Table I. Genes investigated in this study with known or putative involvement in sugar signaling and Suc-to-starch conversion.

Protein Name	Genea	Barley1 Probe Set	DEb	Organc	Foldd	Reference
ADP-glucose pyrophosphorylase large subunit	HvAPL1	Contig5267_at	No	U	1.37	Villand et al. (1992)
ADP-glucose pyrophosphorylase large subunit	HvAPL2	Contig3390_at	(1)	U	1.83	Eimert et al. (1997)
ADP-glucose pyrophosphorylase small subunit	HvAPS1a/b	Contig2267_s_at	No	U	1.35	Thorbjornsen et al. (1996)
ADP-glucose pyrophosphorylase small subunit	HvAPS2	No probe set		U		Johnson et al. (2003)
ADP-glucose transporter	HvNST1	Contig7529_at	(6)	U	2.39	Patron et al. (2004)
α-Amylase 1	HvAMY1	Contig7088_at	n.d.	U		Radchuk et al. (2009)
α-Amylase 2	HvAMY2	Contig3952_at	n.d	n.d.		Radchuk et al. (2009)
α-Amylase 3	HvAMY3	Contig3953_s_at	No	n.d.	1.12	Radchuk et al. (2009)
α-Amylase 4	HvAMY4	EBma03_SQ002_M07_at	No	P	1.35	Radchuk et al. (2009)
α-Glucan phosphorylase	HvPHO1	No probe set		U		Radchuk et al. (2009)
α-Glucan phosphorylase, cytosolic	HvPHO2	Contig6517_at		U	0.50	Radchuk et al. (2009)
β-Amylase 1	HvBAM1	Contig1406_at	No	U	1.41	Radchuk et al. (2009)
β-Amylase 2	HvBAM2	Contig1411_s_at	No	U	1.34	Radchuk et al. (2009)
β-Amylase 3	HvBAM3	Contig8246_at	n.d.	U		Radchuk et al. (2009)
β-Amylase 4	HvBAM4	No probe set		U		Radchuk et al. (2009)
β-Amylase 5	HvBAM5	Contig11522_at	(1)	U	5.21	Radchuk et al. (2009)
β-Amylase 6	HvBAM6	No probe set		U		Radchuk et al. (2009)
β-Amylase 7	HvBAM7	No probe set		U		Radchuk et al. (2009)
β-Amylase 8	HvBAM8	Contig10917_at	No	U	1.38	Edner et al. (2007)
Cell wall invertase 1	HvCWINV1	Contig11241_at	(3)	U	2.28	Weschke et al. (2003)
Cell wall invertase 2	HvCWINV2	Contig6787_at	No	U	1.48	Weschke et al. (2003)
Disproportionating enzyme 1	HvDPE1	Contig26451_at	No	U	1.49	Radchuk et al. (2009)
Disproportionating enzyme 2	HvDPE2	Contig6654_at	No	U	1.48	Radchuk et al. (2009)
Ferredoxin-NADP reductase, putative	FNR1-like	baak21d06_s_at	(4)	U	1.96	Balmer et al. (2006)
Ferredoxin-thioredoxin reductase, putative	FTR-like	Contig14916_at	No	P	1.16	Balmer et al. (2006)
Fructan 1-exohydrolase	Hv1-FEH	Contig7811_s_at	(3)	U	2.21	Nagaraj et al. (2004)
Glucan, water dikinase 1	HvGWD1	Contig18313_at	(4)	U	2.08	Edner et al. (2007)
Glucan, water dikinase 2	HvGWD2	Contig14761_at	n.d.	U		Edner et al. (2007)
Granule-bound starch synthase 1a	HvGBSS1a	Contig694_at	No	U	1.32	Patron et al. (2002)
Granule-bound starch synthase 1b	HvGBSS1b	Contig12208_at	(4)	U	1.80	Patron et al. (2002)
Hexokinase 1	HvHXK1	Contig12296_at	(2)	P	1.72	E. Mangelsen (unpublished data)
Hexokinase 2	HvHXK2	Contig17401_at	No	P	1.42	E. Mangelsen (unpublished data)
Hexokinase 3	HvHXK3	Contig14657_at	No	U	1.38	E. Mangelsen (unpublished data)
Hexokinase 5	HvHXK5	Contig4153_at	No	U	1.20	E. Mangelsen (unpublished data)
Isoamylase 1	HvISA1	Contig7560_at	No	P	1.11	Sun et al. (1999)
Isoamylase 2	HvISA2	Contig13547_at	No	E	1.24	Radchuk et al. (2009)
Isoamylase 3	HvISA3	Contig14990_at	(6)	U	1.38	Radchuk et al. (2009)
Limit dextrinase (pullulanase)	HvLD	Contig11648_at	(3)	U	1.86	Burton et al. (1999)
NADPH-dependent thioredoxin reductase 2	HvNTR2	HB22M22r_s_at	No	U	1.50	Shahpiri et al. (2008)
Phosphoglucan, water dikinase	HvPWD	No probe set		U		Kotting et al. (2005)
Plant glycogenin-like starch initiation protein 1	HvPGSIP1	rbags11k20_s_at	No	U	1.28	Chatterjee et al. (2004)
Plant glycogenin-like starch initiation protein 2	HvPGSIP2	Contig3977_at	(3)	U	4.01	Chatterjee et al. (2004)
SNF1-related protein kinase a	HvSnRK1a	Contig3529_at	No	E	1.33	Hannappel et al. (1995)
SNF1-related protein kinase b	HvSnRK1b	HVSMEc0011O22r2_at	No	U	1.54	Hannappel et al. (1995)
Starch-branching enzyme I	HvSBEI	No probe set		U		Sun et al. (1997)
Starch-branching enzyme IIa	HvSBEIIa	Contig3761_at	No	U	1.42	Sun et al. (1998)
Starch-branching enzyme IIb	HvSBEIIb	Contig3762_s_at	(5)	E		Sun et al. (1998)
Starch synthase I	HvSSI	Contig1808_at	No	U	1.59	Li et al. (2003)
Starch synthase IIa	HvSSIIa	Contig20469_at	No	U	1.85	Li et al. (2003)
Starch synthase IIb	HvSSIIb	No probe set		U		Radchuk et al. (2009)
Starch synthase IIIa	HvSSIIIa	No probe set		U		Radchuk et al. (2009)
Starch synthase IIIb	HvSSIIIb	Contig10722_at	(6)	U	2.96	Radchuk et al. (2009)
Starch synthase IV	HvSSIV	Contig13138_at	No	U	1.26	Radchuk et al. (2009)
Sucrose synthase 1	HvSuSy1	Contig361_s_at	No	U	2.05	Guerin and Carbonero (1997)
Sucrose synthase 2	HvSuSy2	Contig823_at	No	U	1.40	Guerin and Carbonero (1997)
Sucrose transporter 1	HvSUT1	Contig4612_at	No	U	1.44	Weschke et al. (2000)
Sucrose transporter 2	HvSUT2	rbah43d09_s_at	(3)	U	1.66	Weschke et al. (2000)
Sucrose:fructan-6-fructosyltransferase	Hv6-SFT	Contig3392_at	(4)	U	2.64	Nagaraj et al. (2004)
Sucrose:sucrose-1-fructosyltransferase	Hv1-SST	Contig4521_s_at	No	U	1.41	Nagaraj et al. (2004)
Sugar transporter 1	HvSTP1	Contig3479_at	(5)	U	1.91	Weschke et al. (2003)
Sugar transporter 2	HvSTP2	No probe set		U		Weschke et al. (2003)
Sugar transporter 3	HvSTP3	Contig6135_s_at	No	U	1.26	Weschke et al. (2003)
Thioredoxin f	Trx f-like	Contig4022_at	(6)	U	4.06
Thioredoxin h1	HvTrx h1	Contig171_at	No	P	1.38	Maeda et al. (2003)
Thioredoxin h2	HvTrx h2	Contig2980_s_at	No	P	1.09	Maeda et al. (2003)
Thioredoxin h, putative	Trx h-like	HV06G09u_s_at	(6)	P	1.63	Maeda et al. (2003)
Thioredoxin m, putative	Trx m-like	Contig26351_at	(3)	E	2.09	Balmer et al. (2006)
Thioredoxin-like 1	Trx-like 1	Contig5236_at	(6)	U	2.15	Balmer et al. (2006)
Trehalose-6-phosphate phosphatase, putative	TPP-like	HS16E24u_s_at	(3)	U	2.81	Ramon et al. (2009)
Trehalose-6-phosphate synthase, putative	TPS-like	Contig3373_s_at	(6)	U	2.14	Ramon et al. (2009)
WRKY transcription factor 34	HvWRKY34	Contig10471_at	No	U	1.61	Mangelsen et al. (2008)
WRKY transcription factor 41	HvWRKY41	Contig12033_at	(3)	U	1.78	Mangelsen et al. (2008)
WRKY transcription factor SUSIBA2	HvWRKY46	Contig7243_at	No	U	1.10	Sun et al. (2003)

^aPreviously annotated barley genes carry the prefix “Hv”; gene annotations based on best BLAST matches in Arabidopsis or rice (Oryza sativa) carry the suffix “-like.”

^bDE according to the calculation of 2,091 DE probe sets. Number of the set is given in parentheses. n.d., No signal detected.

^cPresence of transcript according to Sreenivasulu et al. (2008). E, Endosperm; n.d., no signal detected; P, pericarp; U, unspecific.

^dAmplitude of the diurnal fluctuation of gene expression given as the ratio of the median normalized maximum signal intensity to the median normalized minimum signal intensity.