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Genes 2017, 8(10), 238; doi:10.3390/genes8100238

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

1
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea
2
Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Korea
3
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea
4
Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju 63240, Korea
5
TheragenEtex Bio Institute, Suwon 16229, Korea
6
Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea
7
Department of Biosystems Engineering, Chungbuk National University, Chungju 28644, Korea
8
Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 2 August 2017 / Revised: 17 September 2017 / Accepted: 18 September 2017 / Published: 21 September 2017
(This article belongs to the Section Plant Genetics and Genomics)
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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. View Full-Text
Keywords: Angelica gigas Nakai; next generation sequencing (NGS); simple sequence repeat (SSR) Angelica gigas Nakai; next generation sequencing (NGS); simple sequence repeat (SSR)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Gil, J.; Um, Y.; Kim, S.; Kim, O.T.; Koo, S.C.; Reddy, C.S.; Kim, S.-C.; Hong, C.P.; Park, S.-G.; Kim, H.B.; Lee, D.H.; Jeong, B.-H.; Chung, J.-W.; Lee, Y. Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing. Genes 2017, 8, 238.

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