loci. Of the 174 primer pairs, 45 (25.9%) were also applicable to Saccharum and 33 (19.0%) to Miscanthus species. These markers would provide a valuable tool for estimating genetic diversity and constructing linkage maps in E. arundinaceus, which would be useful for genetic study and breeding.

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Acknowledgements

We thank the staff of the Forage Plant Breeding and Genetics group at NARO-ILGS who provided technical assistance with the experiments and the staff of the sugarcane improvement project team at JIRCAS-TARF for their great help and their contribution to the data analysis. This study was supported by research grants from the National Agriculture and Food Research Organization (no. 220a0) and the Japan International Research Center for Agricultural Sciences (no. 001750).

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Authors and Affiliations

  1. Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS-TARF), Ishigaki, Okinawa, 907-0002, Japan

    Shin-ichi Tsuruta & Yoshifumi Terajima

  2. Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO-ILGS), Nasushiobara, Tochigi, 329-2793, Japan

    Masumi Ebina, Makoto Kobayashi & Wataru Takahashi

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  1. Shin-ichi Tsuruta
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  2. Masumi Ebina
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  3. Makoto Kobayashi
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  4. Wataru Takahashi
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  5. Yoshifumi Terajima
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Correspondence to Shin-ichi Tsuruta.

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Fig. S1

Percentage of primer pairs that amplified a certain number of fragments (1–6) in each E. arundinaceus accession. (GIF 429 kb)

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Tsuruta, Si., Ebina, M., Kobayashi, M. et al. Development and validation of genomic simple sequence repeat markers in Erianthus arundinaceus . Mol Breeding 37, 71 (2017). https://doi.org/10.1007/s11032-017-0675-z

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