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Identification of an Isogenic Semidwarf Rice Cultivar Carrying the Green Revolution sd1 Gene by Multiplex Codominant ASP-PCR and SSR Markers

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Abstract

The rice cultivar Hikarishinseiki, a semidwarf isogenotype of Koshihikari carrying the Green Revolution sd1 gene, is increasingly grown in both Japan and the United States. Here, we report DNA diagnosis for Hikarishinseiki targeting its Jukkoku-type sd1 locus, which codes for a defective gibberellin 20-oxidase, with a 1 bp substitution in exon 1 (Jukkoku-type GA20ox-2 mutant allele: Jukkoku_GA20ox-2). An allele-specific primer (ASP)-polymerase chain reaction (PCR) with primers SD1F3 and SD1JR gave a PCR product specific to Jukkoku_GA20ox-2. In addition, ASP-PCR with primers SD1F3 and SD1NRM (which contains a mismatch at the third nucleotide from the 3′-terminus of SD1NR) gave a PCR product specific to non-Jukkoku_GA20ox-2. Multiplex ASP-PCR using SD1F3, VIC dye-labeled SD1JR, and FAM dye-labeled SD1NRM enabled simultaneous codominant detection of Jukkoku_GA20ox-2 and non-Jukkoku_GA20ox-2 among 188 cultivars. Also, Hikarishinseiki is identifiable by RM253 polymorphism from 11 cultivars carrying Jukkoku_GA20ox-2. Taken together, our results establish a methodology for distinguishing Hikarishinseiki.

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Acknowledgments

The authors would like to express our gratitude to Japan Science and Technology Agency (JST) for the Grant-in-Aid for Adaptable and Seamless Technology Transfer Program through Target-driven R&D (nos. 08150094 and 08001167) that supported this work.

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  1. Motonori Tomita

    Present address: Research Institute of Green Science and Technology, Shizuoka University, 836, Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

Authors and Affiliations

  1. Food Testing and Hygiene Inspection Department, Mitsubishi Chemical Medience Corporation, 25-11, Azusawa 4-chome, Itabashi-ku, Tokyo, 174-0051, Japan

    Yoshiki Naito

  2. Molecular Genetics Laboratory, Faculty of Agriculture, Tottori University, 101, Minami 4-chome, Koyama-cho, Tottori, 680-8553, Japan

    Motonori Tomita

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  1. Yoshiki Naito
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Correspondence to Motonori Tomita.

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Naito, Y., Tomita, M. Identification of an Isogenic Semidwarf Rice Cultivar Carrying the Green Revolution sd1 Gene by Multiplex Codominant ASP-PCR and SSR Markers. Biochem Genet 51, 530–542 (2013). https://doi.org/10.1007/s10528-013-9584-y

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