Table 1. List of differentially expressed transcription factors with a putative function in the development of CR primordia.

CR: Crown root, CK: Cytokinin, GA: Gibberellin, IAA: Auxin, QC: Quiescent center.

					FC
Regulation	TF family	Gene	RAP-DB id	MSU id	Early	Intermediate	Late	Coexpression cluster	Description	References
Upregulated	AP2	OsPLT5	Os01g0899800	LOC_Os01g67380	2.06	2.19		midnightblue	CR formation and development, maintainance of stem cell activity around QC / activation by IAA, repression by CK	[29]
		OsPLT3	Os02g0614000	LOC_Os02g37070	7.76	7.53	3.98	midnightblue
		OsPLT4	Os04g0474200	LOC_Os04g39570		2.31		skyblue
		OsPLT1	Os04g0653300	LOC_Os04g55970	2.74	2.9	3.08	skyblue
		OsPLT6	Os11g0295900	LOC_Os11g19060	2.75	2.96		skyblue	maintainance of stem cell activity around QC / activation by IAA, repression by CK	[29]
	C3H	C3H13	Os02g0161200	LOC_Os02g06584	2.58		2.01	skyblue	coding for BRI1-interacting protein; bri1 mutant has a mild root phenotype	[30]
	ERF	ERF61	Os05g0331700	LOC_Os05g29810	5.8	4.78		skyblue	in cucumber, ortholog is strongly expressed in melatonin-induced lateral root formation	[31]
	GRAS	OsSCR1	Os11g0124000	LOC_Os11g03110	3.32			midnightblue	OsSCR1 is specifically expressed in the CR endodermis, whereas OsSHR1 is expressed in the stele. OsSCR1 and OsSHR1 interact with each other when produced in yeast, similar to SCR and SHR in Arabidopsis. Experimental evidence suggest that OsSCR1 and OsSHR1 control the division of the epidermis-endodermis initial cells in rice.	[32]
		OsSHR1	Os07g0586900	LOC_Os07g36820	2.44			midnightblue
	LSD	OsLOL2/OsLSD5	Os01g0612700	LOC_Os01g39710	4.94	5.34	5.14	skyblue	involved in regulation of GA synthesis	[33]
Downregulated	ARF	OsARF5	Os02g0138100	LOC_Os02g04510	-1.86	-2.52	-3.18	yellow	ARF5 is downregulated in the crl6 mutant / ARF5 in Arabidopsis controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes	[34, 35]
		OsARF24	Os12g0446370	LOC_Os12g29520			-1.55	orange	dimerizes with OsARF23 to promote RMD expression, triggering changes in F-actin organization required for auxin-mediated cell growth	[36]
	ERF	ERF99/OsEREBP2	Os01g0868000	LOC_Os01g64460		-2.2	-2.14	yellow	implied in the integration of mechanical signals for root curling through interaction with OsHOS1	[37]
		ERF79	Os02g0594000	LOC_Os02g34790		-2	-1.74	yellow	member of the class VIIIb of AP2/ERF family, ortholog of Arabidopsis DRN, expressed in center of meristems / PUCHI, DRN, and DRNL interdependently contribute to cellular fate decisions	[38, 39]
		ERF120	Os06g0222370	LOC_Os06g11860	-1.91	-2.11	-2.09	yellow	direct target of OsNAC genes described to alter root architecture	[40]
		CRL5	Os07g0124400	LOC_Os07g02947	-1.88	-2.1	-2.12	yellow	auxin‐induced CRL5 promotes crown root initiation through repression of cytokinin signaling by positively regulating OsRR1	[41]
	LBD	OsLBD3-6	Os03g0659700	LOC_Os03g42747	-1.96	-2.28	-3.41	yellow	downregulated in osiaa13 mutant / similar to Arabidopsis ASL18/LBD16, ASL16/LBD29, ASL20/LBD18 and rice CRL1/ARL1	[16, 42]
	MYB	OsMYBS60	Os12g0124700	LOC_Os12g03147	-2.97	-3.29	-3.66	blue	associated with 37–60 cm depth dry weight trait / plays a dual role in abiotic stress responses in Arabidopsis through its involvement in stomatal regulation and root growth	[43, 44]
	TCP	OsTCP7	Os02g0632800	LOC_Os02g39347	-5.9	-13.86	-20.34	yellow	AtTCP7 in Arabidopsis / in Arabidopsis, overexpression leads to shorter roots; likely to play a role in cell proliferation by restricting G1/S phase transition	[45, 46]
	WRKY	OsWRKY108	Os01g0821300	LOC_Os01g60600		-2.25	-1.93	orange	downregulated in OsRR6-ox line, a negative regulator of CK signaling, which showed poorly developed root systems	[47]

(References cited in table reported here for purpose of reference list generation: Li and Xue 2011 [29], Nakamura 2006 [30], Zhang [31], Kitomi 2018 [32], Xu and He 2007 [33], Xu 2017 [34], Krogan 2016 [35], Li 2014 [36], Lourenço 2015 [37], Chandler 2018 [38], Chandler and Werr [39], Chung et al [40], Kitomi 2011 [41], Kitomi 2012 [42], Takehisa 2012 [16], Phung et al [43], Oh et al [44], Yao 2007 [45], Wang 2014 [46], Hirose 2007 [47]).