Table I.

Validation of array results by qPCR and marker distribution

Typea	Locus	Description	Log Ratio Arrayb	Log Ratio qPCRbc
MV1	At1g19320	Thaumatin family protein	3.11	3.78
MV2	At1g65300	MADS box transcription factor (PHE2/AGL38)	2.97	3.3
MV3	At3g23060	Zinc finger (C3HC4-type RING finger) family	2.91	1.7
MV4	At5g27000	Kinesin-like protein (ATK4)	2.78	3.91
M1	At1g65330	MADS box transcription factor (PHE1/AGL37)	2.45	ND
MV5	At2g32460	R2R3 MYB transcription factor (MYB101)	2.45	3.98
M2	At4g25530	Homeodomain-containing transcription factor (FWA)	2.43	3.16
MV6	At2g32370	Homeodomain-containing transcription factor	2.37	2.59
M3	At3g24220	9-cis-Epoxycarotenoid dioxygenase (NCED6)	2.24	ND
M4	At1g71890	Suc-proton symporter (SUC5)	2.17	ND
MV7	At1g09500	Alcohol dehydrogenase	1.89	2.69
MV8	At3g05310	GTP and calcium ion-binding protein	1.88	2.35
M5	At2g35670	C2H2 transcription factor (FIS2)	1.83	ND
MV9	At3g54560	Histone H2a protein (HTA11)	1.76	2.73
M6	At1g02580	Polycomb family protein (MEA)	1.74	1.68
MV10	At1g69770	Chromomethylase family protein (CMT3)	1.55	2.86
MV11	At3g11400	G-subunit of eukaryotic initiation factor (EIF3)	1.16	1.48
MV12	At1g17130	Cell cycle control protein-related	1.13	2.95
MV13	At3g55010	Cycloligase (PUR5)	1.12	1.2
M7	At3g19160	Cytokinin synthase (IPT8)	1.12	ND
MV14	At4g28840	Unknown protein	1.06	2.11
MV15	At3g61300	C2 domain-containing protein	1.05	0.74
MV16	At5g65710	ATP-binding kinase (HSL2)	0.86	0.33

^aMV1 to MV16 are genes that gave a range of differential expression in the array data, and M1 to M7 are endosperm marker genes identified from the literature.

^bLog ratio array and log ratio qPCR correspond to log₂ values for the ratio of expression between whole silique and LCM endosperm samples.

^cRelative expression by qRT-PCR was calculated by comparison with the ACTIN2 (At3g18780) reference gene. ND, Not determined.