Gene expression changes during short day induced terminal bud formation in Norway spruce

Epitype-inducing temperatures drive DNA methylation changes during somatic embryogenesis in the long-lived gymnosperm Norway spruce

An epigenetic memory of the temperature sum experienced during embryogenesis is part of the climatic adaptation strategy of the long-lived gymnosperm Norway spruce. This memory has a lasting effect on the timing of bud phenology and frost tolerance in the resulting epitype trees. The epigenetic memory is well characterized phenotypically and at the transcriptome level, but to what extent DNA methylation changes are involved have not previously been determined. To address this, we analyzed somatic epitype embryos of Norway spruce clones produced at contrasting epitype-inducing conditions (18 and 28°C). We screened for differential DNA methylation in 2744 genes related mainly to the epigenetic machinery, circadian clock, and phenology. Of these genes, 68% displayed differential DNA methylation patterns between contrasting epitype embryos in at least one methylation context (CpG, CHG, CHH). Several genes related to the epigenetic machinery (e.g., DNA methyltransferases, ARGONAUTE) and the control of bud phenology (FTL genes) were differentially methylated. This indicates that the epitype-inducing temperature conditions induce an epigenetic memory involving specific DNA methylation changes in Norway spruce.

MADS-box transcription factors determine the duration of temporary winter dormancy in closely related evergreen and deciduous Iris spp

Winter dormancy (WD) is a crucial strategy for plants coping with potentially deadly environments. In recent decades, this process has been extensively studied in economically important perennial eudicots due to changing climate. However, in evergreen monocots with no chilling requirements, dormancy processes are so far a mystery. In this study, we compared the WD process in closely related evergreen (Iris japonica) and deciduous (I. tectorum) iris species across crucial developmental time points. Both iris species exhibit a 'temporary' WD process with distinct durations, and could easily resume growth under warm conditions. To decipher transcriptional changes, full-length sequencing for evergreen iris and short read RNA sequencing for deciduous iris were applied to generate respective reference transcriptomes. Combining results from a multipronged approach, SHORT VEGETATIVE PHASE and FRUITFULL (FUL) from MADS-box was associated with a dormancy- and a growth-related module, respectively. They were co-expressed with genes involved in phytohormone signaling, carbohydrate metabolism, and environmental adaptation. Also, gene expression patterns and physiological changes in the above pathways highlighted potential abscisic acid and jasmonic acid antagonism in coordinating growth and stress responses, whereas differences in carbohydrate metabolism and reactive oxygen species scavenging might lead to species-specific WD durations. Moreover, a detailed analysis of MIKCCMADS-box in irises revealed common features described in eudicots as well as possible new roles for monocots during temporary WD, such as FLOWERING LOCUS C and FUL. In essence, our results not only provide a portrait of temporary WD in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants.

Interactive Effects of Light Quality during Day Extension and Temperature on Bud Set, Bud Burst and PaFTL2, PaCOL1-2 and PaSOC1 Expression in Norway Spruce (Picea abies (L.) Karst.)

Light and temperature are crucial factors for the annual growth rhythm of tree seedlings of the boreal and temperate zone. Dormant, vegetative winter buds are formed under short days (SD) and altered light quality. In the conifer Norway spruce, expression of FTL2 increases and PaCOL1-2 and PaSOC1 decrease under light regimes, inducing bud set. Although temperature is known to modulate the timing of bud set, information about combined effects of light climate and temperature on bud phenology and gene expression is limited. We studied the interactive effects of temperature (18, 22/24 °C) and day extension with blue (B), red (R) or far-red (FR) light or different R:FR ratios compared to SD on growth–dormancy cycling and expression of FTL2, PaCOL1-2 and PaSOC1 in Norway spruce seedlings. Day-extension with B light and all treatments involving FR light sustained shoot elongation, with increased growth at higher temperature. The R light treatment resulted in delayed/prevented bud set compared to SD, with more delay/prevented bud set at 24 °C than 18 °C. This was associated with lower PaFTL2-transcript levels at 24 °C and more rapid subsequent bud burst. For the growth-sustaining treatments (long days, FR and B light), the PaFTL2-transcript levels were generally lower and those of PaCO1-2 and PaSOC1 higher compared with SD and R light. In conclusion, our results demonstrate more reduced/prevented bud set and faster bud burst with increased temperature under day extension with R light, indicating less deep dormancy than at lower temperature. Also, sustained shoot elongation under the B light treatment (27 µmol m−2 s−1) in contrast to the lower B light-irradiances tested previously (≤13 µmol m−2 s−1), demonstrates an irradiance-dependent effect of day extension with B light.

The dehydrins gene expression differs across ecotypes in Norway spruce and relates to weather fluctuations

Norway spruce has a broad natural distribution range, which results in a substantial variety of its physiological and genetic variation. There are three distinct altitudinal ecotypes described in this tree species. The physiological optimum of each ecotype may be shifted due to ongoing climate change, especially in traits associated with water demand that might be crucial for adaptation. Dehydrins are proteins that help to mitigate the adverse effects of dehydration. Dehydrin gene expression patterns appeared to be a suitable marker for plant stress assessment. Genetically determined differences in response between individuals and populations were formerly studied, however, mainly in controlled conditions. We evaluated ecotypic variation in dehydrin gene expression in a clonal bank comprised of all three ecotypes. A genetic relationship among targeted trees was uncovered utilizing GBS (Genotyping by Sequencing) platform. We sampled 4-6 trees of each ecotype throughout 15 months period. Subsequently, we assessed the RNA expression of dehydrin genes by qRT-PCR. For this study, we deliberately selected dehydrins from different categories. Our findings detected significant differences among ecotypes in dehydrin expression. The association of recorded climatic variables and individual gene expression across the study period was evaluated and revealed, for certain genes, a correlation between dehydrin gene expression and precipitation, temperature, and day-length.

Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming

In higher-latitude trees, temperature and photoperiod control the beginning and end of the photosynthetically active season. Elevated temperature (ET) has advanced spring warming and delayed autumn cooling while photoperiod remains unchanged. We assessed the effects of warming on the length of the photosynthetically active season of three provenances of Pinus strobus L. seedlings from different latitudes, and evaluated the accuracy of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI) for tracking the predicted variation in spring and autumn phenology of photosynthesis among provenances. Seedlings from northern, local and southern P. strobus provenances were planted in a temperature-free-air-controlled enhancement (T-FACE) experiment and exposed to ET (+1.5/3°C; day/night). Over 18 months, we assessed photosynthetic phenology by measuring chlorophyll fluorescence, gas exchange, leaf spectral reflectance and pigment content. During autumn, all seedlings regardless of provenance followed the same sequence of phenological events with the initial downregulation of photosynthesis, followed by the modulation of non-photochemical quenching and associated adjustments of zeaxanthin pool sizes. However, the timing of autumn downregulation differed between provenances, with delayed onset in the southern provenance (SP) and earlier onset in the northern relative to the local provenance, indicating that photoperiod at the provenance origin is a dominant factor controlling autumn phenology. Experimental warming further delayed the downregulation of photosynthesis during autumn in the SP. A provenance effect during spring was also observed but was generally not significant. The vegetation indices PRI and CCI were both effective at tracking the seasonal variations of energy partitioning in needles and the differences of carotenoid pigments indicative of the stress status of needles. These results demonstrate that PRI and CCI can be useful tools for monitoring conifer phenology and for the remote monitoring of the length of the photosynthetically active season of conifers in a changing climate.

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.

Photoperiodic Regulation of Growth-Dormancy Cycling through Induction of Multiple Bud-Shoot Barriers Preventing Water Transport into the Winter Buds of Norway Spruce

Whereas long days (LDs) sustain shoot elongation, short days (SDs) induce growth cessation and formation of dormant buds in young individuals of a wide range of temperate and boreal tree species. In specific conifers, including Norway spruce, photoperiodic control of bud development is associated with the formation of a plate of thick-walled cells, denoted as the crown, at the base of the bud. Information about cellular characteristics of this crown region is limited. We aimed to test whether the crown region is an important SD-induced barrier ensuring dehydration of the developing winter bud by preventing water influx. Using microscopy and synchrotron techniques, we show here that under LD, cell walls in growing shoot tips had highly methyl-esterified homogalacturonan pectin. During SD-induced bud development, the homogalacturonan in the crown region was de-methyl-esterified, enabling Ca2+ binding and crosslinking, a process known to decrease cell wall water permeability by reducing pectin pore size. In addition, there was abundant callose deposition at plasmodesmata in the crown region, and xylem connections between the bud and the subtending shoot were blocked. Consistent with reduced water transport across the crown region into the bud, uptake of fluorescein in shoot tips was blocked at the base of the bud under SD. Upon transfer from SD to bud-break-inducing LD, these processes were reversed, and aquaporin transcript levels significantly increased in young stem tissue after 4 weeks under LD. These findings indicate that terminal bud development is associated with reduced water transport through decreased cell wall permeability and blocking of plasmodesmata and xylem connections in the crown structure. This provides further understanding of the regulatory mechanism for growth-dormancy cycling in coniferous tree species such as Norway spruce.

The epigenetic memory of temperature during embryogenesis modifies the expression of bud burst-related genes in Norway spruce epitypes

Epigenetic memory affects the timing of bud burst phenology and the expression of bud burst-related genes in genetically identical Norway spruce epitypes in a manner usually associated with ecotypes. In Norway spruce, a temperature-dependent epigenetic memory established during embryogenesis affects the timing of bud burst and bud set in a reproducible and predictable manner. We hypothesize that the clinal variation in these phenological traits, which is associated with adaptation to growth under frost-free conditions, has an epigenetic component. In Norway spruce, dehydrins (DHNs) have been associated with extreme frost tolerance. DHN transcript levels decrease gradually prior to flushing, a time when trees are highly sensitive to frost. Furthermore, EARLY BUD BREAK 1 genes (EBB1) and the FT-TFL1-LIKE 2-gene (PaFTL2) were previously suggested to be implied in control of bud phenology. Here we report an analysis of transcript levels of 12 DHNs, 3 EBB1 genes and FTL2 in epitypes of the same genotype generated at different epitype-inducing temperatures, before and during spring bud burst. Earlier flushing of epitypes originating from embryos developed at 18 °C as compared to 28 °C, was associated with differential expression of these genes between epitypes and between buds and last year's needles. The majority of these genes showed significantly different expressions between epitypes in at least one time point. The general trend in DHN expression pattern in buds showed the expected reduction in transcript levels when approaching flushing, whereas, surprisingly, transcript levels peaked later in needles, mainly at the moment of bud burst. Collectively, our results demonstrate that the epigenetic memory of temperature during embryogenesis affects bud burst phenology and expression of the bud burst-related DHN, EBB1 and FTL2 genes in genetically identical Norway spruce epitypes.

A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

BACKGROUND

MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.

RESULTS

We identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.

CONCLUSIONS

Most Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.

Adaptation to seasonality and the winter freeze

Flowering plants initially diversified during the Mesozoic era at least 140 million years ago in regions of the world where temperate seasonal environments were not encountered. Since then several cooling events resulted in the contraction of warm and wet environments and the establishment of novel temperate zones in both hemispheres. In response, less than half of modern angiosperm families have members that evolved specific adaptations to cold seasonal climates, including cold acclimation, freezing tolerance, endodormancy, and vernalization responsiveness. Despite compelling evidence for multiple independent origins, the level of genetic constraint on the evolution of adaptations to seasonal cold is not well understood. However, the recent increase in molecular genetic studies examining the response of model and crop species to seasonal cold offers new insight into the evolutionary lability of these traits. This insight has major implications for our understanding of complex trait evolution, and the potential role of local adaptation in response to past and future climate change. In this review, we discuss the biochemical, morphological, and developmental basis of adaptations to seasonal cold, and synthesize recent literature on the genetic basis of these traits in a phylogenomic context. We find evidence for multiple genetic links between distinct physiological responses to cold, possibly reinforcing the coordinated expression of these traits. Furthermore, repeated recruitment of the same or similar ancestral pathways suggests that land plants might be somewhat pre-adapted to dealing with temperature stress, perhaps making inducible cold traits relatively easy to evolve.

Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage

In flowering plants, homologs of the Arabidopsis phosphatidylethanolamine-binding protein (PEBP) FLOWERING LOCUS T (FT) are key components in controlling flowering time. We show here that, although FT homologs are found in all angiosperms with completed genome sequences, there is no evidence to date that FT-like genes exist in other groups of plants. Through phylogeny reconstructions and heterologous expression, we examined the biochemical function of the Picea (spruces) and Pinus (pines) PEBP families - two gymnosperm taxa phylogenetically distant from the angiosperms. We have defined a lineage of gymnosperm PEBP genes, termed the FT/TERMINAL FLOWER1 (TFL1)-like genes, that share sequence characteristics with both the angiosperm FT- and TFL1-like clades. When expressed in Arabidopsis, FT/TFL1-like genes repressed flowering, indicating that the proteins are biochemically more similar to the angiosperm TFL1-like proteins than to the FT-like proteins. This suggests that the regulation of the vegetative-to-reproductive switch might differ in gymnosperms compared with angiosperms. Molecular evolution studies suggest that plasticity at exon 4 contributes to the divergence of FT-like function in floral promotion. In addition, the presence of FT-like genes in basal angiosperms indicates that the FT-like function emerged at an early stage during the evolution of flowering plants as a means to regulate flowering time.

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.

Cold acclimation and floral development in almond bud break: insights into the regulatory pathways

In temperate fruit trees, seasonal dormancy and cold acclimation have a major impact on blooming time and, consequently, fruit production. To gain insight into the still unclear molecular processes underlying blooming, expression of genes putatively involved in the cold response was studied in almond (Prunus dulcis Mill.), which is the earliest fruit tree in the family Rosaceae to bloom. The transcript levels of two C-repeat binding factor (PdCBF) genes and one of their putative targets, PdDehydrin1 (PdDHN1), were analysed in flower buds and shoot internodes during seasonal dormancy up to bud break. In parallel, expression of candidate genes related to flower development was also followed. In a 2-year study, PdCBF2 showed a progressive increase in transcript abundance during the autumn in close correlation with cold acclimation, while high transcript levels of PdCBF1 and PdDHN1 were already found by summer. After bud break, with temperatures still within the chilling range, both PdCBF genes and PdDHN1 were found to sharply reduce transcription in flower buds and internodes, suggesting damping of CBF-mediated cold signalling during growth resumption, in correlation with cold hardiness decline. Flower bud break was also followed by a decrease in the expression of PdGA20OX, a candidate gene involved in gibberellin biosynthesis, and an increase in the expression of two homeotic genes related to floral organ development, PdMADS1 and -3. These genes may also be relevant players in the regulation of anthesis in this model Rosaceae species.