Rice Science ›› 2022, Vol. 29 ›› Issue (1): 76-88.DOI: 10.1016/j.rsci.2021.12.007
• Research Paper • Previous Articles Next Articles
Zhang Chengming1, Nobuhiro Tanaka2, Maria Stefanie Dwiyanti1, Matthew Shenton2, Hayato Maruyama1, Takuro Shinano1, Chu Qingnan3, Xie Jun4, Toshihiro Watanabe1()
Received:
2021-01-01
Accepted:
2021-05-13
Online:
2022-01-28
Published:
2022-01-01
Contact:
Toshihiro Watanabe
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.
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Fig. 1. Boxplot showing log 10 concentrations of 15 essential elements (P, K, S, Ca, Mg, Fe, Mn, Zn, Cu, B, Mo, Ni, Cl?, SO42? and NO3?) in rice shoots and roots.
Element | Shoot | Root | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
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 | |
SO42‒ | 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 |
Table 1. Variations in elemental concentrations in shoots and roots among 120 rice varieties.
Element | Shoot | Root | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
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 | |
SO42‒ | 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 |
Fig. 3. Correlation heatmaps for aus shoots (A), aus roots (B), indica shoots (C), indica roots (D), japonica shoots (E) and japonica roots (F). nly significant (P < 0.05) correlations are displayed in the Pearson’s correlation analysis. The circle in upper triangle matrix represents significant correlation. A larger circle indicates a stronger correlation between the row and the column variables. The red circle indicates a positive correlation coefficient, and the blue indicates a negative one. * and ** in lower triangle matrix represent P < 0.05 and P < 0.01, respectively.
Fig. 4. Combination of principal component analysis (PCA) score plots and loading plots for all samples (A), shoots (B) and roots (C). EA, JP, SA and SEA represent East Asia (except Japan), Japan, South Asia and Southeast Asia, respectively.
ID | Variety | Subspecies | High | Low | |||
---|---|---|---|---|---|---|---|
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, SO42‒ | 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, SO42‒ | Se | ‒ | ‒ | |
WRC23 | Lebed | japonica | ‒ | ‒ | Ni | Cr, Cs | |
WRC24 | Pinulupot 1 | indica | ‒ | ‒ | S, B | Cs | |
WRC25 | Muha | aus | ‒ | ‒ | S, SO42‒ | 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, SO42‒ | Cs | ‒ | ‒ | |
WRC55 | Tupa 729 | japonica | K, NO3‒ | Cs | ‒ | ‒ | |
WRC57 | Milyang 23 | indica | Fe, Ni | Cr | ‒ | ‒ | |
WRC58 | Neang Menh | indica | S, SO42‒ | Na | Mn, B | As | |
WRC60 | Hakphaynhay | indica | S, SO42‒ | ‒ | 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 | ‒ | ‒ |
Table 2. Highest and lowest multi-element accumulation varieties for elements in shoots.
ID | Variety | Subspecies | High | Low | |||
---|---|---|---|---|---|---|---|
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, SO42‒ | 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, SO42‒ | Se | ‒ | ‒ | |
WRC23 | Lebed | japonica | ‒ | ‒ | Ni | Cr, Cs | |
WRC24 | Pinulupot 1 | indica | ‒ | ‒ | S, B | Cs | |
WRC25 | Muha | aus | ‒ | ‒ | S, SO42‒ | 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, SO42‒ | Cs | ‒ | ‒ | |
WRC55 | Tupa 729 | japonica | K, NO3‒ | Cs | ‒ | ‒ | |
WRC57 | Milyang 23 | indica | Fe, Ni | Cr | ‒ | ‒ | |
WRC58 | Neang Menh | indica | S, SO42‒ | Na | Mn, B | As | |
WRC60 | Hakphaynhay | indica | S, SO42‒ | ‒ | 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 | ‒ | ‒ |
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