Species Relationships of Lycoris Endemic to Korea Evaluated by RAPD and Snps of Nrdna-ITS Regions
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Hort. Environ. Biotechnol. 52(2):145-151. 2011. DOI 10.1007/s13580-011-0100-1 Research Report Species Relationships of Lycoris Endemic to Korea Evaluated by RAPD and SNPs of nrDNA-ITS Regions Yong Kweon Yoo1, Tao Yuan2, Jong Suk Lee3, Ae Kyung Lee4, Mark S. Roh5, Siro Kurita6, and Jeung Keun Suh4* 1Division of Life Science, Mokpo National University, Muan 534-729, Korea 2College of Landscape Architecture, Beijing Forestry University, Beijing, PR China 3Department of Horticulture, Chungnam National University, Daejeon 305-764, Korea 4School of Bio-Resources Science, Dankook University, Cheonan 330-714, Korea 5US Department of Agriculture, Agricultural Research Service, US National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD 20705, USA 6Laboratory of Phylogenetic Botany, Chiba University, Chiba 263-8522, Japan *Corresponding author: [email protected] Received May 17, 2010 / Accepted December 20, 2010 GKorean Society for Horticultural Science and Springer 2011 Abstract. This study was performed to investigate the species relationships and variation of Lycoris Herb. (Amaryllidaceae) species using random amplification of polymorphic DNA (RAPD) markers. Also, single nucleotide polymorphisms (SNPs) of internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2 regions in Lycoris sanguinea var. koreana were analyzed. All accessions formed 6 major clusters; cluster A with all L. sanguinea and L. chejuensis; cluster B with 3 accessions of L. flavescens; cluster C with 8 accessions of F. flavescens var. flavescens; cluster D with 10 accessions of L. uydoensis; cluster E with L. chinensis var. sinuolata and 4 accessions of L. uydoensis; and cluster F with all L. radiata. Five haplotypes were observed; L. sanguinea and L. chejuensis having the haplotype 1 with bases of CTTATATATAT; L. chinensis var. sinuolata and all L. flavescens. Lycoris incarnata and L. aurea, non-endemic to Korea had haplotype 2 and 5, respectively. Genetic variations in L. flavescens, L. chinensis var. sinuolata, and L. uydoensis are revealed based on the analysis of molecular variances (AMOVA) and haploid types analyzed by sequence analysis. It is suggested that L. chejuensis may result from hybridization involving L. sanguinea var. koreana due to a close affinity between L. sanguinea complex and L. chejuensis. Nomenclature for L. chejuensis and L. flavescens whether they should be described as a hybrid origin should be discussed in the future. Additional key words: genetic variance, hybrid origin, internal transcribed spacer region, molecular markers, random amplification of polymorphic DNA, single nucleotide polymorphisms =bhfcXiWh]cb Based on the morphological characters, L. chinensis var. sinuolata, L. sanguinea var. koreana, L. flavescens, L. The genus Lycoris consists of about 20 species distributed uydoensis, and L. radiata var. radiata were divided into two in warm temperate zones mainly in China, Korea, and Japan (Tae and Ko, 1995b) or four groups (Tae and Ko, 1996), (Hsu et al., 1994). Lycoris chejuensis K. H. Tae & S. C. Ko and based on RAPD analysis into two or three (Tae and Ko, (L. × chejuensis S. Kurita & P.S. Hsu), L. chinensis Traub. 1997a, 1997b) or one group (Tae et al., 2008), and these var. sinuolata K. Tae et S. Ko ex K. Tae et S. Ko, L. flaves- groupings differed greatly among studies. Lycoris flavescens cens M. Kim & S. Lee, L. sanguinea var. koreana (Nakai) and L. chejuensis, for example, belonged to the same group T. Koyama (L. koreana Nakai), and L. uydoensis M. Kim, in all studies, which is different from the previous study L. radiata (L’Hér.) Herb. var. radiata, and L. squamigera (Roh et al., 2002). Maxim. have been reported endemic to Korea (Kim, 2004; Difficulty to identify Lycoris species based on the mor- Kim and Lee, 1991; Kurita and Hsu, 1998; Lee and Kim, phology could be solved by molecular markers generated 1987; Tae and Ko, 1993, 1995a, 2003; Tae et al., 1987). from randomly amplified polymorphic DNA (RAPD) (Roh 146 Yong Kweon Yoo, Tao Yuan, Jong Suk Lee, Ae Kyung Lee, Mark S. Roh, Siro Kurita, and Jeung Keun Suh et al., 2002). Using isozyme, genetic variance was reported AUhYf]U`g UbX AYh\cXg only in L. flavescens (Lee et al., 2001). Describing the new species of hybrid was difficult due to a phenotypic inter- D`Ubh AUhYf]U`g mediacy (Gottlieb, 1972; Rieseberg, 1997), morphological Lycoris species from the south-western part of Korea characters can not be used effectively for germplasm with a were collected as indicated (Table 1 and Fig. 1). Over 7 very minor difference. The genetic variations were revealed years, they were verified by floral morphology (Fig. 5 and in Lycoris species using inter simple sequence repeat (ISSR) Roh et al., 2002). Total genomic DNA was isolated from 50 analysis (Shi et al., 2006) and RAPD (Roh et al., 2002). mg dried as described (Roh et al., 2006) and quantified by Single nucleotide polymorphisms (SNPs) (Brooks, 1999) of NanoDrop D-1000 Spectrophotometer (Thermo Fisher Scie- internal transcribed spacer regions and the 5.8S ribosomal ntific Waltham, MA, USA). DNA region (nrDNA-ITS region) have been useful for identification at inter-specific levels in Corylopsis (Roh et F5D8 UbX 8UhU 5bU`mg]g al., 2007) and Lycoris (Shi et al., 1998). Six RAPD primers (A9, A11, B13, B17, and B18; Operon Extensive studies on the relationships among Lycoris Technologies, Alameda, CA) were selected (Roh et al., species native to Korea and their genetic diversities using 2002) and polymerase chain reaction (PCR) was performed molecular markers had not been performed except L. flave- and the amplified products were separated on an agarose gel scens using the isozyme markers. Therefore, this study was and stained as described previously (Joung and Roh, 2004; carried out to investigate the relationships among species and Roh et al., 2007). Polymorphic RAPD bands ranging from the genetic diversities of Lycoris species collected from 400 bp to 1,500 bp were scored and the corresponding matrix diverse geographic locations using molecular markers gene- was used to construct a dendrogram using the interior-bran- rated by RAPD and SNPs of nrDNA-ITS regions. ching (IB) test applied to the neighbour-joining (NE) by 6 Fig. 1. Overall collection sites of Lycoris native to Korea. Sites (1; Is. Uy, 2; Te. Naeso, 3; Te. Sunwoon, 4; Te. Bagyang/Mt. Naejang, 5; Mt. Chuwol, 6; Mt. Boolgap, 7; Mt. Gyeryong, 8; Fig. 2. Dendrogram constructed by the neighbor-joining analyzed Sancheon, 9; Daecheon, 10; Anduck valley and Odeung, and by interior branching test generated from RAPD markers. 11; Eoreum. The collection sites for germplasm in China and Bootstrap values > 70% following 1,000 replications are indicated Japan are not indicated. next to the relevant nodes. Hort. Environ. Biotechnol. 52(2):145-151. 2011. 147 Molecular Evolutionary Genetics Analysis (MEGA, version radiata var. radiata (48, 56, 58, 60-62), L. uydoensis (A: 4.0; Tamura et al., 2007). 33-37; B: 63-71, 82), and L. chejuensis (A: 73-81; B: 72). Based on the RAPD dendrogram (Fig. 2), accessions Data was then analyzed for analysis of the molecular variance were grouped into six species and 7 sub-populations among (AMOVA) and Nei’s genetic distance was calculated by the species; L. chinensis var. sinuolata (A; 1-8, 15, 16; B: Nei’s unbiased measures of genetic distance (Nei, 1978) 9-14; C: 17, 30; D: 29), L. sanguinea var. koreana (18 - 28, using Arlequin ver. 3.1 (Excoffier et al., 2005). 31, 32), L. flavescens (A:49-55, 57, 59; B: 83-85) , L. Table 1. List of the Lycoris accessions with collection location and the source of germplasm. Accession numberz Scientific name Remarksy 1, 3, 5, 6, 7, 13, 14 L. chinensis var. sinuolata Mt. Boolgap, Yeongkwang, Cheonnam-Province, valley 1. 5 - light flower colorx 8, 9, 10, 11 L. chinensis var. sinuolata Mt. Boolgap, Yeongkwang, Cheonnam-Province, valley 2 15, 16 L. chinensis var. sinuolata Mt. Boolgap, Yeongkwang, Cheonnam-Province, valley 3 17 L. chinensis var. sinuolata Te. Bagyang, Changsung-Kun, Cheonnam-Province, temple garden 18 L. chinensis var. sinuolata Mt. Sunwoon, Kochang-Kun, Cheonbuk-Province. S. B. Park 19 L. chinensis var. sinuolata Mt. Sunwoon, Kochang-Kun, Cheonbuk-Province. hill 1 21, 22 L. sanguinea var. koreana Te. Bagyang, Changsung-Kun, Cheonnam-Province, valley 1 23, 24 L. sanguinea var. koreana Te. Bagyang, Changsung-Kun, Cheonnam-Province, valley 2 20, 25, 26, 27, 28 L. sanguinea var. koreana Te. Bagyang, Changsung-Kun, Cheonnam-Province, hill 2 (accession no. 20), valley 3 (accession no. 25 �G 28) 29, 30, 33, 34 L. sanguinea var.koreana Mt. Chuwol, Damyang-Kun, Cheonnam-Province, valley 1. 30 - light flower color 31, 32 L. chinensis var. sinuolata Mt. Chuwol, Damyang-Kun, Cheonnam-Province, valley 1. 31 -light flower color; 32 - light flower color 41 L. uydoensis Mt. Gyeryong, Gongju-Shi, Chungnam-Province, Mr. Choi’s resident, transplanted 42 L. uydoensis Chido-Ri, Is. Uy Cheonbuk-Province 43, 44, 45 L. uydoensis Yougol valley, Is. Uy Mr. Choi’s residence 46 L. sanguinea var. sanguinea Eikou Ooyabu and Mr. Oono, Japan 47 L. sanguinea var. kiusiana Eikou Ooyabu and Mr. Oono, Japan 48 L. chinensis var. chinensis Z. Zhao, Beijing Agricultural University, Beijing, China 49 L. incarnata Anduck valley, Joongmoon, Jeju, Korea 53 L. sanguinea var. koreana Jeju, Korea, white flower, collected as L. chejuensis 55 L. sanguinea var. sanguinea S. Kurita, Chiba University, Chiba, Japan 56 L. sanguinea var. kiusiana S. Kurita, Chiba University, Chiba, Japan. Collected from Nagasaki, Japan 57 L. longituba var. longituba S. Kurita, Chiba University, Chiba, Japan 58 L. × albiflora S. Kurita, Chiba University, Chiba, Japan. Collected from Kagoshima, Japan 59 L. radiata var. pumila S. Kurita, Chiba University, J Chiba, Japan. Collected from China 60 L. radiata var.