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Research Article
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Use of Random Amplified Polymorphic DNA Markers to Estimate
Heterosis and Combining Ability in Tomato Hybrids |
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A. Mirshamsi,
M. Farsi,
F. Shahriari
and
H. Nemati
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ABSTRACT
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Random Amplified Polymorphic DNAs (RAPD) were used to estimate
genetic distances and determine the correlation between genetic distance
and hybrid performance of 29 tomato lines that were the parents in a diallel
mating design. Among 97 observed bands, 69 showed polymorphism and were
used for establishing genetic distances based on the Nei coefficient between
parents. A UPGMA dendrogram and Multi-Dimensional Scaling (MDS) analysis
based on Nei genetic distances clearly clustered each group, confirming
the variation at a molecular level. Correlations between genetic distances
of the parents and performances of hybrids were established for various
quantitative traits. Significant correlations were found between RAPD
markers estimated genetic distances and MPH, HPH, SCA for some traits.
The low correlation between parental genetic distances and hybrid performances
for some quantitative traits suggested that RAPD markers have low linkage
to Quantitative Trait Loci (QTLs) or have inadequate genome coverage for
these traits. The results indicated that RAPD markers can be used as a
tool for determining the extent of genetic diversity among tomato lines,
for allocating genotypes into different groups and also to aid in the
choice of the superior crosses to be made among tomato lines, so reducing
the number of crosses required under field evaluation.
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INTRODUCTION
Nearly one hundred years after Shull`s proposal of
hybrid breeding, recognition of lines with superior cross performance
is still the most costly and time-consuming phase in hybrid development
projects. The general procedure is to assess the performance of crosses
between lines from different heterotic groups through extensive field
tests (such as open-pollinated progeny test, topcross test, polycross
test, single cross test, diallel cross mating and line x tester analysis).
If lines could be screened and superior crosses predicted before field
evaluation, this would greatly enhance the efficiency of hybrid breeding
programs (Melchinger et al., 1990).
In tomato, prediction of hybrid performance and heterosis
is important and has attracted large interest over the past decades. Recently,
advances in genome research have generated new tools in predicting heterosis
and hybrid performance using molecular markers in hybridization projects
(Zhang et al., 1996). Genetic diversity between lines for molecular
markers has been considered as a possible way for predicting heterosis
and combining ability. The impetus for this approach stems from the positive
association between heterosis and indirect measures of genetic diversity
reported for crosses among lines of maize. Furthermore, quantitative genetic
theory shows that for any degree of dominance greater than zero, heterosis
expressed in a cross is a function of the allele frequency differences
in parents (Melchinger et al., 1990; Zhang et al., 1996).
The use of markers to assess the genetic divergence among pairs of lines
has been suggested as a mean to overcome the drawbacks referred to above,
allowing the prediction of hybrid performance. Various investigators have
used markers to assess directly the genetic diversity of parental genotypes.
Isozymes, Restriction Fragment Length Polymorphism (RFLP), Random Amplified
Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP)
have been used to estimate genetic diversity of parental genotypes in
several experiments.
The use of isozymes (Heidrich-Sobrino and Corderio, 1975)
and RFLP (Goldshalk et al., 1990; Lee et al., 1984, 1989;
Bernardo, 1992, 1993; Duddley, 1991, Ajmone-Marsan et al., 1998)
has been proposed to predict hybrid performance from the genetic divergence
of lines. However, the correlations of the genetic distance based on isozymes
and the grain yield of the hybrids are too low to be useful to predict
hybrid performance. In maize (Zea mays L.), results indicated that
isozyme allelic differences between lines are not predictive of hybrid
performance (Lamkey et al., 1987; Price et al., 1986). In
rice (Oryza sativa L.). Peng et al. (1988) did not find
any association between the magnitude of heterosis in F1 and
isozyme variation among parents. However, he suggested that esterase and
peroxidase patterns in the parents may be of value for predicting F1
yield heterosis.
RFLP markers have proved useful for assigning maize to heterotic
groups and for detecting relationships among them (Smith et al.,
1990; Dudley et al., 1991; Melchinger et al., 1991; Bernardo,
1993). The association of RFLP-based genetic distance with F1
performance and heterosis has been tested in several studies (Lee et
al., 1984, 1989; Goldshalk et al., 1990; Melchinger et al.,
1990, 1991, 1992; Boppenmaier et al., 1992; Bernardo, 1993; Zhang
et al., 1994, 1995, 1996; Cerna et al., 1997; Zhao et al.,
1999; Benchimol et al., 2000) with the results appearing to be
highly dependent on the origin of parental inbreds. A study reported significant
correlations between RFLP-based genetic distances and heterosis for yield
in Maize, suggesting that measures of similarity calculated from RFLP
data could allow maize breeders to predict combination of lines resulting
in high-yielding single-cross hybrids (Smith et al., 1990). However
some studies conducted in maize indicated that there is no relationship
between RFLP markers and heterosis expression (Dudley et al., 1991;
Goldshalk et al., 1990; Lee et al., 1989; Melchinger et
al., 1990).
In rice (Zhang et al., 1994, 1995) showed the relationship
between marker heterozygosity and hybrid performance and heterosis in
a number of characters, including yield and yield component traits and
found mostly low correlation between general heterozygosity and F1
performance and heterosis. In contrast, very high correlations were detected
between midparent heterosis and specific heterozygosity for a number of
traits other than yield and yield components.
A significant improvement in the correlations between genetic
distance and hybrid performance was noted in maize and alfalfa by using
AFLP markers in comparison with RFLP markers (Ray and Lerma, 1999; Wu,
1999).
RAPD markers have also been used to determine the extent
of diversity among lines, for allocating genotypes into different groups
and to aid in the choice of superior crosses to be made (Arcade et
al., 1996; Lanza and Souza, 1997; Wu, 1999; Parentoni et al.,
2001).
The aim of the present study was to investigate the relationships
between genetic dissimilarity of the parental lines and hybrid performance
in tomato. RAPD markers were selected because of the high number of markers
that can be generated in a short time and technically they are easy to
use. The different steps of the study are to assessment of genetic variability
among lines and parental lines involved in a diallel mating design, to
study of the relationships between genetic distance and hybrid performance
for various quantitative traits and to the evaluation of the potential
of marker-based genetic distance in predicting the performance of tomato
hybrids.
MATERIALS AND METHODS
Parental lines and crosses: Plant materials used in this study are shown in Table
1. Seeds were obtained from breeding programs in Florida, Russia,
Italy and the collection of the Tomato Genetic Resource Center (TGRC).
Out of 29 lines, fifteen lines selected in early field evaluation (Data
not shown) and were inter-mated in all possible pairs excluding reciprocals
to form a half diallel crosses, during the cropping season 2000, in Ferdowsi
University of Mashhad and produced 105 hybrids. Greenhouse
experiment: Out of 105 F1 hybrids,
twenty-one hybrids and their seven parental lines were randomly selected
and examined for agronomic performance in the
Table 1: |
List of tomato lines used in
this study |
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1: Tomato Genetic Resource Center;
2: Institute of Food and Agricultural
Sciences; 3: Vavilov Research Center of Plant Production |
greenhouse, in a randomized complete block design with two
replications, during the year 2001. The field management included: irrigation,
weed control, fertilizer and pesticide applications, essentially the same
as under normal conditions of tomato production. Three plants of each
hybrids were examined for eight quantitative characters namely: Plant
Height (PLH), Yield per plant (Y), Fruit Weight (FW), Fruit Number (FN),
Days to Flowering (DFL), Days to Ripening (DRP), Leaf numbers to first
inflorescence (LI), Days from Flowering to Ripening (DF-DR). Based on
the analysis of hybrids, by means of analysis of variance, the sums of
squares were portioned into general and specific combining abilities using
diallel analysis method (2) proposed by Griffing (1956).
DNA extraction: For each parental line, genomic DNA was extracted
from 0.5 g of young leaves, harvested in bulk from four to five weeks
old plants per genotype. DNA was extracted using a modified Dellaporta
procedure (Dellaporta et al., 1983). DNA concentration was determined
by spectrophotometer, following procedures supplied by the manufacturer.
Agarose gel electrophoresis also was carried out for DNA quantity and
quality analysis. For use in PCR, the DNA was diluted with TE buffer (10
mM Tris-HCl, pH 8.0, 0.1 mM EDTA) to 50 ng µL-1 and stored
at 4°C until used for RAPD analysis.
DNA amplification: A series of optimization experiments were conducted
by changing the concentrations of template DNA, primers and MgCl2
to determine which condition gave the strongest and the most reproducible
patterns. RAPD amplification was performed in a reaction volume of 25
µL, containing 50 ng template DNA, 0.2 µM dNTPs, 1.5 mM MgCl2,
17.5 pmol primer (Cinagen Inc.), One micro Taq polymerase and 10X PCR
buffer (10 mM Tris-HCl, 50 mM KCl). Controls run with each amplification,
included at least one sample of the reaction mix with no template DNA.
PCR cycles consisted of initial denaturation at 94°C for 4 min, followed
by 35 cycles of amplification, each having denaturation at 94°C for 1
min, annealing at 36°C for 1 min and extension at 72°C for 2 min. A final
extension step at 72°C for 10 min was followed by termination of the cycle
at 4°C. Following amplification, PCR products (10 µL) were loaded in 1.2%
agarose gels and separated by electrophoresis at 75 v for about 3 h. RAPD
fragments were stained with ethidium bromide and photographed on UV photo
documentation system. The size of amplification products was determined
by comparison with 1 kb DNA ladder (MBI Fermentas) and using labwork software.
Data scoring and statistical analysis: As RAPD markers are dominant
markers, presence and absence represent the two allelic forms at a locus.
The presence and absence of
Table 2: |
Genetic distance matrix in
percentage for 29 genotypes estimated on the basis of RAPD marker |
 |
bands were recorded for each parent. The genetic similarity index (GS NL)
was determined from the RAPD pattern of individual plants in each population
according to the Nei coefficient (Nei and Li, 1979).
GSNL = 2N11/(2N11+N01+N10) |
N11 |
: |
No. of bands shared by both parents P1
and P2. |
N01 |
: |
Total No. of bands presented by parents P1. |
N10 |
: |
Total No. of bands presented by parents P2. |
For clarity, only strong and reproducible bands were scored as present (1)
or absent (0) for calculating Nei coefficient of similarity. Ambiguities
were scored as missing data. The genetic distance D was deduced from genetic
similarity as D = 1-S. The dissimilarity matrix ( Table 2)
was used to construct the dendrogram using UPGMA and to do Multi-Dimensional
Scaling (MDS) analysis employing the STATISTICA ver.5.5.
Pair-wise genetic distances between the seven parental lines, based on
the RAPD analysis, were examined to find any possible association with
yield performance of the 21-hybrid. The relationship between Nie genetic
distances and General Combining Abilities (GCA), Specific Combining Abilities
(SCA), High Parent Heterosis (HPH), mid Parent Heterosis (MPH) and Mean
were evaluated by Pearson correlations.
RESULTS
Marker polymorphisms: Twenty 10-mer primers were used for the
ability to detect polymorphism in 4 randomly chosen tomato lines (LA1793,
LA3006, BOIII and KalGN3). The primers that presented the highest degree
of polymorphism were selected for this study. These primers produced a
total of 97 reproducible bands, which 71.1% of them were polymorphic.
An average of 24.2 bands per primer was obtained, ranging from 290 to
3500 bp (Fig. 1), mostly concentrated from 400 to 2100
bp. The UPMGA dendrogram based on Nei`s genetic distances (Fig.
2A) showed three clusters: one comprising the Russian lines and two
others clusters included TGRC lines and majority of the Italian cultivars.
The frequencies of the intra-group polymorphic markers were 62.5, 77.08
and 78.04%, respectively. Also, maximum average of polymorphic markers
was 0.299 and the minimum was 0.179. The MDS analysis of 29 tomato lines
(Fig. 2B) indicated very little difference in clustering
among sub-groups; however, in general this MDS analysis confirmed the
cluster results.
Hybrid performance and heterosis: There were significant differences
in the performance of the crosses in all studied traits. The amounts of
heterosis differed drastically among the crosses and also varied widely
from one trait to another (Table 3). The results of
diallel analysis indicated that variation among crosses was attributed
primarily to GCA effects, however, SCA effects were also significant except
for LI and FN (data not shown). This behavior would be expected if additive
effects were of major importance.
Relation of hybrid performance and heterosis with genetic distance:
In general our results showed positive correlations between genetic
distances based on RAPD markers and genetic parameters such as SCA, GCA,
MPH, HPH and mean of hybrids (Table 4). Significant
 |
Fig. 1: |
RAPD profiles for 29 tomato lines
using primer OPJ-10 (5`-AAGCCCGAGG-3`). Lanes are as follows
from left to right: 1 kb DNA ladder (MBI Fermentas), LA3035,
R2, LA1793, C17, Kingston, LA0611, LA0588, LA3168, LA0643, R22,
Super H, B3, LA3898, Fla7771, KalGN3, Re1, Viva, LA3899, 1 kb
DNA ladder, LA3000, IL2-377, LA3728A, LA3247, LA2374, LA3006,
LA3723, IL-345, BoIII, LA2443, LA3004, (H2O) Negative
Control |
 |
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Fig. 2: |
(A) Dendrogram among 29 tomato
lines resulting from UPGMA cluster analysis based on Nei coefficient.
(B) Two-dimensional plot from multidimensional analysis of 29
tomato lines based on RAPD data |
Table 3: |
Measurements of SCA. MPH.
and HPH value for the 21 hybrids of diallel cross |
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Plant height (PLH), Days to
flowering (DFL), Days from flowering to ripening (DF-DR), Days
to ripening (DRP), Fruit number (FN), Fruit weight (FW), Leaf
numbers to 1st inflorescence (LI), Yield per plant (Y), Mid-Parent
Heterosis (MPH), High Parent Heterosis (HPH), Specific Combining
Ability (SCA) |
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Fig. 3: |
Correlation between RAPD`s estimated genetic distance
and Specific Combining Ability (SCA), Mid Parent Heterosis (MPH),
High Parent Heterosis (HPH) and mean of some study traits. Plant
height (PLH), Yield per plant (Y), Fruit Weight (FW), Fruit Number
(FN), Days to Flowering (DFL), Days to Ripening (DRP), Leaf numbers
to 1st inflorescence (PLH), Days from flowering to ripening (DF-DR),
High Parent Heterosis (HPH), Mid-Parent Heterosis (MPH), Specific
Combining Ability (SCA) |
Table 4: |
|
 |
Plant height (PLH), Days to
flowering (DFL), Days from flowering to ripening (DF-DR), Days
to ripening (DRP), Fruit number (FN), Fruit weight (FW), Leaf
numbers to 1st inflorescence (LI), Yield per plant (Y), Mid-Parent
Heterosis (MPH), High Parent Heterosis (HPH), Specific Combining
Ability (SCA) |
correlations (p< 0.10%) were found between D of the parents and performances
of the hybrids for some quantitative traits. MPH for FW (R = 0.45), Y
(R = 0.42) and LI (R = 0.48) were positively correlated with the genetic
distances of parents. Also, our results indicated that significant correlations
were found between genetic distances and HPH for DFL (R = 0.39), DRP (R
= 0.34). Significant correlations were found between SCA in absolute values
for Y (R = 0.39), LI (R = 0.39) and genetic distances. However, in other
traits these correlations were not significant (p< 0.10%). Finally, a
positive significant correlation (p< 0.10%) between genetic distance and
mean of FN (R = 0.42), DRP (R = 0.40), was observed ( Fig.
3).
DISCUSSION
Since present results showed a positive correlation between RAPD-based
genetic distances and SCA, MPH, HPH and mean of most traits, it can be
expected that some of the RAPD markers are linked to QTLs; although a
lower significant correlation (p< 0.10) were observed in some cases, in
absolute values, these estimates were generally small. One possible reason
could be the fact that the calculation of marker genetic distance includes
many markers not linked to yield or yield components. Bernardo (1992)
identified the following conditions for the effective prediction of hybrid
performance using molecular markers: strong dominance effects, the allele
frequencies at individual loci in parental lines should be negatively
correlated, high trait heritability, the narrow range variation of average
parental allele frequencies, 30-50% of QTL have to be linked to molecular
markers and not more than 20-30% of molecular markers have to be randomly
dispersed or unlinked to QTLs (Bernardo, 1992). Estimation of gene action
involved in the expression of traits, the level of additive effects and
the degree of dominance also are very important in developing a breeding
method for the trait of interest. Alleles with dominance or additive phenotypic
effects influence heritability differently, depending on whether they
are in homozygous or heterozygous conditions (Mohammadi et al.,
2002). In tomato, some of these conditions may not be met and current
knowledge may not be sufficient to establish the effectiveness of molecular
markers as predictors for heterosis expression of yield. For instance,
most gene actions reported in tomato for economically important traits
are additive and heritability estimates are low (Burdick, 1954; Mittal
and Singh, 1977; Singh and Singh, 1984). In other instances, even though
relationships between QTLs and molecular markers have been reported (Doganlar
and Tanksley, 2000), no relationships have yet been determined between
RAPD markers and QTLs for yield. Low or negative correlation between RAPD-based
genetic distance and mean of traits, in the results may be indicated that
these traits have complex inheritance and low heritability.
Since we have found a positive correlation between RAPD-based
genetic distance and FN, DRP, it can be expected that some of the RAPD
markers are linked to QTLs. Also, fruit number is a trait with high heritability
and dominance effects, which is in agreement with Bernardo`s predictions.
The assessment of the effectiveness of RAPD markers in breeding
tomato for yield and economically important traits may need further consideration.
The evaluation of the association between RAPD marker diversity and the
expression of heterosis would require more genotypes in hybrid combinations
and also that the RAPD marker used to estimate genetic divergence should
be linked to QTLs of the traits. Another reason for the poor association
between genetic distance and MPH, HPH in crosses could be due to using
the arbitrarily selected primers to estimate the Quantitative Trait Loci
(QTLs) affecting yield. Different loci affecting yield expression in different
crosses or loci with multiple alleles and epistatic effects may also reduce
the correlation. The type of markers used may be decisive in determining
the relationships between genotypes. Indeed, the RAPD markers allow the
amplification of any site of the genome, especially in non-coding regions
that are more likely to accumulate mutations and to generate greater polymorphism
between individuals or between species than coding regions such as isozyme
loci (Arcade et al., 1996).
The identification of individual loci that code for quantitative
traits would be a more suitable approach to an understanding of their
way of expression and predicting hybrid performance. The influence of
genetic distance would not have resulted from cumulative effects of single-locus
heterozygosity but mainly from the accumulation of different and favorable
alleles provided by parents (Arcade et al., 1996).
In conclusion, the analysis of relationship between genetic
distances of the parents and hybrid performances using RAPD markers has
provided important results. Firstly other techniques would not have been
likely to produce as many markers in the same period of time. This observation
is in agreement with other researches (Jain et al., 1994; Vaillancourt
et al., 1995). However, it should be kept in mind that bands of
similar size are not necessarily homologous and that their sequence homology
should be checked either by hybridization or sequencing. RAPD markers
are, however, dominant markers and an imprecision always remains regarding
the genotype of the parents with respect to homozygosity or heterozygosity
for the marker alleles.
Secondly, there is a significant and positive correlation
between genetic distance of the parents and performance of the hybrids.
This result represents a potential selection criterion in breeding program
if some yield component are the desired characters. Crosses should then
be carried out in order to ensure a maximal genetic distance between parents.
Concerning other traits such as plant height, investigations
should focus on the identification of marker linked to QTLs involved in
expression of the character and could lead to a marker-assisted selection
scheme in the tomato breeding.
According to present results, RAPD-based genetic distances
could be used to help in the choice of the crosses to be made among tomato
lines and in this way reducing the number of hybrids to be evaluated.
ACKNOWLEDGMENT We thank TGRC
(Tomato Genetic Resource Center) and Prof. John Warner Scott (Florida
University) for kindly providing seeds used in this study and excellent
technical assistance.
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