Research Article

Development of Polymorphic SSR Markers in Chinese Water Chestnut Based on RAD-seq  

Lianfang He1 , Weiqing Dong1 , Zuyang Qiu2 , Huiping Jiang1 , Lili Liu2 , Qi Chen3 , Shiyu Huang1
1 Institute of Biotechnology, Guanxi Zhuang Nationality Autonomous Region Academy of Agricultural Sciences, Nanning, 530007, China
2 Lipu Municipal Bureau of Agriculture and Rural Affairs, Lipu, 546600, China
3 Nanning New Technical Entrepreneur Center, Nanning, 530007, China
Author    Correspondence author
Molecular Plant Breeding, 2023, Vol. 14, No. 18   doi: 10.5376/mpb.2023.14.0018
Received: 11 Sep., 2023    Accepted: 18 Sep., 2023    Published: 22 Sep., 2023
© 2023 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

He F.L., Dong W.Q., Qiu Z.Y., Jiang H.P., Liu L.L., Chen Q., and Huang S.Y., 2023, Development of polymorphic SSR markers in Chinese water chestnut based on RAD-seq, Molecular Plant Breeding, 14(18): 1-10 (doi: 10.5376/mpb.2023.14.0018)


Chinese water chestnut (Eleocharis dulcis) is an important characteristic vegetable that grows in shallow waters. In order to develop simple sequence repeat (SSR) molecular markers for genetics research on Eleocharis dulcis, simplified genome sequencing by restriction-site associated DNA sequencing (RAD-seq), SSR search and primer design were performed. A total of 5039 SSR loci were detected, from which 4 137 pairs of primer were designed. Among them, the proportion of tri-nucleotides motifs was the highest (1 894), accounting for 45.89% of the total loci; followed by di-nucleotide with 1 406, accounting for 34.07%.. A total of 100 pairs of randomly selected primers were verified. 93% of the primers were successfully amplified. To assess the polymorphism of these primers, two varieties of Chinese water chestnuts were used to amplify the SSR marker using 83 pairs of primers. The 83 pairs of primers generated a total of 232 fragments. A total of 128 fragments were polymorphic. 60 pairs of primers out of 83 pairs generated at least one polymorphic band, and the ratio of polymorphic primers was 72.28%. These SSR markers developed from RAD tags were proved to be effective, which will provide a useful tool for genetic diversity research and molecular breeding in Chinese water chestnuts.

RAD sequencing; SSR; Chinese water chestnut; Molecular marker
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