Table 1.

Functional Profiling of phy-Regulated Early-Response Genes for Photomorphogenic Phenotypes

(Class) Numbers	Arabidopsis Genome Initiative Number	Protein Name Designation	Functional Category	T-DNA Line (in This Study)	Mutant Line Designation	Insertion/Transcript	Hypocotyl Length		Cotyledon Area (Rc)	Reported Function for This Locus
							FRc	Rc
(I) Aberrant photomorphogenic phenotype displayed
1	At2g46790AI	APRR9	Transcription		prr9-11	null1	None	Tall	Small	Circadian rhythms
2	At2g46970AR	PIL1	Transcription	SALK_025372	pil1-2	Null^	Tall	Tall	Small
					pil1-12	Null2	Hyposensitive in R, FR, and Low R/FR			Shade avoidance2
3	At5g11260AI	HY5	Transcription	SAIL_19_G04	hy5-101	S+26^	Tall	Tall	Small
					hy5-13,4	Null3,4	Hyposensitive in R, FR, B, WL			Transcription
4	At2g02950AI	PKS1	Signaling	SAIL_828_H11	pks1-101	−552^	Short	Short	Large
					pks15	Null5	phyA VLFR in FRp			phyA signaling5
5	At2g46340AI	SPA1	Signaling		spa1-3RLD,6,7	Null6,7	Short	Short	Large	Suppressor of phyA6,7
6	At2g37970AI	SOUL family	Unknown	SAIL_1280_E03	soul1	−35^	None	Short	Large	ND
7	At2g40080AI	ELF4	Signaling	SAIL_1244_G01	elf4-1018	Null8	None	Tall	Small	phyB signaling8
(II) Parallel, unidirectional defect in both hypocotyl and cotyledon photoresponsiveness displayed
8	At3g10910AI	RING-ZFN	Transcription	SAIL_256_C02		418^	None	Short	Small	ND
9	At3g21150AI	B-box type ZF	Transcription	SALK_059534		670^	None	Short	Small	ND
10	At5g24120AI	SIGE	Transcription	SALK_141383		383^	Short	Short	Small	ND
11	At5g37260AI	CCA1-L	Transcription	SALK_074896		1192^	Tall	Tall	Large	ND
12	At1g78820AI	Putative EP1	Signaling	SAIL_639_F10		1110^	Short	Short	Small	ND
13	At2g20750AR	β-Expansin	Growth	SAIL_345_G11		519^	None	Short	Small	Loosen cell wall
14	At1g61890AI	MATE	Unknown	SAIL_749_F06		−211^	Short	Short	Small	ND
(III) Aberrant photoresponsive phenotype in hypocotyl only displayed
15	At1g01060AI	LHY	Transcription		lhy-101	Null	Short	Short	None
					lhy-11, -12, -13le,9	LoF9	Same as wild-type in LD conditions			Circadian rhythms
16	At2g31380AI	STH (ZF3)	Transcription	SAIL_786_F08		−442^	Short	Short	None	ND
17	At3g47500ABI	Dof-type ZF	Transcription	SAIL_434_G09		651^	None	Short	None	ND
18	At4g25480AI,BI	CBF3	Transcription	SAIL_244_D02		48^	None	Short	None	Cold tolerance10
19	At2g42870AR	Expressed	Unknown	SAIL_668_E10		S+10^	Short	Short	None	ND
20	At4g14690AI	ELIP1	Unknown	SAIL_667_C04		1316^	Short	Short	None	Photoprotection11
(IV) No aberrant seedling phenotype displayed
21	At1g18330AI	EPR112	Transcription	SAIL_195_F11		602^	None	None	None	Slave oscillator12
22	At2g44910AR	ATHB413	Transcription	SALK_104843		1365^	None	None	None	Shade avoidance13
23	At2g46830AI	CCA1	Transcription		cca1-1w,14	Null14	None	None	None	Circadian rhythms14
24	At3g02380AI	COL215	Transcription	SAIL_70_F03		−258^	None	None	None	Circadian-regulated15
25	At3g21330AR	bHLH08716	Transcription	SALK_066339		487^	None	None	None	ND
26	At4g16780AR	HAT417	Transcription	SALK_106790		162^	None	None	None	Development17
27	At5g44260AR	Putative ZF	Transcription	SAIL_1277_D05		360^	None	None	None	ND
28	At1g78070AI	WD-40 protein	Signaling	SAIL_1264_G10		−4^	None	None	None	ND
29	At2g30040AI	Putative PK	Signaling	SAIL_1175_F12		981^	Short*	None	None	ND
30	At4g26850AI	VTC2	Unknown	SAIL_769_H05		620^	None	None	None	ND
31	At4g27520AI	Plastocyanin-L	Unknown	SAIL_437_B03		−206^	None	None	None	ND
32	At5g52250AI	COP1-L	Unknown	SALK_060638		298^	None	None	None	ND

List of 32 genes analyzed, including Arabidopsis Genome Initiative loci and designated protein names. The corresponding mutant lines isolated in this work (SAIL or SALK lines) and previously identified mutant lines are indicated. The predicted T-DNA insertion sites within the respective genes, relative to the start codon, are shown. In some mutant lines, the T-DNA insertion sites were upstream of the start codon (−) or downstream of the stop codon (S+). Based on the statistical significance (see Supplemental Figures 3 and 4 online) of differences observed in hypocotyl length and cotyledon area between wild-type and mutant seedlings grown in Rc light, genes were grouped into four classes, as indicated. Functions previously reported for some of the genes are listed. One of the lines (line 29) displays a short-hypocotyl phenotype only in FRc light (asterisk). ^, transcript not detected in the mutant (see Supplemental Figures 2 and 5 online). AI, phyA early-induced genes; AR, phyA early-repressed genes; BI, phyB early-induced gene; ABI, phyA/B early-induced gene; R, red light; FR, far-red light; B, blue light; WL, white light; FRp, far-red pulse; VLFR, very-low-fluence response; LD, long day (16-h-light/8-h-dark cycles); Lof, loss of function; ND, not determined; le, Landsberg erecta (wild type); rld, RLD (wild type); w, Wassilewskija (wild type). References are designated as follows: 1, Eriksson et al. (2003); 2, Salter et al. (2003); 3, Koornneef et al. (1980); 4, Ang et al. (1998); 5, Lariguet et al. (2003); 6, Hoecker et al. (1998); 7, Hoecker et al. (1999); 8, Khanna et al. (2003); 9, Mizoguchi et al. (2002); 10, Gong et al. (2002); 11, Hutin et al. (2003); 12, Kuno et al. (2003); 13, Carabelli et al. (1993); 14, Green and Tobin (1999); 15, Ledger et al. (2001); 16, Bailey et al. (2003); 17, Schena et al. (1993).