PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume.

BACKGROUND: Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'. RESULTS: There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation. CONCLUSIONS: Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.

Dormancy regulator Prunus mume DAM6 promotes ethylene-mediated leaf senescence and abscission.

Leaf senescence and abscission in autumn are critical phenological events in deciduous woody perennials. After leaf fall, dormant buds remain on deciduous woody perennials, which then enter a winter dormancy phase. Thus, leaf fall is widely believed to be linked to the onset of dormancy. In Rosaceae fruit trees, DORMANCY-ASSOCIATED MADS-box (DAM) transcription factors control bud dormancy. However, apart from their regulatory effects on bud dormancy, the biological functions of DAMs have not been thoroughly characterized. In this study, we revealed a novel DAM function influencing leaf senescence and abscission in autumn. In Prunus mume, PmDAM6 expression was gradually up-regulated in leaves during autumn toward leaf fall. Our comparative transcriptome analysis using two RNA-seq datasets for the leaves of transgenic plants overexpressing PmDAM6 and peach (Prunus persica) DAM6 (PpeDAM6) indicated Prunus DAM6 may up-regulate the expression of genes involved in ethylene biosynthesis and signaling as well as leaf abscission. Significant increases in 1-aminocyclopropane-1-carboxylate accumulation and ethylene emission in DEX-treated 35S:PmDAM6-GR leaves reflect the inductive effect of PmDAM6 on ethylene biosynthesis. Additionally, ethephon treatments promoted autumn leaf senescence and abscission in apple and P. mume, mirroring the changes due to PmDAM6 overexpression. Collectively, these findings suggest that PmDAM6 may induce ethylene emission from leaves, thereby promoting leaf senescence and abscission. This study clarified the effects of Prunus DAM6 on autumn leaf fall, which is associated with bud dormancy onset. Accordingly, in Rosaceae, DAMs may play multiple important roles affecting whole plant growth during the tree dormancy induction phase.

Genome-wide identification and comprehensive analysis of the AP2/ERF gene family in Prunus sibirica under low-temperature stress.

BACKGROUND: AP2/ERF transcription factors are involved in the regulation of growth, development, and stress response in plants. Although the gene family has been characterized in various species, such as Oryza sativa, Arabidopsis thaliana, and Populus trichocarpa, studies on the Prunus sibirica AP2/ERF (PsAP2/ERF) gene family are lacking. In this study, PsAP2/ERFs in P. sibirica were characterized by genomic and transcriptomic analyses. RESULTS: In the study, 112 PsAP2/ERFs were identified and categorized into 16 subfamilies. Within each subfamily, PsAP2/ERFs exhibited similar exon-intron structures and motif compositions. Additionally, 50 pairs of segmentally duplicated genes were identified within the PsAP2/ERF gene family. Our experimental results showed that 20 PsAP2/ERFs are highly expressed in leaves, roots, and pistils under low-temperature stress conditions. Among them, the expression of PsAP2/ERF21, PsAP2/ERF56 and PsAP2/ERF88 was significantly up-regulated during the treatment period, and it was hypothesised that members of the PsAP2/ERF family play an important role inlow temperature stress tolerance. CONCLUSIONS: This study improves our understanding of the molecular basis of development and low-temperature stress response in P. sibirica and provides a solid scientific foundation for further functional assays and evolutionary analyses of PsAP2/ERFs.

Ecological drivers of flower-leaf sequences: aridity and proxies for pollinator attraction select for flowering-first in the American plums.

Across temperate forests, many tree species produce flowers before their leaves emerge. This flower-leaf phenological sequence, known as hysteranthy, is generally described as an adaptation for wind pollination. However, this explanation does not address why hysteranthy is also common in biotically pollinated taxa. We quantified flower-leaf sequence variation in the American plums (Prunus, subg. Prunus sect. Prunocerasus), a clade of insect-pollinated trees, using herbaria specimens and Bayesian hierarchical modeling. We tested two common, but rarely interrogated hypotheses - that hysteranthy confers aridity tolerance and/or pollinator visibility - by modeling the associations between hysteranthy and related traits. To understand how these phenology-trait associations were sensitive to taxonomic scale and flower-leaf sequence classification, we then extended these analyses to all Prunus species in North America. Our findings across two taxonomic levels support the hypotheses that hysteranthy may help temporally partition hydraulic demand to reduce water stress and increase pollinator visibility - thereby reducing selective pressure on inflorescence size. Our results provide foundational insights into the evolution of flower-leaf sequences in the genus Prunus, with implications for understanding these patterns in biotically pollinated plants in general. Our approach suggests a path to advance these hypotheses to other clades, but teasing out drivers fully will require new experiments.

Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring.

Understanding the process of Prunus species floral development is crucial for developing strategies to manipulate bloom time and prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries (Prunus cerasus) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we show floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A genomic DNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified many genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to Reproductive Meristem B3 domain-containing proteins. Additionally, we determined that the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry-suggesting several major regulators of bloom time are located on Prunus chromosome 4.

Fall Applications of Ethephon Modulates Gene Networks Controlling Bud Development during Dormancy in Peach (Prunus Persica).

Ethephon (ET) is an ethylene-releasing plant growth regulator (PGR) that can delay the bloom time in Prunus, thus reducing the risk of spring frost, which is exacerbated by global climate change. However, the adoption of ET is hindered by its detrimental effects on tree health. Little knowledge is available regarding the mechanism of how ET shifts dormancy and flowering phenology in peach. This study aimed to further characterize the dormancy regulation network at the transcriptional level by profiling the gene expression of dormant peach buds from ET-treated and untreated trees using RNA-Seq data. The results revealed that ET triggered stress responses during endodormancy, delaying biological processes related to cell division and intercellular transportation, which are essential for the floral organ development. During ecodormancy, ET mainly impeded pathways related to antioxidants and cell wall formation, both of which are closely associated with dormancy release and budburst. In contrast, the expression of dormancy-associated MADS (DAM) genes remained relatively unaffected by ET, suggesting their conserved nature. The findings of this study signify the importance of floral organogenesis during dormancy and shed light on several key processes that are subject to the influence of ET, therefore opening up new avenues for the development of effective strategies to mitigate frost risks.

Rhizosphere microorganisms enhance in vitro root and plantlet development of Pyrus and Prunus rootstocks.

MAIN CONCLUSION: The in vitro application of rhizosphere microorganisms led to a higher rooting percentage in Pyrus Py12 rootstocks and increased plant growth of Pyrus Py170 and Prunus RP-20. The rooting of fruit tree rootstocks is the most challenging step of the in vitro propagation process. The use of rhizosphere microorganisms to promote in vitro rooting and plant growth as an alternative to the addition of chemical hormones to culture media is proposed in the present study. Explants from two Pyrus (Py170 and Py12) rootstocks and the Prunus RP-20 rootstock were inoculated with Pseudomonas oryzihabitans PGP01, Cladosporium ramotenellum PGP02 and Phoma sp. PGP03 following two different methods to determine their effects on in vitro rooting and plantlet growth. The effects of the microorganisms on the growth of fully developed Py170 and RP-20 plantlets were also studied in vitro. All experiments were conducted using vermiculite to simulate a soil system in vitro. When applied to Py12 shoots, which is a hard-to-root plant material, both C. ramotenellum PGP02 and Phoma sp. PGP03 fungi were able to increase the rooting percentage from 56.25% to 100% following auxin indole-3-butyric acid (IBA) treatment. Thus, the presence of these microorganisms clearly improved root development, inducing a higher number of roots and causing shorter roots. Better overall growth and improved stem growth of treated plants was observed when auxin treatment was replaced by co-culture with microorganisms. A root growth-promoting effect was observed on RP-20 plantlets after inoculation with C. ramotenellum PGP02, while P. oryzihabitans PGP01 increased root numbers for both Py170 and RP-20 and increased root growth over stem growth for RP-20. It was also shown that the three microorganisms P. oryzihabitans PGP01, C. ramotenellum PGP02 and Phoma sp. PGP03 were able to naturally produce auxin, including indole-3-acetic acid (IAA), at different levels. Overall, our results demonstrate that the microorganisms P. oryzihabitans PGP01 and C. ramotenellum PGP02 had beneficial effects on in vitro rooting and plantlet growth and could be applied to in vitro tissue culture as a substitute for IBA.

Simultaneously measuring pulse-amplitude-modulated (PAM) chlorophyll fluorescence of leaves at wavelengths shorter and longer than 700 nm.

PAM fluorescence of leaves of cherry laurel (Prunus laurocerasus L.) was measured simultaneously in the spectral range below 700 nm (sw) and above 700 nm (lw). A high-sensitivity photodiode was employed to measure the low intensities of sw fluorescence. Photosystem II (PSII) performance was analyzed by the saturation pulse method during a light response curve with subsequent dark phase. The sw fluorescence was more variable, resulting in higher PSII photochemical yields compared to lw fluorescence. The variations between sw and lw data were explained by different levels of photosystem I (PSI) fluorescence: the contribution of PSI fluorescence to minimum fluorescence (F0) was calculated to be 14% at sw wavelengths and 45% at lw wavelengths. With the results obtained, the validity of an earlier method for the quantification of PSI fluorescence (Genty et al. in Photosynth Res 26:133-139, 1990, https://doi.org/10.1007/BF00047085 ) was reconsidered. After subtracting PSI fluorescence from all fluorescence levels, the maximum PSII photochemical yield (FV/FM) in the sw range was 0.862 and it was 0.883 in the lw range. The lower FV/FM at sw wavelengths was suggested to arise from inactive PSII reaction centers in the outermost leaf layers. Polyphasic fluorescence transients (OJIP or OI1I2P kinetics) were recorded simultaneously at sw and lw wavelengths: the slowest phase of the kinetics (IP or I2P) corresponded to 11% and 13% of total variable sw and lw fluorescence, respectively. The idea that this difference is due to variable PSI fluorescence is critically discussed. Potential future applications of simultaneously recording fluorescence in two spectral windows include studies of PSI non-photochemical quenching and state I-state II transitions, as well as measuring the fluorescence from pH-sensitive dyes simultaneously with chlorophyll fluorescence.

Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana).

Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf color. Using enrichment and correlation network analysis, we found that anthocyanin accumulation differed in different colored leaves and that the accumulation of malvidin 3-O-glucoside (violet) and pelargonidin 3-O-glucoside (orange-red) significantly correlated with the leaf color change from green to purple-red. The flavonoid biosynthesis genes (PAL, CHS and CHI) and their transcriptional regulators (MYB, HD-Zip and bHLH) exhibited specific increased expression during the purple-red periods. Two genes encoding enzymes in the anthocyanin biosynthetic pathway, UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) and anthocyanidin 3-O-glucosyltransferase (BZ1), seem to be critical for suppressing the formation of the aforesaid anthocyanins. In PRL, the expression of the genes encoding for UGFT and BZ1 enzymes was substantially higher than in leaves of other colors and may be related with the purple-red color change. These results may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana.

Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species.

BACKGROUND: Flesh color is one of the most important traits for the commercial value of peach fruit. To unravel the underlying regulatory network in Prunus mira, we performed an integrated analysis of the transcriptome and metabolome of 3 fruit types with various flesh pigmentations (milk-white, yellow and blood) at 3 developmental stages (pit-hardening, cell enlargement and fruit ripening). RESULTS: Transcriptome analysis showed that an intense transcriptional adjustment is required for the transition from the pit-hardening to the cell enlargement stage. In contrast, few genes were differentially expressed (DEGs) from the cell enlargement to the fruit ripening stage and importantly, the 3 fruits displayed diverse transcriptional activities, indicating that difference in fruit flesh pigmentations mainly occurred during the ripening stage. We further investigated the DEGs between pairs of fruit types during the ripening stage and identified 563 DEGs representing the 'core transcriptome' associated with major differentiations between the 3 fruit types, including flesh pigmentation. Meanwhile, we analyzed the metabolome, particularly, at the ripening stage and uncovered 40 differential metabolites ('core metabolome') between the 3 fruit types including 5 anthocyanins, which may be the key molecules associated with flesh coloration. Finally, we constructed the regulatory network depicting the interactions between anthocyanins and important transcripts involved in fruit flesh coloration. CONCLUSIONS: The major metabolites and transcripts involved in fruit flesh coloration in P. mira were unraveled in this study providing valuable information which will undoubtedly assist in breeding towards improved fruit quality in peach.

Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume.

BACKGROUND: Long non-coding RNAs (lncRNAs) are transcripts more than 200 bp in length do not encode proteins. Up to the present, it has been reported that lncRNAs play an essential role in developmental processes through their regulatory functions. However, their characteristics, expression inheritance patterns, and functions in Prunus mume are quite unidentified. RESULTS: In this present study, we exposed the specific characters of pistil development process between single pistil cv 'Qingjia No.2' (QJN2) and multiple pistils cv 'Da Yu' (DY). We found that early October is the key stage for pistil differentiation. The similarity epidermis was observed between two types of pistil. We also further investigated a complete pistil development lncRNA profiles through RNA-seq in Prunus mume. 2572 unique lncRNAs and 24,648 genes mapped to Prunus mume genome, furthermore, 591 novel lncRNAs were predicted. Both unique lncRNAs and novel lncRNAs are shorter in length than the mRNAs, and the overall expression level of lncRNAs was lower than mRNAs in Prunus mume. 186 known lncRNAs, 1638 genes and 89 novel lncRNAs were identified as significant differential expressed in QJN2 compared with DY. We predicted 421 target genes of differentially expressed known lncRNAs (DEKLs) and 254 target genes of differentially expressed novel lncRNAs (DENLs). 153 miRNAs were predicted interacted with 100 DEKLs while 112 miRNAs were predicted interacted with 55 DENLs. Further analysis of the DEKLs showed that the lncRNA of XR_514690.2 down-regulated its target ppe-miR172d, and up-regulated AP2, respectively. Meanwhile, the other lncRNA of TCONS_00032517 induced cytokinin negative regulator gene A-ARR expression via repressing its target miRNA ppe-miR160a/b in DY. At the same time we found that the AP2 expression was significantly up-regulated by zeatin (ZT) treatment in flower buds. Our experiments suggest that the two lncRNAs of XR_514690.2 and TCONS_00032517 might contribute the formation of multiple pistils in Prunus mume. CONCLUSION: This study shows the first characterization of lncRNAs involved in pistil development and provides new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development in Prunus mume.

A comparison of two centrifuge techniques for constructing vulnerability curves: insight into the 'open-vessel' artifact.

A vulnerability curve (VC) describes the extent of xylem cavitation resistance. Centrifuges have been used to generate VCs for decades via static- and flow-centrifuge methods. Recently, the validity of the centrifuge techniques has been questioned. Researchers have hypothesized that the centrifuge techniques might yield unreliable VCs due to the open-vessel artifact. However, other researchers reject this hypothesis. The focus of the dispute is centered on whether exponential VCs are more reliable when the static-centrifuge method is used rather than the flow-centrifuge method. To further test the reliability of the centrifuge technique, two centrifuges were manufactured to simulate the static- and flow-centrifuge methods. VCs of three species with open vessels of known lengths were constructed using the two centrifuges. The results showed that both centrifuge techniques produced invalid VCs for Robinia because the water flow through stems under mild tension in centrifuges led to an increasing loss of water conductivity. In addition, the injection of water in the flow-centrifuge exacerbated the loss of water conductivity. However, both centrifuge techniques yielded reliable VCs for Prunus, regardless of the presence of open vessels in the tested samples. We conclude that centrifuge techniques can be used in species with open vessels only when the centrifuge produces a VC that matches the bench-dehydration VC.

Activity maintenance of the excised branches and a case study of NO2 exchange between the atmosphere and P. nigra branches.

The efficient maintenance of the activity of excised branches is the powerful guarantee to accurately determine gas exchange flux between the detached branches of tall trees and the atmosphere. In this study, the net photosynthetic rate (NPR) of the excised branches and branches in situ were measured simultaneously by using two photosynthetic instruments to characterize the activity of the excised branches of Phyllostachys nigra. The ratio of normalized NPR of excised branches to NPR in situ was used to assess the photosynthetic activity of detached branches. Based on photosynthetic activity, an optimal hydroponics protocol for maintaining activity of excised P. nigra branches was presented: 1/8 times the concentration of Gamborg B5 vitamin mixture with pH = 6. Under the best cultivation protocol, photosynthetic activity of excised P. nigra branches could be maintained more than 90% within 6 hr in the light intensity range of 200-2000 µmol/(m2·sec) and temperature range of 13.4-28.7°C. The nitrogen dioxide (NO2) flux differences between in situ and in vitro branches and the atmosphere were compared using double dynamic chambers. Based on the maintenance method of excised branches, the NO2 exchange flux between the excised P. nigra branches and the atmosphere (from -1.01 to -2.72 nmol/(m2·sec) was basically consistent with between the branches in situ and the atmosphere (from -1.12 to -3.16 nmol/(m2 sec)) within 6 hr. Therefore, this study provided a feasible protocol for in vitro measurement of gas exchange between tall trees and the atmosphere for a period of time.

DRO1 influences root system architecture in Arabidopsis and Prunus species.

Roots provide essential uptake of water and nutrients from the soil, as well as anchorage and stability for the whole plant. Root orientation, or angle, is an important component of the overall architecture and depth of the root system; however, little is known about the genetic control of this trait. Recent reports in Oryza sativa (rice) identified a role for DEEPER ROOTING 1 (DRO1) in influencing the orientation of the root system, leading to positive changes in grain yields under water-limited conditions. Here we found that DRO1 and DRO1-related genes are present across diverse plant phyla, and fall within the IGT gene family. The IGT family also includes TAC1 and LAZY1, which are known to affect the orientation of lateral shoots. Consistent with a potential role in root development, DRO1 homologs in Arabidopsis and peach showed root-specific expression. Promoter-reporter constructs revealed that AtDRO1 is predominantly expressed in both the root vasculature and root tips, in a distinct developmental pattern. Mutation of AtDRO1 led to more horizontal lateral root angles. Overexpression of AtDRO1 under a constitutive promoter resulted in steeper lateral root angles, as well as shoot phenotypes including upward leaf curling, shortened siliques and narrow lateral branch angles. A conserved C-terminal EAR-like motif found in IGT genes was required for these ectopic phenotypes. Overexpression of PpeDRO1 in Prunus domestica (plum) led to deeper-rooting phenotypes. Collectively, these data indicate a potential application for DRO1-related genes to alter root architecture for drought avoidance and improved resource use.

Light energy partitioning, photosynthetic efficiency and biomass allocation in invasive Prunus serotina and native Quercus petraea in relation to light environment, competition and allelopathy.

This study addressed whether competition under different light environments was reflected by changes in leaf absorbed light energy partitioning, photosynthetic efficiency, relative growth rate and biomass allocation in invasive and native competitors. Additionally, a potential allelopathic effect of mulching with invasive Prunus serotina leaves on native Quercus petraea growth and photosynthesis was tested. The effect of light environment on leaf absorbed light energy partitioning and photosynthetic characteristics was more pronounced than the effects of interspecific competition and allelopathy. The quantum yield of PSII of invasive P. serotina increased in the presence of a competitor, indicating a higher plasticity in energy partitioning for the invasive over the native Q. petraea, giving it a competitive advantage. The most striking difference between the two study species was the higher crown-level net CO2 assimilation rates (Acrown) of P. serotina compared with Q. petraea. At the juvenile life stage, higher relative growth rate and higher biomass allocation to foliage allowed P. serotina to absorb and use light energy for photosynthesis more efficiently than Q. petraea. Species-specific strategies of growth, biomass allocation, light energy partitioning and photosynthetic efficiency varied with the light environment and gave an advantage to the invader over its native competitor in competition for light. However, higher biomass allocation to roots in Q. petraea allows for greater belowground competition for water and nutrients as compared to P. serotina. This niche differentiation may compensate for the lower aboveground competitiveness of the native species and explain its ability to co-occur with the invasive competitor in natural forest settings.

Substantial Epigenetic Variation Causing Flower Color Chimerism in the Ornamental Tree Prunus mume Revealed by Single Base Resolution Methylome Detection and Transcriptome Sequencing.

Epigenetic changes caused by methylcytosine modification participate in gene regulation and transposable element (TE) repression, resulting in phenotypic variation. Although the effects of DNA methylation and TE repression on flower, fruit, seed coat, and leaf pigmentation have been investigated, little is known about the relationship between methylation and flower color chimerism. In this study, we used a comparative methylomic⁻transcriptomic approach to explore the molecular mechanism responsible for chimeric flowers in Prunus mume "Danban Tiaozhi". High-performance liquid chromatography-electrospray ionization mass spectrometry revealed that the variation in white (WT) and red (RT) petal tissues in this species is directly due to the accumulation of anthocyanins, i.e., cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and peonidin 3-O-glucoside. We next mapped the first-ever generated methylomes of P. mume, and found that 11.29⁻14.83% of the genomic cytosine sites were methylated. We also determined that gene expression was negatively correlated with methylcytosine level in general, and uncovered significant epigenetic variation between WT and RT. Furthermore, we detected differentially methylated regions (DMRs) and DMR-related genes between WT and RT, and concluded that many of these genes, including differentially expressed genes (DEGs) and transcription factor genes, are critical participants in the anthocyanin regulatory pathway. Importantly, some of the associated DEGs harbored TE insertions that were also modified by methylcytosine. The above evidence suggest that flower color chimerism in P. mume is induced by the DNA methylation of critical genes and TEs.

Crosstalk of PmCBFs and PmDAMs Based on the Changes of Phytohormones under Seasonal Cold Stress in the Stem of Prunus mume.

Plants facing the seasonal variations always need a growth restraining mechanism when temperatures turn down. C-repeat binding factor (CBF) genes work essentially in the cold perception. Despite lots of researches on CBFs, the multiple crosstalk is still interesting on their interaction with hormones and dormancy-associated MADS (DAM) genes in the growth and dormancy control. Therefore, this study highlights roles of PmCBFs in cold-induced dormancy from different orgens. And a sense-response relationship between PmCBFs and PmDAMs is exhibited in this process, jointly regulated by six PmCBFs and PmDAM4-6. Meantime, GA3 and ABA showed negative and positive correlation with PmCBFs expression levels, respectively. We also find a high correlation between IAA and PmDAM1-3. Finally, we display the interaction mode of PmCBFs and PmDAMs, especially PmCBF1-PmDAM1. These results can disclose another view of molecular mechanism in plant growth between cold-response pathway and dormancy regulation together with genes and hormones.

Analysis of differentially expressed genes and adaptive mechanisms of Prunus triloba Lindl. under alkaline stress.

BACKGROUND: Prunus triloba Lindl. is a naturally salt-alkaline-tolerant plant with several unique characteristics, and it can be used as the rootstock of Chinese plum (Prunus salicina Lindl.) in saline-alkaline soils. To comprehensively investigate the alkaline acclimation mechanisms in P. triloba, a series of analyses were conducted under alkaline stress, including analyses of the kinetics of molecular and physiological changes, and leaf microstructure. RESULTS: To understand the kinetics of molecular changes under short-term alkaline stress, we used Illumina HiSeq 2500 platform to identify alkaline stress-related differentially expressed genes (DEGs) in P. triloba. Approximately 53.0 million high-quality clean reads were generated from 59.6 million raw reads, and a total of 124,786 unigenes were obtained after de novo assembly of P. triloba transcriptome data. After alkaline stress treatment, a total of 8948 unigenes were identified as DEGs. Based on these DEGs, a Gene Ontology (GO) enrichment analysis was conducted, suggesting that 28 genes may play an important role in the early alkaline stress response. In addition, analysis of DEGs with the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that pathways were significant at different treatment time points. A significant positive correlation was found between the quantitative real-time PCR (qRT-PCR) results and the RNA-Seq data for seven alkaline-related genes, confirming the reliability of the RNA-Seq results. Based on physiological analysis of P. triloba in response to long-term alkaline stress, we found that the internal microstructures of the leaves of P. triloba changed to adapt to long-term alkaline stress. Various physiological indexes indicated that the degree of membrane injury increased with increasing duration of alkaline stress, affecting photosynthesis in P. triloba seedlings. CONCLUSIONS: This represents the first investigation into the physiology and transcriptome of P. triloba in response to alkaline stress. The results of this study can enrich the genomic resources available for P. triloba, as well as deepening our understanding of molecular and physiological alkaline tolerance mechanisms in P. triloba. This will also provide new insights into our understanding of alkaline acclimation mechanisms in Chinese plum (Prunus salicina) trees.

Recognition of a wide-range of S-RNases by S locus F-box like 2, a general-inhibitor candidate in the Prunus-specific S-RNase-based self-incompatibility system.

Many species in the Rosaceae, the Solanaceae, and the Plantaginaceae exhibit S-RNase-based gametophytic self-incompatibility (GSI). This system comprises S-ribonucleases (S-RNases) as the pistil S determinant and a single or multiple F-box proteins as the pollen S determinants. In Prunus, pollen specificity is determined by a single S haplotype-specific F-box protein (SFB). The results of several studies suggested that SFB exerts cognate S-RNase cytotoxicity, and a hypothetical general inhibitor (GI) is assumed to detoxify S-RNases in non-specific manner unless it is affected by SFB. Although the identity of the GI is unknown, phylogenetic and evolutionary analyses have indicated that S locus F-box like 1-3 (or S locus F-box with low allelic sequence polymorphism 1-3; SLFL1-3), which are encoded by a region of the Prunus genome linked to the S locus, are good GI candidates. Here, we examined the biochemical characteristics of SLFL1-3 to determine whether they have appropriate GI characteristics. Pull-down assays and quantitative expression analyses indicated that Prunus avium SLFL1-3 mainly formed a canonical SCF complex with PavSSK1 and PavCul1A. Binding assays with PavS(1,3,4,6)-RNases showed that PavSLFL1, PavSLFL2, and PavSLFL3 bound to PavS(3)-RNase, all PavS-RNases tested, and none of the PavS-RNases tested, respectively. Together, these results suggested that SLFL2 has the appropriate characteristics to be the GI in sweet cherry pollen, while SLFL1 may redundantly work with SLFL2 to detoxify all S-RNases. We discuss the possible roles of SLFL1-3 as the GI in the Prunus-specific S-RNase-based GSI mechanism.

Insights into the Prunus-Specific S-RNase-Based Self-Incompatibility System from a Genome-Wide Analysis of the Evolutionary Radiation of S Locus-Related F-box Genes.

Self-incompatibility (SI) is an important plant reproduction mechanism that facilitates the maintenance of genetic diversity within species. Three plant families, the Solanaceae, Rosaceae and Plantaginaceae, share an S-RNase-based gametophytic SI (GSI) system that involves a single S-RNase as the pistil S determinant and several F-box genes as pollen S determinants that act via non-self-recognition. Previous evidence has suggested a specific self-recognition mechanism in Prunus (Rosaceae), raising questions about the generality of the S-RNase-based GSI system. We investigated the evolution of the pollen S determinant by comparing the sequences of the Prunus S haplotype-specific F-box gene (SFB) with those of its orthologs in other angiosperm genomes. Our results indicate that the Prunus SFB does not cluster with the pollen S of other plants and diverged early after the establishment of the Eudicots. Our results further indicate multiple F-box gene duplication events, specifically in the Rosaceae family, and suggest that the Prunus SFB gene originated in a recent Prunus-specific gene duplication event. Transcriptomic and evolutionary analyses of the Prunus S paralogs are consistent with the establishment of a Prunus-specific SI system, and the possibility of subfunctionalization differentiating the newly generated SFB from the original pollen S determinant.