Biochemical and Metabolomics on Rice Cultivars

doi:10.1016/j.rsci.2018.08.007

Abstract

Abstract:

Plant metabolites are important for both plant life and human nutrition. However, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the different rice metabolome and isozymes which are highly versatile and non-destructive as bio-markers. Five isozymes peroxidase, catalase, malate dehydrogenase, alcohol dehydrogenase (ADH), polyphenol oxidase were studied to characterize the thirty rice cultivars and two hybrids KRH-2 and KRH-4 along with their parental lines. Among the zymograms, ADH was found to be useful for the detection of cultivars, like CTH1, IR64, IR30864, with an R_m value of 0.549. The metabolomics of rice cultivars by using gas chromatography coupled with mass spectrometry instrument with selected reaction monitoring mode software identified the 66 metabolites in the rice samples, including amino, organic, fatty acids, alcohols and sugars (mono-/dis-accharides). All metabolites investigated varied significantly among rice samples. Jaya had the higher number of metabolites (15) with a peak for each metabolite, followed by Jyothi (13). This study demonstrated a powerful tool and provided a high-quality data for understanding the plant metabolome and isozymes, which may help bridge the gap between the genome and phenome.

Key words: gas chromatography, mass spectrometry, isozyme, spectroscopy, metabolomics, rice

Puttaswamaiah Ranjitha Hurugalavadi, Gowda Rame, Nethra Nagarajappa, Amruta Narayanappa, Kumar Kandikattu Hemanth. Biochemical and Metabolomics on Rice Cultivars[J]. Rice Science, 2019, 26(3): 189-194.

Figures/Tables 4

References 23

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CN	Compound Name	Quantification peak				Confirming peak
CN	Compound Name	RT(min)	Precursor	Product	CE	Precursor	Product	CE
1	l-Alanine, N-(trimethylsilyl)-, trimethylsilyl ester	6.37	99	69	30	99	71	10
2	Glycine, N-(trimethylsilyl)-, trimethylsilyl ester	5.69	100.1	59.1	10	174.1	59.1	20
3	Phosphoric acid, bis(trimethylsilyl)monomethyl ester	6.92	78.1	64	12	78.1	71.3	12
4	L-Valine, N-(trimethylsilyl)-, trimethylsilyl ester	7.44	148.8	450	30	148.8	75	10
5	2-(4-Methoxyphenyl)-2-(4-trimethoxysilyloxy)propane	8.73	11.4	45.6	18	118.4	75.2	8
6	Butane, 2,3-bis(trimethylsiloxy)-	10.06	116.1	43	28	116.1	45.1	18
7	1,2-Bis(trimethylsiloxy)ethane	10.48	102.1	45.1	20	102.1	58	30
8	Silanamine, N,N'-methanetetraylbis[1,1,1-trimethyl-	11.55	133	115	10	163.1	133.1	10
9	Ethylbis(trimethylsilyl)amine	12.32	144.1	43	32	144.1	58.1	32
10	N,N'-Bis(trimethylsilyl)trifluoroacetamidine	13.36	299.1	151.1	10	300.5	74.1	10
11	Glycerol, tris(trimethylsilyl) ether	13.43	116.9	59.1	10	116.9	89.1	10
12	Butanedioic acid, bis(trimethylsilyl) ester	14.14	74.8	47	10	148.5	45.2	30
13	N,O,O-Tris(trimethylsilyl)-L-threonine	14.94	205.5	205.3	10	218.2	45	30
14	Serine, N,O-bis(trimethylsilyl)-, trimethylsilyl ester	15.37	100.6	86.1	10	117.1	43	30
15	Threitol, 1,2,3,4-tetrakis-O-(trimethylsilyl)-, D-	16.57	229.1	47	32	229.1	131.1	12
16	Amine, N,N,N-tris((trimethylsilyloxy)ethyl)-	17.04	189.7	147.1	10	233.1	73.1	10
17	Decanoic acid, trimethylsilyl ester	17.23	100	59.1	10	115	59.1	20
18	Butanedioic acid, [(trimethylsilyl)oxy]-, bis (trimethylsilyl) ester	17.35	205.3	117.1	8	205.3	147.1	8
19	3-Trifluoromethylbenzylamine, N,N-dinonyl	17.53	232.1	100.1	8	232.1	188.2	8
20	Arabinofuranose, 1,2,3,5-tetrakis-O-(trimethylsilyl)-	17.73	171.1	73.1	22	314.1	73.1	22
21	Myo-Inositol, 1,2,3,4,5,6-hexakis-O-(trimethylsilyl)-	19.12	128.1	73.1	10	246.1	73.1	20
22	Oleic acid, trimethylsilyl ester	19.24	232.2	73.1	22	262.3	82.1	12
23	Myristic acid, 2,3-bis(trimethylsiloxy)propyl ester	19.94	231.1	116.1	8	231.1	132.2	8
24	D-(+)-Trehalose, octakis(trimethylsilyl) ether	20.84	204.8	117.1	10	204.8	147.2	10
25	D-Turanose, heptakis(trimethylsilyl)- Isomer 1	21.59	299.2	147.2	20	299.2	225.2	10
26	α-D-Galactopyranoside, methyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	21.81	155.1	45	28	156	45.1	28
27	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)- isomer 1	22.41	437.4	191.2	10	437.4	257.2	10
28	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)- isomer 2	22.69	273.1	67.1	10	273.1	183.2	10
29	Silane, [[(3β,24R)-ergost-5-en-3-yl]oxy]trimethyl-	23.3	285.2	95.2	12	285.2	131.1	12
30	β-Sitosterol trimethylsilyl ether	22.86	518.5	188.3	12	518.5	428.3	12
31	D-Glucose, 4-O-[2,3,4,6-tetrakis-O-(trimethylsilyl) -β-D-galactopyranosyl]-2,3,5,6-tetrakis-O-(trimethylsilyl)-	24.34	191.1	45.1	30	191.1	147.2	10
32	2-O-Glycerol-α-d-galactopyranoside, hexa-TMS isomer 1	25.02	218.1	73.1	8	218.1	100.1	8
33	D-Turanose, heptakis(trimethylsilyl)- isomer 3	27.31	73.1	45.1	12	73.1	58	22
34	9,19-Cyclolanostan-3-ol, 24-methylene-, (3β)-	28.15	305.2	147.2	8	305.2	217.2	8
35	2-Methyl-2(p-methoxy)mandelate, bis(trimethylsilyl)-	30.27	202.1	45.1	32	202.1	58	32
36	α-D-Galactopyranoside, methyl 2,3,4,6-tetrakis-O-(trimethylsilyl)Isomer1	30.7	81	79.1	10	337.2	131.1	10
37	β-D-Xylopyranose,1,2,3,4-tetrakis-O-(trimethylsilyl)-	30.82	339.5	75.1	20	339.5	131.1	10
38	β-D-Xylopyranose, 1,2,3,4-tetrakis-O-(trimethylsilyl)	32.65	146.9	45	30	146.9	131.2	10
39	D-Turanose, heptakis(trimethylsilyl)- Isomer 2	32.78	85	43.9	12	98.1	55.1	12
40	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)-	34.4	211.2	71.1	10	343.5	95.1	10
41	β-D-Xylopyranose, 1,2,3,4-tetrakis-O-(trimethylsilyl)-	34.64	318.4	147.2	20	318.4	215.2	10
42	9-Octadecenoic acid, 2-[(trimethylsilyl)oxy]-1-[[(trimethylsilyl)oxy]methyl]ethyl ester	34.73	225.1	79.1	10	225.1	93.1	10
43	Sucrose, octakis(trimethylsilyl) ether	35.27	117	47.1	20	117	75.1	10
44	Sucrose, octakis(trimethylsilyl) ether	38	147.1	45.1	32	147.1	131.1	12
45	β-D-Galactopyranoside, methyl 2,3-bis-O-(trimethylsilyl)-, cyclic methylboronate	39.09	352.7	169.2	10	362.7	170.2	10
46	Myo-Inositol, pentakis-O-(trimethylsilyl)-, bis(trimethylsilyl) phosphate	40.81	361.4	169.1	10	361.4	243.3	10
47	2-Pyrrolidinone, 1-(9-octadecenyl)-	41	103	45.1	20	103	58.1	30
48	α-L-Galactopyranose, 6-deoxy-1,2,3,4-tetrakis-O-imethylsilyl)-	41.54	399.3	81.1	10	399.3	95.5	10
49	9,12-Octadecadienoic acid (Z,Z)-, trimethylsilyl ester	42.68	298.9	147.1	20	298.9	225.2	10
50	Tryptophan, bis(trimethylsilyl)-	42.81	373.4	167.1	12	373.4	211.2	12
51	Hexadecanoic acid, trimethylsilyl ester	43	361.1	169.2	10	361.1	243.3	10
52	N,O,O'-Tris-(trimethylsilyl)tyrosine	43.67	147.2	45.1	32	147.2	131.1	12
53	Mannose, 2,3,4,5,6-pentakis-O-(trimethylsilyl)-, D-	44.71	204	73.1	10	204	189.2	10
54	β-Hydroxypyruvic acid, trimethylsilyl ether, trimethylsilyl ester	44.81	147.3	131.1	10	129.3	45	20
55	Tetradecanoic acid, trimethylsilyl ester	45.01	488.7	222.8	20	488.7	223.5	10
56	1,2,3-Propanetricarboxylic acid, 2-[(trimethylsilyl)oxy]-, tris(trimethylsilyl) ester	45.85	357.1	225.1	18	357.1	341.2	8
57	l-Glutamine, tris(trimethylsilyl) deriv.	46.57	205.2	45.3	30	205.2	190.1	10
58	Phosphoric acid, bis(trimethylsilyl) 2,3-bis[(trimethylsilyl)oxy]propyl ester	46.81	222	45.1	32	222	194.1	12
59	Arabinitol, pentakis-O-(trimethylsilyl)-	48.44	211	115.1	30	211	133.1	10
60	L-Asparagine, N,N2-bis(trimethylsilyl)-, trimethylsilyl ester	48.84	343.2	95.2	20	434.2	121.1	10
61	Glutamic acid, N-(trimethylsilyl)-, bis(trimethylsilyl) ester, L-	50.16	357.3	95.1	20	357.3	107.1	20
62	L-Aspartic acid, N-(trimethylsilyl)-, bis(trimethylsilyl) ester	51.24	362.5	169.2	12	362.5	170.2	12
63	Acetic acid, iodo-, trimethylsilyl ester	52.13	147	105.1	10	147	119.1	10
64	α-D-Glucopyranoside, 1,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-fructofuranosyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	53.49	217.2	45.1	28	361.2	169.2	8
65	D-Glucose, 4-O-[2,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-galactopyranosyl]-2,3,5,6-tetrakis-O-(trimethylsilyl)-	54.95	217.1	45.1	32	217.1	143.1	12
66	α-D-Glucopyranoside, 1,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-fructofuranosyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	59.21	204.1	45.1	30	204.1	189.2	10

CN	Compound Name	Quantification peak				Confirming peak
CN	Compound Name	RT(min)	Precursor	Product	CE	Precursor	Product	CE
1	l-Alanine, N-(trimethylsilyl)-, trimethylsilyl ester	6.37	99	69	30	99	71	10
2	Glycine, N-(trimethylsilyl)-, trimethylsilyl ester	5.69	100.1	59.1	10	174.1	59.1	20
3	Phosphoric acid, bis(trimethylsilyl)monomethyl ester	6.92	78.1	64	12	78.1	71.3	12
4	L-Valine, N-(trimethylsilyl)-, trimethylsilyl ester	7.44	148.8	450	30	148.8	75	10
5	2-(4-Methoxyphenyl)-2-(4-trimethoxysilyloxy)propane	8.73	11.4	45.6	18	118.4	75.2	8
6	Butane, 2,3-bis(trimethylsiloxy)-	10.06	116.1	43	28	116.1	45.1	18
7	1,2-Bis(trimethylsiloxy)ethane	10.48	102.1	45.1	20	102.1	58	30
8	Silanamine, N,N'-methanetetraylbis[1,1,1-trimethyl-	11.55	133	115	10	163.1	133.1	10
9	Ethylbis(trimethylsilyl)amine	12.32	144.1	43	32	144.1	58.1	32
10	N,N'-Bis(trimethylsilyl)trifluoroacetamidine	13.36	299.1	151.1	10	300.5	74.1	10
11	Glycerol, tris(trimethylsilyl) ether	13.43	116.9	59.1	10	116.9	89.1	10
12	Butanedioic acid, bis(trimethylsilyl) ester	14.14	74.8	47	10	148.5	45.2	30
13	N,O,O-Tris(trimethylsilyl)-L-threonine	14.94	205.5	205.3	10	218.2	45	30
14	Serine, N,O-bis(trimethylsilyl)-, trimethylsilyl ester	15.37	100.6	86.1	10	117.1	43	30
15	Threitol, 1,2,3,4-tetrakis-O-(trimethylsilyl)-, D-	16.57	229.1	47	32	229.1	131.1	12
16	Amine, N,N,N-tris((trimethylsilyloxy)ethyl)-	17.04	189.7	147.1	10	233.1	73.1	10
17	Decanoic acid, trimethylsilyl ester	17.23	100	59.1	10	115	59.1	20
18	Butanedioic acid, [(trimethylsilyl)oxy]-, bis (trimethylsilyl) ester	17.35	205.3	117.1	8	205.3	147.1	8
19	3-Trifluoromethylbenzylamine, N,N-dinonyl	17.53	232.1	100.1	8	232.1	188.2	8
20	Arabinofuranose, 1,2,3,5-tetrakis-O-(trimethylsilyl)-	17.73	171.1	73.1	22	314.1	73.1	22
21	Myo-Inositol, 1,2,3,4,5,6-hexakis-O-(trimethylsilyl)-	19.12	128.1	73.1	10	246.1	73.1	20
22	Oleic acid, trimethylsilyl ester	19.24	232.2	73.1	22	262.3	82.1	12
23	Myristic acid, 2,3-bis(trimethylsiloxy)propyl ester	19.94	231.1	116.1	8	231.1	132.2	8
24	D-(+)-Trehalose, octakis(trimethylsilyl) ether	20.84	204.8	117.1	10	204.8	147.2	10
25	D-Turanose, heptakis(trimethylsilyl)- Isomer 1	21.59	299.2	147.2	20	299.2	225.2	10
26	α-D-Galactopyranoside, methyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	21.81	155.1	45	28	156	45.1	28
27	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)- isomer 1	22.41	437.4	191.2	10	437.4	257.2	10
28	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)- isomer 2	22.69	273.1	67.1	10	273.1	183.2	10
29	Silane, [[(3β,24R)-ergost-5-en-3-yl]oxy]trimethyl-	23.3	285.2	95.2	12	285.2	131.1	12
30	β-Sitosterol trimethylsilyl ether	22.86	518.5	188.3	12	518.5	428.3	12
31	D-Glucose, 4-O-[2,3,4,6-tetrakis-O-(trimethylsilyl) -β-D-galactopyranosyl]-2,3,5,6-tetrakis-O-(trimethylsilyl)-	24.34	191.1	45.1	30	191.1	147.2	10
32	2-O-Glycerol-α-d-galactopyranoside, hexa-TMS isomer 1	25.02	218.1	73.1	8	218.1	100.1	8
33	D-Turanose, heptakis(trimethylsilyl)- isomer 3	27.31	73.1	45.1	12	73.1	58	22
34	9,19-Cyclolanostan-3-ol, 24-methylene-, (3β)-	28.15	305.2	147.2	8	305.2	217.2	8
35	2-Methyl-2(p-methoxy)mandelate, bis(trimethylsilyl)-	30.27	202.1	45.1	32	202.1	58	32
36	α-D-Galactopyranoside, methyl 2,3,4,6-tetrakis-O-(trimethylsilyl)Isomer1	30.7	81	79.1	10	337.2	131.1	10
37	β-D-Xylopyranose,1,2,3,4-tetrakis-O-(trimethylsilyl)-	30.82	339.5	75.1	20	339.5	131.1	10
38	β-D-Xylopyranose, 1,2,3,4-tetrakis-O-(trimethylsilyl)	32.65	146.9	45	30	146.9	131.2	10
39	D-Turanose, heptakis(trimethylsilyl)- Isomer 2	32.78	85	43.9	12	98.1	55.1	12
40	1,2-Propanediol-1-phosphate, tris(trimethylsilyl)-	34.4	211.2	71.1	10	343.5	95.1	10
41	β-D-Xylopyranose, 1,2,3,4-tetrakis-O-(trimethylsilyl)-	34.64	318.4	147.2	20	318.4	215.2	10
42	9-Octadecenoic acid, 2-[(trimethylsilyl)oxy]-1-[[(trimethylsilyl)oxy]methyl]ethyl ester	34.73	225.1	79.1	10	225.1	93.1	10
43	Sucrose, octakis(trimethylsilyl) ether	35.27	117	47.1	20	117	75.1	10
44	Sucrose, octakis(trimethylsilyl) ether	38	147.1	45.1	32	147.1	131.1	12
45	β-D-Galactopyranoside, methyl 2,3-bis-O-(trimethylsilyl)-, cyclic methylboronate	39.09	352.7	169.2	10	362.7	170.2	10
46	Myo-Inositol, pentakis-O-(trimethylsilyl)-, bis(trimethylsilyl) phosphate	40.81	361.4	169.1	10	361.4	243.3	10
47	2-Pyrrolidinone, 1-(9-octadecenyl)-	41	103	45.1	20	103	58.1	30
48	α-L-Galactopyranose, 6-deoxy-1,2,3,4-tetrakis-O-imethylsilyl)-	41.54	399.3	81.1	10	399.3	95.5	10
49	9,12-Octadecadienoic acid (Z,Z)-, trimethylsilyl ester	42.68	298.9	147.1	20	298.9	225.2	10
50	Tryptophan, bis(trimethylsilyl)-	42.81	373.4	167.1	12	373.4	211.2	12
51	Hexadecanoic acid, trimethylsilyl ester	43	361.1	169.2	10	361.1	243.3	10
52	N,O,O'-Tris-(trimethylsilyl)tyrosine	43.67	147.2	45.1	32	147.2	131.1	12
53	Mannose, 2,3,4,5,6-pentakis-O-(trimethylsilyl)-, D-	44.71	204	73.1	10	204	189.2	10
54	β-Hydroxypyruvic acid, trimethylsilyl ether, trimethylsilyl ester	44.81	147.3	131.1	10	129.3	45	20
55	Tetradecanoic acid, trimethylsilyl ester	45.01	488.7	222.8	20	488.7	223.5	10
56	1,2,3-Propanetricarboxylic acid, 2-[(trimethylsilyl)oxy]-, tris(trimethylsilyl) ester	45.85	357.1	225.1	18	357.1	341.2	8
57	l-Glutamine, tris(trimethylsilyl) deriv.	46.57	205.2	45.3	30	205.2	190.1	10
58	Phosphoric acid, bis(trimethylsilyl) 2,3-bis[(trimethylsilyl)oxy]propyl ester	46.81	222	45.1	32	222	194.1	12
59	Arabinitol, pentakis-O-(trimethylsilyl)-	48.44	211	115.1	30	211	133.1	10
60	L-Asparagine, N,N2-bis(trimethylsilyl)-, trimethylsilyl ester	48.84	343.2	95.2	20	434.2	121.1	10
61	Glutamic acid, N-(trimethylsilyl)-, bis(trimethylsilyl) ester, L-	50.16	357.3	95.1	20	357.3	107.1	20
62	L-Aspartic acid, N-(trimethylsilyl)-, bis(trimethylsilyl) ester	51.24	362.5	169.2	12	362.5	170.2	12
63	Acetic acid, iodo-, trimethylsilyl ester	52.13	147	105.1	10	147	119.1	10
64	α-D-Glucopyranoside, 1,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-fructofuranosyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	53.49	217.2	45.1	28	361.2	169.2	8
65	D-Glucose, 4-O-[2,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-galactopyranosyl]-2,3,5,6-tetrakis-O-(trimethylsilyl)-	54.95	217.1	45.1	32	217.1	143.1	12
66	α-D-Glucopyranoside, 1,3,4,6-tetrakis-O-(trimethylsilyl)-β-D-fructofuranosyl 2,3,4,6-tetrakis-O-(trimethylsilyl)-	59.21	204.1	45.1	30	204.1	189.2	10