Introduction C

Tomato is one of the world's most popular and widely cultivated vegetables. For many low-income
farmers in the tropical cocitries it is one of the essential food and cash crops. It

pt
is predominantly rich in vitamin C and^m^erals, particularly phosphorus, potassium and calcium,
and is highly appreciated in different dishes. It is an economically important crop

o
with most countries, carrying in much needed resources. As the botanical name of tomato

according to the Linnaean taxonomic ssification was Solanum lycopersicum, on the othe r hand
(Miller et al, 2009) suggested the name of the genus
Lycopersicon (Latin-Wolf Peach) and subsequently suggested the name Lycopersicon esculentum for
cultivated tomato and

Lycopersicon pimpinellifolium for native tomato. Whilst other classification algorithms have been
proposed since then, the Miller classification has turned out to be the norm because of its common
usage. Fungal Plant pathogens form a significant limiting critical role in the development of tomato.
Recognizing the differentiation between pathogenic and nonpathogenic diseases is important for
successful disease control, and identifying the type of microorganism that causes an infectious
disease. Tomatoes watered by sprinklers that
humidify the leaves and fruit seem to be more susceptible to induce disease outbreak than those

irrigated by drip or furrow. Tomato plants are mostly vulnerable to biotic stresses like (fungi, bacteria,

viruses and nematodes) and environmental factors like (temperature, sunlight, malnutrition etc.)

(Caldwell et al, 2005). These pathogens are infectious and can spread from plant to plant in a field,

sometimes very quickly when conditions are favourable for the weather for disease outbreak. Fungi

seem to be the most common mode of infectious diseases in plants and can be very harmful. Damping-

off, Early blight, Septoria leaf spot,

Late blight, Cercospora leaf mould, Fusarium wilt, Grey leaf spot, Powdery mildew,

Verticillium wilt, White mould, Alternaria stem canker, Corky root rot, Didymella stem rot,

Fusarium crown and root rot, Fusarium foot rot, Southern blight, Buckeye rot are the most common

pathogens that threaten tomatoes.

Tomato (Solanum lycopersicum L.) is the second most important fruit or vegetable crop next to potato

(Solanum tuberosum L.), with approximately 182.3 million tons of tomato fruits produced on 4.85

million ha each year (FAOSTAT, 2019). Asia accounts for 61.1% of global tomato production, while

Europe, America, and Africa produced 13.5%, 13.4%, and 11.8% of the total tomato yield, respectively.

Tomato yields are highly variable, ranging from more than 508 tons per ha in the

Netherlands to fewer than 1.5 tons per ha in Somalia in 2017 (FAOSTAT, 2019), with an average global
yield of 376 tons per ha. Tomato consumption is concentrated in China, India, North Africa, the Middle
East, the US, and Brazil with tomato consumption per capita, ranging from 61.9 to 198.9 kg per capita
(FAOSTAT, 2019). Tomato is a member of the Solanaceae family, which includes several other
economically important crops such as potato, pepper (Capsicum annuum L.), and eggplant (Solanum
melongena L.), representing one of the most valuable plant families for vegetable and fruit crops.
Tomatoes contain many health-promoting compounds and

are easily integrated as a nutritious part of a balanced diet (Marti

et al., 2016). In addition to consuming the fresh fruits, consumers

use tomatoes in processed products such as soups, juices, and

sauces (Krauss et al., 2006; Li et al., 2018b). Over the last decade,

consumers have become more aware of foods as a source of

health benefits and their roles in prevention of several chronic

diseases and dysfunctions (Pem and Jeewon, 2015). Although a wealth of functional foodstuffs have

been created to fulfil these requirements, it is important to note that the consumption of “conventional

foods” such as fruits and vegetables is more

effective for this purpose (Viuda-Martos et al., 2014).

The nutritional importance of tomatoes is largely explained by

their various health-promoting compounds, including vitamins,

carotenoids, and phenolic compounds (Raiola et al., 2014; Liu et al.,

2016; Marti et al., 2016; Li et al., 2018b). These bioactive compounds

have a wide range of physiological properties, including antiinflammatory, anti-allergenic, antimicrobial,

vasodilatory,

antithrombotic, cardio-protective, and antioxidant effects (Raiola

et al., 2014). Tomatoes are rich in carotenoids, representing the

main source of lycopene in the human diet (Viuda-Martos et al.,

2014). Carotenoids and polyphenolic compounds contribute to the

nutritional value of tomatoes and improve their functional attributes

and sensory qualities, including taste, aroma, and texture (Raiola et al., 2014;Tohge and Fernie,
2015;Marti et al., 2016). Tomatoes also have the naturally occurring antioxidantsVitamins C and E
(Agarwal and Rao, 2000; Martf et al., 2016) as well as large amounts of metabolites, such as sucrose,
hexoses, citrate, malate, and ascorbic acid (Li et al., 2018b).

Tomato fruit quality and metabolite biosynthesis are affected by plant growing conditions (Diouf et al.,
2018). Tomato production is challenged by several problems around the world, including the scarcity of
water resources, soil salinization, and other abiotic stresses (Fahad et al., 2017; Gharbi et al., 2017; Zhou
et al., 2019). In particular, in countries with a Mediterranean climate, including some regions in
southern Europe and North and South America, tomato cultivation is increasingly confronted with
limiting conditions such as drought and salinity, which ultimately reduce the competitiveness of tomato
farmers in these areas. This, in turn, impacts the integrity of the ecosystem, contributing to the
relocation (abandonment) of rural sectors.
In addition to its economic and nutritional importance, tomatoes have become the model for the study
of fleshy fruit

development (Karlova et al., 2014;Kim et al., 2018; Li et al., 2018b).

The entire tomato genome has been sequenced, serving as a rich

genomic resource, and both genetic and physical maps and

molecular markers are available for this species (The Tomato

Genome Consortium, 2012; Suresh et al., 2014; Zhao et al., 2019).

Moreover, a range of well-characterized monogenic mutants,

TILLING populations, wild tomato species, recombinant inbred

lines and genome editing tools are available (Eshed and Zamir,
1994; Minoia et al., 2010; Perez-Martin et al., 2017; Li et al., 2018b;

Martin-Pizarro and Pose, 2018; Tomato Genetics Resource

Center, 2019; Rothan et al., 2019). Several databases contain

gene expression analysis data (Fei et al., 2006; Suresh et al.,

2014; Zouine et al., 2017; Shinozaki et al., 2018b), while recentprogress in tomato metabolomics has
provided substantial information about the primary and specialized metabolism of this species and the
pathways involved in molecular biosynthesis and turnover (Luo, 2015; Tieman et al., 2017; Zhu et al.,
2018).

Dramatic metabolic changes occur during tomato fruit development (Carrari and Fernie, 2006). Tomato
is a climacteric fruit, meaning it undergoes a surge in respiration and ethylene production at the onset
of ripening (Li et al., 2019a).

As ripening progresses, tomato fruits transit from partially photosynthetic to true heterotrophic tissues
through the parallel differentiation of chloroplasts into chromoplasts and the dominance of carotenoids
and lycopene in the cells of the ripe fruits (Carrari and Fernie, 2006). The ripening process has evolved
to make fruit palatable to the organisms that consume them and disperse their seeds. In doing so,
ripening activates pathways that generally influence the levels of pigments, sugars, acids, and aroma-
associated volatiles to make the fruit more appealing, while simultaneously promoting tissue softening
and degradation to permit easier seed release (Matas et al., 2009). In this review, we provide an
overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic
and hormonal control of fruit development and ripening, after which we document the primary
metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism.
Links between primary and secondary metabolic pathways are further highlighted by the importance of
pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to
several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on
tomato fruit metabolism and quality.
Fungi

A Fungus is one of the most diverse microorganisms that inhabit different environmental sources such
as soil, plant parts (leaves, root and fruits), water and food sources (Maheswari and Komalavalli, 2013,
Sartori et al., 2013;

Rebecca et al., 2012). The growth and distribution of fungi are affected by different environmental
factors such as temperature, pH, moisture, degree of aeration, amount and type of nutrients (Gaddeyya
et al., 2012).

Soil fungi play an important and vital role in maintaining soil fertility and productivity, and are
influenced by a number of factors, including soil properties and human activities (Bao et al., 2012). Fungi
are very important organisms that inhabit the soil. They play an important part in nutrition and
processes that lead to the improvement of the health and development of the plant (Mulani and
Turukmane, 2014). However, the surface of the plant leaves and fruits is inhabited by several
microorganisms, including filamentous fungi and yeast A Fungus is one of the most diverse
microorganisms

that inhabit different environmental sources such as soil,

plant parts (leaves, root and fruits), water and food sources

(Maheswari and Komalavalli, 2013, Sartori et al., 2013;

Rebecca et al., 2012). The growth and distribution of fungi

are affected by different environmental factors such as

temperature, pH, moisture, degree of aeration, amount and

type of nutrients (Gaddeyya et al., 2012).

Soil fungi play an important and vital role in

maintaining soil fertility and productivity, and are

influenced by a number of factors, including soil

properties and human activities (Bao et al., 2012). Fungi

are very important organisms that inhabit the soil. They

play an important part in nutrition and processes that lead to the improvement of the health and
development of the plant (Mulani and Turukmane, 2014). However, the surface of the plant leaves and
fruits is inhabited by several

microorganisms, including filamentous fungi and yeast that cause the deterioration and spoilage of
vegetables and

fruits. This makes Fungi a high-priority concern because

plants are food sources for consumers and are of great

economic importance to farmers (Prabakaran et al., 2011).

Udoh et al., (2015) isolated a number of fungi species

from some edible fruits and vegetables that were

responsible for post-harvest spoilage of some edible fruits

and vegetables. To solve these serious problems, there is

still a need for the isolation and identification of

filamentous fungi to have that under control, and prevent

their damage of the agricultural crops.

The real number of fungi is still unknown; on the other hand, only 5-13 % of the overall evaluated
worldwide fungal species have been characterized (Maheswari and

Komalavalli, 2013). Thus, the fungal Isolation and identification from the different environmental

sources is still very essential for the viewing and recognizing of more species, editing scientific

classification, evaluating their effects in nature, and supplying strains for ecological remediation,

biological control, and industrial aspects (Blackwell, 2011).

The morphology of a fungal colony in filamentous fungi results from growing as fibers (hypha), that are

cylindrical, threadlike 2-10 in diameter structures, long up to several centimeters, with different

observations of colony features such as color, size, shape visible by the naked eye which was used

classically to identify fungi (Lima and Borba, 2001). The morphology of fungi was observed under a

compound microscope to examine the shapes forming from the arrangement of spores (Gaddeyya et
al., 2012). The morphological and biochemical identifications of fungi sometimes face many problems

such as: the need for a great time, requiring high skill, and generating various morpho/biotypes within

one species.

The use of molecular identification is fast, sufficient, reproducible, and can provide high specificity to
distinguish between the species and subspecies of fungi unlike the morphological and biochemical tests
used in the laboratory diagnosis of fungi (liu et al., 2000; Sugita and

Nishikawa, 2003).

Molecular identification techniques based on total fungal DNA extraction provide a unique barcode for
the determination and identification of different fungal isolates up to a species level (Landeweert et al.,
2003). Molecular identification using this barcode has turned into an essential tool for mycologists
studying fungal taxonomy, molecular evolution, population genetics or fungus-plant interactions (Moller
et al., 1992). The identification of fungi using molecular techniques is carried out by the sequencing of
PCR amplified part of 18S rRNA genes with universal primers to fungal species (Monod et al., 2005;
Hensel and Holden, 1996). Factors determining the quality of tomato fruits

Factors that influence product quality can be divided in two groups: Intrinsic factors

(color, shape, and freedom of defects) and internal attributes such as texture, sweetness, acidity, aroma,
flavor, shelf life and nutritional value (Hewett, 2006). Growers are mainly basing their decisions, as
regards which cultivars to produce, on intrinsic factors desired by the buyer (FAO, 1989),

Crop management together with external conditions during the pre-harvest period will determine the
quality of the product (FAO, 1989, Hewett, 2006), and during the best circumstances, this quality may be
kept during the post-harvest period when quality improvements are not possible (FAO, 1989).
2.1 Nutritional factors
2.1.1 Carotenoids, including lycopene
Carotenoids are well known as natural compounds involved
in reducing the risk of
development of several types of diseases such as diabetes,
gastrointestinal and cardiovascular diseases e.g. by reducing
the amount of oxidized low density lipoproteins (Hyman et
al., 2004, Rao and Rao, 2007, Preedy and Watson, 2008).
Carotenoids are also known to prevent development of
degenerative diseases such as blindness, xerophthalmia and
degeneration of muscles (Paliyath et al., 2008). In addition,
carotenoids have been correlated to anticancer properties of
stomach, lung and prostate cancer (Giovannucci, 1999,
Wang et al., 2016). A recent study have shown that high-risk
prostate cancer patients, constantly consuming lycopene
through intake of
a tomato sauce during a period of 4 years, significantly
reduced their risk to contract
prostate cancer. These patients also became low-risk
prostate cancer patients after
the 4 years period of lycopene consumption (Wang et al.,
2016). The health benefits of carotenoids have been
attributed to their function as natural antioxidants.
Lycopene is the major antioxidant carotenoid in tomato
followed by P
carotenoid (Hyman et al., 2004). Furthermore, a-carotene, P-
carotene and P-cryptoxanthin are precursors of vitamin A,
which is not the case for all carotenoids
(Institute of Medicine, 2000, Apel and Bock, 2009).
Bioavailability of the carotenoids is highly important as
related to their impact for
human nutrition. Homogenization and heat treatments are
common steps in transforming fresh tomato to other food
commodities. Homogenization is normally
breaking down the aggregated structures of the cell by
changing the fiber network.
However, homogenization at 90°C in 30 minutes was shown
to not chanae the fiber
2.1.2 Vitamin C including ascorbic acid
Tomato is an important source for humans of vitamin C,
including ascorbic acid and
some, generally low, amounts of dehydroascorbic acid. No
significant differences
was found in quantity of ascorbic acid for different types of
tomatoes, e.g. salad
tomato versus those for processing. However, ascorbic acid
was among the components in tomato highly sensitive to
thermal degradation (Abushita etal., 2000). Red
tomatoes contain approximately 19 mg of vitamin C (Nunes,
2008) and depending
of the cultivar and growing conditions ascorbic acid contents
is around 100 g of fresh red tomato (Abushita etal., 2000).
Synthesis and accumulation of ascorbic acid have been
correlated with the maturity
stage of tomatoes. Ripening tomatoes under storage
conditions was shown to decrease the content of ascorbic
acid in the tomatoes with up to 50% as compared to
vine ripe tomatoes, demonstrating that accumulation of
ascorbic acid is favored if
the fruit reaches the maturity stage on the plant (Nunes,
2008). Salt stress during
growth of tomato enhances the concentration of sugars,
organic acids and amino
acids, all characters being well appreciated by consumers
(Passam et al., 2007).
The vitamin C content in fresh tomatoes could be preserved
under storage conditions if modified atmosphere conditions
was applied with a polyolefin films as an
enclosure barrier with enough 02 permeability to avoid
anaerobic respiration
(Passam et al., 2007). Exclusion of such barriers between the
tomatoes and the atmosphere lead to the disappearance of
vitamin C within 3 days (FAO, 1989). Also,
ififramin C i mrlr^r htiafr mnrlitinnc A A 1 QQQ 、
2.1.3 Polyphenols contents and antioxidant properties
Polyphenols are bioactive natural compounds present in
vegetables, fruits and seeds
(Quideau, 2011). A bioactive compound could be essential
or nonessential for humans, but is mostly considered
beneficial for the human health (Biesalski et al.,
2009). Polyphenols can also be seen as "secondary
metabolites" which presence are
correlated to corresponding genes, although the content
is also being influenced by
the environment (Siracusa et al., 2012).
Polyphenol compounds are characterized by their
phenolic structure in natural products (Tsao, 2010) and
various types are soluble or insoluble in water
(Papadopoulou and Frazier, 2004). The most common
polyphenols in tomatoes are flavonoids, hydroxycinnamic
acids and anthocyanins (Siracusa et al., 2012, Verhoeyen
et al., 2002, Bovy et al., 2002), and the polyphenols are
predominantly present in the tomato peel. In tomatoes,
30 different phenolic compounds have been determined
being present; coffeic acid, caffeic acid-o-hexoside,
chlorogenic acid, coumaroylquinic acid, coumeric acid-o-
hexoside, cryptocholorogeic acid, dicaffeoylquinic acid,
eriodictyol-o-hexoside, ferulic acid, ferulic acid -o-
hexoside,
feruoylquinic acid -o -hexoside, gallic acid, homovanillic
acid, kaempferol-o-rutinoside-hexoside, kaempferol-3-o-
glucoside, kaempferol-3-o-rutinoside,
naringenin, naringen-in-o-dihexoside, naringenin-o-
hexoside, neochlorogenic acid, o-acetylprunin, phloretin-
c-diglycoside, phloridzin-c-diglycoside, protocate-chuic
acid, prunin (naringenin-7-o-glucoside), quercetin, rutin-o-
hexoside- pentoside, rutin-o-hexoside, rutin-o-pentoside,
rutin (quercetin 3-o- rhamnosyl-glucoside)
(Vallverdu-Queralt et al., 2010).
The physien growth and development of pathogen
resistance (Harbone, 1995). Polyphenols' role in
protecting the plant from the attack of viruses and other
microorganism has