Gabino Ríos

IVIA, Ceará, Ceará, Brazil

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Publications (22)53.14 Total impact


  • No preview · Article · Feb 2016 · Tree Genetics & Genomes
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    ABSTRACT: Bud dormancy is an evolutionary adaptation of perennial plants to the seasonal fluctuation of temperatures in temperate climates, affected by intrinsic and environmental signals. Recent investigations point to a relevant role of epigenetic mechanisms in the regulation of bud dormancy. We have performed a chromatin immunoprecipitation sequencing (ChIP-seq) analysis of histone H3 lysine-27 trimethylation (H3K27me3), a chromatin mark associated with stable gene silencing, in dormant (D) and dormancy-released (ND) buds of peach (Prunus persica). H3K27me3 regions were more abundant in gene-rich euchromatic zones of chromosomes and associated with gene bodies. The dormancy regulators DORMANCY-ASSOCIATED MADS-box (DAM)1, DAM4, DAM5 and DAM6 were found significantly enriched in H3K27me3 in ND samples, in close agreement with their dormancy-specific expression. The DAM locus was modified at specific short regions, allowing the uneven regulation of distinct DAM genes. Additional regulatory factors related to meristem activity and flowering genes from Arabidopsis thaliana were differentially H3K27 trimethylated, which suggests that meristem reactivation and flower development could be also epigenetically regulated in reproductive buds of peach. A (GA)n motif and CACTA-type transposon-related sequences were found over-represented in H3K27me3 regions.
    No preview · Article · Jun 2015 · Tree Genetics & Genomes
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    ABSTRACT: Release of bud dormancy in perennial plants resembles vernalization in Arabidopsis thaliana and cereals. In both cases, a certain period of chilling is required for accomplishing the reproductive phase, and several transcription factors with the MADS-box domain perform a central regulatory role in these processes. The expression of DORMANCY-ASSOCIATED MADS-box (DAM)-related genes has been found to be up-regulated in dormant buds of numerous plant species, such as poplar, raspberry, leafy spurge, blackcurrant, Japanese apricot, and peach. Moreover, functional evidence suggests the involvement of DAM genes in the regulation of seasonal dormancy in peach. Recent findings highlight the presence of genome-wide epigenetic modifications related to dormancy events, and more specifically the epigenetic regulation of DAM-related genes in a similar way to FLOWERING LOCUS C, a key integrator of vernalization effectors on flowering initiation in Arabidopsis. We revise the most relevant molecular and genomic contributions in the field of bud dormancy, and discuss the increasing evidence for chromatin modification involvement in the epigenetic regulation of seasonal dormancy cycles in perennial plants.
    Full-text · Article · Jun 2014 · Frontiers in Plant Science
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    ABSTRACT: The reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach. We have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time. We identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.
    Full-text · Article · Feb 2014 · BMC Plant Biology
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    ABSTRACT: 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). 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. The presence of few gene hybridization abnormalities, corroborated by gene dosage measurements, were hypothetically due to the segregation of hemizygous alleles and minor genomic rearrangements occurring during the haploidization procedure. In conclusion, these plants that are valuable genetic and breeding materials contain completely homozygous and essentially intact genomes.
    Full-text · Article · Sep 2013 · BMC Plant Biology
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    ABSTRACT: Background The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in the tapetal cells and its proper deposition on the pollen surface are essential for the development of viable pollen. The beginning of microsporogenesis and pollen maturation in perennial plants from temperate climates, such as peach, is conditioned by the duration of flower bud dormancy. In order to identify putative genes involved in these processes, we analyzed the results of previous genomic experiments studying the dormancy-dependent gene expression in different peach cultivars. Results The expression of 50 genes induced in flower buds after the endodormancy period (flower-bud late genes) was compared in ten cultivars of peach with different dormancy behaviour. We found two co-expression clusters enriched in putative orthologs of sporopollenin synthesis and deposition factors in Arabidopsis. Flower-bud late genes were transiently expressed in anthers coincidently with microsporogenesis and pollen maturation processes. We postulated the participation of some flower-bud late genes in the sporopollenin synthesis pathway and the transcriptional regulation of late anther development in peach. Conclusions Peach and the model plant Arabidopsis thaliana show multiple elements in common within the essential sporopollenin synthesis pathway and gene expression regulatory mechanisms affecting anther development. The transcriptomic analysis of dormancy-released flower buds proved to be an efficient procedure for the identification of anther and pollen development genes in perennial plants showing seasonal dormancy.
    Full-text · Article · Jan 2013 · BMC Genomics
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    ABSTRACT: Background Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo ‘Piel de sapo’ (‘PS’) and C. melo ‘Pat 81’, with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. Results Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. ‘PS’ responded with a more rapid infection response than ‘Pat 81’ at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in ‘PS’ declined from 451 to 359, while the total number of differentially expressed transcripts in ‘Pat 81’ increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in ‘Pat 81’ compared to ‘PS’ suggested that JA response might be partially responsible for their observed differences in resistance. Conclusions As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.
    Full-text · Article · Nov 2012 · BMC Genomics
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    ABSTRACT: The effect of different chilling and gibberellin treatments on growth and development of the peach rootstocks 'Nemaguard' and 'GF305' was studied. A factorial experiment was designed combining cold treatments (0, 5, 15 and 30 days at 4°C temperature) and GA3 concentrations (0, 100 and 200 mg/L). The variables considered were: percentage of germination, number of internodes, plant height and the ratio plant height/number of internodes. Results showed an overall growth increase as a consequence of chilling and gibberellin addition; however the behaviour of the two assayed rootstocks was slightly different. In general terms, 'Nemaguard' responded well to 5 days cold and chilling treatments did not improve growth in a relevant way, whereas 'GF305' showed a more gradual effect of the chilling and gibberellin treatments on the studied parameters.
    No preview · Article · Oct 2012 · Acta horticulturae
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    ABSTRACT: Reproductive meristems and embryos display dormancy mechanisms in specialized structures named respectively buds and seeds that arrest the growth of perennial plants until environmental conditions are optimal for survival. Dormancy shows common physiological features in buds and seeds. A genotype-specific period of chilling is usually required to release dormancy by molecular mechanisms that are still poorly understood. In order to find common transcriptional pathways associated to dormancy release, we analyzed the chilling-dependent expression in embryos of certain genes that were previously found related to dormancy in flower buds of peach. We propose the presence of short and long-term dormancy events affecting respectively the germination rate and seedling development by independent mechanisms. Short periods of chilling seem to improve germination in an abscisic acid-dependent manner, whereas the positive effect of longer cold treatments on physiological dwarfing coincides with the accumulation of phenylpropanoids in the seed.
    Full-text · Article · May 2012 · PLoS ONE
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    ABSTRACT: With 2 figures and 2 tables Dormancy has been defined as the inability to initiate growth from meristem under favourable environmental conditions. The length of dormancy is a genotype-specific trait that limits the climatic adaptability of temperate crops, as peach. A better knowledge of the genes involved in dormancy may provide genetic tools for an early assessment of the trait in breeding programmes. Recent studies on the molecular aspects of dormancy provided an initial description of candidate genes involved in bud dormancy maintenance and release in peach. In this paper, we compare the chilling requirement for dormancy release of five peach cultivars with the expression of five genes and ESTs related to bud dormancy: DAM5, DB396 (ppa007606m), DB247 (ppa012188m), SB280 (ppa006974m) and PpB63 (ppa008309m). Results indicated that gene expression analysis could contribute to estimate the chilling requirement for dormancy release of new cultivars.
    Full-text · Article · Apr 2012 · Plant Breeding
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    ABSTRACT: To better understand the molecular and physiological mechanisms underlying maintenance and release of seasonal bud dormancy in deciduous trees, we previously made four different libraries enriched in cDNA from dormant buds, dormancy-released buds, and buds from the peach 'Springlady' and 'Zincal-5', with different chilling requirements. In this work we analyze by RT-PCR the mRNA accumulation of some of these genes and describe the dormancy-dependent expression of two peach genes similar to Arabidopsis VIN3 and FT. As expected, DAM genes showed reduced expression during dormancy release in buds, whereas several peroxidase-like coding genes, among others, were drastically up-regulated after dormancy release. The peach homologues of VIN3 and FT genes increased their expression from November to January, suggesting a link with the vernalization pathway in Arabidopsis.
    Full-text · Article · Mar 2012 · Acta horticulturae
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    ABSTRACT: During fruit ripening a loss of firmness occurs, which is a key factor limiting postharvest life. In apricot, Prunus armeniaca L., a wide range of fruit firmness at commercial maturity has been observed in different cultivars. Endopolygalacturonase (endoPG) activity has been reported to be associated with differences in firmness in many fruit species, but never in apricot. In this paper, we reported the identification of an apricot cDNA (PaPG) coding for an endoPG-like protein with 393 amino acids. Protein sequence comparison with known polygalacturonases (PGs) revealed that multiple features as conserved domains and functional residues and a predicted signal peptide were present in PaPG. Moreover, a phylogenetic analysis of this and other plant PGs placed PaPG into a clade containing endoPGs expressed in fruit, abscission and dehiscence zones without a propeptide sequence, very close to PRF5 from peach (Prunus persica L. Batsch). PaPG gene expression increased during postharvest storage of the fruit, correlating with fruit softening and ethylene release, and it responded to exogenous ethylene treatments. We localized the PaPG gene in apricot linkage group 4 after genetic mapping based on SNP analysis, in a position apparently syntenic to the PRF5 locus from peach. Results obtained offer genetic evidence supporting the hypothesis that PaPG and PRF5 are orthologous genes, and consequently position PaPG as a gene of interest for studies on fruit softening in apricot, and contribute to the development of molecular tools for breeding apricots with longer shelf life.
    Full-text · Article · Oct 2011 · Postharvest Biology and Technology
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    ABSTRACT: • Bud dormancy release in many woody perennial plants responds to the seasonal accumulation of chilling stimulus. MADS-box transcription factors encoded by DORMANCY ASSOCIATED MADS-box (DAM) genes in peach (Prunus persica) are implicated in this pathway, but other regulatory factors remain to be identified. In addition, the regulation of DAM gene expression is not well known at the molecular level. • A microarray hybridization approach was performed to identify genes whose expression correlates with the bud dormancy-related behaviour in 10 different peach cultivars. Histone modifications in DAM6 gene were investigated by chromatin immunoprecipitation in two different cultivars. • The expression of DAM4-DAM6 and several genes related to abscisic acid and drought stress response correlated with the dormancy behaviour of peach cultivars. The trimethylation of histone H3 at K27 in the DAM6 promoter, coding region and the second large intron was preceded by a decrease in acetylated H3 and trimethylated H3K4 in the region of translation start, coinciding with repression of DAM6 during dormancy release. • Analysis of chromatin modifications reinforced the role of epigenetic mechanisms in DAM6 regulation and bud dormancy release, and highlighted common features with the vernalization process in Arabidopsis thaliana and cereals.
    Full-text · Article · Sep 2011 · New Phytologist
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    ABSTRACT: The survival of the citrus industry is critically dependent on genetically superior cultivars. Improvements in these traits through traditional techniques are unfortunately extremely difficult due to the unusual combination of biological characteristics of citrus. Genomic science holds promise of improvements in breeding and the main goal of our group is to develop genomics tools for the generation of new genotypes. We pursue the identification of candidate genes, alleles and genotypes improving citrus fruit quality and performance, correlating phenotypic analyses, metabolic profiling and gene expression. At completion, genes and alleles with major functions in nutritional quality and stress tolerance could be selected and genotypes with improved fruit composition searched among existing or generated collections. This goal is supported by two complementary strategies the identification of genes of agricultural interest by the use of mutants and microarrays and the elucidation of the citrus genome sequence. In this communication the efforts we are developing in this first approach are revised while the other strategy will be resumed elsewhere.
    No preview · Article · Mar 2011 · Acta horticulturae
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    ABSTRACT: Citrus (Citrus spp.) is the main fruit tree crop in the world and therefore has a tremendous economical, social and cultural impact in our society. In recent years, our knowledge on plant reproductive biology has increased considerably mostly because of the work developed in model plants. However, the information generated in these species cannot always be applied to citrus, predominantly because citrus is a perennial tree crop that exhibits a very peculiar and unusual reproductive biology. Regulation of fruit growth and development in citrus is an intricate phenomenon depending upon many internal and external factors that may operate both sequentially and simultaneously. The elements and mechanisms whereby endogenous and environmental stimuli affect fruit growth are being interpreted and this knowledge may help to provide tools that allow optimizing production and fruit with enhanced nutritional value, the ultimate goal of the Citrus Industry. In this chapter we review the progress that has taken place in the physiology of citrus fruiting during recent years and present the current status of major research topics in this area.
    Full-text · Article · Jan 2011
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    ABSTRACT: Citrus (Citrus spp.) is the main fruit tree crop in the world and therefore has a tremendous economical, social and cultural impact in our society. In recent years, our knowledge on plant reproductive biology has increased considerably mostly because of the work developed in model plants. However, the information generated in these species cannot always be applied to citrus, predominantly because citrus is a perennial tree crop that exhibits a very peculiar and unusual reproductive biology. Regulation of fruit growth and development in citrus is an intricate phenomenon depending upon many internal and external factors that may operate both sequentially and simultaneously. The elements and mechanisms whereby endogenous and environmental stimuli affect fruit growth are being interpreted and this knowledge may help to provide tools that allow optimizing production and fruit with enhanced nutritional value, the ultimate goal of the Citrus Industry. In this chapter we review the progress that has taken place in the physiology of citrus fruiting during recent years and present the current status of major research topics in this area.
    Full-text · Book · Jan 2011
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    ABSTRACT: External ripening in Citrus fruits is morphologically characterized by a colour shift from green to orange due to the degradation of chlorophylls and the accumulation of carotenoid pigments. Although numerous genes coding for enzymes involved in such biochemical pathways have been identified, the molecular control of this process has been scarcely studied. In this work we used the Citrus clementina mutants 39B3 and 39E7, showing delayed colour break, to isolate genes potentially related to the regulation of peel ripening and its physiological or biochemical effects. Pigment analyses revealed different profiles of carotenoid and chlorophyll modification in 39B3 and 39E7 mutants. Flavedo from 39B3 fruits showed an overall delay in carotenoid accumulation and chlorophyll degradation, while the flavedo of 39E7 was devoid of the apocarotenoid β-citraurin among other carotenoid alterations. A Citrus microarray containing about 20,000 cDNA fragments was used to identify genes that were differentially expressed during colour change in the flavedo of 39B3 and 39E7 mutants respect to the parental variety. The results highlighted 73 and 90 genes that were respectively up- and down-regulated in both mutants. CcGCC1 gene, coding for a GCC type transcriptional factor, was found to be down-regulated. CcGCC1 expression was strongly induced at the onset of colour change in the flavedo of parental clementine fruit. Moreover, treatment of fruits with gibberellins, a retardant of external ripening, delayed both colour break and CcGCC1 overexpression. In this work, the citrus fruit ripening mutants 39B3 and 39E7 have been characterized at the phenotypic, biochemical and transcriptomic level. A defective synthesis of the apocarotenoid β-citraurin has been proposed to cause the yellowish colour of fully ripe 39E7 flavedo. The analyses of the mutant transcriptomes revealed that colour change during peel ripening was strongly associated with a major mobilization of mineral elements and with other previously known metabolic and photosynthetic changes. The expression of CcGCC1 was associated with peel ripening since CcGCC1 down-regulation correlated with a delay in colour break induced by genetic, developmental and hormonal causes.
    Full-text · Article · Dec 2010 · BMC Plant Biology
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    ABSTRACT: To better understand the molecular and physiological mechanisms underlying maintenance and release of seasonal bud dormancy in perennial trees, we identified differentially expressed genes during dormancy progression in reproductive buds from peach (Prunus persica [L.] Batsch) by suppression subtractive hybridization (SSH) and microarray hybridization. Four SSH libraries were constructed, which were respectively enriched in cDNA highly expressed in dormant buds (named DR), in dormancy-released buds (RD) and in the cultivars with different chilling requirement, 'Zincal 5' (ZS) and 'Springlady' (SZ), sampled after dormancy release. About 2500 clones picked from the four libraries were loaded on a glass microarray. Hybridization of microarrays with the final products of SSH procedure was performed in order to validate the selected clones that were effectively enriched in their respective sample. Nearly 400 positive clones were sequenced, which corresponded to 101 different unigenes with diverse functional annotation. We obtained DAM4, 5 and 6 genes coding for MADS-box transcription factors previously related to growth cessation and terminal bud formation in the evergrowing mutant of peach. Several other cDNAs are similar to dormancy factors described in other species, and others have been related to bud dormancy for the first time in this study. Quantitative reverse transcription polymerase chain reaction analysis confirmed differential expression of cDNAs coding for a Zn-finger transcription factor, a GRAS-like regulator, a DNA-binding protein and proteins similar to forisome subunits involved in the reversible occlusion of sieve elements in Fabaceae, among others.
    Full-text · Article · Mar 2010 · Tree Physiology
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    ABSTRACT: Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.
    Full-text · Article · Sep 2008 · BMC Genomics
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    ABSTRACT: Citrus is the most economically important fruit crop in the world. Citrus fruits are classified as hesperidiums, berries of very special organization characterized by a juicy pulp made of vesicles within segments. Besides the typical fruit components, citrus fruit contain many organic compounds necessary for human diet and an extraordinary number of metabolites displaying valuable properties for health. In citrus, the concept of fruit quality comprises several other aspects intimately related to human health apart from physical attributes and diet components. Citrus also possess a rare combination of intriguing biological characteristics including an unusual reproductive biology, a non‐climacteric fruit ripening and several specific tree‐traits. The combination of these characteristics suggests that the study of fruit growth regulation in citrus may reveal original mechanisms based on explicit molecular differences and on exclusive genes. Citrus is, therefore, an excellent model to study fruit quality because of its peculiar fruiting, singular biochemistry and economical relevance. In this chapter, the progress that has been carried out in the research on the molecular determinants related to development and fruit quality of citrus is reviewed. The review also intends to provide a physiological frame for the implementation of the information generated during the past years. Molecular background is provided on the current status of principal reproductive processes related to fruit quality mainly flowering, fruiting, ripening, and abscission. We also have focused on main characteristic secondary bioactive compounds, as major contributors of aroma and flavour and finally, on the abiotic stresses influencing development and fruit growth.
    No preview · Article · Jan 2008 · Advances in Botanical Research