American Journal of Plant Sciences, 2011, 2, 255-261
doi:10.4236/ajps.2011.22027 Published Online June 2011 (
Copyright © 2011 SciRes. AJPS
Biodiversity in a Tomato Germplasm for Free
Amino Acid and Pigment Content of Ripening
Guillermo Raúl Pratta1,2, Gustavo Rubén Rodríguez1,2, Roxana Zorzoli2,3, Liliana Amelia Picardi2,3,
Estela Marta Valle1,4
1National Council for Scientific and Technical Research, Buenos Aires, Argentina; 2 Chair of Genetics, Agronomic Sciences Faculty,
National University of Rosario, Zavalla, Argentine; 3Council for Research of the National University of Rosario, Zavalla, Argentine;
4 Institute of Molecular and Cell Biology of Rosario, CONICET/Biochemical and Pharmaceutical Sciences Faculty, Suipacha,
Rosario, Argentine.
Received March 8th, 2011; revised March 25th, 2011; accepted May 6th, 2011.
Free amino acid and pigment composition in fruits at two ripening stages from a selected tomato germplasm was stud-
ied. The aims were contributing to knowledge on variability of ripening metabolism and identifying more consistently
the genetic background of the plant material under analysis. Significant differences (p < 0.05) were found among rip-
ening stages and among genotypes within ripening stage for all amino acids and pigments except by asparagine,
alanine and chlorophyll b contents. The highest relative amino acid content corresponded to glutamate, glutamine, and
GABA though some genotypes had relatively high asparagine content. Glutamate, glutamine and GABA performed op-
positely: the former increa sed along ripening while the latter two decreased in their relative content. A Principal Com-
ponents (PC) analysis was applied, determining that metabolites hav ing the greatest contribution to genera l variability
were threonine, serine, glutamate, glutamine, glycine, isoleucine, leucine, tyrosine, phenylalanine, lycopene and beta-
carotene, which showed the highest association with PC1. Alanine and chlorophylls a and b were highly associated to
PC2. These two first PC explained the 62% of the to tal variation, and genotypes were distributed according to the rip-
ening stage in their coordinates. Accordingly, a Hierarchical Clustering resulted in a dendrogram having a relatively
high cophenetic correlation (0.70), in which two well defined groups were obtained according to ripening stage. These
results verified the existence of variability in the metabolism of ripening fruit for amino acids and pigments, and al-
lowed to identify unequivocally a set of selected tomato germplasm according to the fruit metabolic profiles in these two
ripening stages.
Keywords: Solanum Section Lycopersicon, Plant Breeding , Plant Genetic Resources, Multivariate Analysis
1. Introduction
From an evolutionary viewpoint, tomato (Solanum ly-
copersicum) ripening could be considered as a transition
from a green stage that prevents fruit consumption (hence
protecting the developing seeds) to a ripe stage in which
its attributes are optimum to attract predators, which
consume fruit and help to disperse mature seeds [1]. This
transition includes morphological, biochemical and phy-
siological changes that lead to acquisition of appropriate
color, texture, flavor, among other traits determining fruit
quality. Some of these changes are variations in free
amino acids and pigment composition [2,3]. Glutamate
percent content noticeably increased between mature
green and red ripe stages, simultaneously to a reduction in
glutamine and GABA levels in tomato varieties [4].
From a productive viewpoint, the conservation of red
ripe attributes during a longer time prolongs the opportu-
nity of fruit commercialization, especially for the fresh
market [5]. Shelf life is a measure for the period of tomato
quality adequate maintenance, and has been reported as
negatively correlated to glutamate relative molar content
of ripe mature fruits [6]. Long shelf life tomatoes have been
currently obtained by introgressing spontaneous ripening
mutant genes such as nor, rin, alc and Nr, or by genetic
transformation [7]. Both strategies have disadvantages,
Biodiversity in a Tomato Germplasm for Free Amino Acid and Pigment Content of Ripening Fruits
because spontaneous mutations present pleiotropic effects
that diminish fruit quality and transgenic food are not well
accepted by public opinion even presently [5].
Exotic germplasm of Solanum section Lycopersicon
comprises S. lycopersicum var. cerasiforme, the closest
relative S. pimpinellifolium, and other 10 wild species.
They are invaluable plant genetic resources contributing
abiotic and biotic resistance or tolerance genes but also for
increasing fruit quality and prolonging shelf life [8,9].
Seventeen recombinant inbred lines from an interspecific
cross S. lycopersicum cv. Caimanta x S. pimpinellifolium
LA722 were obtained after six selfing cycles with an-
tagonistic-divergent selection for fruit weight and shelf
life [10] and characterized by quantitative fruit traits, total
pericarp polypeptide profiles and AFLP markers [11,12].
A wide variation was found for all analyzed phenotypic
and molecular attributes.
The general goal of this research was to study free amino
acid and pigment composition in this selected tomato
germplasm, with the aims of contributing to know- ledge
on variability of ripening metabolism, identifying more
consistently the RILs genetic background, and verifying
associations between glutamate content and fruit shelf life.
2. Materials and Methods
2.1. Plant Material
Ten seeds of RILs 4, 10, 12 and 15 together with the
experimental testers, parents Caimanta and LA722 (Fig-
ure 1), were sown in seedling trays on August under a
glasshouse. Then plants were grown at the experimental
field station “José F. Villarino” located at latitude 33°S
and longitude 61°W, from October to March under
greenhouse conditions. Previous to the transplantation,
the soil (a typical argiudol) was fertilized with poultry grit.
The crop was watered twice a week, levels of irrigation
that were sufficient to avoid water stress during the plants
growing period. Mean values of fruit shelf life (in days)
were: Caimanta = 13.00, LA722 = 18.60, RIL4 = 16.21,
RIL 10 = 21.17, RIL12 = 17.41 and RIL15 = 12.79 (av-
eraged from [10] and [12]).
2.2. Determination of Amino Acids and Pigment
Samples of tomato fruits (four per line) were harvested at
the mature green stage (MG, when fruit is green but stops
growing) and red ripe stage (RR, when fruit is completely
red but still firm). Pericarp tissue of harvested fruits was
obtained by removing the locule tissue and seeds and then
they were stored at –80˚C until analysis [2]. Pericarp tissue
(0.5 - 1 g fresh weight) was extracted with 5 ml chloro
form/methanol (1.5/3.5 v/v) and the amino acids relative
Figure 1. Fruits of four tomato Recombinant Inbred Lines
(RIL) and their parents Solanum lycopersicum cv. Caimanta
and S. pimpinellifolium LA722, the experimental testers.
composition was determined in the methanolic phase by
derivatization with ninhydrin or o-phthaldialdehyde using
an amino acids analyzer following [4]. Pigments were
determined according to [3].
2.3. Statistical Analysis
Distribution’s normality of total free amino acids and
pigment contents (in μmol·mg–1 fresh weight and mg·100
g–1 fresh weight, respectively) and each amino acid per-
cent composition was analyzed following [13]. Com-
parisons were made by a hierarchical ANOVA for vari-
ables having normal distribution, in which the principal
source of variation was ripening stage and the nested
source of variation was genotype within ripening stage.
Kruskall-Wallis test was applied for variables displaying
not normal distribution. Mean values were calculated
from three independent experiments in all cases. The
Pearson correlation coefficients (r) among all variables
(including the averaged shelf life values) were calculated
[14]. Multivariate Analysis of Principal Components and
Hierarchical Clustering with Ward method and Euclidean
distances were used to identify metabolites (amino acids
and pigments) mostly contributing to general variability
and to assess the importance of each source of variation
(genotype and ripening stage) in categorizing the obtained
set of results [15] to get a data mining approach on me-
tabolic changes occurring during tomato ripening.
3. Results
Mean values of each amino acid relative molar content,
and total amino acid and pigment contents of the pericarp
fruit at MG and RR stages of the four RILs and the parents
are in Table 1. All variables, except by total free amino
Copyright © 2011 SciRes. AJPS
Biodiversity in a Tomato Germplasm for Free Amino Acid and Pigment Content of Ripening Fruits
Copyright © 2011 SciRes. AJPS
acid content and the threonine and valine relative molar
contents, were normally distributed (W > 0.95; ns). Sig-
nificant differences (p < 0.05) were found among ripening
stages and among genotypes within ripening stage in all
cases except by the relative contents of asparagine and
alanine and chlorophyll b content. For these variables,
significant differences were found among genotypes wit-
hin ripening stage but not among ripening stages.
In all genotypes, the total amino acid content at RR
stage was higher than at MG stage except by the tester
Caimanta, in which no difference was detected among
stages. In most cases, the highest relative amino acid
content corresponded to glutamate, glutamine, and GABA
though some genotypes (LA722 and RIL4) had relatively
high relative asparagine content. Additionally, glutamate,
glutamine and GABA performed oppositely given that the
former increased from MG to RR while the latter two
decreased in their relative molar content. As expected,
chlorophyll a content diminished from MG to RR, chlo-
rophyll b also decreased or remained constant, according
to the genotype source of variation, while lycopene and
beta-carotene increased among ripening stages, the mag-
nitude of such changes widely depending on the genotype.
In general, the wild tester LA722 showed the greatest
values for all pigments.
Just a few (34 of 190, i.e., nearly 18%) correlation
coefficients among metabolites were significant (data not
shown). Some of the remarkable correlation coefficients
Table 1. Relative molar composition of free amino acids, and total amino acid (AA) and pigment contents in the pericarp
tissue of tomato fruits at two ripening stages in different selected genotypes (four Recombinant Inbred Lines—RIL—and
their parents, Caimanta of Solanum lycopersicum and LA722 of S. pimpinellifolium).
Genotypes Caimanta LA722 RIL4 RIL10 RIL12 RIL15
Metabolite/Ripening Stage MG RR MGRR MGRR MGRR MG RR MGRR
mg·100 g–1 fresh weight
Chlorophyll a 1.36 0.32 6.73 1.77 1.47 0.40 3.36 0.852.17 2.56 1.570.30
Chlorophyll b 0.67 1.39 2.27 1.99 0.85 1.05 4.37 0.551.68 3.56 0.790.43
Lycopene 0.75 15.15 0.96 22.68 0.64 12.94 1.27 24.47 1.71 19.90 0.177.93
Beta-carotene 0.24 3.98 0.52 6.55 0.49 3.70 0.723.22 0.43 2.56 0.461.45
Relative molar content of free amino acids (%)
Aspartate 0.38 9.18 1.21 1.68 0.59 2.34 0.99 2.132.15 3.56 1.831.13
Threonine 7.58 1.25 3.76 0.97 6.781.72 1.590.21 1.92 0.24 2.482.74
Serine 8.02 1.74 8.69 2.81 5.34 3.28 2.05 0.8114.09 1.08 5.591.83
Asparagine 10.40 3.53 17.6834.316.6319.729.444.312.33 1.17 13.486.04
Glutamate 13.35 58.26 16.09 44.74 19.88 36.284.8661.74 26.37 78.83 6.7247.11
Glutamine 25.58 13.6624.983.5729.7823.1617.803.4714.93 6.10 44.2420.08
Glycine 2.02 0.79 1.47 0.96 1.940.51 0.520.19 1.35 0.38 0.981.61
Alanine 2.48 2.75 5.03 2.44 1.74 2.461.97 1.476.20 2.61 1.562.76
Valine 4.16 1.24 3.39 2.34 3.30 0.862.54 1.147.44 0.98 1.921.31
Isoleucine 2.62 0.38 1.10 0.20 2.310.77 0.600.12 0.93 0.31 1.380.58
Leucine 1.54 0.53 0.46 0.33 1.570.51 0.430.11 0.75 0.22 1.050.63
Tyrosine 1.88 0.41 1.05 0.23 1.20 0.100.45 0.120.60 0.29 0.520.13
Phenylalanine 3.88 1.05 1.58 0.96 3.92 0.680.82 0.481.25 0.57 1.802.14
GABA 12.38 3.83 8.611.81 10.84 4.04 53.9520.9515.56 1.80 13.326.53
Others 3.73 1.40 4.90 2.65 4.18 3.56 1.99 2.75 4.13 1.86 3.135.38
Total AAs (μmol·mg–1 fresh weight) 25.03 24.668.3620.5915.4140.5317.4733.971.52 17.71 3.515.46
G: fruits at mature green ripening stage, RR: fruits at red ripe ripening stage, Caimanta and LA722 were the experimental testers.
Biodiversity in a Tomato Germplasm for Free Amino Acid and Pigment Content of Ripening Fruits
were those between glutamate and glutamine (r = –0.79, p
< 0.01), threonine, glycine, isoleucine, leucine, tyrosine
and phenylalanine (r > 0.75, p < 0.001 in all cases), serine,
alanine and valine (r > 0.72, p < 0.01 in all cases), iso-
leucine and lycopene (r = –0.72, p < 0.01), and lycopene
and beta-carotene (r = 0.87, p < 0.001). On the other hand,
GABA, asparagine, and chlorophyll a and b had no sig-
nificant correlation with any metabolite, though chloro-
phyll b at MG was positively associated with fruit shelf
life (r = 0.90, p < 0.01). Other metabolites associated with
this latter trait were leucine at RR (r = –0.92, p < 0.01),
alanine at RR (r = –0.85, p < 0.05) and lycopene at RR (r =
0.88, p < 0.05) but the previously reported correlation
with glutamate at RR [6] was not confirmed in this ex-
periment (r = 0.21, ns).
The two first Principal Components (PC1 and PC2)
explained the 62% of the total variation in metabolite
composition of MG and RR tomato fruits. If PC3 was also
considered, this percentage increases to 72% but only PC1
and PC2 will be further analyzed. Metabolite contribu-
tions to PC1 and PC2 (i.e., the respective eigenvalues and
the association among each original variable and both PCs)
are shown in Table 2. The metabolites having the more
remarkable correlation coefficients (threonine, serine,
glutamate, glutamine, glycine, isoleucine, leucine, tyro-
sine, phenylalanine, lycopene and beta-carotene) also had
the greatest contribution to general variability and the
highest association with PC1. Alanine and chlorophylls a
and b were highly associated to PC2. Figure 2 shows the
distribution of genotypes by ripening stage (and also of
each metabolite) in the PC1 and PC2 coordinates. A clear
separation by ripening stage was obtained in the axis of
PC1, which explained the greatest proportion of total
variability (46%, Table 2). It should be considered as an
extent of variability according to ripening metabolism,
indicating that threonine, serine, valine, glutamine, gly-
cine, isoleucine, leucine, tyrosine, and phenylalanine
relative molar content were higher at MG while glutamate
relative content and lycopene and beta-carotene contents
were higher at RR, though there were some genotype
exceptions (RIL10 MG and RIL15 RR, Figure 2). PC2,
which explained a lesser proportion of general variability
(16%), better accounted for genotype biodiversity, and
separations in this axis are more noticeable at the MG
stage (Figure 2). Hence, genotypic differences are less
important at RR.
Hierarchical Clustering confirmed PC results. The
dendrogram had a relatively high cophenetic correlation
(0.70) and two well defined groups were obtained accord-
ing to ripening stage, one including all genotypes at MG
and RIL15 at RR, and the other, the remaining genotypes
at RR (Figure 3). In the first group, separation among
genotypes occurred at a higher distances that in the second
Table 2. Eigenvalue composition of Principal Components 1
and 2 (PC1 and PC2, respectively) and associations among
metabolites and each Principal Component (a1 and a2,
Metabolite PC1 a1 PC2 a2
Aspartate (%) –0.18 –0.54 –0.05 -–0.09
Threonine (%) 0.29 0.89 –0.20–0.35
Serine (%) 0.24 0.72 0.24 0.43
Asparagine (%) –0.02 –0.07 –0.04 –0.06
Glutamate (%) –0.25 –0.77 –0.11 –0.20
Glutamine (%) 0.24 0.72 –0.10–0.17
Glycine (%) 0.29 0.88 –0.10–0.18
Alanine (%) 0.09 0.27 0.39 0.69
Valine (%) 0.21 0.65 0.27 0.49
Isoleucine (%) 0.30 0.91 –0.18–0.32
Leucine (%) 0.29 0.86 –0.24–0.42
Tyrosine (%) 0.27 0.83 –0.07–0.12
Phenylalanine (%) 0.28 0.85 v0.25–0.45
GABA (%) 0.03 0.09 0.24 0.42
Others (%) 0.21 0.64 0.01 0.02
Total AA (μmol·mg–1) –0.16 –0.48 –0.28 –0.50
Chlorophyll a (mg·100 g–1) 0.09 0.26 0.41 0.72
Chlorophyll b (mg·100 g–1) –0.09 –0.28 0.38 0.68
Lycopene (mg·100 g–1) –0.29 –0.89 –0.13 –0.24
Beta-carotene (mg·100 g1) –0.26 –0.79 –0.15 –0.26
group, RIL10 being a discrepant genotype at MG. RIL15
had the minor differences between ripening stages, while
the most discrepant genotype at RR was the tester Cai-
manta, the cultivated parent.
4. Discussion
As previously reported, a wide range of variability was
found in this experiment for tomato pericarp free amino
acid composition, and total amino acids and pigments
content [6,7,8]. Greatest variability was detected among
mature green and red ripe stages than among genotypes,
indicating that these attributes are primarily ripening-
regulated [16] and constitute one of the biological changes
taking place during such a transition [17]. In fact, as
demonstrated by Hierarchical Clustering, ripening stages
could be identified by each amino acid relative molar
composition, and total free amino acids and pigments
content. For the latter attributes, association is visually
Copyright © 2011 SciRes. AJPS
Biodiversity in a Tomato Germplasm for Free Amino Acid and Pigment Content of Ripening Fruits259
Figure 2. Distribution of metabolites (circles) and tomato genotypes (rhombus, four Recombinant Inbred Lines—RIL—and
the parents Solanum lycopersicum cv. Caimanta and S. pimpinellifolium LA722, the experimental testers) at mature green
(MG) and red ripe (RR) stages in the coordinates of Principal Components 1 and 2 (PC1 and PC2, respectively).
Figure 3. Dendrogram of the four tomato Recombinant Inbred Lines (RIL) and the parents Solanum lycopersicum cv.
Caimanta and S. pimpinellifolium LA722, the experimental testers, at two ripening stages: mature green (MG) and red ripe
Copyright © 2011 SciRes. AJPS
Biodiversity in a Tomato Germplasm for Free Amino Acid and Pigment Content of Ripening Fruits
noticeable, but for amino acids composition, different
physiological functions were proposed. Glutamate was
proposed as a precursor of chlorophyll [18], hence the
increase in its percent composition towards the end of
ripening could be due to the cessation of chlorophyll bio-
synthesis. On the other hand, another role was claimed for
glutamate [17], given that even a mutant defective in
chlorophyll degradation also shown the increase at ripe
stage [3]. As an “umami taste” is provoked by glutamate,
the higher glutamate relative molar content in all tomato
germplasm analyzed ([19,20] in addition to the already
mentioned authors) could have an attracting to mammal-
ian predators function [21]. Interestingly, genotype bio-
diversity was higher in fruits at mature green stage than at
red ripe stage. As wild germplasm was analyzed here, this
finding suggesting an evolutive conservation across dif-
ferent genetic backgrounds of optimum attributes to at-
tract fruit predators so assuring seed dispersion [7]. Cor-
relation between glutamate composition at RR and fruit
shelf life proposed by [6] was not confirmed in this ex-
periment, probably due to differences in gene frequencies
among populations studied in both reports. Spontaneous
mutant homozygote genotypes having marked pleiotropic
effects on tomato many ripening associated traits were
studied in that report, which could explain the significant
correlation found in that study. However, significant as-
sociations of shelf life with pigments (chlorophyll b at
mature green and lycopene at red ripe stages) and other
amino acids (leucine and alanine at red ripe stages) were
detected in this set of recombinant inbred lines and their
parents. This interesting finding should be further ex-
plored, since the correlation coefficients were high and
positive with pigments, and high and negative with amino
acids. Accordingly, the wild parent LA722 was the
genotype contributing the highest values of both pigments
and fruit shelf life, and the lesser values of both amino
acids at the corresponding ripening stages.
Other important modification in amino acid metabolism
during tomato ripening transition was the increase in
asparagine levels in the wild tester LA722, also shown by
RIL4. In previous reports [2-4,6], asparagine decreased
from mature green to red ripe in different tomato geno-
types (normal and mutant for ripening cultivars, the wild
variety S. lycopersicum var. cerasiforme) as well as
glutamine and GABA. These two latter were the most
abundant amino acids together with the previously men-
tioned glutamate. The different performance of asparagine
in LA722 and RIL4 was similar to the currently observed
performance of glutamate in most tomato genotypes. Such
an increase in glutamate was even observed in LA722 and
RIL4, though the ratio glutamate at red ripe: glutamate at
mature green stages was lower in both genotypes than in
the remaining ones, hence alternative metabolic functions
related to the ammonium assimilation/dissimilation cycle
[16] during ripening transition could be taking place in the
wild germplasm. The alternative function and parallel
performance of glutamate/asparagine in these genotypes
would also contribute to identify more consistently the
RILs genetic background, since one of them were more
similar to the wild parent while the others performed as
the cultivated Caimanta, which evidences gene segrega-
tion and recombination during the selection process. Ad-
ditionally, the lack of association among glutamate con-
tent and fruit shelf life reported by [6] could also be ex-
plained by this evident variability in ripening amino acids
Finally, the great contribution of threonine, serine,
valine, glycine, isoleucine, tyrosine, and phenylalanine
relative molar content to variability among ripening stages,
detected by both single correlation and Principal Com-
ponent analyses, deserves further studies to elucidate its
physiological meaning, since there are no antecedents in
their contribution to tomato ripening.
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