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A study on relative abundance, composition and length variation of microsatellites in 18 underutilized crop species

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Abstract

In the present work, genomic DNA libraries for 18 underutilized crop species (including 11 dicot and 7 monocot species) were enriched for several di- and tri- nucleotide microsatellites by using an optimized procedure. About 500–960 clones from each library were sequenced and all the sequences were characterized to have a comparative look on relative abundance, composition and length variations of perfect microsatellites among different crops. Sequence analysis revealed contrasting differences in the abundance of di- and tri-nucleotide microsatellites with the predominance of tri-nucleotide microsatellites in 11 crops and that of di-nucleotides in other 8 crops. Among di-nucleotide microsatellites, AG/GA class was the most abundant in all the crops except for four crops in which AC/CA class was predominant. Among tri-nucleotide repeats, AGC/GCA/CAG class was the most abundant in eight crops followed by AGG/GGA/GAG class in four crops, whereas in the remaining six crops, the most abundant class was highly variable. The longest di- and tri-nucleotide repeats were observed in Chinese cabbage and mungbean with the average lengths of 70 and 57 base pairs, respectively. These observations revealed species-specific in the distributions of microsatellite repeat motifs. The present study provides highly valuable information that can be useful in targeted development of specific microsatellites markers for genetic analysis of these underutilized crops.

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Acknowledgement

This study was supported by the faculty research fund of Konkuk University, Seoul, Republic of Korea in 2008.

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Authors and Affiliations

  1. Genetic Resources Division, National Institute of Agricultural Biotechnology, RDA, 225, Seodun-dong, Suwon, Kyunggi, 441-707, Republic of Korea

    Jae-Woong Yu, Anupam Dixit, Kyung-Ho Ma & Jong-Wook Chung

  2. Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-Gu, Seoul, 143-701, Republic of Korea

    Jae-Woong Yu, Jong-Wook Chung & Yong-Jin Park

  3. Rice DNA & Quality Testing Laboratory, Basmati Export Development Foundation, SVBP University of Agriculture & Technology, Meerut, 250110, Uttar Pradesh, India

    Anupam Dixit

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  1. Jae-Woong Yu
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  2. Anupam Dixit
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  3. Kyung-Ho Ma
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  4. Jong-Wook Chung
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  5. Yong-Jin Park
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Correspondence to Yong-Jin Park.

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Yu, JW., Dixit, A., Ma, KH. et al. A study on relative abundance, composition and length variation of microsatellites in 18 underutilized crop species. Genet Resour Crop Evol 56, 237–246 (2009). https://doi.org/10.1007/s10722-008-9359-1

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