Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit

Authors: ZUO, JINHUA - Boyce Thompson Institute; GRIERSON, DONALD - University Of Nottingham; COURTNEY, LANCE - Cornell University; WANG, YUNXIANG - Beijing Academy Of Agricultural Sciences; GAO, LIPU - Beijing Academy Of Agricultural Sciences; ZHAO, XIAOYAN - Beijing Academy Of Agricultural Sciences; ZHU, BENZHONG - China Agricultural University; LUO, YUNBO - China Agricultural University; WANG, QING - Beijing Academy Of Agricultural Sciences; Giovannoni, James

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/7/2020
Publication Date: 4/20/2020
Citation: Zuo, J., Grierson, D., Courtney, L., Wang, Y., Gao, L., Zhao, X., Zhu, B., Luo, Y., Wang, Q., Giovannoni, J.J. 2020. Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit. Plant Journal. https://doi.org/10.1111/tpj.14778.
DOI: https://doi.org/10.1111/tpj.14778

Interpretive Summary: Fruit ripening is a complex plant process necessary for the distribution of plant seeds and with practical implications to human food and nutritional security. The ripening process is regulated by environmental, genetic and hormonal signals that are coordinated by molecular systems which integrate these inputs to influence ripening. Controlling shelf-life, storage and nutrition in addition to other consumer quality attributes (appearance, flavor, texture) for consumers depends on understanding these processes such that aspects can be influenced (e.g. by temperature, air composition or genetic means) to the benefit of consumers. Here we explore complex genetic participants in the molecular control of ripening and identify gene targets and molecular processes that regulate them.

Technical Abstract: Tomato fruit ripening is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes rendering fruit attractive, palatable and nutritious. Ripening requires initiation, activation and coordination of key pathways at the transcriptional and post-transcriptional levels that lead to ethylene synthesis and downstream ripening events determining quality. We studied wild-type, Gr and r mutant fruits at the coding and noncoding transcriptomic, metabolomic, and genome methylation levels. Numerous differentially expressed noncoding RNAs were identified and quantified and potential ceRNAs regulation models were constructed. Multiple gene methylation changes were linked to the ethylene pathway and ripening processes. A combined analysis of genome methylation changes, lncRNAs, circRNAs, miRNAs and fruit metabolites revealed many differentially expressed (DE) genes with differentially methylated regions (DMRs) encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by DE noncoding RNAs. These included ACO2 , CTR1 , ERF2 , ERF5 , PSY1, ZISO and NCED . Understanding the functioning of this intricate genetic regulatory network provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.