During the early stages of seedling development, besides the genetic developmental program, the gravity and light signals guide the seedling establishment and determine the plant architecture (Yoshihara and Iino, 2007; Li et al., 2007, Li et al., 2019). The cultivated rice and its wild relatives have a varying degree of in-built tolerance to submergence (flooding) and anaerobic germination that allows germination of direct seeded rice and coleoptile elongation under flooded conditions (Fukao and Bailey-Serres 2008; Septiningsih et al. 2009; Alam et al. 2020). Thus, an interplay involving four distinct biological processes, namely seed germination, submergence response, gravitropism, and phototropism, leads to the development of a plant's upper ground organs (i.e., stem, leaves) and underground roots. To elucidate this TF network, we re-analyzed the differentially expressed genes (DEG) from Hsu et al. (2017) and identified 57 TFs that showed a positive correlation in their expression. In the second step, we analyzed the promoter region of these 57 TFs coding genes to score potential TF-target relationships. Finally, we constructed a TF network based on the two lines of evidence (co-expression and the presence of TF binding site(s) in the target gene's promoter). Based on literature reviews, we synthesized gene, reaction, and pathway summaries and added additional genes in this network. In this TFs-network, rice homeobox genes OSH1, OSH15, OSH71 are known to express before organ differentiation during early embryogenesis and are important for the shoot apical meristem development (Sato et al., 1996; Tsuda et al., 2011); Sub1A, Sub1B, ERFs, and WRKYs transcription factors involved in submergence tolerance (Peņa-Castro et al., 2011; Alam et al., 2020; Septiningsih et al. 2009; Jung et al., 2010; Lin et al., 2019); and transcription factors of Myb, NAC, and ZFP families and RERJ1 etc. involved in the cell, tissue and organ development, hormone signaling, and abiotic stress tolerance (Kiribuchi et al., 2004; Seo et al., 2011; Dai et al., 2012; El-Kereamy et al., 2012; Yang et al., 2012; Miyamoto et al., 2013; Xiong et al., 2014; Chowrasia et al., 2018; He et al., 2021). It is noteworthy that transcription of LAZY1, an important gene involved in shoot gravitropism (Li et al., 2007; Yoshhara and Iino, 2007), is regulated by OSH1, OSNAC1, NAC77, ZFP36, OSTCP18, OSPCF8, OSERF25, OSERF29 and OSERF32 during seed germination and coleoptile development. LAZY1 does not have any binding site in the promoter region of any TFs in this network. Furthermore, rice LAZY1 has two subcellular locations, the plasma membrane and nucleus. LAZY1 interacts with BRXL4 (or BRXL1) in the plasma membrane and forms a complex that is required for subsequent nuclear localization of the LAZY1 (Li et al., 2019). LAZY1 acts as a TF in the nucleus and regulates the expression of genes involved in shoot gravitropism and tiller angle determination through negative regulation of basipetal polar auxin transport and positive regulator of lateral auxin transport (Li et al., 2007). Unlike rice LAZY1, nuclear localization of its Arabidopsis ortholog AtLAZY1 is not essential for its function (Li et al., 2019). In addition, we find TFs linked to important agronomic traits in this network, for example, OsMPH1 involved in regulating plant height and yield improvement (Zhang et al., 2017).
