Transcriptiome Analysis for Identifying Possible Gene Regulations at the Initial Growth Stage of Maize

The root plays an important role during plant development and growth, i.e., water absorption, plant body maintenance, and nutrient storage. In this study, we attempted to determine root-specific genes at the initial developmental stages of maize by using network-based transcriptome analysis. RNA-seq was performed using maize shoots and roots at different developmental stages of root emergence (6 – 10 days after planting, VE) and one week after plant emergence (V2). A total of 1,286 differentially expressed genes (DEGs) were detected in both tissues. Many DEGs involved in metabolic pathways exhibited altered mRNA levels between VE and V2. In addition, we observed gene expression changes for 113 transcription factors and found five enriched cis-regulatory elements in the 1-kb upstream regions of both DEGs. The network-based transcriptome analysis showed two modules as co-expressed gene clusters differentially expressed between the shoots and roots during plant development. The DEGs of one module exhibited gene expressional coherence in the maize root tips, suggesting that their functional relationships are associated with the initial developmental stage of the maize root. Finally, we confirmed reliable mRNA levels of the hub genes in the potential sub-network related to initial root development at the different developmental stages of VE, V2, and two weeks after plant emergence (V3).

Acknowledgments:This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (grant no. NRF-2015R1D1A4A01015702) as well as a grant from the Golden Seed Project, Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development of Korea (RDA), and the Korea Forest Service (KFS) (project no. 213001-04-4-SB920).