Table 1.

Numbers of differentially expressed genes (DEG) in Meloidogyne graminicola-infected and control root tips in susceptible rice (Oryza sativa ‘Nipponbare’; Nip) and resistant rice (Oryza glaberrima TOG5681; Tog)

Category	Expressed genes	Rice species	Induced genes				Repressed genes				Total DEGs
			2 dpi	4 dpi	8 dpi	Total	2 dpi	4 dpi	8 dpi	Total
All MSU7 genes	29 984	Nip	362 (1·2 %)	1972 (6·6 %)	2823 (9·4 %)	3494 (11·6 %)	46 (0·2 %)	937 (3·1 %)	1221 (4·1 %)	1503 (5·0 %)	4997 (16·7 %)
		Tog	1228 (4·1 %)	2641 (8·8 %)	2801 (9·3 %)	3584 (11·9 %)	49 (0·2 %)	347 (1·2 %)	339 (1·1 %)	548 (1·8 %)	4132 (13·8 %)
		Common	199	982	1331	1828	1	162	160	270
Signalling	16	Nip	0	1	0	1	0	0	0	0	1
		Tog	0	0	0	0	0	0	0	0	0
SA	14	Nip	1	2	2	3	0	0	0	0	3
		Tog	4	4	2	4	0	0	0	0	4
Lignin	21	Nip	0	2	2	2	0	1	1	1	3
		Tog	3	2	2	4	0	0	0	0	4
Flavonoids and terpenoids	64	Nip	3	12	7	16	0	8	8	11	27
		Tog	9	11	12	18	4	4	10	12	30
JA	26	Nip	1	4	4	7	0	0	0	0	7
		Tog	3	5	4	5	0	0	0	0	5
Ethylene	19	Nip	0	2	2	3	0	2	3	3	6
		Tog	0	2	3	3	0	0	0	0	3
Callose	4	Nip	0	0	0	0	0	0	0	0	0
		Tog	0	0	0	0	0	0	0	0	0
PR proteins	4	Nip	1	2	1	2	0	0	0	0	2
		Tog	4	4	3	4	0	0	0	0	4
PR13: thionins	25	Nip	1	3	5	5	2	11	8	11	16
		Tog	0	1	0	1	0	6	8	9	10
QTL	323	Nip	2	28	44	49	1	15	17	24	73
		Tog	14	34	39	45	1	6	3	7	52
Resistance	359	Nip	2	26	35	43	1	11	11	12	55
		Tog	16	47	45	56	2	3	2	4	60
Candidate genes	875	Nip	11 (1·1 %)	82 (8·6 %)	102 (10·6 %)	131 (13·7 %)	4 (0·4 %)	48 (5 %)	48 (5 %)	62 (6·5 %)	193 (22·1 %)
		Tog	53 (5·5 %)	110 (11·5 %)	110 (11·5 %)	140 (14·6 %)	7 (0·7 %)	19 (2·0 %)	23 (2·4 %)	32 (3·3 %)	172 (19·7 %)