Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx

Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement

High species diversity, hybridization potential, broad geographical dispersal range and ornamental characteristics (i.e., attractive size, shape, structure, flowers, and evergreen) have fetched a good international market for Rhododendron. However, most species are restricted to specific geographic areas due to their habitat specificity in acidic soil and cold climates, resulting many species being classified under threat categories of the IUCN. In this review, advances in research on Rhododendron for improvement to floral display quality and stress resistance have been described. The low genetic barrier among species has created opportunities for extensive hybridization and ploidy alteration for introducing quality and adaptive traits during the development of new varieties. Recent technological advances have supported investigations into the mechanism of flower development, as well as cold tolerance and pathogen resistance mechanisms in the Rhododendron. However, most of the species have limited adaptability to drought, line-tolerance, pathogen resistance, and high-temperature conditions and this resistance ability present in few species largely remains unexplored. Additionally, the available genetic diversity and genomic information on species, and possibilities for their application in molecular breeding have been summarized. Overall, genomic resource data are scarce in the majority of the members of this genus. Finally, various research gaps such as genetic mapping of quality traits, understanding the molecular mechanism of quality-related traits and genomic assortment in Rhododendron members have been discussed in the future perspective section.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04006-6.

Infrared thermography of in situ natural freezing and mechanism of winter-thermonasty in Rhododendron maximum

Evergreen leaves of Rhododendron species inhabiting temperate/montane climates are typically exposed to both high radiation and freezing temperatures during winter when photosynthetic biochemistry is severely inhibited. Cold-induced "thermonasty," that is, lamina rolling and petiole curling, can reduce the amount of leaf area exposed to solar radiation and has been associated with photoprotection in overwintering rhododendrons. The present study was conducted on natural, mature plantings of a cold-hardy and large-leaved thermonastic North American species (Rhododendron maximum) during winter freezes. Infrared thermography was used to determine initial sites of ice formation, patterns of ice propagation, and dynamics of the freezing process in leaves to understand the temporal and mechanistic relationship between freezing and thermonasty. Results indicated that ice formation in whole plants is initiated in the stem, predominantly in the upper portions, and propagates in both directions from the original site. Ice formation in leaves initially occurred in the vascular tissue of the midrib and then propagated into other portions of the vascular system/venation. Ice was never observed to initiate or propagate into palisade, spongy mesophyll, or epidermal tissues. These observations, together with the leaf- and petiole-histology, and a simulation of the rolling effect of dehydrated leaves using a cellulose-based, paper-bilayer system, suggest that thermonasty occurs due to anisotropic contraction of cell wall cellulose fibers of adaxial versus abaxial surface as the cells lose water to ice present in vascular tissues.

Time-series RNA-Seq transcriptome profiling reveals novel insights about cold acclimation and de-acclimation processes in an evergreen shrub of high altitude

The high-altitude alpine regions are characterized by highly variable and harsh environmental conditions. However, relatively little is known about the diverse mechanisms adopted by alpine plants to adapt to these stressful conditions. Here, we studied variation in transcriptome and physiological adjustments occurring across the year at high elevation environments in the leaf tissue of Rhododendron anthopogon, an evergreen shrub of Himalaya. The samples were collected at 12 different time-points, from August until snowfall in November 2017, and then from June to September 2018. It was observed that with a drop in both ambient air temperature and photoperiod towards onset of winter, the freezing resistance of plants increased, resulting in 'cold acclimation'. Further, 'de-acclimation' was associated with a decrease in freezing resistance and increase in photosynthetic efficiency of leaves during spring. A considerable amount of variation was observed in the transcriptome in a time-dependent sequential manner, with a total of 9,881 differentially expressed genes. Based on gene expression profiles, the time-points could be segregated into four clusters directly correlating with the distinct phases of acclimation: non-acclimation (22-August-2017, 14-August-2018, 31-August-2018), early cold acclimation (12-September-2017, 29-September-2017), late cold acclimation (11-October-2017, 23-October-2017, 04-November-2017, 18-September-2018) and de-acclimation (15-June-2018, 28-June-2018, 14-July-2018). Cold acclimation was a gradual process, as indicated by presence of an intermediate stage (early acclimation). However, the plants can by-pass this stage when sudden decrease in temperature is encountered. The maximum variation in expression levels of genes occurred during the transition to de-acclimation, hence was 'transcriptionally' the most active phase. The similar or higher expression levels of genes during de-acclimation in comparison to non-acclimation suggested that molecular functionality is re-initiated after passing through the harsh winter conditions.

Identification and genetic diversity analysis of hybrid offspring of azalea based on EST-SSR markers

Azalea is a world famous flower with high economic and ornamental value. The breeding of new azalea varieties is mainly done by cross breeding. However, there is a risk that cross breeding may cause errors in the hybrid offspring due to contamination by exogenous pollen. Therefore, the identification of hybrid offspring is an important part of azalea breeding. In this study, the parents of three hybrid combinations and their 88 F1 hybrid offspring were selected to screen 15 pairs of EST-SSR primers to identify the authenticity of azalea hybrid offspring. The results showed that the authenticity of 88 azalea F1 hybrid progenies could be determined by at least four primer pairs. Genetic diversity analysis of azalea hybrid progeny revealed that the number of alleles and polymorphic information content of the progeny increased to different degrees, and the more distant the genetic distance between parents, the richer the polymorphic information. It is suggested that EST-SSR molecular marker can be applied for the early identification and genetic diversity analysis of the progeny of azalea hybrids. This method is of positive significance for improving the breeding efficiency of new varieties and exploring the genetic background of azalea.

Photoprotection conferring plant tolerance to freezing stress through rescuing photosystem in evergreen Rhododendron

Light stress is one of the important stresses for winter survival in evergreens, especially for plants with broad leaves, like evergreen rhododendrons. Photoprotection has been shown to upregulate dramatically in rhododendrons during winter, but whether it directly contributes to enhancing the freezing tolerance is still unknown. In this study, we found that the expression and circadian rhythm of an early light-induced protein (ELIP)-RhELIP3-which exerts photoprotection in Rhododendron 'Elsie Lee', could be impacted by both photoperiod and low temperature, with low temperature being the predominant inducer. Arabidopsis overexpressing RhELIP3 displayed significantly stronger freezing tolerance and better photosystem II function after a 3-day recovery from freezing treatment. Moreover, RhHY5 binds with the RhELIP3 promoter to activate its expression. Arabidopsis overexpressing RhHY5 exhibited stronger freezing tolerance and better photosystem II function. AtELIP1 and AtELIP2 were significantly induced in RhHY5-overexpressed Arabidopsis at low temperatures. We also discovered that RhBBX24 binds directly to RhELIP3 promoter and suppresses its expression. RhBBX24 can also interact with RhHY5 and inhibit the interaction of RhHY5-RhELIP3. RhELIP3, RhHY5, and RhBBX24 exhibited similar circadian rhythms under low temperature with short period. Overall, our investigation highlights that photoprotection is involved in improving the freezing tolerance of evergreen rhododendrons.

The relationship of cold acclimation and extracellular ice formation to winter thermonasty in two Rhododendron species and their F1 hybrid

PREMISE

Thermonastic leaf movements in evergreen Rhododendron species have been used to study plant strategies for winter photoprotection. To add to the current fundamental understanding of this behavior, we addressed the following questions: (1) Is the cold-acclimated (CA) state necessary for thermonasty, and do cold-induced leaf movements also occur in non-acclimated (NA) plants? (2) Which of the two movements, leaf rolling versus curling, is more responsive to freezing, if any, in a non-thermonastic species? (3) What is the temporal relationship between extracellular freezing and thermonasty? (4) What genetic inferences can be drawn from leaf movement in an F₁ hybrid relative to its parents?

METHODS

A temperature-controlled, gradual cooling regime was used to quantify freeze-induced leaf movements. Infrared thermography was used to confirm extracellular ice-formation in leaves.

RESULTS

Both NA and CA plants of thermonastic species exhibited thermonasty, but leaf rolling/curling increased significantly in CA plants. In the cold-acclimated condition, a non-thermonastic species showed almost no rolling during freezing, while the thermonastic species and F₁ hybrid did, the latter exhibiting a response intermediate to the parents. Freezing-induced leaf curling in the non-thermonastic species and the F₁ hybrid was equivalent and significantly less than the degree of curling in the thermonastic species.

CONCLUSIONS

Milder thermonasty in NA than CA leaves could be associated with differential anisotropy in the rolling forces and/or response of aquaporins to freezing. Leaf movements in the hybrid suggest that leaf rolling and curling are additive and dominant genetic traits, respectively. Infrared thermography confirms that ice formation in tissues precedes cold-induced thermonasty in R. catawbiense.

Transcriptomic responses of Microcystis aeruginosa under electromagnetic radiation exposure

Electromagnetic radiation is an important environmental factor. It has a potential threat to public health and ecological environment. However, the mechanism by which electromagnetic radiation exerts these biological effects remains unclear. In this study, the effect of Microcystis aeruginosa under electromagnetic radiation (1.8 GHz, 40 V/m) was studied by using transcriptomics. A total of 306 differentially expressed genes, including 121 upregulated and 185 downregulated genes, were obtained in this study. The differentially expressed genes were significantly enriched in the ribosome, oxidative phosphorylation and carbon fixation pathways, indicating that electromagnetic radiation may inhibit protein synthesis and affect cyanobacterial energy metabolism and photosynthesis. The total ATP synthase activity and ATP content significantly increased, whereas H+K+-ATPase activity showed no significant changes. Our results suggest that the energy metabolism pathway may respond positively to electromagnetic radiation. In the future, systematic studies on the effects of electromagnetic radiation based on different intensities, frequencies, and exposure times are warranted; to deeply understand and reveal the target and mechanism of action of electromagnetic exposure on organisms.

Factors affecting freezing tolerance: a comparative transcriptomics study between field and artificial cold acclimations in overwintering evergreens

Cold acclimation (CA) is a well-known strategy employed by plants to enhance freezing tolerance (FT) in winter. Global warming could disturb CA and increase the potential for winter freeze-injury. Thus, developing robust FT through complete CA is essential. To explore the molecular mechanisms of CA in woody perennials, we compared field and artificial CAs. Transcriptomic data showed that photosynthesis/photoprotection and fatty acid metabolism pathways were specifically enriched in field CA; carbohydrate metabolism, secondary metabolism and circadian rhythm pathways were commonly enriched in both field and artificial CAs. When compared with plants in vegetative growth in the chamber, we found that the light signals with warm air temperatures in the fall might induce the accumulation of leaf abscisic acid (ABA) and jasmonic acid (JA) concentrations, and activate Ca²⁺ , ABA and JA signaling transductions in plants. With the gradual cooling occurrence in winter, more accumulation of anthocyanin, chlorophyll degradation, closure/degradation of photosystem II reaction centers, and substantial accumulation of glucose and fructose contributed to obtaining robust FT during field CA. Moreover, we observed that in Rhododendron 'Elsie Lee', ABA and JA decreased in winter, which may be due to the strong requirement of zeaxanthin for rapid thermal dissipation and unsaturated fatty acids for membrane fluidity. Taken together, our results indicate that artificial CA has limitations to understand the field CA and field light signals (like short photoperiod, light intensity and/or light quality) before the low temperature in fall might be essential for complete CA.

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant

BACKGROUND

Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis).

RESULTS

In this study, the AS transcriptional landscape was characterized in the tea plant genome using high-throughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents.

CONCLUSION

Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.

Identification and Characterization of Five Cold Stress-Related Rhododendron Dehydrin Genes: Spotlight on a FSK-Type Dehydrin With Multiple F-Segments

Dehydrins are a family of plant proteins that accumulate in response to dehydration stresses, such as low temperature, drought, high salinity, or during seed maturation. We have previously constructed cDNA libraries from Rhododendron catawbiense leaves of naturally non-acclimated (NA; leaf LT₅₀, temperature that results in 50% injury of maximum, approximately -7°C) and cold-acclimated (CA; leaf LT₅₀ approximately -50°C) plants and analyzed expressed sequence tags (ESTs). Five ESTs were identified as dehydrin genes. Their full-length cDNA sequences were obtained and designated as RcDhn 1-5. To explore their functionality vis-à-vis winter hardiness, their seasonal expression kinetics was studied at two levels. Firstly, in leaves of R. catawbiense collected from the NA, CA, and de-acclimated (DA) plants corresponding to summer, winter and spring, respectively. Secondly, in leaves collected monthly from August through February, which progressively increased freezing tolerance from summer through mid-winter. The expression pattern data indicated that RcDhn 1-5 had 6- to 15-fold up-regulation during the cold acclimation process, followed by substantial down-regulation during deacclimation (even back to NA levels for some). Interestingly, our data shows RcDhn 5 contains a histidine-rich motif near N-terminus, a characteristic of metal-binding dehydrins. Equally important, RcDhn 2 contains a consensus 18 amino acid sequence (i.e., ETKDRGLFDFLGKKEEEE) near the N-terminus, with two additional copies upstream, and it is the most acidic (pI of 4.8) among the five RcDhns found. The core of this consensus 18 amino acid sequence is a 11-residue amino acid sequence (DRGLFDFLGKK), recently designated in the literature as the F-segment (based on the pair of hydrophobic F residues it contains). Furthermore, the 208 orthologs of F-segment-containing RcDhn 2 were identified across a broad range of species in GenBank database. This study expands our knowledge about the types of F-segment from the literature-reported single F-segment dehydrins (FSK_n) to two or three F-segment dehydrins: Camelina sativa dehydrin ERD14 as F₂S₂K_n type; and RcDhn 2 as F₃SK_n type identified here. Our results also indicate some consensus amino acid sequences flanking the core F-segment in dehydrins. Implications for these cold-responsive RcDhn genes in future genetic engineering efforts to improve plant cold hardiness are discussed.

Comparative analysis of the response and gene regulation in cold resistant and susceptible tea plants

Cold environment is the main constraint for tea plants (Camellia sinensis) distribution and tea farming. We identified two tea cultivars, called var. sinensis cv. Shuchazao (SCZ) with a high cold-tolerance and var. assamica cv. Yinghong9 (YH9) with low cold-tolerance. To better understand the response mechanism of tea plants under cold stress for improving breeding, we compared physiological and biochemical responses, and associated genes expression in response to 7-day and 14-day cold acclimation, followed by 7-day de-acclimation in these two tea cultivars. We found that the low EL50, low Fv/Fm, and high sucrose and raffinose accumulation are responsible for higher cold tolerance in SCZ comparing with YH9. We then measured the expression of 14 key homologous genes, known as involved in these responses in other plants, for each stages of treatment in both cultivars using RT-qPCR. Our results suggested that the increased expression of CsCBF1 and CsDHNs coupling with the accumulation of sucrose play key roles in conferring higher cold resistance in SCZ. Our findings have revealed key genes regulation responsible for cold resistance, which help to understand the cold-resistant mechanisms and guide breeding in tea plants.

Proteome dynamics of cold-acclimating Rhododendron species contrasting in their freezing tolerance and thermonasty behavior

To gain a better understanding of cold acclimation in rhododendron and in woody perennials in general, we used the 2D-DIGE technique to analyze the rhododendron proteome during the seasonal development of freezing tolerance. We selected two species varying in their cold acclimation ability as well as their thermonasty response (folding of leaves in response to low temperature). Proteins were extracted from leaves of non-acclimated (NA) and cold acclimated (CA) plants of the hardier thermonastic species, R. catawbiense (Cata.), and from leaves of cold acclimated plants of the less hardy, non-thermonastic R. ponticum (Pont.). All three protein samples (Cata.NA, Cata.CA, and Pont.CA) were labeled with different CyDyes and separated together on a single gel. Triplicate gels were run and protein profiles were compared resulting in the identification of 72 protein spots that consistently had different abundances in at least one pair-wise comparison. From the 72 differential spots, we chose 56 spots to excise and characterize further by mass spectrometry (MS). Changes in the proteome associated with the seasonal development of cold acclimation were identified from the Cata.CA-Cata.NA comparisons. Differentially abundant proteins associated with the acquisition of superior freezing tolerance and with the thermonastic response were identified from the Cata.CA-Pont.CA comparisons. Our results indicate that cold acclimation in rhododendron involves increases in abundance of several proteins related to stress (freezing/desiccation tolerance), energy and carbohydrate metabolism, regulation/signaling, secondary metabolism (possibly involving cell wall remodeling), and permeability of the cell membrane. Cold acclimation also involves decreases in abundance of several proteins involved in photosynthesis. Differences in freezing tolerance between genotypes can probably be attributed to observed differences in levels of proteins involved in these functions. Also differences in freezing tolerance may be attributed to higher levels of some constitutive protective proteins in Cata. than in Pont. that may be required to overcome freeze damage, such as glutathione peroxidase, glutamine synthetase, and a plastid-lipid-associated protein.

De Novo Assembly of Transcriptome and Development of Novel EST-SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing

Transcriptome sequences generated by next-generation sequencing (NGS) technologies can be utilized to rapidly detect and characterize a large number of gene-based microsatellites from different plants. Rhododendron rex Lévl. is a perennial woody species from the family Ericaceae and an endangered plant with high ornamental value endemic to Southwestern China. Nevertheless, the genetic and genomic information of R. rex remain unknown. In this study, we performed transcriptome sequencing for R. rex leaf samples, and generated large transcript sequences for functional characterization and development gene-associated SSR markers. A total of 164,242 unigenes were assembled and 115,089 (70.07%) unigenes were successfully annotated in public databases. In addition, a total of 15,314 potential EST-SSRs were identified, and the frequency of SSRs in the R. rex unigenes was 9.32%, with an average of one EST-SSR per 5.65 kb. The most abundant type was repeated di-nucleotide (54.63%), followed by mono- (26.03%) and tri-nucleotide (18.51%) repeats. Based on the SSR-containing sequence, 100 primer pairs were randomly selected and synthesized and used for assessment of the polymorphism. Thirty-six primer pairs were polymorphic and revealed polymorphism among 20 individuals from four R. rex populations. A total of 197 alleles were identified, with an average of 5.472 alleles per locus. The Polymorphism Information Content ranged from 0.154 to 0.870, with a mean of 0.482. The newly developed EST-SSR markers exhibited high transferability (58.33-83.33%) among the six subgenera. Thus, these novel EST-SSR markers developed would provide valuable sequence resources for population structure, genetic diversity analysis, and genetic resource assessments of R. rex and its related species.

Genome-environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica

The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome-environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural Fagus sylvatica populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150 m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC.

Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions

BACKGROUND

Activation of numerous protective mechanisms during cold acclimation is important for the acquisition of freezing tolerance in perennial ryegrass (Lolium perenne L.). To elucidate the molecular mechanisms of cold acclimation in two genotypes ('Veyo' and 'Falster') of perennial ryegrass from distinct geographical origins, we performed transcriptome profiling during cold acclimation using RNA-Seq.

METHODS

We cold-acclimated plants from both genotypes in controlled conditions for a period of 17 days and isolated Total RNA at various time points for high throughput sequencing using Illumina technology. RNA-seq reads were aligned to genotype specific references to identify transcripts with significant changes in expression during cold acclimation.

RESULTS

The genes induced were involved in protective mechanisms such as cell response to abiotic stimulus, signal transduction, redox homeostasis, plasma membrane and cell wall modifications, and carbohydrate metabolism in both genotypes. 'Falster' genotype, adapted to cold climates, showed a stronger transcriptional differentiation during cold acclimation, and more differentially expressed transcripts related to stress, signal transduction, response to abiotic stimulus, and metabolic processes compared to 'Veyo'. 'Falster' genotype also showed an induction of more transcripts with sequence homology to fructosyltransferase genes (FTs) and a higher fold induction of fructan in response to low-temperature stress. The circadian rhythm network was perturbed in the 'Veyo' genotype adapted to warmer climates.

CONCLUSION

In this study, the differentially expressed genes during cold acclimation, potentially involved in numerous protective mechanisms, were identified in two genotypes of perennial ryegrass from distinct geographical origins. The observation that the circadian rhythm network was perturbed in 'Veyo' during cold acclimation may point to a low adaptability of 'Veyo' to low temperature stresses. This study also revealed the transcriptional mechanisms underlying carbon allocation towards fructan biosynthesis in perennial ryegrass.

Breeding blueberries for a changing global environment: a review

Today, blueberries are recognized worldwide as one of the foremost health foods, becoming one of the crops with the highest productive and commercial projections. Over the last 100 years, the geographical area where highbush blueberries are grown has extended dramatically into hotter and drier environments. The expansion of highbush blueberry growing into warmer regions will be challenged in the future by increases in average global temperature and extreme fluctuations in temperature and rainfall patterns. Considerable genetic variability exists within the blueberry gene pool that breeders can use to meet these challenges, but traditional selection techniques can be slow and inefficient and the precise adaptations of genotypes often remain hidden. Marker assisted breeding (MAB) and phenomics could aid greatly in identifying those individuals carrying adventitious traits, increasing selection efficiency and shortening the rate of cultivar release. While phenomics have begun to be used in the breeding of grain crops in the last 10 years, their use in fruit breeding programs it is almost non-existent.

Comparative transcriptome profiling of a desert evergreen shrub, Ammopiptanthus mongolicus, in response to drought and cold stresses

Background

The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. However, few studies have focused on their comparisons especially using non-model plants with strong tolerance to both stresses. Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. is the only evergreen broadleaf shrub grown in the central Asian desert and it has very strong cold and drought tolerance. To provide further insights into plant tolerance, the transcriptome profiles of drought- and cold-treated A. mongolicus seedlings were analyzed using Illumina technology and differentially expressed genes (DEGs) were compared.

Results

A comprehensive transcriptome of A. mongolicus was sequenced using pooled mRNA extracted from drought-, cold-stressed and unstressed seedlings as well as leaves from naturally grown shrub. These sequences were assembled into 86058 unigenes, of which 51014 unigenes had an annotated function and 2440 encoded transcription factors (TFs). Transcriptome profiles were analyzed in A. mongolicus seedlings after drought and cold treatments at three time points (2, 8 and 24 h). Between 3917 and 6102 unigenes were identified as DEGs at a single time point in both stresses. Among these DEGs 2028 and 2026 DEGs were common across the three time points of drought and cold treatments respectively, and 971 DEGs were co-regulated by both stresses. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The most pronounced findings are that flavonoid biosynthesis genes were enriched in the DEGs co-up-regulated by both stresses; while membrane protein genes and genes related to chloroplast were abundant in the DEGs specifically up-regulated by drought or cold, respectively. Furthermore, the DREB, ERF, NAC and WRKY TFs were predominantly co-up-regulated by both stresses.

Conclusions

The present study provides the most comprehensive transcriptome resource and the first dynamic transcriptome profiles of A. mongolicus under drought and cold stresses. This information will deepen our understanding of plant tolerance to drought and cold. The up-regulated DEGs will be valuable for further investigations of key genes and molecular mechanisms involved in the adaptation of A. mongolicus to harsh environments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-671) contains supplementary material, which is available to authorized users.

Is expression of aquaporins (plasma membrane intrinsic protein 2s, PIP2s) associated with thermonasty (leaf-curling) in Rhododendron?

It is postulated that leaf thermonasty (leaf curling) in rhododendrons under sub-freezing temperatures is caused by water redistribution due to extracellular freezing. We hypothesize that aquaporins (AQPs), the transmembrane water-channels, may be involved in regulating water redistribution and thus leaf curling. Our experimental system includes two Rhododendron species with contrasting leaf curling behavior whereby it was observed in R. catawbiense but not in R. ponticum. We compared leaf movements and the expression of two AQPs, i.e. R. catawbiense/ponticum plasma-membrane intrinsic protein 2 (Rc/RpPIP2;1 and Rc/RpPIP2;2), in the two species under freezing-rewarming and dehydration-rehydration cycles. To determine the relationship between extracellular freezing and leaf-curling, we monitored leaf-curling in R. catawbiense with or without controlled ice-nucleation. Our data indicate that extracellular freezing may be required for leaf curling. Moreover, in both species, PIP2s were up-regulated at temperatures that fell in ice-nucleation temperature range. Such up-regulation could be associated with the bulk-water efflux caused by extracellular freezing. When leaves were frozen beyond the ice-nucleation temperature range, PIP2s were continuously down-regulated in R. catawbiense along with the progressive leaf curling, as also observed for RcPIP2;2 in dehydrated leaves; as leaves uncurled during re-warming/rehydration, RcPIP2 expression was restored. On the other hand, R. ponticum, a non-curling species, exhibited substantial up-regulation of RpPIP2s during freezing/dehydration. Taken together, our data suggest that RcPIP2 down-regulation was associated with leaf curling. Moreover, the contrasting PIP2 expression patterns combined with leaf behavior of R. catawbiense and R. ponticum under these two cycles may reflect different strategies employed by these two species to tolerate/resist cellular dehydration.

Identification of stress-responsive genes in Ammopiptanthus mongolicus using ESTs generated from cold- and drought-stressed seedlings

BACKGROUND

Ammopiptanthus mongolicus is the only evergreen broadleaf shrub in the northwest desert of China, which can survive long-term aridity and extremely cold environments. In order to understand the genetic mechanisms underlying stress tolerance and adaptation to unfavorable environments of woody plants, an EST approach was used to investigate expression patterns of A. mongolicus in response to abiotic stresses.

RESULTS

ESTs were generated from a cDNA library constructed from A. mongolicus seedlings subjected to cold and drought stresses. Analysis of 5,637 cDNA sequences led to the identification of 5,282 ESTs and 1,594 unigenes, which were denoted as the AmCDUnigene set. Of these, 70% of unigenes were annotated and classified into 12 functional categories according to Gene Ontology, and 30% of unigenes encoded unknown function proteins, suggesting some of them were novel or A. mongolicus specific genes. Using comparative analysis with the reported genes from other plants, 528 (33%) unigenes were identified as stress-responsive genes. The functional classification of the 528 genes showed that a majority of them are associated with scavenging reactive oxygen species, stress response, cellular transport, signal transduction and transcription. To further identify candidate abiotic stress-tolerance genes, the 528 stress-responsive genes were compared with reported abiotic stress genes in the Comparative Stress Genes Catalog of GCP. This comparative analysis identified 120 abiotic stress-responsive genes, and their expression in A. mongolicus seedlings under cold or drought stress were characterized by qRT-PCR. Significantly, 82 genes responded to cold and/or drought stress. These cold- and/or drought-inducible genes confirmed that the ROS network, signal transduction and osmolyte accumulation undergo transcriptional reorganization when exposed to cold or drought stress treatments. Additionally, among the 1,594 unigenes sequences, 155 simple sequence repeats (SSRs) were identified.

CONCLUSION

This study represents a comprehensive analysis of cold and/or drought stress-responsive transcriptiome of A. mongolicus. The newly characterized genes and gene-derived markers from the AmCDUnigene set are valuable resources for a better understanding of the mechanisms that govern stress tolerance in A. mongolicus and other related species. Certain up-regulated genes characterizing these processes are potential targets for breeding for cold and/or drought tolerance of woody plants.

Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation

BACKGROUND

There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits.

RESULTS

Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%.

CONCLUSIONS

These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry.

Generation and Analysis of Expressed Sequence Tags from Chimonanthus praecox (Wintersweet) Flowers for Discovering Stress-Responsive and Floral Development-Related Genes

A complementary DNA library was constructed from the flowers of Chimonanthus praecox, an ornamental perennial shrub blossoming in winter in China. Eight hundred sixty-seven high-quality expressed sequence tag sequences with an average read length of 673.8 bp were acquired. A nonredundant set of 479 unigenes, including 94 contigs and 385 singletons, was identified after the expressed sequence tags were clustered and assembled. BLAST analysis against the nonredundant protein database and nonredundant nucleotide database revealed that 405 unigenes shared significant homology with known genes. The homologous unigenes were categorized according to Gene Ontology hierarchies (biological, cellular, and molecular). By BLAST analysis and Gene Ontology annotation, 95 unigenes involved in stress and defense and 19 unigenes related to floral development were identified based on existing knowledge. Twelve genes, of which 9 were annotated as “cold response,” were examined by real-time RT-PCR to understand the changes in expression patterns under cold stress and to validate the findings. Fourteen genes, including 11 genes related to floral development, were also detected by real-time RT-PCR to validate the expression patterns in the blooming process and in different tissues. This study provides a useful basis for the genomic analysis of C. praecox.

A novel cold-regulated gene from Camellia sinensis, CsCOR1, enhances salt- and dehydration-tolerance in tobacco

In present research, the full-length cDNA and the genomic sequence of a novel cold-regulated gene, CsCOR1, were isolated from Camellia sinensis L. The deduced protein CsCOR1 contains a hydrophobic N-terminus as a signal peptide and a hydrophilic C-terminal domain that is rich in glycine, arginine and proline. Two internal repetitive tridecapeptide fragments (HSVTAGRGGYNRG) exist in the middle of the C-terminal domain and the two nucleotide sequences encoding them are identical. CsCOR1 was localized in the cell walls of transgenic-tobaccos via CsCOR1::GFP fusion approach. The expression of CsCOR1 in tea leaves was enhanced dramatically by both cold- and dehydration-stress. And overexpression of CsCOR1 in transgenic-tobaccos improved obviously the tolerance to salinity and dehydration.

Identification of genes associated with cold acclimation in perennial ryegrass

Cold acclimation dramatically increases freezing tolerance in many temperate plant species. An understanding of cold acclimation is important for extending adaptation areas of perennial ryegrass. Freezing tolerance is greatly increased in perennial ryegrass cv. 'Caddyshack' after cold acclimation. Genes differentially regulated during cold acclimation were identified by analyzing the abundance of expressed sequence tags (ESTs) randomly sampled from two cDNA libraries, one constructed from 14-d cold-acclimated (CA; LT(50)=-12.2 degrees C) and the other from nonacclimated (NA; LT(50)=-7.6 degrees C) leaves of 'Caddyshack'. More than 1400 quality ESTs were generated for each library. Over 60 EST groups were either increased or decreased three times or more in the CA library than in the NA library. Functional classification showed that for nine gene ontology (GO) subcategories, the ratio of CA ESTs to NA ESTs increased twice or more, whereas the ratio decreased by half or more for seven other GO subcategories. Expression analysis of 23 selected genes confirmed that 19 of them exhibited expression patterns consistent with the EST abundance analysis. Our results suggest that up-regulation of cold-regulated (COR), dehydration-responsive, and ice recrystallization inhibition (IRI) genes, and down-regulation of photosynthesis and respiration-related genes are important to increasing freezing tolerance in perennial ryegrass.

Screening of genes induced by salt stress from Alfalfa

An alfalfa cDNA library induced by salt stress was constructed by suppression subtraction hybridization (SSH) technology. Total RNA from 10-day-old seedlings was used as a "driver," and total RNA from seedlings induced by salt was used as a "tester". One hundred and nineteen clones identified as positive clones by reverse Northern dot-blotting resulted in 82 uni-ESTs comprised of 16 contigs and 66 singletons. Blast analysis of deduced protein sequences revealed that 51 ESTs had identity similar to proteins with known function, while 24 could not be annotated at all. Most of the annotated sequences were homologous to genes involved in abiotic or biotic stress in plants. Among these proteins, beta-amylase, fructose-1,6-bisphosphate, aldolase, and sucrose synthase are related to osmolyte synthesis; a CCCH-type zinc finger protein, DNA binding protein, His-Asp phosphotransfer protein, and the RelA/SpoT protein partake in transcription regulation and signal transduction; and ribulose-l,5-bisphosphate carboxylase/oxygenase, chlorophyll a/b binding proteins, and an early light-inducible proteins are related to photosynthesis. In addition, several ESTs, similar to genes from other plant species, closely involved in salt stress were isolated from alfalfa, such as an aquaporin protein, a late embryogenesis-abundant protein, and glutathione peroxidase.

RcDhn5, a cold acclimation-responsive dehydrin from Rhododendron catawbiense rescues enzyme activity from dehydration effects in vitro and enhances freezing tolerance in RcDhn5-overexpressing Arabidopsis plants

Dehydrins (DHNs) are typically induced in response to abiotic stresses that impose cellular dehydration. As extracellular freezing results in cellular dehydration, accumulation of DHNs and development of desiccation tolerance are believed to be key components of the cold acclimation (CA) process. The present study shows that RcDhn5, one of the DHNs from Rhododendron catawbiense leaf tissues, encodes an acidic, SK(2) type DHN and is upregulated during seasonal CA and downregulated during spring deacclimation (DA). Data from in vitro partial water loss assays indicate that purified RcDhn5 protects enzyme activity against a dehydration treatment and that this protection is comparable with acidic SK(n) DHNs from other species. To investigate the contribution of RcDhn5 to freezing tolerance (FT), Arabidopsis plants overexpressing RcDhn5 under the control of 35S promoter were generated. Transgenic plants exhibited improved 'constitutive' FT compared with the control plants. Furthermore, a small but significant improvement in FT of RcDhn5-overexpressing plants was observed after 12 h of CA; however, this gained acclimation capacity was not sustained after a 6-day CA. Transcript profiles of cold-regulated native Arabidopsis DHNs (COR47, ERD10 and ERD14) during a CA time-course suggests that the apparent lack of improvement in cold-acclimated FT of RcDhn5-overexpressing plants over that of wild-type controls after a 6-day CA might have been because of the dilution of the effect of RcDhn5 overproduction by a strong CA-induced expression of native Arabidopsis DHNs. This study provides evidence that RcDhn5 contributes to freezing stress tolerance and that this could be, in part, because of its dehydration stress-protective ability.

Functional dissection of hydrophilins during in vitro freeze protection

In plants, Late Embryogenesis Abundant (LEA) proteins typically accumulate in response to low water availability conditions imposed during development or by the environment. Analogous proteins in other organisms are induced when exposed to stress conditions. Most of this diverse set of proteins can be grouped according to properties such as high hydrophilicity and high content of glycine or other small amino acids in what we have termed hydrophilins. Previously, we showed that hydrophilins protect enzyme activities in vitro from low water availability effects. Here, we demonstrate that hydrophilins can also protect enzyme activities from the adverse effects induced by freeze-thaw cycles in vitro. We monitored conformational changes induced by freeze-thaw on the enzyme lactate dehydrogenase (LDH) using the fluorophore 1-anilinonaphthalene-8-sulfonate (ANS). Hydrophilin addition prevents enzyme inactivation and this effect is reflected in changes in the ANS-fluorescence levels determined for LDH. We further show that for selected plant hydrophilins, removal of certain conserved domains affects their protecting capabilities. Thus, we propose that hydrophilins, and in particular specific protein domains, have a role in protecting cell components from the adverse effects caused by low water availability such as those present during freezing conditions by preventing deleterious changes in protein secondary and tertiary structure.

Rhododendron catawbiense plasma membrane intrinsic proteins are aquaporins, and their over-expression compromises constitutive freezing tolerance and cold acclimation ability of transgenic Arabidopsis plants

Extracellular freezing results in cellular dehydration caused by water efflux, which is likely regulated by aquaporins (AQPs). In a seasonal cold acclimation (CA) study of Rhododendron catawbiense, two AQP cDNAs, RcPIP2;1 and RcPIP2;2, were down-regulated as the leaf freezing tolerance (FT) increased from -7 to approximately -50 degrees C. We hypothesized this down-regulation to be an adaptive component of CA process allowing cells to resist freeze-induced dehydration. Here, we characterize full-length cDNAs of the two Rhododendron PIPs, and demonstrate that RcPIP2s have water channel activity. Moreover, RcPIP2s were over-expressed in Arabidopsis, and FT of transgenic plants was compared with that of wild-type (WT) controls. Data indicated a significantly lower constitutive FT and CA ability of RcPIP2-OXP plants (compared with WT) due, presumably, to their lower ability to resist freeze desiccation. A relatively higher dehydration rate of RcPIP2-OXP leaves (than WT) supports this notion. Phenotypic and microscopic observations revealed bigger leaf size and mesophyll cells of RcPIP2-OXP plants than WT. It is proposed that lower FT of transgenic plants may be associated with their leaf cells' propensity to greater mechanical stress, that is, volume strain per unit surface, during freeze-thaw-induced contraction or expansion. Additionally, greater freeze injury in RcPIP2-OXP plants could also be attributed to their susceptibility to potentially faster rehydration (than WT) during a thaw.

Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break

Endodormant grapevine buds require a period of chilling before they break and begin to grow. Custom Vitis bud cDNA microarrays (9,216 features) were used to examine gene expression patterns in overwintering Vitis riparia buds during 2,000 h of 4 degrees C chilling. Three-node cuttings collected concurrently with buds were monitored to determine dormancy status. Chilling requirement was fulfilled after 1,500 h of chilling; however, 2,000 h of chilling significantly increased the rate of bud break. Microarray analysis identified 1,469 significantly differentially expressed (p value < 0.05) array features when 1,000, 1,500, and 2,000 h of chilling were compared to 500 h of chilling. Functional classification revealed that the majority of genes were involved in metabolism, cell defense/stress response, and genetic information processing. The number of significantly differentially expressed genes increased with chilling hour accumulation. The expression of a group of 130 genes constantly decreased during the chilling period. Up-regulated genes were not detected until the later stages of chilling accumulation. Hierarchical clustering of non-redundant expressed sequence tags revealed inhibition of genes involved in carbohydrate and energy metabolism and activation of genes involved in signaling and cell growth. Clusters with expression patterns associated with increased chilling and bud break were identified, indicating several candidate genes that may serve as indicators of bud chilling requirement fulfillment.

Expressed sequence tag analysis of the response of apple (Malus x domestica'Royal Gala') to low temperature and water deficit

Leaf, bark, xylem and root tissues were used to make nine cDNA libraries from non-stressed (control) 'Royal Gala' apple trees, and from 'Royal Gala' trees exposed to either low temperature (5 degrees C for 24 h) or water deficit (45% of saturated pot mass for 2 weeks). Over 22 600 clones from the nine libraries were subjected to 5' single-pass sequencing, clustered and annotated using blastx. The number of clusters in the libraries ranged from 170 to 1430. Regarding annotation of the sequences, blastx analysis indicated that within the libraries 65-72% of the clones had a high similarity to known function genes, 6-15% had no functional assignment and 15-26% were completely novel. The expressed sequence tags were combined into three classes (control, low-temperature and water deficit) and the annotated genes in each class were placed into 1 of 10 different functional categories. The percentage of genes falling into each category was then calculated. This analysis indicated a distinct downregulation of genes involved in general metabolism and photosynthesis, while a significant increase in defense/stress-related genes, protein metabolism and energy was observed. In particular, there was a three-fold increase in the number of stress genes observed in the water deficit libraries indicating a major shift in gene expression in response to a chronic stress. The number of stress genes in response to low temperature, although elevated, was much less than the water deficit libraries perhaps reflecting the shorter (24 h) exposure to stress. Genes with greater than five clones in any specific library were identified and, based on the number of clones obtained, the fold increase or decrease in expression in the libraries was calculated and verified by semiquantitative polymerase chain reaction. Genes, of particular note, that code for the following proteins were overexpressed in the low-temperature libraries: dehydrin and metallothionein-like proteins, ubiquitin proteins, a dormancy-associated protein, a plasma membrane intrinsic protein and an RNA-binding protein. Genes that were upregulated in the water deficit libraries fell mainly into the functional categories of stress (heat shock proteins, dehydrins) and photosynthesis. With few exceptions, the overall differences in downregulated genes were nominal compared with differences in upregulated genes. The results of this apple study are similar to other global studies of plant response to stress but offer a more detailed analysis of specific tissue response (bark vs xylem vs leaf vs root) and a comparison between an acute stress (24-h exposure to low temperature) and a chronic stress (2 weeks of water deficit).

Overexpression of a Panax ginseng tonoplast aquaporin alters salt tolerance, drought tolerance and cold acclimation ability in transgenic Arabidopsis plants

Water movement across cellular membranes is regulated largely by a family of water channel proteins called aquaporins (AQPs). Since several abiotic stresses such as, drought, salinity and freezing, manifest themselves via altering water status of plant cells and are linked by the fact that they all result in cellular dehydration, we overexpressed an AQP (tonoplast intrinsic protein) from Panax ginseng, PgTIP1, in transgenic Arabidopsis thaliana plants to test its role in plant's response to drought, salinity and cold acclimation (induced freezing tolerance). Under favorable conditions, PgTIP1 overexpression significantly increased plant growth as determined by the biomass production, and leaf and root morphology. PgTIP1 overexpression had beneficial effect on salt-stress tolerance as indicated by superior growth status and seed germination of transgenic plants under salt stress; shoots of salt-stressed transgenic plants also accumulated greater amounts of Na(+) compared to wild-type plants. Whereas PgTIP1 overexpression diminished the water-deficit tolerance of plants grown in shallow (10 cm deep) pots, the transgenic plants were significantly more tolerant to water stress when grown in 45 cm deep pots. The rationale for this contrasting response, apparently, comes from the differences in the root morphology and leaf water channel activity (speed of dehydration/rehydration) between the transgenic and wild-type plants. Plants overexpressed with PgTIP1 exhibited lower (relative to wild-type control) cold acclimation ability; however, this response was independent of cold-regulated gene expression. Our results demonstrate a significant function of PgTIP1 in growth and development of plant cells, and suggest that the water movement across tonoplast (via AQP) represents a rate-limiting factor for plant vigor under favorable growth conditions and also significantly affect responses of plant to drought, salt and cold stresses.

Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions

Our laboratory has been working toward increasing our understanding of the genetic control of cold hardiness in blueberry (Vaccinium section Cyanococcus) to ultimately use this information to develop more cold hardy cultivars for the industry. Here, we report using cDNA microarrays to monitor changes in gene expression at multiple times during cold acclimation under field and cold room conditions. Microarrays contained over 2,500 cDNA inserts, approximately half of which had been picked and single-pass sequenced from each of two cDNA libraries that were constructed from cold acclimated floral buds and non-acclimated floral buds of the fairly cold hardy cv. Bluecrop (Vaccinium corymbosum L.). Two biological samples were examined at each time point. Microarray data were analyzed statistically using t tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). Interestingly, more transcripts were found to be upregulated under cold room conditions than under field conditions. Many of the genes induced only under cold room conditions could be divided into three major types: (1) genes associated with stress tolerance; (2) those that encode glycolytic and TCA cycle enzymes, and (3) those associated with protein synthesis machinery. A few of the genes induced only under field conditions appear to be related to light stress. Possible explanations for these differences are discussed in physiological context. Although many similarities exist in how plants respond during cold acclimation in the cold room and in the field environment, there are major differences suggesting caution should be taken in interpreting results based only on artificial, cold room conditions.

Identification and expression analysis of cold-regulated genes from the cold-hardy Citrus relative Poncirus trifoliata (L.) Raf

Citrus is a cold-sensitive genus and most commercially important varieties of citrus are susceptible to freezes. On the other hand, Poncirus trifoliata (L.) Raf. is an interfertile Citrus relative that can tolerate temperatures as low as -26 degrees C when fully cold acclimated. Therefore, it has been used for improving cold tolerance in cold-sensitive commercial citrus rootstock varieties and in attempts to improve scion varieties. In this study, cDNA libraries were constructed from both 2-day cold-acclimated and from non-acclimated Poncirus seedlings using a subtractive hybridization method with the objective of identifying cold-regulated genes. A total of 192 randomly picked clones, 136 from the cold-induced library and 56 from the cold-repressed library, were sequenced. The majority of these clones showed sequence homology to previously identified cold-induced and/or environmental stress-regulated genes in Arabidopsis. In addition, some of them shared homology with cold and/or environmental stress-induced genes previously identified in other herbaceous and woody perennial plants and some showed no homology with sequences in GenBank. When these 192 cDNAs were analyzed by reverse northern blot with cold-acclimated and non-acclimated probes, 92 of the cDNAs displayed significantly increased expression, ranging from 2 to 49-fold, during cold acclimation; all 92 were from the cold-induced library. Surprisingly no clones displayed significantly repressed expression in response to cold. Analysis of a number of selected genes individually in northern blots of mRNA from cold-acclimated and non-acclimated plants largely confirmed the reverse northern analysis, verifying induction of expression of selected cDNAs in response to cold. The results showed that subtractive hybridization is an efficient method for identification of cold-induced genes in plants with limited sequence information available. This study also revealed that genes induced during cold acclimation of the cold-hardy citrus relative P. trifoliata are similar to those in Arabidopsis, indicating that similar pathways may be present and activated during cold acclimation in woody perennial plants.

Identification of cold acclimation-responsive Rhododendron genes for lipid metabolism, membrane transport and lignin biosynthesis: importance of moderately abundant ESTs in genomic studies

We have previously analysed expressed sequence tags (ESTs) from non-acclimated (NA) and cold-acclimated (CA) Rhododendron leaves, and identified highly abundant complementary DNAs (cDNAs) possibly involved in cold acclimation. A potentially significant, but relatively unexplored, application of these EST data sets is the study of moderately abundant cDNAs, such as those picked only 1-3 times from each Rhododendron EST library containing approximately 430 ESTs. Using statistical tests and Northern blots, we established that the probability of differential expression of moderately abundant cDNAs based on the EST data is, indeed, a reasonably accurate predictor of their 'true' upregulation or downregulation as 11 out of 13 cDNAs (85%) studied fit this criterion. The analyses also revealed four aspects of cold acclimation in Rhododendron leaf tissues. Firstly, the concomitant upregulation of long-chain acyl-coenzyme A (acyl-CoA) synthetase, CTP:cholinephosphate cytidylyltransferase and delta-12 fatty acid desaturase in CA leaf tissues suggests that phospholipid biosynthesis and desaturation are important components of cold hardening in Rhododendron. Secondly, upregulation of plastidic nicotinamide adenine dinucleotide phosphatemalic enzyme (NADP-ME) in CA tissues suggests that malate is an important source of acetyl-CoA used for fatty acid biosynthesis during cold acclimation. Thirdly, down-regulation of plasma membrane intrinsic protein (PIP)2-1 aquaporin and upregulation of gated outward rectifying K+ channel (GORK) in CA tissues may be associated with the protection of overwintering leaves from freeze-induced cellular dehydration. Fourthly, upregulation of coumarate 3-hydroxylase may be associated with cell wall thickening in CA tissues. Physiological implications of these results, which reveal potentially novel regulations of cold acclimation in overwintering woody evergreens, are discussed. This work highlights the importance of also investigating low/moderately abundant ESTs (in addition to highly abundant ones) in genomic studies, in that it offers an effective strategy for identifying stress-related genes, especially when large-scale cDNA sequencing/microarray studies are not possible.

Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja

BACKGROUND

Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining.

RESULTS

As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109) leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST) sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO) hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443-DT084445).

CONCLUSION

The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants.

Photoprotection in an ecological context: the remarkable complexity of thermal energy dissipation

This review places photoprotection into the context of ecology and species diversity. The focus is on photoprotection via the safe removal - as thermal energy - of excess solar energy absorbed by the light collecting system, which counteracts the formation of reactive oxygen species. An update on the surprisingly complex, multiple variations of thermal energy dissipation is presented, placing these different forms into ecological and genetic contexts. Zeaxanthin-facilitated, flexible thermal dissipation associated with the PsbS protein and controlled by the trans-thylakoid pH gradient apparently occurs ubiquitously in plants, and can become sustained (and thus less flexible) at low temperatures. Long-lived, slow-growing plants with low intrinsic capacities for photosynthesis have greater capacities for this flexible dissipation than short-lived, fast-growing species. Furthermore, potent, but inflexible (zeaxanthin-facilitated) thermal dissipation, prominent in evergreen species under prolonged environmental stress, is characterized with respect to the involvement of photosystem II core rearrangement and/or degradation as well as the absence of control by trans-thylakoid pH and, possibly, PsbS. A role of PsbS-related proteins in photoprotection is discussed.

Intron-flanking EST-PCR markers: from genetic marker development to gene structure analysis in Rhododendron

With a long-term goal of constructing a linkage map of Rhododendron enriched with gene-specific markers, we utilized Rhododendron catawbiense ESTs for the development of high-efficiency (in terms of generating polymorphism frequency) PCR-based markers. Using the gene-sequence alignment between Rhododendron ESTs and the genomic sequences of Arabidopsis homologs, we developed 'intron-flanking' EST-PCR-based primers that would anneal in conserved exon regions and amplify across the more highly diverged introns. These primers resulted in increased efficiency (61% vs. 13%; 4.7-fold) of polymorphism-detection compared with conventional EST-PCR methods, supporting the assumption that intron regions are more diverged than exons. Significantly, this study demonstrates that Arabidopsis genome database can be useful in developing gene-specific PCR-based markers for other non-model plant species for which the EST data are available but genomic sequences are not. The comparative analysis of intron sizes between Rhododendron and Arabidopsis (made possible in this study by aligning of Rhododendron ESTs with Arabidopsis genomic sequences and the sequencing of Rhododendron genomic PCR products) provides the first insight into the gene structure of Rhododendron.