Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Susu Guo; Yanhai Ji; Yanyan Zheng; Christopher B Watkins; Lili Ma; Qing Wang; Hao Liang; Chunmei Bai; Anzhen Fu; Ling Li; Demei Meng; Mingchi Liu; Jinhua Zuo

doi:10.3389/fpls.2023.1142913

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Front Plant Sci. 2023 Mar 8:14:1142913. doi: 10.3389/fpls.2023.1142913. eCollection 2023.

Authors

Susu Guo^{1

2

3

4

5}, Yanhai Ji^{2

3

4

5}, Yanyan Zheng^{2

3

4

5}, Christopher B Watkins⁶, Lili Ma⁷, Qing Wang^{2

3

4

5}, Hao Liang^{2

3

4

5}, Chunmei Bai^{2

3

4

5}, Anzhen Fu^{2

3

4

5}, Ling Li⁷, Demei Meng¹, Mingchi Liu^{2

3

4

5}, Jinhua Zuo^{2

3

4

5}

Affiliations

¹ State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China.
² Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
³ Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
⁴ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
⁵ Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
⁶ School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, NY, Ithaca, United States.
⁷ College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China.

Abstract

Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.

Keywords: ATAC-seq; metabolome; storage; tomato; transcription factor; transcriptome.

Grants and funding

This work was supported by the Special innovation ability construction fund of the Beijing Academy of Agricultural and Forestry Sciences (20230418 and 20210437), the National Natural Science Foundation of China (32072284), the China Agriculture Research System of MOF and MARA (CARS-23 and GARS-23-G-06), the Research Project of Tianjin Education Commission (2021KJ111).