Eggplant: January 2013

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Eggplant
Chapter · January 2013

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116 Genetics, Genomics and Breeding of Peppers and Eggplants
7
Eggplant
Amy Frary1 and Sami Doganlar2 Corresponding author? S.
Doganlar
ABSTRACT
Solanum melongena is an Old World species complex that includes weedy
and wild relatives as well as primitive cultivars and landraces of the
important vegetable crop eggplant. While the origins of cultivated
eggplant are obscure, most evidence suggests an Indo-Chinese centre
of domestication. Sexual promiscuity within eggplant and its relatives
blurs species boundaries, making taxonomic relationships difficult
to decipher. Furthermore, attempts to define finer-scale evolutionary
relationships are thwarted by low levels of genetic variation (despite
considerable morphological diversity) in cultivated eggplant. The
main breeding objectives in the crop are to increase yield by heterosis
breeding, introduce disease and pest resistances from wild germplasm,
and improve fruit quality through selection for parthenocarpy and
elevated levels of key secondary metabolites (anthocyanins and
phenolics). Extensive germplasm resources collected in Asia and Europe
hold considerable potential for the genetic improvement of the crop;
however, the introgression of traits from wild relatives is hampered
by low fertility in hybrids. A variety of molecular markers have been
used to characterize the germplasm collections. This work has helped
both to classify species and to identify potentially valuable sources
of heterozygosity for modern cultivars. Molecular markers have also
been used to construct linkage maps of the eggplant genome. The close
relationship between eggplant, tomato and pepper has facilitated this
work as well as made the Solanaceae a model for comparative genomics.
The molecular genetic maps developed in eggplant have been used
both for the tagging of simply inherited traits and the localization of
the loci underlying complex morphological characters. Quantitative
trait analysis of interspecific mapping populations indicates that
1
Mount Holyoke College, South Hadley, Massachusetts, USA.
2
Izmir Institute of Technology, Izmir, Turkey.
Eggplant 117
wild germplasm holds promise for improving fruit yield and quality.
These analyses also suggest that the conservation of gene function and
position between the tomato and eggplant genomes should allow the
knowledge gained in tomato to be leveraged for the improvement of
eggplant. The development of an integrated molecular linkage map,
generation of expressed sequence data and a growing interest in
the potential nutritional and medicinal benefits of eggplant promise
productive years ahead.
Keywords: Solanum melongena, Evolution, Germplasm, Breeding,
Mapping
1. Economic Importance
Solanum melongena, known variously as eggplant, brinjal and aubergine, is
an important vegetable crop throughout Asia and the Mediterranean region
where its fruits are a key ingredient of national and regional cuisines. While
worldwide production of this Old World solanaceous crop species lags
behind that of its New World kins, potato and tomato, 43 million tons (t) of
eggplant were harvested from 1.7 million hectares (Ha) of land in 2009 (FAO
2009). Asia is the principal centre of eggplant production. In 2009, China
grew 26 million tons of the crop on 740,000 Ha and India 10 million tons
on 600,000 Ha. While far less of the crop was grown in Egypt (1.2 million
t; 50,000 Ha) and Turkey (820,000 t; 27,000 Ha), these two countries are
ranked as the 3rd and 4th largest producers of eggplant worldwide. Other
notable producers are Indonesia (450,000 t; 46,000 Ha), Iraq (396,000 t; 21,000
Ha), Japan (349,000 t; 10,400 Ha), Italy (245,000 t; 9400 Ha), Spain (205,000
t; est. 3500 Ha) and the Philippines (201,000 t; 21,000 Ha) (FAO 2009). The
average yield (26 t/Ha) ranges considerably, depending on environmental
and cultural conditions with the highest yields achieved in the Netherlands
(460 t/Ha) from F1 hybrids grafted onto disease resistant rootstocks and
grown under highly controlled greenhouse conditions.
2. Nutritional Properties
While the fruit of the eggplant is used extensively in Asian, Indian and
Mediterranean cookery, its nutritional value is modest (Gebhardt and
Thomas 2002). Despite being a poor source of protein (1.0g/100g fresh
weight), provitamin A (27 IU/100g) and vitamin E (0.30 mg/100g) (USDA
2011), eggplant is rich in some minerals and antioxidants. For example, 100
g of eggplant (fresh weight) can provide ~5 percent of the recommended
daily amount (RDA)of phosphorus, potassium and copper as well as ~10
percent of the daily intake of phenolics (Raigón et al. 2008). Anthocyanins,
another important class of antioxidants, are found in abundance in the
richly pigmented peel of the fruit (Azuma et al. 2008). Extensive research
into the health benefits provided by the free radical scavenging properties
of both phenolics and anthocyanins has been conducted in recent years
(Kaur and Kapoor 2001; Liu 2003). In addition, the alkaloids produced by
eggplant and its wild relatives have been reported to induce apoptosis in
tumor cells (Kuo et al. 2000; Cham 2007). Thus, while eggplant has been
used in traditional Chinese and Indian medicine for centuries (Daunay
and Janick 2007; Daunay et al. 2007), the biological bases of its merits as a
medicinal plant have only recently been revealed.
3. Brief History of the Crop

The origins of cultivated eggplant are somewhat obscure. Phylogenetic
studies have revealed that Solanum incanum is the closest relative of
S. melongena (Lester and Hasan 1991). However, S. incanum itself is a species
complex that encompasses up to 27 species and 81 taxa (Bitter 1923) endemic
to eastern Africa and the Middle East. These taxa have been divided into
four separate and diverse groups (A-D) of wild eggplant relatives on the
basis of their distribution and morphological characters (Lester and Hasan
1991). It has been hypothesized that S. incanum group C arose as plants of
groups A and B spread from Africa to the Middle East and became adapted
to local conditions. Then, continuing its eastward migration, group C
S. incanum reached Asia and diverged to produce S. melongena. Group D
represents the types that were moved to South Africa and adapted to the
arid conditions there (Daunay et al. 2001).
Like S. incanum, S. melongena is a species complex that comprises four
distinct groups (E-H) (Lester and Hasan 1991; Mace et al. 1999). Group F
(also known as S. cumingii) is the likely ancestor of domesticated eggplant
and includes weedy forms found widely in Indochina and Indonesia. Group
G (S. ovigerum) represents domesticated primitive cultivars and landraces
with small round or oblong fruits which grow throughout Southeast Asia.
Group H (S. melongena) includes the large-fruited advanced cultivars that are
grown in agricultural fields and greenhouses worldwide. Evidence suggests
that S. melongena Group E (S. insanum) arose as revertants from group G
forms (Lester and Hasan 1991; Mace et al. 1999). This group includes weedy
plants with wild attributes. While the direct evidence in support of this
scenario of evolution and domestication in eggplant is currently scarce, an
analysis of DNA sequences (ITS, waxy and trnT-F) from eggplant and its
wild and weedy relatives indicates that the progenitors of eggplant arose
in Africa (Weese and Bohs 2010).
Based on the current distribution of S. melongena group F, it is possible
to deduce an Indo-Chinese centre of origin and domestication for eggplant.
Moreover, because of eggplant’s importance as a food, medicinal and
Eggplant 119
ornamental plant to the ancient civilizations of this region, the spread and
the early history of the crop can been studied through the examination of
historical records, literature and iconography (Daunay and Janick 2007;
Daunay et al. 2007; Wang et al. 2008). Eggplant is frequently mentioned
by various common names in Sanskrit documents, some of which date to
300 BCE (Daunay and Janick 2007). The earliest known written record of
cultivated eggplant in Chinese literature dates to 59 BCE (Wang et al. 2008).
Thus, eggplant is a crop that dates to antiquity. Around the 8th century,
eggplant spread eastward to Japan and then westward to the Mediterranean
(perhaps brought by Muslim conquerors) (Frary et al. 2007). Descriptions
in Chinese literature (6th-18th centuries) as well as images of eggplant
from Chinese and European herbals (dating to the 14th–17th centuries)
depict the progressive changes in fruit sizes, shapes, and colors wrought
by domestication and cultivation: from small round white fruit to larger
fruit of various hues (white, green, violet and almost black) and shapes
(round, oblong, long and thin) (Daunay and Janick 2007; Wang et al. 2008)
(Fig. 7-1). Changes in the flavour of eggplant (from bitter to sweet) have
also been gleaned from Chinese writings (Wang et al. 2008).
Kindly indicate A,B,C &

D
A B C D
Figure 7-1 Depictions of eggplant in Chinese literature: (A) Tu Jing Bencao (AD 1069), (B)
Bencao Gangmu (AD 1590), (C) Sancai Tu Hui (AD 1609), (D) Zhiwu Ming Shi Tu Kao (AD 1848).
Reproduced by permission of the Chinese Academy of Sciences. (Used with permission from
Wang et al. 2008, Oxford University Press.)
4. Taxonomy
S. melongena is a member of the Solanae tribe within the Solanaceae family.
This tribe includes the New World crop plants: potato (S. tuberosum), tomato
(S. lycopersicum) and pepper (Capsicum sp.). Eggplant is further classified
as one of the “spiny solanums”, Solanum subgenus Leptostemonum. This
subgenus includes 350–450 species of New and Old World plants, typified
by leaf and stem prickles (Levin et al. 2006). Two other species commonly
referred to as eggplants, Solanum macrocarpon (gboma eggplant) and
S. aethiopicum (scarlet eggplant), also belong to this group. Both are
cultivated in Africa as fruit and vegetable crops. Taxonomic relationships

in the subgenus and particularly within eggplant and its relatives are
confusing; extensive morphological diversity and interspecific crossability
blurs species boundaries and evolutionary relationships. Nevertheless,
the Old World species reliably group as a clade in molecular phylogenies
of the subgenus (Levin et al. 2006). Wild and weedy forms of S. incanum
cluster separately from S. melongena, and scarlet and gboma eggplants fall
outside of the incanum-melongena complex (Weese and Bohs 2010). The low
levels of genetic variation combined with sexual promiscuity within the
S. melongena complex make it difficult to determine finer-scale evolutionary
relationships (Weese and Bohs 2010).
5. Botanical Description
In its primitive form, eggplant is a tall, woody perennial plant with large
leaves. Prickles on the stem, leaves and calyx are typical. Andromonoecious
flowers with five connate sepals, five connate petals and five stamens fused to
the corolla are produced in small cymes (one to five flowers/inflorescence).
Flowers are generally self-pollinate although cross-pollination may occur
in nature as a result of heterostyly and insect visitation. The fruit, berries,
are small and thick-skinned, green and hard at maturity and unpalatable
because they are bitter and seedy. Wild eggplants are distributed in tropical
regions of Africa and Asia. Domestication, the cultivation and breeding
have resulted in a smaller plant that is grown as an annual crop worldwide.
Eggplant is a field crop in the Middle East and much of Asia, but greenhouse
production is on the rise, especially in Europe and Japan (Daunay 2008).
Cultivated forms usually lack prickles and produce perfect flowers that are
often solitary. Fruits have thin skin, soft flesh and are larger, less seedy and
less bitter than wild types. A diversity of fruit shapes exists among cultivars,
with round, ovate, oblong, fasciated, elongate and serpentine forms. Fruit
size varies widely along with shape. Fruit length ranges from 4 to 45 cm
and diameter from 2 to 35 cm. A 100-fold difference in fruit weight (15 g to
1.5 kg) is seen among varieties. Fruit colors are linked to the variable presence
of chlorophyll (green) and anthocyanin (red and purple) pigments in the
developing fruit. White, green, violet, purple and almost black varieties have
been selected, some with contrasting stripes or streaks (Swarup 1995; Frary
et al. 2007). Eggplant’s genome consists of approximately 956 Mbp (Bennett
and Leitch 2010); it is a diploid with a base chromosome number of 12.
6. Germplasm
Collections of eggplant cultivars, landraces, relatives and wild species in
Asia include ~1,800 accessions in India (National Bureau of Plant Genetic
Eggplant 121
Resources, NBPGR, New Delhi) (Gangopadhyay et al. 2010), nearly 2000

accessions in China (Institutes of Vegetables Crops, IVC, Nanjing and
Hangshu) (Mao et al. 2008) and ~400 lines in Japan (National Institute
of Agrobiological Sciences, NIAS, Tsukuba). Some germplasm resources
have also been collected in Southeast Asia (Wivutvongvana et al. 1984;
Sakata et al. 1996), Indonesia (Gousset et al. 2005), Africa (Lester et al.
1990) and the Middle East (Sadder et al. 2007). A comprehensive database
of eggplant-related germplasm holdings in Europe (estimated to include
~6,000 accessions) (Daunay et al. 2003) was compiled by the EGGNET
(Eggplant Genetic Resources Network) project, a network of public and
private sector researchers from Netherlands, France, Italy, Spain, Greece,
Germany and UK. The database is currently curated by the European
Cooperative Programme for Plant Genetic Resources (ECPGR), Nijmegen,
Netherlands. The Germplasm Resources Information Network (GRIN)
database at the USDA maintains over 800 lines of S. melongena and related
species, including the African eggplants.
Tremendous morphological diversity is available in primitive cultivars,
landraces and weedy species within S. melongena. In addition, the wild
progenitor, S. incanum represents an important source of resistance to
biotic and abiotic stresses (Swarup 1995). Useful germplasm for the
genetic improvement of cultivated eggplant can also be found among wild
allied species, many of which harbour disease and pest resistance genes
(reviewed in Collonnier et al. 2001). Eggplant can be easily crossed with a
wide variety of these spiny solanums. However, while 19 related species
have been employed in the breeding of eggplant, only four of them yield
fertile progeny when crossed with S. melongena: S. incanum, S. linnaeanum,
S. macrocarpon and S. aethiopicum (Collonnier et al. 2001). Thus, in practical
terms, the introgression of donor genes from more distantly related eggplant
relatives is challenging.
7. Classical Genetics and Traditional Breeding

While Solanum lycopersicum (tomato) was an important model organism
in early classical mapping efforts, S. melongena was essentially ignored in
this regard. With the exception of anthocyanin accumulation (Nolla 1932;
Janick and Topoleski 1963; Tigchelaar et al. 1968), very few phenotypic
traits have been mapped in eggplant. The quantitative nature of many
key agronomic characters has complicated inheritance studies in this as
in other crop species. With the advent of molecular linkage maps and the
concomitant development of comparative genomics, attention once focused
exclusively on tomato has widened to encompass eggplant (as well as potato
and pepper). Genome-wide characterization of eggplant through molecular
mapping can facilitate breeding on a number of levels. The inheritance of
complex traits can be more easily analyzed, unwanted genotypes can be

culled from breeding populations earlier via marker-assisted selection and
germplasm can be screened more efficiently for desirable traits (Frary et
al. 2007).
The main objectives of eggplant breeders have been to increase yield to
incorporate disease and pest resistance into the crop and to improve fruit
quality. Improved tolerance to abiotic stress is another important goal. Since
the discovery of heterosis in eggplant (Kakizaki 1931) breeding efforts have
increasingly focused on developing hybrids with enhanced productivity
from inbred materials. As a result, most commercial cultivars are F1 hybrids.
And yet, eggplant breeding is hampered by the labor-intensive aspects of
hybrid seed production. Manual emasculation and pollination of the inbred
parents is time-consuming and expensive. Therefore, efforts to introduce
cytoplasmic male sterility (CMS) into breeding lines of eggplant are ongoing.
Male sterile lines have been generated by interspecific crosses between
S. melongena (as the male parent) and S. violaceum (Isshiki and Kawajiri 2002),
S. virginianum (Khan and Isshiki 2008), S. grandifolium (Saito et al. 2009a)
and S. anguivi (Khan and Isshiki 2010), followed by several generations
of backcrossing to S. melongena. In all of these cases, the incorporation of
the foreign species’ cytoplasm had the desired effect of reducing pollen
production or pollen fertility but leaving seed fertility unaltered. The
successful integration of CMS in commercial hybrid seed production
demands that the sterility be stable in a range of genetic backgrounds (Saito
et al. 2009a) and that nuclear fertility restorer (Rf) genes be present. Such
genes have been identified in progenies from crosses with S. anguivi (Khan
and Isshiki 2010) and S. grandifolium (Saito et al. 2009a).
In addition to heterosis breeding, advances in eggplant productivity
have been achieved by grafting S. melongena onto tomato (S. lycopersicum
and S. hirsutum) as well as more closely related species (S. torvum,
S. aethiopicum, S. macrocarpon and S. incanum) (Daunay 2008; Gisbert et al.
2011). Increased vigour of the scion as well as earlier fruit maturity are
some of the benefits of grafting (Khah 2005; Gisbert et al. 2011). In addition,
grafting is used as a means of conferring resistance to soil pathogens onto
susceptible eggplant cultivars, thereby boosting yield (Bletsos et al. 2003;
reviewed in Daunay 2008).
The diseases of greatest economic concern in eggplant are the wilts
caused by Ralstonia solanacearum (bacterial wilt), Fusarium oxysporum f.
sp. melongenae, and Verticillium dahliae. Fruit and shoot borer (Leucinodes
orbonalis) is the most significant insect pest. Aphids (Aphis gossypii),
nematodes (Meloidogyne spp.) and little leaf disease (caused by a
mycoplasma) also impact yield (Daunay 2008). While disease and pest
resistance levels are generally quite low in commercial varieties, tolerance
has been identified in a number of wild relatives of eggplant (reviewed in
Eggplant 123
Collonnier et al. 2001), and efforts are ongoing to introgress resistance genes
into cultivated germplasm. The success of such crosses depends in large
part on the phylogenetic distance between the parents, the S. melongena
genotype and the direction of the cross (Schaff et al. 1982; Bletsos et al. 2000).
A major obstacle has been cross-species incompatibilities that appear as
low fertility or sterility in the interspecific hybrids and are often attributed
to meiotic irregularities (Schaff et al. 1982; Behera and Singh 2002; Bletsos
et al. 2004). Chromosome doubling (achieved via colchicine treatment or
anther culture) has been an effective means of restoring hybrid fertility in
insert h some cases (Issiki et al. 2000; Issiki and Taura et al. 2003).
Somatic hybridization is another strategy that has been used to create
interspecific eggplant hybrids (Kameya et al.1990; Jarl et al. 1999; Collonnier
et al. 2003; Iwamoto et al. 2007). Although such hybrids typically express the
desired trait they also have a tendency toward sterility. While exceptions
to this have been reported (Borgato et al. 2007; Iwamoto et al. 2007), the
integration of somatic hybrids into breeding programs is further hampered
by their tetraploid nature. Anther culture, however, has proven to be useful
for bringing such lines back to diploidy (Rizza et al. 2002; Rotino et al. 2005).
Regardless of the trait of interest, when trying to introgress genes from wild
species into cultivated germplasm, it is critical that meiotic recombination
occurs between homeologues of the two parental species. Evidence for such
chromosomal exchange has been found in S. melongena + S. aethiopicum
somatic hybrids (Rizza et al 2002; Rotino et al. 2005; Toppino et al. 2008a).
Such hybrids could be employed to transfer bacterial and Fusarium wilt
resistances into eggplant.
Fruit quality traits include the flavour and texture of the flesh, the
thickness, color and glossiness of the skin and the storability of the harvested
fruit. Recently, there has been an emphasis on breeding for parthenocarpy
(the development of seedless fruits) (Fig. 7-2). Parthenocarpy ensures fruit
set and development under otherwise adverse environmental conditions,
such as sub- or supra-optimal temperatures and humidity levels, low light
and heavy rain or strong wind. In addition, seedless fruits typically are less
bitter, have softer flesh and brown less quickly than their seeded counterparts
(Donzella et al. 2000). Treating flowering plants with phytohormones can
induce parthenocarpy, however the labor and expense associated with such
treatments can be prohibitive (Kikuchi et al. 2008a). A more sustainable
approach is to select for the trait, and parthenocarpic cultivars have been
developed in this way (Kikuchi et al. 2008b; Saito et al. 2009b).
Anthocyanin pigments are significant determinants of fruit quality in as well as
eggplant because of not only their obvious effects on color but also their
antioxidant activity and potential health benefits (Noda et al. 2000; Sadilova
et al. 2006; Nisha et al. 2009). An increased interest in plant secondary
metabolites has thus shifted attention towards breeding for these pigments
Figure 7-2 The exterior and interior of fruit of two eggplant hybrids: a transgenic
parthenocarpic line containing the iaaM gene (P10) and a control (C10). (Used with permission
from Acciarri et al. 2002, licensee BioMed Central Ltd.)
Color image of this figure appears in the color plate section at the end of the book.
and other compounds that impact nutritional quality. Several recent studies
have focused on determining the antioxidant content in eggplant cultivars,
landraces and related species (Azuma et al. 2008; Mennella et al. 2010). Thus,
the anthocyanin profiles of numerous accessions of eggplant and related
species have been compared; and, based on the radical-scavenging activities
of purified pigments, it has been suggested that lines containing the
anthocyanin delphinidin 3-glucoside should have the highest antioxidant
properties (Azuma et al. 2008).
Over 14 different phenolic compounds, another important class of
antioxidant, have been identified in eggplant accessions (Stommel and
Whitaker 2003). Researchers in Taiwan, Spain, Turkey and Italy have
measured total phenolics in a number of varieties and hybrids (Hanson et
al. 2006; Raigón et al. 2008; Okmen et al. 2009; Mennella et al. 2010). The
results of these studies indicate that the levels of phenolics in the different
lines are fairly variable (~2-fold variation was generally observed in the
studies) and that it should be possible to select materials with enhanced
antioxidant capacity for breeding purposes. Because phenolics contribute
toward oxidative browning of cut fruit, a negative quality trait, a tradeoff
between these two attributes would seem to be necessary. However,
heritability studies in over 100 eggplant varieties and landraces suggest
Eggplant 125
that only around 20 percent of the variability in degree of browning can

be attributed to phenolics levels, suggesting that it should be possible to Within the S.
obtain lines with high phenolics content but acceptable levels of oxidative melongena
browning (Prohens et al. 2007, 2008). germplasm tested,
Other secondary metabolites of interest in eggplant are the
pickling varieties
glycoalkaloids solamargine and solasonine, which are present in all three
cultivated species, S. melongena, S. aethiopicum and S. macrocarpon (Mennella held the highest
et al. 2010; Sánchez-Mata et al. 2010). Solamargine has been investigated concentration of
as a possible anti-cancer agent (Kuo et al. 2000; Shiu et al. 2007), and both solamargine
compounds appear to be effective in killing parasitic trypanosomatids (Sánchez-Mata et
(Hall et al. 2006). However, the levels of these two glycoalkaloids in some
al. 2010)
allied species (namely, S. macrocarpon, S. sodomaeum, S. aethiopicum and
S. integrifolium) may be high enough to warrant the concern about potential insert space
toxicity should these species be usedin S. melongena breeding programs
(Mennella et al. 2010; Sánchez-Mata et al. 2010). Within the S. melongena
germplasm tested, pickling varieties held the highest concentration of
solamargine (Sánchez-Mata et al. 2010). Further assessment of the safety of
these compounds is necessary before they become a breeding priority.
8. Genetic Engineering
Eggplant has proven very amenable to genetic engineering; protocols for
the regeneration of plants from in vitro cell and tissue cultures, somatic
hybridization and Agrobacterium -m ediated transformation are well
established in the crop (reviewed in Rajam and Kumar 2007). As described
previously, somatic hybridization has been a particularly useful tool in
transferring disease resistances into eggplant from wild relatives. Insect
resistance, on the other hand, has been the primary goal of transformation
experiments in S. melongena. Cry genes coding for the insecticidal crystal
protein endotoxin from Bacillus thuringiensis have been inserted into the
eggplant genome via Agrobacterium-mediated transformation in several
experiments. The resulting regenerants have shown resistance to Colorado
potato beetle (Leptinotarsa decemlineata) (Arpaia et al. 1997; Hamilton et al. , where the fruit
1997) and fruit and shoot borer (Leucinodes orbonalis) (Kumar et al. 1998; Pal and shot borer
et al. 2009). However, in India attempts to introduce commercial varieties causes extensive
of transgenic eggplant carrying the Cry1Ac gene, where the fruit and shoot yield losses,
borer causes extensive yield losses, have thus far been unsuccessful (Shelton
2010). Aphid resistance in eggplant has also been achieved through insertion
of the rice oryzacystatin gene (Ribeiro et al. 2006), and the tomato Mi-1.2
gene was found to increase eggplant’s tolerance to the root-knot nematode
species Meloidogyne javanica (Goggin et al. 2006).
Parthenocarpic eggplant lines have been engineered through the
introduction of the iaaMgene from Pseudomonas syringae pv. savastanoi
insert space
(Rotino et al. 1997; Acciarri et al 2002). This gene plays a key role in the
biosynthesis of auxin, the plant hormone that is used to induce parthenocarpy
in eggplant when environmental conditions are unfavorable for fruit set
and development. In practice, treatment of plants with phytohormones is
laborious, time-consuming and expensive. Thus, the potential economic
benefits of transgene-induced parthenocarpy are considerable. In addition to
the enhanced quality expected of seedless fruit, genetically-modified (GM)
eggplants gave higher yields in both field and greenhouse (Donzella et al.
2000; Acciarri et al. 2002). Elevated levels of tolerance to salt, drought and
cold temperature stresses were observed in genetically-modified eggplants
carrying the mannitol-1-phospho dehydrogenase (mtlD) gene (Prabhavati
et al. 2002). Although several noteworthy successes have been realized in
the genetic engineering of eggplant, consumer wariness of GM vegetable
crops is such that commercial growers have not adopted transgenic varieties yet
yet.
9. Diversity Analysis
The morphological, agronomic and molecular diversity of eggplant and
allied species has been examined by a number of researchers in efforts
to assess genetic relatedness to characterize germplasm collections and
to guide breeding programs towards promising lines. In most of the
morphological studies, the vegetative, floral and fruit traits that were
analyzed correspond to the primary characterization descriptors developed
by EGGNET. A variety of molecular markers have been utilized, including
allozymes, chloroplast DNA, random amplified polymorphic DNA (RAPD),
simple sequence repeat (SSR), inter-simple sequence repeat (ISSR), amplified
fragment length polymorphism (AFLP) and sequence-related amplified
polymorphism (SRAP) markers.
The advantages of molecular traits over morphological ones in assessing
both diversity and relatedness in eggplant have been highlighted by a
number of studies. A study of 16 descriptors in 98 accessions of S. melongena
and the African eggplants, S. aethiopicum and S. macrocarpon, demonstrated
that considerable morphological diversity exists both within and between
species (Polignano et al. 2010). Cluster analysis of the phenotypic data
resulted in three groups that were unrelated to the classification of an
accession (subspecies, botanical or variety group, cultivar or population),
thus suggesting that morphology is an unreliable predictor of genetic
status. The authors, therefore, suggest that molecular markers are an
essential means of categorizing germplasm collections. Allozyme and RAPD
data suggest that while S. melongena, S. insanum (used to denote weedy
forms) and S. incanum (the wild progenitor of cultivated eggplant) are
morphologically distinct, they are very similar at the genetic level (Karihaloo
Eggplant 127
and Gottlieb 1995; Karihaloo et al. 1995). Even though weedy eggplants
show more diversity than the cultivated accessions, the authors suggest
that separate species designations are meaningless. Similarly, restriction
fragment length polymorphism (RFLP) analysis of chloroplast DNA from
S. melongena and related species indicated that taxonomic relationships as
deduced from morphological characters are somewhat unreliable (Sakata
and Lester 1997).
However, similar dendrograms have been obtained from both molecular
data (AFLP and RAPD markers) and phenotypic data in comparative
analyses of Solanum accessions (eggplant cultivars, landraces and related
species) (Furini and Wunder 2004; Sadder et al. 2007). In addition, both
morphological and molecular data were seen to be useful in the correct
classification of previously unnamed and mis-named lines (Furini and
Wunder 2004), suggesting that morphological traits still have a place in
phylogenetic analysis of this taxonomically confusing group of plants.
Obviously, the choice of markers and accessions will have a large
impact on the conclusions drawn from molecular analyses of diversity.
Thus, while low genetic diversity was detected within S. melongena with
microsatellite markers (Nunome et al. 2003a,b), other markers, including
RAPD (Singh et al. 2006), SSR (Behera et al. 2006), genic SSRs (Stàgel et al.
2008; Tümbilen et al. 2011a) and SRAP (Li et al. 2010), have been generated,
which reveals substantial variation both within S. melongena and among
allied species. Some of these markers are sufficiently variable to reveal
phylogenetic relationships (Furini and Wunder 2004; Behera et al. 2006;
Stàgel et al. 2008; Isshiki et al. 2008; Li et al. 2010). Highly discriminatory
ISSR and RAPD markers which are useful for fingerprinting cultivars have
also been developed (Isshiki et al. 2008; Tiwari et al. 2009).
Regardless of the marker type used, it is clear that although
morphologically diverse, cultivated eggplant has a much narrower genetic
background than related allied species, including S. incanum, the aggregate
of species that includes the progenitor of S. melongena (Nunome et al.
2003a; Tümbilen et al. 2011a). This low diversity has been attributed to
a founder effect that likely occurred during the migration of S. incanum
from Africa to Asia as well as the genetic bottleneck within S. melongena
that probably accompanied the transition to the domesticated form. A
comparison of variability in commercial cultivars (both F1 and nonhybrids)
and landraces within black-fruited accessions of S. melongena uncovered
much higher levels of phenotypic and genotypic (based on polymorphism
in SSR markers) diversity among landraces than commercial materials
(Muñoz-Falcón et al. 2008). Moreover, the F1 hybrids were revealed to share
a very limited gene pool. Therefore, although domestication and breeding
efforts have served to constrain diversity within eggplant, landraces and
non-hybrid varieties are potentially valuable sources of heterozygosity for

modern cultivars.
Thus, pockets of diversity can be found within local varieties of eggplant.
Comparing traditional Spanish cultivars to four control accessions on the
basis of morphology and AFLP markers, Prohens et al. (2005) discovered
that “round” cultivars showed greater genetic diversity than “semi-long”,
“long” and “listada de Gandía” types (the four classes of local varieties).
Sufficient levels of overall variability were found to suggest that Spain is
a secondary centre of diversity for eggplant. A separate examination of
“listada de Gandía” (a well-known heirloom) and other “listada” (striped)
accessions from Spain and elsewhere revealed that the Spanish “listada”
lines could be distinguished by their spinier calyces and heavier fruit as well
as slower reproductive development (Muñoz-Falcón et al. 2008). And while
“listada de Gandía” showed low levels of genetic diversity, the absence
of three AFLP fragments in those accessions represent a unique genetic
fingerprint that could enable legal protection of this heirloom variety.
Turkey is also considered a secondary centre of eggplant diversity, given
the wide range of types cultivated in that country. Varieties are designated
as “round”, “semi-long”, and “long”, and these forms are used differently
in preparing Turkish cuisine. Morphological and molecular AFLP analysis
in 67 eggplant lines from the Turkish national germplasm collection showed
the greatest phenotypic variability in “round” and “semi-long” forms.
While these different morphological types did not form separate clusters
on the basis of the molecular data, genetic similarity levels in the accessions
(0.30 to 0.95) were indicative of intermediate diversity (Tümbilen et al.
2011b). The value of preserving local germplasm as well as the advantages
of molecular tools in the efficient classification and management of such studies
germplasm are made apparent by these recent researches (Prohens et al.
2005; Muñoz-Falcón et al. 2008; Tümbilen et al. 2011b). Genotypic data from
molecular markers can be easily obtained within a couple of weeks of seed
germination whereas phenotypic evaluation of vegetative and reproductive
traits can take a month or more. Once generated, such markers can also be
integrated into gene mapping studies.
10. Molecular Linkage Maps

10.1 A History
As previously mentioned, initial mapping efforts in the Solanaceae focused
on the two most important crops in the family, tomato (S. lycopersicum) and
potato (S. tuberosum) (Tanksley et al. 1992). The first linkage map for eggplant
was developed on the basis of a population of 168 F2 individuals generated
from a cross between S. melongena breeding lines from Japan (EPL1) and
Eggplant 129
India (WCGR112-8) (Nunome et al. 1998). Segregation analysis of 94 RAPD

markers yielded a map encompassing 716.7 cM and 13 linkage groups with
an average marker spacing of 8.8 cM. The subsequent characterization of
AFLP markers in this population [using MapMaker/EXP 3.0 (Lander et
al. 1987)] improved the density of the map; 191 markers (88 RAPD and 93
AFLP) spanning 779.2 cM were spaced on average 4.9 cM apart on 21 linkage
groups (Nunome et al. 2001). However, because the number of linkage
groups far exceeded eggplant’s chromosome number of 12, the fragmentary
and incomplete nature of the map was obvious. The addition of seven
polymorphic SSR markers brought the linkage groups down to 17 (Nunome
et al. 2003b). More recently, a large number of SSRs were characterized in this
intraspecific population and a 959.1 cM map consisting of 14 linkage groups
and 236 SSR markers at an average spacing of 4.3 cM was generated using
Mapmaker/EXP 3.0 (Lander et al. 1987; Nunome et al. 2009). Clustering
of the genomic SSR markers in heterochromatic chromosomal regions was
observed, as expected, given the unequal distribution of microsatellites
within the genome (Broun and Tanksley 1996).
An interspecific cross, S. linnaeanum MM195 x S. melongena MM738, was
used to create a molecular map of the eggplant genome based on tomato
markers (Doganlar et al. 2002a). Thus, 58 F2 progeny were genotyped, and
a map comprising 233 RFLP markers and spanning 1480 cM and 12 linkage
groups was constructed using Mapmaker v. 2.0 software (Lander et al. 1987).
This map had the distinct advantage of allowing direct comparisons to be
made between the eggplant and tomato genomes (discussed later). Using
JoinMap v. 1.3 (Stam 1993) Sunseri et al. (2003) also generated a linkage
map from an interspecific S. sodomeum (= S. linneanum) × S. melongena F2
population (48 individuals). The map is based on segregation data for 117
RAPD and 156 AFLP markers that range over 736 cM on 12 linkage groups,
with an average marker interval of 2.7 cM.
More recently, a high-resolution synteny map of eggplant was
constructed by placing 110 COSII markers on the Doganlar et al. (2002a)
map (Wu et al. 2009a) (Fig. 7-3). The COSII markers were developed from
single copy genes conserved in the Solanaceae and Rubiaceae; and, as
their position in the Arabidopsis genome is known, they are useful tool
for comparative mapping in diploid plant species (Wu et al. 2006). The
augmented eggplant map comprises 289 orthologous markers (110 COSII
+ 179 tomato-derived RFLPs), spaced on average every 6.1 cM over a total
map distance of 1535 cM (Wu et al. 2009a). Because of the syntenic nature of
the tomato and eggplant genomes, the locations of an additional 522 COSII
markers in the eggplant genome can be deduced. Thus, these researchers
have calculated that a total of 869 molecular markers of known position
are available in S. melongena.
Figure 7-3 Genetic map of eggplant. Framework markers (LOD > 3) are in bold and by
tick marks, interval markers (2 ≤ LOD ≤ 3) are in bold italics; all other markers are LOD <
2; cosegregating markers are alongside vertical bars. Chromosomal locations of markers on
the tomato map are indicated by ~Tx after the marker name. Each tomato chromosome is
color coded (see bottom of figure) and the corresponding segments of each eggplant linkage
group are colored accordingly. (Used with permission from Wu et al. 2009a, Springer Science
+ Business Media.)
Eggplant 131
While the molecular maps constructed thus far have employed

segregating F2 populations, the possibility of using a doubled haploid
(DH) population for mapping AFLP markers in eggplant was explored by
Barchi et al. (2010). F1 hybrids derived from a cross between two eggplant
breeding lines, one carrying a gene for Fusarium resistance introgressed
from S. aethiopicum and the other a susceptible line were subjected to anther
culture and 93 of the resulting DH individuals were screened with 170
AFLP markers. Of these, 68 percent showed distorted segregation making Please check the detail as
the population unusable for mapping analysis. In contrast, segregation the total adds up to 236
ratios were not skewed in an F2 population obtained by selfing the F1 instead of 238.
hybrids. Thus, 141 of these individuals were genotyped for 238 markers
(212 AFLPs + 22 SSRs + 1 RFLP + 1 CAPS). The resulting map, constructed
3 CAPS
using JoinMap v. 4.0 (van Ooijen 2006), encompasses 718.7 cM on 12 linkage
groups with an average density of one marker every 3.0 cM. The inclusion
of 20 SSR markers from the Nunome et al. (2009) map permitted alignment
and comparison of the maps; marker order and distances were found to
be in close agreement.
10.2 Applications
10.2.1 Comparative Mapping
The close relationship of eggplant and potato to tomato, the first plant species
for which a high density molecular linkage map was created (Tanksley et
al. 1992), has facilitated comparative genomics within the Solanaceae. By
using tomato RFLP markers as the basis for their eggplant map, Doganlar
et al. (2002a) reported the existence of 28 chromosomal rearrangements, 23
inversions and five translocations in eggplant as compared to tomato. In
contrast, only five inversions distinguish the tomato and potato genomes
(Tanksley et al. 1992). Thus, eggplant is estimated to be three- to six-fold
more diverged from tomato than potato; and the rate of divergence between
eggplant and tomato approximates 0.19 rearrangements/chromosome/
million years (assuming 12 million years of evolution between these
two species (Wikstrom et al. 2001)). This is considered a rather moderate
rate of evolution within angiosperms. Comparative mapping in tomato,
potato and eggplant leads one to conclude that evolution in solanaceous
genomes has largely involved paracentric inversions and translocations.
Furthermore, fluorescence in situ hybridization (FISH) mapping of the
entirety of chromosome 6 in seven Solanum species has given insight into
the particulars of these changes; thus, one of the paracentric inversions
previously thought to have occurred within the eggplant lineage is actually
specific to the tomato genome (Lou et al. 2010).
Figure 7-4 Comparative maps of the tomato and eggplant genomes. Color coding is the same
as in Fig. 3. Centromere positions are indicated by white dots. Solid lines connect markers
mapped at LOD ≥ 2 on both maps; dashed lines connect markers mapped at LOD < 2 on either
map. (Used with permission from Wu et al. 2009a, Springer Science + Business Media.)
Eggplant 133
The recent development of COSII markers in plants has paved the

way for even broader comparisons among plant genomes (Wu et al. 2006).
Anchored in the Arabidopsis genome, these markers show remarkable
synteny (conservation of gene order and content), which spans 37 regions
in the eggplant and tomato genomes (Wu et al. 2009a) (Fig. 7-4). Genetic
analysis of the COSII markers has thus helped to explain the mechanisms
of chromosome evolution in these two species. For example, the combined
COSII-RFLP map reveals inversions on eggplant chromosomes 1, 2, 6,
and 11 that were not detected in the RFLP map (Doganlar et al. 2002a).
Furthermore, as these markers have also been mapped in pepper (Wu et
al. 2009b), it can be inferred that while most of the inversions are specific
to the eggplant lineage, some occurred during the divergence of potato
and tomato from their most recent common ancestor with eggplant (Wu
et al. 2009a). The comparative mapping efforts undertaken with the COSII
markers provide important information about genome evolution as well
as useful tools (i.e., molecular markers) for trait mapping and germplasm
characterization.
10.2.2 Mapping and Tagging of Simply Inherited Traits

As a consequence of the relatively late development of genetic maps in
eggplant, few genes have been positioned or tagged within its genome. For
the most part, such studies have focused on genes controlling resistances
to the major diseases and pests of eggplant. As levels of such resistance
are typically low in cultivated materials within S. melongena, finding and
tagging these resistances in wild germplasm has been a priority, so that
marker-assisted selection for these traits can be implemented in eggplant
breeding programs.
Verticillium wilt resistance (derived from S. linnaeanum) was found
linked to two genomic regions in the Sunseri et al. (2003) AFLP map. Bulked
segregant analysis (BSA) of resistant and susceptible individuals was used
to identify molecular markers linked to Fusarium resistance in eggplant
(Mutlu et al. 2008; Toppino et al. 2008b). In one case, resistance genes were
introduced into S. melongena lines from S. aethiopicum and S. integrifolium
via somatic hybridization (Toppino et al. 2008b). RAPD markers linked to
these resistance loci, which proved to be allelic, were then identified and
used to create CAPS markers. Tests of the CAPS markers in segregating
progenies indicated that they could help facilitate selection for the trait.
Similarly, two sequence characterized amplified region (SCAR) markers
were generated for a dominant Fusarium resistance gene introgressed into
a Turkish eggplant line from a Malaysian genotype (Mutlu et al. 2008). The
results of preliminary screens with these SCAR markers suggest that the
gene might be specific to the Malaysian accession as it was not detected
in the other S. melongena accessions and the wild species tested. BSA of F2
progeny from a cross between Chinese inbred lines, one susceptible and one
highly resistant to bacterial wilt, (Ralstonia solnancearum), enabled tagging of
the resistance gene (Cao et al. 2009). An RAPD fragment was then converted
into a SCAR marker, which proved effective in distinguishing between
resistant and susceptible plants. While generally considered a complex
trait, peel color in eggplant was also tagged using bulked line analysis
(BLA) (Liao et al. 2009). The development of a SCAR marker associated
with reddish to dark purple pigmentation of the peel should facilitate
selection for this key fruit quality trait. Advances in marker development
and their application in eggplant will undoubtedly accelerate the rate at
which economically important traits are tagged and increase the role of
marker-assisted selection in breeding programs.
10.2.3 Quantitative Trait Mapping

Although tomato was a forerunner in the realm of quantitative trait mapping
in plants, eggplant has lagged behind. Only as comprehensive linkage
maps have become available has it been possible to study the inheritance of
polygenic characters in this crop. The first such a trait mapped in eggplant
was fruit shape which was analyzed in the S. melongena EPL1 × WCGR112-8
F2 population developed by Nunome et al. (1998). A quantitative trait loci
(QTL) for this character was detected on linkage group (LG) 10 of their
RAPD map using the interval analysis function of Mapmaker/QTL v. 1.1
(Lincoln et al. 1992). In their combined RAPD-AFLP map, approximately
25 percent of the phenotypic variation in fruit shape was localized to the
corresponding region of LG 2 (LG 10 having been re-named LG 2) (Nunome
et al. 2001). The pigmentation of fruit, stem and calyx tissue was shown to be
linked to loci on four linkage groups, with the most significant marker-trait
association (explaining ~25, 50 and 68 percent of the phenotypic variation
in fruit, stem and calyx color, respectively) on LG 7 (Nunome et al. 2001).
The genetic bases underlying a wide range of complex morphological
traits were examined by Doganlar et al. (2002b) and Frary et al. (2003) in
the S. linnaeanum MM195 x S. melongena MM738 F2 mapping population.
Fourteen traits related to domestication (fruit size and shape as well as
the prickliness and color of leaves, stems and fruit) were measured in two
locations (Doganlar et al. 2002b). A total of 62 significant (P ≤ 0.01) QTLs
were detected by linear point regression and confirmed by simple interval
analysis (LOD ≥ 2.4) using QGene software (Nelson 1997). However, as
growth conditions varied widely between the locations (greenhouse in
New York vs. field in France), only 15 QTLs were detected as having a
significant impact on corresponding traits at both locations. Nevertheless,
it was possible to pinpoint the loci underlying traits of particular interest
Eggplant 135
to eggplant breeders. Thus, two loci on linkage groups 2 and 9 controlled

the majority of the variation in fruit size: fw2.1 (23 percent PVE) and fw9.1
(44 percent PVE). Similarly, fruit shape was determined by just two loci: fs2.1
(20 percent PVE) and fs7.1 (29 percent PVE). These same QTLs have been
mapped in tomato (Grandillo et al. 1999; Frary et al. 2000) and pepper (Ben
Chaim et al. 2001), indicating that these genes are conserved more broadly
within Solanaceae. A single major locus on LG 6 determined the degree of
plant prickliness (controlling as much as 79 percent of leaf prickle variation)
while a single locus on LG 10 accounted for anthocyanin content in all
plant tissues, explaining as much as 93 percent of the phenotypic variation.
Daunay et al. (2004) suggest that this locus corresponds to their putative
A, a dominant gene determining anthocyanin presence in the epidermis
of various plant parts. Thus, the results of QTL analysis of domestication
traits in eggplant support those in other crops; selection pressures exerted
on a relatively small number of genetic loci over the course of domestication
and cultivation have had profound and dramatic effects on plant form and
function (Doebley et al. 1997).
In an analysis of 18 traits determining leaf, flower and fruit size, shape,
appearance and development, Frary et al. (2003) identified 63 significant
QTLs (P ≤ 0.01). Interestingly, at 46 percent of these loci, alleles from the wild
parent were found to confer unexpected effects on phenotype. In several
such cases, the wild alleles were responsible for producing transgressive
effects, wherein the phenotype of the progeny was superior to that of either
parent. For example, S. linnaeanum alleles were linked to improvements
in flower and fruit number, fruit set, calyx size and fruit glossiness. These
traits have major impacts on fruit yield and quality; thus, wild germplasm
is a valuable genetic resource for the improvement of complex agronomic
traits in cultivated eggplant. As with the domestication traits, some of the
QTLs detected in eggplant correspond to loci controlling the quantitative
inheritance of the same morphological characters in tomato and potato. This
conservation of gene function and position has significant implications in
terms of genome evolution within Solanum, and the subsequent discovery
of extensive synteny between eggplant and tomato (Wu et al. 2009a) comes
as less of a surprise in light of these earlier QTL-based studies. In practical
terms, as tomato has been a model system for both classical and molecular
genetics, much of the knowledge gained in tomato is readily transferrable
to eggplant breeding and improvement.
11. Genomic Resources

Given eggplant’s close relationship with the other solanaceous vegetable
crops, researchers can easily leverage the extensive resources developed
for tomato, potato and pepper and other nightshade family members
for enhancing understanding of eggplant genetics and evolution. The

SOL Genomics Network (SGN) (http://solgenomics.net/) is a relational
database/website that curates all of the resources currently available for the
Solananceae (Bombarely et al. 2011). SGN provides access to the molecular
linkage maps of tomato, potato and eggplant as well as information
about a range of marker types and links to mutant databases. Moreover,
SGN provides all of the published gene or expressed sequence tag (EST)
sequences from solanaceous species in a comparative genomics format
as well as, at the time of writing, pre-publication draft assemblies of the
genomes of Solanum lycopersicum (cultivated tomato) and S. pimpinellifolium
(its wild progenitor). In addition to these resources, a set of 16,000 ESTs
has been created from 60,000 cDNA clones from different developmental
stages and tissues of eggplant (Fukuoka et al. 2010). While this unigene set
is estimated to cover only ~35 percent of the transcriptome, it nevertheless
provides a wealth of information specific to eggplant and with tremendous
potential to impact work in comparative and functional genomics as well
as phylogenetics in Solanum.
12. Future Prospects

There is much scope for future work in Solanum melongena. While still
in its early stages, sequencing of eggplant’s transcriptome will enable
comparisons with other sequenced genomes thereby expanding resources
for those interested in eggplant. An integrated molecular linkage map,
which will combine RFLP, COSII and AFLP markers on the S. linnaeanum ×
S. melongena F2 population is on the horizon (S. Doganlar, pers. comm.). With
over 1,000 markers, this high density map should make it easier to explore
aspects of gene and genome evolution in the Solanaceae as well as to locate
the regions of the eggplant genome that control qualitative and quantitative
traits of interest. Disease and pest resistances are much needed in the crop;
thus, we can anticipate that marker-assisted selection will become an
increasingly important tool in eggplant breeding as a means of facilitating
the introgression of such genes from wild relatives. Breeding programmes
are also likely to focus on improving the nutritional composition of the
crop, particularly as regards anthocyanin and phenolic levels. Additional
work to characterize antioxidant activity in cultivars, landraces and allied
species will help in selecting the best germplasm for these traits. One can
also imagine that the medicinal benefits of eggplant might lead to the plant
being grown not as a vegetable crop but for its glycoalkaloids. As eggplant’s
nutritional benefits become more widely realized and higher yields are
achieved through genetic improvement, eggplant should gain worldwide
importance as a vegetable crop.
Eggplant 137
Acknowledgement
We are grateful to Anne Frary, Izmir Institute of Technology, Turkey, for
valuable comments on the manuscript. This work was supported by a Career
Project (TUBITAK 104T224) from the Scientific and Technical Research
Council of Turkey to Sami Doganlar.
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Chapter · January 2013

Amy Frary Sami Doganlar

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3. Brief History of the Crop

Kindly indicate A,B,C &

cultivated in Africa as fruit and vegetable crops. Taxonomic relationships

Resources, NBPGR, New Delhi) (Gangopadhyay et al. 2010), nearly 2000

7. Classical Genetics and Traditional Breeding

complex traits can be more easily analyzed, unwanted genotypes can be

that only around 20 percent of the variability in degree of browning can

non-hybrid varieties are potentially valuable sources of heterozygosity for

10. Molecular Linkage Maps

India (WCGR112-8) (Nunome et al. 1998). Segregation analysis of 94 RAPD

While the molecular maps constructed thus far have employed

The recent development of COSII markers in plants has paved the

10.2.2 Mapping and Tagging of Simply Inherited Traits

10.2.3 Quantitative Trait Mapping

to eggplant breeders. Thus, two loci on linkage groups 2 and 9 controlled

11. Genomic Resources

for enhancing understanding of eggplant genetics and evolution. The

12. Future Prospects

Nisha P, Abdul Nazar P, Jayamurthy P (2009) A comparative study on antioxidant activities

S. aethiopicum L. group gilo as a source of resistance to Fusarium oxysporum f. sp. melongenae.

Pineda O, Roder S, Wing RA, Wu W, Young ND (1992) High-density molecular linkage

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