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Melatonin acts both as an antioxidant and as a growth regulatory substance in plants. Pseudomonas fluorescens endophytic bacterium has been shown to produce melatonin and increase plant resistance to abiotic stressors through increasing endogenous melatonin. However, in bacteria, genes are still not known to be melatonin-related. Here, we reported that the bacterial phenylalanine 4-hydroxylase (PAH) may be involved in the 5-hydroxytryptophan (5-HTP) biosynthesis and further influenced the subsequent production of melatonin in P. fluorescens. The purified PAH protein of P. fluorescens not only hydroxylated phenylalanine but also exhibited l-tryptophan (l-Trp) hydroxylase activity by converting l-Trp to 5-HTP in vitro. However, bacterial PAH displayed lower activity and affinity for l-Trp than l-phenylalanine. Notably, the PAH deletion of P. fluorescens blocked melatonin production by causing a significant decline in 5-HTP levels and thus decreased the resistance to abiotic stress. Overall, this study revealed a possible role for bacterial PAH in controlling 5-HTP and melatonin biosynthesis in bacteria, and expanded the current knowledge of melatonin production in microorganisms.

Background Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach. Results In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed. Conclusions The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

Summary Plant stature is one important factor that affects the productivity of peach orchards. However, little is known about the molecular mechanism(s) underlying the dwarf phenotype of peach tree. Here, we report a dwarfing mechanism in the peach cv. FenHuaShouXingTao (FHSXT). The dwarf phenotype of ‘FHSXT’ was caused by shorter cell length compared to the standard cv. QiuMiHong (QMH). ‘FHSXT’ contained higher endogenous GA levels than did ‘QMH’ and did not response to exogenous GA treatment (internode elongation). These results indicated that ‘FHSXT’ is a GA‐insensitive dwarf mutant. A dwarf phenotype‐related single nucleotide mutation in the gibberellic acid receptor GID1 was identified in ‘FHSXT’ (GID1c S191F), which was also cosegregated with dwarf phenotype in 30 tested cultivars. GID1cS191F was unable to interact with the growth‐repressor DELLA1 even in the presence of GA. ‘FHSXT’ accumulated a higher level of DELLA1, the degradation of which is normally induced by its interaction with GID1. The DELLA1 protein level was almost undetectable in ‘QMH’, but not reduced in ‘FHSXT’ after GA 3 treatment. Our results suggested that a nonsynonymous single nucleotide mutation in GID1c disrupts its interaction with DELLA1 resulting in a GA‐insensitive dwarf phenotype in peach.

Recently, there is an increased interest in the function of polyamine (PA) catabolism during fruit ripening, but little is known about its role during the ripening of peach (Prunus persica L.). In this study, the contents of both free and conjugated PAs markedly decreased as the peach fruit ripened. However, RNA-seq analysis showed that the transcript levels of PA synthesis–related genes increased, suggesting that the decreasing PA content during peach ripening was associated with PA catabolism. To better understanding the function of PA catabolism in peach ripening, genes encoding potential polyamine oxidases (PAOs), which are involved in PA catabolism, were identified across the peach genome. Four putative PAO genes (PpePAO1-PpePAO4) were identified in peach using the recently released genome database. The mRNA level of PpePAO1 was significantly increased during peach fruit ripening. Detection of free PAs in tobacco leaves transiently over-expressing PpePAO1 suggested that this gene is probably involved in terminal catabolism of PA. Treatment with the PAO inhibitor guazatine significantly reduced ethylene production and flesh softening of peach fruit, decreased the expression levels of fruit ripening-related genes, and significantly decreased the expression level of PpePAO1 and PAO activity, while PA contents were dramatically higher compared to control treatments. Our results suggests that PpePAO1-mediated PA catabolism is associated with decreased PA content during peach fruit ripening. These data provide valuable knowledge for better understanding the roles of PA catabolism in peach development and ripening.

Adventitious root (AR) formation is indispensable for vegetative asexual propagation. Indole-3-butyric acid (IBA) functioned indirectly as precursor of IAA in regulating AR formation. Ethylene affects auxin synthesis, transport, and/or signaling processes. However, the interactions between auxin and ethylene that control AR formation in apple have not been elucidated. In this study, we investigated the effects of IBA and its interaction with ethylene on AR development in apple. The results revealed that IBA stimulated the formation of root primordia, increased the number of ARs, and upregulated expression of genes (MdWOX11, MdLBD16, and MdLBD29) involved in AR formation. Comparison of different periods of IBA application indicated that IBA was necessary for root primordium formation, while long time IBA treatment obviously inhibited root elongation. RNA-seq analysis revealed that many plant hormone metabolism and signal transduction related genes were differentially expressed. IBA stimulated the production of ethylene during AR formation. Auxin inhibiting ARs elongation depended on ethylene. Together, our results suggest that the inhibitory role of auxin on AR elongation in apples is partially mediated by stimulated ethylene production.

Plant growth caused by ambient temperature is thought to be regulated by a complex transcriptional network. A temperature-sensitive peach (Prunus persica) was used to explore the mechanisms behind shoot internode elongation at elevated temperatures. There was a significantly positive correlation between the length of the terminal internode (TIL) and the maximum temperature three days prior to the measuring day. Four critical growth stages (initial period and initial elongation period at lower temperature, rapid growth period and stable growth period at higher temperature) were selected for comparative RNA-seq analysis. About 6.64G clean bases were obtained for each library, and 88.27% of the data were mapped to the reference genome. Differentially expressed gene (DEG) analysis among the three pairwise comparisons resulted in the detection of several genes related to the shoot elongation in temperature-sensitive peach. HSFAs were up-regulated in response to the elevated temperature, while the up-regulated expression of HSPs might influence hormone signaling pathways. Most of DEGs involved in auxin, abscisic acid and jasmonic acid were up-regulated, while some involved in cytokinin and brassinosteroid were down-regulated. Genes related to ethylene, salicylic acid and circadian rhythm were also differentially expressed. Genes related to aquaporins, expansins, pectinesterases and endoglucanase were up-regulated, which would promote cell elongation. These results lay a foundation for further dissection of the regulatory mechanisms underlying shoot elongation at elevated temperatures.

Witches’ broom disease, caused by phytoplasma, is currently the most destructive disease of jujube. Tetracycline derivatives have been used to treat witches’ broom, and can allow recovery from the phytoplasma infection. Genes related to jasmonic acid (JA) biosynthesis and JA-induced protein-like play roles in phytoplasma infection. Jujube shoots (Ziziphus jujuba Mill. ‘Huizao’) infected by phytoplasma were excised and grown in vitro before treatment with tetracycline. RNA-Seq and iTRAQ analyses of samples treated for different lengths of time were performed during recovery from jujube witches’ broom (JWB) symptoms and diminishing presence of phytoplasma. Phytoplasma was not detected by PCR in the shoots after 6 months of tetracycline treatment (MTT). RNA-Seq and iTRAQ analyses identified 26,790 genes and 6184 proteins from jujube shoot samples. There were 272 differentially expressed genes (DEGs) and 20 differentially expressed proteins (DEPs) between the 3 and 6 MTT samples, respectively. The largest number and the greatest changes of DEGs and DEPs were for those related to alpha-linolenic acid metabolism, jasmonate biosynthesis, and jasmonate induced protein-like (JIPs). JA content slightly decreased at the sixth month compared with the third month. The research avenues explored here showed that genes in the JA biosynthesis pathway, proteins that respond to JA (JIPs), and JA content itself were concurrently regulated during JWB recovery. Alpha-linolenic acid metabolism pathway had higher RichFactor in comparisons between the 3 and 6 MTT samples during JWB recovery, which suggesting JA played vital roles during JWB recovery. The results in this study will help us to understand the roles JA plays in host-phytoplasma interactions during recovery and infection of JWB.

Ethylene plays an important role in the grape rachis, where its production can be 10 times higher than in the berry. VvACS1 is the only rachis-specific ACC synthase (ACS) gene, and its expression is coincident with ethylene production in the rachis of Vitis vinifera 'Thompson seedless'. VvACS1 was cloned and ectopically expressed in tomato (Solanum lycopersicum 'Moneymaker'). Lateral buds were increased in two- or four-week-old 35s∷VvACS1 transgenic tomato plants after transplanting. Compared with wild-type (WT) plants, the transgenic tomato plants showed higher expression of the VvACS1 gene in the flowers, leaves, rachis, and fruits. There was no obvious difference of ACS activity in the fruit of tomato, and only increased ACS activity in the rachis of tomato. Ethylene production was decreased in flowers, leaves, and fruits (seven weeks after full bloom), while the relative expression of endogenous tomato ACS1 and ACS6 genes was not down-regulated by the ectopic expression of VvACS1. These results imply that post-transcriptional or post-translational regulation of ACS may occur, resulting in lower ethylene production in the transgenic tomato plants. Moreover, expression of VvACS1 in tomato resulted in decreased auxin and increased zeatin contents in the lateral buds, as well as reduced or delayed formation of adventitious roots in lateral bud cuttings. RNA-Seq and qRT-PCR analyses of rooted lateral bud cuttings indicated that the relative expression levels of the genes for zeatin O-glucosyltransferase-like, auxin repressed/dormancy-associated protein, and ERF transcription factors were higher in transgenic tomatoes than in WT, suggesting that ethylene may regulate auxin transport and distribution in shoots and that adventitious root formation employs coordination between auxin and ethylene.

Background Jujube witches' broom (JWB), caused by a phytoplasma, devastates jujube tree (Ziziphus jujuba) growth and production in Asia. Although host responses to phytoplasmas are studied at the phenotypic, physiological, biochemical and molecular levels, it remains unclear how a host plant responds at the molecular level during the primary stage of infection. Methods To understand the response of the jujube tree to JWB infection, leaves were sampled at different times during the phytoplasma infection. Transcriptomic analyses at six stages were performed to reveal how phytoplasma infection affects Chinese jujube gene expression through the determination of the key differentially expressed genes (DEGs), and their related pathways. Quantitative real-time PCR was applied to validate 10 differentially expressed genes at different JWB phytoplasma infection stages. Results A total of 25,067 unigenes were mapped to jujube genome reference sequences. In the first infection stage (0–2 weeks after grafting (WAG), a total of 582 jujube genes were differentially regulated but no visible symptoms appeared. Quite a few DEGs related to abscisic acid (ABA) and cytokinin (CTK) were down-regulated, while some related to jasmonic acid (JA) and salicylic acid (SA) were up-regulated, Genes related to plant-pathogen interaction were also differentially expressed. In the second infection stage (37–39WAG), witches' broom symptoms were visible, and a total of 4373 DEGs were identified. Genes involved in biosynthesis and signal transduction of ABA, brassinosteroid (BR), CTK, ethylene (ET), and auxin (IAA), GA, JA and SA, plant-pathogen interaction, flavonoid biosynthesis genes were significantly regulated, suggesting that jujube trees activated defense factors related to SA, JA, ABA and secondary metabolites to defend against phytoplasma infection. By the third infection stage (48–52WAG), serious symptoms occurred and 3386 DEGs were identified. Most DEGs involved in biosynthesis and signal transduction of JA, SA and GA were up-regulated, while those relating to ABA were down-regulated. Genes involved in plant-pathogen interaction were up- or down-regulated, while phenylpropanoid and flavonoid biosynthesis genes were significantly up-regulated. Meanwhile, DEGs involved in photosynthesis, chlorophyll and peroxisome biosynthesis, and carbohydrate metabolism were down-regulated. These results suggested that phytoplasma infection had completely destroyed jujube trees' defense system and had disturbed chlorophyll synthesis and photosynthetic activity in the infected leaves at the late stage, resulting in yellow leaves and other JWB symptoms. Discussion The results in this report suggested that phytohormone biosynthesis and signal transduction, photosynthesis, and secondary metabolism all played important roles in the battle between colonization and defense in the interaction between Ca. Phytoplasma ziziphi and jujube.

Ethylene is important during the berry development and in the last stages of rachis development or rachis senescence. Since grapes develop in a cluster that comprises both the fruit berry and the nonfruit rachis, we measured the release of ethylene from both tissues. Detached berries from Vitis vinifera ‘Ruby Seedless’ and ‘Thompson Seedless’ showed that ethylene release peaks at the beginning of berry development and at veraison. Ethylene production in the rachis was higher than that in the berry and had an obvious peak before harvest in ‘Thompson Seedless’. In both cultivars, ethephon treatment induced ethylene production in the rachis but not in the berry. Expression of 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS) and ACC oxidase (ACO) genes showed diverse temporal and spatial patterns in ‘Thompson Seedless’ and ‘Ruby Seedless’. For most gene family members, the low ACS expression levels were observed in berry and rachis. Expression levels of most of the ACS and ACO genes did not correlate with ethylene released in the same organ. The transcriptional level of VvACS1 did correlate with ethylene evolution in rachis of ‘Thompson Seedless’ during berry development and storage, which suggested that VvACS1 may have important roles in rachis senescence. In berries of ‘Thompson Seedless’ and ‘Ruby Seedless’, the transcriptional levels of VvACO1, VvACS2, and VvACS6 coincided with ethylene production, indicating possible roles in berry development. Expression of VvACS2–VvACO9 and VvACO1–VvACO3 was not consistent with ethylene production during storage or in response to ethephon treatment, which suggests that the expression of ACS and ACO was affected by other stress factors after harvest.

Jujube witches’ broom (JWB) is caused by infection with a phytoplasma. A multi-omics approach was taken during graft infection of jujube by JWB-infected scion through the analysis of the plant transcriptome, proteome and phytohormone levels. A high number of differentially expressed genes (DEGs) were identified 37 weeks after grafting (WAG), followed by observation of typical symptoms of JWB at 48 WAG. At 37 WAG, the majority of the upregulated DEGs and differentially expressed proteins (DEPs) were related to flavonoid biosynthesis, phenylalanine metabolism and phenylpropanoid biosynthesis. Two of the four upregulated proteins were similar to jasmonate-induced protein-like. Among the downregulated genes, the two most populated GO terms were plant–pathogen interaction and plant hormone signal transduction (mainly for tryptophan metabolism). Moreover, phytoplasma infection resulted in reduced auxin content and increased jasmonate content, indicating that auxin and jasmonic acid have important roles in regulating jujube responses during the first and second stages of phytoplasma infection. At 48 WAG, the two largest groups of upregulated genes were involved in phenylpropanoid biosynthesis and flavonoid biosynthesis. Both genes and proteins involved in carbon metabolism and carbon fixation in photosynthetic organisms were downregulated, indicating that photosynthesis was affected by the third stage of phytoplasma infection. A multi-omics approach sheds light on the mechanisms of infection and defense at play between jujube trees and an enigmatic pathogen. Phytoplasmas are unculturable bacterial parasites discovered only a few decades ago, which cause deformed growths known as ‘witch's brooms’ in woody plants. A team at Henan Agricultural University, led by Jiancan Feng, explored the mechanisms of phytoplasma infection in the jujube tree (Ziziphus jujuba), by grafting healthy trees with infected branches. They employed a multi-pronged approach, analyzing the trees' gene activity, protein production, and hormone levels following infection. Their results suggest that the plant hormones auxin and jasmonic acid play important early roles in response to phytoplasma infection and that, as the witch's broom developed, processes such as photosynthesis were negatively impacted. These findings underpin future research towards preventing this devastating disease.

Resveratrol contributes to a plant’s tolerance of various abiotic and biotic stresses and is highly beneficial to human health. A search for elite alleles affecting resveratrol production was undertaken to find useful grapevine germplasm resources. Resveratrol levels in both berry skins and leaves were determined in 95 grapevine accessions (including 50 wild Chinese grapevine accessions and 45 cultivars) during two consecutive years. Resveratrol contents were higher in berry skins than in leaves and in wild Chinese grapevines than in grapevine cultivars. Using genotyping data, 79 simple sequence repeat (SSR) markers linked to 44 stilbene synthase (STS) genes were detected in the 95 accessions, identifying 40 SSR markers with higher polymorphisms. Eight SSR marker loci, encompassing 19 alleles, were significantly associated with resveratrol content on (P

The composition and content of anthocyanins were surveyed by HPLC–MS for assessing genotypic variation in berry skin of 110 grape cultivars, including 3 species and 5 interspecific hybrids. Twenty-nine anthocyanins were identified. For total anthocyanin content, Vitis vinifera and hybrids of Vitis labrusca and V. vinifera were low, and in general, wild species and rootstock were higher than interspecific hybrids, and wine grapes were higher than table grapes in the same species. As regards the composition of anthocyanins, malvidin-derivatives were the most abundant anthocyanins in the majority of germplasms. All anthocyanins were monoglucoside derivatives in V. vinifera , but all the other Vitis germplasms had both mono- and di-glucoside derivatives. Moreover, peonidin-derivatives and malvidin 3- O -glucoside were, respectively, main anthocyanins in table and wine grapes of V. vinifera . Via principal component analysis, the distribution of the cultivars in a scatter plot depended upon their total anthocyanins content, mono- and di-glucoside derivatives .

Effects of salicylic acid (SA), ultraviolet radiation (UV-B and UV-C) on the trans-resveratrol (Res) inducement of the skin of harvested grape berries were studied with three grape cultivars Takasuma, Tano Red and Carigane. Split plot design tests were adopted to compare the effects of UV-B and UV-C radiation on Res inducement of different cultivars. Results showed that spraying 100 mg·L−1 SA markedly enhanced Res contents in the skins of harvested berries for the three selected cultivars. However, the effect of SA varied with the cultivars, and Res inducement by SA was more effective to Tano Red than Takasuma and Carigane. UV-B or UV-C irradiation significantly increased Res contents in grape skins and UV-C was more effective than UV-B. The effects of UV types and dosages on Res inducement depended upon cultivars. In the range of 0–3.6 kJ·m−2, the Res contents in the skins of the three grape cultivars were enhanced along with the increase of dosages of UV-B and UV-C.

This study was conducted to develop a protocol for rapid callus induction and subsequent shoot regeneration in Zizyphus jujuba Mill. ‘Huizao’. The best callus induction (95%) was obtained from young expanding leaves between the third and fifth nodes in vitro jujube shoots in MS media supplemented with 0.5 mg/L benzylamino purine (6-BA), 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2, 4-D), and 0.5 mg/L silver nitrate (AgNO3). Incubation in darkness had non-significant effects on callus induction frequency of leaf explants, while callus formation of leaf was observed five to seven days earlier in one or two weeks of dark incubation. For shoot regeneration, the results showed that combination of zeatin (ZT) and, indole-3-acetic acid (IAA) was found to be more effective than that of 6-BA and indole-3-butyric acid (IBA). A maximum of 37.34% callus differentiation occurred in MS medium supplemented with2.0 mg/L ZT and 0.1 mg/L IAA. Key words: Callus induction, shoot regeneration, Zizyphus jujuba.