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Mehreen Lateef - One of the best experts on this subject based on the ideXlab platform.

Manuel Talon - One of the best experts on this subject based on the ideXlab platform.

  • transcriptomic analysis of Citrus Clementina mandarin fruits maturation reveals a mads box transcription factor that might be involved in the regulation of earliness
    BMC Plant Biology, 2019
    Co-Authors: Javier Terol, Francisco R Tadeo, José M. Nueda, Daniel Ventimilla, Manuel Talon
    Abstract:

    Harvest time is a relevant economic trait in Citrus, and selection of cultivars with different fruit maturity periods has a remarkable impact in the market share. Generation of early- and late-maturing cultivars is an important target for Citrus breeders, therefore, generation of knowledge regarding the genetic mechanisms controlling the ripening process and causing the early and late phenotypes is crucial. In this work we analyze the evolution of the transcriptome during fruit ripening in 3 sport mutations derived from the Fina clementine (Citrus Clementina) mandarin: Clemenules (CLE), Arrufatina (ARR) and Hernandina (HER) that differ in their harvesting periods. CLE is considered a mid-season cultivar while ARR and HER are early- and late-ripening mutants, respectively. We used RNA-Seq technology to carry out a time course analysis of the transcriptome of the 3 mutations along the ripening period. The results indicated that in these mutants, earliness and lateness during fruit ripening correlated with the advancement or delay in the expression of a set of genes that may be implicated in the maturation process. A detailed analysis of the transcription factors known to be involved in the regulation of fruit ripening identified a member of the MADS box family whose expression was lower in ARR, the early-ripening mutant, and higher in HER, the late-ripening mutant. The pattern of expression of this gene during the maturation period was basically contrary to those of the ethylene biosynthetic genes, SAM and ACC synthases and ACC oxidase. The gene was present in hemizygous dose in the early-ripening mutant. Our analysis provides new clues about the genetic control of fruit ripening in Citrus and allowed the identification of a transcription factor that could be involved in the early phenotype.

  • Transcriptomic analysis of Citrus Clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness
    BMC, 2019
    Co-Authors: Javier Terol, José M. Nueda, Daniel Ventimilla, Francisco Tadeo, Manuel Talon
    Abstract:

    Abstract Background Harvest time is a relevant economic trait in Citrus, and selection of cultivars with different fruit maturity periods has a remarkable impact in the market share. Generation of early- and late-maturing cultivars is an important target for Citrus breeders, therefore, generation of knowledge regarding the genetic mechanisms controlling the ripening process and causing the early and late phenotypes is crucial. In this work we analyze the evolution of the transcriptome during fruit ripening in 3 sport mutations derived from the Fina clementine (Citrus Clementina) mandarin: Clemenules (CLE), Arrufatina (ARR) and Hernandina (HER) that differ in their harvesting periods. CLE is considered a mid-season cultivar while ARR and HER are early- and late-ripening mutants, respectively. Results We used RNA-Seq technology to carry out a time course analysis of the transcriptome of the 3 mutations along the ripening period. The results indicated that in these mutants, earliness and lateness during fruit ripening correlated with the advancement or delay in the expression of a set of genes that may be implicated in the maturation process. A detailed analysis of the transcription factors known to be involved in the regulation of fruit ripening identified a member of the MADS box family whose expression was lower in ARR, the early-ripening mutant, and higher in HER, the late-ripening mutant. The pattern of expression of this gene during the maturation period was basically contrary to those of the ethylene biosynthetic genes, SAM and ACC synthases and ACC oxidase. The gene was present in hemizygous dose in the early-ripening mutant. Conclusions Our analysis provides new clues about the genetic control of fruit ripening in Citrus and allowed the identification of a transcription factor that could be involved in the early phenotype

  • this provisional pdf corresponds to the article as it appeared upon acceptance fully formatted pdf and full text html versions will be made available soon cytological and molecular characterization of three gametoclones of Citrus Clementina
    2013
    Co-Authors: Esther Carrera, Benedetta Chiancone, Chunxian Chen, Dominique Dambier, Patrick Ollitrault, Wenwu Guo, Kevin Kwok, Marcos Antonio Machado, Mikeal L Roose, Manuel Talon
    Abstract:

    Abstract Background Three gametoclonal plants of Citrus Clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control.

  • comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self incompatibility response of Citrus Clementina
    BMC Plant Biology, 2012
    Co-Authors: Marco Caruso, Stefano La Malfa, Gaetano Distefano, Manuel Talon, Paz Merelo, Angela Roberta Lo Piero, Francisco R Tadeo, Alessandra Gentile
    Abstract:

    Reproductive biology in Citrus is still poorly understood. Although in recent years several efforts have been made to study pollen-pistil interaction and self-incompatibility, little information is available about the molecular mechanisms regulating these processes. Here we report the identification of candidate genes involved in pollen-pistil interaction and self-incompatibility in clementine (Citrus Clementina Hort. ex Tan.). These genes have been identified comparing the transcriptomes of laser-microdissected stylar canal cells (SCC) isolated from two genotypes differing for self-incompatibility response ('Comune', a self-incompatible cultivar and 'Monreal', a self- compatible mutation of 'Comune'). The transcriptome profiling of SCC indicated that the differential regulation of few specific, mostly uncharacterized transcripts is associated with the breakdown of self-incompatibility in 'Monreal'. Among them, a novel F-box gene showed a drastic up-regulation both in laser microdissected stylar canal cells and in self-pollinated whole styles with stigmas of 'Comune' in concomitance with the arrest of pollen tube growth. Moreover, we identify a non-characterized gene family as closely associated to the self-incompatibility genetic program activated in 'Comune'. Three different aspartic-acid rich (Asp-rich) protein genes, located in tandem in the clementine genome, were over-represented in the transcriptome of 'Comune'. These genes are tightly linked to a DELLA gene, previously found to be up-regulated in the self-incompatible genotype during pollen-pistil interaction. The highly specific transcriptome survey of the stylar canal cells identified novel genes which have not been previously associated with self-pollen rejection in Citrus and in other plant species. Bioinformatic and transcriptional analyses suggested that the mutation leading to self-compatibility in 'Monreal' affected the expression of non-homologous genes located in a restricted genome region. Also, we hypothesize that the Asp-rich protein genes may act as Ca2+ "entrapping" proteins, potentially regulating Ca2+ homeostasis during self-pollen recognition.

  • development of ssr markers from Citrus Clementina rutaceae bac end sequences and interspecific transferability in Citrus p148
    Abstracts of Plant and Animal Genomes XIXth Conference San Diego CA (USA) January 15-19 2011, 2011
    Co-Authors: Frederique Ollitrault, Jose Antonio Pina, Luis Navarro, Javier Terol, Manuel Talon, Patrick Ollitrault
    Abstract:

    Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences (BES) of Citrus Clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata , C. maxima , C. medica , C. sinensis , C. aurantium , C. paradisi , C. lemon , C. aurantifolia, and some papedas (wild Citrus), using a capillary electrophoresis fragment analyzer. Intra and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps. (Resume d'auteur)

Patrick Ollitrault - One of the best experts on this subject based on the ideXlab platform.

  • fdr and srd are meiotic mechanisms involved in unreduced pollen gamete formation in a diploid hybrid between clementine and sweet orange
    Abstract book Sustainable citriculture: the role of applied knowledge, 2016
    Co-Authors: Houssem Rouiss, Luis Navarro, Patrick Ollitrault, Jose Cuenca, Pablo Aleza
    Abstract:

    A diploid hybrid between Citrus Clementina and C. sinensis (CDO) was used as male parent in 4x x 2x sexual hybridizations with tetraploid Fina clementine and Moncada mandarin as female parents to produce triploid hybrids. Unexpectedly, in addition to some triploids, a total of seventy-two tetraploid plants were obtained, 62 plants from Fina x CSO and ten from Moncada x CSO. SSR and SNP markers analysis releaved that recovered tetraploid plants were hybrids arising from unreduced pollen gametes. A maximum-likelihood methodology based on parental heterozygosity restitution (PHR) of markers close to the centromeres was used to identify the mechanism underlying 2n pollen gamete formation. Thirty five tetraploid hybrids were identified to arise from FDR (56%) and 18 from SDR (29%) mechanisms. Inconclusive data were obtained for nine tetraploid hybrids. The pattern of variation of PHR values of ten SSR and twi SNP markers located along linkage groups 1 and 2 confirmed our results at population level. To our knowledge this is the first report in Citrus of progenies of tetraploid hybrids recovered from 2n pollen gametes and the first description of coexistence of two meiotic mechanisms (SDR and FDR) producing unreduced pollen gametes. (Texte integral)

  • genetic mapping of centromeres in the nine Citrus Clementina chromosomes using half tetrad analysis and recombination patterns in unreduced and haploid gametes
    BMC Plant Biology, 2015
    Co-Authors: Pablo Aleza, Luis Navarro, Jose Cuenca, Maria Jose Hernandez, Jose Juarez, Patrick Ollitrault
    Abstract:

    Mapping centromere locations in plant species provides essential information for the analysis of genetic structures and population dynamics. The centromere’s position affects the distribution of crossovers along a chromosome and the parental heterozygosity restitution by 2n gametes is a direct function of the genetic distance to the centromere. Sexual polyploidisation is relatively frequent in Citrus species and is widely used to develop new seedless triploid cultivars. The study’s objectives were to (i) map the positions of the centromeres of the nine Citrus Clementina chromosomes; (ii) analyse the crossover interference in unreduced gametes; and (iii) establish the pattern of genetic recombination in haploid clementine gametes along each chromosome and its relationship with the centromere location and distribution of genic sequences. Triploid progenies were derived from unreduced megagametophytes produced by second-division restitution. Centromere positions were mapped genetically for all linkage groups using half-tetrad analysis. Inference of the physical locations of centromeres revealed one acrocentric, four metacentric and four submetacentric chromosomes. Crossover interference was observed in unreduced gametes, with variation seen between chromosome arms. For haploid gametes, a strong decrease in the recombination rate occurred in centromeric and pericentromeric regions, which contained a low density of genic sequences. In chromosomes VIII and IX, these low recombination rates extended beyond the pericentromeric regions. The genomic region corresponding to a genetic distance < 5cM from a centromere represented 47% of the genome and 23% of the genic sequences. The centromere positions of the nine Citrus chromosomes were genetically mapped. Their physical locations, inferred from the genetic ones, were consistent with the sequence constitution and recombination pattern along each chromosome. However, regions with low recombination rates extended beyond the pericentromeric regions of some chromosomes into areas richer in genic sequences. The persistence of strong linkage disequilibrium between large numbers of genes promotes the stability of epistatic interactions and multilocus-controlled traits over successive generations but also maintains multi-trait associations. Identification of the centromere positions will allow the development of simple methods to analyse unreduced gamete formation mechanisms in a large range of genotypes and further modelling of genetic inheritance in sexual polyploidisation breeding schemes.

  • this provisional pdf corresponds to the article as it appeared upon acceptance fully formatted pdf and full text html versions will be made available soon cytological and molecular characterization of three gametoclones of Citrus Clementina
    2013
    Co-Authors: Esther Carrera, Benedetta Chiancone, Chunxian Chen, Dominique Dambier, Patrick Ollitrault, Wenwu Guo, Kevin Kwok, Marcos Antonio Machado, Mikeal L Roose, Manuel Talon
    Abstract:

    Abstract Background Three gametoclonal plants of Citrus Clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control.

  • development of ssr markers from Citrus Clementina rutaceae bac end sequences and interspecific transferability in Citrus p148
    Abstracts of Plant and Animal Genomes XIXth Conference San Diego CA (USA) January 15-19 2011, 2011
    Co-Authors: Frederique Ollitrault, Jose Antonio Pina, Luis Navarro, Javier Terol, Manuel Talon, Patrick Ollitrault
    Abstract:

    Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences (BES) of Citrus Clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata , C. maxima , C. medica , C. sinensis , C. aurantium , C. paradisi , C. lemon , C. aurantifolia, and some papedas (wild Citrus), using a capillary electrophoresis fragment analyzer. Intra and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps. (Resume d'auteur)

  • development of ssr markers from Citrus Clementina rutaceae bac end sequences and interspecific transferability in Citrus
    American Journal of Botany, 2010
    Co-Authors: Frederique Ollitrault, Jose Antonio Pina, Luis Navarro, Javier Terol, Manuel Talon, Patrick Ollitrault
    Abstract:

    Premise of the study: Indel markers were developed from BAC-end sequences of Citrus Clementina cv. Nules. Transferability and polymorphism were tested in the Citrus genus to estimate the potential of indel markers mined from a single genotype for use in genetic studies. o Methods and Results: Using polyacrylamide gel electrophoresis and DNA silver staining, 89 indel markers were tested for their transferability and polymorphism. Thirty-eight markers were selected. Heterozygosity in C. Clementina cv. Nules was confirmed for 33 of these indel pairs. A preliminary diversity study using a capillary electrophoresis fragment analyzer was conducted with 21 indels using 45 accessions representing Citrus genus diversity. Intraspecific and interspecific polymorphisms were observed. o Conclusions: These results indicate the utility of indel markers developed from sequence data of a single genotype of interspecific origin. In Citrus, these markers will be useful for genetic mapping, germplasm characterization, and phylogenetic assignment of DNA fragments. (Resume d'auteur)

Maria Germana - One of the best experts on this subject based on the ideXlab platform.

  • microspore embryogenesis through anther culture in Citrus Clementina hort ex tan
    Methods of Molecular Biology, 2016
    Co-Authors: Benedetta Chiancone, Maria Germana
    Abstract:

    Anther culture is a biotechnological method that allows to obtain, in one step, homozygous plants, very important to plant breeding, due to their numerous applications in mutation research, selection, genome sequencing, genetic analysis, and transformation. To induce the microspores, i.e., the immature male gametes, to switch from the normal gametophytic pathway to the sporophytic one, it is necessary to submit them to a type of stress, such as high or low temperature, starvation, or magnetic field. Stress can be applied to the donor plants and/or the floral buds or the anthers or the isolated microspores, before or during the culture. In this chapter, the protocol to induce gametic embryogenesis from anther culture of several cultivars of Citrus Clementina Hort. ex Tan. is reported.

  • early embryo achievement through isolated microspore culture in Citrus Clementina hort ex tan cvs monreal rosso and nules
    Frontiers in Plant Science, 2015
    Co-Authors: Benedetta Chiancone, P S Testillano, Ivett Barany, Valeria Gianguzzi, Marines Marli Gniech Karasawa, A Abdelgalel, Daniela Torello Marinoni, Roberto Botta, Maria Germana
    Abstract:

    Microspore embryogenesis is a method of achieving complete homozygosity from plants. It is particularly useful for woody species, like Citrus, characterized by long juvenility, a high degree of heterozygosity and often self-incompatibility. Anther culture is currently the method of choice for microspore embryogenesis in many crops. However, isolated microspore culture is a better way to investigate the processes at the cellular, physiological, biochemical and molecular levels as it avoids the influence of somatic anther tissue. To exploit the potential of this technique, it is important to separate the key factors affecting the process and, among them, culture medium composition and particularly the plant growth regulators and their concentration, as they can greatly enhance regeneration efficiency. To our knowledge, the ability of meta-Topolin, a naturally occurring aromatic cytokinin, to induce gametic embryogenesis in isolated microspores of Citrus has never been investigated. In this study, the effect of two concentrations of meta-Topolin instead of benzyladenine or zeatin in the culture medium was investigated in isolated microspore culture of two genotypes of Citrus. After eleven months of isolated microspore culture, for both genotypes and for all the four tested media, the microspore reprogramming and their sporophytic development was observed by the presence of multinucleated calli and microspore-derived embryos at different stages. Microsatellite analysis of parental and embryo samples was performed to determine the embryo alleles constitution of early embryos produced in all tested media, confirming their origin from microspores. To our knowledge, this is the first successful report of Citrus microspore embryogenesis with isolated microspore culture in Citrus, and in particular in Citrus Clementina Hort. ex Tan, cvs. ‘Monreal Rosso’ and ‘Nules’.

  • early embryo achievement through isolated microspore culture in Citrus Clementina hort ex tan cvs monreal rosso and nules
    Frontiers in Plant Science, 2015
    Co-Authors: Benedetta Chiancone, P S Testillano, Ivett Barany, Valeria Gianguzzi, Marines Marli Gniech Karasawa, A Abdelgalel, Daniela Torello Marinoni, Roberto Botta, Maria Germana
    Abstract:

    Microspore embryogenesis is a method of achieving complete homozygosity from plants. It is particularly useful for woody species, like Citrus, characterized by long juvenility, a high degree of heterozygosity and often self-incompatibility. Anther culture is currently the method of choice for microspore embryogenesis in many crops. However, isolated microspore culture is a better way to investigate the processes at the cellular, physiological, biochemical, and molecular levels as it avoids the influence of somatic anther tissue. To exploit the potential of this technique, it is important to separate the key factors affecting the process and, among them, culture medium composition and particularly the plant growth regulators and their concentration, as they can greatly enhance regeneration efficiency. To our knowledge, the ability of meta-Topolin, a naturally occurring aromatic cytokinin, to induce gametic embryogenesis in isolated microspores of Citrus has never been investigated. In this study, the effect of two concentrations of meta-Topolin instead of benzyladenine or zeatin in the culture medium was investigated in isolated microspore culture of two genotypes of Citrus. After 11 months of isolated microspore culture, for both genotypes and for all the four tested media, the microspore reprogramming and their sporophytic development was observed by the presence of multinucleated calli and microspore-derived embryos at different stages. Microsatellite analysis of parental and embryo samples was performed to determine the embryo alleles constitution of early embryos produced in all tested media, confirming their origin from microspores. To our knowledge, this is the first successful report of Citrus microspore embryogenesis with isolated microspore culture in Citrus, and in particular in Citrus Clementina Hort. ex Tan, cvs. 'Monreal Rosso' and 'Nules.'

  • characterization of leaf essential oil composition of homozygous and heterozygous Citrus Clementina hort extan and its ancestors
    Journal of Essential Oil Bearing Plants, 2013
    Co-Authors: Maria Germana, Benedetta Chiancone, Eristanna Palazzolo, Filippo Saiano
    Abstract:

    Clementine is a natural tangor, resulting from an interspecific cross between mandarin and sweet orange. Gametic embryogenesis, allowing the single-step development of complete homozygous line from the heterozygous parents, increases the efficiency of perennial crop breeding programs. Tri-haploids have been regenerated through pollen embryogenesis (specifically, by anther culture) of Citrus Clementina Hort. ex Tan., cv. Nules. Two of them (HOMO1 and HOMO2) have been acclimatized and grafted in vivo in 2000. Research regarding the chemical characteristics of plant regenerated by pollen embryogenesis or gynogenesis are useful to study the “gametoclonal variation”, as well as for further application of haploidy technology in Citrus breeding. For these reasons and with the aim to characterize these homozygous clementine genotypes, in this study leaf essential oils were extracted by Clevenger apparatus and their chemical composition was investigated by capillary GC-MS, comparing them with oils obtained from th...

  • effect of polyamines on in vitro anther culture of Citrus Clementina hort ex tan
    Plant Cell Tissue and Organ Culture, 2006
    Co-Authors: Benedetta Chiancone, Annalisa Tassoni, Nello Bagni, Maria Germana
    Abstract:

    The improvement of the induction rate in Citrus anther culture is important for taking practical advantage of the haploid potential in breeding. The influence of polyamines on anther culture of Citrus Clementina, cv Nules, with particular attention to the free, soluble and insoluble-conjugated polyamine levels, has been investigated. Putrescine, spermidine and putrescine plus spermidine, were added to the standard induction medium. Before culture, spermidine was the most abundant among the free polyamines detected in anthers. The exogenous supply of either putrescine or spermidine, either independently or combined, effected greater uptake and accumulation of polyamines. The addition of 2 mM spermidine to the medium stimulated gametic embryogenesis in clementine Nules, whereas putrescine did not influence embryo production. Regenerants were mostly tri-haploids; a few doubled-haploids and no haploid plants were obtained.

Jin-zhi Zhang - One of the best experts on this subject based on the ideXlab platform.

  • genome wide identification and characterization of squamosa promoter binding protein sbp genes involved in the flowering development of Citrus Clementina
    Biomolecules, 2019
    Co-Authors: Ren-fang Zeng, Jing-jing Zhou, Sheng-rui Liu, Zhi-meng Gan, Jin-zhi Zhang
    Abstract:

    SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus Clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus Clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

  • Genome-Wide Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina
    MDPI AG, 2019
    Co-Authors: Ren-fang Zeng, Jing-jing Zhou, Sheng-rui Liu, Zhi-meng Gan, Jin-zhi Zhang
    Abstract:

    SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus Clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus Clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron⁻exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis

  • Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus Clementina).
    Plant Molecular Biology, 2018
    Co-Authors: Tian-jia Liu, Jing-jing Zhou, Jin-zhi Zhang
    Abstract:

    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.

  • Identification of the Genetic Variation and Gene Exchange between Citrus Trifoliata and Citrus Clementina
    MDPI AG, 2018
    Co-Authors: Tian-jia Liu, Jing-jing Zhou, Zhi-meng Gan, Fa-yi Chen, Jin-zhi Zhang
    Abstract:

    To identify the genetic variation between Citrus trifoliata and Citrus Clementina, we performed genome resequencing on the two Citrus species. Compared with the Citrus reference genome, a total of 9,449,204 single-nucleotide polymorphisms (SNPs) and 846,615 insertion/deletion polymorphisms (InDels) were identified in the two Citrus species, while 1,868,115 (19.77%) of the SNPs and 190,199 (22.47%) of the InDels from the two Citrus species were located in the genic regions. Meanwhile, a total of 8,091,407 specific SNPs and 692,654 specific InDels were identified in the two Citrus genotypes, yielding an average of 27.32 SNPs/kb and 2.34 InDels/kb. We identified and characterized the patterns of gene exchanges in the grafted Citrus plants by using specific genetic variation from genome resequencing. A total of 4396 transporting genes across graft junctions was identified. Some specific genetic variation and mobile genes was also confirmed by Sanger sequencing. Furthermore, these mobile genes could move directionally or bidirectionally between the scions and the rootstocks. In addition, a total of 1581 and 2577 differentially expressed genes were found in the scions and the rootstocks after grafting compared with the control, respectively. These genetic variations provide fundamental information on the genetic basis of important traits between C. trifoliata and C. Clementina, as the transport of genes would be applicable to horticulture crops