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Development of simple sequence repeat markers in the halophytic turf grass Sporobolus virginicus and transferable genotyping across multiple grass genera/species/genotypes

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Abstract

Simple sequence repeat (SSR) markers are highly informative and widely used in genetic studies and plant breeding. Sporobolus virginicus is a halophytic turf grass that shows a high tolerance to salinity of up to 1.5 M NaCl. In the present study, we developed 148,411 SSR markers on 48,512 transcriptome contigs derived from RNA sequencing data. Of 33 randomly selected SSR markers, 23 (69.7%) produced clean amplification products, and an average of 1.25 alleles per marker was detected in S. virginicus genotypes. These markers were also examined by detecting polymorphisms across 19 different genera/species/genotypes in Poaceae, resulting in a high percentage (40%) of transferability. The sequencing of amplified products from these genera/species/genotypes revealed a high level of sequence similarity; however, substitutions, deletions, and insertions were detected not only in the objective SSRs but also in their flanking sequences. This is the first study on SSR marker development from S. virginicus. These SSR markers are useful for mapping the genes in and the breeding of S. virginicus and also for comparative genomics across genera/species/genotypes in Poaceae.

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Acknowledgements

This work was partially supported by the New Technology Development Foundation to Y. T. This work was partially supported by MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014-2018), and Research Funding for Computational Software Supporting Program from Meiji University to K. Y. Computations were partially performed on the NIG (National Institute of Genetics) SuperComputer Facilities hosted at NIG/ROIS (Research Organization of Information and Systems).

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  1. Naoki Yamamoto

    Present address: Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, 1301, Metro Manila, Philippines

Authors and Affiliations

  1. School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan

    Chisato Endo, Takamitsu Kurusu & Yuichi Tada

  2. Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan

    Naoki Yamamoto, Masaaki Kobayashi, Yukino Nakamura, Koji Yokoyama & Kentaro Yano

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  1. Chisato Endo
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Correspondence to Yuichi Tada.

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Chisato Endo and Naoki Yamamoto have contributed equally to this work.

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Supplementary material 1 (XLSX 11542 kb)

10681_2017_1846_MOESM2_ESM.pdf

Fig. S1 Gel images of simple sequence repeat (SSR) bands. Polyacrylamide gel electrophoresis (PAGE) image of polymerase chain reaction (PCR) products amplified by 20 SSR primer pairs from 19 genera/species/genotypes in Poaceae. M, DNA size marker, lanes 1–19, from left to right, S. virginicus, OKN1, 4, 5, 9, 10, and 11, NGT1, 2, and 3, perennial ryegrass (Lolium perenne), Italian ryegrass (L. multiflorum), Kentucky bluegrass (Poa pratensis), bent grass (Agrostis tenuis), Brachypodium distachyon, manila grass (Zoysia matrella), Japanese lawn grass (Z. japonica), corn (Z. mays), and rice (Oryza sativa).  Supplementary material 2 (PDF 321 kb)

10681_2017_1846_MOESM3_ESM.pdf

Fig. S2 Sequence similarities in polymerase chain reaction (PCR) products amplified by selected expressed sequence tag-simple sequence repeat (EST-SSR) primer pairs from 19 genera/species/genotypes in Poaceae. PCR products amplified by MSv302 (A) and MSv310 (B). Supplementary material 3 (PDF 93 kb)

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Endo, C., Yamamoto, N., Kobayashi, M. et al. Development of simple sequence repeat markers in the halophytic turf grass Sporobolus virginicus and transferable genotyping across multiple grass genera/species/genotypes. Euphytica 213, 56 (2017). https://doi.org/10.1007/s10681-017-1846-z

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