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Genes (Basel). 2017 Sep 21;8(10). pii: E238. doi: 10.3390/genes8100238.

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing.

Author information

1
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea. kjs8789@chungbuk.ac.kr.
2
Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Korea. urspower@korea.kr.
3
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea. sese7510@nate.com.
4
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea. kimot@korea.kr.
5
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea. ksch992@korea.kr.
6
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea. suumani@gmail.com.
7
Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju 63240, Korea. kimsec@korea.kr.
8
TheragenEtex Bio Institute, Suwon 16229, Korea. changpyo.hong@theragenetex.com.
9
TheragenEtex Bio Institute, Suwon 16229, Korea. singi.park@theragenetex.com.
10
Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea. hobang@ibiomedic.co.kr.
11
Department of Biosystems Engineering, Chungbuk National University, Chungju 28644, Korea. leedh@chungbuk.ac.kr.
12
Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea. bhjeong@jbnu.ac.kr.
13
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea. jwchung73@chungbuk.ac.kr.
14
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea. leeyi22@hanmail.net.

Abstract

Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

KEYWORDS:

Angelica gigas Nakai; next generation sequencing (NGS); simple sequence repeat (SSR)

Conflict of interest statement

The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; nor in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

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