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Functional Domain Marker (FDM): an In Silico Demonstration in Solanaceae Using Simple Sequence Repeats (SSRs)

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Abstract

A simple sequence repeat–functional domain marker (SSR-FDM) relies on development of molecular markers for putative functional domains using simple sequence repeats and in silico annotated information of those sequences using biological databases. A total of 148,921 tomato ESTs and 115,598 pepper ESTs were analyzed, resulting in the identification of 439 tomato SSR-FDMs and 489 pepper SSR-FDMs. Among them, 54 pepper SSR-FDMs were tested on pepper. Several genomic databases were used for the in silico annotation of the SSR-FDM sequences that revealed a wide range of candidate genes. This study demonstrates that SSR-FDMs provide information regarding transcribed genetic markers and putative function as a genomic resource database for Solanaceae. This system could be applied to the development of a functional marker database for any crop species.

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Acknowledgments

We would like to thank all members of the Plant Genomics Center in the Korea Research Institute of Bioscience and Biotechnology who assisted in this study. We thank Suk-Yoon Kwon, Jae Bok Yoon, and Jung-Heon Han for providing the pepper DNAs and F2 lines of pepper mapping population CM334 × Chilsungcho and map data. We are grateful to David J. Plunkett at Syngenta Seeds Inc. for his constructive and pertinent suggestions on the manuscript. This research was supported by grants from the Center for Plant Molecular Genetics and Breeding Research, the Crop Functional Genomics Center, and the Plant Diversity Resource Center; one of the 21st Century Frontier Research Programs of Ministry of Education, Science and Technology.

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Authors and Affiliations

  1. Syngenta Seeds Inc., 317 330th Street, Stanton Minnesota, 55018, USA

    Ju-Kyung Yu

  2. Bioinformatics Research Center, Korea Research Institute of Biotechnology and Bioscience, 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, South Korea

    Hyojung Paik, Jae Pil Choi, Jun-Kyoung Choe & Cheol-Goo Hur

  3. Pepper and Breeding Institute Business Incubator, College of Agriculture and Life Science, Seoul National University, Suwon, 441-853, South Korea

    Jung-Heon Han

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  1. Ju-Kyung Yu
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  2. Hyojung Paik
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  3. Jae Pil Choi
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  4. Jung-Heon Han
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  5. Jun-Kyoung Choe
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Corresponding authors

Correspondence to Ju-Kyung Yu or Cheol-Goo Hur.

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Ju-Kyung Yu and Cheol-Goo Hur equally contributed to the correspondense.

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Yu, JK., Paik, H., Choi, J.P. et al. Functional Domain Marker (FDM): an In Silico Demonstration in Solanaceae Using Simple Sequence Repeats (SSRs). Plant Mol Biol Rep 28, 352–356 (2010). https://doi.org/10.1007/s11105-009-0154-8

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  • DOI: https://doi.org/10.1007/s11105-009-0154-8

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