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Construction of Phylogenetic Tree for <Emphasis Type= J. Plant Res. 110: 187-193, 1997 Journal of Plant Research (~) by The Botanical Society of Japan 1997 Construction of Phylogenetic Tree for Nicotiana Species Based on RAPD Markers Yung-Luen Yu and Tsai-Yun Lin Department of Life Science, National Tsing Hua Universiry, No. 101, Sec. 2, Kuang Fu Road, Hsinchu, 30043, Taiwan, R.O.C. To apply random amplified polymorphlc DNA for ana- sequence. The polymorphisms observed may result from lysis of phylogenetic relationshipe, we used 34 synthetic nucleotide substitutions, insertions, or deletions. The oligonucleotides as primers to examine interspecific and major advantages of this analysis are that (1) the informa- intraspeciflc variations among 18 genotypes, nine species tion of DNA sequence is not required, (2) the protocol is of Nicotlana. The nine species used in this study belong relatively easy to perform, (3) only a small quantity (ng) of to sections Tomentosae and Alatae. In addition, we DNA is needed, (4) a large number of samples can be attempted to clarity the taxonomic position of N. sylves- processed simultaneously in a short period of time, (5) tris. A total of 354 distinct DNA fragments were the technique can be applied to a broad range of species obtained by polymerase chain reaction. Pair-wise com- (Welsh and McClelland 1990, Martin et al. 1991, Reiter et parisons of unique and shared amplification products al. 1992, Torres et al. 1993, Chaparro et al. 1994, Yu and were used to generate Jaccard's similarity coefficients Nguyen 1994), and (6) no radioactive reagent is utilized in and Nei and U's similarity coefficients with the computer the assay. software of numerical taxonomy and multivariate ana- To apply RAPD for analysis of phylogenetic relation- lysis system. On the basis of the dendrogram construct- ships, nine species from two sections of Nicotiana ed with the similarity coefficients, the 18 Nlcotlana (Tomentosae and Alatae) were examined. Nicotiana genotypes were divided Into two clusters. The classifi- sylvestris is considered a member of Alatae (Goodspeed cation analyzed by RAPD markers is in accordance with 1954). However, Kostoff (1943) observed that F1 hybrids the classification of Goodspeed that N. sylvestris is a of N. sylvestris and any other species in section Alatae member of section Alatae. had lower chromosome associations than F1 hybrids of N. sylvestris and any member of section Tomentosae had. Key words: Nicotlana m Phylogenetic tree m RAPD Hence, he regarded N. sylvestris as a member of section Tomentosae. In this study, we performed RAPD assay to analyze the phylogenetic relationships among 18 The natural distribution of the genus Nicotiana, family genotypes of Nicotiana and determine the taxonomic Solanaceae, is limited to America (75%), Australia and a position of N. sylvestris. few islands of the South Pacific (25%). The estimated 60 species of Nicotiana are classified into 14 sections based Materials and Methods upon distribution and morphological and cytogenetic characteristics (Goodspeed 1954). For example, inflores- Table1 lists the 18 genotypes of nine species of cence expression in section Tomentosae is in thyrse Nicotiana used in this experiment which were provided by panicles except in N. glutinosa. The inflorescence of the US Department of Agriculture (USDA) and the Taiwan section Alatae shows monochasia, often extending di- Tobacco Research Institute (TTRI). Plants were kept in a chasial forks. The traditional taxonomy is established growth chamber under conditions of 22 C day/22 C night primarily on the basis of morphology, distribution and and with light irradiance of 200 ~mol m-2 s-' for 14 hr day -1. cytology. However, factors like the environment, multi- Genomic DNA was extracted and purified according to the genic inheritance, or partial and complete dominance method of Rogers and Bendich (1988) with modifications. often confound the expression of a genetic trait (Tingey Young leaf tissue (1.0 g) was ground in liquid nitrogen and and del Tufo 1993). then mixed with 1.0ml of 2% CTAB extraction Molecular markers such as isozymes and restriction buffer (2% CTAB, 100 mM Tris HCI (pH 8.0), 20 mM fragment length polymorphisms (RFLPs) have been exten- EDTA (pH 8.0), 1.4 M NaCI and 2% /~-mercaptoethanol). sively applied for genetic studies and plant breeding After incubation at 65 C for 5 min with vigorous shaking, (Beckmann and Soller 1983, Tanksley et al. 1989, Yang et the lysate was extracted with an equal volume of chloro- al. 1992). Random amplified polymorphic DNA (RAPD) form/isoamyl alcohol (24 : 1), and centrifuged at 11 • for analysis is based on the amplification of random DNA 10 min. The aqueous phase was transferred to a fresh segments with single primers of the arbitrary nucleotide tube containing 1/10 volume of the 10% CTAB buffer (10% 188 Y.-L. Yu and T.-Y. Lin Table 1. The genotypes in Nicotiana used for RAPD analysis fications were performed with a programmable thermal controller (MJ Research Inc) programmed for 2 cycles of 2 Chromo- Acc. min at 94 C, 1 min at 36 C and 2 min at 72 C, followed by Section Species no. no.some (2n) Source 43 cycles of 1 min at 94 C, 1 min at 36 C and 2 min at 72 C. After all cycles were completed, the reactions were Alatae held at 72 C for 10 min and slowly cooled to 4 C. The N. Iongiflora (NIo) 30 20 USDA DNA fragments amplified were analyzed by electropho- 30A 20 USDA resis in 1.5% NuSieve (FMC) agarose gels running in 1X 30B 20 USDA TBE buffer (89 mM Tris, 89 mM boric acid and 2 mM 30C 20 USDA EDTA) at 150 V for 3.5 hr. The gels were then stained N. plumbaginifolia (Np) 4,3A 20 USDA with ethidium bromide and photographed under UV light. 43B 20 USDA All the amplifications were tested at least twice for re- 43s 20 USDA producibility. N. bonariensis (Nb) 18 "l-rRI Photographs from ethidium bromide stained agarose N. a/ata (Na) 3 18 USDA gels were used for RAPD analysis. Bands on gels were N. /angsdorffii (Nla) 28A 18 USDA scored as present (1) or absent (0) for all the taxa studi- 28B 18 USDA ed. Pair-wise comparisons of these taxa were analyzed N. sylves~ris (Ns) 56A 24 USDA with the computer software of the numerical taxonomy Tomentosae and multivariate analysis system (NTSYS-pc, version 1.80; N. otophora (No) 38 24 USDA Rohlf 1993) and Jaccard's similarity coefficient and Nei and Li's similarity coefficient. The similarity coefficients 38A 24 USDA obtained were then used to construct a dendrogram using 38B 24 USDA the unweighted pair-group method with arithmetical aver- 30(3 24 USDA ages (UPGMA) employing the sequential, agglomerative, N. tomentosiformis (Nt) 24 "I-FRI hierarchical and nested clustering (SAHN) routine in 24 "H'RI N. glutinosa (Ng) NTSYS programs. Results CTAB and 0.7 M NaCI) and extracted with an equal volume of chloroform/isoamyl alcohol (24:1). DNA was The size of the amplified fragments ranged from 0.2 to precipitated with the addition of an equal volume of CTAB 1.5 kb. The profile of the amplified products obtained precipitation buffer (1% CTAB, 50 mM Tris ~ HCI (pH 8.0) with primer 48 is shown in Figure 1. Of the 354 amplified and 10 mM EDTA (pH 8.0)) and recovered by centrifuga- products, 339 (95.8%) were polymorphic and 15 (4.2%) tion for 15 min at 3,500Xg after incubation at --70 C for were monomorphic (Table 2). For each primer evaluated, 15 min. The pellet was dried and redissolved in high-salt the number of amplified products ranged from 6 to 14. In TE buffer (10 mM Tris ~ HCI (pH 8.0), 1 mM EDTA (pH 8.0) terms of the Nicotiana species, the products obtained with and 1 M NaCI), and then precipitated by ethanol. The the 34 primers ranged from 108 (N. glutinosa) to 158 (N. pellet was washed with 80% ethanol, dried under vacuum Iongiflora accession 30 C) and had an average of 4.1 and resuspended in sterile deionized water. The DNA amplified fragments per primer (Table3). Amplified samples were aliquoted and stored at -20 C prior to use. polymorphic DNA fragments were scored for computer To produce distinct DNA bands, genomic DNA from N. analysis based on Jaccard's similarity coefficients and Iongiflora accession 30 C and N. plumbaginifolia acces- Nei and Li's similarity coefficients and ranged from 0.099 sion 43C was used to screen 400 random oligonu- to 0.980 and 0.181 to 0.990, respectively (Table 4). The cleotides (decamers) with G-I-C contents of 50-80%, result of pair-wise comparisons indicated that Ficus which were obtained from Dr. J.B. Hobbs at the Oligonu- awkeotsang Makino was the most distantly related to all cleotide Synthesis Laboratory, Nucleic Acid-Protein Ser- genotypes in Nicotiana. vice Unit, University of British Columbia (UBC-1 to 100, 201 All of the genotypes in Nicotiana had similarity indices to 300, 401 to 500 and 601 to 700). Thirty-four primers ranging from 0.142 to 0.980 based on Jaccard's similarity (Table 2) were selected for amplification of DNA frag- coefficients and from 0.248 to 0.990 based on Nei and Li's ments with genomic DNA of 18 Nicotiana genotypes and of similarity coefficients (Figure2). Interestingly, the 18 Ficus awkeotsang Makino (jelly fig) as a control. genotypes analyzed were obviously divided into two Genomic DNA amplifications were performed according to clusters, A and B, on the basis of both Jaccard's and Nei the method of Williams et al. (1993) with some modifica- and Li's similarity coefficients.
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