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Identification of high-efficiency SSR markers for assessing watermelon genetic purity

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Abstract

Genomic simple sequence repeat (SSR) markers were used to fingerprint and determine genetic similarity (GS) of the watermelon breeding lines, as well as the purity of their hybrid derivatives. Cluster analysis and Jaccard’s distance coefficients using the unweighted pair group method with arithmetic mean (UPGMA) have classified these lines into three major groups. Notwithstanding, the genetic background of these lines is narrow as revealed by the restricted GS coefficients. Fifty-five sets of SSR markers were employed in this study. Fourteen of these markers were polymorphic between the breeding lines and were used for assessing hybrid purity. Cross-checking assay validated nine SSR markers as informative SSR markers for purity detection of these hybrids. To confirm the accuracy and efficiency of these markers, their derived PCR products were further sequenced, and ClSSR09643, ClSSR18153 and ClSSR01623 were selected as high-efficiency SSR markers. Interestingly, SSR markers ClSSR09643 and ClSSR18153 were broadly applied for purity detection of more than two different hybrids, while SSR marker ClSSR01623 behaved as a specific marker for purity detection in this study. Genetic purity of six commercial watermelon hybrids was definitely evaluated using these SSR markers. Genetic purity of all tested hybrids exceeded 96% while the field purity was above 98%. Genetic purity test was an emergency for identifying off-types and selfed female in a lot of hybrid seeds. Here, we elucidated the potential of nine SSR markers including three with higher breeding selection efficiency. We recommended them to seed company for purity improvement of watermelon commercial hybrid varieties.

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Acknowledgements

We are thankful to the Chinese leaders for establishing and promoting Talents projects in Jiangsu Province and Suqian city. This work is supported by the funding from two talent projects ‘2017 Jiangsu province Entrepreneurial innovation talent program’ and ‘2017 Suqian city Entrepreneurial innovation leading talent program’.

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    Authors and Affiliations

    1. Jiangsu Green Port Modern Agriculture Development Company, NanCai Township Road No. 1, Suqian city, 223800, People’s Republic of China

      Xia Lu, Yawo Mawunyo Nevame Adedze, Zhijun Deng, Luhua Teng, Xuelai Zhang, Gang Sun, Longting Si & Wenhu Li

    2. Catholic University Institute of Buea, P.O. Box 563, Buea, Cameroon

      Gilbert Nchongboh Chofong

    3. Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350000, People’s Republic of China

      Mamadou Gandeka

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    1. Xia Lu
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    Correspondence to Longting Si or Wenhu Li.

    Additional information

    Corresponding editor: H. A. Ranganath

    Xia Lu and Yawo Mawunyo Nevame Adedze contributed equally to this work. AYMN, SLT and LWH designed the project. LX, AYMN, DZJ, TLH and ZXL conducted the field experiments. LX and AYMN performed the laboratory tests. AYMN and LX analysed the data. AYMN drafted the manuscript. AYMN and LX worked on figures and tables presentation and rearrangement. CGN and GM proof read the manuscript and conducted English editing. CGN performed a critical revision of the article. All authors read and approved the final manuscript.

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    Lu, X., Adedze, Y.M.N., Chofong, G.N. et al. Identification of high-efficiency SSR markers for assessing watermelon genetic purity. J Genet 97, 1295–1306 (2018). https://doi.org/10.1007/s12041-018-1027-4

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