Tropical Plant Biol.

(2017) 10:18–29
DOI 10.1007/s12042-016-9181-4

The Sweet Passion Fruit (Passiflora alata) Crop: Genetic

and Phenotypic Parameter Estimates and QTL Mapping
for Fruit Traits
Guilherme da Silva Pereira 1 & Larissa Di Cassia Laperuta 1 & Endson Santana Nunes 1 &
Lourdes Chavarría 1 & Maria Marta Pastina 2 & Rodrigo Gazaffi 3 & Isaías Olívio Geraldi 1 &
Antonio Augusto Franco Garcia 1 & Maria Lucia Carneiro Vieira 1

Received: 29 January 2016 / Accepted: 15 August 2016 / Published online: 1 September 2016
# Springer Science+Business Media New York 2016

Abstract Despite their economic importance, some tropical each trait. Principal component analysis on TS, WS and WP
crop species are largely neglected when it comes to showed that the first two principal components (PCs)
conducting genetic studies characterizing target traits for accounted for 93.6 % of the total variability. CIM analyses
breeding. Herein, genetic and phenotypic parameters as well on these two PCs revealed five putative QTLs controlling
quantitative trait loci (QTL) are described for the first time in a variation for these three traits simultaneously. Thus, genetic
full-sib progeny of sweet passion fruit (Passiflora alata). A improvement for sweet passion fruit should be based on cor-
hundred F1 individuals were evaluated in two locations for relations between traits and QTL-related information can be a
seven fruit traits: diameter of fruit (DF, in mm), length of fruit useful tool.
(LF, in mm), weight of fruit (WF, in g), thickness of fruit skin
(TS, in mm), weight of fruit skin (WS, in g), weight of fruit Keywords Composite interval mapping . Genetic
pulp (WP, in g) and soluble solids (SS, in °Brix). Mixed parameters . Index selection . Mixed model . Passiflora .
models fitted complex, unstructured genetic variance- Tropical fruit species
covariance matrices for all traits in phenotypic analysis.
Because of important genetic correlations among skin and
pulp traits, multiplicative index selection to select the most
promising individuals was successfully applied. A previously Abbreviations
reported integrated map supported composite interval map- AFLP Amplified fragment length polymorphism
ping (CIM) analyses. In total, we found 22 QTLs mapped in AIC Akaike information criterion
seven out of nine linkage groups. Heritabilities (from 59.8 % BIC Bayesian information criterion
to 82.7 %) and proportion of phenotypic variance explained CIM Composite interval mapping
by the QTLs (from 42.0 % to 64.3 %) were comparable for DF Diameter of fruit
GEI Genotype-environment interaction
Communicated by: Yann-Rong Lin LF Length of fruit
LG Linkage groups
Electronic supplementary material The online version of this article
LOD Logarithm of the odds
(doi:10.1007/s12042-016-9181-4) contains supplementary material,
which is available to authorized users. MI Multiplicative index
PC Principal component
* Maria Lucia Carneiro Vieira PCA Principal component analysis
mlcvieir@usp.br QTL Quantitative trait loci
REML Restricted maximum likelihood
1
Escola Superior de Agricultura BLuiz de Queiroz^, Departamento de RS Response to selection
Genética, Universidade de São Paulo, Piracicaba 13418-900, Brazil RS% Response to selection in percentage
2
Embrapa Milho e Sorgo, Sete Lagoas 35701-970, Brazil SD Selection differential
3
Centro de Ciências Agrárias, Universidade Federal de São Carlos, SS Total soluble solids
Araras 13565-905, Brazil TS Thickness of fruit skin
Tropical Plant Biol. (2017) 10:18–29
VCOV Variance-covariance
WF Weight of fruit
WP Weight of fruit pulp
WS Weight of fruit skin
Introduction
Almost all of today’s commercial crops reflect the results of
ongoing breeding efforts, most focused on longstanding goals
such as quality, storage potential and yield (reviewed in
Nocker and Gardiner 2014). Although such efforts have been
successful in generating plant cultivars, overall there is a lack
of genetic and breeding information for many tropical fruit
species. This makes it difficult to raise the selection gain to
higher levels. Genetic diversity at intra- and inter-population
levels is quite unexploited, and most planting materials are
selected based only on visual assessments of phenotype per-
formance or seed-raised cultivars produced by uncontrolled
pollination. Commercial production is based on a rather lim-
ited number of cultivars that are poorly characterized for ge-
netic traits. Additionally, the variable gene pools in germ-
plasm collections cannot be fully utilized without the system-
atic evaluation of existing resources (reviewed in Ray 2002).
Consequently, many of these crops are still grown only on a
small commercial scale.
In Brazil, for instance, passion fruit cultivation is a relative-
ly recent activity and has earned the country an outstanding
position as the world’s main producer. Long-term breeding
programs have just begun and the most recent Brazilian sur-
vey on agricultural production showed that 58,089 ha were
planted, yielding 838,244 tons of fruits (IBGE 2013).
Commercial crops are based almost on a single native species,
the yellow passion fruit (Passiflora edulis), occupying over
90 % of all plantations. Its edible and aromatic fruits are used
in juice concentrate blends that are consumed worldwide. The
crop provides a good alternative source of employment and
income to small farmers.
A second species, the sweet passion fruit (P. alata), is na-
tive to the Brazilian plateau and the eastern Amazon region,
but only low-intensity farming is found in the South and
Southeast of Brazil (reviewed in Cerqueira-Silva et al.
2014). It is appreciated for its typical aroma and flavor char-
acteristics and can therefore reach up to triple the yellow pas-
sion fruit price at local fresh fruit markets. Moreover, pharma-
cologists have found that the vines of Passiflora species,
mainly P. alata, contain bioactive compounds (see Ingale
and Hivrale 2010), which are employed widely as a traditional
medicine because of its sedative activity (Dhawan et al. 2004;
Klein et al. 2014).
Both the yellow and sweet passion fruits are diploid
(2n = 18) (Cuco et al. 2005; Souza et al. 2008) and outcrossing
species (Bruckner et al. 1993; Ferreira et al. 2010) with
19
perfect, insect-pollinated flowers (Fig. 1a). Self-
incompatibility is an important component of their reproduc-
tive system and it is genetically controlled by an S locus that is
actually a cluster of linked loci. A gametophytic mechanism is
also involved (Suassuna et al. 2003; Madureira et al. 2014).
Interestingly, natural population phenotypes are highly vari-
able. Exploiting the favorable attributes of a wild species,
P. setacea, the Brazilian Agricultural Research Corporation
released a novel passion fruit cultivar in 2013 (http://www.
cpac.embrapa.br/lancamentoperola/). Nevertheless, there is
still a lack of uniformity on some plantations due to the
absence of improved varieties selected for adaptation to
location-specific conditions and resistance to major diseases.
Genetic studies using appropriate field experimental de-
signs have been conducted for both yellow and purple forms
of P. edulis (Moraes et al. 2005; Gonçalves et al. 2007; Silva
et al. 2009; Silva et al. 2016). In fact, studying the genetic
architecture of quantitative traits may be useful in plant breed-
ing since they provide a better understanding of any genetic
correlation that might be observed between traits, genotype-
environment interactions (GEI), etc. Breeding programs could
take advantage of properly modeled phenotypic data by using
a mixed model approach and restricted maximum likelihood
(REML) estimation. Moreover, understanding the contribu-
tion of genetic and environmental factors to the phenotype
and consequently obtaining heritability estimates are of great
importance. All this information combined should help plant
breeders to take some important decisions. For instance, by
modeling the genetic variance-covariance (VCOV) structure
for the genotype effect grouped within different environments,
mixed models should provide a straightforward representation
of GEI (Malosetti et al. 2013). Provided that heterogeneous
variances matrices are selected over the homoscedastic-
ity, distinct genotype means are expected depending on
the environment.
Integrated genetic maps are currently available for P. edulis
(Oliveira et al. 2008a) and P. alata (Pereira et al. 2013). They
are based on the method implemented in OneMap software
(Margarido et al. 2007; Mollinari et al. 2009) that takes a
mixture of distinct segregation patterns and estimates a single
map for F1 populations (Wu et al. 2002a; Wu et al. 2002b)
rather than the two maps (one for each parent) generated by
the double pseudo-testcross approach (Grattapaglia and
Sederoff 1994). In particular, the sweet passion fruit map
reported by Pereira et al. (2013) compiled both dominant
and codominant loci, including either anonymous or
putative functional markers. In addition, Gazaffi et al.
(2014) recently published a model for quantitative trait
loci (QTL) mapping for outcrossing species based on
composite interval mapping (CIM) (Zeng 1994) and inte-
grated maps. By combining the benefits of the existing
map and the QTL mapping model, further studies in sweet
passion fruit became feasible.
20
Fig. 1 The sweet passion fruit crop (Passiflora alata): Flowers visited by
carpenter bees (Xylocopa spp.), the main insect pollinators (a); Growing
vines (left) and plants setting fruits (right) in the experimental area (b);
Variation in the diameter, length and color of the fruits (c); Variation in the
thickness of fruit skin and content of the sweet pulp (d)
Therefore, the aims of the present study were (i) to estimate
genetic and phenotypic parameters of traits related to fruit
quality, such as heritability, genetic correlations and expected
response to selection based on appropriate mixed modeling,
and (ii) to characterize the genetic architecture of QTLs un-
derlying these traits using the CIM model for full-sib
progenies.
Results
Analysis of Phenotypic Data Using a Mixed Model
Statistical Approach
Phenotypic data from 100 full-sibs were obtained from the
first harvest year at two locations (A and B) in Southeast
Brazil using a 10×10 square lattice design with three replica-
tions. The progeny resulted from a cross between two P. alata
accessions, 2(12) and SV3, the respective female and male
parents. The averages of 10 fruits per plot were obtained to
examine seven fruit traits: diameter of fruit (DF, in mm),
length of fruit (LF, in mm), weight of fruit (WF, in g), thick-
ness of fruit skin (TS, in mm), weight of fruit skin (WS, in g),
weight of fruit pulp (WP, in g), and soluble solids (SS, in
°Brix). We analyzed the data based on a mixed model ap-
proach, including significance tests for fixed effects and iden-
tification of appropriate VCOV structures of random effects.
Tropical Plant Biol. (2017) 10:18–29
The fixed effect of location was significant (p < 0.001) for
all seven traits according to the Wald statistics. Unstructured
models for genetic VCOV matrices GM were selected for all
traits, since they have shown the lowest values for Akaike
(AIC) (Akaike 1974) and Bayesian (BIC) (Schwarz 1978)
information criteria (Supplemental Table 1). Therefore, all
models selected here were based on structures allowing
heteroscedasticity for the genetic VCOV matrices. For the
DF and LF traits, the largest genetic variances were found at
location A, whereas for the other traits the largest variances
were found at location B (Table 1). Regarding the genetic
VCOV structures, we can state that GEI occurs since genetic
variation is different at each location. These structures also
show that covariances (and thus correlations) were significant
between environments, evidenced by repeated measurements
for genotypes across locations. For all traits, genetic correla-
tions between locations were very high, i.e., rA , B ≥ 0.70
(Table 1), indicating that the norm of reaction for each geno-
type was the same or very similar in both environments.
Therefore, GEI should be detected as a complex pattern, most-
ly in terms of changing mean performance but with just a few
changes in genotype ranking across locations. For the resid-
ual VCOV structures, only identity matrices were select-
ed for locations and replicates, except for TS, which
showed the smallest AIC and BIC values for a diagonal
matrix across locations.
Genetic and Phenotypic Parameter Estimates
and Expected Responses to Selection
Estimates based on mixed models of genetic and phenotypic
variances, heritabilities and coefficients of variation are shown
in Table 2. Results showed that the precision of the field ex-
periments was good for hypothesis tests, since the respective
lowest and highest coefficient of variation (CV) values were
3.42 % (SS) and 21.34 % (WP). These values are relatively
low considering that the experiment was performed using a
semi perennial species and large experimental areas (> 4.5 ha)
(Fig. 1b). As expected for a full-sib progeny, heritabilities on a
genotype-mean basis (H 2means ) were relatively high for all
traits and ranged from 0.598 (WP) to 0.827 (SS). Since clones
are selected so that all types of genetic variance can be
exploited, these heritability values are of special importance
because they can be used to predict responses to selection
(RS), as shown below.
The distribution of the adjusted phenotypic means regard-
ing each trait as well as the pairwise genetic correlation and
scatter plots are shown in Fig. 2. Genotypic correlation coef-
ficients were highly significant (p < 0.01) among all the fol-
lowing traits: DF, LF, WF, TS, WS and WP. The SS trait
showed low negative (or null) genotypic correlation for all
traits. In sweet passion fruit breeding, it is important to have
Tropical Plant Biol. (2017) 10:18–29 21

Table 1 Genetic correlations between traits related to the size and shape of
variances (diagonal) and Trait a Location
the fruits, e.g., between DF and LF.
covariances (below
diagonal) from the A B For selecting 30 % full-sibs with the desired fruit traits, we
selected matrices for the created four scenarios. The first three scenarios were based on
genetic effect at locations DF A 0.8691 0.8990 the three traits separately (single-trait): selecting against TS,
A and B for seven fruit B 0.7379 0.7751 selecting against WS and selecting for WP. In a fourth scenario,
traits in a sweet passion
LF A 1.0070 0.9845 selection was based on a multiplicative index (MI) that com-
fruit full-sib progeny.
Genetic correlations B 0.9810 0.9860 bines all three variables (multi-trait). The expected RS varied
between environments WF A 1.2770 0.8024 according to the selection strategy (Table 3), having large
are in bold type (above B 1.1300 1.5530
diagonal)
values for WP when single-trait selection is applied. Since TS
TS A 0.4050 0.9383 and WS are undesired, RS is negative when single-trait selec-
B 0.4123 0.4767 tion is applied for each individual trait. However, in these cases
WS A 1.4480 0.8510 WP was also reduced. Selection based on the MI produced
B 1.3380 1.7070 satisfactory results when responses were highly correlated, op-
WP A 0.6180 0.6913 timizing gain for WP and losses for TS and WS. Selection for
B 0.5116 0.8862 increasing WP while TS and WS are reduced, a major benefit to
SS A 2.3110 0.8448 growers, may result in an average reduction in all other traits.
B 2.0440 2.5330 MI was the only approach that had the opposite effect on RS. In
a
the other selection scenarios, decreasing TS or WS also de-
Diameter of fruit (DF, in mm), length of
fruit (LF, in mm), weight of fruit (WF, in
creased WP. The same undesired result occurs by selecting
g), thickness of fruit skin (TS, in mm), for increased WP, since TS and WS also increase after selection.
weight of fruit skin (WS, in g), weight of The superior clones selected based on the MI approach, and
fruit pulp (WP, in g), and soluble solids the adjusted phenotypic means for each trait aimed at improv-
(SS, in °Brix)
ing fruit quality are shown in Supplemental Table 2. Comparing
the trait values, especially the mean (and minimum-maximum)
pear-shaped fruits with a greater proportion of pulp.
values shown in Table 2, there is a reduction in amplitude,
Moreover, high TS and WS values are undesirable for both
mainly related to fruit size (DF and LF). Individuals selected
consumers and farmers who want cultivars with increased
as promising are more uniform in size and shape compared to
WP. Examining the correlation coefficients, WP is positively
all full-sibs. Regardless of progeny size (30 full-sibs), there is
correlated with TS and WS (0.28 and 0.69, respectively), in-
still a certain variation, especially for WF and WS.
dicating that selection for increasing WP should result in a
certain increment in TS and WS if this is not carefully consid-
ered during selection. Note that selecting fruits with the QTL Mapping
highest WF values results mainly in increased WS, since the
correlation is 0.98, compared to WP, with a correlation of QTL analyses were carried out using the CIM model (Zeng
0.69. Finally, there were important positive genotypic 1994) for full-sib progenies (Gazaffi et al. 2014) and a

Table 2 Genetic and phenotypic parameter estimates for seven fruit broad-sense heritabilities on an individual-plant basis (H 2plants ) and on a
traits in a sweet passion fruit full-sib progeny: mean (minimum and genotype-mean basis (H 2means ), and coefficient of variation (CV, in
maximum, in parenthesis), genotypic variance (σb2G ), phenotypic percentage)
variance among individuals (σb2P ) and among genotype means (σb2P ),

Traita Mean (Min - Max) CV

σb2G σb2P σb2P H 2plants H 2means (%)

DF 71.10 (63.71–80.46) 12.670 31.180 17.096 0.406 0.741 5.797

LF 114.13 (98.75–129.10) 47.990 97.610 58.644 0.492 0.818 6.122
WF 193.20 (123.85–289.95) 1111.000 2380.600 1476.197 0.467 0.753 16.355
TS 10.05 (8.71–11.57) 0.416 0.830 0.505 0.501 0.823 6.351
WS 149.84 (95.40–235.80) 870.800 1682.500 1096.127 0.518 0.794 17.151
WP 43.35 (29.05–60.01) 42.770 147.080 71.467 0.291 0.598 21.336
SS 18.86 (17.21–21.66) 0.845 1.416 1.021 0.597 0.827 3.419
a
Diameter of fruit (DF, in mm), length of fruit (LF, in mm), weight of fruit (WF, in g), thickness of fruit skin (TS, in mm), weight of fruit skin (WS, in g),
weight of fruit pulp (WP, in g) and soluble solids (SS, in °Brix)
22 Tropical Plant Biol. (2017) 10:18–29

Fig. 2 Histograms (diagonal), 100 115 130 9.0 10.5 30 45 60

scatter plots (lower diagonal) and
genotypic correlations (upper DF

75
diagonal, *p < 0.05, **p < 0.01, 0.67*** 0.89*** 0.59*** 0.88*** 0.59*** −0.14ns
***
p < 0,001, nsnon-significant)

65
for seven fruit traits in a sweet

130
passion fruit full-sib progeny:
diameter of fruit (DF, in mm), LF

115
length of fruit (LF, in mm), weight 0.81*** 0.45*** 0.78*** 0.60*** −0.26**
of fruit (WF, in g), thickness of

100
fruit skin (TS, in mm), weight of
fruit skin (WS, in g), weight of
WF

250
fruit pulp (WP, in g), and soluble
solids (SS, in °Brix) 0.70*** 0.98*** 0.69*** −0.17ns

150
TS
10.5

0.75*** 0.28** −0.03ns

9.0

100 160 220

WS
0.55*** −0.14ns
60

WP
45

−0.23*
30

SS

20
18
65 75 150 250 100 160 220 18 20

previous integrated linkage map for the population (Pereira each for DF and WF, three each for LF, WS and WP, four for
et al. 2013). CIM results for each fruit trait are shown in SS, and five for TS. QTLs were located in seven out of nine
Table 4, while a representation of all mapped QTLs is given linkage groups (LGs), mainly in LG I (seven QTLs) and LG IV
in Supplemental Fig. 1. Altogether, we found 22 QTLs: two (five QTLs). These two LGs contain over 50 % of all mapped

Table 3 Selection differential (SD), response to selection (RS), and RS based on a multiplicative index (MI) (Elston 1963) intended to reduce
in percentage (RS%) in four different selection scenarios for seven fruit skin-related measurements (TS and WS) and increment pulp-related
traits in a sweet passion fruit full-sib progeny. Selection for 30 individuals measurements (WP), simultaneously. Bold numbers represent the target
were performed over three single-traits (TS, WS and WP), separately and for each selection scenario

Traita Selection against TS Selection against WS Selection for WP Selection using MIb

SD RS RS% SD RS RS% SD RS RS% SD RS RS%

DF –1.596 –1.183 –1.66 –3.703 –2.745 –3.86 2.205 1.634 2.30 –0.100 –0.074 –0.10
LF –2.642 –2.162 –1.89 –5.227 –4.277 –3.75 3.788 3.100 2.72 0.841 0.688 0.60
WF –22.209 –16.715 –8.65 –34.714 –26.126 –13.52 24.814 18.675 9.67 1.417 1.067 0.55
TS –0.671 –0.552 –5.50 –0.478 –0.394 –3.92 0.169 0.139 1.38 –0.136 –0.112 –1.12
WS –20.517 –16.299 –10.88 –30.375 –24.131 –16.10 16.645 13.223 8.82 –2.632 –2.091 –1.40
WP –1.802 –1.079 –2.49 –4.318 –2.584 –5.96 7.397 4.427 10.21 3.433 2.054 4.74
SS 0.026 0.022 0.11 0.360 0.297 1.58 –0.087 –0.072 –0.38 0.101 0.083 0.44
a
Diameter of fruit (DF, in mm), length of fruit (LF, in mm), weight of fruit (WF, in g), thickness of fruit skin (TS, in mm), weight of fruit skin (WS, in g),
weight of fruit pulp (WP, in g), and soluble solids (SS, in °Brix)
Table 4 Quantitative trait loci (QTLs) identified using composite interval mapping analyses for seven fruit traits in a sweet passion fruit full-sib progeny from 2(12) × SV3. Global and effect-specific
logarithm of the odds ratio (LOD) scores for QTLs, and the proportion of phenotypic variance explained by each QTL (R2P ) and by all QTLs (R2T ), as a percentage, are also provided

Traita QTL LGb Position (cM) 95 % support Closest marker Global LOD Additive effect on 2(12) Additive effect on SV3 Dominance effect Segregation
interval (cM)c R2P (%) R2T (%)
Estimate LOD Estimate LOD Estimate LOD

DF DF.1 I 34.00 22.00–47.00 D2-E40M60_447 10.91 26.1 42.0 –1.467 4.51 1.429 8.79 –0.623 1.93 1:1:1:1
DF.2 IV 73.99 48.76–79.87 C-P35M48_118 4.78 14.9 –0.969 3.88 0.475 0.83 0.320 0.44 1:2:1
LF LF.1 I 189.95 179.00–205.00 D2-E41M49_150 12.42 31.4 52.7 1.199 1.57 3.450 11.84 0.661 0.55 1:1:1:1
Tropical Plant Biol. (2017) 10:18–29

LF.2 II 40.46 30.00–53.44 D2-E31M59_129 4.00 10.7 –1.214 1.56 1.595 2.57 0.246 0.06 1:2:1
LF.3 IV 93.51 91.64–110.65 D2-E33M48_262 7.56 13.9 –2.402 6.49 1.275 1.96 0.571 0.45 1:1:1:1
WF WF.1 I 71.05 65.00–87.00 A-E31R06_257–9 11.33 28.4 43.8 –4.743 1.04 16.545 10.52 –0.221 0.00 1:1:1:1
WF.2 IV 93.85 80.00–110.65 D1-E35M49_210 7.36 18.2 –11.497 5.70 7.589 2.58 1.143 0.06 1:2:1
TS TS.1 I 35.00 10.00–55.81 D2-E40M60_447 4.36 7.2 64.3 –0.208 2.52 0.159 2.21 –0.003 0.00 1:2:1
TS.2 II 56.00 35.00–70.15 D1-E35R04_171 3.92 7.7 –0.112 1.64 –0.119 2.18 –0.020 0.06 1:2:1
TS.3 III 62.20 52.30–95.75 D2-E36R07_208 5.65 11.4 0.166 1.45 0.127 1.36 0.067 0.35 1:2:1
TS.4 IV 99.00 83.80–110.65 D2-E32M50_336 10.04 17.5 –0.250 7.66 0.159 3.51 –0.008 0.01 1:2:1
TS.5 VI 61.00 45.00–68.17 C-E31R01_330 4.01 6.1 –0.022 0.06 0.175 3.97 0.063 0.52 1:1
WS WS.1 I 25.36 9.00–41.00 D2-E40M60_447 11.33 22.4 51.2 –11.486 4.13 12.737 9.40 –5.522 1.92 1:1:1:1
WS.2 III 86.00 67.00–85.75 A-PE015_204–15 3.99 9.2 5.193 1.44 5.274 1.55 4.297 1.02 3:1
WS.3 IV 102.97 87.49–113.55 D2-P36M48_135 8.20 17.4 –12.125 6.74 6.438 2.30 2.402 0.29 1:1:1:1
WP WP.1 I 71.05 62.00–79.39 A-E31R06_257–9 9.73 20.5 52.6 –0.554 0.42 2.918 9.19 –0.362 0.16 1:1
WP.2 II 47.63 44.00–56.00 C-E32M58_499 9.56 16.2 –1.659 2.89 2.893 8.40 0.432 0.24 1:1:1:1
WP.3 III 73.00 52.30–95.75 D2-E31R06_199 3.67 7.4 1.563 1.83 0.606 0.35 1.213 1.04 1:2:1
SS SS.1 I 196.26 191.01–203.00 D2-E41R03_540 10.46 19.6 62.0 0.112 0.71 0.402 9.82 –0.112 0.81 1:1
SS.2 II 106.30 99.35–115.91 A-PA188A_SSCP 13.80 23.6 0.264 4.64 –0.353 7.51 –0.263 4.67 3:1
SS.3 V 190.00 184.70–192.12 C-E31R06_460 9.10 1.8 0.249 1.11 0.730 7.24 0.087 0.25 1:1:1:1
SS.4 VIII 54.23 48.16–59.94 D1-E35R04_223–0 6.80 1.4 –0.239 1.96 –0.676 5.42 0.067 0.27 1:1:1:1
PC1 PC1.1 III 88.00 67.00–95.75 A-PE015_204–15 5.69 7.9 37.8 0.242 2.38 0.247 2.77 0.148 0.94 3:1
PC1.2 IV 95.00 86.00–117.00 D1-E35M49_210 7.99 15.9 –0.414 7.19 0.178 1.50 0.037 0.07 1:1:1:1
PC1.3 V 203.46 184.70–205.00 D2-PA034A_231 3.95 11.3 –0.161 0.87 –0.214 2.03 0.251 1.87 3:1
PC2 PC2.1 II 50.00 43.00–58.84 C-E32M58_499 9.59 29.7 42.2 –0.067 0.15 0.529 9.11 0.157 0.87 1:1:1:1
PC2.2 IV 79.87 61.00–88.99 C-E41M60_387 4.21 12.8 0.326 3.61 0.064 0.16 –0.075 0.22 1:1
a
Diameter of fruit (DF, in mm), length of fruit (LF, in mm), weight of fruit (WF, in g), thickness of fruit skin (TS, in mm), weight of fruit skin (WS, in g), weight of fruit pulp (WP, in g), soluble solids (SS, in
°Brix), and first (PC1) and second (PC2) principal components on TS, WS and WP
b
Linkage groups (LGs) from Pereira et al. (2013)
c
95 % support interval is approximately LOD – 1.5
23
24
QTLs. In addition, four and three QTLs were mapped in LGs II
and III, respectively, and finally one QTL each was mapped in
LGs V, VI and VIII. Thus, LGs VII and IX did not contribute
any quantitative loci. QTLs were declared when the global
logarithm of the odds (LOD) exceeded threshold values ranging
from 3.25 (WP) to 3.74 (TS), as obtained using permutations.
Since QTLs in full-sib progenies can have up to three main
effects (one additive effect for each parent plus one dominance
effect), a total of 66 effects were estimated for all traits
(Table 4). Moreover, the CIM model used here infers the link-
age phase between QTL alleles and flanking markers based on
the signs of the additive effects (Gazaffi et al. 2014). In gen-
eral, we noticed that most QTL alleles from the female parent
2(12) are in repulsion phase (15 negative signals out of 22),
whereas QTL alleles from the male parent SV3 are in coupling
phase (19 positive signals out of 22), even though not all
effect-specific, marginal LOD scores suggested high signifi-
cance (for instance, LOD > 3). Regarding dominance effects,
LOD scores were much lower in comparison to one or both
additive effects, except for WS.2, WP.3 and SS.2 whose dom-
inance effects had similar significance in comparison to one or
both additive effects. For these traits, dominance seemed to
play a role in phenotypic variation.
The proportion of phenotypic variance explained by each
QTL (R2P ) ranged from 1.4 % (SS.4) to 31.4 % (LF.1).
However, since R2P calculations do not take into account the
covariance between all QTL estimates, the numerator may be
inflated. In fact, if covariances are taken into account, the ratio
tends to decrease. The total of variance explained by all QTLs
(R2T ) ranged from 42.0 % (DF) to 64.3 % (TS), which is a very
high considering that a relatively small number of QTLs was
detected (Table 4). These R2T values for each trait are related to
and comparable with the high heritabilities obtained in pheno-
typic analyses, ranging from 59.8 % (WP) to 82.7 % (SS) (see
Table 2). QTLs exhibited segregation ratios of 1:1 (three
QTLs), 3:1 (two), 1:2:1 (eight) and 1:1:1:1 (nine).
Additionally, we explored three correlated traits together
because of their importance in improving the quality of sweet
passion fruit. Principal component analysis (PCA) performed
on TS, WS and WP data resulted in two principal components
(PCs) accounting for more than 90 % of the variance. The first
PC (PC1) accounts for 69.01 % of total variability and appears
to represent a measurement of fruit mass content with a similar
contribution from each trait (TS, WS and WP loadings equal
0.581, 0.653 and 0.485, respectively). The second PC (PC2)
accounts for a further 24.60 % of variability, and consists
primarily of a contrast between pulp (WP loading =0.818)
and skin-related traits (TS and WS loadings = −0.566 and
−0.105, respectively). A biplot of the first two PCs did not
show any clear clusterization (Supplemental Fig. 2). Since the
cumulative proportion of variance for these two PCs added up
to 93.61 %, they were subjected to QTL analysis.
Tropical Plant Biol. (2017) 10:18–29
A further five QTLs were found in total, located in LGs III,
IV and V for PC1 and LGs II and IV for PC2. Fifteen main
effect estimates were calculated as deviations of scaled PC
means (Table 4). LOD profiles of each QTL analysis are
shown in Supplemental Fig. 1. Partial coefficients of determi-
nation (R2P ) ranged from 7.9 % (PC1.1) to 31.4 % (PC2.1).
Altogether, QTLs explained up to 37.8 % and 42.2 % of total
variance (R2T ) for PC1 and PC2, respectively. Interestingly,
QTL regions were once again detected in LG V for traits TS,
WS and WP, although they had already been found in LGs II,
III and IV QTLs in the previous separate analyses. QTLs
exhibited segregation ratios of 1:1 (one QTL), 3:1 (two) and
1:1:1:1 (two).
The current CIM model for full-sib progenies cannot han-
dle multiple traits simultaneously. We are therefore unable to
make any inferences regarding co-located QTLs between
these traits. However, where 95 % support intervals for the
QTL peaks overlap (Table 4), we can assume that there are
some regions controlling genetic variation for more than one
trait simultaneously. In LG II, PC2.1 (at 50.00 cM) was
mapped close to TS.2 (at 56.00 cM) and WP.2 (at
47.63 cM), but with no QTL evidence for WS; in LG III,
PC1.1 (at 88.00 cM) was found near to TS.3 (at 62.20 cM),
WS.2 (at 86.00 cM) and WP.3 (at 73.00 cM); finally, in LG IV,
PC1.2 (at 95.00 cM) and PC2.2 (at 79.87 cM) were mapped
adjacent to TS.4 (at 99.00 cM) and WS.3 (at 102.97 cM), but
there was no QTL evidence for WP in the same region
(Supplemental Fig. 1).
Discussion
Despite their promising utilization in the food and pharmaceu-
ticals industries, non-model crop species, such as those of the
Passiflora genus, tend to be neglected in genomic, classic and
molecular genetic studies. However, efforts have been made
recently to advance in passion fruit genomics and transcripto-
mics favoring breeding (Santos et al. 2014; Munhoz et al.
2015). Moreover, several types of molecular markers have
been used in diversity and genetic mapping studies in a range
of Passiflora species (reviewed by Cerqueira-Silva et al.
2014). For sweet passion fruit, microsatellite markers have
already been described (Penha et al. 2013), helping us to con-
struct an integrated genetic map for the species (Pereira et al.
2013). In fact, as an outbred species, genetic mapping is per-
formed using highly heterozygous parents as well as their full-
sib progenies, which can be propagated clonally and tested in
a number of environments of interest. For breeding purposes,
this means that all genetic variance can be exploited in the
selection of clonal individuals. In genetic mapping, an addi-
tional complication compared to inbred species lies in the fact
that molecular markers as well as QTLs segregate in distinct
Tropical Plant Biol. (2017) 10:18–29
patterns (Wu et al. 2002a; Gazaffi et al. 2014) and this must be
taken into account. Finally, for effective marker-assisted se-
lection, it is important to know the linkage phase between
QTLs and flanking markers, as well as the genetic architecture
of the trait. This is because we cannot observe QTLs, but we
can infer their effect on an individual phenotype once the
observed genotypes have been found using molecular
markers. Moreover, if dominance is important for the trait,
its effect on the phenotype obviously relies on the interaction
between the QTL alleles to be selected from the parents.
Besides improving fruit yield, sweet passion fruit selection
aims to establish a standard fruit shape and size, i.e., pear-
shaped, 8–14 cm long, 4–10 cm in diameter and weighing
100–400 g. The best commercial packaging consists of card-
board boxes holding about 3.0 kg of fruits sorted by size and
type, with the number of fruits ranging from 8 to 10 or 12
fruits per box. There is clear evidence on the lack of unifor-
mity in sweet passion fruits available on the market. Since it is
mainly consumed in natura, it is necessary to ensure that the
standards for shape, size, and weight translate into pulp con-
tent. For the selected genotypes (Supplemental Table 2), we
have tried to increase the pulp content and improve fruit qual-
ity, so we expect to produce fruits with less phenotypic vari-
ation, 10–13 cm long and 6–8 cm in diameter, weighing 150–
280 g and yielding more pulp (Fig. 1c-d).
The outer skin of the fruit and the sweet pulp (Fig. 1d)
usually vary in color from smooth yellow to orange-colored.
Since the fruits will be consumed mainly in natura, an evenly
distributed sweetness is expected, not exceeding around 20
°Brix of SS. Except for color-related traits, not evaluated here-
in, all the previous characteristics matched our F1 population
(Table 2). However, the skin was around 10 mm thick,
considered excessive in comparison to yellow passion
fruit skin (less than 5 mm). Thus, decreasing the skin
thickness while increasing pulp mass has become another
important goal for breeders.
In the present study, phenotypic data relative to seven fruit
quality traits were obtained at two locations for an F1 popula-
tion. Mixed modeling showed that complex, unstructured ge-
netic VCOV matrices fit all traits (Supplemental Table 1) and
allowed us to make inferences on the existence of GEI. In this
case, selecting individuals based on their joint rather than
marginal adjusted means is possible because genetic correla-
tions between environments were consistently high for all the
traits (Table 1). Additionally, when correlated traits (Fig. 2) are
targeted in a breeding program, index selection ought to be
more appropriate. We successfully used a multiplicative,
weight-free index selection approach (Elston 1963), which
resulted in the expected decrements in TS and WS while
incrementing WP. Because of positive correlations, selection
based on a single trait causes the remaining two traits to in-
crement or decrement concurrently (Table 3), which is unde-
sirable. Interestingly, the biplot of the first two PCs shows
25
high similarity between those individuals located in the first
(upper-right) quadrant (location of the projection of WP), and
the 30 full-sibs ranked by the index selection used herein
(Supplemental Fig. 2). In fact, although all the values for
PC1 are positive, the values for PC2 have opposite signs,
positive for WP and negative for TS and WS, allowing
promising individuals to be segregated. Some dissimilar-
ities are to be expected since there is some residual vari-
ation not captured in the PCs.
In yellow passion fruit, simultaneous selection of traits has
already been reported. Larger desired gains involving length
and width of fruit and a higher number of fruits per plant, for
example, were achieved by using the same weight-free index
used here (Oliveira et al. 2008b). It also appeared to work
correctly for the number of fruits and skin thickness in a
two-phased selection (Rosado et al. 2012). In fact, both direct
and indirect single trait selection seem to be inappropriate,
since although the response for the targeted single trait is
good, the response for other usually correlated traits is ad-
verse. Thus, successful selection programs for passion fruits
should be based on index selection in order to deal with more
than one trait of interest at a time (Oliveira et al. 2008b;
Rosado et al. 2012).
Also, some interesting observations regarding both genetic
correlations and broad-sense heritabilities on a genotype-
mean basis have emerged from yellow passion fruit studies.
For example, Moraes et al. (2005) studied 100 full-sibs de-
rived from a single wide cross and genetic correlations were
very similar, mostly among DF, LF and WF (higher than
0.632). On the other hand, a WP-related measurement showed
very low correlation or none at all with these traits (ranging
from −0.159 to 0.127). Regarding SS, all correlations were
negative or null (from −0.268 to −0.003). In addition, for
DF, LF, WF and SS, heritabilities ranged from 52.6 % to
79.3 % as observed in the present study. The WP-related mea-
surement showed the highest heritability (83.2 %).
Heritabilities were also reported by Oliveira et al. (2008b)
and Silva et al. (2009) respectively for 16 and 26 half-sib
progenies of yellow passion fruit. The values were lower than
(from 28.0 % to 57.0 %; Oliveira et al. 2008a, b) or close to
(from 58.7 % to 83.5 %; Silva et al. 2009) those we found for
the WF, DF and LF traits. For the WP-related and TS mea-
surements respectively, heritabilities were 28.0 % (Oliveira
et al. 2008b) and 40.7 % (Silva et al. 2009). Correlations
among DF, LF and WF were high (Oliveira et al. 2008b;
Silva et al. 2009), but negative (−0.498) between WF and
WP-related measurements (Oliveira et al. 2008b). This WP-
related measurement consists simply of the ratio of WP to WF
(percentage), which makes our WP measurement comparable.
This apparent inconsistence between yellow and sweet
passion fruits in respect of correlations involving WP
measurements can be explained by the breeding process that
has supposedly worked well for the yellow passion fruit but
26
still falls short of the desired outcome for the sweet passion
fruit. Finally, the TS evaluated by Silva et al. (2009) showed
strong correlations (higher than 0.657) with DF, LF and WF,
similar to our findings herein.
By mapping QTLs using the CIM model for F1 popula-
tions, we obtained a full description of 22 genomic regions
controlling variation in fruit-related traits with estimates of
additive parent-specific as well as dominance effects
(Table 4). The contributions of both parents were similar and
significant, and the differences related to additive effects were
due to linkage phases between QTL allele and flanking
markers, which were predominantly in repulsion in 2(12)
and in coupling in SV3. Most of the LOD scores associated
with additive effects were higher than those associated with
dominance effects, indicating that the loci controlling these
traits may have an additive basis, although LOD scores for
three dominance effects were similar to the additive ones.
Also, distinct QTL segregation patterns were inferred from
the presence of informative markers mapped onto linkage
groups, and multipoint conditional probabilities were intro-
duced into the mapping approach by using an integrated
map (Gazaffi et al. 2014).
To our knowledge, this is the first genetic study under field
conditions on the sweet passion fruit, and the first QTL map-
ping report on fruit quality traits in Passiflora species. For
other important fruit crops, however, fruit quality traits have
been investigated; apple (e.g., Kenis et al. 2008; Potts et al.
2013) and tomato (e.g., Chen et al. 1999; Saliba-Colombani
et al. 2001; Chang et al. 2014), for instance, are some of the
most studied. Causse et al. (2002) emphasize that just a few
tomato chromosome regions control fruit-related traits due to
the presence of clustered QTLs. They also argue that this
could account for the detection of correlations between several
fruit traits in the species. In a multi-trait analysis, QTLs were
found for fruit weight and diameter, as well as soluble solids,
accounting for between 12.4 % and 40.9 % of phenotypic
variation. In sweet cherry (Zhang et al. 2009), peach
(Eduardo et al. 2011) and pear (Zhang et al. 2013), similar
observations corroborate the existence of a small number of
QTLs with larger effects underlying variation in fruit traits.
These findings support the idea of conducting further fine
mapping analysis to characterize these regions deeply using
candidate genes or positional QTL cloning approaches
(Causse et al. 2002). Particularly in tomato, an arsenal of
postgenomic tools has allowed the identification of the geno-
mic regions underlying traits related to fruit metabolism, and
fruit and plant growth (reviewed in Alseekh et al. 2015).
In the present study, mapping of PCs was an attempt to
identify QTL underlying variability simultaneously for three
correlated traits of breeding interest. Using CIM, it is not pos-
sible to test for pleiotropic or linked loci in a single-trait anal-
ysis. However, by looking at the nearest QTL peaks (and
associated 95 % support intervals), we can assume that some
Tropical Plant Biol. (2017) 10:18–29
regions contribute to more than one trait. Four out of five
QTLs for PCs were closely mapped to QTLs for TS, WS
and WF (Table 4; Supplemental Fig. 1), while only one region
(PC1.3) was newly discovered as a putative region with ef-
fects on the three traits simultaneously. These five QTLs for
the PCs might explain the high genetic correlations observed
among the three traits. A PC is a linear combination of vari-
ables in the matrix of correlation between traits, and thus it
captures the information in this matrix. In our data, the first
two PCs explain a significant part of the matrix, showing that
there are important correlations between traits. In finding
QTLs for the PCs, we are therefore mapping QTLs controlling
variations between correlated traits. In addition, co-localized
QTLs in LG IV found exclusively using single-trait analyses
for TS and WS as well as different effect magnitudes for QTLs
in LG I and II can be explored when selecting for increased
WP and decreased TS and WS.
In conclusion, there are important genetic correlations be-
tween fruit-related traits in P. alata which are hypothesized as
due to putative shared regions controlling the genetic variation
described herein. More importantly, progress can be made in
genetically improving plants with targeted traits in breeding pro-
grams because there are unlinked loci, and appropriate method-
ology could be used in a multi-trait selection scenario. Although
preliminary, the findings in this study may assist in P. alata
breeding initiatives because, based on breeder interest and ge-
netic architecture, fruit traits are useful for early and marker-
assisted selection. Since unfavorable genotypes can be discarded
early on, significant progress should be made at the beginning of
breeding programs. Moreover, if breeders decide to repeat the
cross from the same parents, it is possible for all new genotypes
in the progeny to be assigned breeding values based only on
molecular data, since the QTL study has already been per-
formed. This could, in theory, speed up the breeding process.
Methods
Plant Material
A full-sib progeny (F1 population) consisting of 100 individ-
uals was used. It was derived from a single cross between two
distinct plant accessions of P. alata, the female parent denoted
as 2(12) and the male SV3. The female belongs to a progeny
of a wild accession of P. alata that was collected in a locality
between the Brazilian Amazon and Cerrado ecosystems
(15°13′ S, 59°20′ W) (for details, see Ferreira et al. 2010).
The male parent was an indoor selection cultivated in the
Southeast of Brazil (22°17′ S, 51°23′ W). Parent SV3 is more
vigorous, develops earlier and its leaf size and biomass are
higher than those of parent 2(12). It produces medium-sized
to small egg-shaped fruits weighing 130 to 150 g. The skin is
thinner and the aromatic pulp plentiful and of a strong orange
Tropical Plant Biol. (2017) 10:18–29
color. Parent 2(12) produces rounder, larger fruits
weighing 200 to 230 g. The skin is thicker and there
is less pulp. The pulp is of a pale color with an almost
imperceptible yellow tinge.
Controlled pollinations were performed under greenhouse
conditions where the F1 population seeds were collected and
germinated in a mixture of soil and commercial potting sub-
strate (1:1). Once the individual plants had grown, 20 rooted
cuttings from each F1 genotype were obtained and then
transplanted in the same mixture to fully develop.
Phenotypic Data
Field experiments were set up at two locations in Southeastern
Brazil: Piracicaba (22°47′ S, 48°07′ W, 500 m above sea level)
and Descalvado (21°54′ S, 47°37′ W, 679 m above sea level)
in February and April 2008, respectively. These two locations
(respectively A and B herein) have distinct soils, sandy at A
and clayey at B. A 10×10 square lattice design was used,
replicated three times in A, and two in B. Plots were 15 m
long with three plants (clones) tied and supported on wire
trellises 2.0 m high. Plants were spaced 5 m apart and rows
3 m apart. Supplementary irrigation and periodic pruning was
carried out to stimulate new shoots and individualize the
growing vines.
Experimental data were collected over the first harvest pe-
riod that ranged from September 2008 to March 2009. Fruits
were collected at maturity, i.e., when the skin color turned
from green to pale orange. The average of 10 fruits per plot
were obtained for examining seven fruit traits: diameter of
fruit (DF, in mm) at the widest point, length of fruit (LF, in
mm), weight of fruit (WF, in g), thickness of fruit skin (TS, in
mm) at the widest point, weight of fruit skin (WS, in g),
weight of fruit pulp (WP, in g), and total soluble solids (SS,
in °Brix). DF, LF and TS were measured using a digital caliper
and WF and WS using a digital scale. WP was calculated by
subtracting WS from WF, and SS was measured using a por-
table sucrose refractometer with 0–32 °Brix scale.
Phenotypic Analyses and Multiplicative Index Selection
Calculation
A multi-location mixed model was used to obtain the adjusted
means to perform subsequent QTL mapping analyses and to
obtain genetic correlations among traits and rank genotypes
for selection. Analyses were run for each trait in GENSTAT 16th
edition (VSN International 2014) based on REML using the
following linear model:
yi jkm ¼μþl m þrk ðmÞ þb jðkmÞ þgim þεi jkm
where yijkm is the phenotype of the ith genotype (i = 1 , … , I;
I = 100) in block j in replicate k at location m, μ is the overall
27
mean, lm is the fixed effect of the mth location (m = 1, M = 2),
rk(m) is the random effect of the kth replicate (k = 1 , … , K;
K = 2 or K = 3 depending on the location) at location m, bj(km)
is the random effect of the jth block in replicate k at location m,
gim is the random effect of the ith genotype at location m, and
εijkm is the random residual error. For genotypes, it was as-
sumed that vector g = (g11, … , gIM)′ has a multivariate nor-
mal distribution with zero mean vector and genetic VCOV
matrix G = GM ⊗ II, i.e., g∼N ð0;GÞ, where ⊗ represents the
Kronecker direct product of both genetic GM and identity II
matrices with respective dimensions M × M, and I × I is the
number of locations and genotypes. Three different models
for the GM matrix were examined and compared via AIC
and BIC. These models were based on identical variances
between locations (identity matrix), heterogeneous vari-
ances between locations with no covariance (diagonal ma-
trix), and heterogeneous variances including covariance
between locations (unstructured matrix). Genetic correla-
tions between locations A and B were calculated directly
from variance (σb2A and σb2B ) and covariance (σbA;B ) genetic
qffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi

estimates as rA;B ¼ σbA;B = σb2A σb2B Þ (Malosetti et al.
2013). For residuals, it was assumed that ε∼N ð0;RÞ,
where ε = (ε1111, … , εIJLM)′ and R is the residual VCOV
matrix, which was examined and compared via AIC and
BIC for several structures regarding locations and repli-
cates after selection for GM. Phenotypic correlations be-
tween traits were calculated over joint adjusted means
such as the standard Pearson product-moment coefficient
and tested assuming a significant global level of 0.05 in R
software (http://www.cran.r-project.org).
Broad-sense heritabilities on an individual-plant basis
2
(H plants ) were computed based on variance component esti-
mates assuming identity structure for the GM matrix by using
the ratio σb2G =σb2P , where σb2G equals the genotypic variance and
σb2P equals the phenotypic variance among individuals for each
trait. We also computed the ratio σb2G =σb2P in order to provide
approximate measurements of broad-sense heritabilities on a
genotype-mean basis (H 2means ), where σb2P equals the pheno-
typic variance among genotype means for each trait, using the
number of environments as the numerator of GEI variance
estimates, and the total number of plots as the numerator of
residual error variance estimates (Holland et al. 2003).
Finally, we defined a multiplicative index selection in order
to select 30 genotypes that combine the highest WP values
and the lowest TS and WS values to satisfy consumer require-
ments. Following the procedures proposed by Elston (1963),
the multiplicative index (MI) for each individual i was obtain-
ed as M I i ¼ ∏Tt¼1 ðyit −λt Þ where yit is the adjusted mean of
the ith genotype for the tth trait (t = 1 , 2; T = 3) and λt is the
lower bound to the tth trait. In addition to this selection sce-
nario, we also ranked 30 genotypes for another three single-
28
trait scenarios: selecting against WP, against TS, and for WS.
Then, we compared the selection differential (SD), i.e., the
difference between selected-group mean and full-sib progeny
mean, the response to selection (RS) as a product of SD and
H 2means for these four scenarios, and the response to selection
in percentage (RS%) as a ratio of RS to the full-sib progeny
mean multiplied by 100.
QTL Mapping Analyses
QTL analyses were run on a version of the FULLSIBQTL R
package (Gazaffi et al. 2014) using the integrated linkage
map constructed with 549 markers genotyped in 180 individ-
uals (Pereira et al. 2013). A sample of this F1 population
containing 100 individuals was evaluated in the field as pre-
viously described and used in the QTL mapping analyses.
We ran composite interval mapping (Zeng 1994) for each
trait using the linear model for full-sib progenies described in
Gazaffi et al. (2014). Conditional probabilities for QTL geno-
types were obtained based on multipoint maximum likelihood
using hidden Markov models (Wu et al. 2002b) as implement-
ed in the OneMap R package (Margarido et al. 2007;
Mollinari et al. 2009). The estimation method was based on
the expectation-maximization algorithm. Each model was
based on a search grid of 1 cM and avoiding a window of
15 cM around each QTL position being tested. Five cofactor
markers were included in the model using stepwise selection
based on the AIC in order to control eventual locus effects
outside the mapping interval. The threshold value for evidence
of putative QTLs was obtained at a 95 % significance level for
1000 permutations (Churchill and Doerge 1994) according to
the modification proposed by Chen and Storey (2006).
Because the fruit skin is thick and the sweet pulp is low in
mass, it is important to reduce TS and WS and increase WP
concurrently. This requires a better knowledge of the genetic
architecture underlying these traits. To this end, PCA was
performed on TS, WS and WP standardized adjusted means
in order to produce additional traits, which potentially sum-
marize the variation for these three traits combined. PCs ac-
counting for a cumulative proportion of variance of over 90 %
were investigated using the CIM approach. The steps involved
in building the CIM model were similar to those previously
applied to single-trait analyses.
For each CIM model, we estimated existing QTL parent-
specific additive and dominance effects, and reported global
and effect-specific LOD scores for each QTL position.
Linkage phase and segregation patterns of the QTLs, as well
as the proportions of phenotypic variance explained respec-
tively by each QTL and by all QTLs as partial (R2P ) and total
(R2T ) coefficients of determination were also provided. Finally,
a 95 % support interval for each QTL peak was estimated from
LOD − 1.5 approximation (Da Costa e Silva et al. 2012).
Tropical Plant Biol. (2017) 10:18–29
Acknowledgments The authors wish to thank the Fundação de
Amparo à Pesquisa do Estado de São Paulo (FAPESP, Brazil) for its
financial support and the fellowships awarded to GSP, MMP and RG.
Our thanks also to the Conselho Nacional de Desenvolvimento Científico
e Tecnológico (CNPq, Brazil) for the fellowships awarded to PhD stu-
dents (ESN and LDCL) and researchers (IOG, AAFG and MLCV).
Finally, we would also like to thank Carlos A. de Oliveira for his excellent
technical assistance, Mr. H. Borgonove for providing an experimental
area on his private farm at Descalvado, Brazil and Mr. Steve Simmons
for proofreading the manuscript.
Compliance with Ethical Standards
Conflict of Interest The authors declare no conflict of interest.
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