Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Abstract

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA–DEmRNA, 281 DEmiRNA–DElncRNA, and 23 DEmiRNA–DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.

Multi-omics revolution to promote plant breeding efficiency

“…While lncRNAs serve as important regulators in several vital biological processes and circRNAs functioned as miRNA sponges, transcriptional and splicing regulators, and moderators of primary gene expression in plants ( Lai et al., 2018 ; Waititu et al., 2020 ). Whole-transcriptome sequencing in plants was used to create the global landscape of these mRNAs in plants, such as maize ( Liu et al., 2022a ) Chinese cabbage ( Shi et al., 2022 ) citrus ( Fu et al., 2019 ).…”

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

“… The numbers represent the total number of circRNAs identified in each study ( Bai et al., 2021 ; Bao et al., 2019 ; Bian et al., 2021 ; Chen et al., 2017 , 2022 ; Darbani et al., 2016 ; Dong et al., 2021 ; Eisenberg and Levanon, 2018 ; Fu et al., 2019 , 2020 ; Ghorbani et al., 2018 ; Han et al., 2021 ; He et al., 2020 ; Hong et al., 2020 ; Jiang et al., 2021 ; Li et al., 2020a , 2020b , 2021a ; Liang et al., 2019 ; Liu et al., 2017 , 2019c , 2020a , 2021a ; Luo et al., 2020 ; Lv et al., 2020 ; Ma et al., 2021a , 2021b ; Medina et al., 2021 ; Meng et al., 2018 ; Pan et al., 2018 ; Qin et al., 2018 ; Ren et al., 2018 ; Salih et al., 2021 ; Shi et al., 2021 , 2022 ; Shu et al., 2021 ; Sun et al., 2016 , 2020 , 2021 , Tang et al., 2018 ; Tong et al., 2018 ; Wang et al., 2017a , 2017b , 2018a , 2018b , 2019c , 2019e , 2020a , 2021a , 2021b , 2021c , 2022a , 2022b , Wu et al., 2020 ; ...…”