Integrating life cycle assessment and a farmer survey of management practices to study environmental impacts of peach production in Beijing, China.

While intensive peach production has expanded rapidly in recent years, few studies have explored the environmental impacts associated with specific regional systems or the optimal management strategies to minimize associated environmental risks. Here, data from a survey of 290 native farmers were used to conduct a life cycle assessment to quantify the acidification potential (AP), global warming potential (GWP), eutrophication potential (EP), and reactive nitrogen (Nr) losses in peach production in Pinggu District, Beijing. Total annual Nr losses, and GWP, AP, and EP values for peach production in Pinggu District were respectively 10.7 kg N t-1, 857 kg CO2-eq t-1, 12.9 kg SO2-eq t-1, and 4.1 kg PO4-eq t-1. The principal driving factors were fertilizer production, transportation, and application, which together accounted for 94%, 67%, 75%, and 94% of Nr losses, GWP, AP, and EP, respectively. In the high yield, high nitrogen-use efficiency (HH) group, relative values of Nr losses, GWP, AP, and EP were respectively 33%, 25%, 39%, and 32% lower than the overall averages for 290 orchards. Further analyses indicate that improved farming practices such as decreasing application rates of fertilizers, increasing proportion of base fertilization rate, and proper fertilization frequency in the HH group were the main reasons for these orchards' better performance in peach yields and partial factor productivity of nitrogen fertilizer, and their reduced environmental impacts. These results highlight the need to optimize nutrient management in peach production in order simultaneously to realize both environmental sustainability and high productivity in the peach production system.

Ppe.XapF: High throughput KASP assays to identify fruit response to Xanthomonas arboricola pv. pruni (Xap) in peach.

Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. We developed simple, accurate, and efficient DNA assays (Ppe.XapF) based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit that allows breeders to cull seedlings at the greenhouse stage. The objective of this research was to validate newly developed DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Our study confirms that with only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, individuals carrying susceptible alleles can be identified. Use of these efficient and accurate Ppe.XapF KASP tests resulted in 44% reduction in seedling planting rate in the Clemson University peach breeding program.

Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening.

Real-time quantitative PCR (RT-qPCR) is a powerful tool to detect and quantify transcription abundance, and the stability of the reference gene determines its success. However, the most suitable reference gene for different genotypes and tobacco rattle virus (TRV) infected fruits was unclear in peach (Prunus persica L. Batsch). In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable variability of gene expression in all experimental conditions. Furthermore, to confirm the validity of the reference genes, the expression levels of PpACO1, PpEIN2, and PpPL were normalized at different fruit storage periods. In summary, our results provide guidelines for selecting reliable reference genes in different genotypes and TRV-infected fruits and lay the foundation for accurate evaluation of gene expression for RT-qPCR analysis in peach.

PpIAA1 and PpERF4 form a positive feedback loop to regulate peach fruit ripening by integrating auxin and ethylene signals.

The signaling pathways of both auxin and ethylene regulate peach fruit ripening via the Aux/IAA and ERF transcription factors, respectively. However, the molecular mechanisms that coordinate both auxin and ethylene signals during peach fruit ripening remain unclear. In this study, we show that PpIAA1 and PpERF4 act as key players in a positive feedback loop, and promote peach fruit ripening by directly binding to and enhancing the activity of target gene promoters. PpIAA1 increased the expression of the ethylene biosynthesis gene PpACS1. Furthermore, PpERF4 enhanced the transcription of PpACO1 and PpIAA1 genes by binding to their promoters. Additionally, PpIAA1 and PpERF4 bound to each other to form a complex, which then enhanced the transcription of abscisic acid biosynthesis genes (PpNCED2 and PpNCED3) and the fruit softening gene (PpPG1) to levels higher than those achieved by each transcription factor individually. Moreover, overexpression of PpIAA1 in tomato accelerated fruit ripening and shortened the fruit shelf-life by increasing the production of ethylene and the expression levels of ripening regulator genes. Collectively, these results advance our understanding of the molecular mechanisms underlying peach fruit ripening and softening via auxin and ethylene signaling pathways.

Meta-analysis of RNA-Seq studies reveals genes with dominant functions during flower bud endo- to eco-dormancy transition in Prunus species.

In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. Each species and/or cultivar requires exposure to low winter temperature followed by warm temperatures, quantified as chilling and heat requirements, to remove the physiological blocks that inhibit budburst. A comprehensive meta-analysis of transcriptomic studies on flower buds of sweet cherry, apricot and peach was conducted, by investigating the gene expression profiles during bud endo- to ecodormancy transition in genotypes differing in chilling requirements. Conserved and distinctive expression patterns were observed, allowing the identification of gene specifically associated with endodormancy or ecodormancy. In addition to the MADS-box transcription factor family, hormone-related genes, chromatin modifiers, macro- and micro-gametogenesis related genes and environmental integrators, were identified as novel biomarker candidates for flower bud development during winter in stone fruits. In parallel, flower bud differentiation processes were associated to dormancy progression and termination and to environmental factors triggering dormancy phase-specific gene expression.

Identifying sources of metabolomic diversity and reconfiguration in peach fruit: taking notes for quality fruit improvement.

The metabolomic content determines many of the important features of a fruit, such as its taste, flavor, color, nutritional value, and abiotic or biotic resistance. Peach (Prunus persica (L.) Batsch) is one of the best genetically characterized species used as a model for Rosaceae, the drupes of which are a source of minerals, vitamins, fiber, and antioxidant compounds for healthy diets around the world. During the last few years, a great advance in the analysis of the metabolic diversity and reconfiguration in different peach varieties in response to developmental and environmental factors has occurred. These studies have shown that the great phenotypic diversity among different peach varieties is correlated with differential metabolomic content. Besides, the fruit metabolome of each peach variety is not static; on the contrary, it is drastically configured in response to both developmental and environmental signals, and moreover, it was found that these metabolic reconfigurations are also variety dependent. In the present review, the main sources of metabolic diversity and conditions that induce modifications in the peach fruit metabolome are summarized. It is postulated that comparison of the metabolic reconfigurations that take place among the fruits from different varieties may help us better understand peach fruit metabolism and their key drivers, which in turn may aid in the future design of high-quality peach fruits.

PbSRT1 and PbSRT2 regulate pear growth and ripening yet displaying a species-specific regulation in comparison to other Rosaceae spp.

Epigenetic regulation is crucial to ensure a coordinated control of the different events that occur during fruit development and ripening. Sirtuins are NAD+-dependent histone deacetylases involved in the regulation of gene expression of many biological processes. However, their implications in the Rosaceae family remains unexplored. Accordingly, in this work, we demonstrated the phylogenetic divergence of both sirtuins among Rosaceae species. We then characterized the expression pattern of both SRT1 and SRT2 in selected pome and stone fruit species. Both SRT1 and SRT2 significantly changed during the fruit development and ripening of apple, nectarine and pear fruit, displaying a different expression profile. Such differences could explain in part their different ripening behaviour. To further unravel the role of sirtuins on the fruit development and ripening processes, a deeper analysis was performed using pear as a fruit model. In pear, PbSRT1 gene expression levels were negatively correlated with specific hormones (i.e. abscisic acid, indole-3-acetic acid, gibberellin A1 and zeatin) during the first phases of fruit development. PbSRT2 seemed to directly mediate pear ripening in an ethylene-independent manner. This hypothesis was further reinforced by treating the fruit with the ethylene inhibitor 1-methylcyclopropene (1-MCP). Instead, enhanced PbSRT2 along pear growth/ripening positively correlated with the accumulation of major sugars (R2 > 0.94), reinforcing the idea that sugar metabolism may be a target of epigenetic modifications during fruit ripening. Overall, the results from this study point out, for the first time, the importance that sirtuins have in the regulation of fruit growth and ripening of pear fruit by likely regulating hormonal and sugar metabolism.

Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated 'Madoka' Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening.

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as 'Madoka' to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

Selection and validation reference genes for qRT-PCR normalization in different cultivars during fruit ripening and softening of peach (Prunus persica).

Quantitative real-time PCR (qRT-PCR) has been emerged as an effective method to explore the gene function and regulatory mechanisms. However, selecting appropriate reference gene (s) is a prerequisite for obtaining accurate qRT-PCR results. Peach is one of important fruit in Rosaceae and is widely cultivated worldwide. In this study, to explore reliable reference gene (s) in peach with different types during fruit ripening and softening (S1-S4), nine candidate reference genes (EF-1α, GAPDH, TBP, UBC, eIF-4α, TUB-A, TUB-B, ACTIN, and HIS) were selected from the whole-genome data. Then, the expression levels of the nine selected genes were detected using qRT-PCR in three peach types, including 'Hakuho' (melting type), 'Xiacui' (stony hard type), 'Fantasia' and 'NJC108' (non-melting type) cultivars were detected using qRT-PCR. Four software (geNorm, NormFinder, BestKeeper and RefFinder) were applied to evaluate the expression stability of these candidate reference genes. Gene expression was characterized in different peach types during fruit ripening and softening stages. The overall performance of each candidate in all samples was evaluated. The Actin gene (ACTIN) was a suitable reference gene and displayed excellent stability in 'Total' set, 'Hakuho' samples, S3 and S4 fruit developmental stages. Ubiquitin C gene (UBC) showed the best stability in most independent samples, including 'Fantasia', 'NJC108', S2 sets. Elongation factor-1α gene (EF-1α) was the most unstable gene across the set of all samples, 'NJC108' and S2 sets, while showed the highest stability in 'Xiacui' samples. The stability of candidate reference genes was further verified by analyzing the relative expression level of ethylene synthase gene of Prunus persica (PpACS1) in fruit ripening and softening periods of 'Hakuho'. Taken together, the results from this study provide a basis for future research on the mining of important functional genes, expression patterns and regulatory mechanisms in peach.

PpEBB1 directly binds to the GCC box-like element of auxin biosynthesis related genes.

EARLY BUD-BREAK 1 (EBB1) can promote bud break, and this function is likely conserved in woody plants. To get a more comprehensive understand of its function, peach (Prunus persica var. nectarina cultivar Zhongyou 4) PpEBB1 was overexpressed in Arabidopsis; the resultant phenotypes, including curved leaves, abnormal development of floral organs and low seed set, were similar to those of DORNRÖSCHEN-LIKE (DRNL) overexpression, indicating that PpEBB1 was a putative ortholog of AtDRNL. PpEBB1 bound to the GCC box-like element in the STYLISH1/SHI RELATED SEQUENCE5 (STY1/SRS5) promoter of peach, which has been proposed to occur in Arabidopsis as well. A GCC box-like element was also found in the YUCCA1 (YUC1) promoter, and PpEBB1 could bind to this element and activate the expression of YUC1. In addition to the elevated auxin content in the PpEBB1-oe plants as observed in our previous study, these results suggest that PpEBB1 can regulate auxin biosynthesis by directly activating related genes. Besides, we screened a zinc finger RING-finger protein, MYB30-INTERACTING E3 LIGASE 1 (PpMIEL1), showing interaction with PpEBB1, suggesting that the stability of PpEBB1 might be influenced by PpMIEL1 through ubiquitination.

Reduced expression of a subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1ßγ, confers flat fruit abortion in peach by regulating sugar and starch metabolism.

BACKGROUND: Fruit abortion is a major limiting factor for fruit production. In flat peach, fruit abortion is present in the whole tree of some accessions during early fruit development. However, the physiological factors and genetic mechanism underlying flat fruit abortion remain largely elusive. RESULTS: In this study, we have revealed that the fertilization process was accomplished and the reduction of sucrose and starch contents might result in flat fruit abortion. By combining association and gene expression analysis, a key candidate gene, PpSnRK1ßγ, was identified. A 1.67-Mb inversion co-segregated with flat fruit shape altered the promoter activity of PpSnRK1ßγ, resulting in much lower expression in aborting flat peach. Ectopic transformation in tomato and transient overexpression in peach fruit have shown that PpSnRK1ßγ could increase sugar and starch contents. Comparative transcriptome analysis further confirmed that PpSnRK1ßγ participated in carbohydrate metabolism. Subcellular localization found that PpSnRK1ßγ was located in nucleus. CONCLUSIONS: This study provides a possible reason for flat fruit abortion and identified a critical candidate gene, PpSnRK1ßγ, that might be responsible for flat fruit abortion in peach. The results will provide great help in peach breeding and facilitate gene identification for fruit abortion in other plant species.

Double NCED isozymes control ABA biosynthesis for ripening and senescent regulation in peach fruits.

During ripening, peach fruits (Prunus persica L. Batsch) rapidly progress to the senescent stage, resulting in a brief shelf life. Abscisic acid (ABA) plays an important role in regulating the ripening process, both in climacteric and non-climacteric fruits. A key enzyme for ABA biosynthesis in higher plants is 9-cis-epoxycarotenoid dioxygenase (NCED). In this study, two NCED isozymes, PpNCED1 and PpNCED5, were identified in peach fruits. While both NCED genes had similar transcriptional patterns (up-regulation) at the beginning of peach ripening, PpNCED5 showed a consistently lower expression level than PpNCED1. During the post-harvest stage, gene expression of PpNCED1 declined, while PpNCED5 expression increased relative to PpNCED1 expression. Considering the dynamic process of ABA accumulation during fruit ripening and senescence in peach, this study indicates that both NCED genes cooperatively control ABA biosynthesis in peach fruits. Moreover, spatio-temporal expression and transcriptional response to hormone and abiotic stress suggested that there is functional divergence between PpNCED1 and PpNCED5 genes in peach. A carotenoid-rich callus system was used to verify the function of PpNCED1 and PpNCED5. In the transgenic callus system, both PpNCED1 and PpNCED5 isozymes promoted ABA biosynthesis, which likely accelerated cell senescence through activating ROS signals. The results from this study provide evidence supporting an ABA biosynthetic regulation process via the two NCED genes in peach fruit, and suggest a mechanism of ABA-induced fruit ripening and senescence.

Developmental stages of peach, plum, and apple fruit influence development and fecundity of Grapholita molesta (Lepidoptera: Tortricidae).

Host plant attributes are essential factors determining the population dynamics of herbivorous insects. The developmental stage of host plants, in particular, may affect the biology of Grapholita molesta (Busck), a possibility that has rarely been examined. Here we assessed the effect of developmental stage of plum, peach, and apple fruits on the development and fecundity performance of G. molesta, along with an examination of the firmness and sugar content of the fruits. Among the fruits collected earliest (May 31), plum and apple were better food sources for G. molesta compared to peach in terms of development, reproduction, and life table parameters. However, despite the higher sugar content in peach, G. molesta larvae showed a lower rate of fruit penetration in peach, probably due to fruit firmness. In the later-collected fruit (June 25), both peach and apple were better than plum, as peach and apple were softer and had higher sugar content. Nevertheless, the penetration rate of larva was still low in peach probably due to pubescence on the fruit surface. Although the plum fruits in the later collection date were softer with higher sugar content, there was a negative impact on the development and reproduction because fruits started to liquefy earlier. In conclusion, the developmental stage of fruits with changes in fruit firmness or sugar content affected the development and reproduction of G. molesta, and apple would be the best food source.

The outer influences the inner: Postharvest UV-B irradiation modulates peach flesh metabolome although shielded by the skin.

UV-B-driven modulation of secondary metabolism in peach fruit by enhancing the biosynthesis of specific phenolic subclasses, is attracting interest among consumers. However, current literature explored the UV-B-induced metabolic changes only in peach skin subjected to direct UV-B irradiation. Accordingly, this study aimed to understand whether UV-B radiation penetrates the fruit skin and is able to induce metabolic changes also within the inner flesh. Peaches were UV-B-irradiated either 10 or 60 min, and the flesh was sampled after 24 and 36 h. Non-targeted metabolomics revealed that UV-B has a strong impact on peach flesh metabolome, determining an initial decrease after 24 h, followed by an overall increase after 36 h, particularly for terpenoids, phenylpropanoids, phytoalexins and fatty acids in the 60 min UV-B-treated samples (+150.02, +99.14, +43.79 and +25.44 log2FC, respectively). Transmittance analysis indicated that UV-B radiation does not penetrate below the skin, suggesting a possible signalling pathway between tissues.

Accurate non-destructive prediction of peach fruit internal quality and physiological maturity with a single scan using near infrared spectroscopy.

The development of precise and reliable near infrared spectroscopy (NIRS)-based non-destructive tools to assess physicochemical properties of fleshy fruit has been challenging. A novel crop load × fruit developmental stage protocol for multivariate NIRS-based prediction models calibration to non-destructively assess peach internal quality and maturity was followed. Regression statistics of the prediction models highlighted that dry matter content (DMC, R2 = 0.98, RMSEP = 0.41%), soluble solids concentration (SSC, R2 = 0.96, RMSEP = 0.58%) and index of absorbance difference (IAD, R2 = 0.96, RMSEP = 0.08) could be estimated accurately with a single scan during fruit growth and development. Thus, the impact of preharvest factors such as crop load and canopy position on peach quality and maturity was evaluated. Large-scale field validation showed that heavier crop loads reduced peach quality (DMC, SSC) and delayed maturity (IAD) and upper canopy position advanced both mainly in the moderate crop loads. This calibration protocol can enhance NIRS adaptation across tree fruit supply chain.

Assessment of organic acid accumulation and its related genes in peach.

Fruit acidity is an important determinant of peach organoleptic quality, but its regulatory mechanism remains elusive. Measurement of organic acids in ripe fruits of seventy-five peach cultivars revealed the predominant components malate and citrate, accompanied by quinate. Organic acid accumulation increased at early stages of fruit growth, but exhibited a more dramatic reduction in low-acid cultivar during later stages of fruit development compared to high-acid cultivars. Low-acid cultivars showed citrate degradation and less transport of malate into the vacuole due to up- and down-regulation of a GABA pathway gene GAD and a malate transporter gene ALMT9, respectively. The NAD-MDH1 gene might control the rate-limiting step in malate synthesis, while three genes, PDK, PK, and ADH, could affect citrate synthesis through the pyruvate-to-acetyl-CoA-to-citrate pathway. Altogether, these results suggested that malate accumulation is controlled at the level of metabolism and vacuolar storage, while metabolism is crucial for citrate accumulation in peach.

Regulation of growth in peach roots by exogenous hydrogen sulfide based on RNA-Seq.

Hydrogen sulfide (H2S) has been shown to regulate many physiological processes of plants. In this study, we observed that 0.2 mM sodium hydrosulfide (NaHS), a donor of H2S, can regulate the root architecture of peach seedlings, increasing the number of lateral roots by 40.63%. To investigate the specific mechanisms by which H2S regulates root growth in peach, we used RNA sequencing and heterologous expression technology. Our results showed that exogenous H2S led to a 44.50% increase in the concentration of endogenous auxin. Analyses of differentially expressed genes (DEGs) revealed that 963 and 1113 genes responded to H2S on days one and five of treatment, respectively. Among the DEGs, 26 genes were involved in auxin biosynthesis, transport, and signal transduction. Using weighted correlation network analysis, we found that the auxin-related genes in the H2S-specific gene module were disproportionately involved in polar transport, which may play an important role in H2S-induced root growth. In addition, we observed that the expression of LATERAL ORGAN BOUNDARIES DOMAIN 16 (PpLBD16) was significantly up-regulated by exogenous application of H2S in peach. Overexpression of PpLBD16 in an Arabidopsis system yielded a 66.83% increase in the number of lateral roots. Under exposure to exogenous H2S, there was also increased expression of genes related to cell proliferation, indicating that H2S regulates the growth of peach roots. Our work represents the first comprehensive transcriptomic analysis of the effects of exogenous application of H2S on the roots of peach, and provides new insights into the mechanisms underlying H2S-induced root growth.

Environmental behavior and influencing factors of glyphosate in peach orchard ecosystem.

In this paper, several experiments were carried out to study the environmental behavior and influencing factors of glyphosate (PMG) in peach orchard ecosystem. The results of field experiments showed that PMG and its metabolite aminomethylphosphonic acid (AMPA) were detected in peach tree leaves and peach tree fruits, although PMG was only sprayed on the soil. The residues of PMG and AMPA in peach tree leaves were ~0.1 mg/kg and ~0.5 mg/kg and in peach tree fruits were ~0.01 mg/kg and 0.07-0.11 mg/kg, respectively. By conducting a series of laboratory simulation experiments, the environmental factors affecting the degradation of PMG were screened and evaluated. The results showed that PMG metabolized much faster in loess soil than red soil and black soil (with the DT50 of 11.6 days, 62.4 days, and 34.1 days, respectively). By analyzing the basic properties of the soil, we investigated the effects of pH, moisture content, organic matter (exogenous biochar) and ambient temperature using orthogonal experiments, and the results were further confirmed by microbial experiment. The results showed that alkaline conditions (pH = 7.8/9), high water content (25%) and microorganisms could promote the degradation of PMG. Sterile soil environment had a negative impact on the metabolic behavior of PMG to AMPA.

Transcriptome Analysis of Genes Involved in Cold Hardiness of Peach Tree (Prunus persica) Shoots during Cold Acclimation and Deacclimation.

We analyzed the transcriptomes in the shoots of five-year-old 'Soomee' peach trees (Prunus persica) during cold acclimation (CA), from early CA (end of October) to late CA (middle of January), and deacclimation (DA), from late CA to late DA (middle of March), to identify the genes involved in cold hardiness. Cold hardiness of the shoots increased from early to late CA, but decreased from late CA to late DA, as indicated by decreased and increased the median lethal temperature (LT50), respectively. Transcriptome analysis identified 17,208 assembled transcripts during all three stages. In total, 1891 and 3008 transcripts were differentially expressed with a |fold change| > 2 (p < 0.05) between early and late CA, and between late CA and late DA, respectively. Among them, 1522 and 2830, respectively, were functionally annotated with gene ontology (GO) terms having a greater proportion of differentially expressed genes (DEGs) associated with molecular function than biological process or cellular component categories. The biochemical pathways best represented both periods from early to late CA and from late CA to late DA were 'metabolic pathway' and 'biosynthesis of secondary metabolites'. We validated these transcriptomic results by performing reverse transcription quantitative polymerase chain reaction on the selected DEGs showing significant fold changes. The relative expressions of the selected DEGs were closely related to the LT50 values of the peach tree shoots: 'Soomee' shoots exhibited higher relative expressions of the selected DEGs than shoots of the less cold-hardy 'Odoroki' peach trees. Irrespective of the cultivar, the relative expressions of the DEGs that were up- and then down-regulated during CA, from early to late CA, and DA, from late CA to late DA, were more closely correlated with cold hardiness than those of the DEGs that were down- and then up-regulated. Therefore, our results suggest that the significantly up- and then down-regulated DEGs are associated with cold hardiness in peach tree shoots. These DEGs, including early light-induced protein 1, chloroplastic, 14-kDa proline-rich protein DC2.15, glutamate dehydrogenase 2, and triacylglycerol lipase 2, could be candidate genes to determine cold hardiness.

Transcript profiling provides insights into molecular processes during shoot elongation in temperature-sensitive peach (Prunus persica).

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.