Cucumis melo L. is an important horticultural crop whose cultivation is limited by environmental stresses. The Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family is central to auxin signaling and plant stress adaptation, yet its functions in melon are unclear. This study identified and characterized the Aux/IAA family in melon to elucidate its roles under stress. Twenty nine CmAux/IAA genes from the melon genome were identified, and phylogenetically classified into eight clades. Collinearity analysis indicated that segmental duplication primarily drove the family's expansion. Promoter analysis revealed cis-regulatory elements linked to development, hormone response, and stress. Transcriptome analysis showed that these genes display characteristic spatiotemporal expression patterns across tissues, and respond differentially to abiotic (salt, drought, chilling, heat, low light), and biotic (downy mildew, powdery mildew, bacterial fruit blotch) stresses. Specifically, CmAux/IAA11 was a core drought-responsive gene; CmAux/IAA26 and 28 were up-regulated under chilling; CmAux/IAA12 and 14 likely function in heat and low light adaptation, respectively. Regarding biotic stress, CmAux/IAA16 responded to downy mildew, CmAux/IAA11 may confer constitutive resistance to powdery mildew, while CmAux/IAA5 and 26 are inducible resistance genes, and elevated expression of CmAux/IAA14, 15, and 26 in susceptible cultivars suggested a negative regulatory role during bacterial fruit blotch. Our findings provide a foundation for functional studies of CmAux/IAA genes, and new insights into melon stress responses.

Spines are an important trait of cucumber fruit that affects commercial quality, smoothness, transportation, storage, and pesticide residue retention. Spine Base Size1 (CsSBS1), a C2H2 zinc-finger transcription factor, has been identified as a determinant of cucumber fruit spine size, though its molecular mechanism remains unclear. Here, our study found that exogenous ethylene treatment partially restored the small spine base phenotype in the Cssbs1 near-isogenic line (NIL) S-SB and knockout lines, while the ethylene inhibitor aminoethoxyvinylglycine reduced spine base size in wild-type L-SB plants. Further investigation revealed that CsSBS1 directly bound to the promoter of the ethylene-biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase 2 (CsACO2) and activated its expression. Silencing CsACO2 through RNA interference inhibited fruit spine base expansion in wild-type plants, whereas enhanced CsACO2 expression resulted in larger spine bases in S-SB plants. Additionally, knockout of CsTTG1 led to smaller fruit spine bases and decreased ethylene release. Genetic and biochemical analyses indicated that CsTTG1 enhances CsSBS1-mediated transcriptional activation of CsACO2. Overall, our results reveal a CsSBS1-CsTTG1 regulatory module that regulates fruit spine base size via CsACO2-mediated ethylene biosynthesis in cucumber.

Fruits are an important source of a healthy diet due to their essential nutrients for daily intake. Melon is known as a significant fruit crop of the Cucurbitaceae family based on its various dietary benefits, but its shelf life needs to be maintained for long-term usage. 1-Methylcyclopropene (1-MCP) is a cyclopropene-derived synthetic plant growth regulator (PGR) that is used for significantly delaying the ripening process and maintaining the shelf life of climacteric fruits during storage. In this study, freshly harvested melon fruits were fumigated with various concentrations (1.0 µL·L−1, 2.0 µL·L−1, and 3.0 µL·L−1) of 1-MCP treatment for 12 h (h) and stored at low temperature (8 ± 1 °C) for 30 days (d). The obtained results showed that 1-MCP fumigation coupled with low-temperature treatment maintains the postharvest shelf life of melon fruit. It was noticed that the increase in color hue (a* (red/green), b* (blue/yellow), L* (lightness)) was slowed down and the external fresh color was effectively maintained. At the same time, the firmness, soluble solids, titratable acids (TAs), and vitamin C (VC) content seemed to be maintained at a high level; weight loss and cell permeability were reduced; respiratory intensity and ethylene emission were inhibited; and the accumulation of superoxide anions and malondialdehyde (MDA) was also reduced. In addition, an upsurge in the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) was noticed in melon fruits under the combined treatment of 1-MCP and low-temperature storage as compared with the control group (CK, without treatment), indicating that 1-MCP treatment can effectively enhance the antioxidant metabolism of melon fruits during storage. Overall, we can recommend that the 3.0 µL·L−1 concentration of 1-MCP had the best effect on maintaining the internal and external quality of sweet melon fruit during storage.

Melon (Cucumis melo L.) is a globally important fruit crop, but progress in molecular breeding has been hampered by limited functional dissection of genes associated with agronomic traits. Therefore, we developed a comprehensive genome resource based on the C. melo ssp. agrestis accession 13C. This resource includes a complete telomere-to-telomere genome assembly, including accurate quantification of 45S rDNA copy number in melon, a transcriptome atlas from 31 tissue samples, a phenotypically diverse EMS-induced mutant library and a stable transformation system. By sequencing 1,125 M2 families, we identified about 660,000 variants, which cover 97.33% of the annotated gene space. Leveraging these integrated resources, we identified and functionally characterized several key genes, including CLAVATA3 INSENSITIVE RECEPTOR KINASES 2 (CmCIK2), which regulates carpel number; PARA-AMINOBENZOIC ACID SYNTHASE (CmACDS), a central regulator of folate biosynthesis; and a mutant allele of the known gynoecious gene WIP DOMAIN PROTEIN 1 (CmWIP1). In addition, we discovered a specific EMS-induced variant in the fruit ripening regulator CmNAC-NOR, and further validated its function by generating targeted mutants. The CmNAC-NOR mutants exhibited delayed fruit ripening, thus providing a valuable resource for improving ripening traits in agrestis accessions. To facilitate broader utilization, we developed the Melon Information Resource, available at https://zhanglab.qau.edu.cn/melon/index.php, an integrated platform housing 13C comprehensive genome resources and associated convenient analysis tools. This unified and accession-specific resource offers unprecedented opportunities to accelerate gene discovery and trait improvement in melon through functional genomics and molecular breeding.

The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F2 generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping. Genes controlling stripe color were located in an 85.284kb region on chromosome 9, which contained five candidate genes. Combined with parental phenotypes, chlorophyll contents of rinds and stripes were assayed. Gene sequence alignment and transcriptional level analysis of parental lines predicted Cla97C09G175170 (encoding a two-component response regulator-like protein, APRR2) as the best candidate gene for stripe color trait. Two SNPs in the ClAPRR2 coding region caused amino acid substitutions, but were not located in the conserved domain, while a 12bp insertion caused premature translation termination and a 35 amino acid deletion in the conserved domain and may have affected ClAPRR2 function in ZXG1555. Subcellular localization analysis showed that ClAPRR2 was expressed in the ZXG1555 cell membrane but was located in the nucleus and cell membrane of COS. Nucleotide polymorphisms and deletions were also detected in the promoter region between parental lines and caused cis-acting element variations. Luciferase activity suggested that promoter variations may not be the main factor in the regulation of ClAPRR2 expression.

The root-knot nematode (Meloidogyne incognita) poses a major threat to global agriculture by impairing root function, reducing nutrient uptake, and ultimately limiting seed development and crop productivity. This study investigated the molecular and metabolic defense responses of Cucumis metuliferus (prickly pear) to M. incognita infection. Gene expression and metabolic pathway reprogramming in M. incognita-infected roots were examined using integrated transcriptomics and metabolomics approaches. The identified genes were involved in stress responses and defense activation. Furthermore, metabolite profiling revealed significant shifts in secondary metabolite production, with an upregulation of defense-related compounds like jasmonic acid, salicylic acid, and prostaglandins. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis highlighted critical pathways such as biotin metabolism and nucleotide metabolism, underscoring the adaptive metabolic responses of C. metuliferus plants. GO (Gene Ontology) analysis from the integrated transcriptomics and metabolomics data highlighted significant upregulation of enzymatic pathways, transporter activities, and reorganization of cellular structures. Furthermore, KEGG pathway analysis revealed activation of secondary metabolite biosynthesis, immune-related signaling pathways, and metabolic reprogramming including increased carbon metabolism and nucleotide biosynthesis. This study provides a valuable molecular framework for breeding of M. incognita-resistant cultivars, ultimately supporting more stable seed distribution and agricultural productivity in M. incognita-prone regions.

Melon (Cucumis melo L.) is a fruit crop in the world; fruit size and fruit shape are major traits for melon quality. Fruit length is a crucial indicator affecting fruit size and shape, but few genes regulating this trait have been identified. Here, we identified the transcription factor CmFUL1 (FRUITFULL) as a candidate for regulating fruit length using genome-wide association analysis (GWAS) and phylogenetic analysis. CmFUL1 is mainly expressed during flower and ovary development by tissue-specific expression. Transcriptional analysis revealed that CmFUL1 expression levels exhibited a negative correlation with fruit length across diverse melon germplasm. Furthermore, functional characterization demonstrated that CmFUL1 acts as a negative regulator of fruit elongation, CR-Cmful1 mutants generated by CRISPR-Cas9 showing enhanced longitudinal fruits. This repressive role was evolutionarily conserved, as heterologous overexpression of CmFUL1 in tomato consistently inhibited fruit elongation. Collectively, the results suggested that CmFUL1 is a candidate gene involved in regulating fruit length in melon, and provided genetic resources for molecular breeding of melon.

Copper is crucial for plant growth and development, but excess copper can damage the leaves of melons.We constructed a genetic population using M625 (copper sensitive) and M972 (copper tolerant) materials for precise localization. Under copper stress, we quantified the levels of reactive oxygen species (ROS), antioxidant enzyme activities, hormone contents, copper accumulation, and conducted a detailed examination of leaf structural characteristics. Bulk segregant analysis sequencing (BSA-seq) revealed that the CmCt gene was located within a 1.2 Mb interval on chromosome 5. The initial localization interval was 166.86 kb, and this interval was shortened to 29.05 kb after the analysis of 1200 F2 individuals. There were a total of 6 genes in the interval, among which only MEL03C031073.2 (CmCt, Cucumis melo Copper tolerance) encodes a nonspecific lipid-transfer protein-like protein with non synonymous mutations. We further investigated and found that the gene is subcellular localized in the endoplasmic reticulum (ER), and its changes in the natural population (copper sensitivity and copper tolerance) are consistent with those of the parents. The results of the relevant physiological and biochemical indices of the parental plants subjected to copper stress (2 g/L) indicated a gradual increase in the levels of ROS, malondialdehyde (MDA), jasmonic acid (JA), and salicylic acid (SA). Concurrently, peroxidase (POD) activity exhibited an increase, while the activities of catalase (CAT) and superoxide dismutase (SOD) initially rose before subsequently declining. Moreover, there are differences in cellular structure between copper tolerant and copper sensitive melons, and copper tolerant materials exhibit stronger antioxidant defense capabilities.

Identification of global transcriptional events is crucial for genome annotation, as accurate annotation enhances the efficiency and comparability of genomic information across species. However, the annotation of transcripts in the cucumber genome remains to be improved, and many transcriptional events have not been well studied. We collected 1,904 high-quality public cucumber transcriptome samples from the National Center for Biotechnology Information (NCBI) to identify and annotate transcript isoforms in the cucumber genome. Over 44.26 billion Q30 clean reads were mapped to the cucumber genome with an average mapping rate of 92.75

Melon is a globally cultivated horticultural crop with a predominantly hybrid commercial seed market in China. Seedling morphology, particularly hypocotyl color, is a valuable trait for rapid F1 hybrid seed purity assessment. While green hypocotyls are common, white hypocotyls are rare in melon germplasm. This study identified a mutant with white hypocotyl but green leaves from the heavy ion beam mutant library. Genetic analysis revealed that a single recessive gene controlled the white hypocotyl, designated CmGhc1. A single-base deletion in the fifth exon of CmGhc1 led to a truncated CmGhc1 lacking the HTH-MYB DNA binding domain, likely affecting its transcriptional activity. CmGhc1 was localized in the nucleus, and yeast two-hybrid analysis and a dual-LUC assay demonstrated it as a transcription repressor. Furthermore, a KASP marker (hc1) was developed and verified as a functional marker for breeding white hypocotyl germplasms in melon. RNA-seq data revealed that CmGhc1 significantly affected the transcription of genes related to chlorophyll metabolism and photosynthesis in hypocotyl. In summary, these findings contribute to our understanding of chloroplast biogenesis and provide a valuable tool for melon breeding.

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and heat tolerance of XIS cucumber seedlings. Using bulked segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1, and HTT3.2, with a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, with a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb by using kompetitive allele-specific PCR (KASP) markers. Based on structural variants (SVs) and single-nucleotide polymorphisms (SNPs), we found the LTT6.1 is covered by a high divergent region including a 50 kb deletion in the XIS49 genome, which affects the gene structure of lipase abhydrolase domain containing 6 (ABHD6, Csa_6G032560). Accordingly, there is a very big difference in lipid composition, but not in other osmoprotectants like free amino acids and fatty acids, between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty-acid-related processes are major aspects in the domestication of the XIS group cucumber. LTT6.1 is a particularly special region positioned nearby lipid-related selective sweeps. These studies above suggested that the lipid-related domestication of XIS cucumbers should account for their extreme cold sensitivity.

Complete disruption of critical genes is generally accompanied by severe growth and developmental defects, which dramatically hinder its utilization in crop breeding. Identifying subtle changes, such as single-nucleotide polymorphisms (SNPs), in critical genes that specifically modulate a favorable trait is a prerequisite to fulfill breeding potential. Here, we found 2 SNPs in the E-class floral organ identity gene cucumber (Cucumis sativus) SEPALLATA2 (CsSEP2) that specifically regulate fruit length. Haplotype (HAP) 1 (8G2667A) and HAP2 (8G2667T) exist in natural populations, whereas HAP3 (8A2667T) is induced by ethyl methanesulfonate mutagenesis. Phenotypic characterization of 4 near-isogenic lines and a mutant line showed that HAP2 fruits are significantly longer than those of HAP1, and those of HAP3 are 37.8% longer than HAP2 fruit. The increasing fruit length in HAP1-3 was caused by a decreasing inhibitory effect on CRABS CLAW (CsCRC) transcription (a reported positive regulator of fruit length), resulting in enhanced cell expansion. Moreover, a 7638G/A-SNP in melon (Cucumis melo) CmSEP2 modulates fruit length in a natural melon population via the conserved SEP2-CRC module. Our findings provide a strategy for utilizing essential regulators with pleiotropic effects during crop breeding. Single-nucleotide changes in a flower development-related gene contribute to fruit length variations in cucurbits via differential inhibitory effects on transcription and cell expansion.

Fruit diameter is one of important agronomy traits that has greatly impacts fruit yield and commercial value in cucumber (Cucumis sativus L.). Hence, we preliminary mapping of fruit diameter was conducted to refine its genetic locus. In this study, to genetic mapping of QTLs that control cucumber fruit diameter, a F2 population with 120 individuals was developed by the East Asian line ‘9930’ (known as narrow fruit diameter) and the European-type cucumber ‘EU224’ (known as wide fruit diameter). Then a Genotyping-by-Sequencing (GBS)-based genetic map with 5662 markers was constructed and the total length is 656.177 cM, with average marker interval of 0.116 cM. Based on this high-density genetic map, a major QTL qfd1.1 related to fruit diameter was detected with a markedly high LOD score 4.07 located approximately 300 kb interval on Chromosome 1 (located between Chr1:1654704–1958556). To confirm qfd1.1 that detected by F2 population, we performed genetic mapping of fruit diameter with an introgression line (IL) about fruit diameter. We developed two KASP markers (FD-1 and FD-2) related to the fruit diameter. Based on this, we inserted the European cucumber EU224 into the qfd1.1 range and targeted widening the fruit diameter of the 9930 cucumber variety, further indicating that qfd1.1 is a new locus regulating the fruit diameter of cucumber. Our findings will support breeders in their research on cucumber fruit diameter.

Seed size (SS) constitutes a pivotal trait in watermelon breeding. In this study, we present findings from an examination of two watermelon accessions, namely, BW85 and F211. Seeds from BW85 exhibited a significant enlargement compared to those of F211 at 13 days after pollination (DAP), with the maximal disparity in seed length and width manifesting at 17 DAP. A comprehensive study involving both metabolic and transcriptomic analyses indicated a significant enrichment of the ubiquinone and other terpenoid-quinone biosynthesis KEGG pathways. To detect the genetic region governing seed size, a BSA-seq analysis was conducted utilizing the F2 (BW85 × F211) population, which resulted in the identification of two adjacent QTLs, namely, SS6.1 and SS6.2, located on chromosomes 6. SS6.1 spanned from Chr06:4847169 to Chr06:5163486, encompassing 33 genes, while SS6.2 ranged from Chr06:5379337 to Chr06:5419136, which included only one gene. Among these genes, 11 exhibited a significant differential expression between BW85 and F211 according to transcriptomic analysis. Notably, three genes (Cla97C06G113960, Cla97C06G114180, and Cla97C06G114000) presented a differential expression at both 13 and 17 DAP. Through annotation, Cla97C06G113960 was identified as a ubiquitin-conjugating enzyme E2, playing a role in the ubiquitin pathway that mediates seed size control. Taken together, our results provide a novel candidate gene influencing the seed size in watermelon, shedding light on the mechanism underlying seed development.

One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation.

A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.

Powdery mildew (PM), a common disease of many major crop species, including melon (Cucumis melo L.), affects plant growth and fruit quality and seriously reduces production. Using a combined morphological and molecular approach, we attribute the PM pathogen that naturally occurs in melon to Podosphaera xanthii, and specifically to physiological race 1. An investigation into the genetic basis of PM resistance in melon using the resistant accession 'PI 164637' and susceptible counterpart 'HDZ' reveals dominant inheritance of PM resistance at the seedling stage, supported by F2 and backcross population segregation ratios. Adult plant assessments indicate a major gene with an additive effect for PM resistance. Bulk segregant analysis coupled with high-throughput sequencing identified a significant quantitative trait locus on chromosome 6 that is associated with PM resistance. Genetic mapping narrowed down the candidate region to 63.5 kb using InDel molecular markers, harboring 12 candidate genes. The marker chr06_indel_5 047 127 demonstrated high accuracy in screening PM resistance in an F2 segregating population and 30 inbred lines as natural populations. Functional annotation and expression analysis of candidate genes revealed that MYB transcription factor MELO3C006700, GATA transcription factor MELO3C028829 and heparanase-like protein MELO3C006697 are promising candidate genes for PM resistance in melon. The genetic architecture underlying this resistance in melon offers valuable insights for breeding programs, and the identified markers, especially chr06_indel_5 047 127, may enable practical applications for marker-assisted selection in developing PM-resistant melon varieties.

The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A similar to 4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light. Structural variation in quantitative trait loci affects hypocotyl elongation in Xishuangbanna cucumber.

Fruit skin color is a critical agronomic trait determining fruit quality, but the mechanisms governing melon (Cucumis melo L.) fruit skin pigmentation remain inadequately characterized. We performed cytological, transcriptomic, and whole-genome bisulfite sequencing (WGBS) comparative analyses on two near-isogenic lines (NILs) at different developmental stages: the green-skinned (GS) and white-skinned (WS) melon. The enriched functions among the 536 identified differentially expressed genes (DEGs) were related to chloroplast development, pigment metabolism, and photosynthetic pathway. The genes in these pathways were downregulated in the WS line, potentially contributing to the decreased chlorophyll content and abnormal chloroplast development in WS. WGBS analysis revealed that the levels of genomic DNA methylation in WS progressively exceeded those in GS as the fruits developed. The integrated analysis of the transcriptome and methylome identified DMR-associated DEGs (CHLI, CRD1, PORA, and HCAR) involved in chlorophyll metabolism. Notably, PORA exhibited downregulated expression and was hypermethylated in WS fruits during two developmental stages, showing a coordinated expression with the chlorophyll contents in developing WS and GS fruits. Furthermore, we identified a transcription factor gene, MELO3C011576, that was closely associated with the expression of PORA and chlorophyll levels across three developmental stages in both NILs. We speculate that PORA positively regulates chlorophyll biosynthesis in the two NILs, with its expression may be co-controlled by DNA methylation and transcription factors.

To investigate the effects of LED white light treatment (LWT) on the storage quality of postharvest ‘Zaosu’ pears, as well as its role in maintaining fruit greenness and delaying senescence, pear fruits were treated with intermittent irradiation using LED white light for 12 h per day, with a light source distance of 30 ± 1 cm and a photon flux density of 151 μmoL/(m2·s) at 25 °C. The results showed that LWT preserved the postharvest quality of ‘Zaosu’ pear fruit by reducing weight loss and ascorbic acid degradation and promoting the ratio of sugar and organic acid. Meanwhile, LWT also substantially inhibited the respiration intensity and ethylene production during the storage process. Accordingly, the expressions of genes related to ethylene biosynthesis and signaling were reduced in LWT fruit. Notably, LWT retarded the decrease in chlorophyll content of fruit by increasing the activities of enzymes associated with chlorophyll synthase. Additionally, LWT also suppressed the chlorophyll degradation-related enzymes and their gene expressions in pear peel. These findings suggest that a moderate light irradiation can delay the de-green progress and benefit post-harvest storage of ‘Zaosu’ pear.