Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabidopsis thaliana

In Arabidopsis thaliana, the flowering time is regulated through the circadian clock that measures day-length and modulates the photoperiodic CO-FT output pathway in accordance with the external coincidence model. Nevertheless, the genetic linkages between the major clock-associated TOC1, CCA1 and LHY genes and the canonical CO-FT flowering pathway are less clear. By employing a set of mutants including an extremely early flowering toc1 cca1 lhy triple mutant, here we showed that CCA1 and LHY act redundantly as negative regulators of the photoperiodic flowering pathway. The partly redundant CCA1/LHY functions are largely, but not absolutely, dependent on the upstream TOC1 gene that serves as an activator. The results of examination with reference to the expression profiles of CO and FT in the mutants indicated that this clock circuitry is indeed linked to the CO-FT output pathway, if not exclusively. For this linkage, the phase control of certain flowering-associated genes, GI, CDF1 and FKF1, appears to be crucial. Furthermore, the genetic linkage between TOC1 and CCA1/LHY is compatible with the negative and positive feedback loop, which is currently believed to be a core of the circadian clock. The results of this study suggested that the circadian clock might open an exit for a photoperiodic output pathway during the daytime. In the context of the current clock model, these results will be discussed in connection with the previous finding that the same clock might open an exit for the early photomorphogenic output pathway during the night-time.     

Genes underlying quantitative variation in ecologically important traits: PIF4 (PHYTOCHROME INTERACTING FACTOR 4) is associated with variation in internode length,flowering time,and fruit set in Arabidopsis thaliana

Association studies utilize the action of recombination over numerous generations to identify loci that underlie quantitative traits. We use a candidate‐gene association approach, segregation analyses and analyses of local linkage disequilibrium (LD) to evaluate the potentially causal effects of molecular variation at PIF4 (PHYTOCROME INTERACTING FACTOR 4) on ecologically important traits in Arabidopsis thaliana. A preliminary analysis of sequence diversity in 14 natural genotypes revealed one intermediate‐frequency replacement polymorphism at PIF4. A sample of 161 natural accessions was genotyped at PIF4 and screened for average length of early internodes, inflorescence length, days to flowering and flowering interval (days between bolting and flowering) under high‐ and low‐density environments to test for genotype‐phenotype associations. PIF4 was associated with early internode lengths, while the PIF4× treatment interaction was associated with flowering interval in the panel of 161 accessions. Further, in a set of recombinant inbred lines that segregate for the PIF4 polymorphism, nucleotide substitutions at PIF4 co‐segregated with early internode lengths, days to flowering and fruit set, suggesting that cryptic population structure in the association‐mapping panel and attendant LD with a physically distant locus do not account for the observed association. Finally, in a panel of pseudochromosomes from 20 re‐sequenced genotypes, LD appeared to decay rapidly in the immediate vicinity of PIF4, suggesting that flanking loci contribute little to the observed association. In sum, the results suggest that PIF4 causally affects early internode lengths on the primary inflorescence, potentially via effects on reproductive timing and that these traits in turn affect fitness.     

Gene TAENIATA is a novel negative regulator of the Arabidopsis thaliana homeobox genes KNAT1, KNAT2, KNAT6, and STM

Mutant Arabidopsis thaliana taeniata (tae) plants are characterized by an altered morphology of leaves and the inflorescence. At the beginning of flowering, the inflorescence produces fertile flowers morphologically intermediate between a shoot and a flower. The recessive mutation tae also causes the formation of ectopic meristems and shoot rosettes on leaves. The expressivity of the mutant characters depend on the temperature and photoperiod. Analysis of the activity of KNOX class I genes in the leaves of the tae mutant has demonstrated the expression of genes KNAT2 and STM and an increase in the expression of genes KNAT1 and KNAT6 compared to wild-type leaves. These data indicate that the TAE gene negatively regulates the KNAT1, KNAT2, KNAT6, and STM genes.     

Gravity control of growth form in Brassica rapa and Arabidopsis thaliana (Brassicaceae): Consequences for secondary metabolism

How gravity influences the growth form and flavor components of plants is of interest to the space program because plants could be used for food and life support during prolonged missions away from the planet, where that constant feature of Earth's environment does not prevail. We used plant growth hardware from prior experiments on the space shuttle to grow Brassica rapa and Arabidopsis thaliana plants during 16-d or 11-d hypergravity treatments on large-diameter centrifuge rotors. Both species showed radical changes in growth form, becoming more prostrate with increasing g-loads (2-g and 4-g). In Brassica, height decreased and stems thickened in a linear relationship with increasing g-load. Glucosinolates, secondary compounds that contribute flavor to Brassica, decreased by 140% over the range of micro to 4-g, while the structural secondary compound, lignin, remained constant at ～15% (w/w) cell wall dry mass. Stem thickening at 4-g was associated with substantial increases in cell size (47%, 226%, and 33% for pith, cortex, and vascular tissue), rather than any change in cell number. The results, which demonstrate the profound effect of gravity on plant growth form and secondary metabolism, are discussed in the context of similar thigmostresses such as touch and wind.     

Structure and expression of the U5 snRNA gene of Arabidopsis thaliana. Conserved upstream sequence elements in plant U-RNA genes.

We have previously characterized the U2 small nuclear (sn) RNA gene family of Arabidopsis thaliana. To find out the structural features of upstream and downstream non-coding regions that are shared by different U-RNA genes in higher plants we have isolated the gene encoding a 125 nt-long U5 snRNA of Arabidopsis. Activity of the cloned gene was demonstrated in stably transformed tobacco calli and by transient expression in transfected protoplasts of Nicotiana plumbaginifolia. Southern analysis indicated that the Arabidopsis genome contains 8-9 copies of the U5 gene. Alignment of upstream non-coding regions revealed two elements conserved between all plant U-RNA genes characterized so far: the sequence RTCCCACATCG (-70/-80 region, 100% conservation) and the TATA homology around position -30. The coding regions in all genes are followed by the sequence CAN4-9AGTN (A/T)AA which may correspond to a termination and/or processing signal.     

Gibberellins and stem growth in Arabidopsis thaliana. Effects of photoperiod on expression of the GA4 and GA5 loci.

Arabidopsis thaliana (L.) Heynh. is a quantitative long-day (LD) rosette plant in which stem growth is mediated by gibberellins (CAs). Application of GAs to plants in short-day (SD) conditions resulted in rapid stem elongation and flower formation, with GA4 and GA9 being equally effective, and GA1 showing lower activity. The effects of photoperiod on the levels of endogenous GAs were measured by combined gas chromatography-mass spectrometry with selected ion monitoring. When plants were transferred from SD to LD conditions there was a slight decrease in the level of GA53 and an increase in the levels of C19-GAs, GA9, GA20, GA1, and GA8, indicating that GA 20-oxidase activity is stimulated in LD conditions. Expression of GA5, which encodes GA 20-oxidase, was highest in elongating stems and was correlated with the rate of stem elongation. By contrast, GA4, which encodes 3 beta-hydroxylase, showed low expression in stems and its expression was not correlated with the rate of stem elongation. We conclude that stem elongation in LD conditions is at least in part due to increased expression of GA5, whereas expression of GA4 is not under photoperiodic control.     

A link between cytokinin and ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) that belongs to the AS2/LOB (LATERAL ORGAN BOUNDARIES) family genes in Arabidopsis thaliana

In Arabidopsis thaliana, each member of a large family of AS2/LOB (ASYMMETRIC LEAVES 2/LATERAL ORGAN BOUNDARIES) genes encodes a plant specific protein. They are highly homologous to one other. A mutational lesion in the representative AS2 gene results in the development of anomalous asymmetric leaves, implying that these family members commonly play some roles in plant development. In this study, we found that ectopic overexpression of ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) in transgenic plants displayed a markedly anomalous architecture during the development of adult plants. Then we found that among AS2/LOB family members, ASL9 is distinct from the others in that it is exclusively regulated by the plant hormone cytokinin in a manner dependent on His-Asp phosphorelay signal transduction. We further found that when supplied externally in a medium, cytokinin specifically affected the growth properties of ASL9-ox seedlings. Taken together, the results of this study suggest that the cytokinin-induced ASL9 gene is implicated in regulation of the development of Arabidopsis thaliana.