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A rapid approach for SSR development in Amorphophallus paeoniifolius using RAD-seq

Yong Gao, Si Yin, Chao Liu, Haibo Wang, Honglong Chu, Lizhou Tang

Published on: 20 August 2018

DOI: 10.6165/tai.2018.63.281

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2018 vol.63 no.3 pp.281-285

Abstract

Amorphophallus paeoniifolius is a tuber plant distributed in Southeastern Asia. Methods of rapid and cost-effective molecular marker development are needed for population genetic studies of this species. Simple sequence repeats (SSRs) have been regarded as one of the most informative and versatile DNA markers. However, the traditional SSR development process is laborious and time-consuming. In this study, we reported an approach for SSR development in A. paeoniifolius based on paired-end restriction-site associated DNA sequencing (RAD-seq). A total of 1,537,924 high-quality RAD contigs were assembled, with the average sequence length of 340 bp, and 50,800 SSRs were identified. Ninety SSR primers were randomly selected and validated with 31 individuals of A. paeoniifolius and 16 individuals of Amorphophallus kachinensis. Twenty-three SSR loci were polymorphic in A. paeoniifolius and 13 loci in A. kachinensis. The overall number of alleles per locus ranged from two to seven. Compared with traditional approaches, our study yielded thousands of microsatellite loci in a short time with affordable costs. RAD-seq could be a new method for the development of SSR markers from non-model species.

Keyword: Amorphophallus paeoniifolius, Polymorphism, RAD- seq, SSR development

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