jasmonic acid biosynthesis Jasmonates (JAs) are important intracellular regulators mediating diverse developmental processes, such as seed germination, flower and fruit development, leaf abscission, and senescence |CITS[11607536]|. In addition, jasmonates induce plant defense responses against a group of pathogens |CITS [10066616]| and mechanical or herbivorous insect-driven wounding |CITS [1594598]|. In particular, methyl jasmonate (MeJA) has become a strong candidate for airborne signals that mediate interplant communication for defense responses |CITS[11607107]|.
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Jasmonates are highly significant signaling molecules which regulate biotic and abiotic stress responses and as well as developmental events in plants.

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 (Peña-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).

Gibberellic acid (GA) controls a variety of biological processes in plants, including growth and development. The bioactive gibbrellins bind to the GA receptor GID1 enabling latter to interact with DELLa (SLR1 in rice) protein. In the absence of bioactive GA, DELLA act as a repressor of transcription factors such as of PIF (Phytochrome interacting factor proteins), JAZ (which regulates Jasmonic acid mediated transcription), BZR (which regulates Brassinosteroid induced regulation of transcription). It also transactivates others such as IDD (Intermediate domain) family of proteins. In the presence of bioactive gibberrelins GID1-GA-DELLA/SLR1 complex binds to the Fbox protein GID 2 leading to ubuiquitination of DELLA resulting in proteosomal degradation of the latter.

DELLA/SLR1 in the absence of bioactive GA represses JAZ to release Jasmonic acid induced transcrption repression by JAZ

(-)-jasmonate is converted into (-)-jasmonic acid methyl ester by enzymatic activity of an unknown gene product.

WRKY42 in rice is likely to downregulate the expression of JAZ8-like and other genes involved in Jasmonic acid biosynthesis and signaling.

OsWRKY42 transcription factor shows low expression in the shoot, seed, pollen sperm cell, leaf, and vegetative cell. It is induced in response to drought, cold stress, and salinity. Its expression in leaf is down-regulated in leaf by OsNAC2 (PMID:28074873). It interacts with SAPK3 and HDR1. OsWRKY42 negatively regulates Jasmonic acid induced genes.

MAPK15 kinase expression is induced by jasmonic acid (JA) and salinity. SERF1 has a binding site in MPK15 promoter region. In comparision to wildtype plants, the serf1 mutant plants do not show induction of MPK15 in response to salt-stress. Thus, MPK15 gene expression is directly regulated by SERF1 TF (Schmidt et al., 2013)

Oryza sativa delay of the onset of senescence (OsDOS), encodes a transcription factor that is shown to play a role in repressing jasmonic acid mediated signaling pathway resulting in leaf senescence delay, likely to play a role in panicle development and pollination/fertilization process (PMID: 16778011). The expression of OsDOS was down-regulated during natural leaf senescence, panicle development, and pollination, although its transcripts were accumulated in various organs. RNAi knockdown of OsDOS caused an accelerated age-dependent leaf senescence, whereas its overexpression produced a marked delay of leaf senescence, suggesting that it acts as a negative regulator for leaf senescence (PMID: 16778011). The barley homolog HORVU.MOREX.r3.3HG0236540 is shown to be up-regulated in the roots of egt2 mutant compared to wild-type (Kirschner et al., 2021; PMID: 34446550). Thus, it is a down-regulated target of the EGT2 in roots.

RERJ1/OSBHLH6 (basic helix-loop-helix transcription activator 6) (PubMed:22456953, PubMed:33128314) is involved in control of disease resistance, regulation of salicylic acid (SA) and jasmonic acid (JA) signaling (PubMed:15541369, PubMed:22456953). Regulates shoot growth inhibition in response to jasmonate (PubMed:15541369) and is likely to play a role in the regulation of jasmonate-mediated stress-inducible gene expression (PubMed:22456953). It is upregulated in response to submergence during seed germination and coleoptile growth. Acts as positive regulator of phosphate homeostasis and phosphate signaling by antagonizing SPX4 (PubMed:33128314). it Forms homodimers (PubMed:33128314) and interacts with SPX4 (PubMed:33128314). Expressed in spikelets, leaf mesophyll cells, root tip and root epidermis cells. {ECO:0000269|PubMed:33128314}. Induced by jasmonate (PubMed:15541369, PubMed:15914931, PubMed:22456953), wounding, and drought stress in leaves (PubMed:15914931, PubMed:22456953) and induced by phosphate starvation in shoots (PubMed:33128314). Overexpression of BHLH6 promotes shoot and root phosphate accumulation, and root hair growth and acid phosphatase activity under phosphate sufficiency. {ECO:0000269|PubMed:33128314}.

a gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice.

a gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice.

OsWRKY42 transcription factor shows low expression in the shoot, seed, pollen sperm cell, leaf, and vegetative cell. It is induced in response to drought, cold stress, and salinity. Its expression in leaf is down-regulated in leaf by OsNAC2 (PMID:28074873). It interacts with SAPK3 and HDR1. OsWRKY42 negatively regulates Jasmonic acid induced genes.
WRKY42 negatively regulates Jasmonic acid induced genes

MAPK15 kinase expression is induced by jasmonic acid (JA) and salinity. SERF1 has a binding site in MPK15 promoter region. In comparision to wildtype plants, the serf1 mutant plants do not show induction of MPK15 in response to salt-stress. Thus, MPK15 gene expression is directly regulated by SERF1 TF (Schmidt et al., 2013)

Rice OSWRKY24 transcription activator is upregulated in response to submergence during seed germination and coleoptile growth. It interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element (PubMed:19199048, PubMed:26025535). Negative regulator of both gibberellic acid (GA) and abscisic acid (ABA) signaling in aleurone cells, probably by interfering with GAM1, via the specific repression of GA- and ABA-induced promoters (PubMed:15618416, PubMed:19199048, PubMed:26025535). Expressed in mostly aleurone cells and embryos within the seeds (PubMed:15618416). Also, shows low expression in leaves, roots, and panicles (PubMed:26025535). It is Induced by abscisic acid (ABA) in aleurone cells, embryos, roots and leaves (PubMed:15618416, PubMed:19199048) and down-regulated by gibberellic acid (GA) (PubMed:15618416). Accumulates in response to jasmonic acid (MeJA). Asexpected tevels of transcripts drop rapidly but transiently in the embryos of imbibed seeds.

a gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice.