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High-throughput simple sequence repeat (SSR) markers development for the kelp grouper (<i>Epinephelus bruneus</i>) and cross-species amplifications for Epinephelinae species

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Advances in Bioscience and Biotechnology 2014年第2期5卷 117-130页

作者： Satoshi Kubota Qi Liu Kanonkporn Kessuwan Nobuaki Okamoto Takashi Sakamoto Yoji Nakamura Yuya Shigenobu Takuma Sugaya Motohiko Sano Susumu Uji kazuharu nomura Akiyuki Ozaki Faculty of Marine Science Tokyo University of Ma-rine Science and Technology Tokyo Japan Faculty of Marine Science Tokyo University of Ma-rine Science and Technology Tokyo Japan National Research Institute of Fisheries Science Fi-sheries Research Agency Kanagawa Japan National Research Institute of Aquaculture Fisheries Research Agency Mie Japan National Research Institute of Fisheries Science Fi-sheries Research Agency Kanagawa Japan

The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).

关键词： Kelp Grouper Epinephelus bruneus Repeat Motif Simple Sequence Repeat (SSR) 454 Pyrosequencing Cross-Species Amplification

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