At the end of the day: a common molecular mechanism for photoperiod responses in plants?

Nitrogen deposition favors later leaf senescence in woody species

China has experienced an unprecedented increase in nitrogen deposition over recent decades, threatening ecosystem structure, functioning, and resilience. However, the impact of elevated nitrogen deposition on the date of foliar senescence remains widely unexplored. Using 22,780 in situ observations and long-term satellite-based date of foliar senescence measures for woody species across China, we find that increased nitrogen deposition generally delays date of foliar senescence, with strong causal evidence observed at site-to-region scales. Changes in climate conditions and nitrogen deposition levels jointly controlled the direction of date of foliar senescence trends (advance or delay). The spatial variability of nitrogen deposition effects can be related to plant traits (e.g., nitrogen resorption and use efficiencies), climatic conditions, and soil properties. Moreover, elevated nitrogen deposition delays date of foliar senescence by promoting foliar expansion and enhancing plant productivity during the growing season, while its influence on evapotranspiration may either accelerate or delay date of foliar senescence depending on local water availability. This study highlights the critical role of nitrogen deposition in regulating date of foliar senescence trends, revealing a key uncertainty in modeling date of foliar senescence driven solely by climate change and its far-reaching implications for ecosystem-climate feedbacks.

Genome-wide identification and functional analysis of the longan CONSTANS (CO) family

Longans are among the most economically important subtropical fruits. Its flowering is sensitive to the photoperiod, and flowering time has a significant influence on yield and quality. CONSTANS-like (COL) gene plays a key role in regulating induced flowering in longans. However, the specific role of the COL gene family in the regulation of flowering remains unknown. In this study, 10 DlCOL genes were identified in longans using comprehensive bioinformatics analysis and named based on their physical chromosomal locations. Phylogenetic tree analysis showed that DlCOL genes were divided into three subfamilies, each with a conserved domain. When combined with collinearity analysis, we found DlCOL genes were more closely related to COL genes of dicotyledons. DlCOL family genes are differentially expressed in various longan organs, with DlCOL1, DlCOL3, and DlCOL9 expressed in all organs, with the highest expression levels in floral buds. In the differential expression at different flowering induction stages of 'Sijimi' ('SJ') or 'Shixia' longan ('SX'), DlCOL4 expression was upregulated by 3-fold at the "T1-T2" flowering induction stage in 'SJ', but there was no expression during the three flowering induction stages in 'SX'. Subcellular localization analysis indicated that DlCOL4 is localized in the nucleus. Heterologous transformation of Arabidopsis indicated that DlCOL4 can negatively regulate flowering in transgenic plants. The qRT-PCR (Quantitative real-time PCR) results related to flowering genes indicated that DICOL4 may inhibit flowering by interacting with AtTFL and AtCOL. This study demonstrates the potential functional role of the DlCOL gene and the key role of DlCOL4 in regulating longan flowering.

Photoperiodic control of growth and reproduction in non-flowering plants

Photoperiodic responses shape plant fitness to the changing environment and are important regulators of growth, development, and productivity. Photoperiod sensing is one of the most important cues to track seasonal variations. It is also a major cue for reproductive success. The photoperiodic information conveyed through the combined action of photoreceptors and the circadian clock orchestrates an output response in plants. Multiple responses such as hypocotyl elongation, induction of dormancy, and flowering are photoperiodically regulated in seed plants (eg. angiosperms). Flowering plants such as Arabidopsis or rice have served as important model systems to understand the molecular players involved in photoperiodic signalling. However, photoperiodic responses in non-angiosperm plants have not been investigated and documented in detail. Genomic and transcriptomic studies have provided evidence on the conserved and distinct molecular mechanisms across the plant kingdom. In this review, we have attempted to compile and compare photoperiodic responses in the plant kingdom with a special focus on non-angiosperms.

Beyond floral initiation: the role of flower bud dormancy in flowering time control of annual plants

The phenology of temperate perennials, including the timing of vegetative growth and flowering, is well known to be controlled by seasonal dormancy cycles. Dormant structures are known as buds and have specialized covering structures, symplastic isolation from the plant, and often autonomous stores of carbon and nitrogen reserves. In contrast, in annual plants, our current understanding of the control of the timing of flowering focuses on the mechanisms affecting floral initiation, the transition from a vegetative apical meristem to a inflorescence meristem producing flower primordia in place of leaves. Recently we revealed that annual crops in Brassicaceae exhibit chilling-responsive growth control in a manner closely resembling bud dormancy breakage in perennial species. Here I discuss evidence that vernalization in autumn is widespread and further discuss its role in inducing flower bud set prior to winter. I also review evidence that flower bud dormancy has a more widespread role in annual plant flowering time control than previously appreciated.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

The long road to bloom in conifers

More than 600 species of conifers (phylum Pinophyta) serve as the backbone of the Earth's terrestrial plant community and play key roles in global carbon and water cycles. Although coniferous forests account for a large fraction of global wood production, their productivity relies largely on the use of genetically improved seeds. However, acquisition of such seeds requires recurrent selection and testing of genetically superior parent trees, eventually followed by the establishment of a seed orchard to produce the improved seeds. The breeding cycle for obtaining the next generation of genetically improved seeds can be significantly lengthened when a target species has a long juvenile period. Therefore, development of methods for diminishing the juvenile phase is a cost-effective strategy for shortening breeding cycle in conifers. The molecular regulatory programs associated with the reproductive transition and annual reproductive cycle of conifers are modulated by environmental cues and endogenous developmental signals. Mounting evidence indicates that an increase in global average temperature seriously threatens plant productivity, but how conifers respond to the ever-changing natural environment has yet to be fully characterized. With the breakthrough of assembling and annotating the giant genome of conifers, identification of key components in the regulatory cascades that control the vegetative to reproductive transition is imminent. However, comparison of the signaling pathways that control the reproductive transition in conifers and the floral transition in Arabidopsis has revealed many differences. Therefore, a more complete understanding of the underlying regulatory mechanisms that control the conifer reproductive transition is of paramount importance. Here, we review our current understanding of the molecular basis for reproductive regulation, highlight recent discoveries, and review new approaches for molecular research on conifers.

Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod

Plants can cold acclimate to enhance their freezing tolerance by sensing declining temperature and photoperiod cues. However, the factors influencing genotypic variation in the induction of cold acclimation are poorly understood among perennial grasses. We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod. Next, we identified the temperature required to induce cold acclimation by exposing the 16 genotypes for 7 days at 20-6°C constant temperatures under a 10 or 16 h photoperiod. Cold acclimation initiated at temperatures 5 and 7°C higher in upland than in coastal and lowland genotypes. Among upland genotypes the shorter photoperiod induced cold acclimation at a 1°C higher temperature. Genotypes originating from a more northern latitude initiate cold acclimation at higher temperatures and develop higher maximum freezing tolerances. An earlier response to declining temperatures may provide the upland ecotype with additional time to prepare for winter and provide an advantage when plants are subjected to the rapid changes in fall temperature associated with injurious frosts.

Long-term effects of artificial nighttime lighting and trophic complexity on plant biomass and foliar carbon and nitrogen in a grassland community

The introduction of artificial nighttime lighting due to human settlements and transport networks is increasingly altering the timing, intensity, and spectra of natural light regimes worldwide. Much of the research on the impacts of nighttime light pollution on organisms has focused on animal species. Little is known about the impacts of daylength extension due to outdoor lighting technologies on wild plant communities, despite the fact that plant growth and development are under photoperiodic control. In a five-year field experiment, artificial ecosystems ("mesocosms") of grassland communities both alone or in combination with invertebrate herbivores and predators were exposed to light treatments that simulated street lighting technologies (low-pressure sodium, and light-emitting diode [LED]-based white lighting), at ground-level illuminance. Most of the plant species in the mesocosms did not exhibit changes in biomass accumulation after 5 years of exposure to the light treatments. However, the white LED treatment had a significant negative effect on biomass production in the herbaceous species Lotus pedunculatus. Likewise, the interaction between the white LED treatment and the presence of herbivores significantly reduced the mean shoot/root ratio of the grass species Holcus lanatus. Artificial nighttime lighting had no effect on the foliar carbon or nitrogen in most of the grassland species. Nevertheless, the white LED treatment significantly increased the leaf nitrogen content in Lotus corniculatus in the presence of herbivores. Long-term exposure to artificial light at night had no general effects on plant biomass responses in experimental grassland communities. However, species-specific and negative effects of cool white LED lighting at ground-level illuminance on biomass production and allocation in mixed plant communities are suggested by our findings. Further studies on the impacts of light pollution on biomass accumulation in plant communities are required as these effects could be mediated by different factors, including herbivory, competition, and soil nutrient availability.

A long and stressful day: Photoperiod shapes aluminium tolerance in plants

Aluminium (Al), a limiting factor for crop productivity in acidic soils (pH ≤ 5.5), imposes drastic constraints for food safety in developing countries. The major mechanisms that allow plants to cope with Al involve manipulations of organic acids metabolism and DNA-checkpoints. When assumed individually both approaches have been insufficient to overcome Al toxicity. On analysing the centre of origin of most cultivated plants, we hypothesised that day-length seems to be a pivotal agent modulating Al tolerance across distinct plant species. We observed that with increasing distance from the Equator, Al tolerance decreases, suggesting a relationship with the photoperiod. We verified that long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth habit boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. Furthermore, DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting that photoperiod act as a selective barrier for Al tolerance. A diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. Altogether, photoperiodic control of Al tolerance might contribute to solving the historical obstacle that imposes barriers for developing countries to reach a sustainable agriculture.

Transcriptomic Analysis of Early Flowering Signals in ‘Royal’ Flax

Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.

Field evaluation of transgenic hybrid poplars with desirable wood properties and enhanced growth for biofuel production by bicistronic expression of PdGA20ox1 and PtrMYB3 in wood-forming tissue

BACKGROUND

To create an ideotype woody bioenergy crop with desirable growth and biomass properties, we utilized the viral 2A-meidated bicistronic expression strategy to express both PtrMYB3 (MYB46 ortholog of Populus trichocarpa, a master regulator of secondary wall biosynthesis) and PdGA20ox1 (a GA20-oxidase from Pinus densiflora that produces gibberellins) in wood-forming tissue (i.e., developing xylem).

RESULTS

Transgenic Arabidopsis plants expressing the gene construct DX15::PdGA20ox1-2A-PtrMYB3 showed a significant increase in both stem fresh weight (threefold) and secondary wall thickening (1.27-fold) relative to wild-type (WT) plants. Transgenic poplars harboring the same gene construct grown in a greenhouse for 60 days had a stem fresh weight up to 2.6-fold greater than that of WT plants. In a living modified organism (LMO) field test conducted for 3 months of active growing season, the stem height and diameter growth of the transgenic poplars were 1.7- and 1.6-fold higher than those of WT plants, respectively, with minimal adverse growth defects. Although no significant changes in secondary wall thickening of the stem tissue of the transgenic poplars were observed, cellulose content was increased up to 14.4 wt% compared to WT, resulting in improved saccharification efficiency of the transgenic poplars. Moreover, enhanced woody biomass production by the transgenic poplars was further validated by re-planting in the same LMO field for additional two growing seasons.

CONCLUSIONS

Taken together, these results show considerably enhanced wood formation of our transgenic poplars, with improved wood quality for biofuel production.

Growing in time: exploring the molecular mechanisms of tree growth

Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

Need for speed: manipulating plant growth to accelerate breeding cycles

To develop more productive and resilient crops that are capable of feeding 10 billion people by 2050, we must accelerate the rate of genetic improvement in plant breeding programs. Speed breeding manipulates the growing environment by regulating light and temperature for the purpose of rapid generation advance. Protocols are now available for a range of short-day and long-day species and the approach is highly compatible with other cutting-edge breeding tools such as genomic selection. Here, we highlight how speed breeding hijacks biological processes for applied plant breeding outcomes and provide a case study examining wheat growth and development under speed breeding conditions. The establishment of speed breeding facilities worldwide is expected to provide benefits for capacity building, discovery research, pre-breeding, and plant breeding to accelerate the development of productive and robust crops.

Spatial and temporal shifts in photoperiod with climate change

Climate change causes both temporal (e.g. advancing spring phenology) and geographic (e.g. range expansion poleward) species shifts, which affect the photoperiod experienced at critical developmental stages ('experienced photoperiod'). As photoperiod is a common trigger of seasonal biological responses - affecting woody plant spring phenology in 87% of reviewed studies that manipulated photoperiod - shifts in experienced photoperiod may have important implications for future plant distributions and fitness. However, photoperiod has not been a focus of climate change forecasting to date, especially for early-season ('spring') events, often assumed to be driven by temperature. Synthesizing published studies, we find that impacts on experienced photoperiod from temporal shifts could be orders of magnitude larger than from spatial shifts (1.6 h of change for expected temporal vs 1 min for latitudinal shifts). Incorporating these effects into forecasts is possible by leveraging existing experimental data; we show that results from growth chamber experiments on woody plants often have data relevant for climate change impacts, and suggest that shifts in experienced photoperiod may increasingly constrain responses to additional warming. Further, combining modeling approaches and empirical work on when, where and how much photoperiod affects phenology could rapidly advance our understanding and predictions of future spatio-temporal shifts from climate change.

Willow phenological modelling at different altitudes in central Italy

In order to estimate the impact of climate change on the phenological parameters and to compare them with the historical record, a decision support system (DSS) has been applied employing a Phenological Modelling Platform. Biological observations of two willow species (Salix acutifolia and smithiana Willd) in 3 gardens at different altitudes located in Central Italy were utilized to identify suitable phenological models related to four main vegetative phase timings (BBCH11, BBCH91, BBCH 94, BBCH95), and male full flowering (BBCH 65) clearly identifiable in these species. The present investigation identifies the best phenological models for the main phenophases allowing their practical application as real-time monitoring and plant development prediction tools. Sigmoid model revealed high performances in simulating spring vegetative phases, BBCH11 (First leaves unfolded), and BBCH91 (Shoot and foliage growth completed). Salix acutifolia Willd. development appeared to be more related to temperature amount interpreted by phenological models in comparison to Salix smithiana Willd. above all during spring (BBCH11 and 91), probably due to a different grade of phenotypic plasticity between the 2 considered species.

Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. and Gray)

In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology in Populus trichocarpa to determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017–2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h² = 0.5–0.8) and in lifetime growth (h² = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth.

Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species

Seasonal phenomena in plants are primarily affected by day length and temperature. The shoot transcriptomes of trees grown in the field and a controlled-environment chamber were compared to characterize genes that control annual rhythms and the effects of day length- and temperature-regulated genes in the gymnosperm Japanese cedar (Cryptomeria japonica D. Don), which exhibits seasonally indeterminate growth. Annual transcriptome dynamics were clearly demonstrated by principal component analysis using microarray data obtained under field-grown conditions. Analysis of microarray data from trees grown in a controlled chamber identified 2,314 targets exhibiting significantly different expression patterns under short-day (SD) and long-day conditions, and 2,045 targets exhibited significantly different expression patterns at 15°C (LT; low temperature) versus 25°C. Interestingly, although growth was suppressed under both SD and LT conditions, approximately 80% of the SD- and LT-regulated targets differed, suggesting that each factor plays a unique role in the annual cycle. The top 1,000 up-regulated targets in the growth/dormant period in the field coincided with more than 50% of the SD- and LT-regulated targets, and gene co-expression network analysis of the annual transcriptome indicated a close relationship between the SD- and LT-regulated targets. These results indicate that the respective effects of day length and temperature interact to control annual transcriptome dynamics. Well-known upstream genes of signaling pathways responsive to environmental conditions, such as the core clock (LHY/CjLHYb and CCA1/CjLHYa) and PEBP family (MFT) genes, exhibited unique expression patterns in Japanese cedar compared with previous reports in other species, suggesting that these genes control differences in seasonal regulation mechanisms between species. The results of this study provide new insights into seasonal regulation of transcription in Japanese cedar.

Bark Features for Identifying Resonance Spruce Standing Timber

Measuring the acoustic properties of wood is not feasible for most luthiers, so identifying simple, valid criteria for diagnosis remains an exciting challenge when selecting materials for manufacturing musical instruments. This article aims to verify whether the bark qualities as a marker of resonance wood are indeed useful. The morphometric and colour traits (in CIELab space) of the bark scales were compared with the structural (width and regularity of the growth rings and of the latewood) and acoustic features (transverse sound velocity, radiation ratio, impedance, and wood basic density) of the wood from 145 standing and 10 felled spruce trees, which are considered a resource of the resonance wood in the Romanian Carpathians. It has been emphasized that the spruce trees with acoustic and structural features that match the requirements for the manufacture of violins have a bark phenotype distinguishable by colour (higher redness, lower yellowness and brightness)—as well as by scale shape (higher slenderness and width). The south-facing side of the trunk and the external side of the scale are best for identifying resonance trees by their bark. Additionally, the mature bark phenotypes denote topoclinal variations and do not depend on tree age. Moreover, the differences among bark phenotypes are noticeable to the naked eye.

Nutrient availability alters the correlation between spring leaf-out and autumn leaf senescence dates

Leaf senescence (LS) affects tree fitness, species distribution and ecosystem structure and functioning. The drivers of LS and the processes underlying it have been studied, but the studies have mainly focused on environmental cues and have mainly been based on statistical analyses using in situ data sets. Experimental investigation and field verification of the processes and drivers are thus urgently needed. We conducted a nutrient-addition experiment after a spring-warming experiment in which an ~40-day range of leaf-out (LO) dates was induced in horse chestnut (Aesculus hippocastanum) and beech (Fagus sylvatica) saplings. We found that both increased nutrient supply and advanced LO date significantly affected the timing of LS, but their effects were opposite, as the former delayed and the latter advanced the senescence. The effects of nutrient supply and LO interacted species specifically. In chestnut, the delay of senescence caused by fertilization increased with the delay of LO and was thus stronger for individuals that flushed late in the spring. On the contrary, in beech the delay of senescence caused by fertilization decreased with the delay of LO and was insignificant for individuals with the latest LO. The experimental findings for beech were confirmed with mature trees at a regional scale. The interactive effect between nutrients and LO on senescence may be associated with variable sensitivity to photoperiod, growth sink limitation and/or direct effect of foliar nutrition on the timing of senescence. Our novel results show that the interactive effects of LO and nutrient supply on the timing of LS should be further addressed experimentally in forthcoming studies. It would also be interesting to consider our results in the further development of phenological models used in assessing the effects of climatic change. The differences found in the present study between horse chestnut and beech suggest that the results found for one species cannot necessarily be generalized to other species, so studies with different temperate tree species are called for.

The influence of spectral composition on spring and autumn phenology in trees

Several recent reviews highlight the molecular mechanisms that underpin phenological responses to temperature and photoperiod; however, these have mostly overlooked the influence of solar radiation and its spectral composition on these processes. For instance, solar radiation in the blue and ultraviolet (UV) regions of the spectrum, as well as the red/far-red (R:FR) ratio, can influence spring and autumn phenology. Solar radiation reaching the Earth changes diurnally and seasonally; however, rising global temperatures, latitudinal range shifts and light pollution are likely to produce novel combinations of phenological cues for tree species. Here, we review the literature on phenological responses to spectral composition. Our objective was to explore the natural variation in spectral composition using radiative transfer models and to reveal any species-specific or ecotype-specific responses relating to latitudinal origin. These responses are likely to be most pronounced at high latitudes where spectral composition varies most throughout the year. For instance, trees from high latitudes tend to be more sensitive to changes in R:FR than those from low latitudes. The effects of blue light and UV radiation on phenology have not been studied as much as those of R:FR, but the limited results available suggest both could be candidate cues affecting autumn leaf colouration and senescence. Failure of more-southern species and ecotypes to adapt and use spectral cues during northwards range shifts could result in mistimed phenology, potentially resulting in frost damage, reduced fitness and limited range expansion. Future areas for research should look to establish how consistently different functional types of tree respond to spectral cues and identify photoreceptor-mediated mechanisms that allow plants to combine information from multiple light cues to coordinate the timing of phenological events. It should then be feasible to consider the synchronous or sequential action of light cues within a hierarchy of environmental factors regulating phenology.

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.

Photoperiod-temperature phase lag: A universal environmental context of seasonal developmental plasticity

Seasonal developmental plasticity, which consists of season-dependent alternations of developmental processes, has evolved to produce optimal phenotypes depending on specific periods in a year. For example, many phenological events in plants, such as flowering, fruiting, bud blast, bud formation, and growth cessation, are often controlled seasonally. Although temperature and photoperiod are the two major seasonal cues for such responses, the importance of phase lag between annual oscillations of the two signals has been unexplored, despite its universal nature in the context of seasonal environments. In this article, the phase-lag calendar hypothesis (New Phytologist, 210, 2016, 399), especially the one between temperature and photoperiod, is explained using meteorological data obtained from central Japan as an example. We set forth to show how, for a narrow window in time of a couple of weeks in a year, simple threshold responses to these two signals that differ in annual oscillation phases are enough to make developmental plasticity to be expressed as phenological events. The properties of the underlying mechanisms of the events in different seasons are further predicted, and the responses are compared with reported empirical examples. Because many organisms have evolved under the phase lag between photoperiod and temperature, the developmental plasticity in response to the phase lag should be evaluated for diverse organisms.

MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod

BACKGROUND

The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod.

RESULTS

A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that "Plant hormone signal transduction" pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant's responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26-58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge.

CONCLUSIONS

These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.

Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations

BACKGROUND

Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices.

RESULTS

The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO₃ were likely epicontrolled by both photoperiod and temperature.

CONCLUSIONS

Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes.

Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations

Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.

Larger temperature response of autumn leaf senescence than spring leaf-out phenology

Climate warming is substantially shifting the leaf phenological events of plants, and thereby impacting on their individual fitness and also on the structure and functioning of ecosystems. Previous studies have largely focused on the climate impact on spring phenology, and to date the processes underlying leaf senescence and their associated environmental drivers remain poorly understood. In this study, experiments with temperature gradients imposed during the summer and autumn were conducted on saplings of European beech to explore the temperature responses of leaf senescence. An additional warming experiment during winter enabled us to assess the differences in temperature responses of spring leaf-out and autumn leaf senescence. We found that warming significantly delayed the dates of leaf senescence both during summer and autumn warming, with similar temperature sensitivities (6-8 days delay per °C warming), suggesting that, in the absence of water and nutrient limitation, temperature may be a dominant factor controlling the leaf senescence in European beech. Interestingly, we found a significantly larger temperature response of autumn leaf senescence than of spring leaf-out. This suggests a possible larger contribution of delays in autumn senescence, than of the advancement in spring leaf-out, to extending the growing season under future warmer conditions.

High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L

The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F₁ population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.

Autumn senescence in aspen is not triggered by day length

Autumn senescence in mature aspens, grown under natural conditions, is initiated at almost the same date every year. The mechanism of such precise timing is not understood but we have previously shown that the signal must be derived from light. We studied variation in bud set and autumn senescence in a collection of 116 natural Eurasian aspen (Populus tremula) genotypes, from 12 populations in Sweden and planted in one northern and one southern common garden, to test the hypothesis that onset of autumn senescence is triggered by day length. We confirmed that, although bud set seemed to be triggered by a critical photoperiod/day length, other factors may influence it. The data on initiation of autumn senescence, on the other hand, were incompatible with the trigger being the day length per se, hence the trigger must be some other light-dependent factor.

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles

BACKGROUND

Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 10⁹ reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation.

RESULTS

We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter.

CONCLUSIONS

Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years

BACKGROUND AND AIMS

Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits.

METHODS

A hybrid Salix viminalis  × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed.

KEY RESULTS

Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production.

CONCLUSIONS

The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations.

Research progress on the autonomous flowering time pathway in Arabidopsis

The transition from vegetative to reproductive growth phase is a pivotal and complicated process in the life cycle of flowering plants which requires a comprehensive response to multiple environmental aspects and endogenous signals. In Arabidopsis, six regulatory flowering time pathways have been defined by their response to distinct cues, namely photoperiod, vernalization, gibberellin, temperature, autonomous and age pathways, respectively. Among these pathways, the autonomous flowering pathway accelerates flowering independently of day length by inhibiting the central flowering repressor FLC. FCA, FLD, FLK, FPA, FVE, FY and LD have been widely known to play crucial roles in this pathway. Recently, AGL28, CK2, DBP1, DRM1, DRM2, ESD4, HDA5, HDA6, PCFS4, PEP, PP2A-B'γ, PRMT5, PRMT10, PRP39-1, REF6, and SYP22 have also been shown to be involved in the autonomous flowering time pathway. This review mainly focuses on FLC RNA processing, chromatin modification of FLC, post-translational modification of FLC and other molecular mechanisms in the autonomous flowering pathway of Arabidopsis.

Evolution of photoperiod sensing in plants and algae

Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review.

Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology

Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).

An insight into the sensitivity of maize to photoperiod changes under controlled conditions

Response of maize to photoperiods affects adaption of this crop to environments. We characterize the phenotypes of four temperate-adapted maize foundation parents, Huangzao 4, Chang 7-2, Ye 478 and Zheng 58, and two tropically adapted maize foundation parents, M9 and Shuang M9 throughout the growth stage under three constant photoperiod regimes in a daily cycle of 24 h at 28 °C, and analysed expression of 48 photoperiod response-associated genes. Consequently, long photoperiod (LP) repressed development of the tassels of photoperiod-sensitive maize lines at V9 stage, and caused subsequent failure in flowering; failure of photoperiod-sensitive maize lines in flowering under LP was associated with lower expression of flowering-related genes; photoperiod changes could make a marked impact on spatial layout of maize inflorescence. The larger oscillation amplitude of expression of photoperiod-responsive genes occurred in LP-sensitive maize lines. In conclusion, failure in development of tassels at V9 stage under LP is an early indicator for judging photoperiod sensitivity. The adaptation of temperate-adapted maize lines to LP is due to the better coordination of expression among photoperiod-sensing genes instead of the loss of the genes. High photoperiod sensitivity of maize is due to high expression of circadian rhythm-responding genes improperly early in the light.

Introducing a sensor to measure budburst and its environmental drivers

Budburst is a key adaptive trait that can help us understand how plants respond to a changing climate from the molecular to landscape scale. Despite this, acquisition of budburst data is constrained by a lack of information at the plant scale on the environmental stimuli associated with the release of bud dormancy. Additionally, to date, little effort has been devoted to phenotyping plants in natural populations due to the challenge of accounting for the effect of environmental variation. Nonetheless, natural selection operates on natural populations, and investigation of adaptive phenotypes in situ is warranted and can validate results from controlled laboratory experiments. To identify genomic effects on individual plant phenotypes in nature, environmental drivers must be concurrently measured, and characterized. Here, we designed and evaluated a sensor to meet these requirements for temperate woody plants. It was designed for use on a tree branch to measure the timing of budburst together with its key environmental drivers; temperature, and photoperiod. Specifically, we evaluated the sensor through independent corroboration with time-lapse photography and a suite of environmental sampling instruments. We also tested whether the presence of the device on a branch influenced the timing of budburst. Our results indicated the following: the temperatures measured by the budburst sensor's digital thermometer closely approximated the temperatures measured using a thermocouple touching plant tissue; the photoperiod detector measured ambient light with the same accuracy as did time lapse photography; the budburst sensor accurately detected the timing of budburst; and the sensor itself did not influence the budburst timing of Populus clones. Among other potential applications, future use of the sensor may provide plant phenotyping at the landscape level for integration with landscape genomics.

Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris)

Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.

Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst]

The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce.

Genetic architecture of spring and autumn phenology in Salix

BACKGROUND

In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa.

RESULTS

All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized.

CONCLUSIONS

This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.

Light quality regulates flowering in FvFT1/FvTFL1 dependent manner in the woodland strawberry Fragaria vesca

Control of flowering in the perennial model, the woodland strawberry (Fragaria vesca L.), involves distinct molecular mechanisms that result in contrasting photoperiodic flowering responses and growth cycles in different accessions. The F. vesca homolog of TERMINAL FLOWER1 (FvTFL1) functions as a key floral repressor that causes short-day (SD) requirement of flowering and seasonal flowering habit in the SD strawberry. In contrast, perpetual flowering F. vesca accessions lacking functional FvTFL1 show FLOWERING LOCUS T (FvFT1)-dependent early flowering specifically under long-days (LD). We show here that the end-of-day far-red (FR) and blue (B) light activate the expression of FvFT1 and the F. vesca homolog of SUPPRESSOR OF THE OVEREXPRESSION OF CONSTANS (FvSOC1) in both SD and LD strawberries, whereas low expression levels are detected in red (R) and SD treatments. By using transgenic lines, we demonstrate that FvFT1 advances flowering under FR and B treatments compared to R and SD treatments in the LD strawberry, and that FvSOC1 is specifically needed for the B light response. In the SD strawberry, flowering responses to these light quality treatments are reversed due to up-regulation of the floral repressor FvTFL1 in parallel with FvFT1 and FvSOC1. Our data highlights the central role of FvFT1 in the light quality dependent flower induction in the LD strawberry and demonstrates that FvTFL1 reverses not only photoperiodic requirements but also light quality effects on flower induction in the SD strawberry.

Effects of nutrient optimization on intra-annual wood formation in Norway spruce

In the Nordic countries, growth of Norway spruce (Picea abies (L.) Karst.) is generally limited by low availability of nutrients, especially nitrogen. Optimizing forest management requires better insight on how growth responds to the environmental conditions and their manipulation. The aim of this study was to analyse the effects of nutrient optimization on timing and the rate of tracheid formation of Norway spruce and to follow the differentiation of newly formed tracheids. The study was performed during two growing seasons in a long-term nutrient optimization experiment in northern Sweden, where all essential macro- and micronutrients were supplied in irrigation water every second day from mid-June to mid-August. The control plots were without additional nutrients and water. Tracheid formation in the stem was monitored throughout the growing season by weekly sampling of microcores at breast height. The onset of xylogenesis occurred in early June, but in early summer there were no significant between-treatment differences in the onset and relative rate of tracheid formation. In both treatments, the onset of secondary cell wall formation occurred in mid-June. The maximum rate of tracheid formation occurred close to the summer solstice and 50% of the tracheids had been accumulated in early July. Optimized nutrition resulted in the formation of ∼50% more tracheids and delayed the cessation of tracheid formation, which extended the tracheid formation period by 20-50%, compared with control trees. The increased growth was mainly an effect of enhanced tracheid formation rate during the mid- and later-part of the growing season. In the second year, the increased growth rate also resulted in 11% wider tracheids. We conclude that the onset and rate of tracheid formation and differentiation during summer is primarily controlled by photoperiod, temperature and availability of nutrients, rather than supply of carbohydrates.

A yeast mitotic activator sensitises the shoot apical meristem to become floral in day-neutral tobacco

True day-neutral (DN) plants flower regardless of day-length and yet they flower at characteristic stages. DN Nicotiana tabacum cv. Samsun, makes about forty nodes before flowering. The question still persists whether flowering starts because leaves become physiologically able to export sufficient floral stimulus or the shoot apical meristem (SAM) acquires developmental competence to interpret its arrival. This question was addressed using tobacco expressing the Schizosaccharomyces pombe cell cycle gene, Spcdc25, as a tool. Spcdc25 expression induces early flowering and we tested a hypothesis that this phenotype arises because of premature floral competence of the SAM. Scions of vegetative Spcdc25 plants were grafted onto stocks of vegetative WT together with converse grafts and flowering onset followed (as the time since sowing and number of leaves formed till flowering). Spcdc25 plants flowered significantly earlier with fewer leaves, and, unlike WT, also formed flowers from axillary buds. Scions from vegetative Spcdc25 plants also flowered precociously when grafted to vegetative WT stocks. However, in a WT scion to Spcdc25 stock, the plants flowered at the same time as WT. SAMs from young vegetative Spcdc25 plants were elongated (increase in SAM convexity determined by tracing a circumference of SAM sections) with a pronounced meristem surface cell layers compared with WT. Presumably, Spcdc25 SAMs were competent for flowering earlier than WT and responded to florigenic signal produced even in young vegetative WT plants. Precocious reproductive competence in Spcdc25 SAMs comprised a pronounced mantle, a trait of prefloral SAMs. Hence, we propose that true DN plants export florigenic signal since early developmental stages but the SAM has to acquire competence to respond to the floral stimulus.

Structure and function of florigen and the receptor complex

In the 1930s, the flowering hormone, florigen, was proposed to be synthesized in leaves under inductive day length and transported to the shoot apex, where it induces flowering. More recently, generated genetic and biochemical data suggest that florigen is a protein encoded by the gene, FLOWERING LOCUS T (FT). A rice (Oryza sativa) FT homolog, Hd3a, interacts with the rice FD homolog, OsFD1, via a 14-3-3 protein. Formation of this tri-protein complex is essential for flowering promotion by Hd3a in rice. In addition, the multifunctionality of FT homologs, other than for flowering promotion, is an emerging concept. Here we review the structural and biochemical features of the florigen protein complex and discuss the molecular basis for the multifunctionality of FT proteins.

Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata

BACKGROUND AND AIMS

The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses.

METHODS

Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization.

KEY RESULTS

The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions).

CONCLUSIONS

The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas.

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714-718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.

The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms

In tree species native to temperate and boreal regions, the activity-dormancy cycle is an important adaptive trait both for survival and growth. We discuss recent research on mechanisms controlling the overlapping developmental processes that define the activity-dormancy cycle, including cessation of apical growth, bud development, induction, maintenance and release of dormancy, and bud burst. The cycle involves an extensive reconfiguration of metabolism. Environmental control of the activity-dormancy cycle is based on perception of photoperiodic and temperature signals, reflecting adaptation to prevailing climatic conditions. Several molecular actors for control of growth cessation have been identified, with the CO/FT regulatory network and circadian clock having important coordinating roles in control of growth and dormancy. Other candidate regulators of bud set, dormancy and bud burst have been identified, such as dormancy-associated MADS-box factors, but their exact roles remain to be discovered. Epigenetic mechanisms also appear to factor in control of the activity-dormancy cycle. Despite evidence for gibberellins as negative regulators in growth cessation, and ABA and ethylene in bud formation, understanding of the roles that plant growth regulators play in controlling the activity-dormancy cycle is still very fragmentary. Finally, some of the challenges for further research in bud dormancy are discussed.

A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling

The transition from the vegetative to reproductive development is a critical event in the plant life cycle. The accurate prediction of flowering time in elite germplasm is important for decisions in maize breeding programs and best agronomic practices. The understanding of the genetic control of flowering time in maize has significantly advanced in the past decade. Through comparative genomics, mutant analysis, genetic analysis and QTL cloning, and transgenic approaches, more than 30 flowering time candidate genes in maize have been revealed and the relationships among these genes have been partially uncovered. Based on the knowledge of the flowering time candidate genes, a conceptual gene regulatory network model for the genetic control of flowering time in maize is proposed. To demonstrate the potential of the proposed gene regulatory network model, a first attempt was made to develop a dynamic gene network model to predict flowering time of maize genotypes varying for specific genes. The dynamic gene network model is composed of four genes and was built on the basis of gene expression dynamics of the two late flowering id1 and dlf1 mutants, the early flowering landrace Gaspe Flint and the temperate inbred B73. The model was evaluated against the phenotypic data of the id1 dlf1 double mutant and the ZMM4 overexpressed transgenic lines. The model provides a working example that leverages knowledge from model organisms for the utilization of maize genomic information to predict a whole plant trait phenotype, flowering time, of maize genotypes.

De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

Background

Transcriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species, and the advent of next-generation sequencing (NGS) technologies has greatly decreased the cost and time required for this process. Transcriptome data are especially desirable in bamboo species, as certain members constitute an economically and culturally important group of mostly semelparous plants with remarkable flowering features, yet little bamboo genomic research has been performed. Here we present, for the first time, extensive sequence and transcript abundance data for the floral transcriptome of a key bamboo species, Dendrocalamus latiflorus, obtained using the Illumina GAII sequencing platform. Our further goal was to identify patterns of gene expression during bamboo flower development.

Results

Approximately 96 million sequencing reads were generated and assembled de novo, yielding 146,395 high quality unigenes with an average length of 461 bp. Of these, 80,418 were identified as putative homologs of annotated sequences in the public protein databases, of which 290 were associated with the floral transition and 47 were related to flower development. Digital abundance analysis identified 26,529 transcripts differentially enriched between two developmental stages, young flower buds and older developing flowers. Unigenes found at each stage were categorized according to their putative functional categories. These sequence and putative function data comprise a resource for future investigation of the floral transition and flower development in bamboo species.

Conclusions

Our results present the first broad survey of a bamboo floral transcriptome. Although it will be necessary to validate the functions carried out by these genes, these results represent a starting point for future functional research on D. latiflorus and related species.

Coordination of plastid and light signaling pathways upon development of Arabidopsis leaves under various photoperiods

Plants synchronize their cellular and physiological functions according to the photoperiod (the length of the light period) in the cycle of 24 h. Photoperiod adjusts several traits in the plant life cycle, including flowering and senescence in annuals and seasonal growth cessation in perennials. Photoperiodic development is controlled by the coordinated action of photoreceptors and the circadian clock. During the past 10 years, remarkable progress has been made in understanding the molecular mechanism of the circadian clock, especially with regard to the transition of Arabidopsis from the vegetative growth to the reproductive phase. Besides flowering photoperiod also modifies plant photosynthetic structures and traits. Light signals controlling biogenesis of chloroplasts and development of leaf photosynthetic structures are perceived both by photoreceptors and in chloroplasts. In this review, we provide evidence suggesting that the photoperiodic development of Arabidopsis leaves mimics the acclimation of plant to various light intensities. Furthermore, the chloroplast-to-nucleus retrograde signals that adjust acclimation to light intensity are proposed to contribute also to the signaling pathways that control photoperiodic acclimation of leaves.

Flowering time and transcriptome variation in Capsella bursa-pastoris (Brassicaceae)

• Flowering is a major developmental transition and its timing in relation to environmental conditions is of crucial importance to plant fitness. Understanding the genetic basis of flowering time variation is important to determining how plants adapt locally. • Here, we investigated flowering time variation of Capsella bursa-pastoris collected from different latitudes in China. We also used a digital gene expression (DGE) system to generate partial gene expression profiles for 12 selected samples. • We found that flowering time was highly variable and most strongly correlated with day length and winter temperature. Significant differences in gene expression between early- and late-flowering samples were detected for 72 candidate genes for flowering time. Genes related to circadian rhythms were significantly overrepresented among the differentially expressed genes. • Our data suggest that circadian rhythms and circadian clock genes play an important role in the evolution of flowering time, and C. bursa-pastoris plants exhibit expression differences for candidate genes likely to affect flowering time across the broad range of environments they face in China.