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Dwarf Tomato Plants Allow for Managing Agronomic Yield Gains with Fruit Quality and Pest Resistance through Backcrossing

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Increased productivity, nutritional quality, and pest resistance have been primary breeding goals. However, managing such increases in a genotype is challenging. In this context, gene introgression using dwarf plants is an alternative; however, there are no dwarf Santa Cruz tomato varieties for direct use in breeding programs. Therefore, the objective of this study was to improve fruit quality and pest resistance through successive backcrossing of dwarf Santa Cruz tomato populations with agronomic potential. Six and 13 dwarf tomato populations obtained from the first and second backcrossing, respectively, the donor parent, and the commercial cultivar ‘Santa Clara’ as the check, totalling 21 treatments, were evaluated. Univariate analysis and computational intelligence were used to evaluate the best genotypes. All agronomic variables showed significant and progressive increases after the first and second backcrossing. The highlighted BC2 populations were Sci#16.1-2, Sci#25.1,1-2, Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.3,1-2, and Sci#8.3,2-2, with significant increases in mean fruit weight, pulp thickness, fruit length and diameter, and acyl sugar content. The selected BC2 populations can be used as male parents to obtain normal hybrids to achieve increased productivity, nutritional quality, and a broader spectrum of pest resistance owing to the presence of acyl sugars in the leaflets.
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Citation: Gomes, D.A.; Machado,
T.G.; Maciel, G.M.; Siquieroli, A.C.S.;
de Oliveira, C.S.; de Sousa, L.A.; da
Silva, H.P. Dwarf Tomato Plants
Allow for Managing Agronomic
Yield Gains with Fruit Quality and
Pest Resistance through Backcrossing.
Agronomy 2022,12, 3087. https://
doi.org/10.3390/agronomy12123087
Academic Editor: Richard G. F. Visser
Received: 28 October 2022
Accepted: 22 November 2022
Published: 6 December 2022
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Attribution (CC BY) license (https://
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4.0/).
agronomy
Article
Dwarf Tomato Plants Allow for Managing Agronomic Yield
Gains with Fruit Quality and Pest Resistance
through Backcrossing
Danilo Araújo Gomes 1, Tardele Gomes Machado 1, Gabriel Mascarenhas Maciel 2,*,
Ana Carolina Silva Siquieroli 3, Camila Soares de Oliveira 1, Luciana Alves de Sousa 1
and Humberto Pereira da Silva 1
1Postgraduate Program in Agronomy, Institute of Agrarian Sciences, Federal University of Uberlândia,
Uberlândia 38410-337, Brazil
2Institute of Agrarian Sciences, Federal University of Uberlândia, Monte Carmelo 38500-000, Brazil
3Institute of Biotechnology, Federal University of Uberlândia, Monte Carmelo 38500-000, Brazil
*Correspondence: gabrielmaciel@ufu.br
Abstract:
Increased productivity, nutritional quality, and pest resistance have been primary breeding
goals. However, managing such increases in a genotype is challenging. In this context, gene introgres-
sion using dwarf plants is an alternative; however, there are no dwarf Santa Cruz tomato varieties
for direct use in breeding programs. Therefore, the objective of this study was to improve fruit
quality and pest resistance through successive backcrossing of dwarf Santa Cruz tomato populations
with agronomic potential. Six and 13 dwarf tomato populations obtained from the first and second
backcrossing, respectively, the donor parent, and the commercial cultivar ‘Santa Clara’ as the check,
totalling 21 treatments, were evaluated. Univariate analysis and computational intelligence were used
to evaluate the best genotypes. All agronomic variables showed significant and progressive increases
after the first and second backcrossing. The highlighted BC
2
populations were Sci#16.1-2, Sci#25.1,1-2,
Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.3,1-2, and Sci#8.3,2-2, with significant increases in mean
fruit weight, pulp thickness, fruit length and diameter, and acyl sugar content. The selected BC
2
populations can be used as male parents to obtain normal hybrids to achieve increased productivity,
nutritional quality, and a broader spectrum of pest resistance owing to the presence of acyl sugars in
the leaflets.
Keywords:
Solanum lycopersicum L.; computational intelligence; dwarf plants; allelochemicals;
nutritional quality
1. Introduction
Tomatoes (Solanum lycopersicum L.) are of great socioeconomic relevance, being one
of the most cultivated vegetables worldwide. In 2020, Brazil produced approximately
4.0 million tons
of tomatoes, accounting for 2.1% of global production [
1
]. Tomatoes exhibit
great diversity and have therefore been classified in the Brazilian market into the following
groups: Minitomato, Salad, Caqui, Santa Cruz, and Saladete [
2
]. Of these, Santa Cruz
tomatoes stand out for their greater postharvest durability, higher yield potential, and
superior organoleptic characteristics than conventional long-shelf-life tomatoes grown in
the country [3].
Field-grown tomato is considered a great financial risk, as the production cost is
substantial because of the high susceptibility of this crop to biotic and abiotic stresses [
4
].
Therefore, higher yield [
5
] and better adaptation to diverse consumption demands have
been the basis of tomato improvement programs.
Increasing tomato productivity involves the enhancement of quantitative inheri-
tance [
6
,
7
]. However, these enhancements become limited in terms of the type of gene
Agronomy 2022,12, 3087. https://doi.org/10.3390/agronomy12123087 https://www.mdpi.com/journal/agronomy
Agronomy 2022,12, 3087 2 of 11
action for productivity. In Minitomato, the use of a dwarf plant as the male parent has been
demonstrated as a very successful alternative to enhance the productivity and nutritional
quality of hybrids [
8
]. This can be achieved by crossing a dwarf parent with a normal-sized
parent [
9
]. Hybrids from a dwarf genitor possess a short internode, resulting in more
compact plants with more clusters per linear meter of stem and, consequently, greater
productivity and fruit quality [
8
,
10
]. Additionally, dwarf plants are rich in allelochemical
acyl sugars [
11
], which are secondary compounds that provide a broad spectrum of pest
resistance [12].
Despite the potential of this strategy, there are no dwarf Santa Cruz populations
for immediate hybrid production. Therefore, backcrossing is essential. The objective
of this breeding method is to introduce a target trait, called the recurrent genitor, into
highly adapted elite genotypes [
13
]. One of the major challenges in this approach is the
management of yield increase while maintaining fruit quality and pest resistance. In this
context, the use of dwarf plants in breeding can be an important alternative, as reported in
Minitomato [8]; however, there has been limited research on Santa Cruz tomatoes. To this
end, the objective of the present study was to achieve fruit quality and pest resistance by
successively backcrossing dwarf Santa Cruz tomato populations with agronomic potential.
2. Materials and Methods
2.1. Materials and Experimental Design
The experiment was conducted from October 2019 to March 2020 at the Experimental
Vegetable Station of the Federal University of Uberlândia (UFU), Monte Carmelo Campus, MG,
Brazil (18
42
0
43.19
00
S, 47
29
0
55.8
00
W; 873 m a.s.l.). The plants were grown in an arch-type
greenhouse (7
×
21 m
2
; 4 m ceiling height), covered with a 150-micron transparent polyethylene
film with additives against ultraviolet rays and lateral anti-insect white mesh curtains.
The genetic material evaluated included six dwarf tomato populations obtained from
the first backcross (BC
1
), 13 dwarf tomato populations obtained from the second backcross
(BC
2
), the donor parent (DP), and the commercial cultivar ‘Santa Clara’ as the check, to-
talling 21 treatments. BC
1
and BC
2
populations were obtained after hybridization between
a homozygous pre-commercial strain of Santa Cruz fruits (UFU-TOM-Mother-2) and the
dwarf strain UFU MC TOM1 [
9
]. The wild Solanum pennellii accession used in the present
study was included to compare resistance to pest arthropods (acyl sugar content). The
commercial check is characterized by indeterminate growth habits and Santa Cruz-type red
fruits. UFU MC TOM1 used as the DP is a homozygous dwarf strain with indeterminate
growth habits and oblong Minitomato-type fruits [
8
,
9
]. As the expression of the dwarf
phenotype is recessive and monogenic [
9
], backcrossing was performed to transfer the
recessive allele.
Sowing was performed in polystyrene trays (200 cells) on 3 October 2019. The seedlings
were transplanted to 5 L plastic pots 36 days after sowing (DAS). Commercial coconut
fiber substrate was used both in the trays and pots. Conventional treatments were applied
throughout the experiment, as recommended for tomato crops in a protected environ-
ment [2].
The experiment followed a randomized block design with 21 treatments and four repli-
cates. The experimental plots comprised six plants distributed in double rows with a spacing
of 0.3 ×0.3 m. The spacing between the double rows was 0.8 m, totaling 504 plants.
2.2. Sample Collection and Evaluation
Harvests were performed weekly from 3 January to 6 March 2020, totaling 10 harvests.
Fruits from each experimental plot were harvested at the full maturity stage, and the
following agronomic traits were evaluated:
Mean fruit weight (g) (MFW): MFW was calculated as the ratio of the mass in grams
and the number of fruits harvested from a plot.
Total soluble solids (
Brix) (TSS): After harvest, pulp juice from the fruits were ana-
lyzed for TSS content using a digital portable refractometer (Atago PAL-1 3810).
Agronomy 2022,12, 3087 3 of 11
Fruit diameter (cm) (FD): The fruit was cut in half vertically and measured along the
horizontal axis with a ruler.
Fruit length (cm) (FL): The fruit was cut in half vertically and measured along the
vertical axis with a ruler.
Fruit shape (FS): FS was calculated as the ratio of transversal and longitudinal diame-
ters (TD/LD). The commercial check was used as the reference of the Santa Cruz segment
for fruit classification.
Pulp thickness (cm) (PT): The fruit was cut in half vertically, and the length between
its skin and the beginning of the lobule was measured with a ruler.
Number of locules (locules fruit
1
) (NL): The fruit was cut in half horizontally and
the locules were counted.
Internode length (cm) (IL): IL was calculated as [(plant height/number of nodes)] on
two central plants of the plot.
Acyl sugar (AS) content (nmols
·
cm
2
of leaflet): At 75 days after sowing, AS content
was measured using a sample comprising eight leaf disks (equivalent to 4.2 cm
2
) from each
plant in the plot, in triplicate. The disks were collected from leaflets in the upper third of
the plants and placed in test tubes. Extraction and quantification followed a previously
described protocol with minor modifications [14].
Regarding nutritional characteristics,
β
-carotene (CC) and lycopene (LC) were ex-
tracted and quantified in triplicate according to previously described procedures [
15
17
].
Briefly, fruit pulp was ground and 1 g was subsequently conditioned in a glass flask con-
taining 3 mL of 100% acetone (Danâmida Ltd.a, Indaiatuba, SP, Brazil). The samples were
protected from light and maintained at 8
C for 48 h. The supernatant was then evaluated
spectrophotometrically (Tecnal Ltd., Piracicaba, SP, Brazil). The absorbance of CC and LC
was recorded at 450 and 470 nm, respectively.
2.3. Statistical Analyses
Statistical assumptions were verified by analyses for normality (Kolmogorov–Smirnov
test), homogeneity (O’Neill and Mathews test), and additivity (Tukey’s test for nonadditiv-
ity). Analysis of variance was performed using the F-test (
α
= 0.05), and mean values were
compared using the Scott–Knott test (
α
= 0.05). Computational intelligence was applied to
analyze genetic similarity using Kohonen self-organizing maps (SOMs).
Typically, SOM learning is achieved in three stages. Initially, synaptic weights are
assigned to different neurons, followed by a competition process. The set of genetic
values of each genotype is allocated to the neuron that best represents it (winning neuron).
This allocation begins the comparison phase, with the winning neuron determining the
approximation of the other neurons from similarity. Finally, the neurons establish the
neighboring neurons and move on to the adaptation stage, characterized by adjustment of
the weight of each variable.
Network training included 5000 epochs per iteration. The adopted model was vali-
dated using different configurations for the number of neurons. The combinations were
tested with varying numbers of rows (2–5) and columns (2–5). Thus, the combination that
best represented the genetic similarity of the analyzed genotypes was the one with four
rows and four columns (16 organizational neurons) with a radius pattern equal to one,
hexagonal neighborhood topology, feedforward network architecture with one input layer
(medium) and one output layer, and Euclidean distance activation function. All analyses
were performed using GENES integrated with R and MATLAB [18].
3. Results
Significant increases in fruit traits were observed in the backcross generations indi-
cating the effectiveness of the backcrossing method in obtaining dwarf tomato genotypes
with fruits belonging to the Santa Cruz segment (Figure 1).
Agronomy 2022,12, 3087 4 of 11
Agronomy 2022, 12, x FOR PEER REVIEW 4 of 11
layer (medium) and one output layer, and Euclidean distance activation function. All
analyses were performed using GENES integrated with R and MATLAB [18].
3. Results
Significant increases in fruit traits were observed in the backcross generations indi-
cating the effectiveness of the backcrossing method in obtaining dwarf tomato genotypes
with fruits belonging to the Santa Cruz segment (Figure 1).
Figure 1. Phenotypic comparison between donor parent (DP) and backcross (BC1 and BC2) popula-
tions. 1, donor parent; 2, Sci#6.1,1-2; 3, Sci#6.1,2-2; 4, Sci#6.1,3-2; 5, Sci#16.2-2; 6, Sci#16.1-2; 7,
Sci#25.1,1-2; 8, Sci#25.1,2-2; 9, Sci#3.1,1-2; 10, Sci#3.1,2-2; 11, Sci#8.2-2; 12, Sci#20.4-2; 13, Sci#8.3,1-2;
14, Sci#8.3,2-2; 15, Sci#6.1.2,5; 16, Sci#16.2.1,3; 17, Sci#3.1.1; 18, Sci#8.2.1; 19, Sci#20.4.1; 20, Sci#8.3,1.2.
3.1. Agronomic Performance of Different Backcross Generations
Both BC2 and BC1 populations differed from the DP population in terms of all agro-
nomic traits evaluated (Table 1) and presented a marked increase in all traits after the
successive backcrossing cycles.
Table 1. Morphological and agronomic characteristics and pest resistance (acyl sugar content) eval-
uated in backcross populations BC2 and BC1 of dwarf tomato, donor parent, check Santa Clara, and
wild Solanum pennellii genotypes.
Genotype Generation MFW PT FL FD FS NL IL AS
Donor parent - 3.61 c 0.20 d 2.95 b 1.61 c 1.83 d 2.00 a 1.26 a 36.28 b
Santa Clara - 26.59 a 0.55 a 3.84 b 3.62 a 1.05 a 2.05 a 7.27 b 25.25 b
Sci#6.1,1-2 BC2 20.32 b 0.47 b 3.77 b 3.26 b 1.15 a 2.75 c 1.99 a 36.63 b
Sci#6.1,2-2 BC2 25.73 a 0.49 b 3.90 b 3.51 a 1.10 a 2.91 c 1.70 a 37.83 b
Sci#6.1,3-2 BC2 20.36 b 0.48 b 3.98 b 3.09 b 1.29 b 2.44 b 2.33 a 47.81 a
Sci#16.2-2 BC2 17.41 b 0.40 c 3.71 b 2.87 b 1.29 b 2.97 c 1.84 a 41.80 a
Sci#16.1-2 BC2 24.11 a 0.50 a 4.16 a 3.37 a 1.23 a 2.86 c 1.95 a 36.55 b
Sci#25.1,1-2 BC2 30.81 a 0.54 a 4.67 a 3.45 a 1.35 b 3.00 c 1.70 a 35.30 b
Sci#25.1,2-2 BC2 28.82 a 0.52 a 4.64 a 3.48 a 1.33 b 2.66 c 1.54 a 37.35 b
Figure 1.
Phenotypic comparison between donor parent (DP) and backcross (BC
1
and BC
2
) pop-
ulations. 1, donor parent; 2, Sci#6.1,1-2; 3, Sci#6.1,2-2; 4, Sci#6.1,3-2; 5, Sci#16.2-2; 6, Sci#16.1-2; 7,
Sci#25.1,1-2; 8, Sci#25.1,2-2; 9, Sci#3.1,1-2; 10, Sci#3.1,2-2; 11, Sci#8.2-2; 12, Sci#20.4-2; 13, Sci#8.3,1-2;
14, Sci#8.3,2-2; 15, Sci#6.1.2,5; 16, Sci#16.2.1,3; 17, Sci#3.1.1; 18, Sci#8.2.1; 19, Sci#20.4.1; 20, Sci#8.3,1.2.
3.1. Agronomic Performance of Different Backcross Generations
Both BC
2
and BC
1
populations differed from the DP population in terms of all agro-
nomic traits evaluated (Table 1) and presented a marked increase in all traits after the
successive backcrossing cycles.
Dwarf populations of both backcross generations (BC
1
and BC
2
) were superior to
the DP population in terms of MFW, PT, and FD. Regarding MFW, the highlighted pop-
ulations included Sci#6.1,2-2, Sci#16.1-2, Sci#25.1,1-2, Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2,
Sci#8.2-2, Sci#20.4-2, Sci#8.3,1-2, and Sci#8.3,2-2 from BC
2
and population Sci#8.2.1 from
BC
1
, with mean weight exceeding 25 g. Regarding PT—an important characteristic for
fruit quality—the highlighted populations included Sci#16.1-2, Sci#25.1,1-2, Sci#25.1,2-2,
Sci#3.1,1-2, Sci#3.1,2-2, Sci#20.4-2, Sci#8.3,1-2, and Sci#8.3,2-2 from BC
2
and Sci#6.1.2,5 and
Sci#8.2.1 from BC
1
, with mean thickness between 0.50 (Sci#16.1-2) and 0.56 (Sci#8.3,2-2) cm.
Regarding FD, the highlighted populations included Sci#6.1,2-2, Sci#16.1-2, Sci#25.1,1-
2, Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.3,1-2, and Sci#8.3,2-2 from BC
2
and Sci#8.2.1
from BC
1
. Regarding FL, which together with FD represents fruit size, only BC
2
populations
Sci#16.1-2, Sci#25.1,1-2, Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.2-2, Sci#20.4-2, Sci#8.3,1-2,
and Sci#8.3,2-2 registered significant increases. Fruits belonging to the Santa Cruz segment
are characterized by an FL/FD value close to 1 [
19
]. Accordingly, all BC
1
populations
were classified as belonging to the Santa Cruz segment. Moreover, the BC
2
populations
(Sci#6.1,1-2, Sci#6.1,2-2, Sci#16.1-2, Sci#20.4-2, Sci#8.3,1-2, and Sci#8.3,2-2) produced fruits
characteristic to the Santa Cruz segment, whereas the remaining populations produced
intermediate, slightly oblong fruits. All populations studied showed reduced NL (
3.0),
characterizing firmer fruits.
Agronomy 2022,12, 3087 5 of 11
Table 1.
Morphological and agronomic characteristics and pest resistance (acyl sugar content)
evaluated in backcross populations BC
2
and BC
1
of dwarf tomato, donor parent, check’ Santa Clara’,
and wild Solanum pennellii genotypes.
Genotype Generation MFW PT FL FD FS NL IL AS
Donor parent - 3.61 c0.20 d2.95 b1.61 c1.83 d2.00 a1.26 a36.28 b
Santa Clara - 26.59 a0.55 a3.84 b3.62 a1.05 a2.05 a7.27 b25.25 b
Sci#6.1,1-2 BC220.32 b0.47 b3.77 b3.26 b1.15 a2.75 c1.99 a36.63 b
Sci#6.1,2-2 BC225.73 a0.49 b3.90 b3.51 a1.10 a2.91 c1.70 a37.83 b
Sci#6.1,3-2 BC220.36 b0.48 b3.98 b3.09 b1.29 b2.44 b2.33 a47.81 a
Sci#16.2-2 BC217.41 b0.40 c3.71 b2.87 b1.29 b2.97 c1.84 a41.80 a
Sci#16.1-2 BC224.11 a0.50 a4.16 a3.37 a1.23 a2.86 c1.95 a36.55 b
Sci#25.1,1-2 BC230.81 a0.54 a4.67 a3.45 a1.35 b3.00 c1.70 a35.30 b
Sci#25.1,2-2 BC228.82 a0.52 a4.64 a3.48 a1.33 b2.66 c1.54 a37.35 b
Sci#3.1,1-2 BC226.12 a0.51 a4.62 a3.35 a1.39 b2.67 c2.03 a32.19 b
Sci#3.1,2-2 BC231.59 a0.54 a4.81 a3.81 a1.28 b2.80 c1.60 a41.10 a
Sci#8.2-2 BC225.01 a0.47 b4.63 a2.92 b1.58 c2.60 c1.97 a43.16 a
Sci#20.4-2 BC232.72 a0.54 a4.76 a3.31 b1.44 b2.77 c1.65 a47.45 a
Sci#8.3,1-2 BC229.61 a0.50 a4.08 a3.71 a1.10 a3.00 c1.76 a40.40 a
Sci#8.3,2-2 BC232.56 a0.56 a4.69 a3.76 a1.24 a2.73 c1.94 a41.86 a
Sci#6.1.2,5 BC119.77 b0.52 a3.36 b3.28 b1.02 a2.41 b1.71 a39.53 b
Sci#16.2.1,3 BC117.93 b0.47 b3.60 b3.05 b1.18 a2.22 a1.57 a39.26 b
Sci#3.1.1 BC114.93 b0.38 c3.27 b3.05 b1.08 a2.92 c1.83 a42.81 a
Sci#8.2.1 BC125.13 a0.52 a3.46 b3.62 a0.95 a2.75 c1.74 a39.91 b
Sci#20.4.1 BC118.64 b0.47 b3.50 b3.12 b1.12 a2.33 b1.82 a31.91 b
Sci#8.3,1.2 BC117.98 b0.45 b3.53 b3.02 b1.18 a2.49 b2.02 a44.21 a
Solanum pennellii - - - - - - - - 50.57 a
KS 1- 0.043 0.646 0.011 0.040 0.010 0.329 0.037 0.839
OM 2- 0.014 0.658 0.056 0.014 0.184 0.021 0.782 0.414
F (Tukey) 3- 0.9380 0.443 0.827 0.528 0.878 0.986 0.982 0.123
MFW, mean fruit weight (g); PT, pulp thickness (cm); FL, fruit length (cm); FD, fruit diameter (cm); FS, fruit shape;
NL, number of locules (locules fruit
1
); IL, internode length (cm); AS, acyl sugar content (nmols
·
cm
2
of leaflet).
Means followed by different letters in the column are significantly different according to the Scott–Knott test at a
significance level of 0.01.
1–3
: Kolmogorov–Smirnov, O’Neill and Mathews, and Tukey’s tests, respectively; Santa
Clara, check/commercial cultivar with low acyl sugar content; Solanum pennellii, check with high acyl sugar.
Improvements aimed at reduced IL in tomato varieties, and consequently, superior
plant architecture are an emerging trend in the market. Thus, the present study used
the cultivar ‘Santa Clara’, which bears fruits belonging to the Santa Cruz segment, as a
reference for inferences on the architecture of plants grown in the field. Specifically, IL was
7.27 cm in the cultivar ‘Santa Clara’, compared with 1.54 and 2.33 cm in Sci#25.1,2-2 and
Sci#6.1,3-2, respectively.
The wild S. pennellii genotype showed the highest AS content (50.57 nmols
·
cm
2
).
Notably, the BC
2
populations (Sci#6.1,3-2, Sci#16.2-2, Sci#3.1,2-2, Sci#8.2-2, Sci#20.4-2,
Sci#8.3,1-2, and Sci#8.3,2-2) and the BC
1
populations (Sci#3.1.1 and Sci#8.3,1.2) did not
differ from the wild genotype in terms of AS content.
3.2. Relative Superiority of BC1and BC2Generations
Overall, compared with the DP, both backcross generations (BC
1
and BC
2
) showed
significantly increased MFW, PT, FL, and FD (Table 1, Figure 2). In the BC
1
generation
,
MFW, PT, and FD were higher than those in DP, with a relative superiority of 428.07%,
134.17%, and 98.13%, respectively (Figure 2). For the same characters, BC
2
generations
showed a relative superiority of 635.49%, 150.76%, and 109.70%, respectively. Moreover,
for FL, compared with DP, the BC2generations achieved a relative superiority of 47.11%.
Agronomy 2022,12, 3087 6 of 11
Agronomy 2022, 12, x FOR PEER REVIEW 6 of 11
The wild S. pennellii genotype showed the highest AS content (50.57 nmols·cm−2). No-
tably, the BC2 populations (Sci#6.1,3-2, Sci#16.2-2, Sci#3.1,2-2, Sci#8.2-2, Sci#20.4-2,
Sci#8.3,1-2, and Sci#8.3,2-2) and the BC1 populations (Sci#3.1.1 and Sci#8.3,1.2) did not dif-
fer from the wild genotype in terms of AS content.
3.2. Relative Superiority of BC1 and BC2 Generations
Overall, compared with the DP, both backcross generations (BC1 and BC2) showed
significantly increased MFW, PT, FL, and FD (Table 1, Figure 2). In the BC1 generation,
MFW, PT, and FD were higher than those in DP, with a relative superiority of 428.07%,
134.17%, and 98.13%, respectively (Figure 2). For the same characters, BC2 generations
showed a relative superiority of 635.49%, 150.76%, and 109.70%, respectively. Moreover,
for FL, compared with DP, the BC2 generations achieved a relative superiority of 47.11%.
Figure 2. Relative superiority of backcross populations BC1 and BC2 for MFW, PT, FL, and FD. Val-
ues are presented as mean ± standard deviation for BC2, BC1, and DP (donor parent).
3.3. Fruit Quality Traits
Both BC1 and BC2 populations showed significant differences (p < 0.05) in terms of all
fruit quality characteristics, as evaluated using the F-test (Table 2).
Table 2. Fruit quality characteristics evaluated in backcross populations BC2 and BC1 of dwarf to-
mato, donor parent, and check Santa Clara’.
Genotype 1 Generation TSS CC LC
Donor parent Donor parent 6.93 a 1.74 a 2.94 c
Santa Clara Check 5.37 b 0.87 b 5.07 a
Sci#6.1,1-2 BC2 4.90 c 1.34 a 2.89 c
Sci#6.1,2-2 BC2 4.80 c 0.88 b 3.08 c
Sci#6.1,3-2 BC2 4.74 c 1.37 a 2.72 c
Figure 2.
Relative superiority of backcross populations BC
1
and BC
2
for MFW, PT, FL, and FD. Values
are presented as mean ±standard deviation for BC2, BC1, and DP (donor parent).
3.3. Fruit Quality Traits
Both BC
1
and BC
2
populations showed significant differences (p< 0.05) in terms of all
fruit quality characteristics, as evaluated using the F-test (Table 2).
All backcross populations and Santa Clara showed lower TSS than the DP population
(6.93
Brix). The dwarf populations highlighted were Sci#16.2-2 (5.74
Brix), Sci#25.1,2-2
(5.51 Brix), and Sci#8.2-2 (5.72 Brix) from BC2and Sci#3.1.1 (5.46 Brix) from BC1.
Regarding total CC, the highest content was recorded for the DP population; BC
2
populations Sci#6.1,1-2, Sci#6.1,3-2, Sci#16.1-2, Sci#25.1,2-2, Sci#8.2-2, and Sci#8.3,1-2; and
BC
1
populations Sci#6.1.2,5, Sci#3.1.1, and Sci#8.3,1.2. Regarding LC, the highest content
was recorded for the cultivar Santa Clara (5.07 mg
·
100 mg
1
). The dwarf populations
highlighted were Sci#16.2-2, Sci#25.1,1-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.2-2, and Sci#8.3,2-2
from BC2and Sci#16.2.1,3, Sci#3.1.1, Sci#8.2.1, and Sci#8.3,1.2 from BC1.
Agronomy 2022,12, 3087 7 of 11
Table 2.
Fruit quality characteristics evaluated in backcross populations BC
2
and BC
1
of dwarf
tomato, donor parent, and check ‘Santa Clara’.
Genotype 1Generation TSS CC LC
Donor parent Donor parent 6.93 a1.74 a2.94 c
Santa Clara Check 5.37 b0.87 b5.07 a
Sci#6.1,1-2 BC24.90 c1.34 a2.89 c
Sci#6.1,2-2 BC24.80 c0.88 b3.08 c
Sci#6.1,3-2 BC24.74 c1.37 a2.72 c
Sci#16.2-2 BC25.74 b0.48 b4.04 b
Sci#16.1-2 BC24.37 c1.40 a2.72 c
Sci#25.1,1-2 BC24.77 c1.10 b2.42 d
Sci#25.1,2-2 BC25.51 b1.27 a2.55 c
Sci#3.1,1-2 BC25.03 c0.87 b2.40 d
Sci#3.1,2-2 BC25.02 c0.91 b2.00 d
Sci#8.2-2 BC25.72 b1.31 a2.42 d
Sci#20.4-2 BC24.99 c0.96 b3.73 b
Sci#8.3,1-2 BC24.58 c1.20 a2.67 c
Sci#8.3,2-2 BC24.42 c1.38 a3.36 b
Sci#6.1.2,5 BC14.68 c1.31 a2.57 c
Sci#16.2.1,3 BC14.15 c1.11 b1.81 d
Sci#3.1.1 BC15.46 b1.41 a2.15 d
Sci#8.2.1 BC14.88 c1.11 b2.15 d
Sci#20.4.1 BC15.03 c1.06 b2.75 c
Sci#8.3,1.2 BC15.03 c1.24 a2.05 d
KS 2- 0.079 0.025 0.046
OM 3- 0.101 0.353 0.480
F (Tukey) 4- 0.487 0.460 0.323
TSS, total soluble solids (
Brix); CC, carotenoid content (mg
·
100 mg
1
); LC, lycopene content (mg
·
100 mg
1
).
1
Means followed by different letters in the column are significantly different from each other according to the
Scott–Knott test at a significance level of 0.05.
2–4
: Kolmogorov–Smirnov, O’Neill and Mathews, and Tukey’s tests,
respectively; Santa Clara, check/commercial cultivar.
3.4. Genetic Dissimilarity between the Tested Genotypes
In a Kohonen SOM, most similar genotypes are grouped within the same neuron. In
contrast, genotypes clustered in different neurons show genetic dissimilarity. Neurons
consist of individuals that have some similarity with the neighboring class, and the most
divergent and intermediate classes constitute the extreme and central regions of the map,
respectively. An output layer comprising 4 rows
×
4 columns was obtained from the
Kohonen SOM. The genotypes evaluated in this study were grouped into 11 distinct
neurons (Figure 3). Each hexagon represents a neuron and the amount of area filled within
a hexagon indicates the concentration of grouped genotypes in that neuron. Thus, the
greater the number of genotypes grouped in a neuron, the greater the filled area.
Neurons I, II, II, and XI included three populations each; neurons V and VIII included
two populations each; and neurons VII, X, and XXI included one population each. Neurons
IX and XIII included the donor parent and check ‘Santa Clara’, respectively. No genotype
was allocated to neurons IV, VI, XIV, XV, and XVI (Figure 3).
Agronomy 2022,12, 3087 8 of 11
Agronomy 2022, 12, x FOR PEER REVIEW 8 of 11
Figure 3. Topological Kohonen self-organizing network and genotype classification in the respec-
tive network neurons. DP, donor parent; Sta. Clara, check Santa Clara.
Neurons I, II, II, and XI included three populations each; neurons V and VIII included
two populations each; and neurons VII, X, and XXI included one population each. Neu-
rons IX and XIII included the donor parent and check Santa Clara, respectively. No gen-
otype was allocated to neurons IV, VI, XIV, XV, and XVI (Figure 3).
4. Discussion
4.1. Feasibility of the Method
The presence of reduced internodes resulting in compact tomato plants is a trend for
new hybrids [8,20]. A dwarf parent was used in the combination for obtaining Minitomato
hybrids, which resulted in hybrids with reduced internodes, and consequently, an in-
creased number of clusters per linear meter of stem and enhanced productivity. The mor-
phology of the leaves and leaflets (Figure 1) was very different when compared to the
findings of recent research carried out with dwarf plants [21].
The marked increases observed in BC2 populations indicate the effectiveness of back-
crossing cycles in the development of dwarf tomato genotypes with Santa Cruz-type
fruits. Such increases in favorable alleles or complementary gene blocks in the develop-
ment of segregating populations allow for the selection of superior genotypes based on
improved traits of interest [22].
At this stage of the breeding program, populations derived from the second back-
cross generation (BC2) should present 87.5% of the genome of the recurrent parent on av-
erage [22]. Melo et al. [23] and García-Fortea et al. [24] have reported satisfactory back-
crossing results in passion fruit, corroborating our findings.
4.2. Effect of Backcrossing on Agronomic Traits, Resistance, and Nutritional Quality of Tomato
In addition to characteristics directly related to tomato fruits and plant architecture,
breeding programs have aimed to introgress alleles linked to insect resistance. With this
objective, several wild tomato species, such as S. pennellii, are used as a source of pathogen
resistance. The major resistance trait of these species has been linked to the presence of
allelochemicals such as ASs [25,26].
Acyl sugars are allelochemicals producing deleterious effects on the life cycle of pest
arthropods, reducing their oviposition and altering their feeding preference [2527]. Dias
et al. [28] highlighted that F2 genotypes selected for high AS content from the interspecific
crosses between S. pennellii and a commercial cultivar were efficient in reducing the
Figure 3.
Topological Kohonen self-organizing network and genotype classification in the respective
network neurons. DP, donor parent; Sta. Clara, check ‘Santa Clara’.
4. Discussion
4.1. Feasibility of the Method
The presence of reduced internodes resulting in compact tomato plants is a trend for
new hybrids [
8
,
20
]. A dwarf parent was used in the combination for obtaining Minitomato
hybrids, which resulted in hybrids with reduced internodes, and consequently, an increased
number of clusters per linear meter of stem and enhanced productivity. The morphology
of the leaves and leaflets (Figure 1) was very different when compared to the findings of
recent research carried out with dwarf plants [21].
The marked increases observed in BC
2
populations indicate the effectiveness of back-
crossing cycles in the development of dwarf tomato genotypes with Santa Cruz-type fruits.
Such increases in favorable alleles or complementary gene blocks in the development of
segregating populations allow for the selection of superior genotypes based on improved
traits of interest [22].
At this stage of the breeding program, populations derived from the second backcross
generation (BC
2
) should present 87.5% of the genome of the recurrent parent on average [
22
].
Melo et al. [
23
] and García-Fortea et al. [
24
] have reported satisfactory backcrossing results
in passion fruit, corroborating our findings.
4.2. Effect of Backcrossing on Agronomic Traits, Resistance, and Nutritional Quality of Tomato
In addition to characteristics directly related to tomato fruits and plant architecture,
breeding programs have aimed to introgress alleles linked to insect resistance. With this
objective, several wild tomato species, such as S. pennellii, are used as a source of pathogen
resistance. The major resistance trait of these species has been linked to the presence of
allelochemicals such as ASs [25,26].
Acyl sugars are allelochemicals producing deleterious effects on the life cycle of
pest arthropods, reducing their oviposition and altering their feeding preference [
25
27
].
Dias et al. [28]
highlighted that F
2
genotypes selected for high AS content from the inter-
specific crosses between S. pennellii and a commercial cultivar were efficient in reducing
the damage caused by tomato leaf miners, thereby being promising for the continuation
of backcrossing cycles. Thus, dwarf populations with high AS levels used in the present
study can be considered important sources of resistance to arthropod pests.
Current tomato breeding programs seek to develop cultivars that are not only produc-
tive but also tasty and rich in nutrients, vitamins, and antioxidants [
29
]. In this perspective,
tomato TSS content is an important trait that is directly linked to the quality of fruit
Agronomy 2022,12, 3087 9 of 11
taste [
30
,
31
]. In the present study, DP fruits presented the highest TSS level. The lower
TSS levels in BC
1
and BC
2
fruits than in DP fruits can be explained by the increased fruit
size in backcross generations, which diluted the sugars and soluble acids and decreased
their concentrations [
32
]. According to Schwarz et al. [
31
], a TSS content of 3.0
Brix is ideal
for tomatoes intended for fresh consumption. Accordingly, all dwarf populations in the
present study exhibited promising genotypes for the development of Santa Cruz strains
with high TSS content and short IL.
4.3. Genetic Similarity Using Kohonen Self-Organizing Maps
Furthermore, to analyze the genetic dissimilarity between genotypes, we used Koho-
nen SOM, which is a computational intelligence strategy demonstrated to be efficient in
identifying similarity patterns among genotypes and distinguishing and classifying them
according to the distance between neurons in the network; as such, the shorter the distance,
the greater is the similarity between genotypes contained in the respective neurons [
33
36
].
In the present study, all BC
1
populations were allocated to neighboring neurons
(neurons I, II, and V), indicating similarity between them. Furthermore, the BC
2
populations
(Sci#6.1,3-2 and Sci#6.1,1-2) were allocated to neurons I and II, respectively, indicating their
similarity to BC
1
populations. Except for Sci#3.1.1 in neuron V, all other populations
allocated to the respective neurons were characterized by small MFW increases. Moreover,
all populations allocated to neurons I, II, and V showed reduced FL (Table 1, Figure 3).
BC
2
populations were distributed in neurons I, II, III, VII, VIII, X, XI, and XI, indicating
moderate similarity between most populations of the respective generation (Figure 3). In
the SOM analysis, all BC
2
and BC
1
populations were allocated to distinct DP neurons,
validating the success of backcrossing cycles in rescuing part of the genetic constitution of
the recurrent parent.
Multivariate techniques, machine learning, and SOMs were used by
Sant’Anna et al. [37]
to study genetic diversity in elite genotypes of rubber trees; they reported consistent results
across these methods. Overall, the authors reported that the methods based on computational
intelligence were highly efficient in detecting similarity among genotypes.
To obtain improved fruit traits, the BC
2
genotypes that stood out were selected for the
third backcrossing cycle, obtaining dwarf tomato lines with Santa Cruz-type fruits.
In Minitomato, selected BC
2
genotypes should be used as the male parent to obtain
normal hybrids with high yields [
8
]. Additionally, selected genotypes can provide hybrids
with a broad spectrum of pest resistance [12] owing to high AS levels.
5. Conclusions
Significant and progressive increases were recorded in all agronomic response vari-
ables after the first and second backcrossing cycles. The BC
2
populations (Sci#16.1-2,
Sci#25.1,1-2, Sci#25.1,2-2, Sci#3.1,1-2, Sci#3.1,2-2, Sci#8.3,1-2, and Sci#8.3,2-2) stood out with
marked improvements in agronomic traits (MFW, PT, FL, and FD), the nutritional quality
of fruits, and AS content of leaflets.
Author Contributions:
Conceptualization, G.M.M.; methodology, D.A.G., T.G.M. and C.S.d.O.; soft-
ware, D.A.G. and C.S.d.O.; validation, D.A.G., T.G.M. and L.A.d.S.; formal analysis, G.M.M. and A.C.S.S.;
investigation, D.A.G. and H.P.d.S.; resources, A.C.S.S.; data curation, G.M.M.;
writing—original
draft
preparation, D.A.G. and T.G.M.; writing—review and editing, G.M.M. and A.C.S.S.; visualization,
A.C.S.S.; supervision, G.M.M.; project administration, G.M.M.; funding acquisition, G.M.M. and A.C.S.S.
All authors have read and agreed to the published version of the manuscript.
Funding:
This research was funded by the Brazilian National Council for Scientific and Technological
Development (CNPq) Grant No 310083/2021-4, Minas Gerais Research Foundation (FAPEMIG),
Coordination for the Improvement of Higher Education Personnel (CAPES), and Federal University
of Uberlândia (UFU).
Data Availability Statement: Not applicable.
Conflicts of Interest: The authors declare no conflict of interest.
Agronomy 2022,12, 3087 10 of 11
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ResearchGate has not been able to resolve any citations for this publication.
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