Genetic Diversity and Phenetic Relationship of Dill (Anethum graveolens L.) by rps16-trnK DNA Sequences
Genetic Diversity and Phenetic Relationship of Dill (Anethum graveolens L.) by rps16-trnK DNA Sequences
Journal of Life Science. 2013. Nov, 23(11): 1305-1310
Copyright © 2013, Korean Society of Life Science
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
  • Received : August 12, 2013
  • Accepted : October 30, 2013
  • Published : November 30, 2013
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About the Authors
정숙, 성
National Agrobiodiversity Center, NAAS, RDA, Suwon 441-717, Korea
종욱, 정
National Agrobiodiversity Center, NAAS, RDA, Suwon 441-717, Korea
기안, 이
National Agrobiodiversity Center, NAAS, RDA, Suwon 441-717, Korea
만정, 강
National Agrobiodiversity Center, NAAS, RDA, Suwon 441-717, Korea
석영, 이
National Agrobiodiversity Center, NAAS, RDA, Suwon 441-717, Korea
만규, 허
Department of Molecular Biology, Dong-eui University, Busan 614-714, Korea

Dill ( Anethum graveolens L.) is an annual herb with a long history and it is mainly used as a spice and as a medicine that is effective as a digestive aid, a sedative, and a narcotic, and that helps remove bad breath. Dill grows wild in the districts along the shores of the Mediterranean Sea, West Asia, China, and Korea. An estimate of the phylogenetic relationships within dill accessions in 20 countries was inferred using data from the rps 16- trn K3-intergenic spacer. The aligned data sets for dill ranged from 747 to 779 nucleotides (bp) as a result of the differences in the insert/delete nucleotides. The sequence variation within the dill accessions was mostly due to nucleotide substitutions, although several small insertions and deletions can be found. Among 100 accessions from 20 countries, the Eastern Asia accessions were more closely related to the North American accessions than to the Central Asia and European accessions. Although some accessions were not congruent completely with geographical locations, the dill accessions with rps 16- trn K analysis resulted in plants with better-resolved clades.
Dill ( Anethum graveolens L.) is one of widespread vegetable herbs belonging to the family Apiaceae (Umbellifera). Dill is also called Hongwhoa or Syrah. Wild and weedy types of dill are widespread in the Mediterranean basin and in West Asia. It is suggested that dill originated from central Asia [18] . Similarly, Grieve [5] suggested that dill originated within an area around the Mediterranean and the South of Russia. Dill has been cultivated for thousands of years as a spice and medicinal purposes. For example, dill was found in mounds of ancient Egyptian history and in the Neolithic period in Switzerland. Dill has spread expanding the territory of the Roman Empire to many countries in the end of the first century BC.
This species contains biologically active constituents including carvone, limouene, dillapiole, borgaptene, umbelleprenin, and γ-sitosterole. In the central Asian countries, dill has been used as spices, stimulant, and carminative. Young leaves of dill can be edible. Essential oil extracted from the seeds has been used as pest control, pickles, and preservatives [4] .
Recently, molecular methods have been used for the identification and evaluation of genetic diversity within dill accessions at the plant population levels [14 , 15] . These results may provide clues to the spread process of dill.
Molecular markers which reveal extensive polymorphism are suitable for discriminating closely related genotypes [11] . However, RAPD (random amplified polymorphic DNA) has a problem of limited repeatability, with the confounding factor that repeating DNA sequences are often amplified [9] .
The rps 16- trn K region in chloroplast DNA usually shows sequence conservation in the regions flanking both trn L exons, whereas the central part is highly variable [13] . Within the intergenic spacer, no secondary-structural elements have been found, which could serve as splicing points, including that rps 16- trn K are probably co-transcribed [3 , 8] . A general feature of cpDNA spacer regions is the occurrence of indels that can be derived from either deletion or duplication of adjacent sequences or occur in non-repetitive regions of the spacer [6] .
We analyzed intraspecific phylogenic relationships within the worldwide accessions in A. graveolens and to compare our results with those of previous studies of this species.
Materials and Methods
- DNA extraction, gene amplification and sequencing
All one hundred samples (five accessions per nation) of dill accessions were obtained from National Agrobiodiversity Center, National Academy of Agricultural Science (Suwon, Gyonggi Province in Korea) and the center collected the samples from 20 countries. Genomic DNA was extracted from fresh leaves after germinating using the DNA Zol Kit (Life Technologies Inc., Grand Island, New York, U.S.A.) according to the manufacturer’s protocol. Total DNA was precipitated with ethanol (-20℃), centrifuged for 30 minutes, washed in 70% ethanol to remove excess salts. DNA pellet was dried and then re-dissolved in 100ul TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). DNA was checked for shearing and concentration by agarose electrophoresis and fluometry, respectively.
Specific primers ( rps 16F:5`-AAAGGKGCTCARCCTACARGAA-3`, trn K5`R: 5`-TACTCTACCRTTGAGTTAGCAAC-3`) were used to amplify the entire length of the sequences for the rps 16 -trn K gene by polymerase chain reaction (PCR) using standard techniques at a 2.5 mmol/l MgCl 2 concentration.
PCR materials (50 ul volume) included 50 ng of genomic DNA, 100 uM of each dNTP, 0.2 uM of each primer, 1x enzyme buffer, and 2 unit of Taq polymerase. The amplification profile was 28 cycles of 94℃ for 30 sec, 42℃ for 60 sec, 72℃ for 60 sec, preceded by an initial denaturation at 94℃ for 90 sec and followed by a final extension at 72℃ for 5 min.
PCR products were separated on 2.0% agarose gels and purified using the QIAquick Gel Extraction Kit (QIAGEN). The amplified fragments were cloned into a bluescript vector and sequenced using ABI Prism 377 Sequencer (Applied Biosystem, USA). At least five clones of each accession were analyzed.
- Alignment and phylogenetic analysis
The chromatogram output for each sample was edited using the software Sequence Navigator 1.0.1 (Applied Biosystems Inc.), and the sequences were manually aligned. New sequences obtained in this study were deposited in GenBank.
An alignment was calculated using the MULTIPLE ALIGNMENT MODE of the Crustal X program. Phylogenetic relationship was estimated by MEGA5 version with maximum parsimony (MP) algorithm [17] . The MP was inferred using heuristic search, branch-swapping options and tree bisection-reconnection. Tajima’s neutrality test [16] was estimated using MEGA5. Bayesian analysis was performed using MrBayes 3.1.2 [12] on the combined matrix. We calculated the MODELTEST 3.7 [10] . The best-fit maximum likelihood model was chosen using the Akaike information criterion (AIC) [1] .
Confidence values for individual branches were determined by a bootstrap analysis with 100 repeated sampling of the data.
The complete sequences of rps 16- trn K regions for the 100 dill accessions in the world were amplified and sequenced with PCR and primers. The aligned data sets for dill ranged from 747 to 779 nucleotides (bp) as results of differences in insert/delete nucleotides ( Table 2 ).
Base frequencies across accessions of 20 countries`Anethum graveolensusingrps16-trnK
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Base frequencies across accessions of 20 countries` Anethum graveolens using rps16-trnK
Alignments of rps 16- trn K regions for the dill accessions were great similarity among the accessions and the unusual rps 16- trn K insert were not shown. Sequence variation within dill was mostly due to nucleotide substitutions, although several small insertions and deletions can be found. Another source of sequence divergence was length variation due to stretches of short repeated that occurred at the sequences of TTTTT and AAAGA.
Alignment of the DNA sequences did not require allowing gaps. Total alignment length was 779 positions, of which 39 were parsimony-informative characters, 76 variable but parsimony-uninformative, and 318 constant characters.
G + C content for dill ranged between 31.1% (Kazakhstan) and 39.7% (China) ( Table 2 ). The base frequencies did not showed the significant difference to the accessions. These values were similar to the mean (33.5%) for the dill alignments except China accession of the rps 16- trn K region.
Substitution pattern and rates were estimated under the Kimura 2-parameter model. The estimated Transition/Transversion biases ( R ) varied from 4.17 to 14.85. Under maximum likelihood fits of 24 different nucleotide substitution models, substitution from G to A was 14.85 and the reverse was 7.79 ( Table 3 ).
Maximum composite likelihood estimate of the pattern of nucleotide substitution
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Each entry shows the probability of substitution (r) from one base (row) to another base (column). For simplicity, the sum of r values is made equal to 100. Rates of different transitional substitutions are shown in bold and those of transversionsal substitutions are shown in italics. The nucleotide frequencies are 35.04% (A), 31.65% (T/U), 18.39% (C), and 14.93% (G). There were a total of 689 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.
BIC score was the lowest at the Kimura parameter with 14938.4 ( Table 4 ). AICc value was the lowest at the Tamura 3-parameter with 14637.4. Assumed or estimated values of transition/transversion bias ( R ) are shown for each model, as well.
Maximum likelihood fits of 24 different nucleotide substitution models
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Models with the lowest BIC scores (Bayesian Information Criterion) are considered to describe the substitution pattern the best. For each model, AICc value (Akaike Information Criterion, corrected), Maximum Likelihood value (lnL), and the number of parameters (including branch lengths) are also presented. Non-uniformity of evolutionary rates among sites may be modeled by using a discrete Gamma distribution (+G) with 5 rate categories and by assuming that a certain fraction of sites are evolutionarily invariable (+I). Whenever applicable, estimates of gamma shape parameter and/or the estimated fraction of invariant sites are shown. Assumed or estimated values of transition/transversion bias (R) are shown for each model, as well. They are followed by nucleotide frequencies (f) and rates of base substitutions (r) for each nucleotide pair. Relative values of instantaneous r should be considered when evaluating them. For simplicity, sum of r values is made equal to 1 for each model. For estimating ML values, a tree topology was automatically computed.
Number of segregating sites was 548 and nucleotide diversity (π) was 0.250. Under the neutral mutation hypothesis, the probability that the Tajima test statistic ( D ) is positive (0.476) is less than 0.5 ( Table 5 ). Therefore, there may be a site at which deletion/insertion, which increases the genetic variation, is operating.
Results from Tajima’s neutrality test forrps16 andtrnK sequences of 20 countries’ dills
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m=number of sequences, S=Number of segregating sites, ps= S/m, Θ=ps/a1, π=nucleotide diversity, and D is the Tajima test statistic.
The main phylogenetic analysis revealed many distinct clades ( Fig. 1 ). The first clade includes three accessions (China, Korea, and Vietnam). Internal nodes were not strongly supported (only 28%). The second clade included Canada and United States and sistered to Mexico. The group was sistered to Mongol and next was Georgia, Kazakhstan, and Germany. Clade of Turkmenistan and Ukrainewas sistered to former group. Internal node of Bulgaria and Turkey was strongly supported (71%) and sistered to Greece. Tajikistan and Armenia were formed one clade and sistered to Russia. In addition, the positions of phylogeny based on rps 16- trn K analysis were not congruenced with the geographical positions.
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The maximum parsimonious tree for 20 countries’ Anethum graveolens based on rps16-trnK analysis using MEGA5.
rps 16- trn K for the one hundred accessions of dill had a total aligned length of 779 bp. Many accessions of dill contained the identical sequences over rps 16- trn K gene, resulting in a single, undifferentiated clade for these samples in the phylogenetic analysis, even though many of these sample accessions had been obtained from very different geographical origins ( Table 1 ). However, the sequences of many dill accessions differed from each other, resulting in clear delineation of all accessions in our analysis. In particular, there are many single nucleotide polymorphisms in these sequences, allowing us to distinguish accessions from other accessions based on the sequence data.
The code names ofAnethum graveolensin 20 countries
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The code names of Anethum graveolens in 20 countries
Study of genetic diversity and phylogenetic analysis in the 135 dill accessions using molecular markers (RAPD) were reported by Suresh et al. [15] . However, their results by RAPD showed little association with the geographic origin of the collecting countries. Some accessions of same country were located in different clades of phylogenetic tree. It might be accounted for a few bands of RAPD markers (142 bands for 135 accessions). In addition, the phenetic results of RAPD were grouped into two major clusters without geographic locations. The rps 16- trn K analysis resulted in trees with better-resolved clades although the present results are not congruent completely with geographical locations. Solouki et al. [14] also reported genetic diversity and morphological traits in 37 accessions of dill in Iran using AFLP (amplified fragment length polymorphism) markers. They concluded that morphological traits showed a high degree of variation among the dill accessions and molecular markers showed a low variation.
Low numbers of bands (fragments) used for RAPD or AFLP markers did not present a good relationships among accessions of dill. In addition, we are unaware of any unique anatomical or morphological traits that would support the union of these accessions of dill. As a pointed by Solouki et al. [14] , dill has shown the phenetic plasticity and morphological traits may be controlled by few genes. RAPD fragments have not made the expected bands related to the morphological similarity. These similar results have been reported other species [2 , 7] .
This study was carried out with the support of “Cooperative Research Program for Agricultural Science & Technology Development (Project No. PJ0086232013 )”, Rural Development Administration, Republic of Korea.
Akaike H. 1974 A new look at statistical model identification Automatic Control 19 716 - 723    DOI : 10.1109/TAC.1974.1100705
Ali G. M. , Yasumoto S. , Katsuta M. S. 2007 Assessment of genetic diversity in sesame (Sesamum indicum L.) detected by Amplified Fragment Length Polymorphism markers Electronic J Biotech 10 12 - 23
Andersson L. , Rova J. H. 1999 The rps16 intron and the phylogeny of the Rubioideae (Rubiaceae) Plant Syst Evol 214 161 - 186    DOI : 10.1007/BF00985737
Bakkali F. , Averbeck S. , Averbeck D. , Idaomar M. 2008 Biological effects of essential oils – a review Food Chem Toxicol 46 446 - 465    DOI : 10.1016/j.fct.2007.09.106
Grieve, M. "Dill". A Modern Herbal
Golenberg E. M. , Clegg M. T. , Durbin M. L. , Doebley J. , Ma D. P. 1993 Evolution of a noncoding region of the chloroplast genome Mol Phylogenet Evol 2 52 - 64    DOI : 10.1006/mpev.1993.1006
Lopez P. A. , Widrlechner M. P. , Simon P. W. , Boylston S. R. T. D. , Isbell T. A. , Bailey T. B. , Gardner C. A. , Wilson L. A. 2008 Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm Genet Resour Crop 55 247 - 275    DOI : 10.1007/s10722-007-9232-7
Oxelman B. , Liden M. , Berglund D. 1997 Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae) Plant Syst Evol 206 393 - 410    DOI : 10.1007/BF00987959
Penner G. A. , Chong J. , Levesque-Lamay M. , Molnar S. I. , Fedak K. G. 1993 Identification of a RAPD marker linked to the oat stem rust gene Pg3 Theor Appl Genet 85 702 - 705
Posada D. , Crandall K. 1998 Modelist: testing the model of DNA substitution Bioinformatics 14 817 - 873    DOI : 10.1093/bioinformatics/14.9.817
Rajaseger G. , Tan T. W. H. , Turner I. M. , Kumar P. R. 1997 Analysis of genetic diversity among Ixora cultivars (Rubiaceae) using random amplified polymorphic DNA Ann Bot 80 355 - 361    DOI : 10.1006/anbo.1997.0454
Ronquist F. , Huelsenbeck J. P. 2003 MrBayes: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1972 - 1974    DOI : 10.1093/bioinformatics/btg261
Shaw J. , Lickey E. B. , Beck J. T. , Farmer S. B. , Liu W. , Miller J. , Siripun K. C. , Winder C. T. , Schilling E. E. , Small R. L. 2005 The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis Am J Bot 92 142 - 166    DOI : 10.3732/ajb.92.1.142
Solouki M. S. , Hoseini S. B. , Tavassoli A. 2012 Genetic diversity in dill (Anethum graveolens L.) populations on the basis of morphological traits and molecular markers African J Biotech 11 3649 - 3655
Suresh S. , Chung J. W. , Sung J. S. , Cho G. T. , Park J. H. , Yoon M. S. 2012 Analysis of genetic diversity and population structure of 135 dill (Anethum graveolens L.) accessions using RAPD markers Genet Resour Crop Evol    DOI : 10.1007/s10722-012-9886-7
Tajima F. 1989 Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism Genetics 123 585 - 595
Tamura K. , Peterson D. , Peterson G. , Stecher G. , Nei M. , Kumar S. 2011 MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Mol Biol Evol 28 2731 - 2739    DOI : 10.1093/molbev/msr121
Zohary D. , Hopf M. 2000 Domestication of plants in the Old World third ed. Oxford University Press NY, USA