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author:("talin, Manuel")
1.  Diversity of floral regulatory genes of japonica rice cultivated at northern latitudes 
BMC Genomics  2014;15:101.
Background
Rice is considered a short day plant. Originally from tropical regions rice has been progressively adapted to temperate climates and long day conditions in part by modulating its sensitivity to day length. Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1) that code for florigens, are known as major regulatory genes of floral transition in rice. Both Hd3a and RFT1 are regulated by Early heading date 1 (Ehd1) and Days to heading on chromosome 2 (DTH2) while Heading date 1 (Hd1) also governs Hd3a expression. To investigate the mechanism of rice adaptation to temperate climates we have analyzed the natural variation of these five genes in a collection of japonica rice representing the genetic diversity of long day cultivated rice.
Results
We have investigated polymorphisms of Hd3a, RFT1, Ehd1, Hd1 and DTH2 in a collection of 57 japonica varieties. Hd3a and RFT1 were highly conserved, displaying one major allele. Expression analysis suggested that RFT1 rather than Hd3a could be the pivotal gene controlling flowering under long day conditions. While few alleles were found in the Ehd1 promoter and DTH2 coding region, a high degree of variation in Hd1, including non-functional alleles, was observed. Correlation analysis between gene expression levels and flowering periods suggested the occurrence of other factors, additionally to Ehd1, affecting RFT1 regulation in long day adapted cultivars.
Conclusions
During domestication, rice expansion was accompanied by changes in the regulatory mechanism of flowering. The existence of non-functional Hd1 alleles and the lack of correlation of their presence with flowering times in plants grown under long day conditions, indicate a minor role of this branch in this process and the existence of an alternative regulatory pathway in northern latitudes. Expression analysis data and a high degree of conservation of RFT1 suggested that this gene could be the main factor regulating flowering among japonica cultivars adapted to northern areas. In the absence of inhibition exerted by Hd1 through repression of Hd3a expression, the role of Ehd1 as a regulator of RFT1 and Hd3a appears to be reinforced. Data also indicated the occurrence of additional regulatory factors controlling flowering.
doi:10.1186/1471-2164-15-101
PMCID: PMC3922420  PMID: 24498868
Flowering; Short day; Rice; Polymorphism; Natural variation
2.  The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker 
PLoS ONE  2013;8(11):e80930.
Pathogens interaction with a host plant starts a set of immune responses that result in complex changes in gene expression and plant physiology. Light is an important modulator of plant defense response and recent studies have evidenced the novel influence of this environmental stimulus in the virulence of several bacterial pathogens. Xanthomonas citri subsp. citri is the bacterium responsible for citrus canker disease, which affects most citrus cultivars. The ability of this bacterium to colonize host plants is influenced by bacterial blue-light sensing through a LOV-domain protein and disease symptoms are considerably altered upon deletion of this protein. In this work we aimed to unravel the role of this photoreceptor during the bacterial counteraction of plant immune responses leading to citrus canker development. We performed a transcriptomic analysis in Citrus sinensis leaves inoculated with the wild type X. citri subsp. citri and with a mutant strain lacking the LOV protein by a cDNA microarray and evaluated the differentially regulated genes corresponding to specific biological processes. A down-regulation of photosynthesis-related genes (together with a corresponding decrease in photosynthesis rates) was observed upon bacterial infection, this effect being more pronounced in plants infected with the lov-mutant bacterial strain. Infection with this strain was also accompanied with the up-regulation of several secondary metabolism- and defense response-related genes. Moreover, we found that relevant plant physiological alterations triggered by pathogen attack such as cell wall fortification and tissue disruption were amplified during the lov-mutant strain infection. These results suggest the participation of the LOV-domain protein from X. citri subsp. citri in the bacterial counteraction of host plant defense response, contributing in this way to disease development.
doi:10.1371/journal.pone.0080930
PMCID: PMC3829917  PMID: 24260514
3.  Early gene expression events in the laminar abscission zone of abscission-promoted citrus leaves after a cycle of water stress/rehydration: involvement of CitbHLH1 
Journal of Experimental Botany  2012;63(17):6079-6091.
Leaf abscission is a common response of plants to drought stress. Some species, such as citrus, have evolved a specific behaviour in this respect, keeping their leaves attached to the plant body during water stress until this is released by irrigation or rain. This study successfully reproduced this phenomenon under controlled conditions (24h of water stress followed by 24h of rehydration) and used it to construct a suppression subtractive hybridization cDNA library enriched in genes involved in the early stages of rehydration-promoted leaf abscission after water stress. Sequencing of the library yielded 314 unigenes, which were spotted onto nylon membranes. Membrane hybridization with petiole (Pet)- and laminar abscission zone (LAZ)-enriched RNA samples corresponding to early steps in leaf abscission revealed an almost exclusive preferential gene expression programme in the LAZ. The data identified major processes such as protein metabolism, cell-wall modification, signalling, control of transcription and vesicle production, and transport as the main biological processes activated in LAZs during the early steps of rehydration-promoted leaf abscission after water stress. Based on these findings, a model for the early steps of citrus leaf abscission is proposed. In addition, it is suggested that CitbHLH1, the putative citrus orthologue of Arabidopsis BIGPETAL, may play major roles in the control of abscission-related events in citrus abscission zones.
doi:10.1093/jxb/ers270
PMCID: PMC3481208  PMID: 23028022
Citrus clementina; cDNA custom macroarray; expression profiling; laminar abscission zone; mandarin; petiole
4.  Identification of a GCC transcription factor responding to fruit colour change events in citrus through the transcriptomic analyses of two mutants 
BMC Plant Biology  2010;10:276.
Background
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.
Results
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.
Conclusions
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.
doi:10.1186/1471-2229-10-276
PMCID: PMC3014968  PMID: 21159189
5.  Tissue-specific transcriptome profiling of the citrus fruit epidermis and subepidermis using laser capture microdissection 
Journal of Experimental Botany  2010;61(12):3321-3330.
Most studies of the biochemical and regulatory pathways that are associated with, and control, fruit expansion and ripening are based on homogenized bulk tissues, and do not take into consideration the multiplicity of different cell types from which the analytes, be they transcripts, proteins or metabolites, are extracted. Consequently, potentially valuable spatial information is lost and the lower abundance cellular components that are expressed only in certain cell types can be diluted below the level of detection. In this study, laser microdissection (LMD) was used to isolate epidermal and subepidermal cells from green, expanding Citrus clementina fruit and their transcriptomes were compared using a 20k citrus cDNA microarray and quantitative real-time PCR. The results show striking differences in gene expression profiles between the two cell types, revealing specific metabolic pathways that can be related to their respective organelle composition and cell wall specialization. Microscopy provided additional evidence of tissue specialization that could be associated with the transcript profiles with distinct differences in organelle and metabolite accumulation. Subepidermis predominant genes are primarily involved in photosynthesis- and energy-related processes, as well as cell wall biosynthesis and restructuring. By contrast, the most epidermis predominant genes are related to the biosynthesis of the cuticle, flavonoids, and defence responses. Furthermore, the epidermis transcript profile showed a high proportion of genes with no known function, supporting the original hypothesis that analysis at the tissue/cell specific levels can promote gene discovery and lead to a better understanding of the specialized contribution of each tissue to fruit physiology.
doi:10.1093/jxb/erq153
PMCID: PMC2905196  PMID: 20519339
Cell wall; citrus; cuticle; epidermis; fruit; laser microdissection; microarray; transcriptome
6.  Effects of antagonists and inhibitors of ethylene biosynthesis on maize root elongation 
Plant Signaling & Behavior  2009;4(12):1154-1156.
During the first days of development, maize roots showed considerable variation in the production of ethylene and the rate of elongation. As endogenous ethylene increases, root elongation decreases. When these roots are treated with the precursor of ethylene aminocyclopropane- 1-carboxylic acid (ACC), or inhibitors of ethylene biosynthesis 2-aminoethoxyvinyl glycine (AVG) or cobalt ions, the root elongation is also inhibited. Because of root growth diminishes at high or reduced endogenous ethylene concentrations, it appears that this phytohormone must be maintained in a range of concentrations to support normal root growth. In spite of its known role as inhibitor of ethylene action, silver thiosulphate (STS) does not change significantly the root elongation rate. This suggests that the action of ethylene on root elongation should occur, at least partially, by interaction with other growth regulators.
PMCID: PMC2819443  PMID: 20514233
2-aminoethoxyvinyl glycine; cobalt; ethylene; root elongation; silver thiosulphate; Zea mays
7.  Comparative transcriptional survey between laser-microdissected cells from laminar abscission zone and petiolar cortical tissue during ethylene-promoted abscission in citrus leaves 
BMC Plant Biology  2009;9:127.
Background
Abscission is the cell separation process by which plants are able to shed organs. It has a great impact on the yield of most crop plants. At the same time, the process itself also constitutes an excellent model to study cell separation processes, since it occurs in concrete areas known as abscission zones (AZs) which are composed of a specific cell type. However, molecular approaches are generally hampered by the limited area and cell number constituting the AZ. Therefore, detailed studies at the resolution of cell type are of great relevance in order to accurately describe the process and to identify potential candidate genes for biotechnological applications.
Results
Efficient protocols for the isolation of specific citrus cell types, namely laminar abscission zone (LAZ) and petiolar cortical (Pet) cells based on laser capture microdissection (LCM) and for RNA microextraction and amplification have been developed. A comparative transcriptome analysis between LAZ and Pet from citrus leaf explants subjected to an in-vitro 24 h ethylene treatment was performed utilising microarray hybridization and analysis. Our analyses of gene functional classes differentially represented in ethylene-treated LAZ revealed an activation program dominated by the expression of genes associated with protein synthesis, protein fate, cell type differentiation, development and transcription. The extensive repertoire of genes associated with cell wall biosynthesis and metabolism strongly suggests that LAZ layers activate both catabolic and anabolic wall modification pathways during the abscission program. In addition, over-representation of particular members of different transcription factor families suggests important roles for these genes in the differentiation of the effective cell separation layer within the many layers contained in the citrus LAZ. Preferential expression of stress-related and defensive genes in Pet reveals that this tissue is likely to be reprogrammed to prevent pathogen attacks and general abiotic stresses after organ shedding.
Conclusion
The LCM-based data generated in this survey represent the most accurate description of the main biological processes and genes involved in organ abscission in citrus. This study provides novel molecular insight into ethylene-promoted leaf abscission and identifies new putative target genes for characterization and manipulation of organ abscission in citrus.
doi:10.1186/1471-2229-9-127
PMCID: PMC2770498  PMID: 19852773
8.  Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome 
BMC Genomics  2008;9:381.
Background
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.
Results
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.
Conclusion
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.
doi:10.1186/1471-2164-9-381
PMCID: PMC2533677  PMID: 18691431
9.  Ethylene-induced differential gene expression during abscission of citrus leaves 
Journal of Experimental Botany  2008;59(10):2717-2733.
The main objective of this work was to identify and classify genes involved in the process of leaf abscission in Clementina de Nules (Citrus clementina Hort. Ex Tan.). A 7 K unigene citrus cDNA microarray containing 12 K spots was used to characterize the transcriptome of the ethylene-induced abscission process in laminar abscission zone-enriched tissues and the petiole of debladed leaf explants. In these conditions, ethylene induced 100% leaf explant abscission in 72 h while, in air-treated samples, the abscission period started later and took 240 h. Gene expression monitored during the first 36 h of ethylene treatment showed that out of the 12 672 cDNA microarray probes, ethylene differentially induced 725 probes distributed as follows: 216 (29.8%) probes in the laminar abscission zone and 509 (70.2%) in the petiole. Functional MIPS classification and manual annotation of differentially expressed genes highlighted key processes regulating the activation and progress of the cell separation that brings about abscission. These included cell-wall modification, lipid transport, protein biosynthesis and degradation, and differential activation of signal transduction and transcription control pathways. Expression data associated with the petiole indicated the occurrence of a double defensive strategy mediated by the activation of a biochemical programme including scavenging ROS, defence and PR genes, and a physical response mostly based on lignin biosynthesis and deposition. This work identifies new genes probably involved in the onset and development of the leaf abscission process and suggests a different but co-ordinated and complementary role for the laminar abscission zone and the petiole during the process of abscission.
doi:10.1093/jxb/ern138
PMCID: PMC2486473  PMID: 18515267
Citrus clementina; cDNA microarray; expression profiling; laminar abscission zone; mandarin; petiole
10.  High-throughput functional annotation and data mining with the Blast2GO suite 
Nucleic Acids Research  2008;36(10):3420-3435.
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
doi:10.1093/nar/gkn176
PMCID: PMC2425479  PMID: 18445632

Results 1-10 (10)