determination of genetic diversity between eggplant and its wild ...

DETERMINATION OF GENETIC DIVERSITY 

BETWEEN EGGPLANT AND ITS WILD 

RELATIVES 

A Thesis Submitted to 

the Graduate School of Engineering and Sciences of 

zmir Institute of Technology 

in Partial Fulfillment of the Requirements for the Degree of 

MASTER OF SCIENCE 

in Molecular Biology and Genetics 

by 

Yeliz TÜMB LEN 

July 2007 

ZM R

We approve the thesis of Yeliz TÜMB LEN 

Date of Signature 

…………………………………………… 18 July 2007 

Assoc. Prof. Dr. Sami DO ANLAR 

Supervisor 

Department of Biology 


…………………………………………… 18 July 2007 

Assoc. Prof. Dr. Anne FRARY 

Co-Supervisor 

Department of Biology 


…………………………………………… 18 July 2007 

Assoc. Prof. Dr. Hülya LB 

Department of Horticulture 

Ege University 

…………………………………………… 18 July 2007 

Assoc. Prof. Dr. Bahattin TANYOLAÇ 

Department of Bioengineering 

Ege University 

…………………………………………… 18 July 2007 

Assist. Prof. Dr. Abdullah KAHRAMAN 

Department of Field Crops 

Harran University 

…………………………………………… 18 July 2007 

Assoc. Prof. Dr. Sami DO ANLAR 

Head of Department 

Izmir Institute of Technology 

……………………………………………. 

Prof. Dr. Barı ÖZERDEM 

Head of the Graduate School

ACKNOWLEDGEMENTS 

I want to present my thanks to my advisor Assoc. Prof. Dr. Sami DO ANLAR 

for his trust and all of his support to me. 

I would like to also thank my co-supervisor Assoc. Prof. Dr. Anne FRARY for 

her great concern, valuable suggestions and kindness. 

I am also grateful to Dr. Osman GÜL EN and Dr. Nedim MUTLU from Alata 

Bahçe Ara tırma Enstitüsü Erdemli, Mersin and Alpaslan K BARO LU from Beckman 

Coulter for all their kind and sincere support during my studies. 

Also, I am grateful for the financial support of the TÜB TAK (The Scientific 

and Technological Research Council of Turkey) during my education of Master of 

Science. 

Finally, I present my gratitude to my dear parents, Birol TÜMB LEN and Serpil 

TÜMB LEN, for their endless support, encouragement and love. 

remembered. 

In memory of my dear older sister Ye im TÜMB LEN, who will always be

ABSTRACT 

DETERMINATION OF GENETIC DIVERSITY BETWEEN 

EGGPLANT AND ITS WILD RELATIVES 

Eggplant (Solanum melongena L.) is an important crop and has a growing 

reputation and is now cultivated globally. It is a valuable member of the human diet in 

Asia, especially in India, which is a primary diversity center of the species. Turkey is 

the first in Europe and is in the first five countries around the world in terms of eggplant 

production. The Solanaceae family to which S. melongena belongs is an important 

family, too. Tomato, potato, tobacco and petunia are some example species of the 

Solanaceae family. This important family with 3000-4000 species shows a high level of 

morphological diversity which results in confusion about its systematics and this 

diversity is at the level of genera, species and cultivars. 

The aims of the studies reported in this thesis were to analyze genetic diversity 

of Turkish eggplants and wild relatives in separate studies with different molecular 

tools. To reveal genetic diversity among eggplant cultivars grown in Turkey, the AFLP 

marker system was applied to the sample genotypes. For the investigation of genetic 

variation between S. melongena and its wild relatives, though, the SSR marker system 

was used. 

For the AFLP data for Turkish eggplants, an r value of 0.97 was obtained which 

was in the best scale. Eigen values reported here were also informative. These results 

showed that the first component analysis explained 64.34% of the variation between 

samples. For three axes, though, a total of 72.21% variation was explained. According to 

the statistical results of SSR analysis, the r value of Solanum species’ genotypic data was 

found to be 0.88. That means the correlation between sample genotypic data and 

dendrogram was found to be high. Due to the other statistical results which were Eigen 

values explained 46.12% of genotypes for first component analysis. With a total value of 

55.28%, the 47 different genotypes were explained by the three principle component axes. 

The results of AFLP studies showed that although a high similarity value was 

observed, diversity was detectable among the accessions. The results of SSR studies 

were also meaningful with their concordance with previous studies and observed 

diversity with a good fit to statistical results. 

iv

ÖZET 

PATLICAN VE YABAN TÜRLER ARASINDAK GENET K 

ÇE TL L N BEL RLENMES 

Patlıcan (Solanum melongena L.) gittikçe artan bir tanınma ile önemli 

ürünlerden bir tanesidir ve u anda küresel olarak üretilmektedir. Özellikle Hindistan 

ba ta olmak üzere, birincil çe itlilik merkezi olan Asya kıtasında, insan beslenmesinde 

önemli bir yeri vardır. Üretim miktarı bakımından Türkiye, Avrupa’ da birinci ve dünya 

da da ilk be ülke arasındadır. S. melongena’nın ait oldu u Solanaceae ailesi de 

önemlidir. 3000-4000 türün yer aldı ı bu önemli aile, morfolojik olarak yüksek düzeyde 

çe itlilik göstermektedir ve bu çe itlilik sistematik açıdan çe itler, türler ve cinsler 

seviyesindedir. 

Bu tezde yapılan çalı maların amacı, Türk patlıcanları ve yabani akrabaları 

arasındaki genetik çe itlili i ayrı ayrı ve farklı moleküler teknikler kullanarak 

belirlemektir. Türkiye’de yeti tirilen patlıcan kültürleri arasındaki genetik çe itlili i 

açı a çıkarmak üzere, AFLP i aretleyici sistemi örnek genotiplere uygulanmı tır. S. 

melongena ve yabani akrabaları arasındaki genetik varyasyonu ara tırmak için ise SSR 

i aretleyici sistemi kullanılmı tır. 

Türk patlıcanları AFLP verileri için, 0.97 r de eri bulunmu tur. Bu de er en iyi 

aralık dahilinde yer almı tır. Ayrıca, rapor edilen Eigen de erleri de oldukça açıklayıcı 

bulunmu tur. Bu sonuçlar, örnekler arasındaki çe itlili in temel bile enler analizi ile ilk 

düzlemde %64.34 oranında açıklandı ını göstermi tir. Üç düzlemde ise, toplam 

varyasyonun %72.21’ i açıklanmı tır. SSR analizlerinin istatistiksel sonuçlarına göre, 

Solanum türleri genotipik verilerinin r de eri 0.88 bulunmu tur. Bu sonuç, örnek 

genotipik data ve dendrogram arasında bulunan ili kinin yüksek oldu u anlamındadır. 

Di er istatistiksel sonuçlara göre, Eigen de erleri, temel bile enler analizi ile ilk 

düzlemde genotiplerin %46.12’ sini açıklamı tır. Toplam %55.28’ lik de er ile, 47 farklı 

genotip, temel bile enler analizindeki ilk üç düzlemde açıklanmı tır. 

AFLP çalı malarının sonuçları, yüksek düzeyde benzerlik de eri gözlenmesine 

ra men, tohum örnekleri arasında varyasyonun tespit edilebilece ini göstermi tir. SSR 

çalı malarının sonuçları, önceki çalı malarla uyumlu ve tespit edilen çe itlilik ise 

istatistiksel olarak anlamlı bulunmu tur. 

v

TABLE OF CONTENTS 

LIST OF FIGURES .......................................................................................................viii 

LIST OF TABLES............................................................................................................ x 

CHAPTER 1. INTRODUCTION .................................................................................. 1 

1.1. Diversity and Systematics..................................................................... 1 

1.2. Genetic Diversity and Molecular Systematics...................................... 3 

1.2.1. Molecular Techniques .................................................................... 4 

1.2.1.1. AFLP...................................................................................... 5 

1.2.1.2. SSR ........................................................................................ 7 

1.3. Solanaceae Family ............................................................................. 11 

1.3.1. Genus Solanum............................................................................. 13 

1.3.2. Eggplant (Solanum melongena).................................................... 14 

1.4. Eggplant Genetic Diversity................................................................. 19 

1.5. Studies of Genetic Diversity in Eggplant .......................................... 24 

CHAPTER 2. MATERIALS AND METHODS.......................................................... 30 

2.1. Materials ............................................................................................. 30 

2.1.1. Plant Material ............................................................................... 30 

2.1.2.Sample DNAs ................................................................................ 35 

2.1.2.1. Extraction............................................................................. 35 

2.1.2.2. Quantity Checking ............................................................... 35 

2.2. Methods .............................................................................................. 37 

2.2.1. AFLP............................................................................................. 37 

2.2.2. SSR ............................................................................................... 39 

2.2.2.1. Design and Checking of the SSR Primers ........................... 39 

2.2.2.2. SSR Protocol........................................................................ 40 

CHAPTER 3. RESULTS AND DISCUSSION OF AFLP DATA .............................. 43 

3.1. Results................................................................................................. 43 

3.1.1. Pre-Experiments and Their Results .............................................. 43 

vi

3.1.2. Analysis and results of the AFLP Data......................................... 46 

3.2. Discussion .......................................................................................... 50 

CHAPTER 4. RESULTS AND DISCUSSION OF SSR DATA................................. 52 

4.1. Results................................................................................................. 52 

4.1.1. Pre-Experiments and Their Results .............................................. 52 

4.1.2. Analysis and Results of the SSR Data.......................................... 61 

4.2. Discussion........................................................................................... 67 

CHAPTER 5. CONCLUSION AND FUTURE PERSPECTIVE................................ 69 

REFERENCES ............................................................................................................... 71 

vii

LIST OF FIGURES 

Figure Page 

Figure 1.1. The relation of genomic data with taxonomy and taxonomic 

definition...................................................................................................... 3 

Figure 1.2. Several techniques that are used in molecular systematics studies. 

The methods for which usefulness has been proven are check- 

marked. ....................................................................................................... 5 

Figure 1.3. The protocol of AFLP technique. ............................................................... 7 

Figure 1.4. The design of genic SSR primers databases and their fields of use. ........... 9 

Figure 1.5. Production and clustering of ESTs from genomic DNA. ......................... 10 

Figure 1.6. The dispersion of Solanaceae family members around the world............. 11 

Figure 1.7. An example of a phylogenetic tree of the Solanaceae family 

indicating morphological traits. ................................................................ 13 

Figure 1.8. Worldwide production of eggplant between the years 1995 and 

2004. ......................................................................................................... 16 

Figure 1.9. Primary and secondary diversity centers of eggplant (Solanum 

melongena L.). Red-colored region is the basic primary diversity 

center while green-colored regions are secondary diversity centers 

and major cultivation areas........................................................................ 16 

Figure 1.10. Examples of fruit diversity in eggplant. .................................................... 18 

Figure 1.11. Plant species used in biological studies are depicted at the order 

level while species belonging to these orders are similarly 

colored. Order Solanales has three species: potato, tomato and 

tobacco and are in blue. ............................................................................ 21 

Figure 1.12. Phylogenetic classification of angiosperms. Solanales order is 

indicated by the arrow. ............................................................................. 23 

Figure 1.13. A detailed view of Solanum genus’ classification. The 

Leptostemonum clade includes eggplant and its close relatives. ............. 24 

Figure 1.14. Number of different types of dinucleotide repeats in humans and 

plants. ........................................................................................................ 29 

viii

Figure 3.1. An example of AFLP study results for three different samples 

(06T122, 06T139 and 06T144) with one primer combination (11. 

primer com). Size standards are not shown in the figure. ........................ 45 

Figure 3.2. A closer view of the same results shown in Figure 3.1. 

Polymorphisms detected within the three samples are indicated by 

arrows. Fragment sizes are indicated above each peak. .......................... 45 

Figure 3.3. Dendrogram showing coefficient of similarity among Turkish 

eggplants and three outgroups. ................................................................. 47 

Figure 3.4. Two-dimensional plot of Turkish eggplant accessions. ........................... 48 

Figure 3.5. Three-dimensional graphs of Turkish eggplants AFLP results................. 49 

Figure 4.1. Amplification results for 19 smSSR primers checked with a single 

DNA. A weaker result is indicated by the arrow. ..................................... 59 

Figure 4.2. Amplification of DNA from 16 wild eggplant accessions with 

smSSR10. Some of the polymorphic bands are indicated by 

arrows. ...................................................................................................... 60 

Figure 4.3. An example of SSR studies for 4 samples (Pedigree numbers: 

06T892, 06T874, 06T893 and 06T877) with one primer pair 

(smSSR39) is shown in the figure. Polymorphism can be detected by 

examining the size of the peaks. ....................................................................... 61 

Figure 4.4. Dendrogram showing similarity among S. melongena and its wild 

relatives. .................................................................................................... 63 

Figure 4.5. Dendrogram showing similarity among S.melangena and as wild 

relatives with clusters indicated. ............................................................... 64 

Figure 4.6. Two-dimensional plot of wild eggplants SSR data. ................................. 65 

Figure 4.7. Three-dimensional plots of wild eggplants SSR data. .............................. 66 

ix

LIST OF TABLES 

Table Page 

Table 2.1. Turkish eggplants characterized by AFLP................................................... 31 

Table 2.2. Eggplant and its wild relatives tested with SSR markers ............................ 33 

Table 2.3. List of eggplant and its wild relatives with number of accessions 

tested ............................................................................................................ 34 

Table 2.4. Turkish Eggplants Nanodrop results. .......................................................... 36 

Table 2.5. Wild Eggplants Nanodrop results. .............................................................. 37 

Table 2.6. Selective primer combinations that were applied to Turkish 

eggplants ...................................................................................................... 38 

Table 2.7. Repeat motifs and sequences for the SSR primers. M13 sequence 

was added to the forward sequence. ........................................................... 41 

Table 3.1. Eigen values representing principal components of the study AFLP 

Turkish eggplants at three dimensions are listed in order. .......................... 46 

Table 4.1. Repeat motifs, numbers of SSRs identified and average repeat 

numbers for the SSRs identified in the eggplant EST library...................... 53 

Table 4.2. SSR primers repeat motifs and sequences ................................................... 55 

Table 4.3. SGN ESTs and their unigene status ............................................................. 57 

Table 4.4. SSR primers selected for use in the analysis and for drawing 

dendrogram .................................................................................................. 62 

Table 4.5. Eigen values representing principal components of the study SSR 

wild eggplants at three dimensions are listed in order................................. 62 

x

1.1. Diversity and Systematics 

CHAPTER 1 

INTRODUCTION 

There are presumably more than 30 million species in the world yet, a 

significant number of different organism types have not been identified. Human beings 

could not imagine the number of species until the possibility to travel to distant and 

remote places and closely examine them. However, the need for giving names to 

organisms is as old as human history. The basic aim was to be able to understand each 

other while explaining something in a short way. Nevertheless, the usage of different 

terminology in different languages or parts of the world or even in the same country but 

in a different region started to make it difficult to follow this basic aim. As a result, 

people started to consider an appropriate way of communication in a scientific way. The 

solution to this problem came in the early 18 th century. A Swedish naturalist, Carolus 

Linnaeus, proposed a system for naming organisms. In this binominal system of 

nomenclature, every organism has two names. The first name which represents the 

genus is written with a capital letter. The second name which is called an epithet is 

special for each organism. Both of these names are written in italics or underlined. This 

nomenclature is important because it is based on the usage of Latin words which serves 

as a common language overall and because of its easiness during the classification 

process. 

Classification is basically the categorization of identified and named organisms 

in a hierarchical way. Identification and naming is then a necessity to be able to classify 

organisms. According to Linnaeus` system, which is the base of modern classification, 

two basic categories were constructed: species and genus. In terms of today’s 

classification systems, organisms were grouped in seven categories which are species, 

genus, family, order, class, phylum for animals or division for plants and kingdom. 

Although there is some disagreement, most recently, all organisms started to be grouped 

into 3 different domains or superkingdoms: Bacteria, Archaea or Eukarya. In addition to 

these, there are also intermediate categories such as sub-, super- or infra- at each 

taxonomic level. The easiness of the binominal system does in fact rely upon the 

1

availability to be broadened or become more complicated without any disorder. All 

these categories are the building blocks of the classification systems which start from 

the narrowest, most concordant groups and expand to the broadest, least similar taxa. 

There are many classification systems based on different considerations. For 

example, people who are mostly interested in the geographical dispersal of organisms 

may classify them according to their habitats. Others may focus on the shape or color of 

a body part and propose a system. However, there are three fundamental systems. In the 

natural classification system, organisms are categorized based on their similarity and 

close relation. Members of higher taxa share less similarity and are less closely related 

and the opposite is true for lower taxa. The second system is an artificial classification 

system. In this system, a character or feature is taken into account and the grouping is 

done in terms of that trait. As an example, the classification of plants upon their 

medicinal properties or economic importance can be given. The last fundamental system 

is used to define fossil organisms and both natural and artificial systems provide data 

that support this definition. With respect to Linnaeus’ classification idea, morphological 

and structural similarities were the major considerations and this method is still in 

usage. Today’s classification of organisms is mainly carried out using the natural 

classification system. 

Systematics is the science which defines diversity of organisms and includes 

their identification, naming and classification. As a result, it has a much more 

broadened aspect than all these proceedings which starts from first finding and then 

naming and place an organism into a taxon in systematics. This aspect also deals with 

the history of organisms on Earth, thus, it takes into account evolution. After being first 

elucidated by Lamarck although with an incorrect assumption and fully explained by 

Darwin using the theory of natural selection, evolutionary relationships of organisms 

have started to be considered within systematics more seriously. In this way, organisms 

can be more accurately grouped and new ones added to the systems in a well-suited 

way. This new way of systematics is called phylogenetics or phylogenetic systematics. 

There are three types of phylogenetic studies: phenetics, cladistics and evolutionary 

systematics (Westhead et al. 2002). The difference between phenetics and cladistics 

depends on the type of data chosen to study evolutionary relationships of organisms. All 

characters are used for phenetics while only shared characters are used for cladistics 

(Westhead et al. 2002). Hence, evolutionary systematics benefits from these two types 

of studies. As a general result for all three, though, phylogenetic trees or dendrograms 

2

are drawn (Li 1997 and Raven et al. 1999b). Specifically phenograms and cladograms 

are terms that are used to refer to the trees drawn from these studies (Raven et al. 1999b 

and WEB_3 2007). 

1.2. Genetic Diversity and Molecular Systematics 

Darwin’s theory which has real importance for systematics is in agreement with 

and supported by several sciences such as genetics, statistics and mathematics and has 

certain building blocks (Raven et al. 1999a and WEB_7 2007). These building blocks 

which are important in evolution are natural selection, genetic drift and founder effects. 

All three affect the same composition: genotype. Evolution can be defined as any 

changes in genotype due to several reasons but basically due to mutations. 

Genetic diversity is different forms of genotype and occurs as a result of changes 

in genetic structure (WEB_2 2007). It potentially leads to speciation in the long term 

due to the process of evolution (Raven et al. 1999a and WEB_2 2007). Diversity in 

genetic composition is the basic feature which increases chance of survival for 

individuals and populations during natural selection (WEB_2 2007). The molecular 

components that form this genetic composition are DNA and proteins and their 

connection to classification is shown in Figure 1.1. (Li 1997, WEB_9 2007). 

Figure 1.1. The relation of genomic data with taxonomy and taxonomic definition. 

(Source: Knapp et al. 2004) 

3

Molecular systematics is the classification of organisms with the help of 

molecular techniques to detect diversity at the molecular level (Li 1997, Raven et al. 

1999b and WEB_9 2007). There are several advantages of using molecular data 

compared to morphological data. Molecular data can be gathered via molecular 

techniques and are more abundant compared to morphological data (Li 1997 and Raven 

et al. 1999b). Even morphologically diverse species can be compared because of 

genotypic data’s higher conservation compared to morphological data which is not only 

related with genotype but also affected by environment (Li 1997 and Raven et al. 

1999b). Also, molecular techniques are open to improvement and every new method 

has increased easiness for application and fewer disadvantages in terms of obtained data 

(Li 1997 and Ranade 2003). As a result, an increased accumulation which is an 

important factor for molecular systematics is present (Li 1997). 

There are three groups of statistical analysis systems used in phylogenetic 

studies (Li 1997, Ranade 2003 and Westhead et al. 2002). These are distance matrix 

methods, maximum likelihood methods and maximum parsimony methods (Li 1997, 

Ranade 2003 and Westhead et al. 2002). According to distance matrix methods, 

distances between any two taxa are calculated and clustering is organized using 

minimum distance (Li 1997, Ranade 2003 and Westhead et al. 2002). Neighbour- 

joining (NJ) and Unweighted Pairgroup Method with Arithmetic Averaging (UPGMA) 

are methods which depend on these kinds of distance values (Ranade 2003). UPGMA 

which is the simplest analysis method is specifically defined to construct phenograms 

while it is also used for phylogenetic trees (Li 1997 and Westhead et al. 2002). 

Maximum likelihood methods try to reach maximum likelihood value while 

constructing the final tree (Westhead et al. 2002 and Ranade 2003). The principle of 

maximum parsimony methods is based on using a minimum number of variables that 

exhibit phylogenetic differences between samples (Li 1997, Westhead et al. 2002 and 

Ranade 2003). 

1.2.1. Molecular Techniques 

There are various molecular techniques used experimentally for several 

purposes. Their usage for taxonomic studies is relatively new. Widespread application is 

reported as starting with protein analysis during the 1960s (Li 1997). This was followed 

4

y DNA-based methods and recombinant technologies of which examples are shown in 

the Figure 1.2. (Li 1997). 

Figure 1.2. Several techniques that are used in molecular systematics studies. The 

methods for which usefulness has been proven are check-marked (Source: 

Ranade 2003). 

Among these various techniques, AFLP and SSR technologies are defined in 

detail because they are of interest for this thesis. 

1.2.1.1. AFLP 

The amplified fragment length polymorphism (AFLP) marker technique was 

first developed by Vos et al. (Vos et al. 1995). It is a PCR-based technique that has the 

advantages of its easiness, speed and specificity (Mohan et al. 1997, Jones et al. 1997 

Henry 1999 and Ranade 2003). The method also relies on restriction digestion of 

genomic DNA and, in fact, is a DNA fingerprinting process (Vos et al. 1995 and 

Ranade 2003). 

AFLP consists of several steps. First, DNA is digested with two different 

enzymes. One of them cuts the DNA in several regions while the other cuts in few 

places: frequent and rare cutters (Vos et al.1995 and Jones et al. 1997). This provides an 

optimized number of DNA fragments, though, the number of fragments or bands, 

compared to other methods, is still high (Vos et al. 1995, Staub and Serquen 1996 and 

5

Mohan et al. 1997). Usually between 50 and 100 bands per individual are obtained (Vos 

et al. 1995 and Staub and Serquen 1996). Enzyme pairs may be changed in experiments 

but the cutting patterns should be appropriate to the method. Some examples of these 

pairs are: EcoR I – Mse I, Pst I - Mse I, EcoR I – Taq I and HindIII - EcoR I (Mace et 

al. 1999 and WEB_6 2007). In this thesis study, specifically, EcoR I – Mse I restriction 

enzyme pairs were used. They have 6 bp and 4 bp recognition sites, respectively 

(Grandillo and Fulton 2002 and Invitrogen 2003). The next step of the protocol is 

related with these restriction sites. Small DNA pieces (adapters) specific for each 

restricted enzyme site are bound to the template DNA (Vos et al. 1995, Jones et al. 1997 

and Ranade 2003). The template DNA plus adapter provides the binding sites for 

primers (Vos et al. 1995 and Jones et al. 1997). There are two PCR amplification steps 

in the protocol. These are called pre-selective and selective amplifications (Vos et al. 

1995 and Invitrogen 2003). While pre-selective amplifications’ primers have one extra 

nucleotide, selective amplification primers have two or three extra bases which may be 

selected differently (Vos et al. 1995, Mohan et al. 1997 and Salamini et al. 2004). These 

bases are responsible for selectivity and are used to increase specificity and decrease or 

increase number of bands (Vos et al. 1995 and Invitrogen 2003). The number of bands 

obtained from the AFLP technique is related with genome size and number of C and G 

bases in the extra nucleotides (Vos et al. 1995 and Invitrogen 2003). The last step is the 

running of samples on polyacrylamide gels and visualization of bands with either 

autoradiography or fluorescent detection (Vos et al. 1995 and Ranade 2003). 

AFLP is a dominant type of marker (Henry 1999 and Ranade 2003). However, a 

large number of fragments and relatively high polymorphism make the technique 

favorable in molecular investigations (Vos et al. 1995, Staub and Serquen 1996, and 

Ranade 2003). Also, no prior sequence knowledge is needed for application of AFLP 

(Grandillo and Fulton 2002). Thus, it is a preferred method especially for taxonomic 

and mapping studies (Mohan et al. 1997 and Ranade 2003). Although it is a random 

process, selective amplifications increase the specificity (Vos et al. 1995 and Ranade 

2003). The results are also reproducible (Mohan et al. 1997 and Henry 1999). 

Disadvantages are generally due to high expenses which are related with the detection 

steps (Staub and Serquen 1996 and Mohan et al. 1997). Automation is applicable, 

though, it is in fact another reason causing increase in expenses (Staub and Serquen 

1996, Mohan et al. 1997 and Ranade 2003). 

6

1.2.1.2. SSR 

Figure 1.3. The protocol of AFLP technique. 

(Source: Invitrogen 2003) 

Simple sequence repeats or microsatellites are terms used to refer to tandemly 

repeated short nucleotide units between 1-5 bps in the genome (Staub and Serquen 

1996, Powell et al. 1996, Jones et al. 1997 and Nunome et al. 2003a). These repeats 

show a genome-wide distribution and can be placed in either genes or non-coding 

regions of the nuclear genome or else in extranuclear genomes (Powell et al. 1996, 

Jones et al. 1997, Nunome et al. 2003b and Varshney et al. 2005). In the genome, this 

distribution is reported to be collected around particular regions of the chromosomes 

7

such as centromeric areas (Nunome et al. 2003b). For the generation of SSR markers 

sequence data are needed (Jones et al. 1997, Nunome et al. 2003b and Varshney et al. 

2005). These data are obtained in two ways. One way is by constructing a genomic 

library and screening using SSR probes (Jones et al. 1997 and Nunome et al. 2003a). 

The other way is based on sequence data supported by publicly available databases 

which comprises gene sequences and cDNA libraries (Nunome et al. 2003a, Nunome et 

al. 2003b and Varshney et al. 2005). ESTs (Expressed sequence tags) are included in the 

second way of accessing microsatellite-related sequence data (Rudd 2003 and Varshney 

et al. 2005). From all the resulting sequences, specific primers for SSRs can then be 

designed (Figure 1.4.). However, difference in the data type that is used classifies SSRs 

as genomic or genic SSRs (Rudd 2003 and Varshney et al. 2005). SSRs designed by 

using EST library data are one of the basic type of genic SSRs. Comparison of these 

SSRs in terms of their advantages and disadvantages was described in the studies of 

Rudd and Varshney et al. (Rudd 2003 and Varshney et al. 2005). Due to being a part of 

conserved regions of the genome, SSR primers designed from EST sequences, are 

expected to be suitable to apply to other related species (Varshney et al. 2005). This 

makes genic SSRs favored in comparison to genomic SSRs. SSRs identified by 

genomic library construction and search can be products of transcribed or non- 

transcribed regions (Varshney et al. 2005 and Nunome et al. 2003b). This feature while 

providing a high rate of polymorphism makes genomic SSRs less transferable among 

species (Varshney et al. 2005). One result of these interpretations is a disadvantage of 

genic SSRs such that less polymorphism is observed for genic SSRs (Varshney et al. 

2005). Another disadvantage is related with the amount of sequence data which is 

publicly available as mentioned above. For example, eggplant was reported in SOL 

Genomics Network (http://sgn.cornell.edu) as having 3,181 ESTs in total (Mueller et al. 

2005). That number was the lowest number within other species mentioned in the same 

study: tomato, potato, pepper and petunia (Mueller et al. 2005). However, sequencing 

studies continue with the continual addition of new data. 

The production of ESTs is a sequencing event and can be directed from each end 

of cDNAs or from both ends (Rudd 2003). As a result, several ESTs are produced 

(Rudd 2003). These ESTs are then clustered to form contigs which include several 

sequence products that overlap and are included in the same region (Rudd 2003 and 

Krane and Raymer 2003). If these contigs include many members, then they are called a 

multi-member sequence assembly (Figure 1.5.). If a cluster includes small portions of a 

8

cDNA, all of which in fact were synthesized from the initial complementary DNA, it is 

referred to as bridged sequence assembly (Figure 1.5.). Last, a cluster that consists of 

single ESTs or small clusters of ESTs are called singletons and small clusters, 

respectively (Figure 1.5.). 

Figure 1.4. The design of genic SSR primers databases and their fields of use. 

(Source: Varshney et al. 2005) 

9

Figure 1.5. Production and clustering of ESTs from genomic DNA. 

(Source: Rudd 2003) 

SSR is a PCR based molecular method (Staub and Serquen 1996 and Jones et al. 

1997). The principle is the detection of polymorphisms resulting from different numbers 

of repeat units in different individuals and is observed codominantly (Powell et al. 1996, 

Jones et al. 1997 and Henry 1999). The level of polymorphism is very high which 

makes SSR an ideal marker for mapping and diversity studies, fingerprinting and 

population genetics (Powell et al. 1996, Jones et al. 1997, Mohan et al. 1997 and 

Nunome et al. 2003a). It has an easy application procedure which is basic PCR 

amplification of the sample and then detection of the bands (Powell et al. 1996 and 

Jones et al. 1997). However, the major disadvantage is related with development of SSR 

primers which is defined above. 

10

1.4. Solanaceae Family 

The Solanaceae is a family in the plant kingdom and is a member of the 

Magnoliophyta division which is more generally referred to as angiosperms or 

flowering plants. The family is one of the five families of the Solanales order which is 

respectively a group within the 10 orders in Asterids (APG II 2003). The family 

includes 90 genera and estimated species number is between 3000-4000 (Knapp et al. 

2004 and WEB_10 2007). 

The Solanaceae family members are well adapted to different environments. 

They show a good dispersal to a wide region in the world and even to places that have 

harsh conditions such as deserts (Knapp et al. 2004, WEB_10 2007 and WEB_4 2007). 

As a result, the Solanaceae plants can be grown in several habitats and distributed 

worldwide (Figure 1.6.). 

Figure 1.6. The dispersion of Solanaceae family members around the world. 

(Source: WEB_10 2007) 

However, the origin of diversity for most solanaceous plants is around tropical 

regions with accumulation around the Amazon and Andes parts of South America, thus 

they have a New World origin (Daunay et al. 2001, Knapp et al. 2004, WEB_10 2007 

and WEB_4 2007). There are a few exceptions, though. For example, Solanum 

melongena (eggplant) and some of its related species are of Asia-Africa origin and are 

domesticated species, thus they are of Old World origin (Daunay et al. 2001, Doganlar 

et al. 2002a and Doganlar et al. 2002 b). 

11

Owing to its inclusion of plant species that are important in relation to human 

diet, health issues and beauty and decorative needs, the family ranks third in economic 

importance (Mueller et al. 2005 and WEB_4 2007). This is also due to the Solanaceae 

consisting of a high number of domesticated species including tomato, pepper, potato, 

petunia, datura, tobacco, eggplant and others (Doganlar et al. 2002b, Mueller et al. 

2005, WEB_10 2007). 

In addition to distribution and usage diversity, morphological diversity among 

the Solanaceae family members which cover genus, species and cultivars is really 

noteworthy (Knapp et al. 2004 and WEB_10 2007). Flowers, fruits and leaves are 

important plant parts used commonly in taxonomy as they were targets of the 

domestication process (Doganlar et al. 2002b, Knapp et al. 2004 and WEB_10 2007). 

Recently, the huge variation for these traits is combined with molecular data for 

phylogenetic studies and an example was presented in the review of Knapp et al. 

(Knapp et al. 2004). In that study, the two forms of solanaceous fruits (berries or 

capsules), growth period (annual or perennial) and structure of the flower 

(actinomorphic or zygomorphic) were taken into account and the resulting tree is in 

Figure 1.7. (Knapp et al. 2004). There are also other morphological traits that show 

differences among the Solanaceae family such as prickles and hairs on several parts of 

the body, height and length of plant and plant organs (Doganlar et al. 2002b and Frary 

et al. 2003). 

12

Figure 1.7. An example of a phylogenetic tree of the Solanaceae family indicating 

morphological traits (Source: Knapp et al. 2004). 

1.4.1. Genus Solanum 

The number of species in the Solanum genus is reported differently according to 

different sources as 1000-1400, 1500-2000 and 1000-2000 species (Sakata and Lester 

13

1994, Isshiki et al. 1994c, Lester 1997, Daunay et al. 1998 and WEB_10 2007). This 

makes Solanum the most crowded genus of the family and almost half of solanaceous 

plants are members of this genus (Doganlar et al. 2002a, Knapp et al. 2004, WEB_10 

2007 and WEB_11 2007). The confusion is not only about the exact number of species 

in the genus or family. It is also related with the number of names used for these 

species. These data are also not constant with over 3000, 3700 and close to 5000 names 

that are referred to in different papers (Sakata et al. 1994, Lester 1997, Daunay et al. 

1998, Daunay et al. 1999, Furini and Wunder 2004). Due to all this indefiniteness and 

the importance of the genus for humans, there are considerable numbers of studies on 

the taxonomy, phylogeny and biotechnology of Solanum species. The importance for 

humans relies on the existence of several important crop plants in the genus. 

1.4.2. Eggplant (Solanum melongena) 

Due to confusion about use of the term eggplant, Lester indicated that eggplant 

may be used as nomenclature to refer to several Solanum species important for human 

diet and health such as Solanum melongena, S. aethiopicum, S. macrocarpon, S. 

quitoense, S. sessiliforum and related species (Lester 1998 and Daunay et al. 2001). 

However, another definition of eggplant only includes three cultivated species: S. 

melongena, S. aethiopicum and S. macrocarpon (Lester 1998, Daunay et al. 2001 and 

Doganlar et al. 2002a). Among these species, S. melongena is commonly referred to as 

eggplant and is of the most interest in published studies and as well as for this thesis 

(Lester 1998). 

The name eggplant comes from the shape and color of the vegetable’s fruit 

(Lester 1998, Economic Research Service, USDA 2006 and National Research Council 

2006). Like an egg in shape and white-colored, this fruit led people to use this term in 

history (Economic Research Service USDA, 2006 and National Research Council, 

2006). However, this fruit of African-origin was superseded by the Asian- domesticated 

species, Solanum melongena (Lester 1998, Daunay et al. 2001, Lester and Daunay 

2003, National Research Council, 2006 and Frary et al. 2007). There are several terms 

used for Solanum melongena. Eggplant, brinjal eggplant, aubergine or guinea squash 

are examples of these terms (Nothmann 1986, Choudhury 1995, Lawande and Chavan 

14

1998, Daunay et al. 1999 and Kashyap et al. 2003). However, Brinjal eggplant is the 

most common name used to refer to Solanum melongena. 

The distribution and production of S. melongena differs according to countries 

and continents. The major production area is the continent Asia where the plant has real 

importance (Choudhury 1995, Lawande and Chavan 1998, Collonier et al. 2001, 

National Research Council 2006 and Frary et al. 2007). India and China are the two 

countries which are the primary cultivation centers and have the highest production 

(Lawande and Chavan 1998, Lester 1998, Daunay et al. 2001, Doganlar et al. 2002a, 

Doganlar et al. 2002b and Economic Research Service, USDA 2006). Thailand, 

Malaysia, Indonesia, and Philippines are the other important producers in Asia 

(Lawande and Chavan 1998, Daunay et al. 2001, Collonnier et al. 2001 and Doganlar et 

al. 2002b). In its own history, cultivation of brinjal eggplant spread to Japan after India 

and China (Frary et al. 2007). Japan is now an important eggplant producer in the world 

(Economic Research Service, USDA 2006). The introduction of eggplant to the west 

was primarily around the Mediterranean region which is the secondary “domestication 

region” and covers Turkey, Syria, and Persia (Nothmann 1986, Daunay et al. 2001, 

Kashyap et al. 2003, WEB_8 2007 and WEB_12 2007). Although later in history, the 

whole south Mediterranean region including countries such as Italy, Spain, France, and 

Greece became eggplant producers (Lawande and Chavan 1998, Daunay et al. 2001, 

Frary et al. 2007 and WEB_8 2007). Today, Turkey ranks the first in Europe in terms of 

total eggplant production (Economic Research Service, USDA 2006). Egypt is the most 

important brinjal eggplant producer in Africa (Economic Research Service, USDA 

2006). America is far behind in terms of production and is reported as 20 th in the world 

and ranks first as an importer (Economic Research Service, USDA 2006). However, 

interest in eggplant has been increasing in the USA especially since the 1990s 

(Economic Research Service, USDA 2006). Overall, brinjal eggplant is now a globally 

cultivated plant species (Daunay et al. 2001, Doganlar et al. 2002a and Frary et al. 

2007). 

15

Figure 1.8. Worldwide production of eggplant between the years 1995 and 2004 

(Source: Economic Research Service, USDA 2006). 

Figure 1.9. Primary and secondary diversity centers of eggplant (Solanum melongena 

L.). Red-colored region is the basic primary diversity center while green- 

colored regions are secondary diversity centers and major cultivation areas 

(Source: WEB_12 2007). 

Eggplant or brinjal eggplant has three varieties differing from each other based 

on morphology affected by physiology and environment (Nothmann 1986, Lawande 

16

and Chavan 1998 and Kashyap et al. 2003). These varieties are var. esculentum, var. 

serpentinum and var. depressum while the generally sold and consumed types are the 

offspring of these varieties (Nothmann 1986, Lawande and Chavan 1998 and Kashyap 

et al. 2003). 

Eggplant (S. melongena) is a warm-loving plant with an ideal growing 

temperature between 22-30ºC, and has an erect and compact growth habit and large 

leaves and perfect flowers (Nothmann 1986 and Lawande and Chavan 1998). Autogamy 

or self-pollination is the usual way of fertilization although cross-pollination is also 

possible by insect (Nothmann 1986, Lawande and Chavan 1998, Daunay et al. 2001 and 

Frary et al. 2007). The plant is a biennial which is grown as an annual in general 

(Nothmann 1986). There is great morphological diversity among S. melongena 

varieties, cultivars, wild and weedy plants and between related species observed for 

several characters. Fruit color, size, shape and taste are the most noticeable traits that 

show differences among individuals (Collonnier et al. 2001, Kashyap et al. 2003, 

Nothmann 1986, Daunay et al. 2001 and Frary et al. 2007). The color differences of 

fruits are basically due to two color pigments’ and their effects on appearance and are 

controlled by more than one gene (Nothmann 1986 and Frary et al. 2007). These 

pigments are chlorophyll a and b and anthocyanins which are in different amounts and 

in combination determine the exact color of the fruit (Nothmann 1986, Daunay et al. 

2001 and Frary et al. 2007). As a result, eggplant fruits can be from white to black in 

color with a gradient of purple, yellow and green (Nothmann 1986, Lawande and 

Chavan 1998 and Daunay et al. 2001). In addition to the skin color uniformity of plants, 

striped or spotted color configurations are possible (Nothmann 1986, Lawande and 

Chavan 1998 and Daunay et al. 2001). The size of eggplant fruits may vary from grams 

to a kilo and vary greatly in length (Nothmann 1986 and Daunay et al. 2001). Another 

variable morphological character is the shape of the eggplant fruits. Round, egg shaped, 

oblong, pear shaped, long and curved are some examples of different forms of the fruits 

(Nothmann 1986, Lawande and Chavan 1998 and Daunay et al. 2001). Figure 1.10. 

shows some examples of different sized, shaped and colored Turkish eggplants. 

17

Figure 1.10. Examples of fruit diversity in eggplant. 

When the taste of eggplant is considered, bitterness is the main concern and 

arises from the accumulation of a chemical in different amounts: glycoalkaloids 

(Lawande and Chavan 1998). The relation between bitterness and glycoalkaloid 

accumulation is directly proportional (Lawande and Chavan 1998). Consumption of the 

fruit is related with the ripening process (Nothmann 1986 and Lawande and Chavan 

1998). Recommended time is before full maturity at which stage seed formation 

dominates (Nothmann 1986 and Lawande and Chavan 1998). 

In addition to those features and morphological differences, there are also other 

important traits that exhibit a wide range of variety in eggplant. Flower color, hairiness, 

leaf shape, parthenocarpy, spines, resistance to pest and diseases are some examples 

(Nothmann 1986, Lawande and Chavan 1998 and Daunay et al. 2001). Spines are the 

physiological structures on several body parts and are common for not only eggplant but 

also the subgenus (Levin et al. 2006). For this reason, subgenus Leptostemonum was 

referred to as Spiny Solanums in the study of Levin et al. (Levin et al 2006). Resistance 

to pest and diseases is really important due to general susceptibility to these agents in 

eggplant which results in serious effects on production and yield (Lawande and Chavan 

1998, Daunay et al. 2001 and Collonnier et al. 2001). 

As reviewed in the study of Lawande and Chavan, the nutrient composition of 

eggplant changes according to cultivars and varieties. However, in general, the 

chemistry of eggplant is mostly composed of moisture: 92.7% (Lawande and Chavan 

1998 and Collonnier et al. 2001). Carbohydrates, proteins, fiber and fat come after 

moisture as 4.0%, 1.4%, 1.3% and 0.3% respectively (Lawande and Chavan 1998 and 

18

Collonnier et al. 2001). Chlorine, phosphorus and sulfur and, with respectively lower 

amounts, calcium and magnesium are abundant in eggplant (Lawande and Chavan 

1998). Vitamin A and C are also important components of this chemical composition 

(Lawande and Chavan 1998 and Collonnier et al. 2001). Glutamic acid and aspartic acid 

are two amino acids that are in the highest quantity among the others for different 

varieties (Lawande and Chavan 1998). 

Although eggplant is mainly considered as a food product, it also has medicinal 

effects (Daunay et al. 2001, Kashyap et al. 2003 and WEB_4 2007). Cholera, diabetes, 

asthma, bronchitis, dysuria, tooth ache and decrease in cholesterol are examples of 

health disorders on which eggplant has positive effects (Daunay et al. 2001 and 

Kashyap et al. 2003). As a family though, Solanaceae includes important genera that 

have pharmacological properties such as Datura, Belladona, Capsicum and Nicotiana 

(WEB_4 2007 and WEB_5 2007). Atropine, nicotine and capsaicin are alkaloid 

derivatives that have impacts on the neural system and epithelium (WEB_5 2007). All 

these chemicals including eggplant glycoalkaloids have a toxic effect in excessive 

amounts while serving as therapeutics in small amounts (WEB_5 2007). 

Related with the chemical composition, it is known that allergy to Solanaceae 

members such as potato, tomato and bell pepper are possible for some individuals 

(Pramod and Venkatesh 2004 and WEB_5 2007). Recently, it has been reported that 

such allergies to eggplant are rare (Pramod and Venkatesh 2004). In that study, three 

allergens were detected by electrophoresis and immunoblotting assays and three 

different people were sampled for their complaints (Pramod and Venkatesh 2004). 

1.5. Eggplant Genetic Diversity 

As mentioned in the third section, the three varieties of S. melongena, the other 

two eggplant species and most of the species belonging to the Leptostemonum subgenus 

are diploids and have a haploid chromosome number of 12 (Choudhury 1995, Daunay 

et al. 2001 and Kashyap et al. 2003). The genus Solanum has not yet been properly 

identified. There is great morphological diversity observed in the genus both at the intra 

and interspecific levels (Furini and Wunder 2004, Karihaloo and Gottlieb 1995). As 

reported in different studies, morphological diversity is also detected between 

individuals of cultivars and between weedy and wild forms of the species (Isshiki et al. 

19

1994b and Karihaloo and Gottlieb 1995). The distribution of the species in a wide 

region in the world and the existence of different origins of diversity and cultivation 

areas makes classification much more complicated (Lester 1997, Daunay et al. 2001, 

Lester and Daunay 2003, Levin et al. 2006 and National Research Council 2006). In 

addition to these problems, classification attempts were generally based on these 

morphological data which were in fact assisting the confusion about systematics (Mace 

et al. 1999b, Daunay et al. 2001, Furini and Wunder 2004 and Doganlar et al. 2002b). 

However, with new technology and as a result of accumulated molecular knowledge, 

genotypic information has started to be integrated into eggplant systematics and 

classification attempts (Daunay et al. 2001). 

The Solanaceae as a family has also importance in genetic studies as well as 

great economic importance (Daunay et al. 2001, Frary et al. 2003 and WEB_4 2007). 

Three of the model systems used in plant genetics today: tomato, potato and tobacco, 

are members of the Solanaceae family. Two of these crops, tomato and potato, belong 

to genus Solanum (WEB_4 2007). Figure 1.11. shows the phylogenetic relationships 

among species used in biological studies. 

20

Figure 1.11. Plant species used in biological studies are depicted at the order level 

while species belonging to these orders are similarly colored. Order 

Solanales has three species: potato, tomato and tobacco and are in purple 

(Source: WEB_14 2007). 

21

Recently with intense interest in tomato and other species of the family, there is 

increased accumulation of genetic data (Mueller et al. 2005). Much of the recent data 

are expressed sequence tags (ESTs) and can be reached online from a network called 

SGN (Mueller et al. 2005). Tomato, potato, pepper, petunia and eggplant all have EST 

libraries available with tomato having the most and eggplant the least ESTs (Mueller et 

al. 2005). The International Sol Project basically aims to produce data for comparative 

studies in the family via first sequencing the whole genome of tomato as a reference 

genome (Mueller et al. 2005 and WEB_4 2007). Sequencing of the tomato genome 

started in 2004 with collaboration between 10 countries (Mueller et al. 2005). Eggplant 

has been largely ignored in these studies end and progress is still behind other species in 

the Solanaceae family. 

The systematics of flowering plants of which the Solanaceae family is a member 

has recently been organized by the Angiosperm Phylogeny Group (APG II 2003 and 

WEB_1 2007). The idea of the group was to obviate the questions and contradictions 

about classification (APG II 2003). The latest phylogenetic classification of 

angiosperms (flowering plants) and a detailed classification are shown in Figure 1.12. 

and Figure 1.13. 

22

Figure 1.12. Phylogenetic classification of angiosperms. Solanales order is indicated by 

the arrow (Source: APG II 2003). 

23

Figure 1.13. A detailed view of Solanum genus’ classification. The Leptostemonum 

clade includes eggplant and its close relatives (Source: WEB_11 2007). 

1.6. Studies of Genetic Diversity in Eggplant 

In addition to morphological data, which has been used classically in taxonomy, 

other fields of science such as embryology, chemistry and anatomy have been used for 

revised classification of organisms (Daunay et al. 2001 and Singh et al. 2006). The 

usage of molecular data in taxonomy and systematics of organisms is the newest 

strategy for increasing accuracy in relation to evolutionary history. Molecular and other 

types of data are also being applied for classification in the Solanaceae family. 

Experiments based on molecular investigations started just three decades ago for this 

family (Daunay et al. 2001). In this view, some of the first studies were carried out at 

the protein level and examined differences in allozyme and isozyme patterns between 

individuals (Isshiki et al. 1994a, Isshiki et al. 1994b, Isshiki et al. 1994c, Karihaloo and 

Gottlieb 1995 and Kaur et al. 2004). Basically in these studies, Solanum melongena, 

commonly known as eggplant was compared with its weedy and wild forms and close 

relatives (Isshiki et al. 1994a, Isshiki et al. 1994b, Isshiki et al. 1994c, Karihaloo and 

24

Gottlieb 1995 and Kaur et al. 2004). The purpose of these studies was to measure 

genetic diversity in those organisms and these types of markers were identified as being 

especially advantageous for cultivar studies (Isshiki et al. 1994a and Isshiki et al. 

1994b). Although having important features that all markers should have such as 

codominancy, stability and also concordance with the previous classification attempts, 

limitations about the number of isozymes available and their possibility of further 

modifications at the cellular level, such as post-translational modification, resulted in 

declined interest in isozymes and allozymes (Staub and Serquen 1996, Daunay et al. 

2001, Kaur et al. 2004 and Isshiki et al. 1994a). Thus, there are not much data 

accumulated from enzyme studies for eggplant (Kaur et al. 2004). However, studies 

based on enzymatic patterns are still being done. Recently, the technique was applied 

with an increased collection of isozymes and plant material and was found to be 

concordant with previous diversity results (Kaur et al. 2004). 

Another way which is used to determine genetic diversity is concentrated on one 

of the extrachromosomal DNAs: the chloroplast genome. So far, several studies were 

done using chloroplast DNA analysis. In the early studies on Solanum melongena and 

its relatives, non-radioactively labeled total chloroplast DNA (cpDNA) was used as 

probe for detection in total DNA (Sakata et al. 1991, Sakata and Lester 1994 and Sakata 

and Lester 1997). The results were satisfactory in terms of data accumulation and 

agreement with previous studies. In addition to this, some interesting results were 

obtained. In the study of Sakata et al. (1997), it was found that morphological diversity 

was not related to cpDNA diversity and that morphologically similar lines could have 

quite different cpDNA patterns (Sakata and Lester 1997). A similar situation for the 

family Solanaceae was reviewed by Knapp et al. (2004). Although supporting important 

data in the taxonomy of Solanum, cpDNA studies are probably more effective for 

higher taxonomic levels due to cpDNAs maternal inheritance pattern and conservation 

(Sakata and Lester 1997, Olmstead et al. 1999 and Daunay et al. 2001). In the review of 

Daunay et al. (2001) it is proposed that the Leptostemonum subgenus which includes 

Melongena section is relatively suitable for cpDNA analysis. 

Recently, studies about cpDNA are mostly concentrated on sequence data. The 

experiments are designed with a combination of different data just from cpDNA or a 

combination of nuclear DNA and cpDNA. In the study of Olmstead et al., restriction 

fragment length differences in the nuclear genome and the sequence of two chloroplast 

genes were used to construct cladograms reflecting phylogeny of the Solanaceae family 

25

(Olmstead et al. 1999). In another study, Levin et al. studied only sequence data for 

phylogenic systematics of subgenus Leptostemonum of the genus Solanum (Levin et al. 

2006). At a higher taxonomic level, Bremer et al. worked with 3 coding and 3 non- 

coding cpDNA regions to observe phylogeny of asterids to which the order Solanales 

belongs (Bremer et al. 2002). Also in this study, they checked the feasibility of using 

non-coding cpDNA regions to study phylogeny in higher taxa (Bremer et al. 2002). 

Today, there are many phylogeny studies using cpDNA genes or non-coding regions in 

different genera. Even in a recent study, it was proposed that as a comparison criterion 

the sequencing of the chloroplast genome is important (Martin et al. 2005). This 

approach represents the same idea that, in general, increased numbers of genes, 

individuals, species or markers give more accurate results (Martin et al. 2005). The 

Solanaceae family is then one step further than other plant families because the cpDNA 

of a member of the family, Nicotiana tabacum, was the first completely sequenced 

chloroplast genome (Olmstead et al. 1999). 

Other detection techniques used for revealing plant diversity depend on nuclear 

genome analysis and use molecular markers (DNA-based markers) (Mohan et al. 1997 

and Jones et al. 1997). Compared to morphological markers, molecular markers are 

noteworthy because they are unaffected by environmental changes and do not change 

the morphology of plants (Mohan et al. 1997, Jones et al. 1997 and Singh et al. 2006). 

Additionally, there are many more molecular markers in comparison to morphological 

markers (Jones et al. 1997). Molecular markers can be observed at any growth stage 

which is one of the most advantageous properties for breeders. The use of molecular 

markers leads to a new application field: marker assisted selection (MAS) (Staub and 

Serquen 1996, Mohan et al. 1997 and Kashyap et al. 2003). Via MAS, breeders can 

benefit from the early detection of traits of interest that have economic and agronomic 

importance (Staub and Serquen 1996 and Mohan et al. 1997). Some of these 

economically important traits are controlled by single genes (Staub and Serquen 1996). 

However, many important traits such as yield are under the control of several genes. In 

such cases, MAS has the most benefits (Staub and Serquen 1996). To summarize, 

molecular markers such as RFLP, RAPD and AFLP are important markers for not only 

eggplant but also for other plant species because they provide data for MAS and 

diversity studies. (Mohan et al. 1997 and Kashyap et al. 2003). 

RFLP is one type of molecular marker. The basic principle of this marker is the 

difference in length of digested pieces of DNA segments (Staub and Serquen 1996 and 

26

Jones et al. 1997). Digestion points are the restriction sites which are recognized by 

restriction enzymes (Staub and Serquen 1996 and Jones et al. 1997). Variation in length 

(polymorphism) is the result of a mutation affecting that restriction site (Jones et al. 

1997). Despite its codominant nature, ability to define unique loci and reliability, RFLP 

has a time consuming protocol with additional steps to visualize bands via labeled 

probes (Staub and Serquen 1996, Mohan et al. 1997 and Jones et al. 1997). However, 

this technique has an important place in molecular markers in that it is the first marker 

type that was used in mapping studies for humans and, later, plants (Mohan et al. 1997). 

The first interspesific genetic linkage map for eggplant was constructed by using RFLP 

marker system (Doganlar et al. 2002). Two examples of diversity studies using RFLP 

are the papers of Isshiki et al. (Isshiki et al. 1998 and Isshiki et al. 2003). In these two 

different studies, they worked on mitochondrial and PCR amplified chloroplast DNA 

(Isshiki et al. 1998 and Isshiki et al. 2003). The aim for both studies was to look for 

complementation of DNA regions (mtDNA and cpDNA) with extracted and digested 

total DNA (Isshiki et al. 1998 and Isshiki et al. 2003). A different and impressive thing 

for the study of Isshiki et al. (1998) was the amplification of specific cpDNA fragments 

which reduced some of the labor during the process (Isshiki et al. 1998). Despite this, 

the results showed that mtDNA and cpDNA were not suitable materials to study 

diversity in Solanum melongena because of low variability (Isshiki et al. 2003). 

RAPD is another molecular marker. It has a PCR (Polymerase Chain Reaction) 

based principle which was firstly defined by two different groups: Welsh and 

McClelland (1990) and Williams et al. (1990) (Staub and Serquen 1996, Mohan et al. 

1997 and Jones et al. 1997). During the assay, just a single primer randomly binds to 

and allows amplification of several DNA regions. Thus, a banding pattern with 5 to 10 

bands is obtained (Staub and Serquen 1996 and Jones et al. 1997). The advantages of 

this marker system rely on its easiness of application which results in reduced cost and 

time (Staub and Serquen 1996 and Jones et al. 1997). However, it usually shows a 

dominant character and generally they are specific to species (Staub and Serquen 1996 

and Jones et al. 1997). In addition to these disadvantages, RAPD markers do not carry 

two of the most important features that a marker should exhibit: reliability and 

reproducibility (Jones et al. 1997). There are several diversity and mapping studies 

about eggplant using RAPD. For example; as reviewed in Kashyap et al., an eggplant 

molecular linkage map was constructed by Nunome et al. and fruit shape and color were 

mapped with RAPD and AFLP markers (Kashyap et al. 2003 and Nunome et al. 2001). 

27

In another study, Karihaloo et al. looked at diversity between Solanum melongena and 

the weedy form insanum (Karihaloo et al. 1995). As a result of this study, it was 

reported that there is no need to define them as different species due to very high 

genetic similarity (Karihaloo et al. 1995). More recently, a study was designed upon 5 

different species of eggplant to determine their diversity by RAPD analysis (Singh et al. 

2006). The genetic differences observed in this study were high and were the result of 

the fact that sampling was commonly from India which is one of the most important 

diversity regions in the world (Singh et al. 2006). 

AFLP is one of the most favorite markers with its many advantages and fewer 

disadvantages as described in Section 1.2.1.1. There are several studies about eggplant 

AFLP. These studies are generally concentrated on diversity of eggplant (Solanum 

melongena) while the results support the suitability of AFLP for that kind of analysis as 

firstly indicated by the study of Mace et al. (Mace et al. 1999b, Furini and Wunder 

2004). In another study of Mace et al., they used AFLP markers to reveal phylogenetic 

relations of Datureae which is a member of the Solanaceae family (Mace et al. 1999a). 

This study showed that AFLP analysis was more informative than isozyme, 

morphological and ITS-1 markers when the same accessions were compared (Mace et 

al. 1999a). Furini and Wunder also studied eggplant and related species. However in 

addition to AFLP data, morphological data were evaluated as a verification tool 

especially for such a diverse and complicated genus (Furini and Wunder 2004). It was 

also emphasized in the study that the way of deciding which plants should be saved in 

the seed banks should be revised by the addition of molecular data (Tanksley and 

McCouch 1997 and Furini and Wunder 2004). AFLP as a technique is also used for 

mapping studies for eggplant as with other plant species (Mohan et al. 1997, Kashyap et 

al. 2003 and Frary et al. 2007). With combinations of other molecular tools, AFLP was 

used for constructing several genetic linkage maps of eggplant (Kashyap et al. 2003 and 

Frary et al. 2007). 

Like AFLP, SSR is an important molecular marker type owing to its significant 

properties which were described in Section 1.2.1.2. Based on these features, SSRs can 

be used in breeding, MAS, mapping, fingerprinting, population genetics and 

phylogenetic studies (Staub and Serquen 1996, Powell et al. 1996, Jones et al. 1997, 

Nunome et al. 2003a, Nunome et al. 2003b and Varshney et al. 2005). Named 

differently for plants and vertebrates as SSRs (Simple Sequence Repeats) and STRs 

(Simple Tandem Repeats), respectively, repeated sequences as markers are really 

28

informative for both plants and vertebrates (Staub and Serquen 1996). The commonly 

observed types of repeats are different between humans and plants and also among plant 

species and it was estimated that 10 fold fewer SSRs are found in plants than humans 

and diagramed as shown in the Figure 1.14. (Powell et al. 1996, Mohan et al. 1997 and 

Nunome et al. 2003a). 

Figure 1.14. Number of different types of dinucleotide repeats in humans and plants. 

(Source: Powell et al. 1996) 

The first study about SSRs in eggplant concentrated on their suitability as a 

marker system for molecular analysis of this plant (Nunome et al. 2003b). In that study, 

Nunome et al. built a linkage map of eggplant that had SSR, AFLP and RAPD markers 

(Nunome et al. 2003b). In another study, Nunome et al. specifically examined 

trinucleotide repeats in eggplant (Nunome et al. 2003a). The reason trinucleotides were 

used was because of their greater suitability for allele differentiation (Nunome et al. 

2003a). 

In this thesis, two separate assays upon two different sample set were applied. 

For the first one, AFLP technique was used to reveal genetic diversity among several 

Turkish local varieties. For the second assay, SSR molecular marker technique was used 

to identify genetic similarity between Solanum melongena and related species. For both 

studies, materials used in the experiments were kit-extracted DNAs of greenhouse- 

grown samples. 

29

2.1. Materials 

2.1.1. Plant Material 

CHAPTER 2 

MATERIALS AND METHODS 

The plant material used in this thesis’ studies can be categorized into two groups 

in terms of two different experimental designs: AFLP and SSR. One group of material 

was Turkish eggplants. The seeds were supplied by Dr. Ayfer Tan; Aegean Agricultural 

Research Institute (AARI), Turkey (Ege Tarımsal Ara tırma Enstitüsü Menemen, 

Türkiye) and these accessions are listed in Table 2.1. 

30

Table 2.1. Turkish eggplants characterized by AFLP. 

Given Genotype 

Numbers 

Pedigree 

Number 

Accession number Cultivar Name 

1 06T53 TR 66688 Burdur Yerli Patlıcan 

2 06T54 TR 66667 Isparta Patlıcan 

3 06T55 TR 66572 U ak Patlıcan 

4 06T56 TR 43010 Çanakkale Kır Patlıcan 

5 06T57 TR 40300 Gaziantep Mor Dolmalik 

6 06T58 TR 37266 Kastamonu Uzun Patlıcan 

7 06T59 TR 66013 Bursa Topan Patlıcan 

8 06T60 TR 43306 Edirne Kırmızı Patlıcan 

9 06T61 TR 66017 Bilecik Kemer Patlıcan 

10 06T62 TR 66012 Eski ehir Tombul Ak 

11 06T63 TR 66559 Kütahya Patlıcan 

12 06T64 TR 62668 Manisa Uzun Patlıcan 

13 06T65 TR 68530 Zonguldak Patlıcan 

14 06T67 TR 70633 Kemer-27 

15 06T68 TR 50591 zmir Patlıcan 

16 06T74 TR 70635 Topan-374 

17 06T75 TR 62004 

18 06T76 TR 52348 

19 06T77 TR 62430 

20 06T78 TR 62423 

21 06T79 TR 62491 

22 06T80 TR 62525 

23 06T82 TR 62581 

24 06T84 TR 62667 

25 06T85 TR 62736 

26 06T86 TR 62776 

27 06T87 TR 62385 

28 06T89 TR 61593 

29 06T91 TR 61563 

30 06T92 TR 61564 

31 06T93 TR 61706 

32 06T94 TR 61518 

33 06T95 TR 61493 

34 06T96 TR 61766 

35 06T97 TR 61856 

36 06T99 TR 62049 

37 06T100 TR 62043 

38 06T102 TR 61985 

39 06T103 TR 62073 

40 06T104 TR 62072 

41 06T105 TR 62139 

42 06T106 TR 62101 

43 06T107 TR 62100 

44 06T108 TR 61956 

45 06T111 TR 66009 

46 06T112 TR 66014 

47 06T113 TR 66011 

31

Table 2.1. Turkish eggplants characterized by AFLP (Cont.). 


Numbers 

Pedigree 

Number 

Accession number Cultivar Name 

48 06T114 TR 66018 

49 06T115 TR 66334 

50 06T116 TR 66331 

51 06T117 TR 55852 

52 06T118 TR 52522 

53 06T120 TR 43134 

54 06T121 TR 43919 

55 06T122 TR 66579 

56 06T123 TR 66584 

57 06T124 TR 66587 

58 06T125 TR 66589 

59 06T126 TR 66597 

60 06T127 TR 66672 

61 06T128 TR 66667 

62 06T129 TR 66687 

63 06T130 TR 66695 

64 06T131 TR 66698 

65 06T132 TR 66701 

66 06T134 TR 66709 

67 06T135 TR 66720 

68 06T136 TR 66728 

69 06T137 TR 66730 

70 06T138 TR 43768 

71 06T139 TR 55862 

72 06T140 TR 55976 

73 06T141 TR 56029 

74 06T142 TR 61540 

75 06T143 TR 61620 

76 06T144 TR 61892 

77 06T146 Black Beauty 

78 06T147 MM738 

79 06T149 Çamlıca 

80 06T148 Dusky 

81 06T875 MM 0195 S. linnaeanum 

82 06T877 MM 0232 S. aethiopicum group Gilo 

83 06T874 MM 0150 S. macrocarpon 

Seeds for 77 different Turkish lines, three non-Turkish cultivars (Black Beauty, 

MM738 and Dusky) and three wild types as outgroups were sown and grown in the 

greenhouse with 10 seeds planted per line. The second group consisted of wild relatives 

of eggplant seeds of which were obtained from Dr. Marie- Christine Daunay; French 

National Research Institute (INRA), France and are listed in Table 2.2. 

32

Table 2.2. Eggplant and its wild relatives tested with SSR markers. 


Numbers 

Pedigree 

Number 

Accession Numbers Species Names 

1 06T860 MM 0661 S. incanum group A 

2 06T861 MM 0574 S. aethiopicum group Kumba 

3 06T862 MM 0497 S. violaceum 

4 06T863 MM 0374 S. viarum 

5 06T865 MM 0577 S. incanum group C 

6 06T866 MM 0498 S. melongena group E 

7 06T867 MM 0376 S. capsicoides 

8 06T868 MM 0373 S. scabrum 

9 06T870 BIRM/S. 2458 S. melongena group H 

10 06T871 LF3.24 S. melongena group H 


12 06T873 MM 0134 S. aethiopicum group Aculeatum 


14 06T875 MM 0195 S. linnaeanum 

15 06T876 MM 0210 S. campylacanthum 

16 06T877 MM 0232 S. aethiopicum group Gilo 

17 06T878 MM 0284 S. sisymbrifolium 

18 06T879 MM 1248 S. incanum group D 

19 06T880 MM 1259 S. anguivi 

20 06T881 MM 1269 S. semilistellatum 

21 06T882 MM 1350 S. melanospermum 

22 06T883 MM 1426 S. incanum group B 



25 06T886 MM 0702 S. incanum 





30 06T892 MM 0738 S. melongena group H 

31 06T893 MM 0824 S. marginatum 

32 06T895 MM 0982 S. anguivi 

33 06T896 MM 1005 S. lidii 


35 06T899 MM 1010 S. melongena group G 


37 06T901 MM 1137 S. dasyphyllum 

38 06T902 MM 1169 S. aculeantrum 

39 06T903 MM 1235 S. lurchellii 

40 06T904 MM 1244 S. incanum group B 



43 06T908 MM 0674 S. lichtensteinii 




47 06T913 MM 0686 S. melongena group F 

33

Eggplant and its wild relatives were represented by total 47 different individuals that 

are encompassed by 20 different species. Within these 20 species; S. incanum, S. melongena 

and S. aethiopicum had individual groups which were represented by several accessions. 

Species with the number of accessions for each group and total number of accessions for each 

species are listed in Table 2.3. Same as Turkish eggplants, wild eggplants were grown in the 

greenhouse and each species were represented by 10 individuals. 

Table 2.3. List of eggplant and its wild relatives with number of accessions tested. 

Species Names Number of accessions Total number of accessions 

1 S. incanum 1 

Group A 4 

Group B 2 

Group C 4 

Group D 4 15 

2 S. melongena 3 

Group E 1 

Group F 1 

Group G 3 8 

Group H 

3 S. aethiopicum 1 

Group Aculeatum 1 

Group Gilo 

Group Kumba 1 3 

4 S. violaceum 1 

5 S viarum 1 

6 S. capsicoides 1 

7 S. scabrum 1 

8 S. macrocarpon 4 

9 S. linnaeanum 

S. 

1 

10 campylacanthum 1 

11 S. sisymbrifolium 1 

12 S. anguivi 2 

13 S. semilistellatum 1 

14 S. melanospermum 1 

15 S. marginatum 1 

16 S. lidii 1 

17 S. dasyphyllum 1 

18 S. aculeantrum 1 

19 S. lurchellii 1 

20 S. lichtensteinii 1 

34

2.1.2.Sample DNAs 

2.1.2.1. Extraction 

For the extraction process, Wizard Genomic DNA Purification Kit, (Promega, 

Madison, WI, USA), was utilized. The protocol was applied with a few modifications. 

Genomic DNA from the fresh and youngest leaves of 10 plants representing each 

individual was extracted separately. Instead of directly using 600 µl Nuclei Lysis 

Solution to each tube, amount was added in two steps. At first step, 250 µl of solution 

was used for grinding. Then remaining 350 µl was added to each tube and ground tissue 

was mixed several times for better homogeneity. Another modification was about 

centrifugation. Instead of 3 min. at 13.000 – 16.000 g, samples were spun at 10.000 g 

for 5 min. at 6 th step in the protocol and 10.000 g for 2 min. at 9 th step. At the 10 th step, 

ethanol washed samples were spun again at 10.000 g for 2 min. After rehydration of 

DNA with DNA rehydration solution, 5 µl DNA per each individual was taken and 

combined in a new tube with the DNAs of the other individuals of the same accession. 

2.1.2.2. Quantity Checking 

Mixed samples were checked in NanoDrop ND-1000 Spectrophotometer 

(NanoDrop Technologies, Inc., Wilmington, DE, USA) to determine the quantity of the 

DNAs. The NanoDrop values of Turkish and Wild eggplants are in Table 2.4. and Table 

2.5. According to these values, the amount of DNA that was used in the experiments 

was adjusted as described in Section 2.2.1. for AFLP experiments and Section 2.2.2.2. 

for SSR experiments. 

35

Table 2.4. Turkish Eggplants Nanodrop Results. 

Pedigree 

Number 

ng/ul 

Pedigree 

Number 

ng/ul 

Pedigree 

Number 

ng/ul 

06T53 663.61 06T86 488.46 06T120 1156.8 

06T54 513.21 06T87 672.35 06T121 1004.07 

06T55 802.84 06T89 715.87 06T122 1048.06 

06T56 806.55 06T91 583.79 06T123 972.8 

06T57 701.71 06T92 456.02 06T124 1959.06 

06T58 706.64 06T93 913.89 06T125 110.35 

06T59 411.32 06T94 687.44 06T126 120.99 

06T60 1224.08 06T95 1113.16 06T127 162.17 

06T61 804.88 06T96 779.57 06T128 47.77 

06T62 514.05 06T97 695.55 06T129 54.64 

06T63 563.4 06T99 478.93 06T130 843.13 

06T64 299.96 06T100 2031.05 06T131 188.59 

06T65 800.29 06T102 738.43 06T132 936.93 

06T66 1638.53 06T103 689.2 06T134 1373.68 

06T67 598.48 06T104 197.12 06T135 1106.52 

06T68 989.15 06T105 917.37 06T136 239.36 

06T74 992.28 06T106 162.26 06T137 98.67 

06T75 1014.87 06T107 4410.06 06T138 2619.18 

06T76 191.73 06T108 1074.34 06T139 1210.54 

06T77 831.69 06T111 124.78 06T140 1148.92 

06T78 741.69 06T112 908.53 06T141 98.54 

06T79 348.19 06T113 811.18 06T142 1236.51 

06T80 102.28 06T114 1047.41 06T143 3085.77 

06T81 782.35 06T115 1798.6 06T144 239.18 

06T82 1255.79 06T116 1450.27 06T146 352.57 

06T83 70.08 06T117 1476.57 06T147 182.34 

06T84 889.27 06T118 116.44 06T149 839.13 

06T85 506.98 06T119 167.45 

36

Table 2.5. Wild Eggplants Nanodrop Results. 

Pedigree 

Pedigree 

Pedigree 

Number ng/ul 

Number ng/ul 

Number ng/ul 

06T860 647.04 06T879 233.24 06T897 447.13 

06T861 960.96 06T880 596.69 06T899 1185.94 

06T862 338.08 06T881 274.93 06T900 389.76 

06T863 429.92 06T882 414.5 06T901 896.81 

06T865 966.16 06T883 317.42 06T902 332.64 

06T866 160.46 06T884 858.41 06T903 118.43 

06T867 1151.32 06T885 225.5 06T904 88.21 

06T868 484.65 06T886 156.09 06T905 698.1 

06T870 944.99 06T887 243.62 06T906 751.88 

06T871 1140.79 06T888 101.97 06T907 440.85 

06T872 877.97 06T889 217.64 06T908 465.78 

06T873 398.95 06T890 244.27 06T909 507.66 

06T874 929.56 06T891 446.42 06T910 331.29 

06T875 628.03 06T892 414.13 06T911 476.01 

06T876 610.16 06T893 683.53 06T913 361.75 

06T877 385.55 06T895 591.43 

06T878 320.47 06T896 331.32 

2.2. Methods 

2.2.1. AFLP 

For AFLP experiments, two different kits were used: Invitrogen AFLP Core 

Reagent Kit and Invitrogen AFLP Starter Primer Kit. Several pre-experiments were 

done to optimize the protocol. The final protocol was the one defined in the user manual 

of AFLP Analysis System I, AFLP Starter Primer Kit, Version B, 2003 with a few 

modifications as described below. Water used during the whole process was either that 

provided with the kit or Sigma Water (Sigma-Aldrich Company, LTD Irvine, Ayrshire 

KA12 8NB, UK). As Taq polymerase, Promega GoTaq DNA Polymerase (Promega, 

Madison, WI, USA) was used in amplification reactions. Prepared samples were 

analyzed with the CEQ 8800 Genetic Analysis System (Beckman Coulter, Inc., 

Fullerton, CA, USA). The chemicals used during this analysis were Sample Loading 

Solution, Size Standard-600, Mineral Oil, Separation Buffer, Separation Gel and 

Separation Capillary Array all of which were Beckman Coulter products. 

37

The protocol consisted of several steps. Firstly, isolated sample DNAs were 

restricted with two enzymes the properties of which were defined in Section 1.2.1.1. 

These two enzymes were EcoR I and Mse I and were supplied in the kit as a mixture. 

Modification in this step was the adjustment of each sample DNA concentration to ~ 

700 ng/µl. 

At the second step, adapters specific to EcoR I and Mse I restriction sites were 

bound to those regions. For this step, no changes were applied. 

Next step included the first PCR reaction. In this step instead of 1:50 dilution, 

PCR products were diluted 1:40: 1 µl sample DNA and 39 µl sample loading solution 

(SLS). 

The second PCR reaction was based on trinucleotide extension of the previous 

step’s samples. In this step, fluorescent labeled primers were used for detection in the 

CEQ 8800 Genetic Analysis System. Different EcoR I primers with different triplets 

were labeled by Sigma-Proligo (Sigma-Aldrich Company, LTD Irvine, Ayrshire, UK). 

These primers were the same as the kit primers and were diluted before use to 1 

pmol/µl. Because there are no defined and recommended primer combinations for 

eggplant for this product, information about suitable primer combinations for other 

related Solanaceous species was used (Invitrogen 2003). Thus, combinations that 

worked well for tomato, pepper and potato were defined. Of the total 22 primer 

combinations, 10 were selected and applied to Turkish eggplants (Table 2.6.). 

Table 2.6. Selective primer combinations that were applied to Turkish eggplants. 

EcoR I / Mse I 

combinations 

E - ACA 

E - ACC 

E - ACT 

E - AAC 

E - AGC 

E - AGG 

M - CAC M - CAT M - CAG M - CAA M - CTA 

(3.pri.com) 

(11.pri.com) 

(5.pri.com) 

(13.pri.com) 

(6.pri.com) 

(7.pri.com) 

(18.pri.com) 

(16.pri.com) 

(17.pri.com) 

(19.pri.com) 

38

Other modifications in this step were using labeled EcoR I primers instead of 

labeling them as described in the user manual. For Mix 1 and for each sample, 2.5 µl 

EcoR I, 1.5 µl Mse I primers were used. 1µl dH2O was added per sample to complete 

the total volume of Mix 1 to 5 µl. Mix 2 was prepared as the manual described and 5 µl 

from Mix 1, 10 µl from Mix 2 and 5 µl DNA were mixed. First PCR profile for this 

selective amplification was chosen due to defined PCR machine properties. 

The last step was the preparation of the samples, for the machine. Selective PCR 

products were first diluted 1:5 with dH2O: 2 µl DNA and 8 µl SLS. Then, a second 

dilution with SLS was done: 3 µl DNA was mixed with 30 µl SLS and 0.5 µl size 

standard-600. 

As appropriate for the size standard that was used, (Size Standard-600, 

GenomeLab, Beckman Coulter, Inc., Fullerton, CA, USA), Frag 4 method in the system 

was chosen. The profile of the method was: capillary temperature 50ºC, denaturation 

temperature 90ºC for 120 sec., injection voltage 2.0kV for 30 sec. and with a separation 

voltage 4.8 kV for 60.0 min. After definition of the plate and method, system was 

started to be run. 

2.2.2. SSR 

2.2.2.1. Design and Checking of the SSR Primers 

For design of SSR primers, an EST library of Solanum melongena with 3181 

sequences was accessed from Sol Genomics Network (WEB_4 2007). SSRs in the 

sequences were found using the SSR Discovery Input program from PBC Public 

Databases (WEB_15 2006). Among these designed primers, the primers that had certain 

repeat numbers were selected for synthesis by Integrated DNA Technologies, Inc. IA, 

USA. In the next step, synthesized primers were checked for amplification in PCR 

reactions. PCR conditions were a preliminary denaturation for 5 min. at 94ºC; 35 cycles 

at 94ºC for 30 s., 50ºC for 1 min., 72ºC for 1 min.; final extension for 5 min at 72ºC and 

hold at 4ºC. For annealing temperature, a general estimation was done with 5ºC less 

then the melting temperature of the SSR primers. Generally, 50ºC was applied to all 

primers. PCR reaction was 25 µl per sample: 2.5 µl 10x PCR Buffer; 0.5 µl dNTP, 0.5 

µl of F primer and R primer; 0.25 µl Taq Polymerase; 18.75 µl dH2O and 2 µl sample 

39

DNA. The products were prepared for gel electrophoresis by adding 2 µl blue juice to 

each sample and the gel was 3% agarose 1xTAE. Samples were electrophoresed for at 

least 4 hours at 120 mA. For visualizing of DNA bands in the gel, ethidium bromide 

was used either by adding it directly to the gel or by staining the gel with an ethidium 

bromide solution after electrophoresis. At last step, these gels were viewed using the 

AlphaImager Gel Documentation System (Alpha Innotech, San Leandro, CA, USA). 

2.2.2.2. SSR Protocol 

As a result of gel electrophoresis, primers giving polymorphic bands were 

detected. These primer combinations’ forward pairs were extended by adding M13 

sequence. M13 sequence was added to the 5’ end of the forward primer whereas the 

reverse primer remained same as previously designed (Table 2.7.). These newly 

designed forward primers and separate fluorescent M13 primers were synthesized by 

Sigma-Proligo (Sigma-Aldrich Company, LTD Irvine, Ayrshire, UK). 

The best PCR conditions and the amounts of components in the experiments 

were determined after several preliminary experiments. PCR reactions were 20 µl total 

for each sample and were composed of 13.15 µl dH2O, 2 µl 10x PCR buffer, 0.4 µl 

dNTP, 0.2 µl Taq Polymerase, 0.75 µl of each primer (F and R primers and M13) and 2 

µl sample DNA. Sample DNA concentrations were adjusted ~10 ng/µl by dilution with 

dH2O. The profile of the PCR was: 94ºC for 5 min.; 94ºC for 30 s., 56ºC for 45 s., 72ºC 

for 45 s. for 27 cycles; 94ºC for 30 s., 53ºC for 45 s., 72ºC for 45 s. for eight cycles; 

72ºC for 10 min, hold at 4ºC. 

Before loading the samples for analysis in the CEQ 8800 Genetic Analysis 

System, PCR products were diluted 1:10 with sample loading solution (SLS). For each 

sample, 3 µl PCR products were diluted with 27 µl SLS and 0.5 µl size standard-600. 

Suitable with the used size standard, Frag 4 method in the system was used. The 

profile of the method was: capillary temperature 50ºC, denaturation temperature 90ºC 

for 120 sec., injection voltage 2.0kV for 30 sec. and with a separation voltage 4.8 kV for 

60.0 min. After definition of the plate and method, system was started to be run. 

40

41 

Table 2.7. Repeat motifs and sequences for the SSR primers. M13 sequence was added to the forward sequence. 

Given Code Repeat Motif and Number Forward Sequence Reverse Sequence 

smSSR01 (ATT)21 TGTAAAACGACGGCCAGTGTGACTACGGTTTCACTGGT GATGACGACGACGATAATAGA 

smSSR02 (TA)9 (GA)8 TGTAAAACGACGGCCAGTATTGAAAGTTGCTCTGCTTC GAAAGAGGAGATCCAGGAGT 

smSSR03 (TA)9 (GA)8 TGTAAAACGACGGCCAGTATTGAAAGTTGCTCTGCTTC GATCGAACCCACATCATC 

smSSR04 (TA)9 (GA)8 TGTAAAACGACGGCCAGTCTCTGCTTCACCTCTGTGTT CCATGAAAGAGAAGATCGAG 

smSSR05 (TA)9 (GA)8 TGTAAAACGACGGCCAGTTCTGCTTCACCTCTGTTCTT AGTAGAGCAACGACGACAAT 

smSSR06 (TA)9 (GA)8 TGTAAAACGACGGCCAGTTCTGCTTCACCTCTGTTCTT GAAAGAGGAGATCGAGGAGT 

smSSR07 (TAA)20 (CGA)8 TGTAAAACGACGGCCAGTTGAATGGAATTACACAAGCA ATTCTCTAAACCTCAGCCAA 

smSSR08 (TAA)20 (CGA)4 - (TAA)22 TGTAAAACGACGGCCAGTAATGCAAACAATTATCAGGG ACAACTCAGCCAGTCGTAAT 

smSSR09 (TTTGC)3 TGTAAAACGACGGCCAGTCACATGGGAACCTACTTACC GACGACCATCAAACAAGAAT 

smSSR10 (TTTGC)3 TGTAAAACGACGGCCAGTAAGCTTCGGAGGAAGATAAG GGGAGATGGAATAAGTCACA 

smSSR11 (AGC)6 TGTAAAACGACGGCCAGTAAACAAACTGAAACCCATGT AAGTTTGCTGTTGCTGCT 

smSSR12 (ACCAA)3 TGTAAAACGACGGCCAGTAAACAGAAACCAGAGTACTTCA CAGAAGAAGGTTCAGTTTGC 

smSSR13 (AT)9 TGTAAAACGACGGCCAGTAGGAATTAACATGGTTCAACA TTCCTCTTACAACCACATCC 

smSSR14 (ATTA)4 TGTAAAACGACGGCCAGTATACCACATCAATCCAAAGC CATCATCATCTTCACAGTGG 

smSSR15 (CCTTT)3 TGTAAAACGACGGCCAGTCTGTGGTTGCCTTATCAGTA TAGTCCAAGGGTTTGATGAC 

smSSR16 (AGA)7 TGTAAAACGACGGCCAGTAAGAATTTGATGTTGAACCG CTTTATCAGCCAATTTCTGG 

smSSR17 (ATAC)4 TGTAAAACGACGGCCAGTTCTTGCCATTTAATTTCCTC CTATGTCCCTATTATGCCCA 

smSSR18 (TAAT)4 TGTAAAACGACGGCCAGTTTAGGCATTTGATTTAGCCT TATGTCCCTAAGCATAACGG 

smSSR19 (GAA)6 TGTAAAACGACGGCCAGTGAACAATGATTCATCGGATT AGTTGATGTTGAATTTCCCA 

smSSR20 (AGA)5 TGTAAAACGACGGCCAGTACAAGGAAGGACACAAACAC ATCTAATCACTGTCGCTGCT 

smSSR21 (TAC)5 TGTAAAACGACGGCCAGTAAGTTTACATGACAGCACCA TTGCCATCATCAATACCATA 

smSSR22 (GCC)5 TGTAAAACGACGGCCAGTCTCCGTCAAATTCCTATCAA GGGAGTCCACATAGAGCATA 

smSSR23 (AAG)5 TGTAAAACGACGGCCAGTAGAGAAGAAGCCAGCAGAA TCTGAATCTCCCGAGAAGTA 

smSSR24 (TCA)5 TGTAAAACGACGGCCAGTGATTTATGGCTTCTGATGGA TCCTAACCCACTTGATGAAC 

smSSR25 (TGA)5 TGTAAAACGACGGCCAGTTCCTAACCCACTTGATGAAC GATTTATGGCTTCTGATGGA 

smSSR26 (AAG)5 TGTAAAACGACGGCCAGTCAACTTCGATCTTCAATTCC TCTGAATCTCCCGAGAAGTA 

smSSR27 (TGT)5 TGTAAAACGACGGCCAGTATACATTTGAGCCGAGAGTG TAAATCTGAGAAGGTCGCAT 

smSSR28 (TCA)5 TGTAAAACGACGGCCAGTCACACTCCTCAGAACTCCAT CAGCAGTACCTCTTGGTCAT 

smSSR29 (CTT)5 TGTAAAACGACGGCCAGTTCCACTTCAATTTCCAAGTC GATCGCTTAGCAGAAGCC 

smSSR30 (GAA)5 TGTAAAACGACGGCCAGTGATCGCTTAGCAGAAGCC TCCACTTCAATTTCCAAGTC 

41

42 

Table 2.7. Repeat motifs and sequences for the SSR primers. M13 sequence was added to the forward sequence (Cont.). 

Given Code Repeat Motif and Number Forward Sequence Reverse Sequence 

smSSR31 (TCC)5 TGTAAAACGACGGCCAGTCTTCCTACCCACACTTCATC TAGGCCGGAGATAGTTGTAA 

smSSR32 (GAA)5 TGTAAAACGACGGCCAGTCCCACTGATCAGAAGAAGTT TAGCACACATCCATACCAAA 

smSSR33 (TCA)5 TGTAAAACGACGGCCAGTTTGCTAGAAATAGCAAAGGG CGTGGTGTGTATGATGCTTA 

smSSR34 (AGA)5 TGTAAAACGACGGCCAGTACAAGGAAGGACACAAACAC ATCTAATCACTGTCGCTGCT 

smSSR35 (ATG)5 TGTAAAACGACGGCCAGTCACCACCAAAGAATTCCTAA TTGCTAGAAATAGCAAAGGG 

smSSR36 (CTG)5 TGTAAAACGACGGCCAGTAGCACCAGGACAATGAATAC CCATTTCTTTCTCGACCTTA 

smSSR37 (AAG)5 TGTAAAACGACGGCCAGTAAAGAAGCTTCCGACGAA CACTTGTTTCAGCACTTTGA 

smSSR38 (GCT)5 TGTAAAACGACGGCCAGTGCCATAGATGAAAGGTCAGA GGATTTATGGACAAGGTGAA 

smSSR39 (TCA)5 TGTAAAACGACGGCCAGTTTGCTAGAAATAGCAAAGGG CGTGGTGTGTATGATGCTTA 

smSSR40 (AAG)5 TGTAAAACGACGGCCAGTTTCTTTGATCTTCAATTCCAA ATGAAGCTGTTCATGATTCC 

smSSR41 (TCA)5 TGTAAAACGACGGCCAGTCTCCTCCTGGTAAGGAGTCT GCAGTATAGAGACGCGAAAT 

smSSR42 (CAC)5 TGTAAAACGACGGCCAGTACAGTACACCAGAAACGGAA GTTACAATGACGGTGGATCT 

smSSR43 (GCT)5 TGTAAAACGACGGCCAGTACACCTAAACAACAACCAGG GGTGGTGTTCAGTCATCTTT 

smSSR44 (CCA)5 TGTAAAACGACGGCCAGTTGCATTTCATACAGAAACCA GCAAGGATATCACTGAGCTG 

smSSR45 (TTC)5 TGTAAAACGACGGCCAGTTTTCTCAACCCAAACTGAAC GCAGCTCTCGCATAGATAGT 

smSSR46 (CAC)5 TGTAAAACGACGGCCAGTGGAAACCTTCATTCACTTCA AGGTCACCGTTACAATTACG 

smSSR47 (AGA)5 TGTAAAACGACGGCCAGTACACGATGATCATAAGGGAG ATCTAATCACTGTCGCTGCT 

smSSR48 (GCT)5 TGTAAAACGACGGCCAGTGCCATAGATGAAAGGTCAGA GGATGGAAAGGATAAGAAGG 

smSSR49 (ATG)5 TGTAAAACGACGGCCAGTTAGTCAACTGCATCACCAGA CCACTCCCACTACTGTCACT 

smSSR50 (ATG)5 TGTAAAACGACGGCCAGTTATCAGTCAACTGCATCACC TGCATTTACGTGAGCTCTAA 

42

3.1. Results 

CHAPTER 3 

RESULTS AND DISCUSSION OF AFLP DATA 

3.1.1. Pre-Experiments and Their Results 

To determine the final form of the protocol described in Section 2.2.1. that gave 

the best results for eggplant samples and their relatives, several preliminary experiments 

were done. These attempts were changes in the amounts of the components or dilution 

ratios. Also, because no primer combinations for the selective PCR amplification step 

were specified for eggplant in the kit protocol, various combinations were tested. 

At first, sample DNA amounts of 0.5 µl, 1 µl, and 1.5 µl were tested. Then, in 

accordance with the recommended amount (250 ng), DNA concentrations were fixed to 

~ 100 ng/ µl. From these dilutions 2.5 µl was taken for each sample and used in the 

restriction digestion step. However, the best results for eggplant samples were ~ 700 ng/ 

µl for restriction digestion. For selective PCR, 5 µl and 7 µl DNA from the previous 

step were tried and 5 µl was determined to be better. 

In the second PCR, although all primers had the same triplet extensions, the 

selective primers for both EcoR I and Mse I were not the kit primers. An important point 

was the need for addition of dNTP which was an extra variable. Different dNTP 

amounts applied in the experiments were 0.4 µl and 0.6 µl. However, due to discordant 

results for both samples and amounts and to eliminate a variable, it was decided that 

Mse I primers would be used from the kit. This was basically because dNTP were 

included with the kit primers. In this step, also, different primers amounts were tested. 

Different from the user manual, 2.5 µl EcoR I and 1.5 µl Mse I were decided to be best 

in the end. 

As mentioned previously in Section 2.2.1., due to a lack of defined data about 

selective primer combinations in the kit manual (Invitrogen 2003), combinations that 

worked best in related species were determined. Twenty two such combinations were 

applied to two different Turkish eggplants and the 10 giving the best results were 

selected (Table 2.6.). Of these 10 combinations, two of them (E-ACT/M-CAG and E- 

43

AAC/M-CAG) were the same as previously published AFLP primer combinations used 

in eggplant (Mace et al. 1999a and Mace et al. 1999b). 

One of the most challenging parts of the experiment which was not mentioned in 

the protocol was the dilution of samples. Two different dilution steps were of concern: 

dilution with water before sample loading solution (SLS) and SLS dilution. Dilutions of 

1:5, 1:10, 1:20 and 1:40 in water after selective PCR were tested. In those tests, 1:20 

was the best resulting dilution ratio. For SLS dilution, three different dilutions were 

tested: 1:5, 1:10 and 1:20. The results of these dilution ratios were related with the 

amount of sample DNA and kit primer used during the experiments. Generally when 

sample DNA volume (water diluted) was high, a higher dilution ratio with SLS and less 

selective kit primer gave better results. If less DNA was taken, more kit primer and less 

SLS worked better. There are also TE (supplied by the kit) dilutions according to 

protocol. For these steps, several attempts were made to find out the best resulting one 

for eggplant samples. The only change was after the first PCR: instead of 1:50, a 1:40 

dilution was applied as described in Section 2.2.1. 

In summary, each component in the experiment and their concentrations were 

sensitive. Less than should be or excess amount of DNA, dNTP, Taq polymerase and 

primers affect the results and sometimes no result may be obtained. The most important 

thing that is emphasized in the manual (Invitrogen 2003) was the purity of DNA. For 

such an importance, extraction of sample DNAs was done with DNA purification kit 

and quantities of DNAs were measured for each sample as described in detailed in 

Section 2.1.2. Results from an AFLP experiment and an expanded view of that figure 

are shown in Figure 3.1. and Figure 3.2. 

44

Figure 3.1. An example of AFLP study results for three different samples (06T122, 

06T139 and 06T144) with one primer combination (11. primer com). Size 

standards are not shown in the figure. 

Figure 3.2. A closer view of the same results shown in Figure 3.1. Polymorphisms 

detected within the three samples are indicated by arrows. Fragment sizes 

are indicated above each peak. 

06T122 11.primer 






45

3.1.2. Analysis and results of the AFLP Data 

For analysis of AFLP data, the results of the experiments were genotyped based on 

the presence and absence of peaks (bands) as 1 and 0, respectively. The preliminary 

analyzed data were then used to draw a dendrogram. In this study, to draw the dendrogram 

of Turkish eggplants, NTSYS-pc version 2.2j, (Applied Biostatistics Inc, Setauket, New 

York, USA), was used. This software consists of several clustering methods including 

UPGMA (unweighted-pair group method arithmetic average) and enables the correlation of 

data and construction of dendrograms with two and three-dimensional plots of the 

components. 

To draw the dendrogram, qualitative data were used to generate a matrix 

determining similarity and dissimilarity among samples. The chosen method was Dice’s 

method (Dice 1945) which is one of the coefficients evaluating similarity of the samples 

(Mohammadi and Prasanna 2003 and Gulsen et al. 2007). The defined similarity matrix 

was then used to draw a dendrogram with the clustering method UPGMA via the SHAN 

module in the software. To decide the efficiency of clustering, the cophenetic 

correlation coefficient was calculated with the Mantel method (1967) (Mohammadi and 

Prasanna 2003). 

As a second step, Principle Component Analysis (PCA) was done to form two- 

dimensional and three-dimensional plots representing samples organization in multiple planes 

(Mohammadi and Prasanna 2003). To do that, a correlation matrix of the data was calculated 

with SIMINT module in the software. Then, Eigen values were calculated with Eigen module 

in the software of which values are listed in Table 3.1. 

Table 3.1. Eigen values representing principal components of the study AFLP Turkish 

eggplants at three dimensions are listed in order. 

Eigenvalue Percent Cumulative 

1 53.40756115 64.3465 64.3465 

2 4.66385657 5.6191 69.9656 

3 1.86849208 2.2512 72.2168 

At the last step, the acquired tree and plots were arranged for the final form 

while samples were labeled and graphs were organized as shown in Figure 3.3., Figure 

3.4. and Figure 3.5. 

46

47 

Figure 3.3. Dendrogram showing coefficient of similarity among Turkish eggplants and three outgroups. 

47

48 

Dim-2 

0.34 

0.17 

-0.00 

Macro. 

Aeth. 

31 

38 

Linna. 

50 

22 

59 37 69 8 

57 

70 18 

40 

65 

49 

45 

80 7643 

23 79 

42 61 7233 

52 74 

44 

60 

6362 

75 66 

48 

35 51 

30 

24 

29 

58 

-0.18 

28 36 

19 

39 20 

41 26 

46 53 

55 

56 

-0.35 

25 21 

34 

3254 

-0.12 0.14 0.40 

Dim-1 

0.66 0.92 

17 

2 

11 

10 

16 

9 

1 

4 

12 

7 

15 3 

5 

13 

6 

14 

Figure 3.4. Two-dimensional plot of Turkish eggplant accessions. 

64 

77 

78 

73 68 

67 

71 

27 

47 

48

49 

8 

16 18 

22 

23 33 

37 

40 

42 

43 

44 

45 

49 

50 52 

57 

59 

60 

61 

62 

63 

64 

65 

66 

67 

68 

69 

70 

72 

73 

74 

75 

76 

77 

78 

79 

80 

Macro. 

Linna. 

Aeth. 

1 

2 

3 

4 

5 

6 

7 

9 10 

11 

12 

13 

14 

15 

17 

19 

20 

21 

24 

25 

26 

27 

28 

29 

30 

31 

32 34 

35 

36 

38 

39 

41 

46 

47 

48 

51 

53 

54 

55 56 

58 

71 

0.34 

0.34 

0.17 

0.17 

-0.00 

-0.00 

Dim-2 

Dim-2 

-0.18 

-0.18 

-0.35 

-0.35 

-0.35 

-0.35 

-0.12 

-0.12 

0.14 

0.14 

-0.17 

-0.17 

0.40 

0.40 

Dim-1 

Dim-1 

0.66 

0.66 

Dim-3 

Dim-3 0.01 

0.01 

0.92 

0.92 

0.18 

0.18 

0.36 

0.36 

8 

16 

18 

22 

23 33 

37 

40 

42 

43 

44 

45 

49 

50 

52 

57 

59 

60 

61 

62 

63 

64 

65 

66 

67 

68 

6970 

72 

73 

74 

75 

76 

77 

78 

79 

80 

Macro. 

Linna. 

Aeth. 

1 

2 

3 

4 

5 

6 

7 

9 

10 

11 

12 

13 

14 

15 

17 

19 

20 

21 

24 

25 

26 

27 

28 

29 

30 

31 

32 

34 

35 

36 

38 

39 

41 

46 

47 

48 51 

53 

54 

55 56 

58 

71 

0.34 

0.34 

0.17 

0.17 

-0.00 

-0.00 

Dim-2 

Dim-2 

0.92 

0.92 

0.66 

0.66 

-0.18 

-0.18 

Dim-1 

Dim-1 

0.40 

0.40 

0.14 

0.14 

-0.35 

-0.35 

-0.35 

-0.35 -0.12 

-0.12 

-0.17 

-0.17 

Dim-3 

Dim-3 

0.01 

0.01 

0.18 

0.18 

0.36 

0.36 

Figure 3.5. Three-dimensional graphs of Turkish eggplants AFLP results. 

49

3.2. Discussion 

One of the statistical results of AFLP analysis was the correlation matrix result: r 

value. In the review of Mohammadi and Prasanna, an r value of more than 0.9 is defined 

as a very good correlation (Mohammadi and Prasanna 2003). For the AFLP data for 

Turkish eggplants, an r value of 0.97 was obtained and indicates that the correlation 

coefficient between the similarity matrix of data and dendrogram was in the best scale 

(Mohammadi and Prasanna 2003). Reported Eigen values were also informative. These 

results showed that the first component explained 64.34% of the variation between 

samples (Table 3.1.). For three axes, a total of 72.21% variation was explained. 

The similarity within the total of 83 samples including three outgroups was 

between 0.29 and 0.95, with a mean value of 0.62 (Figure 3.3.). There were just two 

samples identical with 0.95 similarity, genotype numbers 58 and 12. Among the 

outgroups, Solanum linnaeanum was the closest sample to Turkish eggplants which 

were representative of Solanum melongena. At the point where S. linnaeanum joined to 

most of the genotypes the similarity coefficient was 0.48. Though, from that point, 

Turkish eggplants were separated into two groups with a 0.68 cophenetic correlation 

coefficient. One group which was relatively small consisted of three samples with 

genotype numbers 78, 73 and 68. The other group was a very large one represented by 

73 different genotypes out of 83 (88%) in total (Figure 3.3.). That large group also 

separated into two big groups of 43 and 30 samples in each group (Figure 3.3.). The 

correlation coefficient of these two groups was 0.75 (Figure 3.3.). The least similar 

samples for each of these two groups were genotypes 67 and 22 while 67 belonged to 

the first, and 22 belonged to the second group. 

S. macrocarpon was the least similar outgroup of the three outgroups and had 

0.29 similarity coefficient to all remaining genotypes. S. aethiopicum, though, was 

relatively more similar with a 0.33 coefficient value. Samples which were relatively 

distant from most of the Turkish eggplants even from S. linnaeanum outgroup were S. 

melongena genotypes 77, 64, 38 and 31 (Figure 3.3.). 

The concordance of the results with previous studies was dependent on the 

outgroups similarity to S. melongena. This was because in previous studies, generally, 

the variation between S. melongena and Solanum species was investigated (Sakata et al. 

1991, Isshiki et al. 1998, Mace et al. 1999b, Furini and Wunder 2004, Singh et al. 2006 

50

and Levin et al. 2006). Intraspecies diversity examples, though, were again concentrated 

on S. melongena and its closest relatives such as S. incanum (Sakata and Lester 1994, 

Karihaloo and Gottlieb 1995 and Karihaloo et al. 1995). AFLP studies about S. 

melongena were the studies of Furini and Wunder and Mace et al. (Furini and Wunder 

2004 and Mace et al. 1999b). In these studies, genetic variation or similarity were 

investigated within the Solanaceae family. As a consequence of AFLP results, the 

outgroups’ relatedness to Turkish eggplants (S. melongena) was similar in the results of 

previous studies. Among the species S. linnaeanum, S. aethiopicum and S. 

macrocarpon, S. linnaeanum was the closest relative of S. melongena (Furini and 

Wunder 2004 and Levin et al. 2006). In fact, S. melongena and these outgroups were 

reported as in the same subgenus (Leptostemonum) and closer than the other subgenus 

species (Furini and Wunder 2004). The closeness of S. linnaeanum was a result of 

belonging to the same section, Melongena, while S. aethiopicum and S. macrocarpon 

were reported to belong to Oliganthes section (Furini and Wunder 2004). 

51

4.1. Results 

CHAPTER 4 

RESULTS AND DISCUSSION OF SSR DATA 

4.1.1 Pre-Experiments and Their Results 

As a result of the database search mentioned in Section 2.2.2.1., 158 different 

SGN sequences were identified as having at least one SSR. When the SSRs were 

counted individually, the total number of SSRs increased to 168 as nine of the 

sequences had two SSRs and one had three SSRs (Table 4.1.). In total, seven compound 

repeats were identified meaning that two SSRs followed each other (Table 4.1.). 

Overall, the AT repeat was the most common repeat representing 8.33 % of the total 

(Table 4.1). The longest simple SSR was a TAA SSR with 22 repeat units (Table 4.1.). 

Based on total length, the longest SSR was the compound repeat (TAA)20 (CGA)8, 84 

nucleotides long (Table 4.1.). 

When the repeat motifs were classified in terms of the number of the bases in the 

repeat, it was observed that the most common ones were trinucleotide repeats which 

represented 56.7% of the total (Table 4.1.). TCA and TTC/AAG were the two most 

frequently identified trinucleotide repeats with 8 SSRs identified for each (Table 4.1.). 

52

Table 4.1. Repeat motifs, numbers of SSRs identified and average repeat numbers for 

the SSRs identified in the eggplant EST library. 

Repeat Motif Number of SSRs Identified Average repeat # 

Dinucleotide 

AT/ TA 14/ 2 5,78/ 6,5 

AC 3 6 

GA 1 7 

TC/ AG 1/ 1 5/ 6 

CA 1 8 

Trinucleotide 

TCA 8 4,625 

ATT/ TAA 1/ 1 21/ 22 

ACC/ TGG 2/ 3 4/ 4 

AGA/ TCT 6/ 2 5/ 4 

AGC 4 5,25 

TGC 6 4 

TTC/ AAG 8/ 8 4,375/ 4,5 

CTT/ GAA 4/ 3 4,25/ 5,33 

TAC/ ATG 1/ 3 5/ 5 

AAC/ TTG 2/ 1 4/ 4 

GCA 1 6 

GCC 1 5 

ACT/ TGA 2/ 3 4/ 4,33 

ACA/ TGT 4/ 3 4/ 4,33 

CAT 4 4 

CCG 4 4 

AAT/ TTA 1/ 2 4/ 4 

GTG/ CAC 1/ 4 4/ 4,5 

ATA 2 4 

CCA 2 4,5 

GAT 2 4,5 

TCC 1 5 

GAG 1 4 

CTG 1 5 

GCT 4 4,75 

CAG 1 4 

CAA 3 4 

Tetranucleotide 

CTGG 1 3 

ATAG 2 3 

TTTA 2 3 

ATAC 1 4 

TAAT/ ATTA 1/ 1 4/ 4 

AAAC 1 3 

TGAC 1 3 

Pentanucleotide 

TTTGC 2 3 

ATTTT 1 2 

53

Table 4.1. Repeat motifs, numbers of SSRs identified and average repeat numbers for 

the SSRs identified in the eggplant EST library (Cont.). 

Repeat Motif Number of SSRs Identified Average repeat # 

AAATA 2 2 

AAAAT 3 2 

AATTG 1 2 

AAAAG 1 2 

ACCAA 1 3 

ATAAA 4 2 

CCTTT 1 3 

CATGC 1 2 

TTCCT 1 2 

Compound Repeats 

Dinucleotide 

(TA)9 (GA)8 5 17 

Compound Repeats 

Trinucleotide 

(TAA)20 (CGA)8 1 28 

(TAA)20 (CGA)4 1 24 

The longest SSRs were selected for primer design. The criterion taken into 

account was the number of repeat motifs. Thus, only SSRs containing dinucleotides 

greater than 8, trinucleotides greater than 4, and tetranucleotides greater than 3 units 

long were used for primer design. A total of 50 SSR primer pairs were designed (Table 

4.2.). 

In the next step, the EST sequences having SSRs were analyzed for their 

uniqueness. Thus, the 158 SSR-containing sequences were found to represent 110 

unigenes (Table 4.3.). The remaining 48 sequences were members of these unigene 

families (Table 4.3.). In the table, unique ESTs are listed with (–) in the unigene status 

part (Table 4.3.). The ESTs that are in the same unigene family with other members are 

listed with their SGN EST identifier codes in the status part (Table 4.3.). SGN ESTs 

that in fact belong to an EST family but had no other SSR primers designed for them 

were listed having more than one unigene member but no ESTs in the family (Table 

4.3.). 

54

55 

Table 4.2. SSR primers repeat motifs and sequences. 

Given Code Primer Code Repeat Motif and Number Forward Sequence Reverse Sequence 

smSSR01 sgn|E513845 (ATT)21 GTGACTACGGTTTCACTGGT GATGACGACGACGATAATAGA 55,041 55,346 310 

smSSR02 sgn|E514583 (TA)9 (GA)8 ATTGAAAGTTGCTCTGCTTC GAAAGAGGAGATCCAGGAGT 54,815 54,889 327 

smSSR03 sgn|E514601 (TA)9 (GA)8 ATTGAAAGTTGCTCTGCTTC GATCGAACCCACATCATC 54,815 54,264 145 

smSSR04 sgn|E514602 (TA)9 (GA)8 CTCTGCTTCACCTCTGTGTT CCATGAAAGAGAAGATCGAG 55,529 54,996 320 

smSSR05 sgn|E514645 (TA)9 (GA)8 TCTGCTTCACCTCTGTTCTT AGTAGAGCAACGACGACAAT 55,140 55,047 165 

smSSR06 sgn|E514647 (TA)9 (GA)8 TCTGCTTCACCTCTGTTCTT GAAAGAGGAGATCGAGGAGT 55,140 55,059 315 

smSSR07 sgn|E519315 (TAA)20 (CGA)8 TGAATGGAATTACACAAGCA ATTCTCTAAACCTCAGCCAA 55,129 54,183 240 

(TAA)20 (CGA)4 - 

smSSR08 sgn|E520555 (TAA)22 AATGCAAACAATTATCAGGG ACAACTCAGCCAGTCGTAAT 55,183 54,877 395 

smSSR09 sgn|E513913 (TTTGC)3 CACATGGGAACCTACTTACC GACGACCATCAAACAAGAAT 54,494 55,020 344 

smSSR10 sgn|E513947 (TTTGC)3 AAGCTTCGGAGGAAGATAAG GGGAGATGGAATAAGTCACA 55,452 54,946 248 

smSSR11 sgn|E515884 (AGC)6 AAACAAACTGAAACCCATGT AAGTTTGCTGTTGCTGCT 54,531 54,589 126 

smSSR12 sgn|E516012 (ACCAA)3 AAACAGAAACCAGAGTACTTCA CAGAAGAAGGTTCAGTTTGC 53,397 55,156 313 

smSSR13 sgn|E517027 (AT)9 AGGAATTAACATGGTTCAACA TTCCTCTTACAACCACATCC 54,667 55,033 263 

smSSR14 sgn|E517698 (ATTA)4 ATACCACATCAATCCAAAGC CATCATCATCTTCACAGTGG 54,991 54,721 241 

smSSR15 sgn|E518171 (CCTTT)3 CTGTGGTTGCCTTATCAGTA TAGTCCAAGGGTTTGATGAC 53,832 55,033 116 

smSSR16 sgn|E518867 (AGA)7 AAGAATTTGATGTTGAACCG CTTTATCAGCCAATTTCTGG 55,217 55,070 390 

smSSR17 sgn|E519219 (ATAC)4 TCTTGCCATTTAATTTCCTC CTATGTCCCTATTATGCCCA 54,553 55,149 115 

smSSR18 sgn|E519312 (TAAT)4 TTAGGCATTTGATTTAGCCT TATGTCCCTAAGCATAACGG 54,376 55,387 342 

smSSR19 sgn|E520513 (GAA)6 GAACAATGATTCATCGGATT AGTTGATGTTGAATTTCCCA 54,868 55,468 241 

smSSR20 sgn|E513907 (AGA)5 ACAAGGAAGGACACAAACAC ATCTAATCACTGTCGCTGCT 55,003 55,131 205 

smSSR21 sgn|E514329 (TAC)5 AAGTTTACATGACAGCACCA TTGCCATCATCAATACCATA 54,132 54,840 249 

smSSR22 sgn|E514434 (GCC)5 CTCCGTCAAATTCCTATCAA GGGAGTCCACATAGAGCATA 55,310 55,154 276 

smSSR23 sgn|E515341 (AAG)5 AGAGAAGAAGCCAGCAGAA TCTGAATCTCCCGAGAAGTA 55,388 54,996 338 

smSSR24 sgn|E515827 (TCA)5 GATTTATGGCTTCTGATGGA TCCTAACCCACTTGATGAAC 55,216 55,033 229 

smSSR25 sgn|E515828 (TGA)5 TCCTAACCCACTTGATGAAC GATTTATGGCTTCTGATGGA 55,033 55,216 228 

smSSR26 sgn|E516013 (AAG)5 CAACTTCGATCTTCAATTCC TCTGAATCTCCCGAGAAGTA 54,836 54,996 373 

Left 

TM 

Right 

TM 

Size 

55

56 

Table 4.2. SSR primers repeat motifs and sequences (Cont.). 

Given Code Primer Code Repeat Motif and Number Forward Sequence Reverse Sequence 

smSSR27 sgn|E516784 (TGT)5 ATACATTTGAGCCGAGAGTG TAAATCTGAGAAGGTCGCAT 55,408 55,040 184 

smSSR28 sgn|E517072 (TCA)5 CACACTCCTCAGAACTCCAT CAGCAGTACCTCTTGGTCAT 55,084 55,313 301 

smSSR29 sgn|E517168 (CTT)5 TCCACTTCAATTTCCAAGTC GATCGCTTAGCAGAAGCC 55,167 56,235 188 

smSSR30 sgn|E517192 (GAA)5 GATCGCTTAGCAGAAGCC TCCACTTCAATTTCCAAGTC 56,235 55,167 188 

smSSR31 sgn|E517356 (TCC)5 CTTCCTACCCACACTTCATC TAGGCCGGAGATAGTTGTAA 54,592 55,104 225 

smSSR32 sgn|E517618 (GAA)5 CCCACTGATCAGAAGAAGTT TAGCACACATCCATACCAAA 54,280 54,994 317 

smSSR33 sgn|E517678 (TCA)5 TTGCTAGAAATAGCAAAGGG CGTGGTGTGTATGATGCTTA 54,998 55,550 191 

smSSR34 sgn|E517743 (AGA)5 ACAAGGAAGGACACAAACAC ATCTAATCACTGTCGCTGCT 55,003 55,131 205 

smSSR35 sgn|E517795 (ATG)5 CACCACCAAAGAATTCCTAA TTGCTAGAAATAGCAAAGGG 55,229 54,998 269 

smSSR36 sgn|E517835 (CTG)5 AGCACCAGGACAATGAATAC CCATTTCTTTCTCGACCTTA 55,057 54,620 231 

smSSR37 sgn|E517892 (AAG)5 AAAGAAGCTTCCGACGAA CACTTGTTTCAGCACTTTGA 56,119 54,976 115 

smSSR38 sgn|E517980 (GCT)5 GCCATAGATGAAAGGTCAGA GGATTTATGGACAAGGTGAA 55,288 54,967 211 

smSSR39 sgn|E518064 (TCA)5 TTGCTAGAAATAGCAAAGGG CGTGGTGTGTATGATGCTTA 54,998 55,550 191 

smSSR40 sgn|E518161 (AAG)5 TTCTTTGATCTTCAATTCCAA ATGAAGCTGTTCATGATTCC 55,012 55,105 283 

smSSR41 sgn|E518430 (TCA)5 CTCCTCCTGGTAAGGAGTCT GCAGTATAGAGACGCGAAAT 55,026 54,827 267 

smSSR42 sgn|E518630 (CAC)5 ACAGTACACCAGAAACGGAA GTTACAATGACGGTGGATCT 55,666 54,886 160 

smSSR43 sgn|E519141 (GCT)5 ACACCTAAACAACAACCAGG GGTGGTGTTCAGTCATCTTT 55,073 54,913 333 

smSSR44 sgn|E519591 (CCA)5 TGCATTTCATACAGAAACCA GCAAGGATATCACTGAGCTG 55,129 56,011 233 

smSSR45 sgn|E519680 (TTC)5 TTTCTCAACCCAAACTGAAC GCAGCTCTCGCATAGATAGT 55,252 54,969 172 

smSSR46 sgn|E519853 (CAC)5 GGAAACCTTCATTCACTTCA AGGTCACCGTTACAATTACG 55,167 55,206 272 

smSSR47 sgn|E520160 (AGA)5 ACACGATGATCATAAGGGAG ATCTAATCACTGTCGCTGCT 54,983 55,131 189 

smSSR48 sgn|E520161 (GCT)5 GCCATAGATGAAAGGTCAGA GGATGGAAAGGATAAGAAGG 55,288 55,308 152 

smSSR49 sgn|E520192 (ATG)5 TAGTCAACTGCATCACCAGA CCACTCCCACTACTGTCACT 55,187 55,035 317 

smSSR50 sgn|E520238 (ATG)5 TATCAGTCAACTGCATCACC TGCATTTACGTGAGCTCTAA 54,452 54,788 255 

Left 

TM 

Right 

TM 

Size 

56

57 

SGN EST 

Identifier 

Number of Unigene 

Members 

Table 4.3. SGN ESTs and their unigene status. 

Unigene Status 

ESTs in the Unigene Family 

SGN EST 

Identifier 


Members 



SGN-E513833 1 - SGN-E517356 1 - 

SGN-E513845 3 SGN-E519315 - 520555 

SGN-E513909 - 513941 - 514099 - 515598 - 

SGN-E517380 >1 - 

SGN-E513876 6 

520441 SGN-E517385 1 - 

SGN-E513913 2 SGN-E513947 SGN-E517618 1 - 

SGN-E513907 5 SGN-E517743 - 517980 - 520160 - 520161 SGN-E517645 >1 - 

SGN-E513915 2 SGN-E513916 SGN-E517670 4 SGN-E517903 - 518057 - 519243 

SGN-E513959 1 - SGN-E517672 1 - 

SGN-E513954 4 SGN-E517716 - 517947 - 518931 SGN-E517678 3 SGN-E517795 - 518064 

SGN-E514038 1 - SGN-E517698 >1 - 

SGN-E514161 1 - SGN-E517702 1 - 

SGN-E514249 3 SGN-E514250 - 514252 SGN-E517712 >1 - 

SGN-E514275 1 - SGN-E517804 >1 - 

SGN-E514279 1 - SGN-E517835 1 - 

SGN-E514329 1 - SGN-E517846 1 - 

SGN-E514364 >1 - SGN-E517892 1 - 

SGN-E514405 1 - SGN-E518073 1 - 

SGN-E514434 >1 - SGN-E518083 1 - 

SGN-E514583 4 SGN-E514602 - 514645 - 514647 SGN-E518171 >1 - 

SGN-E514589 1 - SGN-E518430 1 - 

SGN-E514599 1 - SGN-E518441 2 SGN-E519135 

SGN-E514601 1 - SGN-E518630 >1 - 

SGN-E514796 4 SGN-E516027 - 519337 - 519339 SGN-E518715 1 - 

SGN-E514812 2 SGN-E520465 SGN-E518750 1 - 

SGN-E514885 2 SGN-E516490 SGN-E518751 1 - 

SGN-E515218 2 SGN-E515220 SGN-E518838 1 - 

SGN-E515228 1 - SGN-E518850 1 - 

SGN-E515249 >1 - SGN-E518867 1 - 

SGN-E515280 3 SGN-E520089 - 520115 SGN-E518869 1 - 

SGN-E515318 1 - SGN-E518919 1 - 

SGN-E515331 >1 - SGN-E519141 1 - 

SGN-E515341 3 SGN-E516013 - 518161 SGN-E519202 1 - 

SGN-E515531 1 - SGN-E519219 >1 - 

SGN-E515767 1 - SGN-E519312 1 - 

57

58 

SGN EST 

Identifier 

Table 4.3. SGN ESTs and their unigene status (Cont.). 



SGN EST 

Identifier 


Members 

SGN-E515782 


Members 

1 - SGN-E519392 >1 - 

SGN-E515827 2 SGN-E515828 SGN-E519431 1 - 

SGN-E515838 4 SGN-E515840 - 517812 - 517813 SGN-E519467 1 - 

SGN-E515884 1 - SGN-E519591 >1 - 

SGN-E515985 >1 - SGN-E519680 1 - 

SGN-E516001 1 - SGN-E519737 1 - 

SGN-E516012 >1 - SGN-E519853 1 - 

SGN-E516287 2 SGN-E516310 SGN-E520021 1 - 

SGN-E516412 >1 - SGN-E520010 2 SGN-E520012 

SGN-E516480 1 - SGN-E520049 1 - 

SGN-E516525 2 SGN-E516575 SGN-E520056 1 - 

SGN-E516784 1 - SGN-E520120 1 - 

SGN-E516862 >1 - SGN-E520121 1 - 

SGN-E517027 1 - SGN-E520147 >1 - 

SGN-E517041 >1 - SGN-E520154 2 SGN-E520155 

SGN-E517072 1 - SGN-E520192 2 SGN-E520238 

SGN-E517074 >1 - SGN-E520221 2 SGN-E520223 

SGN-E517168 2 SGN-E517192 SGN-E520230 1 - 

SGN-E517174 1 - SGN-E520254 1 - 

SGN-E517185 1 - SGN-E520454 >1 - 

SGN-E517317 1 - SGN-E520470 1 - 

SGN-E517318 1 - SGN-E520513 1 - 



58

After design of the primers and their synthesis, they were checked for 

amplification as described in detail in Section 2.2.2.1. Verification was done using 

DNA from one accession only (Figure 4.1.). As exemplified in Figure 4.1., 19 smSSR 

primers were checked for amplification. Except for the eight primers which gave faint 

bands, all the primers worked successfully with the sample DNA. Generally, single 

bands were observed for the total 50 smSSR primers with a few exceptions as shown in 

Figure 4.2. 

Figure 4.1. Amplification results for 19 smSSR primers checked with a single DNA. 

A weaker result is indicated by the arrow. 

Primers that gave successful amplification were applied to whole DNA samples 

from individuals of wild species to identify the SSRs that revealed polymorphism. In 

Figure 4.2., an example of a polymorphic SSR, smSSR10, is shown. 

59

Figure 4.2. Amplification of DNA from 16 wild eggplant accessions with smSSR10. 

Some of the polymorphic bands are indicated by arrows. 

Before the final protocol for SSR analysis was determined, several preliminary 

experiments were done. These preliminary experiments were based on changes of the 

PCR conditions, the amount of forward, reverse and M13 primers and dilution amount 

of PCR products with sample loading solution (SLS). 

The challenging part about PCR conditions of the SSR experiments with M13 

primer were annealing step cycles (Section 2.2.2.2.). In the study of Schuelke, which 

was primarily taken as reference, 30 cycles were applied in the experiments (Schuelke 

2000). However, the 30 cycle PCR condition was not successful for eggplant samples. 

For this reason; 25, 26, 27 cycled PCR profiles were tried. Within these, 25 cycles also 

did not work for the samples. Also, because of giving weaker PCR products in 

comparison to 27 cycled PCR profile products, 26 cycled PCR profile was not selected. 

Another variable was related to the amount of primers used in the experiments. 

According to the reference study, equal amount of forward, reverse and M13 primers 

were used: 1.0 µl (Schuelke 2000). However, no satisfactory results were obtained by 

these amounts. Decreasing the amount of each primer in different combinations, to 0.75 

µl while the other 2 were stable, did not give different or better results in the end. Final 

volumes of primers which gave successful results were equal amount of each primer: 

0.75 µl. 

The other variant of the SSR experiments with M13 primer was about dilution of 

PCR products with sample loading solution (SLS) (Beckman Coulter, Inc., Fullerton, 

60

CA, USA). 1:5, 1:10, 1:20, and 1:30 were the different SLS dilution ratios of the 

samples. 1:20 and 1:30 resulted in weaker peaks or even no peaks while differing from 

sample to sample. However, 1:5 and 1:10 dilutions gave best results with the 1:10 

dilution applied to the PCR products. 

In Figure 4.3., an example of SSR sample results analyzed by the CEQ 8800 

Genetic Analysis System is shown. 

Figure 4.3. An example of SSR studies for 4 samples (Pedigree numbers: 06T892, 06T874, 

06T893 and 06T877) with one primer pair (smSSR39) is shown in the figure. 

Polymorphism can be detected by examining the size of the peaks. 

4.1.2. Analysis and Results of the SSR Data 

06T892 smSSR 39 

06T874 smSSR 39 

06T893 smSSR 39 

06T877 smSSR 39 

Although a total of 50 primers were designed and applied to the samples (Table 

4.2.), data for only 25 primers, listed in Table 4.4., were used for further analysis. 

61

Table 4.4. SSR primers selected for use in the analysis and for drawing dendrogram. 

Given Codes 

smSSR 09 smSSR 20 smSSR 39 







smSSR 18 smSSR 36 

smSSR 19 smSSR 37 

Seventeen of these selected primers were previously defined as produced from 

unique ESTs. Four of the 25 SSRs share the same EST family with other SSRs that 

were not used in the dendrogram analysis. Therefore, for the purposes of this study, 

they can be considered as unique. The remaining four SSR primers were in two families 

with two SSRs used from each family. Detailed information is given in Table 4.3. 

For the analysis of SSR data, the results of the experiments were grouped based 

on their presence and absence as 1 and 0. This was achieved using the software of the 

CEQ 8800 System. These analyzed data were then used to draw a dendrogram. In this 

study, NTSYS-pc version 2.2j was used to draw the dendrogram of eggplant species. 

The same matrix and dendrogram parameters were used for the wild eggplants as for the 

Turkish eggplant analysis. Eigen values are listed in Table 4.5. The derived tree and 

plots are shown in Figure 4.4., Figure 4.5., Figure 4.6. and Figure 4.7. 

Table 4.5. Eigen values representing principal components of the study SSR wild 

eggplants at three dimensions are listed in order. 

Eigenvalue Percent Cumulative 

1 21.67843519 46.1243 46.1243 

2 2.17524931 4.6282 50.7525 

3 2.12832677 4.5284 55.2809 

62

63 

Figure.4.4. Dendrogram showing similarity among S. melongena and its wild relatives. 

63

64 

Figure 4.5. Dendrogram showing similarity among S.melangena and as wild relatives with clusters indicated. 

1 

2 

3 

4 

5 

6 

64

65 

Dim-2 

0.40 

0.20 

-0.01 

-0.21 

8 

4 

19 

17 

38 

-0.42 

20 

34 

0.28 0.42 0.56 

Dim-1 

0.71 0.85 

3 

39 

25 

33 

2622 

16 

32 

31 

27 

43 

24 

36 

44 

14 

47 

46 

21 

30 

23 

37 

13 

41 

40 

2 12 

Figure 4.6. Two-dimensional plot of wild eggplants SSR data. 

11 

7 

1 

9 

15 

18 

45 

42 

6 

5 

35 

10 

29 

28 

65

66 

10 

11 

1 

2 

3 

4 

5 6 

7 

8 

9 

12 

13 

14 

15 

16 

17 

18 

19 

20 

21 

22 

23 24 

25 

26 

27 

28 

29 

30 

31 

32 

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34 

35 

36 

37 

38 

39 40 

41 

42 

43 

44 

45 

46 

47 

0.40 

0.40 

0.20 

0.20 

Dim-2 

Dim-2 

-0.01 

-0.01 

-0.21 

-0.21 

-0.42 

-0.42 

-0.40 

-0.40 

0.28 

0.28 

0.42 

0.42 

-0.18 

-0.18 

0.56 

0.56 

Dim-1 

Dim-1 

Dim-3 

Dim-3 0.05 

0.05 

0.71 

0.71 

0.85 

0.85 

0.28 

0.28 

0.51 

0.51 

10 

11 

1 

2 

3 

4 

5 

6 

7 

8 

9 

12 

13 

14 

15 16 

17 

18 

19 

20 

21 

22 

23 

24 

25 

26 

27 

28 

29 

30 

31 

32 

33 

34 

35 

36 

37 

38 

39 

40 

41 

42 

43 

44 

45 

46 

47 

0.85 

0.85 

0.71 

0.71 

Dim-1 

Dim-1 

0.56 

0.56 

0.42 

0.42 

0.28 

0.28 

-0.42 

-0.42 

-0.40 

-0.40 

-0.21 

-0.21 

Dim-2 

Dim-2 

-0.01 

-0.01 

0.20 

0.20 

0.40 

0.40 

-0.18 

-0.18 

Dim-3 

Dim-3 

0.05 

0.05 

0.28 

0.28 

0.51 

0.51 

Figure 4.7. Three-dimensional plots of wild eggplants SSR data. 

66

4.2. Discussion 

According to the statistical results of SSR analysis, the r value of Solanum species’ 

genotypic data was found to be 0.88. This value indicates a good fit as defined in the review 

of Mohammadi and Prasanna (Mohammadi and Prasanna 2003). That means the correlation 

between sample genotypic data and dendrogram was found to be high. Other statistical 

results which were Eigen values explained 46.12% of genotypes for fırst component 

analysis (Table 4.5.). With a total value of 55.28%, the 47 different genotypes were 

explained by the three component axes (Table 4.5.). 

The scale of the dendrogram was between 0.32 and 0.88 with a mean value of 0.60 

(Figure 4.4.). According to the least similarity value, genotypes were separated into 2 

groups with 0.32 coefficient. One group consisted of two samples, genotypes 20 and 4 

which were S. semilistellatum and S. viarum, respectively. All the other samples formed 

the other group in the large scale and with 0.36 similarity. There were just two genotypes 

which gave identical results but with a 0.88 correlation coefficient (Figure 4.4.). The second 

most similar samples were Solanum melongena group E and H members (genotype 

numbers 6 and 10) with a 0.86 cophenetic correlation value (Figure 4.5., Group-2). 

In terms of the samples’ clustering, the dendrogram was compatible with the 

expected results and with the previous studies. For example, Solanum incanum, Solanum 

melongena, Solanum macrocarpon members all formed separate clusters (Figure 4.5., 

Group-1, Figure 4.5., Group-2 and Figure 4.5., Group-5). An important grouping was the 

one which included S. incanum and S. melongena clusters with a 0.67 correlation value 

(Figure 4.5., Group-1 and Figure 4.5., Group-2). This result agreed with the interpretation of 

the relative closeness of these 2 species which was reported in several studies (Sakata and 

Lester 1994, Karihaloo et al. 1995, Furini and Wunder 2004, Mace et al. 1999b, Singh et al. 

2006). One point which was quite noteworthy was the separation of different group 

members of S. incanum into different clusters (Figure 4.5., Group-1, Figure 4.5., Group-4 

and Figure 4.5., Group-6). This result showed the diversity among different groups and 

within the same species. Another important grouping was S. macrocarpon which also 

included S. dasyphyllum (Figure 4.5., Group-5). In the recent phylogenetic study of the 

Leptostemonum clade by Levin et al., these two species were included in the same clade 

with a very high similarity. In the same study and in our SSR analysis of eggplant and its 

67

wild relatives, S. campylacanthum and S. incanum were grouped together (Levin et al. 

2006, Figure 4.5., Group-3). 

As a marker system, SSR is accepted as a valuable molecular analysis tool (Powell 

et al. 1996). However, due to their conservative nature and expected low level of 

polymorphism, the usefulness of SSRs derived from ESTs for clustering analysis has been 

questioned (Rudd 2003 and Varshney et al. 2005). However, the overall results of the 

present study were satisfactory in terms of their statistical values and concordance with 

previously published data. The correlation coefficient 0.88 for the highest similarity 

between genotypes and the least 0.32 exhibited a good separation from a conserved region 

of the genome. However, increasing data and sample numbers may increase the accuracy of 

the clustering results. 

68

CHAPTER 5 

CONCLUSION AND FUTURE PERSPECTIVE 

In this thesis, the research was separated into two parts. For both parts, the 

materials used in the experiments were DNAs from greenhouse-grown samples. The 

general aim for each part was to reveal genetic differences or similarities between the 

plant materials which were members of different accessions or species. 

For the first part, materials were Turkish eggplants all of which belonged to 

different accessions of Solanum melongena. To reveal genetic diversity among Turkish 

eggplants and three outgroups, which were Solanum linnaeanum, Solanum aethiopicum 

and Solanum macrocarpon, the AFLP marker system was used because it has been 

proven to be an efficient molecular tool to reveal genetic diversity not only in other 

systems but also in the Solanaceae family (Mace et al. 1999b). Another reason for this 

method’s selection was related with its potential to produce a high amount of genetic 

data. When it was considered that the possible genetic diversity at the intraspecies level 

was low in eggplant, it was determined that as much data as possible should be obtained 

and used in the analysis (Daunay et al. 2001). According to the results of the AFLP 

experiments in Turkish eggplants, this idea was shown to be correct. Statistical results 

were quite satisfactory and a dendrogram was drawn that was concordant with the data 

in these analyses with an r value of 0.97. 

In the second part, the aim was to find genetic diversity between eggplant and its 

wild relatives. From 20 different species, three species clustered into individual groups, 

and a total of 47 different genotypes were tested with SSR marker system. The reason 

for the selection of this marker system was related with its highly polymorphic nature, 

easiness to study and its reliability. However, the design of that marker system is 

laborious work. For that reason, SSR primers for this study were designed from 

eggplant ESTs which were publicly available on SOL Genomics Network 

(http://sgn.cornell.edu). Due to the fact that the source of the primers was ESTs, these 

SSRs were expected to amplify more conserved regions in the genome. That led to a 

relatively low level of polymorphism and diversity within the materials. However, 

analysis of the results and statistical values obtained were in the good scale with a 

correlation coefficient value of 0.88. The concordance within the results and clusters in 

69

the dendrogram also concluded it as a reliable work. However, increase in the amount of 

data may give a better separation of the samples and a better statistical result. 

The overall importance of these studies is related with taxonomic issues and also 

breeding and preservation attempts. Because of confusion about eggplant or in the 

Solanaceae family, genotypic data serves as a powerful means and data source in 

determination of similarity between individuals. This similarity can be at any level in 

the organization of organisms. In addition to this, for the preservation and maintenance 

of crop plants which are important for human health and diet is an important subject. 

This is basically related with diversity conservation. Using the results of this study, the 

most diverse species or accessions can be selected for preservation without any time and 

money lost and species or accessions can be identified accurately in taxonomy. For 

future work, these new SSR primers can be used and integrated into the mapping studies 

of eggplant. 

70

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