A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants

BMC Bioinformatics

Table 3 ABP minimal cut sets (MCSs) with corresponding ABP gene(s) and reactions.

MCS	N-3-D-RXN	LEUCPEL-RXN	D-4-R-RXN	RXN-525	APIGNAR-RXN	RXN-600	RXN-602	RXN-7652	PELUDP-RXN	RXN1F-775	RXN-7775	N-C-S-RXN	Total rxns	Unaffected	Genes/enz in MCS
1	0	0	0	0	1	0	0	0	0	0	0	0	1	3	CHI
2	0	0	0	0	0	0	0	0	0	0	0	1	1	3	CHS
3	1	0	0	0	0	1	0	0	0	0	0	0	2	57	F3H, DFR(cy)
4	1	0	0	0	0	0	0	1	0	0	0	0	2	9	F3H, F3'H(i)
5	0	1	0	0	0	1	0	0	0	0	0	0	2	126	ANS(pg), DFR(cy)
6	0	0	1	0	0	1	0	0	0	0	0	0	2	123	DFR(pg), DFR(cy)
7	1	0	0	0	0	0	1	0	0	0	0	0	2	60	F3H, ANS(cy)
8	0	1	0	0	0	0	1	0	0	0	0	0	2	132	ANS(pg), ANS(cy)
9	0	0	1	0	0	0	1	0	0	0	0	0	2	129	DFR(pg), ANS(cy)
10	0	0	0	0	0	1	0	0	1	0	0	0	2	129	DFR(cy), 3-UGT(pg)
11	0	0	0	0	0	0	1	0	1	0	0	0	2	135	ANS(cy), 3-UGT(pg)
12	1	0	0	0	0	0	0	0	0	1	0	0	2	63	F3H, 3-UGT(cy)
13	0	1	0	0	0	0	0	0	0	1	0	0	2	138	ANS(pg), 3-UGT(cy)
14	0	0	1	0	0	0	0	0	0	1	0	0	2	135	DFR(pg), 3-UGT(cy)
15	0	0	0	0	0	0	0	0	1	1	0	0	2	141	3-UGT(pg), 3-UGT(cy)
16	1	0	0	0	0	0	0	0	0	0	1	0	2	18	F3H, F3H(cy)
17	0	1	0	1	0	0	0	1	0	0	0	0	3	39	ANS, F3'H, F3'H
18	0	0	1	1	0	0	0	1	0	0	0	0	3	36	DFR, F3'H, F3'H
19	0	0	0	1	0	0	0	1	1	0	0	0	3	42	F3'H, F3'H, 3-UGT(pg)
20	0	1	0	1	0	0	0	0	0	0	1	0	3	48	ANS, F3'H, F3H(cy)
21	0	0	1	1	0	0	0	0	0	0	1	0	3	45	DFR, F3'H, F3H(cy)
22	0	0	0	1	0	0	0	0	1	0	1	0	3	51	F3'H(ii), 3-UGT(pg), F3H(cy)
fc	0.50	0.43	0.43	0.33	1	0.50	0.50	0.38	0.43	0.50	0.38	1
Enzymes	1	2	3	4	5	6	7	8	9	10	11	12

Table 3 shows the set of MCSs or ABP gene candidates for genetic changes needed to eliminate anthocyanin production. Some reactions in the top row have been abbreviated and the numbers in the bottom row represent enzymes corresponding to the reactions in the top row; the details are as follows:
Reactions (top row):
N-3-D-RXN: NARINGENIN-3-DIOXYGENASE-RXN
D-4-R-RXN: DIHYDROKAEMPFEROL-4-REDUCTASE-RXN
N-C-S-RXN: NARINGENIN-CHALCONE-SYNTHASE-RXN
Unaffected: Non-affected flav EMs
Enzymes (bottom row):
1: F3H; 2: ANS/LDOX (pg); 3: DFR(pg); 4: F3'H(ii); 5: CHI; 6: DFR(cy); 7: ANS/LDOX (cy); 8: F3'H(i); 9: 3-UGT/UDPG (pg); 10: 3-UGT/UDPG (cy); 11: F3H(cy); 12: CHS
The reactions directly forming the anthocyanin compounds (PELUDP-RXN and RXN1F-775) are identified as the objective functions for which the MCSs are determined. In the last column, parallel enzymes are listed by a single representative: ANS & LDOX corresponding to LEUCPEL-RXN as ANS(pg), ANS & LDOX corresponding to RXN-602 as ANS(cy); 3-UGT & UDPG corresponding to PELUDP-RXN as 3-UGT(pg) and 3UGT & UDPG corresponding to RXN1F-775 as 3-UGT(cy). fc - fragility coefficient. (Refer to Figure 3 legend or List of abbreviations used, for explanation of the abbreviated enzymes.)

ISSN: 1471-2105