Abstract

Background

   Melon is an important horticultural crop cultivated extensively
   worldwide. The size of the fruit navel, the terminal region of melon
   fruits, significantly influences the appearance quality of the fruit.
   However, the regulatory factors and molecular mechanisms governing the
   fruit navel development remain poorly understood in melon.

Results

   In this study, the regulators and mechanisms underlying fruit navel
   development were investigated through phenotypic analysis, RNA
   sequencing (RNA-seq) and RT-qPCR methods. The inbred line ‘T03’ and a
   big fruit navel mutant ‘BFN’ of melon were used as experimental
   materials. RNA-seq analysis identified 116 differentially expressed
   genes (DEGs), including 54 up-regulated and 62 down-regulated genes, in
   both the green bud (GB) and ovary at anthesis (OA) stages of the ‘BFN’
   melon compared to the ‘T03’ melon. Functional enrichment analysis
   revealed that these 116 DEGs were significantly associated with
   “Sesquiterpenoid and triterpenoid biosynthesis”, “Circadian
   rhythm—plant”, “Galactose metabolism” and “Biosynthesis of various
   alkaloids” pathways. There were three (AP2/ERF, MYB and C2H2 types) and
   eight (AP2/ERF, MADS-box, homeobox domain and bZIP types) transcription
   factors presented in up-regulated and down-regulated DEGs, and their
   putative target genes were predicted. Based on KEGG and expression
   analyses, two terpene cyclase/mutase genes (MELO3 C001812 and MELO3
   C004329) were identified as being involved in the “Sesquiterpenoid and
   triterpenoid biosynthesis” pathway, and their transcripts were
   significantly downregulated in all detected development stages (EGB,
   GB, GYB, YB and OA) of ‘BFN’ fruits compared with ‘T03’ fruits.

Conclusions

   The findings of this study elucidate a fundamental regulatory mechanism
   underlying fruit navel formation, and identify two key negative
   regulators, MELO3C001812 and MELO3C004329, involved in the development
   of the fruit navel in melon.

Supplementary Information

   The online version contains supplementary material available at
   10.1186/s12870-025-06444-7.

   Keywords: Melon, Fruit navel development, Transcriptome analysis,
   Expression analysis

Background

   Melon is an important horticultural crop, highly valued by consumers
   for its sweet and flavorful fruit. The flowers of melon are classified
   into male flowers, female flowers and bisexual flowers [[36]1]. Most
   melon cultivars exhibit andromonoecy in which bisexual flowers develop
   into fruits [[37]2]. Under optimal growth conditions, bisexual flowers
   typically take approximately 5 days to progress from visible buds to
   full bloom [[38]3]. During anthesis, pollen from male flowers lands on
   the stigma of the pistil and germinates, the ovule is fertilized in
   virtue of the growth of pollen tubes [[39]4]. Subsequently, the fruit
   undergoes rapid growth driven by cell division and expansion. In
   melons, the morphology of ovary and mature fruit is closely correlated,
   and the fruit shape is predominantly determined prior to flowering
   [[40]3].

   To date, several quantitative trait loci (QTLs) have been identified as
   regulators of fruit length (flqs2.1, flqs3b.1, flqs6a.1, flqs8.1,
   flqs10b.1), fruit diameter (fdqs3a.1, fdqs12.1) and fruit shape
   (fsqs2.1, fsqs8.1, fsqs12.1) in melon [[41]5]. The fruit navel is also
   a critical component of the exterior quality in melon fruit, and the
   size of the fruit navel greatly influences consumer preference and its
   associated economic value. However, the molecular mechanisms underlying
   fruit navel formation in melon remain largely unexplored.

   The fruit navel is the residual trace left after the flower abscises, a
   prominent scar often appears due to the interplay of genotype,
   environmental factors and hormonal regulation, and compromises the
   aesthetic quality of the fruit [[42]6–[43]8]. In tomato, low
   temperature and growth regulators are important factors contributing to
   the formation of navel-like scars at the blossom end of fruits [[44]9].
   Under low temperature condition, abnormal development of flower organs
   leads to the production of navel-like scars at the fruit apex [[45]10].
   Exogenous application of gibberellic acid (GA[3]),
   N-methatolylphthalamic acid, or 2,3,5-triiodobenzoic acid (TIBA)
   promotes the formation of large fruit navels in tomato, and the
   severity of large fruit navel is connected with the plant's
   developmental stage at the time of induction [[46]9, [47]11–[48]13].
   Specifically, auxin plays a direct role in the development of
   pointed-tip fruits in tomato. Knockdown of auxin response factor 7
   (ARF7) leads to the production of heart-shaped fruits [[49]14]. The
   POINTED TIP (PT) gene, which encodes a C2H2-type zinc finger
   transcription factor, has been demonstrated to suppress the formation
   of pointed-tip fruits by downregulating the transcription of FRUTFULL 2
   (FUL2) and altering auxin transport. Consequently, knockout of PT
   results in the development of pointed-tip fruits in tomato [[50]15]. In
   melon, low temperature alters the ultrastructure of the phloem, which
   is responsible for the photoassimilate transport, and inhibits the
   phloem loading [[51]16, [52]17]. Additionally, low temperature also
   results in decreased carbohydrate content in fruits, an altered plant
   metabolism and a significant loss of productivity [[53]18, [54]19]. At
   present, the effects of environmental factors and hormones on the
   formation of fruit navel in melon remain poorly understood, and the key
   regulatory genes involved in this process have yet to be identified.

   Currently, RNA-seq analysis is widely utilized to identify candidate
   genes and regulatory pathways associated with key developmental traits
   in plants. For instance, RNA-seq has been employed to investigate the
   mechanism underlying the formation of bisexual flowers in melon,
   revealing that the ethylene signaling pathway plays a crucial role in
   the initiation of bisexual buds [[55]2]. In this study, the dynamics of
   fruit navel development were examined using the melon inbred line ‘T03’
   and a big fruit navel mutant ‘BFN’. Transcriptome analysis was
   conducted at the green bud (GB) and ovary at anthesis (OA) stages of
   ‘T03’ and ‘BFN’ fruit navels to explore the molecular mechanisms
   governing fruit navel development in melon. The results of this study
   revealed several potential regulators and regulatory networks involved
   in fruit navel development, and providing valuable insights for
   improving the exterior quality of melon as well as its consumer appeal.

Methods

Plant materials and growth conditions

   This study was conducted from March 2023 to August 2024. The melon
   inbred line ‘T03’ (Cucumis melo ssp. agrestis Jeffrey) and a
   spontaneous mutant ‘BFN’ (Cucumis melo ssp. agrestis Jeffrey) were used
   for morphological observation, transcriptome sequencing and reverse
   transcription quantitative polymerase chain reaction (RT-qPCR)
   analyses. The melon inbred line ‘T03’ is a widely cultivated variety in
   Hebei province of China, while ‘BFN’ is a spontaneous mutant derived
   from ‘T03’. The primary difference between ‘T03’ and ‘BFN’ is the size
   of fruit navel. The melon seedlings were cultivated in the greenhouse
   of Hebei Agricultural University at 25–28℃/16–19℃ of light/dark of 16/8
   h. Standard irrigation and pest management practices were followed
   throughout the experiment.

RNA extraction and sequencing

   Total RNA was extracted from the terminal region of ‘T03’ and ‘BFN’
   melon fruits at five developmental stages (early green bud (EGB), green
   bud (GB), green yellow bud (GYB), yellow bud (YB) and ovary at anthesis
   (OA) stages) using the TianGen Quick RNA Isolation Kit (TianGen
   Biotech, China). The quality of the isolated total RNA was evaluated by
   the NanoDrop2000 spectrophotometer (IMPLEN, CA, USA) and 1% RNase-free
   agarose gel electrophoresis. Samples meeting the quality criteria were
   selected for further analyses, and the samples at GB and OA stages were
   chosen to perform RNA-sequencing. Independent samples of melon fruits
   collected before flowering were used for RNA-seq data validation and
   expression analyses of several enzyme-coding genes. For RNA sequencing,
   ten and three fruit navel tissues (indicated by the white frame in
   Fig. [56]1A) were pooled to form one biological replicate for the GB
   and OA stages, respectively. Three biological replicates were performed
   for each set (GB-T03, GB-BFN, OA-T03, OA-BFN). RNA-Seq libraries were
   constructed by Majorbio Bio-Pharm Technology (Shanghai, China) using
   the Illumina Truseq™ RNA Library Prep Kit following the manufacturer’s
   instructions.

Fig. 1.

   [57]Fig. 1
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   Phenotypic traits of fruit navel in ‘T03’ and ‘BFN’ fruits. A
   Comparison of fruit navels in ‘T03’ and ‘BFN’ fruits at the early green
   bud stage, green bud stage, green-yellow bud stage, yellow bud stage,
   ovary at anthesis, fruit at 3 days after pollination (DAP) and 7 DAP,
   fruit at veraison, and mature fruit stages. White frames represent the
   fruit navel tissues used for RNA-sequencing. B Diameter of fruit navel
   in ‘T03’ and ‘BFN’ fruits. Error bars represent ± SD. Asterisks
   indicate significant differences in the diameter of fruit navel in
   ‘BFN’ fruits relative to ‘T03’ fruits (Student t-test: *, P < 0.05; **,
   P < 0.01)

Bioinformatics analysis of RNA-Seq data

   The raw paired end-reads were filtered and subjected to quality
   controlled using fastpusing default parameters [[59]20]. The clean
   reads were then aligned to the Melon Genome
   ([60]http://cucurbitgenomics.org/organism/18) in a directed mode using
   the HISAT2 software [[61]21]. The mapped reads were assembled and
   spliced by StringTie ([62]http://ccb.jhu.edu/software/stringtie/), and
   compared with known transcripts to functionally annotate the potential
   new transcripts [[63]22]. Subsequently, RSEM was employed to quantify
   the read counts for each gene [[64]23], and the Fragments Per Kilobase
   of transcript sequence per Millions reads (FPKM) were calculated.
   Differentially expressed genes (DEGs) between the ‘T03’ and ‘BFN’ fruit
   navels were identified using the DESeq2 R package [[65]24]. The
   P-values were adjusted to control the false discovery rate (FDR) using
   the Benjamini and Hochberg method. DEGs with a fold change > 2 and an
   FDR < 0.05 were considered to be differently expressed.

KEGG enrichment analysis of DEGs

   The 54 up-regulated genes, 62 down-regulated genes in ‘BFN’ compared to
   ‘T03’ fruits, and all 116 DEGs were subjected to Kyoto Encyclopedia of
   Genes and Genomes (KEGG) pathway enrichment analysis. The KEGG pathway
   enrichment was performed by the ClusterProfiler R package [[66]25],
   with the FDR controlled by the Benjamini and Hochberg method. A KEGG
   term was considered significantly enriched if its P-value was less than
   0.05.

Heatmap of DEGs

   The heatmap of DEGs was generated by OriginPro 8.0 (OriginLab
   Corporation, Northampton, MA, USA) based on the read counts. For each
   gene, the highest and lowest transcript levels were normalized to 1.5
   and − 1.5, respectively. The transcript levels in other samples were
   calculated as the relative values and visualized using a color
   gradient.

RT-qPCR verification

   Total RNA extracted from the fruit navels of ‘T03’ and ‘BFN’ melon at
   the EGB, GB, GYB, YB and OA stages was used to synthesize the cDNA
   using the FastQuant cDNA Kit (Tiangen Biotech, China). RT-qPCR was
   performed on a CFX96 Real-time PCR System (Bio-Rad, USA) with SYBR
   Green PCR master Mix (Applied Biosystems, USA). The melon CmACTIN gene
   (MELO3C008032) was used as an internal control. The relative expression
   level of each gene was calculated by the 2^−ΔΔCt method [[67]26].
   Gene-specific primers used for RT-qPCR were listed in Table S1.

Statistical analysis

   Phenotypic data of the fruit navel in ‘T03’ and ‘BFN’ melons were
   measured from three biological replicates. The Student’s t-test (*, P <
   0.05; **, P < 0.01) was used to compare the differences in fruit navel
   diameter between ‘BFN’ and ‘T03’ fruits (Fig. [68]1B). For RT-qPCR
   assays, three biological replicates and three technical replicates were
   performed. The Student’s t-test (*, P < 0.05; **, P < 0.01) was applied
   to assess significant differences in transcript levels relative to the
   GB-T03 sample (Fig. [69]3), while Duncan’s test (lowercase letters, P <
   0.05) was used to compare the expression differences of five putative
   enzyme-coding genes in different fruit developmental stages of melon
   (Fig. [70]7).

Fig. 3.

   [71]Fig. 3
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   RT-qPCR validation of RNA-seq data. Three upregulated and five
   downregulated DEGs identified by RNA-seq were randomly selected for
   RT-qPCR analyses. The expression trends of the selected DEGs detected
   by RT-qPCR were consistent with those obtained from RNA-seq. Error bars
   represent ± SD. Asterisks indicate significant differences in gene
   expression levels compared with the GB-T03 sample (Student t-test: *,
   P < 0.05; **, P < 0.01)

Fig. 7.

   [73]Fig. 7
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   Expression analyses of five putative enzyme-coding genes identified in
   the “Sesquiterpenoid and triterpenoid biosynthesis”, “Galactose
   metabolism” and “Circadian rhythm—plant” pathways. RT-qPCR assays were
   conducted at the early green bud (EGB), green bud (GB), green yellow
   bud (GYB), yellow bud (YB) and ovary at anthesis (OA) stages. Error
   bars represent ± SD. Letters above the columns indicate significant
   differences in transcript levels at P < 0.05 (Duncan’s test)

Results

Phenotypic characteristics of fruit navel in ‘T03’ and ‘BFN’ melon

   Based on corolla color and fruit developmental characteristics, the
   morphology of the fruit navel was observed at the early green bud
   (EGB), green bud (GB), green yellow bud (GYB), yellow bud (YB), ovary
   at anthesis (OA), fruit at 3 days after pollination (DAP), fruit at 7
   DAP, fruit at veraison and mature fruit stages (Fig. [75]1). The melon
   inbred line ‘BFN’ is a spontaneous mutant derived from the inbred line
   ‘T03’, and exhibits a significantly larger fruit navel compared with
   ‘T03’. During the early green bud stage, no obvious morphological
   difference was observed in the terminal region of the ovary between
   ‘T03’ and ‘BFN’ melons. However, the diameter of the fruit navel in
   ‘BFN’ was notably larger than that in ‘T03’ (Fig. [76]1A, B). Starting
   from the green bud stage, the ovary end of ‘BFN’ began to bulge,
   whereas the ovary end of ‘T03’ remained slightly sunken. As a result, a
   prominent navel formed in ‘BFN’ fruits, contrasting with the small and
   smooth navel of ‘T03’ fruits (Fig. [77]1A). At the mature fruit stage,
   the navel diameter of ‘T03’ fruits was 1.57 cm, while that of ‘BFN’
   fruits reached 4.10 cm (Fig. [78]1B).

Transcriptomic characteristics of the fruit navel from ‘T03’ and ‘BFN’ melons

   To investigate the mechanism underlying big fruit navel formation,
   RNA-seq was conducted on the terminal region of ovaries, specifically
   the fruit navel region, in ‘T03’ and ‘BFN’ melons. The ovary at
   anthesis (OA) was selected for sampling due to its ease of
   identification and ability to ensure sampling accuracy. Additionally,
   transcriptome profiling was performed on the fruit navel of ‘BFN’ and
   ‘T03’ at the green bud (GB) stage, in which the fruit navel exhibits
   distinct developmental characteristics. Three biological replicates
   were performed for each set (GB-T03, GB-BFN, OA-T03, OA-BFN), so that a
   total of 12 libraries were produced (Table. S2). In general, 41.56 to
   60.85 million raw reads were generated per sample, and 41.13 to 60.29
   million clean reads were mapped to the melon genome after initial data
   filtering (Table. S2).

   The square of Pearson's correlation coefficient (R^2) was closely
   associated with the developmental stage, and higher R^2 was observed
   among the three biological replicates within each set compared to those
   between different groups (Table. S3). Principal component analysis
   (PCA) revealed clear clustering of samples within the same set, with
   four distinct clusters corresponding to GB-T03, GB-BFN, OA-T03 and
   OA-BFN (Fig. [79]2A). These results indicated that distinct gene
   expression profiles existed in the fruit navel region of ‘BFN’ and
   ‘T03’ ovaries at the green bud and anthesis stages.

Fig. 2.

   Fig. 2
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   Transcriptomic characteristics of fruit navel in ‘T03’ and ‘BFN’ melon.
   A Principal component analysis (PCA) of GB-T03, GB-BFN, OA-T03 and
   OA-BFN samples. B, C Venn diagrams of significantly upregulated (B) and
   downregulated (C) genes in ‘BFN’ fruits compared with ‘T03’ fruits at
   GB and OA stages

Distinct gene expression profiles contributing the formation of fruit navel

   Differential expression genes (DEGs) were identified using a FDR
   threshold of less than 0.05 and a fold change greater than 2 (Table.
   S4). During the green bud stage, 186 genes and 394 genes were
   significantly up-regulated and down-regulated in GB-BFN compared with
   GB-T03, respectively (Fig. [81]2B, C). At the anthesis stage, 1404
   genes were significantly up-regulated and 478 genes were significantly
   down-regulated in the fruit navel of ‘BFN’ compared with that of ‘T03’
   (Fig. [82]2B, C).

   Subsequently, independent samples were collected using the same way as
   for the RNA-seq analysis, and RT-qPCR was conducted to validate the
   DEGs results. Eight DEGs were randomly selected, and the expression
   trends of selected DEGs detected by RT-qPCR were consistent with that
   of RNA-seq data (Fig. [83]3). Compared with the ovary of ‘T03’, three
   genes were significantly up-regulated and five genes were significantly
   down-regulated in the ‘BFN’ melon. The Pearson’s correlation
   coefficient between the RNA-seq and RT-qPCR data was 0.91. These
   results indicated that the RNA-seq results were highly reliable.

   To investigate the mechanism underlying fruit navel formation, DEGs
   exhibiting consistent expression trends in both the OA and GB stages of
   ‘T03’ and ‘BFN’ melons were selected for further study. A total of 116
   DEGs were identified, comprising 54 up-regulated and 62 down-regulated
   genes in the ‘BFN’ melon compared with the ‘T03’ melon during both GB
   and OA phases (Fig. [84]2B, C and Fig. [85]4). Kyoto Encyclopedia of
   Genes and Genomes (KEGG) enrichment analysis revealed that the 54
   up-regulated genes in ‘BFN’ were significantly enriched in
   “Biosynthesis of various alkaloids”, “Biosynthesis of unsaturated fatty
   acids”, “Isoquinoline alkaloid biosynthesis”, “Glycosaminoglycan
   degradation” pathways. The 62 down-regulated genes were significantly
   enriched in “Sesquiterpenoid and triterpenoid biosynthesis”, “Circadian
   rhythm—plant” and “Galactose metabolism” pathways (Fig. [86]5A, B,
   Table S5). KEGG analysis of the 116 DEGs identified four significantly
   enriched pathways including “Sesquiterpenoid and triterpenoid
   biosynthesis”, “Circadian rhythm—plant”, “Galactose metabolism” and
   “Biosynthesis of various alkaloids” (Fig. [87]5C, Table S5). These
   pathways were hypothesized to play a critical role in the fruit navel
   development of melon.

Fig. 4.

   [88]Fig. 4
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   Expression pattern of 116 DEGs between ‘BFN’ and ‘T03’ fruit navels. A
   total of 54 and 62 genes were significantly upregulated and
   downregulated, respectively, in both the GB and OA phases of ‘BFN’
   fruits compared with ‘T03’ fruits. The color blocks represent the
   relative expression levels of genes, with high and low expression shown
   in red and blue color, respectively

Fig. 5.

   [90]Fig. 5
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   Significantly enriched (P < 0.05) KEGG terms in upregulated (A),
   downregulated (B), and all 116 DEGs (C) in the fruit navel of ‘BFN’
   fruits compared with ‘T03’ fruits

Key regulators are involved in the fruit navel formation

   Transcription factors play an important role in regulating gene
   transcription and expression by directly binding to cis-acting elements
   located in the promoter regions of target genes, thereby influencing
   various growth and developmental processes in plants [[92]27]. There
   were three (AP2/ERF, MYB and C2H2 types) and eight (AP2/ERF, MADS-box,
   homeobox domain and bZIP types) transcription factors presented in
   up-regulated and down-regulated DEGs, and their potential target genes
   were predicted from the remaining 51 up-regulated and 54 down-regulated
   DEGs. In the promoter regions of these genes, a total of 13
   up-regulated genes were found to contain the GCC (AGCCGCC) or CRT/DRE
   (A/GCCGAC) cis-acting elements, which are recognized by AP2/ERF
   transcription factors (Fig. [93]6A, Table S6) [[94]28, [95]29]. The
   promoters of 26 and 2 DEGs included the AC (ACCTACC, ACCAACC, ACCTAAC)
   and elicitor-responsive (AATTGACC) elements, which are recognized by
   MYB and C2H2 transcription factors, respectively (Fig. [96]6A, Table
   S6) [[97]30, [98]31]. The same way was conducted for the down-regulated
   DEGs. Specifically, the promoters of 21, 4, 7 and 46 DEGs contained
   cis-acting elements recognized by AP2/ERF, MADS-box (CArG, CC(A
   + T-rich)[6]GG), homeobox domain (HD-ZIP1, CAAT(A/T)ATTG) and bZIP
   (ACGT, CACGT, CACGTC, TACGTA) transcription factors, respectively
   (Fig. [99]6A, Table S6) [[100]27, [101]32, [102]33].

Fig. 6.

   [103]Fig. 6
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   Identification of key regulators involved in fruit navel formation. A
   Analysis of transcription factors in up-regulated and down-regulated
   DEGs. Orange and green color represent up-regulated and down-regulated
   transcription factors, respectively. B Promoter analyses of DEGs
   involved in the “Sesquiterpenoid and triterpenoid biosynthesis”,
   “Galactose metabolism” and “Circadian rhythm—plant” pathways

   Based on the results of KEGG analyses, two terpene cyclase/mutase
   family members (MELO3C001812 and MELO3C004329) were identified as
   participating in the “Sesquiterpenoid and triterpenoid biosynthesis”
   pathways (Table S5). The putative promoter regions of them contained
   cis-acting elements recognized by bZIP transcription factors.
   Additionally, the promoter of MELO3C004329 included cis-acting elements
   for AP2/ERF and homeobox domain transcription factors (Fig. [105]6B).
   Within the “Galactose metabolism” pathway, cis-acting elements for bZIP
   and MADS-box transcription factors were identified in putative
   promoters of MELO3C002287 (Raffinose synthase) and MELO3C025521
   (Hexosyltransferase), respectively (Fig. [106]6B, Table S5).
   Furthermore, a bZIP transcription factor (MELO3C003686) and a chalcone
   synthase (MELO3C014767) were implicated in the “Circadian rhythm—plant”
   pathway (Table S5). The promoter of MELO3C014767 contained cis-acting
   elements for bZIP, AP2/ERF and homeobox domain transcription factors
   (Fig. [107]6B). However, no cis-acting elements for AP2/ERF, MYB or
   C2H2 transcription factors were detected in the promoter region of
   MELO3C022377, a cucumber peeling cupredoxin-like gene involved in the
   “Biosynthesis of various alkaloids” pathway.

   Subsequently, the expression patterns of five putative enzyme-coding
   genes were analyzed at different fruit developmental stages prior to
   fertilization. The transcripts of two terpene cyclase/mutase genes
   (MELO3C001812 and MELO3C004329) were significantly downregulated in all
   detected stages (EGB, GB, GYB, YB and OA) of ‘BFN’ fruits compared with
   ‘T03’ fruits (Fig. [108]7A, B). In contrast, MELO3C002287 exhibited
   significant upregulation at the YB stage in the fruit navel of ‘BFN’
   compared with ‘T03’ (Fig. [109]7C). For MELO3C025521, no significant
   difference in expression levels was observed between ‘BFN’ and ‘T03’
   fruit navels at the EGB, GB and YB stages (Fig. [110]7D). Similarly,
   MELO3C014767 showed a significant increase in expression at the GYB
   stage in the fruit navel of ‘BFN’ compared with ‘T03’, while no
   significant difference was detected at the EGB and YB stages
   (Fig. [111]7E). These results suggested that MELO3C001812 and
   MELO3C004329, involved in the “Sesquiterpenoid and triterpenoid
   biosynthesis” pathway, play a critical role in fruit navel development.

Discussion

   Fruits shape and size exhibit significant variation among different
   melon varieties. Wild melons typically produce small and round fruits,
   whereas cultivated varieties display a remarkable diversity in fruits
   morphology due to continuous domestication [[112]3]. The fruit navel,
   an important component of melon appearance quality, significantly
   influences consumer preferences. However, the formation process and