Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects

doi:10.1016/j.rsci.2021.12.007

Abstract

Abstract:

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.

Key words: ionomic profile, rice genotype, elemental covariation, correlation, principal component analysis

Zhang Chengming, Nobuhiro Tanaka, Maria Stefanie Dwiyanti, Matthew Shenton, Hayato Maruyama, Takuro Shinano, Chu Qingnan, Xie Jun, Toshihiro Watanabe. Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects[J]. Rice Science, 2022, 29(1): 76-88.

Figures/Tables 5

References 57

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Element	Shoot					Root
Element	F value ^a	Contribution (%) ^b	CV of japonica	CV of indica	CV of aus	F value ^a	Contribution (%) ^b	CV of japonica	CV of indica	CV of aus
P	3.31**	63.57	0.14	0.16	0.19	1.08	37.24	0.27	0.29	0.19
K	2.58**	56.71	0.09	0.07	0.09	3.60**	64.69	0.10	0.11	0.10
S	2.76**	58.33	0.13	0.23	0.10	8.10**	80.47	0.14	0.21	0.15
Ca	2.65**	57.34	0.14	0.08	0.08	1.16	37.05	0.10	0.10	0.12
Mg	4.91**	71.38	0.14	0.12	0.11	12.11**	86.03	0.20	0.19	0.17
Fe	1.29	39.48	0.30	0.21	0.28	1.53*	44.64	0.20	0.20	0.37
Mn	3.13**	61.29	0.11	0.11	0.19	3.56**	64.44	0.22	0.16	0.26
Zn	1.54*	43.90	0.17	0.16	0.19	1.32	40.24	0.30	0.17	0.20
Cu	3.74**	65.46	0.15	0.17	0.21	9.13**	82.27	0.15	0.20	0.18
B	2.86**	59.19	0.16	0.25	0.17	0.81	29.09	0.31	0.30	0.47
Mo	2.96**	59.99	0.22	0.16	0.14	3.07**	60.99	0.13	0.11	0.16
Ni	1.05	34.73	0.17	0.51	0.16	1.63*	45.36	0.12	0.13	0.19
Cl^‒	1.24	40.21	0.22	0.19	0.16	1.08	41.28	0.21	0.30	0.26
SO₄^2‒	2.13**	53.69	0.30	0.38	0.28	2.19**	59.04	0.47	0.43	0.44
NO₃^‒	1.57*	45.91	0.28	0.24	0.27	1.39	47.32	0.29	0.35	0.26
Al	0.85	30.21	0.49	0.53	0.36	1.15	37.07	0.25	0.21	0.24
Ba	2.70**	57.80	0.18	0.14	0.14	3.55**	64.35	0.14	0.11	0.19
Na	2.33**	54.19	0.29	0.34	0.30	3.03**	60.61	0.26	0.32	0.30
Sr	2.98**	60.18	0.17	0.16	0.16	2.60**	56.92	0.14	0.12	0.17
As	4.11**	67.56	0.12	0.09	0.10	4.53**	69.71	0.15	0.18	0.24
Cd	8.76**	81.61	0.30	0.19	0.32	6.77**	77.50	0.19	0.20	0.23
Co	2.99**	60.19	0.27	0.21	0.26	4.56**	69.85	0.17	0.17	0.20
Cr	1.67**	46.07	0.52	0.68	0.51	1.47*	42.76	0.20	0.14	0.22
Cs	4.21**	68.07	0.13	0.16	0.20	9.19**	82.37	0.10	0.16	0.18
Li	1.87**	48.69	0.28	0.21	0.21	1.15	36.97	0.20	0.17	0.19
Se	6.11**	75.56	0.14	0.21	0.35	8.83**	81.78	0.18	0.20	0.28

Element	Shoot					Root
Element	F value ^a	Contribution (%) ^b	CV of japonica	CV of indica	CV of aus	F value ^a	Contribution (%) ^b	CV of japonica	CV of indica	CV of aus
P	3.31**	63.57	0.14	0.16	0.19	1.08	37.24	0.27	0.29	0.19
K	2.58**	56.71	0.09	0.07	0.09	3.60**	64.69	0.10	0.11	0.10
S	2.76**	58.33	0.13	0.23	0.10	8.10**	80.47	0.14	0.21	0.15
Ca	2.65**	57.34	0.14	0.08	0.08	1.16	37.05	0.10	0.10	0.12
Mg	4.91**	71.38	0.14	0.12	0.11	12.11**	86.03	0.20	0.19	0.17
Fe	1.29	39.48	0.30	0.21	0.28	1.53*	44.64	0.20	0.20	0.37
Mn	3.13**	61.29	0.11	0.11	0.19	3.56**	64.44	0.22	0.16	0.26
Zn	1.54*	43.90	0.17	0.16	0.19	1.32	40.24	0.30	0.17	0.20
Cu	3.74**	65.46	0.15	0.17	0.21	9.13**	82.27	0.15	0.20	0.18
B	2.86**	59.19	0.16	0.25	0.17	0.81	29.09	0.31	0.30	0.47
Mo	2.96**	59.99	0.22	0.16	0.14	3.07**	60.99	0.13	0.11	0.16
Ni	1.05	34.73	0.17	0.51	0.16	1.63*	45.36	0.12	0.13	0.19
Cl^‒	1.24	40.21	0.22	0.19	0.16	1.08	41.28	0.21	0.30	0.26
SO₄^2‒	2.13**	53.69	0.30	0.38	0.28	2.19**	59.04	0.47	0.43	0.44
NO₃^‒	1.57*	45.91	0.28	0.24	0.27	1.39	47.32	0.29	0.35	0.26
Al	0.85	30.21	0.49	0.53	0.36	1.15	37.07	0.25	0.21	0.24
Ba	2.70**	57.80	0.18	0.14	0.14	3.55**	64.35	0.14	0.11	0.19
Na	2.33**	54.19	0.29	0.34	0.30	3.03**	60.61	0.26	0.32	0.30
Sr	2.98**	60.18	0.17	0.16	0.16	2.60**	56.92	0.14	0.12	0.17
As	4.11**	67.56	0.12	0.09	0.10	4.53**	69.71	0.15	0.18	0.24
Cd	8.76**	81.61	0.30	0.19	0.32	6.77**	77.50	0.19	0.20	0.23
Co	2.99**	60.19	0.27	0.21	0.26	4.56**	69.85	0.17	0.17	0.20
Cr	1.67**	46.07	0.52	0.68	0.51	1.47*	42.76	0.20	0.14	0.22
Cs	4.21**	68.07	0.13	0.16	0.20	9.19**	82.37	0.10	0.16	0.18
Li	1.87**	48.69	0.28	0.21	0.21	1.15	36.97	0.20	0.17	0.19
Se	6.11**	75.56	0.14	0.21	0.35	8.83**	81.78	0.18	0.20	0.28

ID	Variety	Subspecies	High		Low
ID	Variety	Subspecies	Essential element	Nonessential element	Essential element	Nonessential element
JRC06	Kaneko B	japonica	Mn, B	As, Cd, Co, Cr, Se	K	‒
JRC12	Oiran	japonica	Ca, Mg, Mn	Sr, Co, Se	Mo	‒
JRC13	Bouzu Mochi	japonica	Mg, Fe, B, Ni	As, Cd, Se	‒	‒
JRC36	Sekiyama	japonica	‒	‒	K, Zn, Cu, Mo	Ba, Sr
JRC37	Shinyamadaho 2	japonica	‒	Al	S, Ca, Mo	Ba, Sr, Co
JRC40	Akamai	indica	‒	‒	Ca, Zn	Ba, Sr
JRC49	Rikutou Rikuu 2	japonica	‒	‒	Zn, Mo, SO₄^2‒	Na, Li
JRC51	Shinshuu	japonica	‒	‒	NO₃^‒	Na, Sr, Li
WRC04	Jena 035	aus	‒	Li	P	Na, As, Cd, Se
WRC10	Shuusoushu	indica	Cl^‒	‒	‒	Co, Cs
WRC11	Jinguoyin	indica	Zn, Cl^‒	‒	NO₃^‒	Cd
WRC14	IR58	indica	Mg, Mo	Al	‒	Cs
WRC18	Qingyu (Seiyu)	indica	‒	‒	P, Ni	Co, Cs
WRC19	Deng Pao Zhai	indica	‒	‒	Ni	Co, Cr
WRC20	Tadukan	indica	‒	‒	Ni	Co, Cr
WRC21	Shwe Nang Gyi	indica	Mo, SO₄^2‒	Se	‒	‒
WRC23	Lebed	japonica	‒	‒	Ni	Cr, Cs
WRC24	Pinulupot 1	indica	‒	‒	S, B	Cs
WRC25	Muha	aus	‒	‒	S, SO₄^2‒	Cd, Se
WRC26	Jhona 2	aus	K, Zn, Cu	‒	‒	Cr
WRC27	Nepal 8	aus	‒	Li	‒	Cd, Se
WRC29	Kalo Dhan	aus	‒	Na, Li	P, Mg, Mn	Cd, Se
WRC30	Anjana Dhan	aus	K, Zn	Co, Cs	Mg, Mn	‒
WRC32	Tupa 121-3	aus	Mn	‒	Cu, Ni	As
WRC33	Surjamukhi	aus	‒	‒	Mg, Cu, Ni	Ba, Sr
WRC38	Arc 11094	aus	‒	‒	S, Ca, Cu	Sr, As, Se
WRC42	Local Basmati	aus	P, K, NO₃^‒	Se	‒	‒
WRC47	Jaguary	japonica	Ca, Zn, Cu	Al	‒	‒
WRC48	Khau Mac Kho	japonica	P, Ca, Mg, B, Mo	Ba, Na, Sr, As	‒	‒
WRC49	Padi Perak	japonica	P, S, Fe, B, Mo, Ni	Ba, Sr, Co, Cr, Se	‒	‒
WRC50	Rexmont	japonica	P, Fe, Ni	Co, Cr	Cl^-, NO₃^‒	‒
WRC51	Urasan 1	japonica	Ca, Mg, Fe	Ba, Sr, As, Co, Cr	‒	‒
WRC52	Khau Tan Chiem	japonica	Cu, NO₃^‒	Cd	Ca	Al
WRC53	Tima	japonica	S, Mn, SO₄^2‒	Cs	‒	‒
WRC55	Tupa 729	japonica	K, NO₃^‒	Cs	‒	‒
WRC57	Milyang 23	indica	Fe, Ni	Cr	‒	‒
WRC58	Neang Menh	indica	S, SO₄^2‒	Na	Mn, B	As
WRC60	Hakphaynhay	indica	S, SO₄^2‒	‒	P, Fe, B	Al
WRC63	Bleiyo	indica	Zn, Cl^‒	Sr	‒	‒
WRC65	Rambhog	indica	K, S	Cs	Mn	‒
WRC67	Phulba	japonica	Ca, Mn, Cl^‒	Li	‒	‒
WRC68	Khao Nam Jen	japonica	Mg, Cu	Cd, Li	‒	‒

ID	Variety	Subspecies	High		Low
ID	Variety	Subspecies	Essential element	Nonessential element	Essential element	Nonessential element
JRC06	Kaneko B	japonica	Mn, B	As, Cd, Co, Cr, Se	K	‒
JRC12	Oiran	japonica	Ca, Mg, Mn	Sr, Co, Se	Mo	‒
JRC13	Bouzu Mochi	japonica	Mg, Fe, B, Ni	As, Cd, Se	‒	‒
JRC36	Sekiyama	japonica	‒	‒	K, Zn, Cu, Mo	Ba, Sr
JRC37	Shinyamadaho 2	japonica	‒	Al	S, Ca, Mo	Ba, Sr, Co
JRC40	Akamai	indica	‒	‒	Ca, Zn	Ba, Sr
JRC49	Rikutou Rikuu 2	japonica	‒	‒	Zn, Mo, SO₄^2‒	Na, Li
JRC51	Shinshuu	japonica	‒	‒	NO₃^‒	Na, Sr, Li
WRC04	Jena 035	aus	‒	Li	P	Na, As, Cd, Se
WRC10	Shuusoushu	indica	Cl^‒	‒	‒	Co, Cs
WRC11	Jinguoyin	indica	Zn, Cl^‒	‒	NO₃^‒	Cd
WRC14	IR58	indica	Mg, Mo	Al	‒	Cs
WRC18	Qingyu (Seiyu)	indica	‒	‒	P, Ni	Co, Cs
WRC19	Deng Pao Zhai	indica	‒	‒	Ni	Co, Cr
WRC20	Tadukan	indica	‒	‒	Ni	Co, Cr
WRC21	Shwe Nang Gyi	indica	Mo, SO₄^2‒	Se	‒	‒
WRC23	Lebed	japonica	‒	‒	Ni	Cr, Cs
WRC24	Pinulupot 1	indica	‒	‒	S, B	Cs
WRC25	Muha	aus	‒	‒	S, SO₄^2‒	Cd, Se
WRC26	Jhona 2	aus	K, Zn, Cu	‒	‒	Cr
WRC27	Nepal 8	aus	‒	Li	‒	Cd, Se
WRC29	Kalo Dhan	aus	‒	Na, Li	P, Mg, Mn	Cd, Se
WRC30	Anjana Dhan	aus	K, Zn	Co, Cs	Mg, Mn	‒
WRC32	Tupa 121-3	aus	Mn	‒	Cu, Ni	As
WRC33	Surjamukhi	aus	‒	‒	Mg, Cu, Ni	Ba, Sr
WRC38	Arc 11094	aus	‒	‒	S, Ca, Cu	Sr, As, Se
WRC42	Local Basmati	aus	P, K, NO₃^‒	Se	‒	‒
WRC47	Jaguary	japonica	Ca, Zn, Cu	Al	‒	‒
WRC48	Khau Mac Kho	japonica	P, Ca, Mg, B, Mo	Ba, Na, Sr, As	‒	‒
WRC49	Padi Perak	japonica	P, S, Fe, B, Mo, Ni	Ba, Sr, Co, Cr, Se	‒	‒
WRC50	Rexmont	japonica	P, Fe, Ni	Co, Cr	Cl^-, NO₃^‒	‒
WRC51	Urasan 1	japonica	Ca, Mg, Fe	Ba, Sr, As, Co, Cr	‒	‒
WRC52	Khau Tan Chiem	japonica	Cu, NO₃^‒	Cd	Ca	Al
WRC53	Tima	japonica	S, Mn, SO₄^2‒	Cs	‒	‒
WRC55	Tupa 729	japonica	K, NO₃^‒	Cs	‒	‒
WRC57	Milyang 23	indica	Fe, Ni	Cr	‒	‒
WRC58	Neang Menh	indica	S, SO₄^2‒	Na	Mn, B	As
WRC60	Hakphaynhay	indica	S, SO₄^2‒	‒	P, Fe, B	Al
WRC63	Bleiyo	indica	Zn, Cl^‒	Sr	‒	‒
WRC65	Rambhog	indica	K, S	Cs	Mn	‒
WRC67	Phulba	japonica	Ca, Mn, Cl^‒	Li	‒	‒
WRC68	Khao Nam Jen	japonica	Mg, Cu	Cd, Li	‒	‒