Table 8. Number of alkalinity-responsive probesets classified in each putative functional annotation, for each ecotype×organ combination.

Ecotype	Organ	Regulation	Amino acid metabolism	Biodegradation of Xenobiotics	Cell organisation	Cell wall	Development	DNA synthesis	Fermentation	Gluconeogenesis	Glycolysis	Hormone metabolism	Lipid metabolism	Major CHO degradation metabolism	Metal handling	Minor CHO metabolism	Miscelany	N-metabolism	Protein metabolism	Redox proteins	Secondary metabolism	Signalling	Stress	TCA	Transcription factors	Transporters	Unknown genes	Total 1	Total 2	Up/down-regulated genes
Gifu	Leaf	Down	0	1	0	1	0	0	1	0	0	1	0	0	3	0	2	0	0	0	0	1	0	0	1	0	6	17	93	4,5
		Up	0	0	2	0	0	0	0	0	0	1	0	1	2	0	1	0	8	1	1	3	2	0	12	16	26	76
	Root	Down	3	0	1	5	4	4	0	0	0	6	5	2	0	1	20	0	7	2	6	4	7	0	14	12	38	141	382	1,7
		Up	2	0	2	4	4	1	1	0	1	12	4	1	4	3	34	0	24	1	23	17	15	1	21	8	58	241
MG20	Leaf	Down	1	0	1	1	0	0	0	0	0	1	0	0	0	0	2	0	0	0	0	2	0	0	2	0	5	15	93	5,2
		Up	2	0	3	3	0	0	0	0	0	6	3	0	1	1	9	0	7	1	2	2	2	1	9	10	16	78
	Root	Down	2	0	0	0	8	1	2	0	0	0	1	2	1	2	11	2	9	2	2	4	5	0	13	5	37	109	301	1,8
		Up	5	0	1	1	4	1	0	1	3	0	3	0	1	0	34	1	13	1	15	8	4	2	16	21	57	192
Total			15	1	10	15	20	7	4	1	4	27	16	6	12	7	113	3	68	8	49	41	35	4	88	72	243	869	869

Probesets with a mean absolute expression ratio of at least 1.5 (linear scale) and a P-value of P<0.05 in a t-test for significance were classified into the categories shown. Those probesets for which no annotation could be inferred were regarded as unknown.