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| Development of Polymorphic SSR Markers in Rhododendron henanense subsp. lingbaoense Based on RAD-seq |
| ZHOU Xiao-Jun1, *, WANG Hai-Liang2, LI Fang-Ling1, ZHANG Kai2, WANG Yu-Na1, YA Hui-Yuan1 |
1 Life Science College, Luoyang Normal University, Luoyang 471934, China;
2 Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia 472500, China |
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Abstract Rhododendron henanense subsp. lingbaoense belongs to Ericaceae, Rhododendron, and is a rare and endemic species in Henan Province. Because of its narrow distribution and poor natural regeneration, the population size has been shrinking, and systematic research and protection has become increasingly urgent. In order to develop SSR (simple sequence repeat) molecular markers for conservation genetics research on R. henanense subsp. lingbaoense, simplified genome sequencing by restriction-site associated DNA sequencing (RAD-seq), SSR search and primer design were performed. A total of 6 107 SSR loci were detected in 120 970 assembled sequences. Among them, the proportion of di-nucleotide motifs was the highest, accounting for 63.01% of the total loci; followed by tri-nucleotides with 765, accounting for 12.53%. 3 843 pairs of primers were successfully designed for these SSR loci using software Primer Premier 3.0. A total of 100 pairs of primers were randomly selected and verified with 20 individuals of R. henanense subsp. lingbaoense, and 87 were able to amplify the target bands. Fifteen pairs of polymorphic SSR loci were further analyzed using Cervus 3.0, and the polymorphic information content ranged from 0.463 to 0.893 with an average of 0.649. Among them, there were 13 highly polymorphic loci, no deviation from Hardy-Weinberg equilibrium was detected in the 15 loci. Above results could provide data support for the study of SSR markers in R. henanense subsp. lingbaoense and Rhododendron.
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Received: 31 May 2018
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Corresponding Authors:
* , lynubio@126.com
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