Molecular and genetic characterization of a non-climacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit

Regulation of climacteric fruit ripening in melon: recent advances and future challenges

Fruit ripening is a complex and highly regulated process where tomato and strawberry have been the model species classically used for studying climacteric and non-climacteric fleshy fruit ripening types, respectively. Melon has emerged as an alternative ripening model because climacteric and non-climacteric cultivars exist, which makes it possible to dissect the regulation of ripening using a genetic approach. Several quantitative trait loci that regulate climacteric fruit ripening have been identified to date, and their combination in both climacteric and non-climacteric genetic backgrounds resulted in lines with different ripening behaviors, demonstrating that the climacteric intensity can be genetically modulated. This review discusses our current knowledge of the physiological changes observed during melon climacteric fruit ripening such as ethylene production, fruit abscission, chlorophyll degradation, firmness, and aroma, as well as their complex genetic control. From pioneer experiments in which ethylene biosynthesis was silenced, to the recent genetic edition of ripening regulators, current data suggest that the climacteric response is determined by the interaction of several loci under quantitative inheritance. The exploitation of the rich genetic diversity of melon will enable the discovery of additional genes involved in the regulation of the climacteric response, ultimately leading to breeding aromatic melon fruits with extended shelf life.

Thorough Characterization of ETHQB3.5, a QTL Involved in Melon Fruit Climacteric Behavior and Aroma Volatile Composition

The effect of the QTL involved in climacteric ripening ETHQB3.5 on the fruit VOC composition was studied using a set of Near-Isogenic Lines (NILs) containing overlapping introgressions from the Korean accession PI 16375 on the chromosome 3 in the climacteric 'Piel de Sapo' (PS) genetic background. ETHQB3.5 was mapped in an interval of 1.24 Mb that contained a NAC transcription factor. NIL fruits also showed differences in VOC composition belonging to acetate esters, non-acetate esters, and sulfur-derived families. Cosegregation of VOC composition (23 out of 48 total QTLs were mapped) and climacteric ripening was observed, suggesting a pleiotropic effect of ETHQB3.5. On the other hand, other VOCs (mainly alkanes, aldehydes, and ketones) showed a pattern of variation independent of ETHQB3.5 effects, indicating the presence of other genes controlling non-climacteric ripening VOCs. Network correlation analysis and hierarchical clustering found groups of highly correlated compounds and confirmed the involvement of the climacteric differences in compound classes and VOC differences. The modification of melon VOCs may be achieved with or without interfering with its physiological behavior, but it is likely that high relative concentrations of some type of ethylene-dependent esters could be achieved in climacteric cultivars.

Atypical Climacteric and Functional Ethylene Metabolism and Signaling During Fruit Ripening in Blueberry (Vaccinium sp.)

Climacteric fruits display an increase in respiration and ethylene production during the onset of ripening, while such changes are minimal in non-climacteric fruits. Ethylene is a primary regulator of ripening in climacteric fruits. The ripening behavior and role of ethylene in blueberry (Vaccinium sp.) ripening is controversial. This work aimed to clarify the fruit ripening behavior and the associated role of ethylene in blueberry. Southern highbush (Vaccinium corymbosum hybrids) and rabbiteye (Vaccinium ashei) blueberry displayed an increase in the rate of respiration and ethylene evolution, both reaching a maxima around the Pink and Ripe stages of fruit development, consistent with climacteric fruit ripening behavior. Increase in ethylene evolution was associated with increases in transcript abundance of its biosynthesis genes, AMINOCYCLOPROPANE CARBOXYLATE (ACC) SYNTHASE1 (ACS1) and ACC OXIDASE2 (ACO2), implicating them in developmental ethylene production during ripening. Blueberry fruit did not display autocatalytic system 2 ethylene during ripening as ACS transcript abundance and ACC concentration were not enhanced upon treatment with an ethylene-releasing compound (ethephon). However, ACO transcript abundance was enhanced in response to ethephon, suggesting that ACO was not rate-limiting. Transcript abundance of multiple genes associated with ethylene signal transduction was upregulated concomitant with developmental increase in ethylene evolution, and in response to exogenous ethylene. As these changes require ethylene signal transduction, fruit ripening in blueberry appears to involve functional ethylene signaling. Together, these data indicate that blueberry fruit display atypical climacteric ripening, characterized by a respiratory climacteric, developmentally regulated but non-autocatalytic increase in ethylene evolution, and functional ethylene signaling.

The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding

The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, France. Accessions from the collections have geographically diverse origins, are generally well-described and fixed for traits of agronomic or scientific interest and have available passport data. In addition to currently conserving over 10,000 accessions (between 900 and 3000 accessions per crop), the centre maintains scientific collections such as core collections and bi- or multi-parental populations, which have also been genotyped with SNP markers. Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality traits and environmental stress tolerance.

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines "Dulce" (reticulatus, climacteric) and "Tam Dew" (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.

Knock-Out of CmNAC-NOR Affects Melon Climacteric Fruit Ripening

Fruit ripening is an important process that affects fruit quality. A QTL in melon, ETHQV6.3, involved in climacteric ripening regulation, has been found to be encoded by CmNAC-NOR, a homologue of the tomato NOR gene. To further investigate CmNAC-NOR function, we obtained two CRISPR/Cas9-mediated mutants (nor-3 and nor-1) in the climacteric Védrantais background. nor-3, containing a 3-bp deletion altering the NAC domain A, resulted in ~8 days delay in ripening without affecting fruit quality. In contrast, the 1-bp deletion in nor-1 resulted in a fully disrupted NAC domain, which completely blocked climacteric ripening. The nor-1 fruits did not produce ethylene, no abscission layer was formed and there was no external color change. Additionally, volatile components were dramatically altered, seeds were not well developed and flesh firmness was also altered. There was a delay in fruit ripening with the nor-1 allele in heterozygosis of ~20 days. Our results provide new information regarding the function of CmNAC-NOR in melon fruit ripening, suggesting that it is a potential target for modulating shelf life in commercial climacteric melon varieties.

Application and toxicity studies of arabinoxylan and β-D-glucan stearic acid ester composite coatings in extending postharvest storage of peach

Peaches are good source of nutrients and known for their taste and aroma. The highly perishable nature of the peaches tends to decay rapidly during transportation and storage is a serious constraint for efficient transportation and storage. Therefore, the effect of arabinoxylan (AX) and β-D-glucan stearic acid ester (SABG) composite coating material was examined for the postharvest storage quality of peach under storage at 22 ± 2 °C with 85% relative humidity (RH). Both, AX-SABG and shellac (1-2%) coatings significantly reduced the change in the quality attributes like weight loss (1.2-1.4 fold), respiration rate (1.1-1.2 fold), ripening index (1.3-1.5 fold) and firmness (1.3-1.5 fold) during 6 days storage as compared to the uncoated peaches. In addition, AX-SABG (1-2%) coating was more effective in retaining aroma volatiles and reducing disease incidence compared to shellac. Further, acute and chronic toxicological studies have shown no tissue related toxicity and mortality in mice. Our results suggest that AX-SABG as an edible coating has the potential to preserve the fruit quality during 6 days storage at 22 ± 2 °C and extend the postharvest shelf life of peach during storage.

A novel introgression line collection to unravel the genetics of climacteric ripening and fruit quality in melon

Introgression lines are valuable germplasm for scientists and breeders, since they ease genetic studies such as QTL interactions and positional cloning as well as the introduction of favorable alleles into elite varieties. We developed a novel introgression line collection in melon using two commercial European varieties with different ripening behavior, the climacteric cantalupensis 'Védrantais' as recurrent parent and the non-climacteric inodorus 'Piel de Sapo' as donor parent. The collection contains 34 introgression lines, covering 99% of the donor genome. The mean introgression size is 18.16 Mb and ~ 3 lines were obtained per chromosome, on average. The high segregation of these lines for multiple fruit quality traits allowed us to identify 27 QTLs that modified sugar content, altered fruit morphology or were involved in climacteric ripening. In addition, we confirmed the genomic location of five major genes previously described, which control mainly fruit appearance, such as mottled rind and external color. Most of the QTLs had been reported before in other populations sharing parental lines, while three QTLs (EAROQP11.3, ECDQP11.2 and FIRQP4.1) were newly detected in our work. These introgression lines would be useful to perform additional genetic studies, as fine mapping and gene pyramiding, especially for important complex traits such as fruit weight and climacteric ripening.

Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species, allowing the study of the processes that regulate this complex trait with genetic approaches. We phenotyped a population of recombinant inbred lines (RILs), obtained by crossing a climacteric (Védrantais, cantalupensis type) and a non-climcteric variety (Piel de Sapo T111, inodorus type), for traits related to climacteric maturation and ethylene production. Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced, the early onset of ethylene production, and other phenotypes associated with ripening. We characterized a major QTL on chromosome 8, ETHQV8.1, which is sufficient to activate climacteric ripening, and other minor QTLs that may modulate the climacteric response. The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds. A Genome-wide association study (GWAS) using 211 accessions of the ssp. melo further identified two regions on chromosome 8 associated with the production of aromas, one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1. The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening. This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.

Spatio-temporal immunolocalization of extensin protein and hemicellulose polysaccharides during olive fruit abscission

Immunocytochemical and molecular analyses reveal that the disassembly of the cell wall may be mediated by changes in the level and subcellular location of extensin protein and hemicelluloses during olive-fruit abscission. Although cell-wall modification is believed to underlie the changes in organ abscission, information concerning the changes in cell-wall proteins and hemicellulose polysaccharides is still limited. The aim of this work was to analyze the spatio-temporal patterns of the distribution of different extensin proteins and hemicelluloses in the abscission zone (AZ) during natural ripe-fruit abscission in olive (Olea europaea L.). In this study, we employed immunogold labeling in the ripe-fruit AZ during olive AZ cell separation, using an expanded set of monoclonal antibodies that recognize different types of hemicelluloses (LM11, LM15, and LM21), callose (anti-(1,3)-β-D-glucan) and extensin (JIM19) epitopes, and transmission electron microscopy imaging. Our data demonstrate that AZ cell separation was accompanied by a loss of the JIM19 extensin epitopes and a reduction in the detection of the LM15 xyloglucan epitopes in AZ cell walls, whereas AZ cells were found to be enriched with respect to the xylan and callose levels of the cell wall during olive ripe-fruit abscission. By contrast, AZ cell-wall polysaccharide remodeling did not involve mannans. Moreover, in ripe-fruit AZ, quantitative RT-PCR analysis revealed that OeEXT1, OeEXT2, OeXTH9, and OeXTH13 genes were downregulated during abscission, whereas the expression of OeXTH1, OeXTH5, and OeXTH14 genes increased during abscission. Taken together, the results indicate that AZ cell-wall dynamics during olive ripe-fruit abscission involves extensin protein and hemicellulose modifications, as well as related expressed genes. This is the first study available demonstrating temporal degradation of extensin protein and hemicelluloses in the AZ at the subcellular level.

Transcriptome and Hormone Analyses Revealed Insights into Hormonal and Vesicle Trafficking Regulation among Olea europaea Fruit Tissues in Late Development

Fruit ripening and abscission are the results of the cell wall modification concerning different components of the signaling network. However, molecular-genetic information on the cross-talk between ripe fruit and their abscission zone (AZ) remains limited. In this study, we investigated transcriptional and hormonal changes in olive (Olea europaea L. cv Picual) pericarp and AZ tissues of fruit at the last stage of ripening, when fruit abscission occurs, to establish distinct tissue-specific expression patterns related to cell-wall modification, plant-hormone, and vesicle trafficking in combination with data on hormonal content. In this case, transcriptome profiling reveals that gene encoding members of the α-galactosidase and β-hexosaminidase families associated with up-regulation of RabB, RabD, and RabH classes of Rab-GTPases were exclusively transcribed in ripe fruit enriched in ABA, whereas genes of the arabinogalactan protein, laccase, lyase, endo-β-mannanase, ramnose synthase, and xyloglucan endotransglucosylase/hydrolase families associated with up-regulation of RabC, RabE, and RabG classes of Rab-GTPases were exclusively transcribed in AZ-enriched mainly in JA, which provide the first insights into the functional divergences among these protein families. The enrichment of these protein families in different tissues in combination with data on transcript abundance offer a tenable set of key genes of the regulatory network between olive fruit tissues in late development.

Cell Wall Composition and Ultrastructural Immunolocalization of Pectin and Arabinogalactan Protein during Olea europaea L. Fruit Abscission

Cell wall modification is integral to many plant developmental processes where cells need to separate, such as abscission. However, changes in cell wall composition during natural fruit abscission are poorly understood. In olive (Olea europaea L.), some cultivars such as 'Picual' undergo massive natural fruit abscission after fruit ripening. This study investigates the differences in cell wall polysaccharide composition and the localization of pectins and arabinogalactan protein (AGP) in the abscission zone (AZ) during cell separation to understand fruit abscission control in 'Picual' olive. To this end, immunogold labeling employing a suite of monoclonal antibodies to cell wall components (JIM13, LM5, LM6, LM19 and LM20) was investigated in olive fruit AZ. Cell wall polysaccharide extraction revealed that the AZ cell separation is related to the de-esterification and degradation of pectic polysaccharides. Moreover, ultrastructural localization showed that both esterified and unesterified homogalacturonans (HGs) localize mainly in the AZ cell walls, including the middle lamella and tricellular junction zones. Our results indicate that unesterified HGs are likely to contribute to cell separation in the olive fruit AZ. Similarly, immunogold labeling demonstrated a decrease in both galactose-rich and arabinose-rich pectins in AZ cell walls during ripe fruit abscission. In addition, AGPs were localized in the cell wall, plasma membrane and cytoplasm of AZ cells with lower levels of AGPs during ripe fruit abscission. This detailed temporal profile of the cell wall polysaccharide composition, and the pectins and AGP immunolocalization in the olive fruit AZ, offers new insights into cell wall remodeling during ripe fruit abscission.

Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo

BACKGROUND

Cucumis melo is a suitable study material for investigation of fruit ripening owing to its climacteric nature. Long non-coding RNAs have been linked to many important biological processes, such as fruit ripening, flowering time regulation, and abiotic stress responses in plants. However, knowledge of the regulatory roles of lncRNAs underlying the ripening process in C. melo are largely unknown. In this study the complete transcriptome of Cucumis melo L. cv. Hetao fruit at four developmental stages was sequenced and analyzed. The potential role of lncRNAs was predicted based on the function of differentially expressed target genes and correlated genes.

RESULTS

In total, 3857 lncRNAs were assembled and annotated, of which 1601 were differentially expressed between developmental stages. The target genes of these lncRNAs and the regulatory relationship (cis- or trans-acting) were predicted. The target genes were enriched with GO terms for biological process, such as response to auxin stimulus and hormone biosynthetic process. Enriched KEGG pathways included plant hormone signal transduction and carotenoid biosynthesis. Co-expression network construction showed that LNC_002345 and LNC_000154, which were highly expressed, might co-regulate with mutiple genes associated with auxin signal transduction and acted in the same pathways. We identified lncRNAs (LNC_000987, LNC_000693, LNC_001323, LNC_003610, LNC_001263 and LNC_003380) that were correlated with fruit ripening and the climacteric, and may participate in the regulation of ethylene biosynthesis and metabolism and the ABA signaling pathway. A number of crucial transcription factors, such as ERFs, WRKY70, NAC56, and NAC72, may also play important roles in the regulation of fruit ripening in C. melo.

CONCLUSIONS

Our results predict the regulatory functions of the lncRNAs during melon fruit development and ripening, and 142 highly expressed lncRNAs (average FPKM > 100) were identified. These lncRNAs participate in the regulation of auxin signal transduction, ethylene, sucrose biosynthesis and metabolism, the ABA signaling pathway, and transcription factors, thus regulating fruit development and ripening.

QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map

BACKGROUND

Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools.

RESULTS

In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: "Védrantais", from the cantalupensis group, and "Piel de Sapo", from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits.

CONCLUSION

Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.

The sex-determining gene CitACS4 is a pleiotropic regulator of flower and fruit development in watermelon (Citrullus lanatus)

In the species of the Cucurbitaceae family, the occurrence of separate male and female flowers in the same plant (monoecy) is controlled by an ethylene biosynthesis ACS gene, which specifically suppresses the development of stamen in the female flower. In watermelon, a mutation of loss of function in CitACS4 promotes the conversion of female into hermaphrodite flowers, and of monoecious into andromonoecious plants. We have studied whether the ethylene produced by CitACS4 enzyme could also be involved in other ethylene-regulated traits, including pistillate flowering transition and the number of female flowers per plant, the development of floral organs other than stamens, as well as fruit and seed set, and fruit development. A linkage analysis approach was performed in three independent F2 populations segregating for the two alleles of the gene (M, monoecious; m, andromonoecious), and the different traits under study. The CitACS4m allele not only cosegregated with andromonoecy, but also with earlier pistillate transition, an increased number of pistillate flowers per plant, and a slower growth and maturation of petals and carpels, which delayed anthesis time in hermaphrodite flowers. The m allele was also found to be linked to a reduced fruit set, which was not caused by a deficiency in pollination or fertilization. The gene also affected the longitudinal and transverse growth rates of the ovary and fruit, which means that fruits from andromonoecious plants (mm) were rounder than those from monoecious (MM) ones. Taken together, these data indicate that the locus defined by the ethylene biosynthesis and sex-determining gene CitACS4 acts as a pleiotropic regulator of the complete development of the pistillate flower and the earlier development of the fruit.

Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening

Fleshy fruits using ethylene to regulate ripening have developed multiple times in the history of angiosperms, presenting a clear case of convergent evolution whose molecular basis remains largely unknown. Analysis of the fruitENCODE data consisting of 361 transcriptome, 71 accessible chromatin, 147 histone and 45 DNA methylation profiles reveals three types of transcriptional feedback circuits controlling ethylene-dependent fruit ripening. These circuits are evolved from senescence or floral organ identity pathways in the ancestral angiosperms either by neofunctionalisation or repurposing pre-existing genes. The epigenome, H3K27me3 in particular, has played a conserved role in restricting ripening genes and their orthologues in dry and ethylene-independent fleshy fruits. Our findings suggest that evolution of ripening is constrained by limited hormone molecules and genetic and epigenetic materials, and whole-genome duplications have provided opportunities for plants to successfully circumvent these limitations.

Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping

Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL. Thiol acyltransferase (CmThAT1) gene was identified within the QTL interval of its product, S-methyl-thioacetate, a key component of melon fruit aroma. Metabolic activity of CmThAT1-encoded protein was validated in bacteria and in vitro. QTL analysis of flesh color intensity identified a candidate white-flesh gene (CmPPR1), one of two major loci determining fruit flesh color in melon. CmPPR1 encodes a member of the pentatricopeptide protein family, involved in processing of RNA in plastids, where carotenoid and chlorophyll pigments accumulate. Network analysis of > 12 000 eQTL mapped for > 8000 differentially expressed fruit genes supported the role of CmPPR1 in determining the expression level of plastid targeted genes. We highlight the potential of RNA-Seq-based QTL analysis of small to moderate size, advanced RIL populations for precise marker-assisted breeding and gene discovery. We provide the following resources: a RIL population genotyped with a unique set of SNP markers, confined genomic segments that harbor QTL governing 129 traits and a saturated set of melon eQTLs.

ETHQV6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor

Fruit ripening is divided into climacteric and non-climacteric types depending on the presence or absence of a transient rise in respiration rate and the production of autocatalytic ethylene. Melon is ideal for the study of fruit ripening, as both climacteric and non-climacteric varieties exist. Two introgressions of the non-climacteric accession PI 161375, encompassed in the QTLs ETHQB3.5 and ETHQV6.3, into the non-climacteric 'Piel de Sapo' background are able to induce climacteric ripening independently. We report that the gene underlying ETHQV6.3 is MELO3C016540 (CmNAC-NOR), encoding a NAC (NAM, ATAF1,2, CUC2) transcription factor that is closely related to the tomato NOR (non-ripening) gene. CmNAC-NOR was functionally validated through the identification of two TILLING lines carrying non-synonymous mutations in the conserved NAC domain region. In an otherwise highly climacteric genetic background, both mutations provoked a significant delay in the onset of fruit ripening and in the biosynthesis of ethylene. The PI 161375 allele of ETHQV6.3 is similar to that of climacteric lines of the cantalupensis type and, when introgressed into the non-climacteric 'Piel de Sapo', partially restores its climacteric ripening capacity. CmNAC-NOR is expressed in fruit flesh of both climacteric and non-climacteric lines, suggesting that the causal mutation may not be acting at the transcriptional level. The use of a comparative genetic approach in a species with both climacteric and non-climacteric ripening is a powerful strategy to dissect the complex mechanisms regulating the onset of fruit ripening.

The draft genome of MD-2 pineapple using hybrid error correction of long reads

The introduction of the elite pineapple variety, MD-2, has caused a significant market shift in the pineapple industry. Better productivity, overall increased in fruit quality and taste, resilience to chilled storage and resistance to internal browning are among the key advantages of the MD-2 as compared with its previous predecessor, the Smooth Cayenne. Here, we present the genome sequence of the MD-2 pineapple (Ananas comosus (L.) Merr.) by using the hybrid sequencing technology from two highly reputable platforms, i.e. the PacBio long sequencing reads and the accurate Illumina short reads. Our draft genome achieved 99.6% genome coverage with 27,017 predicted protein-coding genes while 45.21% of the genome was identified as repetitive elements. Furthermore, differential expression of ripening RNASeq library of pineapple fruits revealed ethylene-related transcripts, believed to be involved in regulating the process of non-climacteric pineapple fruit ripening. The MD-2 pineapple draft genome serves as an example of how a complex heterozygous genome is amenable to whole genome sequencing by using a hybrid technology that is both economical and accurate. The genome will make genomic applications more feasible as a medium to understand complex biological processes specific to pineapple.

A new genomic library of melon introgression lines in a cantaloupe genetic background for dissecting desirable agronomical traits

BACKGROUND

Genomic libraries of introgression lines (ILs) consist of collections of homozygous lines with a single chromosomal introgression from a donor genotype in a common, usually elite, genetic background, representing the whole donor genome in the full collection. Currently, the only available melon IL collection was generated using Piel de sapo (var. inodorus) as the recurrent background. ILs are not available in genetic backgrounds representing other important market class cultivars, such as the cantalupensis. The recent availability of genomic tools in melon, such as SNP collections and genetic maps, facilitates the development of such mapping populations.

RESULTS

We have developed a new genomic library of introgression lines from the Japanese cv. Ginsen Makuwa (var. makuwa) into the French Charentais-type cv. Vedrantais (var. cantalupensis) genetic background. In order to speed up the breeding program, we applied medium-throughput SNP genotyping with Sequenom MassARRAY technology in early backcross generations and High Resolution Melting in the final steps. The phenotyping of the backcross generations and of the final set of 27 ILs (averaging 1.3 introgressions/plant and covering nearly 100 % of the donor genome), in three environments, allowed the detection of stable QTLs for flowering and fruit quality traits, including some that affect fruit size in chromosomes 6 and 11, others that change fruit shape in chromosomes 7 and 11, others that change flesh color in chromosomes 2, 8 and 9, and still others that increase sucrose content and delay climacteric behavior in chromosomes 5 and 10.

CONCLUSIONS

A new melon IL collection in the Charentais genetic background has been developed. Genomic regions that consistently affect flowering and fruit quality traits have been identified, which demonstrates the suitability of this collection for dissecting complex traits in melon. Additionally, pre-breeding lines with new, commercially interesting phenotypes have been observed, including delayed climacteric ripening associated to higher sucrose levels, which is of great interest for Charentais cultivar breeding.

Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map

Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The F_ST between accessions of cantalupensis and inodorus was 0.23. The F_ST between cantalupensis and various agrestis accessions was in a range of 0.19-0.53 and between inodorus and agrestis accessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.

Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon

The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.

Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties

Background

In climacteric fruit-bearing species, the onset of fruit ripening is marked by a transient rise in respiration rate and autocatalytic ethylene production, followed by rapid deterioration in fruit quality. In non-climacteric species, there is no increase in respiration or ethylene production at the beginning or during fruit ripening. Melon is unusual in having climacteric and non-climacteric varieties, providing an interesting model system to compare both ripening types. Transcriptomic analysis of developing melon fruits from Védrantais and Dulce (climacteric) and Piel de sapo and PI 161375 (non-climacteric) varieties was performed to understand the molecular mechanisms that differentiate the two fruit ripening types.

Results

Fruits were harvested at 15, 25, 35 days after pollination and at fruit maturity. Transcript profiling was performed using an oligo-based microarray with 75 K probes. Genes linked to characteristic traits of fruit ripening were differentially expressed between climacteric and non-climacteric types, as well as several transcription factor genes and genes encoding enzymes involved in sucrose catabolism. The expression patterns of some genes in PI 161375 fruits were either intermediate between. Piel de sapo and the climacteric varieties, or more similar to the latter. PI 161375 fruits also accumulated some carotenoids, a characteristic trait of climacteric varieties.

Conclusions

Simultaneous changes in transcript abundance indicate that there is coordinated reprogramming of gene expression during fruit development and at the onset of ripening in both climacteric and non-climacteric fruits. The expression patterns of genes related to ethylene metabolism, carotenoid accumulation, cell wall integrity and transcriptional regulation varied between genotypes and was consistent with the differences in their fruit ripening characteristics. There were differences between climacteric and non-climacteric varieties in the expression of genes related to sugar metabolism suggesting that they may be potential determinants of sucrose content and post-harvest stability of sucrose levels in fruit. Several transcription factor genes were also identified that were differentially expressed in both types, implicating them in regulation of ripening behaviour. The intermediate nature of PI 161375 suggested that classification of melon fruit ripening behaviour into just two distinct types is an over-simplification, and that in reality there is a continuous spectrum of fruit ripening behaviour.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1649-3) contains supplementary material, which is available to authorized users.

Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.)

Background

A collection of 175 melon (Cucumis melo L.) accessions (including wild relatives, feral types, landraces, breeding lines and commercial cultivars) from 50 countries was selected to study the phenotypic variability for ripening behavior and sugar accumulation. The variability of single nucleotide polymorphisms (SNPs) at 53 selected candidate genes involved in sugar accumulation and fruit ripening processes was studied, as well as their association with phenotypic variation of related traits.

Results

The collection showed a strong genetic structure, defining seven groups plus a number of accessions that could not be associated to any of the groups (admixture), which fitted well with the botanical classification of melon varieties. The variability in candidate genes for ethylene, cell wall and sugar-related traits was high and similar to SNPs located in reference genes. Variability at ripening candidate genes had an important weight on the genetic stratification of melon germplasm, indicating that traditional farmers might have selected for ripening traits during cultivar diversification. A strong relationship was also found between the genetic structure and phenotypic diversity, which could hamper genetic association studies. Accessions belonging to the ameri group are the most appropriate for association analysis given the high phenotypic and molecular diversity within the group, and lack of genetic structure.

The most remarkable association was found between sugar content and SNPs in LG III, where a hotspot of sugar content QTLs has previously been defined. By studying the differences in allelic variation of SNPs within horticultural groups with specific phenotypic features, we also detected differential variation in sugar-related candidates located in LGIX and LGX, and in ripening-related candidates located in LGII and X, all in regions with previously mapped QTLs for the corresponding traits.

Conclusions

In the current study we have found an important variability at both the phenotypic and candidate gene levels for ripening behavior and sugar accumulation in melon fruit. By combination of differences in allelic diversity and association analysis, we have identified several candidate genes that may be involved in the melon phenotypic diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0183-2) contains supplementary material, which is available to authorized users.

Transcriptional control of fleshy fruit development and ripening

Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed microRNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling.

Molecular and functional characterization of CpACS27A gene reveals its involvement in monoecy instability and other associated traits in squash (Cucurbita pepo L.)

A number of Cucurbita pepo genotypes showing instable monoecy or partial andromonoecy, i.e. an incomplete conversion of female into bisexual flowers, have been detected. Given that in melon and cucumber andromonoecy is the result of reduction of ethylene production in female floral buds, caused by mutations in the ethylene biosynthesis genes CmACS7 and CsACS2; we have cloned and characterized two related C. pepo genes, CpACS27A and CpACS27B. The molecular structure of CpACS27A and its specific expression in the carpels of female flowers during earlier stages of flower development suggests that this gene is the Cucurbita ortholog of CmACS7 and CsACS2. CpACS27B is likely to be a paralogous pseudogene since it has not been found to be expressed in any of the analyzed tissues. CpACS27A was sequenced in Bolognese (Bog) and Vegetable Spaghetti (Veg), two monoecious inbred lines whose F2 was segregating for partial andromonoecy. The Bog allele of CpACS27A carried a missense mutation that resulted in a substitution of the conserved serine residue in position 176 by an alanine. Segregation analysis indicated that this mutant variant is necessary but not sufficient to confer the andromonoecious phenotype in squash. In concordance with its involvement in stamen arrest, a reduction in CpACS27A expression has been found in bisexual flower buds at earlier stages of development. This reduction in CpACS27A expression was concomitant with a downregulation of other ethylene biosynthesis and signaling genes during earlier and later stages of ovary development. The role of CpACS27A is discussed regarding the regulation of ethylene biosynthesis and signaling genes in the control of andromonoecy-associated traits, such as the delayed maturation of corolla and stigma as well as the parthenocarpic development of the fruit.

Proteomic analysis during capsicum ripening reveals differential expression of ACC oxidase isoform 4 and other candidates

Capsicum (Capsicum annuum L.) is categorised as a non-climacteric fruit that exhibits limited ethylene production during ripening and the molecular mechanisms associated with this process are poorly understood. A proteomic approach was used to identify the differentially expressed proteins during various ripening stages (Green (G), Breaker Red 1 (BR1) and Light Red (LR)) and the genes associated with their synthesis. From 2D gel electrophoresis (2DGE), seven protein spots were identified as selectively present either in G or BR1 and are involved in carbon metabolism, colour and fruit development, protein synthesis and chaperones or biosynthesis of amino acids and polyamines. One candidate of interest, 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) is known to be involved in ethylene biosynthesis and was only present in BR1 and is related to the tomato ACO isoform 4 (LeACO4) and hence named CaACO4. CaACO4 RNA expression as well as total ACO protein expression in multiple stages of ripening (G, Breaker (B), BR1, Breaker Red 2 (BR2), LR and Deep Red (DR)) corresponded to the 2DGE protein spot abundance in breaker stages. Our findings highlight the involvement of the ethylene pathway in non-climacteric fruit ripening.

Interaction analysis of grapevine MIKC(c)-type MADS transcription factors and heterologous expression of putative véraison regulators in tomato

MIKC(c)-type MADS-domain transcription factors include important regulators of floral development that interact in protein complexes to control the development of floral organs, as described by the ABC model. Members of the SEPALLATA (SEP) and AGAMOUS (AG) MADS clades include proteins involved in stamen and carpel specification and certain members of these families, such as tomato (Solanum lycopersicon) SlRIN and SlTAGL1, have been shown to regulate fruit development and ripening initiation. A number of expression studies have shown that several floral homeotic MADS genes are expressed during grapevine (Vitis vinifera) berry development, including potential homologues of these characterized ripening regulators. To gain insight into the regulation of berry development and ripening in grapevine, we studied the interactions and functions of grapevine floral homeotic MADS genes. Using the yeast 2- and 3-hybrid systems, we determined that the complexes formed during fruit development and ripening may involve several classes of floral homeotic MADS proteins. We found that a heterologously expressed grapevine SEP gene, VviSEP4, is capable of partially complementing the non-ripening phenotype of the tomato rin mutant, indicating that a role for this gene in ripening regulation may be conserved in fleshy fruit ripening. We also found that ectopic expression of a grapevine AG clade gene, VviAG1, in tomato results in the development of fleshy sepals with the chemical characteristics of tomato fruit pericarp. Additionally, we performed 2-hybrid screens on a library prepared from Pinot noir véraison-stage berry and identified proteins that may interact with the MADS factors that are expressed during berry development and that may represent regulatory functions in grape berry development.

Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening

The coexistence of both climacteric and non-climacteric genotypes and the availability of a set of genetic and genomic resources make melon a suitable model for genetic studies of fruit ripening. We have previously described a QTL, ETHQB3.5, which induces climacteric fruit ripening in the near-isogenic line (NIL) SC3-5 that harbors an introgression on linkage group (LG) III from the non-climacteric melon accession PI 161375 in the, also non-climacteric cultivar, "Piel de Sapo" genetic background. In the current study, a new major QTL, ETHQV6.3, on LG VI was detected on an additional introgression in the same NIL. These QTLs are capable, individually, of inducing climacteric ripening in the non-climacteric background, the effects of ETHQV6.3 being greater than that of ETHQB3.5. The QTLs interact epistatically, advancing the timing of ethylene biosynthesis during ripening and, therefore, the climacteric responses. ETHQV6.3 was fine-mapped to a 4.5 Mb physical region of the melon genome, probably in the centromeric region of LG VI. The results presented will be of value in the molecular identification of the gene underlying ETHQV6.3.

Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis

BACKGROUND

Mature-fruit abscission (MFA) in fleshy-fruit is a genetically controlled process with mechanisms that, contrary to immature-fruit abscission, has not been fully characterized. Here, we use pyrosequencing to characterize the transcriptomes of melon abscission zone (AZ) at three stages during AZ-cell separation in order to understand MFA control at an early stage of AZ-activation.

PRINCIPAL FINDINGS

The results show that by early induction of MFA, the melon AZ exhibits major gene induction, while by late induction of MFA, melon AZ shows major gene repression. Although some genes displayed similar regulation in both early and late induction of abscission, such as EXT1-EXT4, EGase1, IAA2, ERF1, AP2D15, FLC, MADS2, ERAF17, SAP5 and SCL13 genes, the majority had different expression patterns. This implies that time-specific events occur during MFA, and emphasizes the value of characterizing multiple time-specific abscission transcriptomes. Analysis of gene-expression from these AZs reveal that a sequential induction of cell-wall-degrading genes is associated with the upregulation of genes involved in endo and exocytosis, and a shift in plant-hormone metabolism and signaling genes during MFA. This is accompanied by transcriptional activity of small-GTPases and synthaxins together with tubulins, dynamins, V-type ATPases and kinesin-like proteins potentially involved in MFA signaling. Early events are potentially controlled by down-regulation of MADS-box, AP2/ERF and Aux/IAA transcription-factors, and up-regulation of homeobox, zinc finger, bZIP, and WRKY transcription-factors, while late events may be controlled by up-regulation of MYB transcription-factors.

SIGNIFICANCE

Overall, the data provide a comprehensive view on MFA in fleshy-fruit, identifying candidate genes and pathways associated with early induction of MFA. Our comprehensive gene-expression profile will be very useful for elucidating gene regulatory networks of the MFA in fleshy-fruit.

[Construction of a melon genetic map with fruit and seed QTLs]

A genetic map of melon was constructed using 143 F2 population developed from a cross between two distant lines Ano2 of Japan and Hami melon K413. The map contains 12 linkage groups and 142 markers, including 121 AFLPs, 16 SSRs, 3 STSs, 2 trait markers and covers 1 014.2 cM. Composite interval mapping (CIM) method was used to detect QTLs involved in melon fruit and seed traits: fruit length (FL), fruit width (FW), fruit shape (length/width, FS), centre sugar (CS), edge sugar (ES), flesh texture (FT), seed length (SL), seed width (SW), seed shape (SS), and seed weight (SW). The result showed that Flesh was located between AFLP markers NDAA and NCFA on C9. A total of 25 QTLs were detected for other traits and some QTLs were co-located with each other. The QTLs Sl5.1, Sw5.1, and Swt5.1 located on linkage C5 between NCA and N73C explained a significant portion of associated phenotypic variation (R2=17%, 19%, 23%). The allele from Ano2 obviously suppressed the length, width, and weight of melon seed; the QTLs between N73A and NFDA on C8 were involved in seed width, shape, and weight; the QTL Fs8.1 on C8 was detected using both F2 and F3 fruit data and explained a significant portion of phenotypic variation 25% and 19%. Fs8.1 showed partly dominant, and the allele from Ano2 sup-pressed elongation of fruit to form round melon. The QTLs related to centre sugar, edge sugar, and fruit texture were also detected in this research.

Polyamine-induced modulation of genes involved in ethylene biosynthesis and signalling pathways and nitric oxide production during olive mature fruit abscission

After fruit ripening, many fruit-tree species undergo massive natural fruit abscission. Olive (Olea europaea L.) is a stone-fruit with cultivars such as Picual (PIC) and Arbequina (ARB) which differ in mature fruit abscission potential. Ethylene (ET) is associated with abscission, but its role during mature fruit abscission remains largely uncharacterized. The present study investigates the possible roles of ET and polyamine (PA) during mature fruit abscission by modulating genes involved in the ET signalling and biosynthesis pathways in the abscission zone (AZ) of both cultivars. Five ET-related genes (OeACS2, OeACO2, OeCTR1, OeERS1, and OeEIL2) were isolated in the AZ and adjacent cells (AZ-AC), and their expression in various olive organs and during mature fruit abscission, in relation to interactions between ET and PA and the expression induction of these genes, was determined. OeACS2, OeACO2, and OeEIL2 were found to be the only genes that were up-regulated in association with mature fruit abscission. Using the inhibition of ET and PA biosynthesis, it is demonstrated that OeACS2 and OeEIL2 expression are under the negative control of PA while ET induces their expression in AZ-AC. Furthermore, mature fruit abscission depressed nitric oxide (NO) production present mainly in the epidermal cells and xylem of the AZ. Also, NO production was differentially responsive to ET, PA, and different inhibitors. Taken together, the results indicate that PA-dependent ET signalling and biosynthesis pathways participate, at least partially, during mature fruit abscission, and that endogenous NO and 1-aminocyclopropane-1-carboxylic acid maintain an inverse correlation, suggesting an antagonistic action of NO and ET in abscission signalling.

A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.)

BACKGROUND

A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS).

RESULTS

Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm.

CONCLUSIONS

Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

BACKGROUND

Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.

RESULT

We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.

CONCLUSION

The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.

Cloning and characterisation of two CTR1-like genes in Cucurbita pepo: regulation of their expression during male and female flower development

Ethylene is an essential regulator of flower development in Cucurbita pepo, controlling the sexual expression, and the differentiation and maturation of floral organs. To study the action mechanism of ethylene during the male and female flower development, we have identified two CTR1 homologues from C. pepo, CpCTR1 and CpCTR2, and analysed their expressions during female and male flower development and in response to external treatments with ethylene. CpCTR1 and CpCTR2 share a high homology with plant CTR1-like kinases, but differ from other related kinases such as the Arabidopsis EDR1 and the tomato LeCTR2. The C-terminal ends of both CpCTR1 and CpCTR2 have all the conserved motifs of Ser/Thr kinase domains, including the ATP-binding signature and the protein kinase active site consensus sequence, which suggests that CpCTR1 and CpCTR2 could have the same function as CTR1 in ethylene signalling. The transcripts of both genes were detected in different organs of the plant, including roots, leaves and shoots, but were mostly accumulated in mature flowers. During the development of male and female flowers, CpCTR1 and CpCTR2 expressions were concomitant with ethylene production, which indicates that both genes could be upregulated by ethylene, at least in flowers. Moreover, external treatments with ethylene, although did not alter the expression of these two genes in seedlings and leaves, were able to upregulate their expression in flowers. In the earlier stages of flower development, when ethylene production is very low, the expression of CpCTR1 and CpCTR2 is higher in male floral organs, which agrees with the role of these genes as negative regulators of ethylene signalling, and explain the lower ethylene sensitivity of male flowers in comparison with female flowers. The function of the upregulation of these two genes in later stages of female flower development, when the production of ethylene is also increased, is discussed.

The fading distinctions between classical patterns of ripening in climacteric and non-climacteric fruit and the ubiquity of ethylene-An overview

The process of fruit ripening is normally viewed distinctly in climacteric and non-climacteric fruits. But, many fruits such as guava, melon, Japanese plum, Asian pear and pepper show climacteric as well as non-climacteric behaviour depending on the cultivar or genotype. Investigations on in planta levels of CO2 and ethylene at various stages of fruits during ripening supported the role and involvement of changes in the rate of respiration and ethylene production in non-climacteric fruits such as strawberry, grapes and citrus. Non-climacteric fruits are also reported to respond to the exogenous application of ethylene. Comparative analysis of plant-attached and plant-detached fruits did not show similarity in their ripening behaviour. This disparity is being explained in view of 1. Hypothetical ripening inhibitor, 2. Differences in the production, release and endogenous levels of ethylene, 3. Sensitivity of fruits towards ethylene and 4. Variations in the gaseous microenvironment among fruits and their varieties. Detailed studies on genetic and inheritance patterns along with the application of '-omics' research indicated that ethylene-dependent and ethylene-independent pathways coexist in both climacteric and non-climacteric fruits. Auxin levels also interact with ethylene in regulating ripening. These findings therefore reveal that the classification of fruits based on climacteric rise and/or ethylene production status is not very distinct or perfect. However, presence of a characteristic rise in CO2 levels and a burst in ethylene production in some non-climacteric fruits as well as the presence of system 2 of ethylene production point to a ubiquitous role for ethylene in fruit ripening.

Engineering melon plants with improved fruit shelf life using the TILLING approach

Background

Fruit ripening and softening are key traits that have an effect on food supply, fruit nutritional value and consequently, human health. Since ethylene induces ripening of climacteric fruit, it is one of the main targets to control fruit over ripening that leads to fruit softening and deterioration. The characterization of the ethylene pathway in Arabidopsis and tomato identified key genes that control fruit ripening.

Methodology/Principal Findings

To engineer melon fruit with improved shelf-life, we conducted a translational research experiment. We set up a TILLING platform in a monoecious and climacteric melon line, cloned genes that control ethylene production and screened for induced mutations that lead to fruits with enhanced shelf life. Two missense mutations, L124F and G194D, of the ethylene biosynthetic enzyme, ACC oxidase 1, were identified and the mutant plants were characterized with respect to fruit maturation. The L124F mutation is a conservative mutation occurring away from the enzyme active site and thus was predicted to not affect ethylene production and thus fruit ripening. In contrast, G194D modification occurs in a highly conserved amino acid position predicted, by crystallographic analysis, to affect the enzymatic activity. Phenotypic analysis of the G194D mutant fruit showed complete delayed ripening and yellowing with improved shelf life and, as predicted, the L124F mutation did not have an effect.

Conclusions/Significance

We constructed a mutant collection of 4023 melon M2 families. Based on the TILLING of 11 genes, we calculated the overall mutation rate of one mutation every 573 kb and identified 8 alleles per tilled kilobase. We also identified a TILLING mutant with enhanced fruit shelf life. This work demonstrates the effectiveness of TILLING as a reverse genetics tool to improve crop species. As cucurbits are model species in different areas of plant biology, we anticipate that the developed tool will be widely exploited by the scientific community.

Mature fruit abscission is associated with up-regulation of polyamine metabolism in the olive abscission zone

This study investigates whether, and how, polyamines (PAs) are involved in mature fruit abscission of olive (Olea europaea L.). Physiological abscission was studied in relation to the activation of the abscission zone (AZ), located between fruit and peduncle, from two olive cultivars where the breakstrength profiles and the scanning electron micrographs illustrated differences in the abscission program, under natural conditions, of mature fruit. The localization and activities of diamine oxidase (DAO), polyamine oxidase (PAO) and PA biosynthetic enzymes, together with PA content were investigated in the fruit AZ during development and abscission. The activities of arginine decarboxylase and S-adenosyl-l-methionine decarboxylase in the fruit AZ were significantly increased and decreased, respectively, by mature fruit abscission, in good agreement with the rise in free putrescine (Put), and content in uncommon PAs there, such as homospermidine and cadaverine, while no significant differences in free spermidine (Spd) and spermine (Spm) contents were detected. By contrast, an abscission-induced decrease was noted in the contents of insoluble conjugated Put, Spd and Spm. The maximum activity of PAO coincided with the maximum content of Spd and Spm, and it was localized mainly in parenchyma cells of pith, while DAO was present mainly in parenchyma cells of pith and cortex as well as at the base of the vascular tissue. These results suggest a clear correlation between the PA distribution and mature fruit abscission. The regulation of PA metabolism is discussed in relation to mature fruit abscission.

A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes

A genetic map of melon enriched for fruit traits was constructed, using a recombinant inbred (RI) population developed from a cross between representatives of the two subspecies of Cucumis melo L.: PI 414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Phenotyping of 99 RI lines was conducted over three seasons in two locations in Israel and the US. The map includes 668 DNA markers (386 SSRs, 76 SNPs, six INDELs and 200 AFLPs), of which 160 were newly developed from fruit ESTs. These ESTs include candidate genes encoding for enzymes of sugar and carotenoid metabolic pathways that were cloned from melon cDNA or identified through mining of the International Cucurbit Genomics Initiative database (http://www.icugi.org/). The map covers 1,222 cM with an average of 2.672 cM between markers. In addition, a skeleton physical map was initiated and 29 melon BACs harboring fruit ESTs were localized to the 12 linkage groups of the map. Altogether, 44 fruit QTLs were identified: 25 confirming QTLs described using other populations and 19 newly described QTLs. The map includes QTLs for fruit sugar content, particularly sucrose, the major sugar affecting sweetness in melon fruit. Six QTLs interacting in an additive manner account for nearly all the difference in sugar content between the two genotypes. Three QTLs for fruit flesh color and carotenoid content were identified. Interestingly, no clear colocalization of QTLs for either sugar or carotenoid content was observed with over 40 genes encoding for enzymes involved in their metabolism. The RI population described here provides a useful resource for further genomics and metabolomics studies in melon, as well as useful markers for breeding for fruit quality.

Ethylene signal transduction elements involved in chilling injury in non-climacteric loquat fruit

Loquat (Eriobotrya japonica Lindl.) is a subtropical fruit, with some cultivars such as 'Luoyangqing' (LYQ) susceptible to chilling injury (CI), while others such as 'Baisha' (BS) are resistant. Although loquats are non-climacteric, modulation of ethylene has an effect on ripening-related post-harvest CI. Therefore the role of ethylene signalling in the development of CI was investigated in fruit of both the LYQ and BS cultivars. Three ethylene receptor genes, one CTR1-like gene, and one EIN3-like gene were isolated and characterized in ripening fruit. All of these genes were expressed differentially within and between fruit of the two cultivars. Transcripts either declined over fruit development (EjERS1a in both cultivars and EjEIL1 in LYQ) or showed an increase in the middle stages of fruit development before declining (EjETR1, EjERS1b, and EjCTR1 in both cultivars and EjEIL1 in BS). The main cultivar differences were in levels rather than in patterns of expression during post-harvest storage. EjETR1, EjCTR1, and EjEIL1 genes showed increased expression in response to low temperature and this was particularly notable for EjETR1, and EjEIL1 during CI development in LYQ fruit. The genes were also differentially responsive to ethylene treatment, 1-methycyclopropene (1-MCP) and low temperature conditioning, confirming a role for ethylene in regulation of CI in loquat fruit.

Non-climacteric fruit ripening in pepper: increased transcription of EIL-like genes normally regulated by ethylene

Only limited information has been published to date on the similarities and differences between climacteric and non-climacteric fruit ripening on transcriptional level. To address this issue, we performed a direct comparative transcriptome analysis between tomato and pepper fruits using heterologous microarray hybridization. Given the significant differences in the morphological, physiological, and biochemical characteristics of pepper and tomato fruits, the existence of extensive common regulons is surprising. This finding suggests the conservation of ripening mechanisms in climacteric and non-climacteric fruits. However, disparate expression profiles were also observed in both fruits. This study revealed that a gene that encodes an enzyme that converts lycopene to downstream carotenoids is induced in pepper but not in tomato. Most of the genes that encode ribosomal proteins are only induced in early fruit-stage pepper fruit and show rapidly diminishing expression in the later developmental stages. The genes involved in ethylene biosynthesis were not induced in pepper fruit. However, the EIL-like genes, ethylene-mediated signaling components, were induced in pepper fruit. Divergent types of transcription factors were expressed in ripening tomato and pepper fruits, suggesting they may be key factors that differentiate these distinct ripening processes.

Melon fruits: genetic diversity, physiology, and biotechnology features

Among Cucurbitaceae, Cucumis melo is one of the most important cultivated cucurbits. They are grown primarily for their fruit, which generally have a sweet aromatic flavor, with great diversity and size (50 g to 15 kg), flesh color (orange, green, white, and pink), rind color (green, yellow, white, orange, red, and gray), form (round, flat, and elongated), and dimension (4 to 200 cm). C. melo can be broken down into seven distinct types based on the previously discussed variations in the species. The melon fruits can be either climacteric or nonclimacteric, and as such, fruit can adhere to the stem or have an abscission layer where they will fall from the plant naturally at maturity. Traditional plant breeding of melons has been done for 100 years wherein plants were primarily developed as open-pollinated cultivars. More recently, in the past 30 years, melon improvement has been done by more traditional hybridization techniques. An improvement in germplasm is relatively slow and is limited by a restricted gene pool. Strong sexual incompatibility at the interspecific and intergeneric levels has restricted rapid development of new cultivars with high levels of disease resistance, insect resistance, flavor, and sweetness. In order to increase the rate and diversity of new traits in melon it would be advantageous to introduce new genes needed to enhance both melon productivity and melon fruit quality. This requires plant tissue and plant transformation techniques to introduce new or foreign genes into C. melo germplasm. In order to achieve a successful commercial application from biotechnology, a competent plant regeneration system of in vitro cultures for melon is required. More than 40 in vitro melon regeneration programs have been reported; however, regeneration of the various melon types has been highly variable and in some cases impossible. The reasons for this are still unknown, but this plays a heavy negative role on trying to use plant transformation technology to improve melon germplasm. In vitro manipulation of melon is difficult; genotypic responses to the culture method (i.e., organogenesis, somatic embryogenesis, etc.) as well as conditions for environmental and hormonal requirements for plant growth and regeneration continue to be poorly understood for developing simple in vitro procedures to culture and transform all C. melo genotypes. In many cases, this has to be done on an individual line basis. The present paper describes the various research findings related to successful approaches to plant regeneration and transgenic transformation of C. melo. It also describes potential improvement of melon to improve fruit quality characteristics and postharvest handling. Despite more than 140 transgenic melon field trials in the United States in 1996, there are still no commercial transgenic melon cultivars on the market. This may be a combination of technical or performance factors, intellectual property rights concerns, and, most likely, a lack of public acceptance. Regardless, the future for improvement of melon germplasm is bright when considering the knowledge base for both techniques and gene pools potentially useable for melon improvement.

The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds

A combined chemical, biochemical and molecular study was conducted to understand the differential accumulation of volatile sesquiterpenes in melon fruits. Sesquiterpenes were present mainly in the rinds of climacteric varieties, and a great diversity in their composition was found among varieties. Sesquiterpenes were generally absent in non-climacteric varieties. Two climacteric melon varieties, the green-fleshed 'Noy Yizre'el', and the orange-fleshed 'Dulce' were further examined. In 'Noy Yizre'el' the main sesquiterpenes accumulated are delta-cadinene, gamma-cadinene and alpha-copaene, while alpha-farnesene is the main sesquiterpene in 'Dulce'. Sesquiterpene synthase activities, mainly restricted to rinds of mature fruits, were shown to generate different sesquiterpenes in each variety according to the compositions found in rinds. EST melon database mining yielded two novel cDNAs coding for members of the Tps gene family termed CmTpsNY and CmTpsDul respectively, that are 43.2% similar. Heterologous expression in E. coli of CmTpsNY produced mainly delta-copaene, alpha-copaene, beta-caryophyllene, germacrene D, alpha-muurolene, gamma-cadinene, delta-cadinene, and alpha-cadinene, while CmTpsDul produced alpha-farnesene only. CmTpsNY was mostly expressed in 'Noy Yizre'el' rind while CmTpsDul expression was specific to 'Dulce' rind. None of these genes was expressed in rinds of the non-climacteric 'Tam Dew' cultivar. Our results indicate that different sesquiterpene synthases encoded by different members of the Tps gene family are active in melon varieties and this specificity modulates the accumulation of sesquiterpenes. The genes are differentially transcriptionally regulated during fruit development and according to variety and are likely to be associated with chemical differences responsible for the unique aromas of melon varieties.

Candidate genes and QTLs for fruit ripening and softening in melon

Different factors affect the quality of melon fruit and among them long shelf life is critical from the consumer's point of view. In melon, cultivars showing both climacteric and non-climacteric ripening types are found. In this study we have investigated climacteric ripening and fruit softening using a collection of near-isogenic lines (NILs) derived from the non-climacteric melon parental lines PI 161375 (SC) and "Piel de Sapo" (PS). Surprisingly, we found that QTL eth3.5 in NIL SC3-5b induced a climacteric-ripening phenotype with increased respiration and ethylene levels. Data suggest that the non-climacteric phenotypes from PI 161375 and "Piel de Sapo" may be the result of mutations in different genes. Several QTLs for fruit flesh firmness were also detected. Candidate genes putatively involved in ethylene regulation, biosynthesis and perception and cell wall degradation were mapped and some colocations with QTLs were observed. These results may provide additional data towards understanding of non-climacteric ripening in melon.

Cloning and characterization of a root sunflower peroxidase gene putatively involved in cell elongation

A cDNA-encoding a peroxidase (Helianthus annuus POX (HaPOX)1) was isolated and characterized from the roots of sunflower seedlings. This gene exhibited homology with other peroxidases from several higher-plant species, and its expression in the root growth was particularly abundant during cell expansion. To elucidate the precise functions of HaPOX1 in sunflower root, we examined its expression pattern in response to several plant growth regulators. Expression of HaPOX1 is down-regulated by abscisic acid (ABA), whereas indole-3-acetic acid (IAA) induced its expression. These results suggest that HaPOX1 expression is differentially regulated by phytohormonal components of signaling cascades. Since IAA appears to participate in the regulation of HaPOX1 expression, we postulate that the peroxidase encoded by HaPOX1 may be involved in the reactions that promote cell elongation during the early stage of root growth.