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

PeerJ

article

Zhe Zhou¹  Yanmin Zhu²  Hengtao Zhang¹  Ruiping Zhang¹  Qiming Gao¹  Tiyu Ding¹  Huan Wang¹  Zhenli Yan¹  Jia-Long Yao¹ 

[1] Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences;Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service;The New Zealand Institute for Plant & Food Research Limited

关键词: Apple;    Transgenic fruit;    Fruit size;    Transcriptome;    Transcription factors;    Coexpression netword;   

DOI  :  10.7717/peerj.12675

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundMicroRNA172 (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.MethodsTo answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data.ResultsOverexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the 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 a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.

【 授权许可】

CC BY