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Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai

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Abstract

Watermelon, Citrullus lanatus Thunb. Matsum. & Nakai is an important vegetable crop worldwide. Due to its narrow genetic base, detection and utilization of the genetic variations, cultivar identification and increasing genetic diversity are some important tasks for watermelon breeders. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for these purposes. In the present study, a core set of 23 highly informative SSR markers was developed for watermelon genetic diversity analysis. Based on whole genome sequencing of 17 watermelon inbred lines, we identified 3.9 million single nucleotide polymorphisms (SNPs) which were used to construct a SNP-based dendrogram for the 17 lines. Meanwhile, from the sequenced genome, 13,744 SSRs were developed, of which 704 were placed on a high-resolution watermelon linkage map. To develop the core set SSR markers, 78 of the 704 mapped SSRs were selected as the candidate markers. Using the SNP-based dendrogram as calibration, 23 SSR markers evenly distributed across the genome were identified as the core marker set for watermelon genetic diversity analysis. Each marker was able to detect 2–7 alleles with polymorphism information content values ranging from 0.45 to 0.82. The dendrograms of 17 watermelon lines based on SNPs, the base set of 78 SSRs and the core set of 23 SSRs were highly consistent. The utility of this core set SSRs was demonstrated in 100 commercial watermelon cultivars and elite lines, which could be placed into six clusters that were largely consistent with previous classification based on morphology and parentage data. This core set of SSR markers should be very useful for genotyping and genetic variation analysis in watermelon.

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Acknowledgments

This work was supported by funds from Beijing Municipal Science & Technology Commission, China (D08070500690803, D111100001311002, KJCX201101010, Z09090501040902 and 5100001); The Ministry of Science and Technology of China (2009BADB8B02, 2010DFB33740, 30972015, 31171980 and 2010AA10A107), and the Ministry of Agriculture of China (CARS-26).

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Authors and Affiliations

  1. National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China

    Haiying Zhang, Hui Wang, Shaogui Guo, Yi Ren, Guoyi Gong & Yong Xu

  2. USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53719, USA

    Yiqun Weng

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  1. Haiying Zhang
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  2. Hui Wang
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  7. Yong Xu
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Correspondence to Yong Xu.

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Zhang, H., Wang, H., Guo, S. et al. Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai. Euphytica 186, 329–342 (2012). https://doi.org/10.1007/s10681-011-0574-z

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