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Non-climacteric fruit ripening in pepper: increased transcription of EIL-like genes normally regulated by ethylene

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Abstract

Only limited information has been published to date on the similarities and differences between climacteric and non-climacteric fruit ripening on transcriptional level. To address this issue, we performed a direct comparative transcriptome analysis between tomato and pepper fruits using heterologous microarray hybridization. Given the significant differences in the morphological, physiological, and biochemical characteristics of pepper and tomato fruits, the existence of extensive common regulons is surprising. This finding suggests the conservation of ripening mechanisms in climacteric and non-climacteric fruits. However, disparate expression profiles were also observed in both fruits. This study revealed that a gene that encodes an enzyme that converts lycopene to downstream carotenoids is induced in pepper but not in tomato. Most of the genes that encode ribosomal proteins are only induced in early fruit-stage pepper fruit and show rapidly diminishing expression in the later developmental stages. The genes involved in ethylene biosynthesis were not induced in pepper fruit. However, the EIL-like genes, ethylene-mediated signaling components, were induced in pepper fruit. Divergent types of transcription factors were expressed in ripening tomato and pepper fruits, suggesting they may be key factors that differentiate these distinct ripening processes.

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Acknowledgements

The authors are grateful to Drs. Woo-Taek Kim, Hwa-Jee Chung, Youn Lee, and Jim Giovannoni for helpful discussion and for critical reading of the manuscript. This work was supported by grants from PDRC (PF0033-01) and CFGC (CG1431) of the 21st Century Frontier Research Program, funded by MOST of the Korean government.

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Authors and Affiliations

  1. Bio-Research Team, Dongbu Advanced Research Team, Daejeon, 305-708, South Korea

    Sanghyeob Lee

  2. Plant Genomic Research Center, KRIBB, Daejeon, 305-806, South Korea

    Sanghyeob Lee, Eun-Joo Chung & Doil Choi

  3. Department of Science and Technology, Chonnam National University, Gwangju, 500-757, South Korea

    Young-Hee Joung

  4. Horticultural Science Program, Seoul National University, Seoul, 151-742, South Korea

    Doil Choi

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  1. Sanghyeob Lee
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  2. Eun-Joo Chung
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Correspondence to Doil Choi.

Electronic supplementary materials

All of the array data used in this study was deposited in ArrayExpress under the accession number E-MEXP-260.

Figure S1

A figure showing a quality control analysis of replicated microarray experiments. (GIF 456 kb)

High resolution image (TIFF 985 kb)

Table S1

A complete list of fruit-specific genes in pepper and tomato. (XLS 352 kb)

Table S2

Genes encoding ribosomal proteins that are up- or down-regulated more than twofold during fruit ripening. (XLS 41 kb)

Table S3

Genes that are differently regulated in the early fruit stages of pepper and tomato. (XLS 106 kb)

Table S4

Genes that are differently regulated in the mature green fruit stages of pepper and tomato. (XLS 90 kb)

Table S5

Genes that are differently regulated in the breaker fruit stages of pepper and tomato. (XLS 112 kb)

Table S6

Genes that are differently regulated in the red ripe fruit stages of pepper and tomato. (XLS 80 kb)

Table S7

Genes used in the comparative expression analysis of pepper and tomato ripening. (XLS 822 kb)

Table S8

Genes used in the comparative expression analysis that showed up- or down-regulation of over twofold during pepper or tomato ripening. (XLS 345 kb)

Table S9

A table of pair-wise correlation coefficients of the replicated array data. (DOC 133 kb)

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Lee, S., Chung, EJ., Joung, YH. et al. Non-climacteric fruit ripening in pepper: increased transcription of EIL-like genes normally regulated by ethylene. Funct Integr Genomics 10, 135–146 (2010). https://doi.org/10.1007/s10142-009-0136-9

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