Analysis of weighted co-regulatory networks in maize provides insights into new genes and regulatory mechanisms related to inositol phosphate metabolism

BMC Genomics

Research Article

Shuai Ma¹  Xiaoqing Liu²  Yunliu Fan²  Ling Jiang²  Chunyi Zhang²  Qianqian Zhao²  Xiaojin Zhou²  Ye Li²  Rumei Chen²  Wenzhu Yang²  Shaojun Zhang² 

[1] Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), 100081, Beijing, China;

关键词: Inositol phosphates;    Metabolism;    Co-regulatory network;    WGCNA;    Candidate gene;   

DOI  :  10.1186/s12864-016-2476-x

 received in 2015-11-02, accepted in 2016-02-16,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundD-myo-inositol phosphates (IPs) are a series of phosphate esters. Myo-inositol hexakisphosphate (phytic acid, IP6) is the most abundant IP and has negative effects on animal and human nutrition. IPs play important roles in plant development, stress responses, and signal transduction. However, the metabolic pathways and possible regulatory mechanisms of IPs in maize are unclear. In this study, the B73 (high in phytic acid) and Qi319 (low in phytic acid) lines were selected for RNA-Seq analysis from 427 inbred lines based on a screening of IP levels. By integrating the metabolite data with the RNA-Seq data at three different kernel developmental stages (12, 21 and 30 days after pollination), co-regulatory networks were constructed to explore IP metabolism and its interactions with other pathways.ResultsDifferentially expressed gene analyses showed that the expression of MIPS and ITPK was related to differences in IP metabolism in Qi319 and B73. Moreover, WRKY and ethylene-responsive transcription factors (TFs) were common among the differentially expressed TFs, and are likely to be involved in the regulation of IP metabolism.Six co-regulatory networks were constructed, and three were chosen for further analysis. Based on network analyses, we proposed that the GA pathway interacts with the IP pathway through the ubiquitination pathway, and that Ca2+ signaling functions as a bridge between IPs and other pathways. IP pools were found to be transported by specific ATP-binding cassette (ABC) transporters. Finally, three candidate genes (Mf3, DH2 and CB5) were identified and validated using Arabidopsis lines with mutations in orthologous genes or RNA interference (RNAi)-transgenic maize lines. Some mutant or RNAi lines exhibited seeds with a low-phytic-acid phenotype, indicating perturbation of IP metabolism. Mf3 likely encodes an enzyme involved in IP synthesis, DH2 encodes a transporter responsible for IP transport across organs and CB5 encodes a transporter involved in IP co-transport into vesicles.ConclusionsThis study provides new insights into IP metabolism and regulation, and facilitates our development of a better understanding of the functions of IPs and how they interact with other pathways involved in plant development and stress responses. Three new genes were discovered and preliminarily validated, thereby increasing our knowledge of IP metabolism.

【 授权许可】

CC BY   
© Zhang et al. 2016