Kun-Song Chen

Zhejiang University, Hang-hsien, Zhejiang Sheng, China

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Publications (42)102.95 Total impact

  • Postharvest Biology and Technology 01/2016; 111:161-167. DOI:10.1016/j.postharvbio.2015.08.012 · 2.63 Impact Factor
  • Scientia Horticulturae 10/2015; 194:278-285. DOI:10.1016/j.scienta.2015.08.018 · 1.50 Impact Factor
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    ABSTRACT: Lignin biosynthesis is regulated by many transcription factors, such as those of the MYB and NAC families. However, the roles of AP2/ERF transcription factors in lignin biosynthesis have been rarely investigated. Eighteen EjAP2/ERF genes were isolated from loquat fruit (Eriobotrya japonica), which undergoes postharvest lignification during low temperature storage. Among these, expression of EjAP2-1, a transcriptional repressor, was negatively correlated with fruit lignification. The dual-luciferase assay indicated that EjAP2-1 could trans-repress activities of promoters of lignin biosynthesis genes from both Arabidopsis and loquat. However, EjAP2-1 did not interact with the target promoters (Ej4CL1). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated protein-protein interactions between EjAP2-1 and lignin biosynthesis-related EjMYB1 and EjMYB2. Furthermore, repression effects on the Ej4CL1 promoter were observed with the combination of EjAP2-1 and EjMYB1 or EjMYB2, while EjAP2-1 with the EAR motif mutated (mEjAP2-1) lost such repression, although mEjAP2-1 still interacted with EjMYB protein. Based on these results, it is proposed that EjAP2-1 is an indirect transcriptional repressor on lignin biosynthesis, and the repression effects were manifested by EAR motifs and were conducted via protein-protein interaction with EjMYBs. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 03/2015; DOI:10.1111/pbi.12351 · 5.68 Impact Factor
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    ABSTRACT: NAC genes have been characterized in numerous plants, where they are involved in responses to biotic and abiotic stress, including low oxygen stress. High concentration of CO2 is one of the most effective treatments to remove astringency of persimmon fruit owing to the action of the accumulated anoxia metabolite acetaldehyde. In model plants, NAC genes have been identified as being responsive to low oxygen. However, the possible relationship between NAC transcription factors and persimmon astringency removal remains unexplored. In the present research, treatment with a high concentration of CO2 (95%) effectively removed astringency of "Mopan" persimmon fruit by causing decreases in soluble tannin. Acetaldehyde content increased in response to CO2 treatment concomitantly with astringency removal. Using RNA-seq and Rapid amplification of cDNA ends (RACE), six DkNAC genes were isolated and studied. Transcriptional analysis indicated DkNAC genes responded differentially to CO2 treatment; DkNAC1, DkNAC3, DkNAC5 and DkNAC6 were transiently up-regulated, DkNAC2 was abundantly expressed 3 days after treatment, while the DkNAC4 was suppressed during astringency removal. It is proposed that DkNAC1/3/5/6 could be important candidates as regulators of persimmon astringency removal and the roles of other member are also discussed.
    International Journal of Molecular Sciences 01/2015; 16(1):1894-906. DOI:10.3390/ijms16011894 · 2.86 Impact Factor
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    ABSTRACT: Bagging is a useful method to improve fruit quality by altering its exposure to light, whereas its effect on fruit volatiles production is inconsistent, and the genes responsible for the observed changes remain unknown. In the present study, single-layer yellow paper bags were used to study the effects of bagging treatment on the formation of C6 aldehydes in peach fruit (Prunus persica L. Batsch, cv. Yulu) over two succeeding seasons. Higher concentrations of n-hexanal and (E)-2-hexenal, which are characteristic aroma volatiles of peach fruit, were induced by bagging treatment. After bagging treatment, peach fruit had significantly higher LOX and HPL enzyme activities, accompanying increased contents of C6 aldehydes. The gene expression data obtained through real-time PCR showed that no consistent significant differences in transcript levels of LOX genes were observed over the two seasons, but significantly up-regulated expression was found for PpHPL1 after bagging treatment In addition, bagging-treated fruit produced more (E)-2-hexenal and had higher expression levels of PpHPL1 during postharvest ripening at room temperature. The regulatory role of the LOX-HPL pathway on the biosynthesis of n-hexanal and (E)-2-hexenal in response to bagging treatment during peach fruit development is discussed in the text.
    Molecules 09/2014; 19(9):13461-13472. DOI:10.3390/molecules190913461 · 2.42 Impact Factor
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    ABSTRACT: Lignin biosynthesis and its transcriptional regulatory networks have been studied in model plants and woody trees. However, lignification also occurs in some fleshy fruit and has rarely been considered in this way. Loquat ( Eriobotrya japonica ) is one such convenient tissue for exploring the transcription factors involved in regulating fruit flesh lignification. Firmness and lignin content of ‘Luoyangqing’ loquat were fund to increase during low-temperature storage as a typical symptom of chilling injury, while heat treatment (HT) and low-temperature conditioning (LTC) effectively alleviated them. Two novel EjMYB genes, EjMYB1 and EjMYB2, were isolated and were found to be localized in the nucleus. These genes responded differently to low temperature, with EjMYB1 induced and EjMYB2 inhibited at 0 °C. They also showed different temperature responses under HT and LTC conditions, and may be responsible for different regulation of flesh lignification at the transcriptional level. Transactivation assays indicated that EjMYB1 and EjMYB2 are a transcriptional activator and repressor, respectively. EjMYB1 activated promoters of both Arabidopsis and loquat lignin biosynthesis genes, while EjMYB2 countered the inductive effects of EjMYB1. This finding was also supported by transient overexpression in tobacco. Regulation of lignification by EjMYB1 and EjMYB2 is likely to be achieved via their competitive interaction with AC elements in the promoter region of lignin biosynthesis genes such as Ej4CL1.
    Journal of Experimental Botany 05/2014; 65(15). DOI:10.1093/jxb/eru208 · 5.79 Impact Factor
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    ABSTRACT: A hypoxic environment is generally undesirable for most plants and stimulates anaerobic metabolism. It is a beneficial treatment, however, for the removal of astringency from persimmon to improve the fruit quality after harvest. High soluble tannins (SCTs) content is one of most important causes of astringency. High CO2 (95%) treatment effectively reduced SCTs in both "Mopan" and "Gongcheng-shuishi" persimmon fruit by causing increases in acetaldehyde. Using RNA-seq and realtime PCR, twelve ethylene response factor genes (DkERF11-22) were isolated and characterized, to determine those responsive to high CO2 treatment. Only two genes, DkERF19 and DkERF22, showed trans-activation effects on the promoters of deastringency-related genes pyruvate decarboxylase genes (DkPDC2 and DkPDC3) and the transcript levels of these genes was enhanced by hypoxia. Moreover, DkERF19 and the previously isolated DkERF9 had additive effects on activating the DkPDC2 promoter. Taken together, these results provide further evidence that transcriptome changes in the level of DkERF mRNAs regulate deastringency-related genes and their role in the mechanism of persimmon fruit deastringency is discussed.
    PLoS ONE 05/2014; 9(5):e97043. DOI:10.1371/journal.pone.0097043 · 3.23 Impact Factor
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    ABSTRACT: The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.
    Molecular Biology Reports 02/2014; 41(7). DOI:10.1007/s11033-014-3297-0 · 1.96 Impact Factor
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    Li Liang · Bo Zhang · Xue-Ren Yin · Chang-Jie Xu · Chong-De Sun · Kun-Song Chen
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    ABSTRACT: Peach fruits are sensitive to chilling injury (CI) during postharvest cold storage and their subsequent shelf-life, which results in loss of quality and market value. Many studies have examined the development of CI, including analyses of changes in biochemical composition, enzyme activity and gene expression; however, the molecular mechanism of CI remains unresolved. Six C-repeat (CRT) / dehydration-responsive element (DRE) binding factor (CBF) genes (PpCBF1-6) were isolated and characterized in peach fruit based on their homology to CBF genes that are available in public Prunus persica genome databases. The expression patterns of these genes were analyzed in response to varying temperatures and durations of treatment. Transcription of PpCBF1/5/6 was induced at low temperatures, whereas expression of other CBF genes remained relatively constant. The results presented here indicate that treating peach fruit with a CI-delaying temperature (0 °C) resulted in a greater accumulation of PpCBF1/5/6 transcripts than that observed in fruit treated with a CI-inducing temperature (5 °C). CBF gene induction was accompanied by a decrease in CI symptoms, including a loss of firmness, flesh browning and increased electrical conductivity, throughout the experimental 21-day cold storage period. An analysis of the upstream nucleotide sequence of CBF genes showed that a cis element inducer of CBF expression 1 (ICEr1) was detected in the promoter of PpCBF1/5/6.
    Plant Molecular Biology Reporter 12/2013; 31(6). DOI:10.1007/s11105-013-0600-5 · 2.37 Impact Factor
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    ABSTRACT: Anthocyanins, being important for both plant functions and human health, were transcriptionally regulated by the MYB–bHLH–WD40 transcription complex. The key MYB regulator for Chinese bayberry (Myrica rubra), MrMYB1, has been characterized in previous studies, while the specific bHLH partner(s) are unknown. In this study, MrbHLH1 and MrbHLH2 were isolated based on their homology to known plant bHLHs involved in anthocyanin biosynthesis regulation. Coordinate expression of MrbHLH1 with MrMYB1 and the anthocyanin biosynthetic genes was observed during fruit development, while MrbHLH2 showed a weaker correlation. Further transient assays in tobacco leaves suggested that MrbHLH1, but not MrbHLH2, was associated with MrMYB1 and triggered significant anthocyanin production. The lack of function of the MrbHLH2 in anthocyanin biosynthesis regulation suggested that different MrbHLH genes within the same phylogenic subfamily have different functions. Overexpression of MrMYB1 and MrbHLH1 in tobacco confirmed the crucial role of MrMYB1–MrbHLH1 in anthocyanin biosynthesis and all of the structural genes from NtCHS were up-regulated by the complex. Dual luciferase assays, however, indicated that MrMYB1 and MrbHLH1 selectively activated five of the eight promoters of biosynthetic genes from bayberry (MrCHI, MrF3′H, MrDFR1, MrANS, MrUFGT), although expression levels of all eight biosynthetic genes including MrCHS and downstream genes were coordinately increased during fruit ripening. Moreover, the interaction between MrbHLH1 and MrMYB1 was confirmed by yeast two-hybrid assay. In conclusion, MrbHLH1, but not MrbHLH2, was the essential partner of MrMYB1 during anthocyanin biosynthesis regulation in tobacco and bayberry, however, the biosynthetic genes in these two species responded differently to the MrMYB1–MrbHLH1 complex.
    Plant Cell Tissue and Organ Culture 12/2013; 115(3). DOI:10.1007/s11240-013-0361-8 · 2.61 Impact Factor
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    ABSTRACT: Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species.Result: RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function' category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species.
    BMC Genomics 10/2013; 14(1):732. DOI:10.1186/1471-2164-14-732 · 4.04 Impact Factor
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    ABSTRACT: The effects of acetylsalicylic acid (ASA) on kiwifruit (Actinidia deliciosa cvs Bruno and Hayward) ethylene biosynthesis and signaling were investigated. Exogenous application of ASA inhibited ethylene production in both whole fruit, and in vitro with flesh discs, and enzymes associated with ethylene biosynthesis (ACS and ACO). The effect of ASA treatment on kiwifruit softening was relatively weak. Combination treatments also had inhibitory effects on fruit ripening, with ASA + C2H4 more effective than C2H4 + ASA. In order to evaluate the effects of ASA on ethylene signaling, twenty-four ethylene signaling components (five ethylene receptors, two CTR1 like genes, four EIN3-like genes and thirteen ERF genes) were analyzed at the transcriptional level. The results indicated that ASA treatment generally inhibited ethylene-induced modulation of ethylene receptor genes, and had little effect on softening-related ethylene signaling components, which suggested that ASA inhibits fruit ripening mainly by interfering directly with ethylene biosynthesis and perception. In addition, the ethylene response factors AdERF1, AdERF3 and AdERF12 were characterized as ASA-responsive genes, and their roles in fruit stress response are also discussed.
    Postharvest Biology and Technology 09/2013; 83:27–33. DOI:10.1016/j.postharvbio.2013.03.012 · 2.63 Impact Factor
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    ABSTRACT: MrMYB1, an R2R3 MYB transcription factor (TF) gene associated with anthocyanin biosynthesis in Chinese bayberry (Myrica rubra Sieb. and Zucc.), was introduced into Arabidopsis and tobacco (Nicotiana tabacum) under the control of the CaMV 35S promoter. Overexpression of MrMYB1 induced anthocyanin accumulation in all tissues of Arabidopsis as well as in petals, ovaries and young seeds of tobacco, but not in tobacco leaves. The anthocyanin biosynthetic pathway, including chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), and the basic helix-loop-helix (bHLH) transcriptional partner TRANSPARENT TESTA8 (TT8), were up-regulated significantly in MrMYB1-overexpressing Arabidopsis. In MrMYB1-overexpressing tobacco petals, ovaries and young seeds, anthocyanin biosynthetic genes and bHLH partners NtAn1a and NtAn1b, were up-regulated. In contrast, high expression of MrMYB1 in transgenic tobacco leaves did not induce the expression of anthocyanin biosynthesis. Unlike in petals and ovaries, the foliar transcript level of NtAn1a and NtAn1b was extremely low and not stimulated by MrMYB1 transformation. These results show that higher expression of an endogenous bHLH partner, either intrinsically or stimulated by exogenous gene transformation, is required for anthocyanin production in plant tissues, and the different abundance in endogenous bHLH transcript accounts for differential accumulation of anthocyanin in Arabidopsis and tobacco leaves. These findings demonstrate that higher levels of expression of an endogenous bHLH partner, either intrinsically or following genetic transformation, are required for anthocyanin production in plant tissues. Moreover, differences in levels of endogenous bHLH transcripts account for observed differential accumulation of anthocyanin in leaves of Arabidopsis and tobacco.
    Plant Cell Tissue and Organ Culture 06/2013; 113(3). DOI:10.1007/s11240-013-0291-5 · 2.61 Impact Factor
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    ABSTRACT: Low temperature storage slows ripening and reduces decay of peach fruit, although storage life is limited due to chilling injury. Intermittent warming (IW) can be used to alleviate fruit chilling injury, however, its effect on aroma remains unknown. Yellow-fleshed peach (Prunus persica L. Batsch cv. Jinxiu) fruit (melting type) was stored at 5 °C or exposed to 20 °C for 1 d every week during storage. Changes in fruit esters, alcohol acyltransferase (AAT) activity and gene expression were investigated. Flesh browning (FB) was observed on the third day of shelf-life at 20 °C after 21 d of storage at 5 °C, while no FB was found in IW-treated fruit for up to 28 d. Significant lower ester contents were found in peach fruit with flesh browning. Expression profiles of PpAAT1 were similar to AAT activity profiles, both of which increased during shelf-life of fruit treated with IW. As precursors of esters, levels of linoleic and linolenic acids were high in IW-treated peach fruit. Treatment with IW effectively alleviated the loss of aroma-related esters associated with FB, and high levels of AAT activity and PpAAT1 expression in IW-treated peach fruit contributed to the formation of the esters.
    Postharvest Biology and Technology 12/2012; 74:42–48. DOI:10.1016/j.postharvbio.2012.07.003 · 2.63 Impact Factor
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    ABSTRACT: • Premise of the study: In Chinese bayberry (Myrica rubra), the available simple sequence repeat (SSR) markers are insufficient to meet the developing demand for genetic and molecular breeding research. This study was aimed at developing a large number of polymorphic expressed sequence tag (EST)-SSRs from the transcriptome of Chinese bayberry.• Methods and Results: Five hundred ninety-four compound EST-SSRs and 5557 noncompound ones were identified from 41239 unigene sequences generated from the transcriptome of M. rubra cv. Biqi. Using 10 Chinese bayberry cultivars, 109 polymorphic EST-SSRs were screened from 412 selected. In total, they generated 389 alleles, with a polymorphism ratio of 93.8%. In addition, it was observed that the polymorphism levels of compound EST-SSRs were somewhat lower than those of noncompound ones.• Conclusions: The 109 polymorphic EST-SSRs developed from the Chinese bayberry transcriptome should greatly promote the development of genetic and molecular breeding studies in this as well as other Myricaceae species.
    American Journal of Botany 11/2012; 99(12). DOI:10.3732/ajb.1200156 · 2.46 Impact Factor
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    ABSTRACT: Organic acid and sugar balance is an important trait for fruit quality. The mandarin, Ponkan (Citrus reticulata Blanco cv. Ponkan) is rich in organic acids even at maturity, thus the fruit provide good material for the study of organic acid degradation. In the present research, hot air (40 °C, 2 d) treatment (HAT) was found to have significant effects on both degradation of the organic acids, especially on citric acid, and accumulation of soluble sugars, especially on fructose and glucose. Genes related to citric acid degradation related (CitAco1, CitAco2, CitAco3, CitIDH1, CitIDH2, CitIDH3, CitGAD4, CitGAD5 and CitGS2) and sucrose metabolism (CitAI1, CitAI3, CitNI1 and CitNI3) were isolated and transcription analyzed. HAT significantly up-regulated CitAco3, CitIDH2/3 and CitGAD4 expression, while having little effect on CitGS2. Sucrose metabolism related genes also differentially responded to HAT, with CitAI genes were induced and CitNI genes were relatively unchanged. It is proposed that HAT drove citric acid degradation via the GABA shunt pathway (especially by modulating CitAco3–CitIDH2/3–CitGAD4 cascade), but not the glycolysis pathway.
    Scientia Horticulturae 11/2012; 147:118–125. DOI:10.1016/j.scienta.2012.09.011 · 1.50 Impact Factor
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    ABSTRACT: The persimmon fruit is a particularly good model for studying fruit response to hypoxia, in particular, the hypoxia-response ERF (HRE) genes. An anaerobic environment reduces fruit astringency by converting soluble condensed tannins (SCTs) into an insoluble form. Although the physiology of de-astringency has been widely studied, its molecular control is poorly understood. Both CO(2) and ethylene treatments efficiently removed the astringency from 'Mopan' persimmon fruit, as indicated by a decrease in SCTs. Acetaldehyde, the putative agent for causing de-astringency, accumulated during these treatments, as did activities of the key enzymes of acetaldehyde synthesis, alcohol dehydrogenase (ADH), and pyruvate decarboxylase (PDC). Eight DkADH and DkPDC genes were isolated, and three candidates for a role in de-astringency, DkADH1, DkPDC1, and DkPDC2, were characterized by transcriptional analysis in different tissues. The significance of these specific isoforms was confirmed by principal component analysis. Transient expression in leaf tissue showed that DkPDC2 decreased SCTs. Interactions of six hypoxia-responsive ERF genes and target promoters were tested in transient assays. The results indicated that two hypoxia-responsive ERF genes, DkERF9 and DkERF10, were involved in separately regulating the DkPDC2 and DkADH1 promoters. It is proposed that a DkERF-DkADH/DkPDC cascade is involved in regulating persimmon de-astringency.
    Journal of Experimental Botany 10/2012; 63(18). DOI:10.1093/jxb/ers296 · 5.79 Impact Factor
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    ABSTRACT: The biosynthesis of volatile compounds in plants is affected by environmental conditions. Lactones are considered to be peach-like aroma volatiles; however, no enzymes or genes associated with their biosynthesis have been characterized. White-fleshed (cv. Hujingmilu) and yellow-fleshed (cv. Jinxiu) melting peach (Prunus persica L. Batsch) fruit were used as materials in two successive seasons and responses measured to four different temperature treatments. Five major lactones accumulated during postharvest peach fruit ripening at 20 °C. Peach fruit at 5 °C, which induces chilling injury (CI), had the lowest lactone content during subsequent shelf life after removal, while 0 °C and a low-temperature conditioning (LTC) treatment alleviated development of CI and maintained significantly higher lactone contents. Expression of PpACX1 and activity of acyl-CoA oxidase (ACX) with C16-CoA tended to increase during postharvest ripening both at 20 °C and during shelf life after removal from cold storage when no CI was developed. There was a positive correlation between ACX and lactones in peach fruit postharvest. Changes in lactone production in response to temperatures are suggested to be a consequence of altered expression of PpACX1 and long-chain ACX activity.
    Plant Cell and Environment 09/2012; 35(3):534-45. DOI:10.1111/j.1365-3040.2011.02433.x · 5.91 Impact Factor
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    ABSTRACT: Ethylene response factors (ERFs) play important roles in fruit ripening and abiotic stress response. After harvest, fruit such as kiwifruit are subject to a range of stresses associated with postharvest handling and storage treatments. There have been few attempts to evaluate fruit ERF responses in relation to such abiotic stress. Stress treatments including low temperature (0 °C), high temperature (35 °C), high CO2 (5%) and high water loss (∼10% RH air) were applied to freshly harvested mature kiwifruit. Expression patterns of 13 AdERF genes were followed. In response to the abiotic stresses, AdERF3, AdERF4, AdERF11, AdERF12 and AdERF14 were constitutively up-regulated, and AdERF1 was generally down-regulated, while the other AdERF genes showed no regular expression patterns. These data showed that AdERF genes differentially respond to abiotic stresses experienced by fruit during postharvest storage.
    Postharvest Biology and Technology 04/2012; 66:1–7. DOI:10.1016/j.postharvbio.2011.11.009 · 2.63 Impact Factor
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    ABSTRACT: Chinese bayberry (Myrica rubra Sieb. and Zucc.) is an important subtropical fruit crop and an ideal species for fruit quality research due to the rapid and substantial changes that occur during development and ripening, including changes in fruit color and taste. However, research at the molecular level is limited by a lack of sequence data. The present study was designed to obtain transcript sequence data and examine gene expression in bayberry developing fruit based on RNA-Seq and bioinformatic analysis, to provide a foundation for understanding the molecular mechanisms controlling fruit quality changes during ripening. RNA-Seq generated 1.92 G raw data, which was then de novo assembled into 41,239 UniGenes with a mean length of 531 bp. Approximately 80% of the UniGenes (32,805) were annotated against public protein databases, and coding sequences (CDS) of 31,665 UniGenes were determined. Over 3,600 UniGenes were differentially expressed during fruit ripening, with 826 up-regulated and 1,407 down-regulated. GO comparisons between the UniGenes of these two types and interactive pathways (Ipath) analysis found that energy-related metabolism was enhanced, and catalytic activity was increased. All genes involved in anthocyanin biosynthesis were up-regulated during the fruit ripening processes, concurrent with color change. Important changes in carbohydrate and acid metabolism in the ripening fruit are likely associated with expression of sucrose phosphate synthase (SPS) and glutamate decarboxylase (GAD). Mass sequence data of Chinese bayberry was obtained and the expression profiles were examined during fruit ripening. The UniGenes were annotated, providing a platform for functional genomic research with this species. Using pathway mapping and expression profiles, the molecular mechanisms for changes in fruit color and taste during ripening were examined. This provides a reference for the study of complicated metabolism in non-model perennial species.
    BMC Genomics 01/2012; 13(1):19. DOI:10.1186/1471-2164-13-19 · 4.04 Impact Factor