Post-harvest quality of melon accessions subjected to salinity.

The objective was to evaluate the behavior of melon genotypes (Cucumis melo L.) in the physical, chemical and biochemical quality of melon fruits as a function of electrical conductivity irrigation water levels (ECw). The experimental design adopted was randomized blocks in a 5 x 3 factorial scheme with five replications. The first factor was represented by five salinity levels (0.5, 1.5, 3.0, 4.5, and 6.0 dS m-1) and the second factor by accessions A35, and A24, and the hybrid Sancho. The physical, chemical and biochemical variables showed a reduction in production, with smaller fruits, with less weight, smaller cavity, with increased pulp thickness for Sancho. Vitamin C and yellow flavonoids increased indicating antioxidant power against ROS. The genotypes showed similar post-harvest behavior, however, the hybrid Sancho stood out over the others, possibly because it is an improved material. Accession A24 presented physiological and biochemical responses that classify it as intolerant.

Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops.

The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.

Bioprospecting of Sechium spp. varieties for the selection of characters with pharmacological activity.

Bioprospecting identifies new sources of compounds with actual or potential economic value that come from biodiversity. An analysis was performed regarding bioprospecting purposes in ten genotypes of Sechium spp., through a meta-analysis of 20 information sources considering different variables: five morphological, 19 biochemical, anti-proliferative activity of extracts on five malignant cell lines, and 188 polymorphic bands of amplified fragment length polymorphisms, were used in order to identify the most relevant variables for the design of genetic interbreeding. Significant relationships between morphological and biochemical characters and anti-proliferative activity in cell lines were obtained, with five principal components for principal component analysis (SAS/ETS); variables were identified with a statistical significance (< 0.7 and Pearson values ≥ 0.7), with 80.81% of the accumulation of genetic variation and 110 genetic bands. Thirty-nine (39) variables were recovered using NTSYSpc software where 30 showed a Pearson correlation (> 0.5) and nine variables (< 0.05), Finally, using a cladistics analysis approach highlighted 65 genetic bands, in addition to color of the fruit, presence of thorns, bitter flavor, piriform and oblong shape, and also content of chlorophylls a and b, presence of cucurbitacins, and the IC50 effect of chayote extracts on the four cell lines.

Non-destructive sugar content assessment of multiple cultivars of melons by dielectric properties.

BACKGROUND: Non-destructive determination of the internal quality of fruit with a thick rind and of a large size is always difficult and challenging. To investigate the feasibility of the dielectric spectroscopy technique with respect to determining the sugar content of melons during the postharvest stage, three cultivars of melon samples (160 melons for each cultivar) were used to acquire dielectric spectra over the frequency range 20-4500 MHz. The three cultivars of melons were divided separately into a calibration set and a prediction set in a ratio of 3:1 by a joint x-y distance algorithm. Partial least squares (PLS) and extreme learning machine (ELM) methods were applied to develop individual-cultivar and multi-cultivar models based on full frequencies (FFs) and effective dielectric frequencies (EDFs) selected by the successive projection algorithm (SPA). RESULTS: The results showed that ELM models demonstrated a better performance than PLS models for the same input dielectric variables. Most of the models built based on the EDFs selected by SPA had a slightly worse performance compared to those based on FFs. For both PLS and ELM methods, the models for multi-cultivars demonstrated a worse calibration and prediction performance compared to those for individual cultivars. When individual-cultivar and multi-cultivar samples were used to build sugar content determination models, the best model was FFs-ELM (Rp  = 0.887, RMSEP = 0.986), FFs-ELM (Rp  = 0.870, RMSEP = 1.028), FFs-PLS (Rp  = 0.882, RMSEP = 1.010) and FFs-ELM (Rp  = 0.849, RMSEP = 1.085) for 'Hongyanliang', 'Xinzaomi', 'Manao' and multi-cultivar melons, respectively. CONCLUSION: The present study indicates that it is possible to develop both individual-cultivar and multi-cultivar models for determining the sugar content of melons based on the dielectric spectroscopy technique. © 2021 Society of Chemical Industry.

Isolation of Cysteine-Rich Peptides from Citrullus colocynthis.

The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

Comparative Transcriptomic Analysis of Two Bottle Gourd Accessions Differing in Fruit Size.

The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in their fruit size. The average fruit length and weight of the cultivar Hang (39.48 cm/624.4 g) were higher than those of the cultivar USA (10.34 cm/152.8 g) at maturity. Transcriptome sequencing and assembly resulted in 89,347 unigenes. A total of 1250 differentially expressed genes (DEG) were found between the two cultivars, including 422 upregulated genes and 828 downregulated genes in Hang as compared to USA. Genes related to cell wall metabolism, phytohormones, cell cycle, and cell division showed significant differential expression between the two cultivars. DEGs encoding transcription factors (TF) from nine TF families were also identified. The ethylene response factor family was the most enriched among these families. Our study provides a basis for further investigations of the molecular regulation of fruit size in bottle gourd.

Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae.

Phylogenomic studies have so far mostly relied on genome skimming or target sequence capture, which suffer from representation bias and can fail to resolve relationships even with hundreds of loci. Here, we explored the potential of phylogenetic informativeness and tree confidence analyses to interpret phylogenomic datasets. We studied Cucurbitaceae because their small genome size allows cost-efficient genome skimming, and many relationships in the family remain controversial, preventing inferences on the evolution of characters such as sexual system or floral morphology. Genome skimming and PCR allowed us to retrieve the plastome, 57 single copy nuclear genes, and the nuclear ribosomal ITS from 29 species representing all but one tribe of Cucurbitaceae. Node support analyses revealed few inter-locus conflicts but a pervasive lack of phylogenetic signal among plastid loci, suggesting a fast divergence of Cucurbitaceae tribes. Data filtering based on phylogenetic informativeness and risk of homoplasy clarified tribe-level relationships, which support two independent evolutions of fringed petals in the family. Our study illustrates how formal analysis of phylogenomic data can increase our understanding of past diversification processes. Our data and results will facilitate the design of well-sampled phylogenomic studies in Cucurbitaceae and related families.

Complete chloroplast genomes of two Siraitia Merrill species: Comparative analysis, positive selection and novel molecular marker development.

Siraitia grosvenorii fruit, known as Luo-Han-Guo, has been used as a traditional Chinese medicine for many years, and mogrosides are its primary active ingredients. Unfortunately, Siraitia siamensis, its wild relative, might be misused due to its indistinguishable appearance, not only threatening the reliability of the medication but also partly exacerbating wild resource scarcity. Therefore, high-resolution genetic markers must be developed to discriminate between these species. Here, the complete chloroplast genomes of S. grosvenorii and S. siamensis were assembled and analyzed for the first time; they were 158,757 and 159,190 bp in length, respectively, and possessed conserved quadripartite circular structures. Both contained 134 annotated genes, including 8 rRNA, 37 tRNA and 89 protein-coding genes. Twenty divergences (Pi > 0.03) were found in the intergenic regions. Nine protein-coding genes, accD, atpA, atpE, atpF, clpP, ndhF, psbH, rbcL, and rpoC2, underwent selection within Cucurbitaceae. Phylogenetic relationship analysis indicated that these two species originated from the same ancestor. Finally, four pairs of molecular markers were developed to distinguish the two species. The results of this study will be beneficial for taxonomic research, identification and conservation of Siraitia Merrill wild resources in the future.

Metabolite Profiling and Quantitation of Cucurbitacins in Cucurbitaceae Plants by Liquid Chromatography coupled to Tandem Mass Spectrometry.

Cucurbitaceae is an important plant family because many of its species are consumed as food, and used in herbal medicines, cosmetics, etc. It comprises annual vines and is rich in various bioactive principles which include the cucurbitacins. These steroidal natural products, derived from the triterpene cucurbitane, are mainly the bitter principles of the family Cucurbitaceae. Their biological activities include anti-inflammatory, hepatoprotective, and anti-cancer activities. A total of 10 species belonging to 6 genera of the Cucurbitaceae family along with Cissampelos pareira (Menispermaceae) were included in this study. A comprehensive profiling of certain natural products was developed using HPLC-QTOF-MS/MS analysis and a distribution profile of several major natural products in this family was obtained. A total of 51 natural products were detected in both positive and negative ionization modes, based on accurate masses and fragmentation patterns. Along with this, quantitation of four bioactive cucurbitacins, found in various important plants of the Cucurbitaceae family, was carried out using multiple reaction monitoring (MRM) approach on an ion trap mass spectrometer. Cucurbitacin Q was found to be the most abundant in C. pareira, while Citrullus colocynthis contained all four cucurbitacins in abundant quantities. The developed quantitation method is simple, rapid, and reproducible.

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits.

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.

Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis.

BACKGROUND: The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data. RESULTS: A set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17 kb), with more rapid decay in euchromatic (8 kb) than heterochromatic (30 kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59 kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars. CONCLUSIONS: The results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons.

Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships.

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.

We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net . The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.

Susceptibility of Fourteen New Cucurbit Species to Gummy Stem Blight Caused by Stagonosporopsis citrulli Under Field Conditions.

At least 24 species of cucurbits from 13 genera are known to be susceptible to gummy stem blight, caused by three species of Stagonosporopsis. Cankers that are formed on crowns and stems play an important role in the disease cycle and the survival of the pathogen. Fourteen cucurbit species of unknown susceptibility representing 12 genera, four taxonomic tribes, and four geographic origins were inoculated with Stagonosporopsis citrulli in Charleston, SC, in spring 2015, spring 2016, and fall 2016 to evaluate their level of susceptibility to gummy stem blight and the ability of the pathogen to reproduce on crown cankers. An additional species, Cucumis melo, was included as a reference due to its known high susceptibility. Data sets of area under the disease progress curve (AUDPC) for foliar severity and crown cankers, final percentage of diseased leaf area, final percentage of plants with cankers, final percentage of plants with fruiting bodies, and rates of increase in canker incidence were analyzed to evaluate susceptibility. Results were similar for datasets of AUDPC and final ratings but there were more differences for AUDPC. In all experiments, Apodanthera sagittifolia, Ecballium elaterium, and Kedrostis leloja were at least as susceptible to foliar blight as the reference C. melo. K. leloja was as susceptible to crown cankers as C. melo in all experiments and A. sagittifolia and E. elaterium were among the species most susceptible to crown cankers in two experiments. Coccinia grandis was highly resistant to gummy stem blight and had a few cankers only in fall 2016. Sicana odorifera and Zehneria pallidinervia also consistently grouped with the most resistant species. Incidence of crown cankers on Cucumis melo and K. leloja increased at the fastest rate of all species in all experiments and had, along with E. elaterium, the highest incidence of crowns with fruiting bodies. In general, the most susceptible species also were most suitable for reproduction of the pathogen and had the fastest disease progression. The tribes Benincaseae and Cucurbiteae had consistently lower levels of foliar blight than Bryonieae and Coniandreae. The tribe Benincaseae had a consistently lower AUDPC for canker incidence than Bryonieae and Coniandreae. The species originating from Europe (E. elaterium) was consistently most susceptible to both symptoms, while African species grouped with the least susceptible species in all experiments. To the best of our knowledge, this is the first report of susceptibility to gummy stem blight of 14 species and the first report of susceptibility of the cucurbit tribes Coniandreae and Gomphogyneae. This expands the host range of Stagonosporopsis citrulli to 37 species representing 21 genera and seven tribes in the family Cucurbitaceae. This study demonstrates the importance of crown cankers as reproductive sites for S. citrulli.

Molecular modelling, dynamics simulation and characterization of antifungal chitinase from Sechium edule.

Chitinases are varied sized proteins which have the ability to degrade chitin and are present in a huge range of organisms like fungi, yeasts, arthropods, humans etc. and have been getting increased attention due to their biocontrol properties. In silico analysis sheds light on the extensive properties of this plant protein. In this paper, a particular antifungal protein Chitinase sourced from Sechium edule from East Khasi Hills, Meghalaya was characterized using an array of bioinformatics tools. The modelled protein showed conserved domains characteristic to glycosyl hydrolase, family 18 superfamily. Likewise, a part of the conserved domain area fits in with xylanase inhibitor Xip-1 and the class ΙΙΙ plant chitinases, for example, concanavalin B, hevamine, which have a GH18 area. The modelled wild type protein exhibited secondary characteristics comprising of 48.8% helix, 62.2% sheets and 13.8% turns, displaying an aliphatic index of 80.53 and instability index of 48.88 inferring upon the fact that the protein is relatively unstable without its appropriate environment. The paper functions as the first attempt to portray molecular dynamics simulation of Chitinase from Sechium edule reinforced by modelling and thorough characteristic analysis of the protein by employing parameters like Ramachandran Plot, Chou and Fasman Secondary Structure prediction, ProtParam etc. Further approaches like protein engineering and activity analysis suggested.

Effects of fungal- and plant-derived non-starch polysaccharides in macrophages

The consumption of fungal- and plant-derived non-starch polysaccharides (NSP) have been associated with reduced risk of cardiovascular diseases and cancer. In addition to promote physiochemical effects on the gastrointestinal tract and serve as substrate for the intestinal microbiota to produce short-chain fatty acids, NSP can interact with immune system cells including macrophages, which are crucial for tissue repair, lipid metabolism and host defense against foreign substances and pathogens. However, the effects of NSP in macrophages depends on their structure. Recently, it was showed that the chayote (Sechium edule) and the fungus Pleurotus albidus are promising sources of NSP with potential immunomodulatory effects in macrophages. In this study, it was explored the effects of cooking on the composition of NSP from chayote and evaluated their biological effects in macrophages. Furthermore, it was optimized a method for the extraction of mushroom NSP and characterized the structure and biological effects of NSP from P. albidus in macrophages. Results showed that the NSP from chayote pulp regulate cytokine secretion and phagocytosis by macrophages, and minor changes in composition during cooking influences their effects in macrophages. Furthermore, NSP from chayote induces cholesterol efflux and inhibits the expression of genes required for NLRP3 inflammasome activation in macrophages previously exposed to cholesterol crystals. Then, it was showed that the optimized method for the extraction of NSP from mushroom reduces by up to half the extraction time commonly required. Furthermore, results showed that P. albidus is source of easily extractable glucans with biological effects in macrophages. Results also suggest that glucans from P. albidus inhibit lipid-induced inflammation and foam-cell formation at distinct levels, with significant effects on NLRP3 inflammasome activation. Taken together, the results suggest that the benefits of chayote NSP is beyond their physical properties on the gastrointestinal tract, and that the P. albidus NSP offers potential health benefits that might be of relevance as a functional food ingredient

O consumo de polissacarídeos não-amido (PNA) de fungos e plantas tem sido associado a redução do risco de doenças cardiovasculares. Além de promoverem efeitos físicos no trato gastrointestinal e serem utilizados como substratos pela microbiota intestinal, os PNA podem interagir com células do sistema imune, como macrófagos, cruciais no reparo tecidual, metabolismo lipídico, e na defesa do organismo contra patógenos. Entretanto, os efeitos em macrófagos dependem da estrutura do PNA. Recentemente, foi observado que o chuchu (Sechium edule) e o fungo Pleurotus albidus são fontes de PNA com potencial efeito sobre macrófagos. Assim, foram avaliados os efeitos dos PNA do chuchu fresco e cozido em macrófagos. Além disso, foi otimizado um método para extração de polissacarídeos de cogumelo, e avaliada a estrutura e os efeitos biológicos dos PNA do P. albidus em macrófagos. Foi observado que os PNA do chuchu regulam a secreção de citocinas e o processo de fagocitose por macrófagos, e alterações na composição de PNA durante o cozimento tem um impacto em seus efeitos biológicos. Além disso, os PNA do chuchu induzem o efluxo de colesterol e regulam a expressão de genes necessários para a ativação do inflamassoma NLRP3 em macrófagos previamente tratados com cristais de colesterol. Também foi demonstrado que o método otimizado de extração de PNA de cogumelos reduz em até pela metade o tempo de extração normalmente empregado. Além disso, foi verificado que o P. albidus é fonte para extração de glicanos com efeitos em macrófagos. Os resultados também sugerem que os glicanos obtidos do P. albidus inibem em diferentes níveis a inflamação induzida por lipídeos e a formação de células espumosas, com efeitos significativos sobre a ativação do inflamassoma NLRP3. Tais diferenças parecem estar associadas à estrutura dos glicanos. Por fim, os resultados sugerem que os benefícios dos PNA do chuchu estão além dos seus efeitos físicos sobre o trato gastrointestinal, e que os PNA do P. albidus promovem benefícios que podem ser relevantes para explorar sua utilização como um alimento ou fonte para extração de ingredientes funcionais

The complete chloroplast genome sequence of Cucumis sativus var. Hardwickii, the wild progenitor of cultivated cucumber.

The complete chloroplast genome sequence of wild cucumber (Cucumis sativus var. hardwickii) was determined and characterized in this study. The genome is of 155 277 bp in length, containing a pair of inverted repeats regions (IRs) of 25 198 bp, which are separated by a large single-copy region of 86 618 bp and a small single-copy region of 18 263 bp. The wild cucumber chloroplast genome has 130 known genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Among these genes, 19 comprise one or two introns. There are 11 tRNA genes present in the IR of the chloroplast genome. Phylogenomic analysis showed that C. sativus var. hardwickii forms a cluster with other Cucumis species with strong bootstrap supports and is closely related to C. sativus var. sativus. This newly sequenced chloroplast genome sequence may provide useful genetic information to explore wild cucumber germplasms for cucumber breeding programs.

Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research.

In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.

Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.).

Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

Microsatellite analysis of genetic relationships between wild and cultivated melons in Northwest and Central China.

The genetic relationships between the wild and cultivated melon accessions from Northwest and Central China were dissected using 22 microsatellite markers. A total of 153 alleles, a high level of expected heterozygosity (0.669), and a low observed heterozygosity (0.156) were detected in the total panel. Differences on the allelic composition and heterozygosity levels were found between the two accession types and the wild accessions revealed a higher level of genetic diversity. The UPGMA analysis of the total panel showed that (a) most wild accessions from Northwest China were clustered independently from the cultivated accessions, and (b) the wild and cultivated accessions from Central China presented a high genetic closeness and showed a divergence from those of Northwest China. Similar positioning of the most accessions was observed with the principal coordinate analysis and STRUCTURE analysis. Pairwise FST and Nei's genetic distance quantified the genetic differentiation among the different accession types and further verified our findings. We concluded that the wild melons from Northwest China have a distinctive genetic background and could be the true wild forms, while the wild melons from Central China showed a close relationship to the local cultivars and could be a return from the cultivated melons in the same region. Our results offer an insight into the genetic resources of the main melon producing regions in China, which is essential for maximizing utilization of the traits of interest in wild melons.