Biology subjects

Chalfun-Junior, A.

Publications and source records attributed to Chalfun-Junior, A..

10 recordsLinked to original sources

bioRxiv2024

A leaf-expressed TERMINAL FLOWER1 ortholog from coffee with alternate splice forms alters flowering time and inflorescence branching in Arabidopsis

Perennial, polycarpic species, such as Coffea sp L. (coffee), exhibit asynchronous flowering while maintaining concomitant vegetative growth. This growth dichotomy is associated directly with fruit development and maturation time. To identify molecular components that underlie asynchronous flowering, we isolated phosphatidylethanolamine binding protein (PEBP) homologs expressed in coffee and identified a gene with high similarity to Arabidopsis TERMINAL FLOWER1-like. In Arabidopsis, interaction of TFL1 (AtTFL1) with bZIP transcription factor floral regulator FD (AtFD) forms a floral repressor complex that maintains inflorescence meristems in an indeterminate state. Unlike AtTFL1, which is expressed only in the shoot apical meristem, CaTFL1 transcript was detected exclusively in coffee leaves. Moreover, this transcript retained an intron, which was not reported for AtTFL1. CaTFL1 was characterized through heterologous expression in Arabidopsis and protein interaction analysis. Ectopic overexpression of CaTFL1 in transgenic Arabidopsis plants caused extreme late flowering or prevented flowering. However, the most severe floral repressive activity occurred in transgenic plants that spliced out the extra intron from CaTFL1. Yeast two hybrid assay revealed that CaTFL1 protein encoded by the spliced mRNA interacts with AtFD, as well as Arabidopsis 14-3-3 protein. These findings suggest that CaTFL1 acts as a leaf-expressed floral repressor, whose activity is controlled by alternate splicing, and may contribute to asynchronous flowering in coffee.

plant biology↗

bioRxiv2024

The contrasting flowering-time among coffee genotypes is associated with ectopic and differential expressions of genes related to environment, floral development, and hormonal regulation

The molecular pathways underlying floral activation and development are well described in model species, but exhibit significant diversity in plants that is poorly understood in crops with complex cycles, such as Coffea arabica L. The reproductive development of coffee plants is biannual, and the flowering time is crucial for the coffee productivity and cup quality. In this study, we explored the plasticity of floral development and flowering-time of contrasting coffee genotypes to understand the associated metabolic and regulatory transcriptional profiles. Firstly, we compared the reproductive development of three coffee genotypes, confirming that Acaua is late flowering, Oeiras is early flowering, and the natural mutant Semperflorens (Sf) exhibits continuous flowering throughout the year. Analysis of sugar and ethylene content revealed quantitative differences between genotypes in both leaves and floral buds. To associate these phenotypic differences with the regulatory developmental pathways, we performed RNA-seq analysis comparing the shoot apical meristems, floral buds and leaves of different genotypes. Our analysis identified 12.478 differentially expressed genes, which showed enriched terms mainly related to hormonal regulation, external stimulus and floral development. Notably, some major players of reproductive development, as homologs of FLOWERING LOCUS T and MADS-box genes, showed contrasting expression patterns, generally being ectopically upregulated in the Sf mutant. These findings were associated with the phenotypic differences among coffee genotypes. In conclusion, the present study improves the understanding of the divergence of floral development in coffee, providing valuable insights for directing breeding programs and future studies aiming at controlling floral development and enhancing crop production.

plant biology↗

bioRxiv2024

SlAN1 is a limiting factor for the light-dependent anthocyanin accumulation in fruit tissues of purple tomato

Anthocyanins are specialized plant metabolites with significant dietary value due to their anti-inflammatory properties. Research indicates that dietary intake of these phenolic compounds contributes to preventing various chronic diseases. As the most consumed vegetable worldwide, tomato (Solanum lycopersicum) is an excellent candidate for anthocyanin-enrichment strategies. In tomato, activation of anthocyanin biosynthesis is light-dependent, but this mechanism has yet to be entirely characterized. We investigated the role of light in anthocyanin biosynthesis in fruits of the purple tomato, which is a near-isogenic line (NIL) derived from wild accessions into cv. Micro-Tom (MT). MT-Aft/atv/hp2 starts accumulating anthocyanin early during fruit development but is restricted to the peel (exocarp and epicarp). Manipulating light incidence in different fruit tissues determined that the absence of anthocyanin accumulation in the flesh results from the sun-blocking effect of the cyanic epicarp on the mesocarp, thus preventing light from penetrating deeper into the fruit. Transcriptional analyses of the fruit peel and flesh revealed that the bHLH transcription factor SlAN1 (Solyc09g065100) is the limiting factor for light-dependent anthocyanin accumulation in both tissues. This research enhances our comprehension of the genetic and environmental regulation of anthocyanin accumulation in fruit tissues, offering valuable insights into plant breeding for human nutrition. HighlightThe expression of the SlAN1 gene is activated in response to light signals, and it is the limiting factor for anthocyanin pigmentation in tomato fruit tissues.

plant biology↗

bioRxiv2023

Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions

The Humulus lupulus L. (hops) is traditionally produced in temperate regions, historically attributed to the belief that vernalization was necessary for reproductive transition. Nevertheless, recent studies have revealed the potential for hop plants to flower in tropical and subtropical climates, thereby reshaping cultivation prospects once the developmental disparities are understood and adapted for optimized production. Here, we delved into the hop phenological cycle and the underlying floral regulatory pathways ultimately, seeking to devise strategies to modulate development and enhance production in regions with low latitudes. In contrast to cultivation in temperate regions, hops grown in the subtropical climate of Minas Gerais, Brazil, flower multiple times throughout the year, independently of the season. Hop is a short-day plant, and in Brazil, the photoperiod is consistently inductive due to daylight hours always being below the described threshold (16,5 h of light critical point). We observed that the reproductive transition of hop initiates after a specific number of nodes, 25 to 28, leading us to hypothesize that this process is primarily controlled by endogenous factors. To explore this issue, we first identified in the hop genome families of miRNAs related to reproductive transition, such as the families MIR156 and MIR172, and the PEBP family which includes the FLOWERING LOCUS T (FT). The expression of miR156 decreased along development inversely to miR172 and in synchrony with the upregulation of HlFT3 and HlFT5. These findings strongly support that the reproductive transition in hops under inductive photoperiodic conditions is primarily regulated by endogenous factors related to development and aging throughout the miRNA and FT-associated pathways. Thus, our study shedded light on the intricate molecular mechanisms that underlie hop floral development paving the way for potential advancements in hop production on a global scale.

plant biology↗

bioRxiv2023

The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming.

O_LINon-coding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. C_LIO_LIWe combined this data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs and tRFs. C_LIO_LIOur differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs and phasiRNAs preferentially accumulate in a stage- specific manner. C_LIO_LIMembers of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family-stage specific manner, related to modulated hormonal responses and transcription factors expression. C_LI Societal Impact StatementThis research holds potential to benefit millions of coffee-producing families in over 60 countries. We uncovered molecular regulatory mechanisms governing flower development, one of the causes for the Coffea arabicas uneven ripening. The absence of uniformity in coffee production, spanning from floral induction to branch senescence, has a detrimental impact on the final products quality. These insights will inform strategies for controlled coffee maturation, leading to improved, uniform harvests.

plant biology↗

bioRxiv2023

Coffee microsporogenesis and related small interfering RNAs biosynthesis have a unique pattern among eudicots suggesting a sensitivity to climate changes.

Recently, the siRNAs pathways, and especially reproductive phasiRNAs, have attracted attention in eudicots since their biological roles are still unknown and their biogenesis took different evolutionary pathways compared to monocots. In this work, we used Coffea arabica L., a recently allotetraploid formed from the hybridization of C. canephora and C. eugenioides unreduced gametes, to explore microsporogenesis and small RNAs related pathways in a eudicot crop. First, we identified the microsporogenesis stages during anther development revealing that pre-meiosis occurs in anthers of 1.5 mm inside floral buds (FBs), whereas meiosis between 1.5 and 4.2 mm FBs, and post-meiosis in FBs larger than 4.2mm. These stages coincide with the Brazilian winter, a period of FBs reduced growth which suggests temperature sensitivity. Next, we identified and quantified the expression of reproductive 21- and 24-nt phasiRNAs during coffee anther development together with their canonical and novel miRNA triggers, and characterized the DCL and AGO families. Our results showed that the pattern of reproductive phasiRNA abundance in C. arabica is unique among described eudicots and the canonical trigger car-miR2275 is involved in the processing of both 21 and 24 nt phasiRNAs. Fourteen DCL genes were identified, but DCL5, related to phasiRNA biosynthesis in monocots, was not according to its specificity for monocots. Thus, our work explored the knowledge gap about microsporogenesis and related siRNAs pathways in coffee, contributing to the control of reproductive development and to the improvement of fertility in eudicots.

plant biology↗

bioRxiv2023

Differential universal ortholog composition of Coffea arabica L. sub-genomes and its contribution to regulatory networks governing essential biological processes

The polyploidy of Coffea arabica is an important trait affecting the evolution of this species. Genetic variability is scarce due to its recent origin as an interspecific hybrid from a single successful crossing event between Coffea canephora and Coffea eugenioides relatives. To further investigate the genomic composition of an allotetraploid we coupled high-throughput methodologies of co-expression analysis and full-length protein coding genes inference. Many of the expected orthologs were found to be missing from one of the two homoeologous chromosomes. The gene expression machinery is mainly represented by single-copy essential orthologs located in the Coffea eugenioides sub-genome. This result suggests a preference of the transcriptional and RNA processing machinery to be regulated by one parental sub-genome. To understand the operational modules of the sub-genomes transcription, we performed co-expression analysis that revealed 23 co-regulated modules. This system-wide approach clarified how biological processes (i.e., photosynthesis, cell wall biogenesis, translation, transcription, catabolism and biosynthesis) are running in synchrony and reinforces that there is an ongoing selective pressure in C. arabica that constrains the number of copies of some universal orthologues. Thus, this work contributes to our understanding of genome evolution in recent polyploids and supports crop breeding programs.

bioinformatics↗

bioRxiv2021

Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials

The behavior of florigen(s) and environment-influenced regulatory pathways that control flowering in tropical perennials with complex phenological cycles is poorly understood. Understanding the mechanisms underlying this process is important for food production in the face of climate change. To explore this, homologs of Arabidopsis florigen FLOWERING LOCUS T (CaFT1) and environment-related regulators CONSTANS (CO), PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and FLOWERING LOCUS C (FLC) were isolated from Coffea sp. L. (Rubiaceae). Overexpression of CaFT1 in Arabidopsis showed typical early-flowering and yeast two hybrid studies indicated CaFT1 binding to bZIP floral regulator, FD, demonstrates that CaFT1 is a coffee orthologue of florigen. Expression of CaFT1 and floral regulators were evaluated over one year using three contrasting genotypes: two C. arabica and one C. canephora. All genotypes showed active CaFT1 transcription from February until October, indicating a potential window for floral induction. CaCO expression, as expected, varied over the day period and monthly with day length, whereas expression of temperature-responsive homologs, CaFLC and CaPIF4, did not correlate with temperature changes. Using coffee as a model, we suggest a continuum of floral induction that allows different starting points for floral activation, which explains developmental asynchronicity and prolonged anthesis events in tropical perennial species. HighlightCoffee florigen CaFT1 and related regulators revealed an extended floral induction window clarifying the asynchronicity and influence of environment for flowering in tropical perennial crops, providing perspectives to its control.

plant biology↗

bioRxiv2021

Crosstalk between Ethylene and ABA during changes in soil water content reveals a role of ACC in coffee anthesis regulation

O_LICoffee (Coffea arabica L.) presents an asynchronous flowering regulated by endogenous and environmental stimulus, and anthesis occurs once plants are rehydrated after a period of water deficit. C_LIO_LIWe evaluated the evolution of Abscisic Acid (ABA), ethylene, 1-aminocyclopropane-1-carboxylate (ACC) content, ACC oxidase (ACO) activity, and expression analysis of the Lysine Histidine Transporter 1 (LHT1) transporter, in roots, leaves and, flower buds from three coffee genotypes (Coffea arabica L. cv Oeiras, Acaua, and Semperflorens) cultivated under field conditions with two experiments. In a third field experiment, the effect of exogenous supply of ACC in coffee anthesis was evaluated. C_LIO_LIWe found an increased ACC level in all tissues from the three coffee genotypes in the re-watering period just before anthesis for all tissues and high expression of the LHT1 gene in flower buds and leaves. Ethylene content and ACO activity decreased from rainy to dry period whereas ABA content increased. Higher number of opened and G6 stage flower buds were observed in the treatment with exogenous ACC. C_LIO_LIThe results showed that the interaction of ABA-ACO-ethylene and intercellular ACC transport among leaves, buds, and roots in coffee favors an increased level of ACC that is most likely, involved as a modulator in coffee anthesis. C_LI

plant biology↗

bioRxiv2020

Elevated temperatures impose transcriptional constraints on coffee genotypes and elicit intraspecific differences in thermoregulation

The projected impact of global warming on coffee production may require the heat-adapted genotypes in the next decades. To identify thermotolerance cellular strategies, we compared the effect of elevated temperature on two commercial Coffea arabica L. genotypes exploring leaf physiology, transcriptome and carbohydrate/protein composition. Growth temperatures were 23/19{degrees}C (day/night), as optimal condition (OpT), and 30/26{degrees}C (day/night) as a possible warmer scenario (WaT). The cv. Acaua showed lower levels of leaf temperature under both conditions compared to cv. Catuai, whereas slightly or no differences for other leaf physiological parameters. Therefore, to explore thermoregulatory pathways the leaf transcriptome was examined using RNAseq. Genotypes showed a marked number of differentially-expressed genes (DEGs) under OpT, however DEGs strongly decrease in both at WaT condition indicating a transcriptional constraint. DEGs responsive to WaT revealed shared and genotype-specific genes mostly related to carbohydrate metabolism. Under OpT, leaf starch content was greater in cv. Acaua although the levels of leaf starch, sucrose, and leaf protein decreased in both genotypes as WaT was imposed. These findings indicate that genotypes with a greater capacity to maintain carbohydrate homeostasis under temperature fluctuations could be more thermotolerant and which may be useful in breeding for a changing climate. HIGHLIGHTIn response to warming, transcriptional differences decrease in coffee genotypes hampering breeding programs. Differences in gene expression and sugar levels confirm intraspecific variation associating thermotolerance to maintenance of energetic homeostasis.

plant biology↗