•The volatiles of 108 citrus accessions were determined, including 22 wild or semi-wild germplasms.•Citrus germplasms that accumulate specific volatile compounds were found.•The clustering results of 34 distinctive volatiles via HCA agreed with classic citrus taxonomy.•MVA pathway is enhanced in the peels of C. ichangensis ‘Huaihua’.The volatile profiles of fruit peels and juice sacs from 108 citrus accessions representing seven species were analyzed. Using GC–MS 162 and 107 compounds were determined in the peels and juice sacs, respectively. In the peels, monoterpene alcohols were accumulated in loose-skin mandarins; clementine tangerines and papedas were rich in sesquiterpene alcohols, sesquiterpenes, monoterpene alcohols and monoterpene aldehydes. β-pinene and sabinene were specifically accumulated in 4 of 5 lemon germplasms. Furthermore, concentrations of 34 distinctive compounds were selected to best represent the volatile profiles of seven species for HCA analysis, and the clustering results were in agreement with classic citrus taxonomy. Comparison of profiles from different growing seasons and production areas indicated that environmental factors play important roles in volatile metabolism. In addition, a few citrus germplasms that accumulated certain compounds were determined as promising breeding materials. Notably, volatile biosynthesis via MVA pathway in C. ichangensis ‘Huaihua’ was enhanced.

•Non-targeted metabolic profiling was performed in different fruit tissues and species.•Differential accumulation patterns of amino acids, flavonoids and limonoids were revealed.•Metabolite profiling of natural variation in 47 individual Citrus accessions was studied.To study the natural variation and spatio-temporal accumulation of citrus metabolites, liquid chromatography tandem mass spectrometry (LC–MS) based metabolome analysis was performed on four fruit tissues (flavedo, albedo, segment membrane and juice sacs) and different Citrus species (lemon, pummelo and grapefruit, sweet orange and mandarin). Using a non-targeted metabolomics approach, more than 2000 metabolite signals were detected, from which more than 54 metabolites, including amino acids, flavonoids and limonoids, were identified/annotated. Differential accumulation patterns of both primary metabolites and secondary metabolites in various tissues and species were revealed by our study. Further investigation indicated that flavedo accumulates more flavonoids while juice sacs contain more amino acids. Besides this, cluster analysis based on the levels of metabolites detected in 47 individual Citrus accessions clearly grouped them into four distinct clusters: pummelos and grapefruits, lemons, sweet oranges and mandarins, while the cluster of pummelos and grapefruits lay distinctly apart from the other three species.

•Main FGs and PMFs are detected simultaneously in fruit tissues of four sweet oranges.•Mechanisms accounting for the differences in FGs composition of citrus may be revealed.•Character of methylation-related gene accounting for PMF biosynthesis may be implied.•Lycopene accumulation may affect the modification of citrus flavonoid biosynthesis.Four main flavanone glycosides (FGs) and four main polymethoxylated flavones (PMFs) were determined in fruits of ‘Cara Cara’ navel orange, ‘Seike’ navel orange, ‘Anliu’ and ‘Honganliu’ sweet orange (Citrus sinensis). No bitter neohesperidosides were detected in the FG profiles, indicating the functional inability of 1,2-rhamnosyltransferase, though relatively high transcription levels were detected in the fruit tissues of ‘Anliu’ and ‘Honganliu’ sweet oranges. Different to the FGs, the PMFs only exist abundantly in the peel and decreased gradually throughout fruit development of sweet oranges, suggesting the expression of methylation-related genes accounting for PMF biosynthesis have tissue-specificity. Significant changes in production of the eight flavonoids were found between red-flesh and blonde-flesh sweet oranges, indicating that lycopene accumulation might have direct or indirect effects on the modification of flavonoid biosynthesis in these citrus fruits.

•4 FCMs were determined in 73 citrus germplasm/accessions for 2 seasons.•16 pummelos flock high rate of 6,7-DHB and bergamottin, and the other flock high EBM.•All 4 FCMs were below the detection level in lemons and trifoliate oranges.•Special citrus germplasms were defined for future drug/juice use based on FCMs.•The traits of dominant FCMs in citrus could be changed by breeding and selection.Due to the furanocoumarin compounds in the fruit, the production and consumption of grapefruit have been affected in the past decades since the ‘grapefruit juice effect’ was declared. To provide elite germplasm and obtain knowledge for future citrus breeding programs, the contents of 4 furanocoumarin monomers (FCMs) in the juice sacs from 73 citrus germplasms were evaluated using ultra-performance liquid chromatography. 6′,7′-Dihydroxybergamottin and bergamottin were dominant in all the tested grapefruits, while there were some pomelos with dominant epoxybergamottin, and some with dominant 6′,7′-dihydroxybergamottin and bergamottin. The contents of FCMs were low or below detection in sweet oranges, mandarins, lemons and trifoliate oranges. The results also show that the dominant patterns of FCMs are genotype-related, and crossing and selection are effective approaches to alter FCM profiles in citrus breeding. Furthermore, the contribution of pomelo as a parent to grapefruit regarding their FCM profiles was discussed.

Volatiles of a wild mandarin, Mangshanyegan (Citrus nobilis Lauriro), were characterized by GC-MS, and their aroma active compounds were identified by aroma extract dilution analysis (AEDA) and gas chromatography–olfactometry (GC-O). The volatile profile of Mangshanyegan was compared with those of other four citrus species, Kaopan pummelo (Citrus grandis), Eureka lemon (Citrus limon), Huangyanbendizao tangerine (Citrus reticulata), and Seike navel orange (Citrus sinensis). Monoterpene hydrocarbons predominated in Mangshanyegan, in particular d-limonene and β-myrcene, which accounted for 85.75 and 10.89% of total volatiles, respectively. Among the 12 compounds with flavor dilution factors (FD) = 27, 8 oxygenated compounds, including (Z)- and (E)-linalool oxides, were present only in Mangshanyegan. The combined results of GC-O, quantitative analysis, odor activity values (OAVs), and omission tests revealed that β-myrcene and (Z)- and (E)-linalool oxides were the characteristic aroma compounds of Mangshanyegan, contributing to the balsamic and floral notes of its aroma.

Eight carotenoids, such as phytoene, α-carotene, violaxanthin, etc., synthesized in citrus callus of 31 genotypes were identified and determined. Though varied with genotypes, the carotenoids composition of callus derived from a certain genotype was stable, while carotenoids contents altered between sub-cultures. Some specific carotenoids were produced in calluses of limited genotypes: β-citraurin was only synthesized in calluses of Nianju tangerine (Citrus reticulata Blanco) and Page tangelo (C. reticulata × C. paradisi); while 9-Z-violaxanthin was only detected in Nianju tangerine and Skaggs Bonanza navel orange (C. sinensis L. Osbeck). Notably, the only carotenoid detected in calluses of Natsudaidai (C. aurantium L.) and other two sweet oranges (C. sinensis L. Osbeck) was phytoene. It implied that citrus calluses could be employed to produce specific carotenoids in the future. To further elucidate the characters of callus carotenoids profile, comparisons of carotenoids profiles was made among calluses, fruit tissues and leaves of four selected citrus genotypes. Results showed that lycopene was not detected in leaves and calluses; nevertheless, both citrus fruits and calluses accumulated phytoene, whereas leaves did not except those of Cara Cara navel orange. It is postulated that citrus callus featured its carotenoids profile different from fruit tissues and leaves. In conclusion, the advantages of using citrus callus as an alternative model research system in understanding the regulation of carotenogenesis have been discussed.

Citrus fruits are rich in carotenoids. In the carotenoid biosynthetic pathway, lycopene β-cyclase (LCYb, EC:1.14.-.-) is a key regulatory enzyme in the catalysis of lycopene to β-carotene, an important dietary precursor of vitamin A for human nutrition. Two closely related lycopene β-cyclase cDNAs, designated CsLCYb1 and CsLCYb2, were isolated from the pulp of orange fruits (Citrus sinensis). The expression level of CsLCYb genes is lower in the flavedo and juice sacs of a lycopene-accumulating genotype Cara Cara than that in common genotype Washington, and this might be correlated with lycopene accumulation in Cara Cara fruit. The CsLCYb1 efficiently converted lycopene into the bicyclic β-carotene in an Escherichia coli expression system, but the CsLCYb2 exhibited a lower enzyme activity and converted lycopene into the β-carotene and the monocyclic γ-carotene. In tomato transformation studies, expression of CsLCYb1 under the control of the cauliflower mosaic virus (CaMV) 35S constitutive promoter resulted in a virtually complete conversion of lycopene into β-carotene, and the ripe fruits displayed a bright orange colour. However, the CsLCYb2 transgenic tomato plants did not show an altered fruit colour during development and maturation. In fruits of the CsLCYb1 transgenic plants, most of the lycopene was converted into β-carotene with provitamin A levels reaching about 700 μg g−1 DW. Unexpectedly, most transgenic tomatoes showed a reduction in total carotenoid accumulation, and this is consistent with the decrease in expression of endogenous carotenogenic genes in transgenic fruits. Collectively, these results suggested that the cloned CsLCYb1 and CsLCYb2 genes encoded two functional lycopene β-cyclases with different catalytic efficiency, and they may have potential for metabolite engineering toward altering pigmentation and enhancing nutritional value of food crops.

•Cutin was formed before wax accumulation, providing the scaffold for wax assembling.•Transition of metabolism of fruits peel occurred from 120 to 150 DAF.•ABA and GL1-like were predicted to be pivotal for wax synthesis.Fruit cuticle, which is composed of cutin and wax and biosynthesized during fruit development, plays important roles in the prevention of water loss and the resistance to pathogen infection during fruit development and postharvest storage. However, the key factors and mechanisms regarding the cuticle biosynthesis in citrus fruits are still unclear. Here, fruit cuticle of ‘Newhall’ navel orange (Citrus sinensis Osbeck) was studied from the stage of fruit expansion to postharvest storage from the perspectives of morphology, transcription and metabolism. The results demonstrated that cutin accumulation is synchronous with fruit expansion, while wax synthesis is synchronous with fruit maturation. Metabolic profile of fruits peel revealed that transition of metabolism of fruit peel occurred from 120 to 150 DAF and ABA was predicted to regulate citrus wax synthesis during the development of Newhall fruits. RNA-seq analysis of the peel from the above two stages manifested that the genes involved in photosynthesis were repressed, while the genes involved in the biosynthesis of wax, cutin and lignin were significantly induced at later stages. Further real-time PCR predicted that MYB transcription factor GL1-like regulates citrus fruits wax synthesis. These results are valuable for improving the fruit quality during development and storage.

•Main bitter compounds determination in ‘Oroblanco’ fruit tissues for three years.•Cold stress partially account for the contents changes of bitter compounds.•Active communication between fruit tissues is suggested.•Self-regulation mechanism of bitter compounds in citrus is suggested.The main bitter compounds nomilin, limonin and naringin in citrus were determined in the fruit tissues of ‘Oroblanco’ (Citrus grandis L. × Citrus paradisi Macf.) throughout three growing seasons. The results showed a higher accumulation of bitter compounds in the first and second year due to the cold stress occurring in the first year, while much lower contents were detected in the third year, indicating a stress alleviation of the tree. In the fruit tissues of ‘Oroblanco’, the flavedo contained undetectable nomilin and the lowest naringin, while the segment membrane contained the highest limonin and nomilin; however, the juice sacs contained the highest naringin, especially in 2008 and 2009. Correlation analysis based on the contents of the three compounds implied that there are active communications between juice sacs and other fruit tissues together with a self-regulation mechanism of bitter compounds in citrus.