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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #386537
Research Project: Utilization of the Rhizosphere Microbiome and Host Genetics to Manage Soil-borne Diseases

Location: Physiology and Pathology of Tree Fruits Research

Title: Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages

Author
item ZHOU, ZHE - Chinese Academy Of Agricultural Sciences
item Zhu, Yanmin
item ZHANG, HENGTAO - Chinese Academy Of Agricultural Sciences
item ZHANG, RUIPING - Chinese Academy Of Agricultural Sciences
item GAO, QIMING - Chinese Academy Of Agricultural Sciences
item YAO, JIA-LONG - Chinese Academy Of Agricultural Sciences
item YAN, ZHENLI - Chinese Academy Of Agricultural Sciences

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2021
Publication Date: 12/22/2021
Citation: Zhou, Z., Zhu, Y., Zhang, H., Zhang, R., Gao, Q., Yao, J., Yan, Z. 2021. Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages. PeerJ. 9:e12675. https://doi.org/10.7717/peerj.12675.
DOI: https://doi.org/10.7717/peerj.12675

Interpretive Summary: Control of gene expression occurs at multiple levels with different mechanisms, and one of the recently discovered gene expression regulation mode is microRNA (miRNA)-directed degradation on specific gene transcripts. MicroRNA172 (miR172) has been linked to apple (Malus x domestica Borkh.) fruit size. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. The present study was designed to understand the regulation scheme of miR172 in developing apple fruit. The global transcriptional changes were compared between transgenic apple with overexpressed miR172 (miR172OX) and non-genetic-modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. Twenty-four libraries and 10338 differential expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. The data indicated that overexpressing of miR172 altered expression of many cell proliferation- and cell expansion-related genes. The potential regulating networks associated with fruit size traits were defined between structural and regulatory genes. There genes include those families of hormone synthesis, signaling pathways and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit. These findings constitute a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.

Technical Abstract: MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. Towards answering this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and non-genetic-modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. 24 libraries and 10338 differential expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. Overexpressing of miR172 altered expression of many cell proliferation- and cell expansion-related genes. The potential regulating networks associated with fruit size triggered traits were defined between structural and regulatory genes, which belong to families of hormone synthesis, signaling pathways and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit, and construct a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.