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Identification of volatile and softening-related genes using digital gene expression profiles in melting peach

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Abstract

To reveal the comprehensive mechanism which is associated with the biosynthesis of volatile compounds and the accompanying texture change, RNA-seq was employed to survey the differentially expressed genes (DEGs), at the transcriptional level, of one cultivar at three stages of ripening and of four melting peach cultivars at harvest stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that highly ranked genes are involved in “Ribosome” and “Plant-pathogen interaction,” “Flavonoid biosynthesis,” “Linoleic acid metabolism,” and “Flavone and flavonol biosynthesis” during the fruit-ripening process. The quantitative real-time PCR (qRT-PCR) validation with 15 aroma and softening-related genes showed high correlation with the RNA-seq results. Transcripts of a nonspecific lipid transfer protein (nsLTP, ppa013554) and an ATP-binding cassette transporter (ABC, ppa002351) increased from the early ripening stage to the commercial harvest stage and then declined in the fully ripening stage. The highest transcript abundance was in the aroma-enriched cv. “Hu Jing Mi Lu” (HJ) and lowest in the cv. “Zhong Hua Shou Tao” with slight aroma. Fifty gene families related to the formation of aroma compounds were found. For peach lactone biosynthesis, we inferred that ppa002510 and ppa002282 may be the two important acyl-CoA oxidase genes correlating with the difference in γ-decalactone concentrations among the four cultivars. The expression of one 3-hydroxyacyl-CoA dehydrogenase gene (HCAD, ppa008854) was upregulated during ripening. Thirteen gene families were associated to fruit softening. Four aquaporin (AQP) genes showed cultivar-specificity for HJ, and one of them, ppa009506, reached maximum accumulation of transcripts at harvest stage. The batch of novel genes (nsLTP, ACX, AOC, ABC, HCAD, AQP) found here facilitates understanding of the molecular mechanism of melting peach aroma biosynthesis and fruit softening.

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Abbreviations

DGE:

Digital gene expression

DEGs:

Differentially expressed genes

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

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Acknowledgments

This work was supported by the State Ministry of Science and Technology of China (2011AA100206 and International Cooperation 1114), China Natural Science Foundation (31372040 and 31401833), The Key Project for New Agricultural Cultivar Breeding in Zhejiang Province, China (2012C12904), and the Scientific Fund for Young Scholars in Shanghai Municipal Agricultural Commission(2014:1–27). We acknowledge Mei-dan Lu for lab work on RNA extraction.

Conflict of interest

The authors declare that they have no conflict of interest.

Authors’ contributions

XWL, YY, JJ, and LPZ performed the experiments, analyzed the data, and drafted the manuscript. XWL, JJ, MLC, and HQZ performed the RNA-seq data analysis. YY contributed to the RNA extraction, qPCR implementation, and data analysis. ZWY, XMW, and JYZ were involved in selection and preparation of fruit samples and quality evaluation. ZSG, HJJ, and PA initiated the project, designed the experiment, and reviewed the manuscript. All authors read and approved the manuscript.

Data archiving statement

For each sample, the raw data files containing reads and quality scores have been deposited to the NCBI’s GEO database (http://www.ncbi.nlm.nih.gov/geo/) and will be submitted to the NCBI Sequence Read Archive (SRA) database by the GEO administrator. As required by GEO, the submitted data included three components: (1) metadata_spreadsheet_peach_DGE (indicating the research title, sample name, sample characteristic, experiment design methods, data processing methods, etc.), (2) processed data files (including all the RPKM value for each gene of each sample, e.g., HJ1_rep1_RPKM), and (3) raw reads data files (e.g., HJ1_rep1.fq). The accession number for each raw read file supplied by SRA is as follows: GSM1574411(HJ1 rep1), GSM1574412(HJ1 rep2), GSM1574413(HJ2 rep1),GSM1574414(HJ2 rep2), GSM1574415(HJ3 rep1), GSM1574416 (HJ3 rep2), GSM1574417(YL2 rep1), GSM1574418(YL2 rep2), GSM1574419(JX2 rep1), GSM1574420(JX2 rep2), GSM1574421(ZH2 rep1), and GSM1574422(ZH2 rep2).

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Authors and Affiliations

  1. Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China

    Xiong-wei Li, Jun Jiang, Li-ping Zhang, Yi Yu, Ming-liang Chai, Hui-juan Jia & Zhong-shan Gao

  2. Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China

    Xiong-wei Li & Zheng-wen Ye

  3. Horticultural Department, Shanghai Municipal Agricultural Technology Extension & Service Center, Shanghai, 201103, China

    Xiu-min Wang & Jing-yi Zhou

  4. Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China

    Hui-qin Zhang

  5. IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Campus UAB-Edifici CRAG, Bellaterra-Cerdanyola del Vallès, 08193, Barcelona, Spain

    Pere Arús

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  1. Xiong-wei Li
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  2. Jun Jiang
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  3. Li-ping Zhang
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  4. Yi Yu
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  9. Hui-qin Zhang
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  11. Hui-juan Jia
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Corresponding authors

Correspondence to Hui-juan Jia or Zhong-shan Gao.

Additional information

Communicated by A. G. Abbott

This article is part of the Topical Collection on Gene Expression

Electronic supplementary material

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Supplementary Figure 1

The distribution of reads on the reference genome, and on reference genes in picture format. X-axis, length of chromosome (Mb): y-axis, the number of reads mapped to the reference genome. (JPEG 212 kb)

Supplementary Figure 2

Scatter plots constructed with log10 (RPKM) value in each transcriptome profile. Correlation analysis of two parallel experiments evaluates the reliability of experimental results as well as operational stability. The closer the correlation value to 1, the better the repeatability between two parallel experiments. For example, with ‘HJ1_1 vs HJ1-2’ the x-axis represents log10 (RPKM) in HJ1-1 and the y-axis represents the value of log10 (RPKM) of the same corresponding gene in the transcriptome profile in HJ1-2. The correlation coefficient of two biological replicates is from 0.936 to 0.965, the high value indicates the reproducibility of our RNA-seq results. (JPEG 116 kb)

Supplementary Figure 3

Histogram of gene ontology (GO) classification of DEGs during three ripening stages of ‘HJ’ under corrected P value<0.05. The DEGs were summarized in three main categories: biological process, molecular function and cellular compound. The y-axis indicates the whole number of differentially expressed genes annotated in the category. The x-axis indicates different GO terms. The red, yellow and blue lines indicate the term corresponds to biological process, molecular function or cellular compound, respectively. (PPTX 71 kb)

Supplementary Figure 4

Histogram of gene ontology (GO) classification of DEGs among four peach varieties under corrected P value<0.05. The DEGs were summarized in three main categories: biological process, molecular function and cellular compound. The y-axis indicates the whole number of differentially expressed genes annotated in the category. The x-axis indicates different GO terms. The red, yellow and blue lines indicate the term corresponds to biological process, molecular function or cellular compound, respectively. (PPTX 77 kb)

Supplementary Figure 5

Histogram of enriched KEGG pathway of DEGs in three comparison groups of three ripening stages of ‘HJ’ under the corrected P value <0.05. X-axis: Significantly enriched KEGG terms. Y-axis: number of DEGs in the corresponding enriched KEGG pathway. (PPTX 69 kb)

Supplementary Figure 6

Histogram of enriched KEGG pathway of DEGs in six comparison groups among four peach varieties under corrected P value <0.05. X-axis: Significantly enriched KEGG terms. Y-axis: number of DEGs in the enriched KEGG pathway. (PPTX 91 kb)

Supplementary Table 1

Characteristics of four peach cultivars and three ripening stages of ‘HJ’. (DOC 35 kb)

Supplementary Table 2

Primer sequences used for qRT-PCR validation of RNA-seq data. (DOC 52 kb)

Supplementary Table 3

One hundred and sixty four genes and gene annotations associated to lipid transfer, aroma formation and texture change during the ripening stages of ‘HJ’. (XLSX 48 kb)

Supplementary Table 4

One hundred and sixty four genes and gene annotations associated to lipid transfer, aroma formation and texture change among 4 different cultivars. (XLSX 34 kb)

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Li, Xw., Jiang, J., Zhang, Lp. et al. Identification of volatile and softening-related genes using digital gene expression profiles in melting peach. Tree Genetics & Genomes 11, 71 (2015). https://doi.org/10.1007/s11295-015-0891-9

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