Melon,
Melon (
Wild melons or the feral forms are mainly found in the centers of origin, Africa and South Asia [
Genetic diversity and relationships of
A total of 191 melon accessions were used in this study (Supplemental Table
Genomic DNA was extracted from young leaf samples of all the accessions using a CTAB procedure described by Doyle and Doyle [
PCR amplification was carried out in a Thermal Cycler (BIORAD C1000™) with the reaction system and amplification program being same to the report of Wang
All the markers were scored as codominant data according to the amplicon size. This resulted in a genotypic matrix that was used to calculate the genetic parameters with the software PowerMarker v3.51 [
To analyze the genetic diversity and relationship of the melon accessions, the genotypic data were imported into the software MEGA6 [
Genetic differentiation among the different groups was measured by calculating pairwise F statistics (
All the 36 SSR markers produced clear band patterns, revealing single-locus variation among the melon accessions. Five genetic parameters (Na, Ne, Ho, He, and PIC) were calculated for the 36 markers estimated from the 191 melon accessions, as shown in Table
Statistics of genetic variation as measured for 36 SSRs estimated from 191 melon accessions.
Marker | Na | Ne | Ho | He | PIC |
| |||||
CM07 | 7 | 5.83 | 0.04 | 0.83 | 0.60 |
CMCT505 | 8 | 3.89 | 0.09 | 0.75 | 0.71 |
SSR011330 | 9 | 3.63 | 0.11 | 0.73 | 0.69 |
SSR012562 | 9 | 3.39 | 0.12 | 0.71 | 0.68 |
gSSR4959 | 6 | 1.95 | 0.03 | 0.49 | 0.46 |
SSR013487 | 16 | 3.41 | 0.16 | 0.71 | 0.69 |
SSR014660 | 14 | 4.75 | 0.05 | 0.79 | 0.78 |
SSR015784 | 6 | 3.69 | 0.11 | 0.73 | 0.68 |
SSR016829 | 9 | 3.97 | 0.14 | 0.75 | 0.71 |
HNM33 | 10 | 4.32 | 0.10 | 0.77 | 0.74 |
HNM12 | 11 | 5.92 | 0.11 | 0.83 | 0.81 |
SSR020162 | 5 | 2.46 | 0.05 | 0.60 | 0.54 |
SSR020947 | 5 | 2.31 | 0.06 | 0.57 | 0.50 |
DE1557 | 12 | 5.25 | 0.03 | 0.81 | 0.79 |
SSR023138 | 8 | 4.20 | 0.16 | 0.76 | 0.74 |
HNM41 | 7 | 1.94 | 0.13 | 0.48 | 0.45 |
DE1103 | 7 | 2.40 | 0.09 | 0.58 | 0.55 |
CMAGN52 | 9 | 3.54 | 0.02 | 0.72 | 0.70 |
CMAGN75 | 13 | 7.67 | 0.05 | 0.87 | 0.86 |
gSSR22419 | 6 | 3.15 | 0.04 | 0.68 | 0.63 |
SSR029474 | 5 | 4.21 | 0.03 | 0.76 | 0.72 |
SSR029716 | 9 | 4.47 | 0.02 | 0.78 | 0.75 |
HNM31 | 8 | 4.04 | 0.09 | 0.75 | 0.71 |
HNM40 | 8 | 4.11 | 0.15 | 0.76 | 0.73 |
CMTC47 | 8 | 3.08 | 0.18 | 0.68 | 0.64 |
SSR033639 | 8 | 4.70 | 0.02 | 0.79 | 0.76 |
CMATN22 | 7 | 3.32 | 0.07 | 0.70 | 0.65 |
CM38 | 9 | 4.81 | 0.11 | 0.79 | 0.76 |
CMTCN8 | 10 | 2.56 | 0.05 | 0.61 | 0.58 |
HSSR010 | 9 | 5.16 | 0.05 | 0.81 | 0.79 |
DM0673 | 12 | 6.08 | 0.11 | 0.84 | 0.82 |
SSR038372 | 5 | 2.29 | 0.05 | 0.56 | 0.47 |
CMGA104 | 9 | 3.68 | 0.05 | 0.73 | 0.69 |
SSR040314 | 10 | 3.51 | 0.06 | 0.72 | 0.67 |
SSR041311 | 11 | 3.56 | 0.04 | 0.72 | 0.70 |
CMGAN80 | 9 | 2.54 | 0.11 | 0.61 | 0.58 |
Mean | 8.72 | 3.88 | 0.08 | 0.72 | 0.68 |
Na: the number of observed alleles.
Ne: the number of effective alleles.
Ho: observed heterozygosity.
He: expected heterozygosity.
PIC: polymorphic information content.
With the SSR genotypic data, a NJ dendrogram (Figure
A neighbor-joining dendrogram showing the genetic affiliations of the 191 melon accessions. All the accessions were divided into four clusters (I, II, III, and IV). Numbers indicate the accession codes as listed in Supplementary Table
The remaining 88 accessions formed cluster IV that covered both the two subspecies (TC, TN, and wild groups), mainly representing by East Asian TN melons (i.e., 75 subspecies
Furtherly, two methods, principal component analysis (PCA) and STRUCUTRE analysis, were used to offer an alternative view of the relationships within the accession collection. On the PCA dendrogram (Figure
Genetic structure of the 191 melon accessions revealed by principal component analysis (PCA) (a) and STRUCTURE analysis (b). The symbols and colors for the accessions correspond to those of the Figure
Since distinct divergences were found among the different groups, the six genetic parameters (Na, Ne, Ho, He, I, and PIC) were computed for each group to compare their diversity levels. As shown in Table
Comparison of genetic diversity for the thick-skinned (TC), thin-skinned (TN), and wild (W) groups.
Accession group | Na | Ne | Ho | He | I | PIC |
| ||||||
TC | 226 | 2.93 | 0.04 | 0.63 | 1.26 | 0.58 |
TN | 256 | 2.87 | 0.07 | 0.59 | 1.26 | 0.55 |
W | 250 | 4.08 | 0.18 | 0.72 | 1.51 | 0.67 |
Na: the number of observed alleles.
Ne: the number of effective alleles.
Ho: observed heterozygosity.
He: expected heterozygosity.
I: Shannon’s information index.
PIC: Polymorphic information content.
A Venn diagram showing the number of alleles specific to a certain group or shared by different groups. TC, TN, and W mean the thick-skinned, thin-skinned, and wild groups, respectively.
To analyze the genetic differentiation of the collection, AMOVA was conducted using accession groups and geographic origins as sources of variation, and showed that 28.70% of the total variation was attributed to the differentiation between groups and 30.44% was to the differentiation between geographic regions (Table
Molecular analyses of variance (AMOVA) among the accession groups and origin regions.
Source of variation | df | Variance components | Percentage of variation | |
| ||||
Among groups | 2 | 58.03 | 28.70 | <0.01 |
Among regions | 2 | 61.54 | 30.44 | <0.01 |
Among individuals | 176 | 75.67 | 37.42 | <0.01 |
Within individuals | 191 | 6.96 | 3.44 | <0.01 |
Groups were defined by the thick-skinned, thin-skinned, and wild accessions.
Regions were defined by South Asia (India and Maldives), East Asia (China, Malaysia, and Japan), West Asia (Iran and Turkey), and Africa (Tunisia).
Pairwise estimates of genetic differentiation among the three accession groups using pairwise
Accession group | TC | TN | W |
| |||
TC | — | 0.380 | 0.293 |
TN | 0.102 | — | 0.319 |
W | 0.083 | 0.100 | — |
TC, TN, and W mean the thick-skinned, thin-skinned, and wild groups.
Pairwise
A diversity of plant germplasms is valuable resources for present and future commercial producers and researchers; they can be used for breeding of new cultivars to meet the demand for food and studying the origin, evolution, and taxonomy of plant species. Melon is such a horticultural crop with abundant diversity. During the past decades, it earned worldwide attentions in scientific research (e.g., developmental biology and genetics) [
To date, genetic diversity and relationships in
The strongest differentiation occurred between TC and TN melons (
In the present research, we used SSR markers separated by polyacrylamide gel. It would be interesting to compare phylogenetic relationships among studied melon accessions using another method like capillary electrophoresis or even other molecular approaches including SNP or DArT markers. Such new researches can confirm or show a conflict with current study for the genetic clustering and it will be the next step for the investigation.
Genetic diversity and relationship are crucial for plant breeding as they determine the efficient utilization of the genetic materials and selection of potential parents. Accurate measurement of genetic diversity and relationship present within an accession collection relies on the molecular markers (e.g., SSR) with stability and even distribution across the genome. The present study revealed an existence of distinct population structure in 191 melon accessions. Indian wild accessions, revealing a close relationship to the local subspecies
The data used to support the findings of this study are included within the article.
The authors declare that there are no conflicts of interest regarding the publication of this paper.
This work was supported by the National Natural Science Foundation of China (31672147), Key Science and Technology Program of Henan Province of China (172102110052), and the Natural Science Foundation of Henan Province of China (162300410150).
Table 1: descriptions of the 191 melon accessions used in the present study. Table 2: the information of the 37 SSR markers used in the present study.