Analysis of CcGASA family members in Citrus clementina (Hort. ex Tan.) by a genome-wide approach

The Gibberellic Acid Stimulated Arabidopsis (GASA) proteins were investigated in the study to help understand their possible roles in fruit trees, particularly in Citrus. A total of 18 CcGASA proteins were identified and characterized in Citrus clementina via a genome-wide approach. It was shown that the CcGASA proteins structurally shared a conserved GASA domain but varied considerably in primary sequences and motif compositions. Thus, they could be classified into three major phylogenetic groups, G1~G3, and two groups, G1 and G3 could be further classified into subgroups. The cis- elements on all CcGASA promoters were identified and categorized, and the associated transcription factors were predicted. In addition, the possible interactions between the CcGASA proteins and other proteins were predicted. All the clues suggested that these genes should be involved in defense against biotic and abiotic stresses and in growth and development. The notion was further supported by gene expression analysis that showed these genes were more or less responsive to the treatments of plant hormones (GA₃, SA, ABA and IAA), and infections of citrus canker pathogen Xanthomonas citri. It was noted that both the segmental and the tandem duplications had played a role in the expansion of the CcGASA gene family in Citrus. Our results showed that the members of the CcGASA gene family should have structurally and functionally diverged to different degrees, and hence, the representative group members should be individually investigated to dissect their specific roles.

A Comparative Study of the Chemical Composition by SPME-GC/MS and Antiradical Activity of Less Common Citrus Species

Citrus secondary metabolites, such as terpene compounds, are very important for human health due to their bioactivity including anti-inflammatory, anti-cancer, and antioxidant effects. In this work, for the first time, the volatile chemical composition of peels and juices from four different Citrus species (C. junos, Citrus × aurantium, C. aurantium 'Bizzarria' and C. medica 'Florentina', commonly known as Yuzu jeune, Oni Yuzu, Bizzarria orange and Florence cedar, respectively) was investigated by Solid-Phase Microextraction-Gas Chromatography/Mass Spectrometry (SPME-GC/MS) technique and the antiradical activity was also examined. The results showed that limonene and γ-terpinene were the main volatile substances detected both in the juices and in the peels, followed by other minority compounds responsible for the phyto-complex of the unique aromas which characterize each individual analyzed Citrus species. Principal component analysis (PCA), performed on volatile compounds, showed both some correlation as well as a clear separation between the juice and the peel of each species. Among them, Oni Yuzu juice was found to be the richest in total polyphenols and flavonoids while its capacity to scavenge ABTS^•+ and DPPH^• radicals was similar to that of Yuzu Jeune and Bizzarria orange.

The Chemical Compositions, and Antibacterial and Antioxidant Activities of Four Types of Citrus Essential Oils

Nanfeng mandarins (Citrus reticulata Blanco cv. Kinokuni), Xunwu mandarins (Citrus reticulata Blanco), Yangshuo kumquats (Citrus japonica Thunb) and physiologically dropped navel oranges (Citrus sinensis Osbeck cv. Newhall) were used as materials to extract peel essential oils (EOs) via hydrodistillation. The chemical composition, and antibacterial and antioxidant activities of the EOs were investigated. GC-MS analysis showed that monoterpene hydrocarbons were the major components and limonene was the predominate compound for all citrus EOs. The antibacterial testing of EOs against five different bacteria (Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Salmonella typhimurium) was carried out using the filter paper method and the broth microdilution method. Kumquat EO had the best inhibitory effect on B. subtilis, E. coli and S. typhimurium with MIC (minimum inhibitory concentration) values of 1.56, 1.56 and 6.25 µL/mL, respectively. All citrus EOs showed the antioxidant activity of scavenging DPPH and ABTS free radicals in a dose-dependent manner. Nanfeng mandarin EO presented the best antioxidant activity, with IC₅₀ values of 15.20 mg/mL for the DPPH assay and 0.80 mg/mL for the ABTS assay. The results also showed that the antibacterial activities of EOs might not be related to their antioxidant activities.

Volatilomic Profiling of Citrus Juices by Dual-Detection HS-GC-MS-IMS and Machine Learning-An Alternative Authentication Approach

A prototype dual-detection headspace-gas chromatography-mass spectrometry-ion mobility spectrometry (HS-GC-MS-IMS) system was used for the analysis of the volatile profile of 47 Citrus juices including grapefruit, blood orange, and common sweet orange juices without requiring any sample pretreatment. Next to reduced measurement times, substance identification could be improved substantially in case of co-elution by considering the characteristic drift times and m/z ratios obtained by IMS and MS. To discriminate the volatile profiles of the different juice types, extensive data analysis was performed with both datasets, respectively. By principal component analysis (PCA), a distinct separation between grapefruit and orange juices was observed. While in the IMS data grapefruit juices not from fruit juice concentrate could be separated from grapefruit juices reconstituted from fruit juice concentrate, in the MS data, the blood orange juices could be differentiated from the orange juices. This observation leads to the assumption that the IMS and MS data contain different information about the composition of the volatile profile. Subsequently, linear discriminant analysis (LDA), support vector machines (SVM), and the k-nearest-neighbor (kNN) algorithm were applied to the PCA data as supervised classification methods. Best results were obtained by LDA after repeated cross-validation for both datasets, with an overall classification and prediction ability of 96.9 and 91.5% for the IMS data and 94.5 and 87.9% for the MS data, respectively, which confirms the results obtained by PCA. Additional data fusion could not generally improve the model prediction ability compared to the single data, but rather for certain juice classes. Consequently, depending on the juice class, the most suitable dataset should be considered for the prediction of the class membership. This volatilomic approach based on the dual detection by HS-GC-MS-IMS and machine learning tools represent a simple and promising alternative for future authenticity control of Citrus juices.

Identification of the 'Haryejosaeng' mandarin cultivar by multiplex PCR-based SNP genotyping

Most satsuma mandarin (Citrus unshiu Marc.) cultivars are difficult to identify in the seedling stage based only on morphological traits. Therefore, simple polymerase chain reaction (PCR)-based single-nucleotide polymorphism (SNP) markers were developed to specifically and rapidly distinguish the 'Haryejosaeng' cultivar, which is generally supplied to breeders of other satsuma mandarin cultivars. SNP markers were verified using high-resolution melt (HRM)-specific primers. PCR was performed to distinguish 'Haryejosaeng' from eight other satsuma mandarin cultivars using six SNP markers (P1-P6) specific for 'Haryejosaeng', with one negative control SNP primer pair. The best results were obtained using three SNP markers (P1, P2, and P5). In the multiplex PCR, markers P1, P2, and P5 yielded 165-, 150-, and 526-base pair amplicons, respectively, in 'Haryejosaeng', distinguishing it from other satsuma mandarin cultivars. The selected SNP markers were validated by HRM with HRM-specific primers. The multiplex PCR with P1/P5 and P2/P5 also identified 'Haryejosaeng' obtained from a farm growing 17 different cultivars of satsuma mandarin. Specific SNP molecular markers were determined for accurately identifying the 'Haryejosaeng' cultivar by multiplex PCR to save the time and costs associated with its supply to breeders of satsuma mandarin.

Characterization of Volatile Organic Compounds of Healthy and Huanglongbing-Infected Navel Orange and Pomelo Leaves by HS-GC-IMS

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is the only natural vector of bacteria responsible for Huanglongbing (HLB), a worldwide destructive disease of citrus. ACP reproduces and develops only on the young leaves of its rutaceous host plants. Olfactory stimuli emitted by young leaves may play an important role in ACP control and HLB detection. In this study, volatile organic compounds (VOCs) from healthy and HLB-infected young leaves of navel orange and pomelo were analyzed by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). A total of 36 compounds (including dimers or polymers) were identified and quantified from orange and 10 from pomelo leaves. Some compounds showed significant differences in signal intensity between healthy and HLB-infected leaves and may constitute possible indicators for HLB infection. Principal component analysis (PCA) clearly discriminated healthy and HLB-infected leaves in both orange and pomelo. HS-GC-IMS was an effective method to identify VOCs from leaves. This study may help develop new methods for detection of HLB or find new attractants or repellents of ACP for prevention of HLB.

Storage Behavior and Cryopreservation of Citrus cavaleriei, an Endangered, Cold-resistant Species of Northeast India with Exceptionally Large Seeds

BACKGROUND

Ichang Papeda (Citrus cavaleriei H.Lév. ex Cavalerie) is a wild and endangered species of NE India that requires urgent preservation of its genetic resources.

OBJECTIVE

To characterize the storage physiology of the seeds and to cryopreserve the embryo and embryonic axis (EA).

MATERIALS AND METHODS

The morphology and storage physiology of the seeds were determined, and the cryopreservation of embryos and EA attempted using various techniques (viz., air desiccation-freezing, vitrification and encapsulation-dehydration).

RESULTS

Weighing up to 4 g, seeds of Citrus cavaleriei are the largest known in the genus. Based on estimates using the seed coat ratio - seed mass (SCR-SM) model there was a very high probability of seed desiccation intolerance, which was validated physiologically; seeds lost vigour on drying below 30% moisture content (MC) and no seeds germinating after drying to <12% MC. Embryos and EAs could be air dried to 25-30% MC and cryopreserved with c. 50% survival. In contrast, EA optimally exposed to PVS2 (20 min) or encapsulated, sucrose pretreated (0.5 M, 24 h) and dehydrated (6 h) had c. 40% survival after cryopreservation.

CONCLUSION

Citrus cavaleriei produces large, recalcitrant seeds that can, nevertheless, be cryopreserved as embryos or isolated EA after air drying to c. 25-30% MC; encapsulation-dehydration and vitrification provide alternative options for the cryopreservation of EA.

A novel fluorescence sensing strategy based on nanoparticles combined with spectral splicing and chemometrics for the recognition of Citrus reticulata 'Chachi' and its storage year

BACKGROUND

The fluorescence sensing method has been increasingly applied in food quality control because it is fast and sensitive. However, its application in quality evaluation is challenging. Using Citri Reticulatae Pericarpium (CRP; dried mandarin orange peel) as an example, we developed a simple and low-cost fluorescence sensing strategy based on nanoparticles combined with spectral splicing and chemometrics for quality evaluation. This method can recognize Citrus reticulata 'Chachi' (CRC) from other CRP cultivars and further identify the storage year.

RESULTS

Nanogold particles and cadmium telluride quantum dots were selected as nanosensors and mixed with aqueous extracts of CRP separately to produce fluorescence quenching spectra. Then, a simple spectral splicing procedure was applied to obtain spliced spectra comprising different combinations of the self-fluorescence and fluorescence quenching spectra of CRP samples. With the aid of partial least-squares discriminant analysis, the new strategy achieved recognition rates of 100% in distinguishing CRC samples from other CRP samples, as well as recognition rates of 100% for the training set and 98.04% for the prediction set in the discrimination of the storage year of CRC. The recognition mechanism is dominated by interactions between the nanoparticles and the fluorescent components in the CRP samples, but other components also have concurrent effects.

CONCLUSIONS

This novel fluorescence sensing strategy not only provides a new tool for the quality evaluation of CRC but also has good prospects for the authentication and traceability of other foods and herbs. Crucially, the developed method is convenient, simple and effective. © 2020 Society of Chemical Industry.

Mineral Content of the Pulp and Peel of Various Citrus Fruit Cultivars

The aim of the study was to compare the mineral content between the peel and the pulp of citrus fruits and to determine which citrus fruit, among orange (Citrus sinensis), pomelo (Citrus maxima), mandarin (Citrus reticulata Blanco), lemon (Citrus limon), key lime (Citrus aurantifolia), and red, yellow, or green grapefruit (Citrus paradisi), is the richest in minerals. The research material consisted of fresh citrus fruits belonging to the genus Citrus L in the family Rutaceae. The fruits were purchased at a supermarket at one time. To prepare laboratory samples, each fruit was cut in half, and one half was homogenized, treating the sample as a whole (peel + flesh), while the other half was peeled and the pulp (F) and peel (P) were homogenized separately. To determine the content of minerals (Na⁺, K⁺, Ca⁺², Mg⁺², Fe⁺², Zn⁺², Cu⁺², Mn⁺², and Se⁺²), the samples were mineralized and analyzed using an Analytik Jena PlasmaQuant PQ 9000 inductively coupled plasma optical emission spectrometer. The content of macro- and micronutrients in the peel of most of the fruits far exceeded their quantity in the pulp. Oranges and pomelos are the fruits richest in iron and copper, so they could be recommended in cases such as hemoglobin production disorders resulting from a deficiency of these elements. Oranges can additionally enrich the body with potassium, phosphorus, and manganese, while lime can be a source of calcium, zinc, sodium, and especially potassium. It should also be noted that all citrus fruits are a very valuable source of potassium, which is needed to ensure the water and electrolyte balance.

Genetic, morphological and chemical investigations reveal the genetic origin of Pompia (C. medica tuberosa Risso & Poiteau) - An old endemic Sardinian citrus fruit

Citrus fruits have been introduced to the Mediterranean area from Asia for centuries and spontaneous crosses have generated several hybrid forms, some of which have had agricultural or industrial success while others have remained niche food or ornamental products, or have disappeared. Pompia (C. medica tuberosa Risso & Poiteau) is an old endemic citrus fruit from Sardinia of unknown genetic origin. Initial phenotypic and molecular characterizations revealed a high degree of similarity with lemon (C. limon (L.) Burm.) and citron (C. medica L.). To identify the ancestors of Pompia, 70 citrus species of the Citrus genus were genotyped with 36 codominant molecular markers (SSR and InDel) of nuclear and cytoplasmic genomes. Diversity analysis and allelic comparisons between each citrus species at each locus indicated that Pompia resembles lemon and limonette of Marrakech, i.e. the result of a cross between sour orange (C. aurantium L.) and citron, where citron was the pollinator. Two Italian citron varieties were identified as potential male parents, i.e. Diamante and Common Poncire. However, we were unable to differentiate varieties of sour oranges because varietal diversification in this horticultural group resulted from DNA sequence variations that SSR or InDel markers could not reveal. Rhob el Arsa and Poncire de Collioure were found to be two synonyms of Pompia. Pompia appeared to be equally distinct from citron, lemon and sour orange based on the overall analysis of the fruit, leaf and seed phenotype, and juice chemical composition. At the leaf level, the Pompia essential oil (EO) composition is close to that of citron whereas the zest is much closer to that of sour orange.

Lignin Accumulation in Three Pumelo Cultivars in Association with Sucrose and Energy Depletion

Lignification, which occurs in many horticultural fruit and vegetables, brings about undesirable texture and unfavorable consumer preference. However, this problem has rarely been studied. In this work, three pumelo cultivars cvs "Hongroumiyou" (HR), "Bairoumiyou" (BR), and "Huangroumiyou" (HuR) were stored at 25 °C for 90 days, and juice sacs were sampled to explore the lignin accumulation and its relationship to sucrose and energy depletion were investigated. The results displayed that HuR contained lower sucrose content, lower ATP level, but higher lignin content compared to BR and HR during postharvest storage, indicating that the sequence according to storage resistance on the basis of lignin content is as follows: HuR < BR < HR. Furthermore, sucrose degradation attributed to enhanced activities of neutral invertase (NI), soluble acid invertase (S-AI), cell wall-bound invertase (B-AI), and energy deficit on account of declined ATP level, showed significantly negative correlation with lignin accumulation, suggesting that lignin accumulation occurrence could induce sucrose degradation and energy deficit during postharvest storage. Additionally, higher activities of phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD) could accelerate lignin synthesis and resulted in lignin accumulation during postharvest pumelo storage.

LOCAL regression applied to a citrus multispecies library to assess chemical quality parameters using near infrared spectroscopy

The non-destructive on-tree measurement of the chemical quality attributes of fruits belonging to the Citrus genus using rapid spectral sensors is of vital interest to citrus growers, allowing them to carry out a selective harvest of any species of Citrus fruit. With this objective, the viability of using of a handheld portable near infrared spectroscopy (NIRS) instrument to predict soluble solid content (SSC), pH, titratable acidity (TA), maturity index and BrimA, in order to measure the optimum harvest time in a group made up of 608 samples belonging to the Citrus genus (378 oranges and 230 mandarins) was evaluated. For each of the parameters analysed, both non-linear regression (LOCAL algorithm) and linear regression (Modified Partial Least Squares, MPLS) strategies were designed and compared. The use of the LOCAL algorithm in the sample group of oranges and mandarins for all the parameters analysed allowed to obtain more robust models than those obtained with MPLS regression, and it could also be extended more easily when routinely applied. The results confirm that NIRS technology combined with non-linear regression strategies such as the LOCAL algorithm can indeed respond to the needs of the Citrus growers and help them to set the optimum harvest time, in this case of oranges and mandarins, by predicting the chemical quality parameters in situ.

Evolutionary dynamics of lincRNA transcription in nine citrus species

Long intergenic non-coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large-scale comparative study of lincRNA transcription patterns in nine citrus species. By strand-specific RNA-sequencing, we identified 18 075 lincRNAs (14 575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8-97.6% of sweet orange (Citrus sinensis) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5-28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6-84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher expression levels and lower tissue specificity than species-specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo (Citrus grandis), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi-miR166c, and two lincRNAs that act as a precursor and target of csi-miR166c, respectively. These lincRNAs together with csi-miR166c could form an eTM166-miR166c-targeted lincRNA regulatory network that possibly affects citrus fruit development.

Characterisation and classification of Citri Reticulatae Pericarpium varieties based on UHPLC-Q-TOF-MS/MS combined with multivariate statistical analyses

INTRODUCTION

Citri Reticulatae Pericarpium (CRP), comprising dried pericarps of Citrus reticulata Blanco and its cultivars, is popularly used for its great medicinal and dietary values. Generally, the pericarps from C. reticulate "Chachi" ("Guangchenpi" in Chinese, GCP) is considered to have superior qualities and merit premium price compared with CRP derived from other cultivars (collectively called "Chenpi" in Chinese, CP). Since its multiple origins and derived economic adulteration, it is significant to systematically compare the chemical profiles of different CRP varieties.

OBJECTIVE

The main objective of this work was to identify the chemical profiles of CRP from different varieties and find out potential chemical markers for differentiating GCP and CP.

METHODS

In the present study, a total of 42 CRP samples from 10 varieties (including GCP and CP) were analysed by ultra-high performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry (UHPLC-Q-TOF-MS/MS) for chemical profiling. Obtained MS/MS data were further employed in multivariate statistical methods to screen the main compounds which contributed to the characterisation and classification of CRP.

RESULTS

As a result, 73 compounds (mainly flavonoids) were identified or tentatively characterised in these CRP samples. Based on the obtained chemical profiles data, GCP and CP samples could be easily discriminated from each other by statistical analyses. Moreover, seven compounds were selected as having the most discriminating features which contributed to the classification of CRP.

CONCLUSION

This work obtains a better understanding of the chemical profiles of different CRP varieties and provides a practical strategy for the authentication of GCP and CP.

Essential Oil Composition and Biological Activity of "Pompia", a Sardinian Citrus Ecotype

Pompia is a Sardinian citrus ecotype whose botanical classification is still being debated. In the present study, the composition of Pompia peel essential oil (EO) is reported for the first time, along with that of the leaf EO, as a phytochemical contribution to the classification of this ecotype. The peel EO was tested for its antioxidant ability (with both the 2,2-diphenyl-1-picarylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) assays). Moreover, its antimicrobial activities were tested for the first time on dermatophytes (Microsporum canis, Microsporum gypseum, and Trichophyton mentagrophytes), on potentially toxigenic fungi (Fusarium solani, Aspergillus flavus, and Aspergillus niger) as well on bacteria (Escherichia coli, Staphylococcus aureus, and Staphylococcus pseudointermedius). The dominant abundance of limonene in the peel EO seems to distinguish Pompia from the Citrus spp. to which it had previously been associated. It lacks γ-terpinene, relevant in Citrus medica EO. Its relative content of α- and β-pinene is lower than 0.5%, in contrast to Citrus limon peel EO. Pompia peel and leaf EOs did not show significant amounts of linalool and linalyl acetate, which are typically found in Citrus aurantium. Pompia peel EO antioxidant activity was weak, possibly because of its lack of γ-terpinene. Moreover, it did not exert any antimicrobial effects either towards the tested bacteria strains, or to dermatophytes and environmental fungi.

Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus clementina Hort. Ex Tan. and its taxonomic implications

BACKGROUND

Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine.

RESULTS

A graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)₃ was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin.

CONCLUSIONS

The composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.

SLAF-Based Construction of a High-Density Genetic Map and Its Application in QTL Mapping of Carotenoids Content in Citrus Fruit

Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3817 molecular markers using specific locus amplified fragment (SLAF) sequencing from a C. reticulata × P. trifoliata F₁ pseudotestcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6, and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL colocalizations for multiple carotenoid constituents were observed on Chr 2, 3, and 9, one of which was located on Chr2:34,654,608-35430715 accounted for 20.1-25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin, and total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.

Comprehensive Metabolomics Analysis of Mandarins ( Citrus reticulata) as a Tool for Variety, Rootstock, and Grove Discrimination

The metabolite profile responsible for the quality of mandarin fruit is influenced by preharvest factors including genotype, rootstock, grove location, etc. In this paper, mandarin varieties were discriminated using metabolomics. Additionally, effects on metabolic profiles due to grove location and rootstock differences were also investigated. Results revealed that mandarin varieties could be differentiated using the metabolite profile, while the compositions of flavonoids have the potential for variety differentiation. With regard to fruits of the same variety, grove location might determine the overall profile of metabolites, whereas rootstock possibly affected composition of secondary metabolites. Pathway enrichment analysis demonstrated that biosynthesis pathways of terpenoids and steroids involving limonene and linalool were highly influenced by variety diversity. Moreover, the flavonoid biosynthesis pathway, involving hesperetin, naringenin, eriodictyol, and taxifolin, was indicated to have a close relationship with rootstock differentiation. This study provides useful and important information with depth for breeding and optimizing preharvest practices.

Genome of Wild Mandarin and Domestication History of Mandarin

Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.

Citrus species and hybrids depicted by near- and mid-infrared spectroscopy

BACKGROUND

Citrus trees are among the most cultivated plants in the world, with a high economic impact. The wide sexual compatibility among relatives gave rise to a large number of hybrids that are difficult to discriminate. This work sought to explore the ability of infrared spectroscopy to discriminate among Citrus species and/or hybrids and to contribute to the elucidation of its relatedness.

RESULTS

Adult leaves of 18 distinct Citrus plants were included in this work. Near- and mid-infrared (NIR and FTIR) spectra were acquired from leaves after harvesting and a drying period of 1 month. Spectra were modelled by principal component analysis and partial least squares discriminant analysis. Both techniques revealed a high discrimination potential (78.5-95.9%), being the best results achieved with NIR spectroscopy and air-dried leaves (95.9%).

CONCLUSION

Infrared spectroscopy was able to successfully discriminate several Citrus species and/or hybrids. Our results contributed also to enhance insights regarding the studied Citrus species and/or hybrids. Despite the benefit of including additional samples, the results herein obtained clearly pointed infrared spectroscopy as a reliable technique for Citrus species and/or hybrid discrimination. © 2018 Society of Chemical Industry.

Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms

Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.

Immunoblotting Quantification Approach for Identifying Potential Hypoallergenic Citrus Cultivars

The inherent allergens of citrus fruits, such as Cit s 1, Cit s 2, Cit s 3 can cause allergic reactions. A better understanding of the genetic factors (cultivar to cultivar) affecting the allergenic potential of citrus fruits would be beneficial for further identification of hypoallergenic genotypes. In the present study, an immunoblotting quantification approach was adopted to assess the potential allergenicity of 21 citrus cultivars, including nine subgroups (tangerine, satsuma, orange, pummelo, grapefruit, lemon, kumquat, tangor, and tangelo). To prepare highly sensitive and specific rabbit polyclonal antibodies, antigenicity of purified rCit s 1.01, rCit s 2.01, and rCit s 3.01 peptides were enhanced with high epitope density in a single protein molecule. The data integration of three citrus allergen quantifications demonstrated that the four pummelo cultivars (Kao Phuang Pummelo, Wanbai Pummelo, Shatian Pummelo, and Guanxi Pummelo) were potential hypoallergenic, compared with other 8 subgroups. Moreover, the immunological analyses with sera of allergic subjects revealed that Shatian Pummelo and Guanxi Pummelo showed the lowest immunoreactivity in 8 representative citrus cultivars. These potential hypoallergenic genotypes are of great significance to not only allergic consumers but also citrus breeders in the genetic improvement of hypoallergenic citrus as breeding resources.

Comparative analysis of juice volatiles in selected mandarins, mandarin relatives and other citrus genotypes

BACKGROUND

Citrus fruit flavor is an important attribute prioritized in variety improvement. The present study compared juice volatiles compositions from 13 selected citrus genotypes, including six mandarins (Citrus reticulata), three sour oranges (Citrus aurantium), one blood orange (Citrus sinensis), one lime (Citrus limonia), one Clementine (Citrus clementina) and one satsuma (Citrus unshiu).

RESULTS

Large differences were observed with respect to volatile compositions among the citrus genotypes. 'Goutou' sour orange contained the greatest number of volatile compounds and the largest volatile production level. 'Ponkan' mandarin had the smallest number of volatiles and 'Owari' satsuma yielded the lowest volatile production level. 'Goutou' sour orange and 'Moro' blood orange were clearly distinguished from other citrus genotypes based on the analysis of volatile compositions, even though they were assigned into one single group with two other sour oranges by the molecular marker profiles.

CONCLUSIONS

The clustering analysis based on the aroma volatile compositions was able to differentiate mandarin varieties and natural sub-groups, and was also supported by the molecular marker study. The gas chromatography-mass spectrometry analysis of citrus juice aroma volatiles can be used as a tool to distinguish citrus genotypes and assist in the assessment of future citrus breeding programs. The aroma volatile profiles of the different citrus genotypes and inter-relationships detected among volatile compounds and among citrus genotypes will provide fundamental information on the development of marker-assisted selection in citrus breeding. © 2017 Society of Chemical Industry.

Chemotaxonomic Classification Applied to the Identification of Two Closely-Related Citrus TCMs Using UPLC-Q-TOF-MS-Based Metabolomics

This manuscript elaborates on the establishment of a chemotaxonomic classification strategy for closely-related Citrus fruits in Traditional Chinese Medicines (TCMs). UPLC-Q-TOF-MS-based metabolomics was applied to depict the variable chemotaxonomic markers and elucidate the metabolic mechanism of Citrus TCMs from different species and at different ripening stages. Metabolomics can capture a comprehensive analysis of small molecule metabolites and can provide a powerful approach to establish metabolic profiling, creating a bridge between genotype and phenotype. To further investigate the different metabolites in four closely-related Citrus TCMs, non-targeted metabolite profiling analysis was employed as an efficient technique to profile the primary and secondary metabolites. The results presented in this manuscript indicate that primary metabolites enable the discrimination of species, whereas secondary metabolites are associated with species and the ripening process. In addition, analysis of the biosynthetic pathway highlighted that the syntheses of flavone and flavone glycosides are deeply affected in Citrus ripening stages. Ultimately, this work might provide a feasible strategy for the authentication of Citrus fruits from different species and ripening stages and facilitate a better understanding of their different medicinal uses.

Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits

The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.

Antioxidant Capacity, Anticancer Ability and Flavonoids Composition of 35 Citrus (Citrus reticulata Blanco) Varieties

Citrus (Citrus reticulate Blanco) is one of the most commonly consumed and widely distributed fruit in the world, which is possessing extensive bioactivities. Present study aimed to fully understand the flavonoids compositions, antioxidant capacities and in vitro anticancer abilities of different citrus resources. Citrus fruits of 35 varieties belonging to 5 types (pummelos, oranges, tangerines, mandarins and hybrids) were collected. Combining li quid chromatography combined with electrospray ionization mass spectrometry (LC-ESI-MS/MS) and ultra-performance liquid chromatography combined with diode array detector (UPLC-DAD), a total of 39 flavonoid compounds were identified, including 4 flavones, 9 flavanones and 26 polymethoxylated flavonoids (PMFs). Each citrus fruit was examined and compared by 4 parts, flavedo, albedo, segment membrane and juice sacs. The juice sacs had the lowest total phenolics, following by the segment membrane. Four antioxidant traits including 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, ferric reducing antioxidant power (FRAP), oxygen radical absorbance capacity (ORAC) and cupric reducing antioxidant capacity (CUPRAC) were applied for the antioxidant capacities evaluation. Three gastric cancer cell lines, SGC-7901, BGC-823 and AGS were applied for the cytotoxicity evaluation. According to the results of correlation analysis, phenolics compounds might be the main contributor to the antioxidant activity of citrus extracts, while PMFs existing only in the flavedo might be closely related to the gastric cancer cell line cytotoxicity of citrus extracts. The results of present study might provide a theoretical guidance for the utilization of citrus resources.

Matrix Effects and Interferences of Different Citrus Fruit Coextractives in Pesticide Residue Analysis Using Ultrahigh-Performance Liquid Chromatography-High-Resolution Mass Spectrometry

The matrix effects of ethyl acetate extracts from seven different citrus fruits on the determination of 80 pesticide residues using liquid chromatography coupled to high-resolution time-of-flight mass spectrometry (UHPLC-(ESI)-HR-TOF) at 4 GHz resolution mode were studied. Only 20% of the evaluated pesticides showed noticeable matrix effects (ME) due to coelution with natural products between t_R = 3 and 11 min. Principal component analysis (PCA) of the detected coextractives grouped the mandarins and the orange varieties, but separated lemon, oranges, and mandarins from each other. Matrix effects were different among species but similar between varieties, forcing the determination of pesticide residues through matrix-matched calibration curves with the same fruit. Twenty-three natural products (synephrine, naringin, poncirin, glycosides of hesperitin, limonin, nomilin, and a few fatty acids, among others) were identified in the analyzed extracts. Twelve of the identified compounds coeluted with 28 of the pesticides under study, causing different matrix effects.

Changes in Anthocyanin Production during Domestication of Citrus

Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

Analysis of Genetic Variation in Brevipalpus yothersi (Acari: Tenuipalpidae) Populations from Four Species of Citrus Host Plants

We studied species diversity and genetic variation among populations of Brevipalpus mites from four species of citrus host plants. We sampled mites on orange, lime, grapefruit and mandarin trees from orchards at six localities distributed in the five most important citrus producing states in Mexico. Genetic variation among citrus host plants and localities were assessed by analysis of nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). Both Brevipalpus yothersi and B. californicus were found at these sites, and B. yothersi was the most abundant species found on all citrus species and in all localities sampled. B. californicus was found mainly on orange and mandarin and only in two of the states sampled. AMOVA and haplotype network analyses revealed no correlation between B. yothersi genetic population structure and geographical origin or citrus host plant species. Considering that a previous study reported greater genetic diversity in B. yothersi populations from Brazil than we observed in Mexico, we discuss the possibility that the Mexican populations may have originated in the southern region of America.

Expression and functional analysis of citrus carotene hydroxylases: unravelling the xanthophyll biosynthesis in citrus fruits

BACKGROUND

Xanthophylls are oxygenated carotenoids and fulfill critical roles in plant growth and development. In plants, two different types of carotene hydroxylases, non-heme di-iron and heme-containing cytochrome P450, were reported to be involved in the biosynthesis of xanthophyll. Citrus fruits accumulate a high amount of xanthophylls, especially β,β-xanthophylls. To date, however, the roles of carotene hydroxylases in regulating xanthophyll content and composition have not been elucidated.

RESULTS

In the present study, the roles of four carotene hydroxylase genes (CitHYb, CitCYP97A, CitCYP97B, and CitCYP97C) in the biosynthesis of xanthophyll in citrus fruits were investigated. Phylogenetic analysis showed that the four citrus carotene hydroxylases presented in four distinct clusters which have been identified in higher plants. CitHYb was a non-heme di-iron carotene hydroxylase, while CitCYP97A, CitCYP97B, and CitCYP97C were heme-containing cytochrome P450-type carotene hydroxylases. Gene expression results showed that the expression of CitHYb increased in the flavedo and juice sacs during the ripening process, which was well consistent with the accumulation of β,β-xanthophyll in citrus fruits. The expression of CitCYP97A and CitCYP97C increased with a peak in November, which might lead to an increase of lutein in the juice sacs during the ripening process. The expression level of CitCYP97B was much lower than that of CitHYb, CitCYP97A, and CitCYP97C in the juice sacs during the ripening process. Functional analysis showed that the CitHYb was able to catalyze the hydroxylation of the β-rings of β-carotene and α-carotene in Escherichia coli BL21 (DE3) cells. Meanwhile, when CitHYb was co-expressed with CitCYP97C, α-carotene was hydroxylated on the β-ring and ε-ring sequentially to produce lutein.

CONCLUSIONS

CitHYb was a key gene for β,β-xanthophyll biosynthesis in citrus fruits. CitCYP97C functioned as an ε-ring hydroxylase to produce lutein using zeinoxanthin as a substrate. The results will contribute to elucidating xanthophyll biosynthesis in citrus fruits, and provide new strategies to improve the nutritional and commercial qualities of citrus fruits.

Tolerance of citrus plants to the combination of high temperatures and drought is associated to the increase in transpiration modulated by a reduction in abscisic acid levels

BACKGROUND

In natural environments, several adverse environmental conditions occur simultaneously constituting a unique stress factor. In this work, physiological parameters and the hormonal regulation of Carrizo citrange and Cleopatra mandarin, two citrus genotypes, in response to the combined action of high temperatures and water deprivation were studied. The objective was to characterize particular responses to the stress combination.

RESULTS

Experiments indicated that Carrizo citrange is more tolerant to the stress combination than Cleopatra mandarin. Furthermore, an experimental design spanning 24 h stress duration, heat stress applied alone induced higher stomatal conductance and transpiration in both genotypes whereas combined water deprivation partially counteracted this response. Comparing both genotypes, Carrizo citrange showed higher phostosystem-II efficiency and lower oxidative damage than Cleopatra mandarin. Hormonal profiling in leaves revealed that salicylic acid (SA) accumulated in response to individual stresses but to a higher extent in samples subjected to the combination of heat and drought (showing an additive response). SA accumulation correlated with the up-regulation of pathogenesis-related gene 2 (CsPR2), as a downstream response. On the contrary, abscisic acid (ABA) accumulation was higher in water-stressed plants followed by that observed in plants under stress combination. ABA signaling in these plants was confirmed by the expression of responsive to ABA-related gene 18 (CsRAB18). Modulation of ABA levels was likely carried out by the induction of 9-neoxanthin cis-epoxicarotenoid dioxygenase (CsNCED) and ABA 8'-hydroxylase (CsCYP707A) while conversion to ABA-glycosyl ester (ABAGE) was a less prominent process despite the strong induction of ABA O-glycosyl transferase (CsAOG).

CONCLUSIONS

Cleopatra mandarin is more susceptible to the combination of high temperatures and water deprivation than Carrizo citrange. This is likely a result of a higher transpiration rate in Carrizo that could allow a more efficient cooling of leaf surface ensuring optimal CO2 intake. Hence, SA induction in Cleopatra was not sufficient to protect PSII from photoinhibition, resulting in higher malondialdehyde (MDA) build-up. Inhibition of ABA accumulation during heat stress and combined stresses was achieved primarily through the up-regulation of CsCYP707A leading to phaseic acid (PA) and dehydrophaseic acid (DPA) production. To sum up, data indicate that specific physiological responses to the combination of heat and drought exist in citrus. In addition, these responses are differently modulated depending on the particular stress tolerance of citrus genotypes.

Anti-Inflammatory Properties and Chemical Characterization of the Essential Oils of Four Citrus Species

Citrus fruits have potential health-promoting properties and their essential oils have long been used in several applications. Due to biological effects described to some citrus species in this study our objectives were to analyze and compare the phytochemical composition and evaluate the anti-inflammatory effect of essential oils (EO) obtained from four different Citrus species. Mice were treated with EO obtained from C. limon, C. latifolia, C. aurantifolia or C. limonia (10 to 100 mg/kg, p.o.) and their anti-inflammatory effects were evaluated in chemical induced inflammation (formalin-induced licking response) and carrageenan-induced inflammation in the subcutaneous air pouch model. A possible antinociceptive effect was evaluated in the hot plate model. Phytochemical analyses indicated the presence of geranial, limonene, γ-terpinene and others. EOs from C. limon, C. aurantifolia and C. limonia exhibited anti-inflammatory effects by reducing cell migration, cytokine production and protein extravasation induced by carrageenan. These effects were also obtained with similar amounts of pure limonene. It was also observed that C. aurantifolia induced myelotoxicity in mice. Anti-inflammatory effect of C. limon and C. limonia is probably due to their large quantities of limonene, while the myelotoxicity observed with C. aurantifolia is most likely due to the high concentration of citral. Our results indicate that these EOs from C. limon, C. aurantifolia and C. limonia have a significant anti-inflammatory effect; however, care should be taken with C. aurantifolia.

Oxygenated heterocyclic compounds to differentiate Citrus spp. essential oils through metabolomic strategies

This study aimed to characterise and discriminate 44 authenticated commercial samples of citrus essential oils (EO) from seven species (bergamot, lemon, bigarade, orange, mandarin, grapefruit, lime) by analysing the non-volatile oxygenated heterocyclic compounds (OHC) by UHPLC/TOF-HRMS, multivariate data analysis (PCA, PLS-DA) and metabolomic strategies; the OHC fraction includes coumarins, furocoumarins, and polymethoxylated flavonoids. Two different approaches were adopted: (i) targeted profiling based on quantifying 18 furocoumarins and coumarins, some of which are regulated by law, and (ii) targeted fingerprinting based on 140 OHCs reported in citrus essential oils, from which 38 discriminant markers were defined. This approach correctly discriminated the Citrus species; its "sensitivity" to relatively low adulteration rate (10%) was highly satisfactory. The proposed method is complementary to that of analysing the citrus EO volatile part by GC techniques.

Diversity among mandarin varieties and natural sub-groups in aroma volatiles compositions

BACKGROUND

Mandarins constitute a large, diverse and important group within the Citrus family. Here, we analysed the aroma volatiles compositions of 13 mandarin varieties belonging to seven genetically different natural sub-groups that included common mandarin (C. reticulata Blanco), clementine (C. clementina Hort. ex. Tan), satsuma (C. unshiu Marcovitch), Mediterranean mandarin (C. deliciosa Tenore), King mandarin (C. nobilis Loureiro), and mandarin hybrids, such as tangor (C. reticulata × C. sinensis) and tangelo (C. reticulata × C. paradisi).

RESULTS

We found that mandarin varieties among tangors ('Temple', 'Ortanique'), tangelos ('Orlando', 'Minneola') and King ('King') had more volatiles, at higher levels, and were richer in sesquiterpene and ester volatiles, than other varieties belonging to the sub-groups common mandarin ('Ora', 'Ponkan'), clementine ('Oroval', 'Caffin'), satsuma ('Okitsu', 'Owari') and Mediterranean mandarin ('Avana', 'Yusuf Efendi'). Hierarchical clustering and principal component analysis accurately differentiated between mandarin varieties and natural sub-groups according to their aroma-volatile profiles.

CONCLUSIONS

Although we found wide differences in aroma-volatiles compositions among varieties belonging to different natural sub-groups, we detected only minor differences among varieties within any natural sub-group. These findings suggest that selecting appropriate parents would enable manipulation of aroma-volatile compositions in future mandarin breeding programmes.

Protective effects of peel and seed extracts of Citrus aurantium on glutamate-induced cytotoxicity in PC12 cell line

Oxidative stress and apoptosis contribute to neuronal degeneration in many neurodegenerative diseases such as Alzheimer's disease. Glutamate is a major excitatory neurotransmitter in the central nervous system (CNS) and is considered responsible for the pathogenesis of many neurological disorders. Reactive oxygen species (ROS) production is thought to be involved in glutamate-induced apoptosis process. In this study, the neuroprotective effects of Citrus aurantium in the glutamate-induced rat's adrenal pheochromocytoma cell line (PC12 cells) were investigated. The cell viability and apoptotic cell death were measured using MTT and propidium iodine (PI)-staining methods, respectively. In addition, intracellular ROS and malondialdehyde (MDA) levels were determined by fluorometric methods. The results showed that glutamate cytotoxicity in PC12 cells was accompanied by an increment of MDA content, ROS generation, and apoptotic induction. However, pretreatment with peel and seed extracts of C. aurantium significantly reduced MDA content, ROS generation, and apoptotic cells. All these findings indicated that C. aurantium protected PC12 cells against glutamate-induced apoptosis by inhibiting ROS production. Therefore, the present study supports that C. aurantium extracts possess neuroprotective effects against glutamate-induced toxicity in PC12 cell line. The protective effect of C. aurantium might be attributed to its antioxidant properties.

The Distribution of Coumarins and Furanocoumarins in Citrus Species Closely Matches Citrus Phylogeny and Reflects the Organization of Biosynthetic Pathways

Citrus plants are able to produce defense compounds such as coumarins and furanocoumarins to cope with herbivorous insects and pathogens. In humans, these chemical compounds are strong photosensitizers and can interact with medications, leading to the "grapefruit juice effect". Removing coumarins and furanocoumarins from food and cosmetics imply additional costs and might alter product quality. Thus, the selection of Citrus cultivars displaying low coumarin and furanocoumarin contents constitutes a valuable alternative. In this study, we performed ultra-performance liquid chromatography coupled with mass spectrometry analyses to determine the contents of these compounds within the peel and the pulp of 61 Citrus species representative of the genetic diversity all Citrus. Generally, Citrus peel contains larger diversity and higher concentrations of coumarin/furanocoumarin than the pulp of the same fruits. According to the chemotypes found in the peel, Citrus species can be separated into 4 groups that correspond to the 4 ancestral taxa (pummelos, mandarins, citrons and papedas) and extended with their respective secondary species descendants. Three of the 4 ancestral taxa (pummelos, citrons and papedas) synthesize high amounts of these compounds, whereas mandarins appear practically devoid of them. Additionally, all ancestral taxa and their hybrids are logically organized according to the coumarin and furanocoumarin pathways described in the literature. This organization allows hypotheses to be drawn regarding the biosynthetic origin of compounds for which the biogenesis remains unresolved. Determining coumarin and furanocoumarin contents is also helpful for hypothesizing the origin of Citrus species for which the phylogeny is presently not firmly established. Finally, this work also notes favorable hybridization schemes that will lead to low coumarin and furanocoumarin contents, and we propose to select mandarins and Ichang papeda as Citrus varieties for use in creating species devoid of these toxic compounds in future breeding programs.

CrWSKP1, an SKP1-like Gene, Is Involved in the Self-Incompatibility Reaction of "Wuzishatangju" (Citrus reticulata Blanco)

Plant S-phase kinase-associated protein 1 (SKP1) genes play crucial roles in plant development and differentiation. However, the role of SKP1 in citrus is unclear. Herein, we described a novel SKP1-like gene, designated as CrWSKP1, from "Wuzishatangju" (Citrus reticulata Blanco). The cDNA sequence of CrWSKP1 is 779 base pairs (bp) and contains an open reading frame (ORF) of 477 bp. The genomic sequence of the CrWSKP1 gene is 1296 bp with two exons and one intron. CrWSKP1 has high identity with SKP1-like genes from other plant species within two conserved regions. Approximately 85% of pollen tubes of self-pollinated CrWSKP1 transgenic tobaccos became twisted at four days after self-pollination. Pollen tube numbers of self-pollinated CrWSKP1 transformants entering into ovules were significantly fewer than that of the control. Seed number of self-pollinated CrWSKP1 transformants was significantly reduced. These results suggested that the CrWSKP1 is involved in the self-incompatibility (SI) reaction of "Wuzishatangju".

[Identification of Pummelo Cultivars Based on Hyperspectral Imaging Technology]

Existing methods for the identification of pummelo cultivars are usually time-consuming and costly, and are therefore inconvenient to be used in cases that a rapid identification is needed. This research was aimed at identifying different pummelo cultivars by hyperspectral imaging technology which can achieve a rapid and highly sensitive measurement. A total of 240 leaf samples, 60 for each of the four cultivars were investigated. Samples were divided into two groups such as calibration set (48 samples of each cultivar) and validation set (12 samples of each cultivar) by a Kennard-Stone-based algorithm. Hyperspectral images of both adaxial and abaxial surfaces of each leaf were obtained, and were segmented into a region of interest (ROI) using a simple threshold. Spectra of leaf samples were extracted from ROI. To remove the absolute noises of the spectra, only the date of spectral range 400~1000 nm was used for analysis. Multiplicative scatter correction (MSC) and standard normal variable (SNV) were utilized for data preprocessing. Principal component analysis (PCA) was used to extract the best principal components, and successive projections algorithm (SPA) was used to extract the effective wavelengths. Least squares support vector machine (LS-SVM) was used to obtain the discrimination model of the four different pummelo cultivars. To find out the optimal values of σ2 and γ which were important parameters in LS-SVM modeling, Grid-search technique and Cross-Validation were applied. The first 10 and 11 principal components were extracted by PCA for the hyperspectral data of adaxial surface and abaxial surface, respectively. There were 31 and 21 effective wavelengths selected by SPA based on the hyperspectral data of adaxial surface and abaxial surface, respectively. The best principal components and the effective wavelengths were used as inputs of LS-SVM models, and then the PCA-LS-SVM model and the SPA-LS-SVM model were built. The results showed that 99.46% and 98.44% of identification accuracy was achieved in the calibration set for the PCA-LS-SVM model and the SPA-LS-SVM model, respectively, and a 95.83% of identification accuracy was achieved in the validation set for both the PCA-LS-SVM and the SPA- LS-SVM models, which were built based on the hyperspectral data of adaxial surface. Comparatively, the results of the PCA-LS-SVM and the SPA-LS-SVM models built based on the hyperspectral data of abaxial surface both achieved identification accuracies of 100% for both calibration set and validation set. The overall results demonstrated that use of hyperspectral data of adaxial and abaxial leaf surfaces coupled with the use of PCA-LS-SVM and the SPA-LS-SVM could achieve an accurate identification of pummelo cultivars. It was feasible to use hyperspectral imaging technology to identify different pummelo cultivars, and hyperspectral imaging technology provided an alternate way of rapid identification of pummelo cultivars. Moreover, the results in this paper demonstrated that the data from the abaxial surface of leaf was more sensitive in identifying pummelo cultivars. This study provided a new method for to the fast discrimination of pummelo cultivars.

[Identification of two varieties of Citri Fructus by fingerprint and chemometrics]

Citri Fructus identification by fingerprint and chemometrics was investigated in this paper. Twenty-three Citri Fructus samples were collected which referred to two varieties as Cirtus wilsonii and C. medica recorded in Chinese Pharmacopoeia. HPLC chromatograms were obtained. The components were partly identified by reference substances, and then common pattern was established for chemometrics analysis. Similarity analysis, principal component analysis (PCA) , partial least squares-discriminant analysis (PLS-DA) and hierarchical cluster analysis heatmap were applied. The results indicated that C. wilsonii and C. medica could be ideally classified with common pattern contained twenty-five characteristic peaks. Besides, preliminary pattern recognition had verified the chemometrics analytical results. Absolute peak area (APA) was used for relevant quantitative analysis, results showed the differences between two varieties and it was valuable for further quality control as selection of characteristic components.

Phloem restriction of viroids in three citrus hosts is overcome by grafting with Etrog citron: potential involvement of a translocatable factor

Viroid systemic spread involves cell-to-cell movement from initially infected cells via plasmodesmata, long-distance movement within the phloem and again cell-to-cell movement to invade distal tissues including the mesophyll. Citrus exocortis viroid (CEVd), hop stunt viroid, citrus bent leaf viroid, citrus dwarfing viroid, citrus bark cracking viroid and citrus viroid V remained phloem restricted when singly infecting Citrus karna, Citrus aurantium and Poncirus trifoliata, but not Etrog citron, where they were additionally detected in mesophyll protoplasts. However, when CEVd-infected C. karna was side-grafted with Etrog citron--with the resulting plants being composed of a C. karna stock and an Etrog citron branch--the viroid was detected in mesophyll protoplasts of the former, thus indicating that the ability of Etrog citron to support viroid invasion of non-vascular tissues was transferred to the stock. Further results suggest that a translocatable factor from Etrog citron mediates this viroid trafficking.

Comparative analysis of three Australian finger lime (Citrus australasica) cultivars: identification of unique citrus chemotypes and new volatile molecules

The volatile constituents of the peel of three cultivars of Australian finger lime (Citrus australasica) were investigated: Alstonville, Judy's Everbearing and Durham's Emerald. Both qualitative and quantitative GC-MS analyses were performed on their peel solvent extract. The results showed that the unique phenotypes of finger lime are also correlated to unique molecular compositions. Each cultivar revealed a different chemotype: limonene/sabinene for cv. Alstonville, limonene/citronellal/isomenthone for cv. Judy's Everbearing, and limonene/citronellal/ citronellol for cv. Durham's Emerald. To the best of our knowledge, these chemotypes have never been reported in any other citrus species. Furthermore, the amounts of some volatile constituents (γ-terpinene, α-pinene, β-pinene, citral), which are generally the major constituents besides limonene in lime species, were surprisingly low in the three cultivars. Comparative GC-MS analysis also showed that some volatile molecules tended to be specific to one cultivar and could therefore be considered as markers. Moreover six molecules were reported for the first time in a citrus extract and confirmed by synthesis. Heart-cutting enantioselective two-dimensional GC-MS was performed to determine the enantiomeric distribution of the major chiral constituents. The combined data on three finger lime cultivars gives evidence of their divergence from other citrus species.

Genome-wide analysis of citrus R2R3MYB genes and their spatiotemporal expression under stresses and hormone treatments

The R2R3MYB proteins represent one of the largest families of transcription factors, which play important roles in plant growth and development. Although genome-wide analysis of this family has been conducted in many species, little is known about R2R3MYB genes in citrus, In this study, 101 R2R3MYB genes has been identified in the citrus (Citrus sinesis and Citrus clementina) genomes, which are almost equal to the number of rice. Phylogenetic analysis revealed that they could be subdivided into 21 subgroups. The evolutionary relationships and the intro-exon organizations were also analyzed, revealing strong gene conservation but also the expansions of particular functional genes during the plant evolution. Tissue-specific expression profiles showed that 95 citrus R2R3MYB genes were expressed in at least one tissue and the other 6 genes showed very low expression in all tissues tested, suggesting that citrus R2R3MYB genes play important roles in the development of all citrus organs. The transcript abundance level analysis during abiotic conditions (NaCl, abscisic acid, jasmonic acid, drought and low temperature) identified a group of R2R3MYB genes that responded to one or multiple treatments, which showed a promising for improving citrus adaptation to stresses. Our results provided an essential foundation for the future selection of the citrus R2R3MYB genes for cloning and functional dissection with an aim of uncovering their roles in citrus growth and development.

Complete chloroplast genome sequence of Omani lime (Citrus aurantiifolia) and comparative analysis within the rosids

The genus Citrus contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the Citrus chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (C. aurantiifolia). The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (C. sinensis) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated Citrus. A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution.

Analysis of biologically active oxyprenylated ferulic acid derivatives in Citrus fruits

4'-Geranyloxyferulic (GOFA) and boropinic acid have been discovered during the last decade as interesting phytochemicals having valuable pharmacological effects as cancer chemopreventive, anti-inflammatory, neuroprotective, and anti-Helicobacter pylori agents. A reverse-phase HPLC-UV/Vis method for the separation and quantification of the title oxyprenylated ferulic acid derivatives in extracts obtained from peels of nine edible Citrus and Fortunella fruits was successfully applied. Concentration values showed a great variation between the different species, being orange (C. sinensis) the fruit richest in GOFA (0.141 ± 0.011 mg/g of exocarp fresh weight) and kumquat (Fortunella japonica) the one in which boropinic acid was recorded as the most abundant phytochemical (0.206 ± 0.002 mg/g of exocarp fresh weight). Both secondary metabolites were not detected only in three species. The set-up methodology showed limits of quantification (LOQ) values, that were able to selectively quantify both GOFA and boropinic acid. Results described herein depict a potential chemopreventive dietary feeding role for the Rutaceae spp. under investigation.

Effect of cultivation line and peeling on food composition, taste characteristic, aroma profile, and antioxidant activity of Shiikuwasha (Citrus depressa Hayata) juice

BACKGROUND

Shiikuwasha (Citrus depressa Hayata) juice from four main cultivation lines subjected to two peeling practices (with or without peeling) were discriminated in terms of quality attributes, represented by sugar and organic acid composition, taste characteristic, aroma profile, and antioxidant activity.

RESULTS

Shiikuwasha juice from these lines had diverse food compositions; 'Izumi kugani' juice had lower acidity but contained more ascorbic acid than that of other cultivation lines. The composition of volatile aroma components was influenced by fruit cultivation line, whereas its content was affected by peeling process (20.26-53.73 mg L(-1) in whole juice versus 0.82-1.58 mg L(-1) in flesh juice). Peeling also caused Shiikuwasha juice to be less astringent and acidic bitter and to lose its antioxidant activity. Moreover, the total phenolic and ascorbic acid content of Shiikuwasha juice positively influenced its antioxidant activity.

CONCLUSION

Each fruit cultivation line had a distinct food composition, taste characteristic, and aroma profile. Peeling in Shiikuwasha juice production might reduce aftertaste, and thus might improve its palatability. Comprehensive information on the effect of cultivation line and peeling on quality attributes will be useful for Shiikuwasha juice production, and can be applied to juice production of similar small citrus fruits.

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.

Genetic diversity among mandarins in fruit-quality traits

A detailed phenotypic analysis of fruit-quality traits was conducted among 46 mandarin varieties within the Israeli Citrus breeding collection, belonging to genetically different natural subgroups, including common mandarin (C. reticulata Blanco), clementine (C. clementina Hort. ex. Tan), satsuma (C. unshiu Marcovitch), Mediterranean mandarin (C. deliciosa Tenore), King mandarin (C. nobilis Loureiro), and mandarin hybrids, such as tangor (C. reticulata × C. sinensis) and tangelo (C. reticulata × C. paradisi). Evaluated qualities included physical attributes (size, shape, color, peel thickness, and seed number); physiological properties (ripening period, peelability, and segmentation); nutritional and biochemical composition (vitamin C, phenol, flavonoid, and carotenoid contents and total antioxidant activity); and sensory attributes (total soluble solids and acid levels, flavor preference, sweetness, sourness, and fruitiness). The results indicated wide genetic variability in fruit-quality traits among mandarin varieties and natural subgroups, and statistical and hierarchical clustering analysis revealed multiple correlations among attributes. Such phenomic analysis is an obligatory requirement for identification of molecular markers for distinct fruit-quality traits and for selection of appropriate parents for future breeding programs.

Characterization by GC–MS of Vietnamese Citrus Species and Hybrids Based on the Isotope Ratio of Monoterpene Hydrocarbons

The isotope ratio of monoterpene hydrocarbons was used to characterize the citrus essential oils from different species and hybrids. Citrus cold-pressed peel oils from Vietnam were analyzed for the composition and isotope ratio of monoterpene hydrocarbons by using gas chromatography-mass spectrometry. A profile of citrus essential oils on the basis of their isotope ratio values and levels of monoterpene hydrocarbons was developed for Vietnamese citrus. The molecular isotope ratios were lower than those calculated from natural abundance of 13C and 2H. In addition, the isotope ratio of the base peaks (m/z 94/93) was significantly different among the citrus essential oils from different species and hybrids. The results would be applicable for the characterization of citrus essential oils from different origins.

[Citrus boron nutrient level and its impact factors in the Three Gorges Reservoir region of Chongqing, China]

To investigate the level of boron nutrient in citrus and its impact factors, a total of 954 citrus leaf samples and 302 soil samples were collected from representative orchards in the 12 main citrus production counties in the Three Gorges Reservoir region of Chongqing to determine the boron content in citrus leaves, as well as the relationships between leaf boron content with soil available boron content, soil pH value, cultivar, rootstock and the age of tree. Results indicated that the leaf samples from 41.6% orchards (< 35 mg x kg(-1)) and the soil samples from 89.4% orchards (< 0.5 mg x kg(-1)) were boron insufficient. The correlation of leaf boron content and soil available boron content was not significant. The soil pH, cultivar, rootstock and the age of tree did affect the leaf boron content. The leaves from the orchards with soil pH of 4.5-6.4 demonstrated significantly higher boron contents than with the soil pH of 6.5-8.5. The leaf boron contents in the different cultivars was ranged as Satsuma mandarin > pomelo > valencia orange > sweet orange > tangor > navel orange. The citrus on trifoliate orange and sour pomelo rootstocks had significantly higher leaf boron contents than on Carrizo citrange and red tangerine rootstocks. Compared with the adult citrus trees (above 8 year-old), 6.6% more of leaf samples of younger trees (3 to 8 year-old) contained boron contents in the optimum range (35-100 mg x kg(-1)).