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Jin-zhi Zhang - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina)
Plant Molecular Biology, 2018Co-Authors: Tian-jia Liu, Chun-gen Hu, Yong-ping Li, Jing-jing Zhou, Jin-zhi ZhangAbstract:Key messageThe comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing.AbstractFruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene–phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.
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Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).
Plant Molecular Biology, 2018Co-Authors: Tian-jia Liu, Jing-jing Zhou, Jin-zhi ZhangAbstract:The comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing. Fruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene-phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.
Enrique Sentandreu - One of the best experts on this subject based on the ideXlab platform.
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effect of ph temperature and maturity on pectinmethylesterase inactivation of citrus juices treated by high pressure homogenization
Lwt - Food Science and Technology, 2014Co-Authors: Jose L Navarro, L Izquierdo, J V Carbonell, Enrique SentandreuAbstract:Abstract The effects of high-pressure homogenization (HPH) at 150 MPa combined with heating at 58, 63 and 68 °C on inactivation of pectinmethylesterase (PME) were studied in orange and Clementine juices. Juices covering a range of total soluble solids (°Bx) to acid ratios (10.2–15.0 in oranges and 9.2–19.4 in Clementines) were adjusted to pH 3.1, 3.5 and 3.9 before homogenization. Results indicated how the residual PME activity of homogenized samples was greatly attenuated by lowering the pH and in a lesser extent by increasing the homogenization temperature (finding orange enzymes more HPH sensitive than their Clementine counterparts). Generally, ripeness of fruits had little influence on PME inactivation (especially in Clementine juices). In any case, orange and Clementine samples with pH 3.1 and homogenized at 68 °C showed residual PME activities below 10% of the initial value from their respective fresh juices.
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total cumulative fast kinetics and cumulative slow kinetics antiradical activities of juices from Clementine citrus clementina Clementine hybrids and satsuma citrus unshiu cultivars and their utility as discriminant variables
European Food Research and Technology, 2007Co-Authors: Enrique Sentandreu, Luis Izquierdo, José M. SendraAbstract:Mandarin juices from three pure Clementine (Citrus clementina Hort. ex Tan.) cultivars: Clemenules, Hernandine and Marisol, two Clementine-hybrid cultivars: Nova (Clementine×tangelo Orlando) and Fortune (Clementine× mandarin Dancy), one mandarin-hybrid cultivar: Ortanique (mandarin×orange) and one satsuma (Citrus unshiu Marc) cultivar: Clauselline have been analysed for determination of total, cumulative fast-kinetics and cumulative slow-kinetics antiradical activities. Total antiradical activity followed the order: pure Clementine and Nova> Ortanique>Fortune and Clauselline. Cumulative fast-kinetics antiradical activity was the major contributor to total antiradical activity, accounting for about 87% as average. Ascorbic acid content was the major contributor to cumulative fast-kinetics antiradical activity, accounting for about 93.5% as average. A weak correlation (r 2=0.151) between total flavanone-7-O-glycosides (FGs, Narirutin, Hesperidin and Didymin) content and cumulative slow-kinetics antiradical activity was observed. However, ascorbic acid and total FGs contents showed a significant negative correlation (r 2=0.658). By using the cumulative fast-kinetics and slow-kinetics antiradical activities as variables, all the assayed juices were significantly discriminated (<0.05) by statistical multivariate discriminant analysis.
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Differentiation of juices from Clementine (Citrus clementina), Clementine-hybrids and satsuma (Citrus unshiu) cultivars by statistical multivariate discriminant analysis of their flavanone-7-O-glycosides and fully methoxylated flavones content as det
European Food Research and Technology, 2007Co-Authors: Enrique Sentandreu, L Izquierdo, José M. SendraAbstract:Mandarin juices from three pure Clementine ( Citrus clementina Hort. ex Tan.) cultivars: Clemenules, Hernandine and Marisol, three Clementine-hybrids: Nova (Clementine×tangelo Orlando), Ortanique (Clementine×orange) and Fortune (Clementine×mandarin Dancy) and one satsuma ( Citrus unshiu Marc) cultivar: Clauselline have been analyzed for simultaneous determination of their flavanone-7- O -glycosides (FGs) and fully methoxylated flavones (FMFs) content, using high-performance liquid chromatography. Statistical multivariate discriminant analysis from the FGs concentration data showed that its discriminant power was rather poor, leading to overlapping between some groups of the assayed cultivars. By contrast, the discriminant power from the FMFs concentration data was very high and only two concentration ratios were needed as discriminant parameters to significantly differentiate between all the assayed cultivars. Moreover, the values of the discriminant parameters were almost independent of the location of the orchards and the maturity stage of the fruits.
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Total, cumulative fast-kinetics and cumulative slow-kinetics antiradical activities of juices from Clementine (Citrus clementina), Clementine-hybrids and satsuma (Citrus unshiu) cultivars and their utility as discriminant variables
European Food Research and Technology, 2006Co-Authors: Enrique Sentandreu, Luis Izquierdo, José M. SendraAbstract:Mandarin juices from three pure Clementine ( Citrus clementina Hort. ex Tan.) cultivars: Clemenules, Hernandine and Marisol, two Clementine-hybrid cultivars: Nova (Clementine×tangelo Orlando) and Fortune (Clementine× mandarin Dancy), one mandarin-hybrid cultivar: Ortanique (mandarin×orange) and one satsuma ( Citrus unshiu Marc) cultivar: Clauselline have been analysed for determination of total, cumulative fast-kinetics and cumulative slow-kinetics antiradical activities. Total antiradical activity followed the order: pure Clementine and Nova> Ortanique>Fortune and Clauselline. Cumulative fast-kinetics antiradical activity was the major contributor to total antiradical activity, accounting for about 87% as average. Ascorbic acid content was the major contributor to cumulative fast-kinetics antiradical activity, accounting for about 93.5% as average. A weak correlation ( r ^2=0.151) between total flavanone-7- O -glycosides (FGs, Narirutin, Hesperidin and Didymin) content and cumulative slow-kinetics antiradical activity was observed. However, ascorbic acid and total FGs contents showed a significant negative correlation ( r ^2=0.658). By using the cumulative fast-kinetics and slow-kinetics antiradical activities as variables, all the assayed juices were significantly discriminated (
Tian-jia Liu - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina)
Plant Molecular Biology, 2018Co-Authors: Tian-jia Liu, Chun-gen Hu, Yong-ping Li, Jing-jing Zhou, Jin-zhi ZhangAbstract:Key messageThe comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing.AbstractFruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene–phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.
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Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).
Plant Molecular Biology, 2018Co-Authors: Tian-jia Liu, Jing-jing Zhou, Jin-zhi ZhangAbstract:The comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing. Fruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene-phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.
N Duranvila - One of the best experts on this subject based on the ideXlab platform.
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effect of a field source mixture of citrus viroids on the performance of nules Clementine and navelina sweet orange trees grafted on carrizo citrange
Plant Disease, 2009Co-Authors: S Bani M Hashemian, Pedro Serra, C J Barbosa, J Juarez, P Aleza, J M Corvera, A Lluch, Jose Antonio Pina, N DuranvilaAbstract:ABSTRACT A field-source mixture of citrus viroids was characterized and shown to contain Citrus exocortis viroid (CEVd), Hop stunt viroid (HSVd), Citrus bent leaf viroid (CBLVd), and Citrus dwarfing viroid (CDVd). Sequencing results showed that: (i) CEVd contained the PL and PR characteristic of class A variants; (ii) HSVd was a noncachexia variant; (iii) CBLVd was related to CVd-Ia variants; (iv) CDVd was a mixture of two types (CVd-IIIa and CVd-IIIb) of variants. The presence of the same type of variants in inoculated Clementine (Citrus clementina ‘Nules’) and sweet orange (C. sinensis ‘Navelina’) trees on Carrizo citrange (Poncirus trifoliata × C. sinensis) rootstocks was confirmed. The effect of infection was determined by assessing the performance of infected and noninfected trees growing in the field. Infection resulted in small trees with reduced canopy, yielding a reduced crop. Fruit characteristics were also affected: (i) Clementine and sweet orange fruits from infected trees were larger than tho...
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a survey of citrus viroids in campania southern italy
Plant Disease, 2005Co-Authors: M Malfitano, M Barone, D Alioto, N DuranvilaAbstract:Within a certification program of citrus, a survey covering 14 citrus fields not previously screened were randomly selected in seven areas of the Campania Region of southern Italy to evaluate the presence and distribution of citrus viroids in the region. During the last 3 years, 112 trees were visually inspected and sampled including 14 ‘Navelina’, 8 ‘Washington navel’, 13 ‘Biondo Commune’, 10 ‘Tarocco’, 6 ‘Valencia late’, 1 ‘Sanguinello’, and 1 ‘Vanilla’ sweet oranges (Citrus sinensis), four sour oranges (C. aurantium), 21 ‘Commune’ and 7 ‘Monreale’ Clementines (C. clementina), 8 ‘Common’ and 2 ‘Avana’ mandarins (C. reticulata), 8 ‘Ovale di Sorrento’ and 6 ‘Zagara’ lemons (C. lemon), 2 Tangelos (C. reticulata × C. paradisi), and 1 grapefruit (C. paradisi). Nearly all (37 of 38) mandarin and Clementine trees showed cachexia-like symptoms. Severe bark scaling that is characteristic of exocortis disease was observed on a single ‘Ovale di Sorrento’ lemon, the only tree incidentally found to be grafted onto t...
Patrick Ollitrault - One of the best experts on this subject based on the ideXlab platform.
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Comparative Genetic Mapping between Clementine Pummelo and Sweet Orange and the Interspecicic Structure of the Clementine Genome
Acta Horticulturae, 2015Co-Authors: Patrick Ollitrault, Javier Terol, Chunxian Chen, Claire T. Federici, Samia Lotfy, Isabelle Hippolyte, Frédérique Ollitrault, Aurélie Bérard, Aurélie Chauveau, José CuencaAbstract:The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly of the reference whole genome sequence based on a Clementine derived haploid. The primary goals of the present study were to establish a Clementine reference map, and to perform comparative mapping with pummelo and sweet orange. Five parental genetic maps were established with SNPs, SSRs and InDels. A medium density reference map (961 markers for 1084.1 cM) of Clementine was established and used by the ICGC to facilitate the chromosome assembly of the haploid genome sequence. Comparative mapping with pummelo and sweet orange revealed that the linear order of markers was highly conserved. Reasonable inferences of most citrus genomes should be obtained by mapping next-generation sequencing data against the haploid reference genome sequence. Skewed segregations were frequent and higher in the male than female Clementine potentially leading to false interpretation of the genetic determinism of phenotypic traits. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange and identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Introgression of pummelo genome fragments were identified in heterozygosity in each chromosome. Moreover, it appeared that the genome of the haploid Clementine used to establish the citrus reference genome sequence was inherited primarily from the 'Mediterranean' mandarin. The usefulness of this genetic map, anchored in the reference whole genome sequence, is discussed. (Resume d'auteur)
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Comparative Genetic Mapping between Clementine, Pummelo and Sweet Orange and the Interspecicic Structure of the Clementine Genome
2012Co-Authors: Patrick Ollitrault, Javier Terol, Chunxian Chen, Claire T. Federici, Samia Lotfy, Isabelle Hippolyte, Frédérique Ollitrault, Aurélie Bérard, Aurélie Chauveau, José CuencaAbstract:The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly of the reference whole genome sequence based on a Clementine derived haploid. The primary goals of the present study were to establish a Clementine reference map, and to perform comparative mapping with pummelo and sweet orange. Five parental genetic maps were established with SNPs, SSRs and InDels. A medium density reference map (961 markers for 1084.1 cM) of Clementine was established and used by the ICGC to facilitate the chromosome assembly of the haploid genome sequence. Comparative mapping with pummelo and sweet orange revealed that the linear order of markers was highly conserved. Reasonable inferences of most citrus genomes should be obtained by mapping next-generation sequencing data against the haploid reference genome sequence. Skewed segregations were frequent and higher in the male than female Clementine potentially leading to false interpretation of the genetic determinism of phenotypic traits. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange and identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Introgression of pummelo genome fragments were identified in heterozygosity in each chromosome. Moreover, it appeared that the genome of the haploid Clementine used to establish the citrus reference genome sequence was inherited primarily from the 'Mediterranean' mandarin. The usefulness of this genetic map, anchored in the reference whole genome sequence, is discussed.
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A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping
BMC Genomics, 2012Co-Authors: Patrick Ollitrault, Javier Terol, Chunxian Chen, Claire T. Federici, Samia Lotfy, Isabelle Hippolyte, Frédérique Ollitrault, Aurélie Bérard, Aurélie Chauveau, José CuencaAbstract:Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.
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Autotetraploid trifoliate orange (Poncirus trifoliata) rootstocks do not impact Clementine quality but reduce fruit yields and highly modify rootstock/scion physiology.
Scientia Horticulturae, 2012Co-Authors: Sajjad Hussain, Laurent Urban, Frank Curk, Claudie Dhuique-mayer, Patrick Ollitrault, François Luro, Raphaël MorillonAbstract:Two autotetraploid (4×) trifoliate orange (Poncirus trifoliata (L.) Raf.) rootstocks and the corresponding diploid (2×) rootstocks were compared for their impact on Clementine " Commune " (Citrus clementina Hort. ex Tan) production and on rootstock/scion physiology. Cumulative fruit yield, fruit quality (sugars, organic acids, carotenoids, hesperidin) and scion physiology (stem growth, leaf starch, sugars, chlorophyll content, phenolic content and gas exchange parameters) were investigated. The cumulative fruit yield over 11 years was lower in 4× rootstock/Clementine associations and correlated with reduced vigor of the Clementine scion. Fruit quality criteria were not affected by the ploidy level of the rootstocks, with the exception of hesperidin content, which was higher with 4× than 2× rootstock/Clementine associations. Leaf chlorophyll and phenolic contents were higher with 4× than 2× rootstock/Clementine associations. In leaves, the rate of photosynthesis and stomatal conductance was much higher with 2× rootstocks; however, the maximum electron transport rate was lower when compared to the 4× rootstocks. Similarly , leaf starch and sugar contents were much higher with 4× than 2×. Taken together, these results demonstrate that the use of 4× rootstocks dramatically changes both tree physiology and fruit yield, without promoting large changes in fruit quality criteria.
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Effects of Nucleo-Cytoplasmic Interactions on Leaf Volatile Compounds from Citrus Somatic Diploid Hybrids
Journal of Agricultural and Food Chemistry, 2005Co-Authors: Anne-laure Fanciullino, Patrick Ollitrault, François Luro, Anne-laure Gancel, Yann Froelicher, Jean-marc BrillouetAbstract:Three diploid citrus somatic hybrids (cybrids) were produced by fusions combining nucellar callus-derived protoplasts of Willow Leaf mandarin (Citrus deliciosa Ten.) and Commune Clementine (Citrus clementina Hort. ex Tan.) with, respectively, leaf protoplasts of Eureka lemon [Citrus limon (L.) Burm.] and Marumi kumquat [Fortunella japonica (Thunb.) Swing.] and leaf protoplasts of Marumi kumquat. Ploidy and origins of the nuclear, chloroplastic, and mitochondrial genomes were investigated by flow cytometry and nuclear and cytoplasmic simple sequence repeat analyses. Volatile compounds were extracted from the leaves of the three cybrids by a pentane/ether (1:1) mixture, analyzed by GC-MS, and compared to those of their parents. The cybrids were found to be very close to their nucleus-giving parent, suggesting that the main information for volatile compounds biosynthesis is contained in the nucleus. However, nucleo-cytoplasmic interactions occurred: the (mandarin + lemon) cybrid, possessing nucleus and chloroplasts of lemon and mitochondria from mandarin, synthesizes more monoterpene alcohols and esters than its nucleus-giving parent; the (Clementine + kumquat) cybrid, possessing nucleus from kumquat and organelles from mandarin, synthesizes more monoterpene and sesquiterpene hydrocarbons and sesquiterpene alcohols than its nucleus-giving parent.
