Molecular-genetic analysis of natural variation in photoperiodic flowering of Arabidopsis thaliana

In Arabidopsis thaliana, the focus of my research, three developmental switches controlling the life cycle can be recognised. The first is germination that separates embryonic from post-embryonic development. The second signals the transition from the juvenile to the adult vegetative phase while the third, flowering, marks the initiation of the reproductive phase (Isabel Baurle and Caroline Dean, Cell 2006). All three exhibit both external (environmental) and endogenous (hormones) regulation. Natural genetic variation, namely phenotypic diversity due to genetic differences between individuals of the same species, has been reported both for germination and flowering initiation (Bentsink et al., PNAS 2006; O Neill et al., TAG 2008). Since individuals of Arabidopsis, commonly referred to as accessions, are collected from a variety of locations, it is believed that this genetic diversity reflects differences in the seasonal oscillations of environmental cues among the collection sites leading to local adaptation. Although natural genetic variation as a tool has been used in the study of flowering initiation in Arabidopsis (Alonso-Blanco and Maarten Koornneef, Trends in Plant Science 2000) a systematic survey that focuses mainly on the photoperiodic aspect of this regulation has been lacking. In order to expand the current knowledge two approaches were designed. First a survey for natural genetic variation in the flowering responses of phylogenetically distant Arabidopsis accessions under six different photoperiods was made. In parallel the transgenic equivalents of the same accessions, carrying a promoter fusion of the flowering time and circadian clock gene GIGANTEA (GI) were screened in the same photoperiods as for flowering time in order to detect for the first time trans-specific natural variation in the circadian regulation of an evening gene. Here I present evidence that natural genetic variation is present in a wide range of photoperiods both for the circadian clock and for flowering initiation per se. The flowering time responses are compared with the ones of mutants and transgenic lines of previously identified flowering time genes and I show that the affected known genes cannot fully cover the different patterns of day length discrimination that the natural accessions exhibit. Five different mapping populations were constructed by selecting interesting accessions from both screens, which led to the identification of new as well as known QTL, which alter various circadian and flowering responses between short and long days of similar duration. Generating advanced genetic material allows fine mapping and eventually cloning of some of the loci, while identification of genome-wide patterns of genetic interactions reveals additional loci that classical QTL mapping approaches cannot detect. Using RT-PCR and in situ hybridisation, I link this novel natural genetic variation between similar long day lengths with molecular variability in the temporal and spatial expression of flowering time genes FT and SOC1 thereby also demonstrating the tight dependence of the SAM floral commitment on the FT florigen. Finally I show that in nature, genetic variability in the property of enhanced photoperiod discrimination under similar long days, is enough to prevent winter flowering in a plant without any requirements for vernalization. Cologne, 200

Viruses affecting lentil (Lens culinaris Medik.) in Greece; incidence and genetic variability of Bean leafroll virus and Pea enation mosaic virus

In Greece, lentil (Lens culinaris Medik.) crops are mainly established with non-certified seeds of local landraces, implying high risks for seed transmitted diseases. During April and May of the 2007–2012 growing seasons, surveys were conducted in eight regions of Greece (Attiki, Evros, Fthiotida, Korinthos, Kozani, Larissa, Lefkada and Viotia) to monitor virus incidence in lentil fields. A total of 1216 lentil samples, from plants exhibiting symptoms suggestive of virus infection, were analyzed from 2007 to 2009, using tissue-blot immunoassays (TBIA). Pea seed-borne mosaic virus (PSbMV) overall incidence was 4.9%, followed by Alfalfa mosaic virus (AMV) (2.4%) and Bean yellow mosaic virus (BYMV) (1.0%). When 274 of the samples were tested for the presence of luteoviruses, 38.8% were infected with Bean leafroll virus (BLRV). Since BLRV was not identified in the majority of the samples collected from 2007 to 2009, representative symptomatic plants (360 samples) were collected in further surveys performed from 2010 to 2012 and tested by ELISA. Two viruses prevailed in those samples: BLRV (36.1%) was associated with stunting, yellowing, and reddening symptoms and Pea enation mosaic virus-1 (PEMV-1) (35.0%) was associated with mosaic and mottling symptoms. PSbMV (2.2%), AMV (2.2%), BYMV (3.9%) and CMV (2.8%) were also detected. When the molecular variability was analyzed for representative isolates, collected from the main Greek lentil production areas, five BLRV isolates showed 95% identity for the coat protein (CP) gene and 99% for the 3’ end region. Three Greek PEMV isolates co-clustered with an isolate from Germany when their CP sequence was compared with isolates with no mutation in the aphid transmission gene. Overall, limited genetic variability was detected among Greek isolates of BLRV and PEMV

FTIP1 Is an Essential Regulator Required for Florigen Transport

FT-INTERACTING PROTEIN 1 is a novel protein that is involved in transporting florigen, a long-known mobile signal that induces flowering in plants in response to day length, from companion cells to sieve elements in the phloem of Arabidopsis

ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize

Higher plants use multiple perceptive measures to coordinate flowering time with environmental and endogenous cues. Physiological studies show that florigen is a mobile factor that transmits floral inductive signals from the leaf to the shoot apex. Arabidopsis FT protein is widely regarded as the archetype florigen found in diverse plant species, particularly in plants that use inductive photoperiods to flower. Recently, a large family of FT homologues in maize, the Zea CENTRORADIALIS (ZCN) genes, was described, suggesting that maize also contains FT-related proteins that act as a florigen. The product of one member of this large family, ZCN8, has several attributes that make it a good candidate as a maize florigen. Mechanisms underlying the floral transition in maize are less well understood than those of other species, partly because flowering in temperate maize is dependent largely on endogenous signals. The maize indeterminate1 (id1) gene is an important regulator of maize autonomous flowering that acts in leaves to mediate the transmission or production of florigenic signals. This study finds that id1 acts upstream of ZCN8 to control its expression, suggesting a possible new link to flowering in day-neutral maize. Moreover, in teosinte, a tropical progenitor of maize that requires short-day photoperiods to induce flowering, ZCN8 is highly up-regulated in leaves under inductive photoperiods. Finally, vascular-specific expression of ZCN8 in Arabidopsis complements the ft-1 mutation, demonstrating that leaf-specific expression of ZCN8 can induce flowering. These results suggest that ZCN8 may encode a florigen that integrates both endogenous and environmental signals in maize

Fruit load modulates flowering-related gene expression in buds of alternate-bearing 'Moncada' mandarin

Background and Aims Gene determination of flowering is the result of complex interactions involving both promoters and inhibitors. In this study, the expression of flowering-related genes at the meristem level in alternate-bearing citrus trees is analysed, together with the interplay between buds and leaves in the determination of flowering. Methods First defruiting experiments were performed to manipulate blossoming intensity in `Moncada¿ mandarin, Citrus clementina. Further defoliation was performed to elucidate the role leaves play in the flowering process. In both cases, the activity of flowering-related genes was investigated at the flower induction (November) and differentiation (February) stages. Key Results Study of the expression pattern of flowering-genes in buds from on (fully loaded) and off (without fruits) trees revealed that homologues of FLOWERING LOCUS T (CiFT), TWIN SISTER OF FT (TSF), APETALA1 (CsAP1) and LEAFY (CsLFY) were negatively affected by fruit load. CiFT and TSF activities showed a marked increase in buds from off trees through the study period (ten-fold in November). By contrast, expression of the homologues of the flowering inhibitors of TERMINAL FLOWER 1 (CsTFL), TERMINAL FLOWER 2 (TFL2) and FLOWERING LOCUS C (FLC) was generally lower in off trees. Regarding floral identity genes, the increase in CsAP1 expression in off trees was much greater in buds than in leaves, and significant variations in CsLFY expression (approx. 20 %) were found only in February. Defoliation experiments further revealed that the absence of leaves completely abolished blossoming and severely affected the expression of most of the flowering-related genes, particularly decreasing the activity of floral promoters and of CsAP1 at the induction stage. Conclusions These results suggest that the presence of fruit affects flowering by greatly altering gene-expression not only at the leaf but also at the meristem level. Although leaves are required for flowering to occur, their absence strongly affects the activity of floral promoters and identity genes.This work was supported by a grant from the Instituto Nacional Investigaciones Agrarias, Spain (RTA2009-00147). M. C. Gonzalez was the recipient of a contract by the Fundacion Agroalimed (Conselleria d'Agricultura, Pesca i Alimentacio, Generalitat Valenciana).Muñoz Fambuena, N.; Mesejo Conejos, C.; Gonzalez Más, MC.; Primo-Millo, E.; Agustí Fonfría, M.; Iglesias, DJ. (2012). Fruit load modulates flowering-related gene expression in buds of alternate-bearing 'Moncada' mandarin. Annals of Botany. 110(6):1109-1118. doi:10.1093/aob/mcs190S110911181106Abe, M. (2005). FD, a bZIP Protein Mediating Signals from the Floral Pathway Integrator FT at the Shoot Apex. Science, 309(5737), 1052-1056. doi:10.1126/science.1115983Bustin, S. (2002). Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. 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Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them

Non-coding variants in cancer: Mechanistic insights and clinical potential for personalized medicine

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them. © 2021 by the authors. Li-censee MDPI, Basel, Switzerland