Journal of Nuclear Agricultural Sciences ›› 2021, Vol. 35 ›› Issue (9): 2016-2026.DOI: 10.11869/j.issn.100-8551.2021.09.2016
• Induced Mutations for Plant Breeding·Agricultural Biotechnology • Previous Articles Next Articles
CAO Liru1(), ZHANG Qianjin1, GUO Zining2, LU Xiaomin1, ZHANG Xin1, WEI Xin1, HUANG-FU Baishu3,*(
), WANG Zhenhua1,*(
)
Received:
2020-06-28
Accepted:
2020-10-04
Online:
2021-09-10
Published:
2021-07-22
Contact:
HUANG-FU Baishu,WANG Zhenhua
曹丽茹1(), 张前进1, 郭子宁2, 鲁晓民1, 张新1, 魏昕1, 皇甫柏树3,*(
), 王振华1,*(
)
通讯作者:
皇甫柏树,王振华
作者简介:
曹丽茹,女,主要从事玉米遗传育种及生物信息学分析。E-mail: caoliru008@126.com
基金资助:
CAO Liru, ZHANG Qianjin, GUO Zining, LU Xiaomin, ZHANG Xin, WEI Xin, HUANG-FU Baishu, WANG Zhenhua. Geneome-Wide Identification and Expression Analysis of Auxin Response Factor Gene Family in Maize[J]. Journal of Nuclear Agricultural Sciences, 2021, 35(9): 2016-2026.
曹丽茹, 张前进, 郭子宁, 鲁晓民, 张新, 魏昕, 皇甫柏树, 王振华. 玉米生长素响应因子基因家族全基因组鉴定及表达分析[J]. 核农学报, 2021, 35(9): 2016-2026.
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URL: https://www.hnxb.org.cn/EN/10.11869/j.issn.100-8551.2021.09.2016
基因编号 Gene name | 基因ID Gene ID | 长度 Length/aa | 结构域 Domain | 分子量 Molecular weight/kDa | 等电点 pI | ɑ-螺旋 ɑ-Helix /% | β-转角 β-Turn /% | 无规则卷曲 Random coil/% | 延伸链 Extender china/% |
---|---|---|---|---|---|---|---|---|---|
ZmARF1 | Zm00001d031064 | 897 | B3,ARF,AUX_IAA | 98.37 | 6.23 | 29.21 | 8.47 | 45.82 | 16.50 |
ZmARF2 | Zm00001d032683 | 681 | B3,ARF | 74.54 | 7.92 | 18.21 | 4.41 | 61.53 | 15.86 |
ZmARF3 | Zm00001d031522 | 1 086 | B3,ARF,AUX_IAA | 120.17 | 6.25 | 27.99 | 6.91 | 45.40 | 19.71 |
ZmARF4 | Zm00001d030801 | 446 | B3,ARF | 48.73 | 8.66 | 14.35 | 3.81 | 59.64 | 22.20 |
ZmARF5 | Zm00001d030803 | 418 | B3,ARF | 46.83 | 7.07 | 18.66 | 3.59 | 57.89 | 19.86 |
ZmARF6 | Zm00001d003601 | 657 | B3,ARF,AUX_IAA | 72.95 | 6.14 | 25.27 | 4.26 | 54.64 | 15.83 |
ZmARF7 | Zm00001d001945 | 935 | B4,ARF,AUX_IAA | 102.87 | 6.12 | 26.95 | 7.17 | 50.37 | 15.51 |
ZmARF8 | Zm00001d001879 | 817 | B5,ARF,AUX_IAA | 90.99 | 6.37 | 30.11 | 6.24 | 47.12 | 16.52 |
ZmARF9 | Zm00001d003011 | 273 | B3,ARF | 29.73 | 7.58 | 17.95 | 5.86 | 56.78 | 19.41 |
ZmARF10 | Zm00001d002929 | 513 | B3,ARF | 55.45 | 6.40 | 14.81 | 3.51 | 65.50 | 16.18 |
ZmARF11 | Zm00001d043431 | 688 | B3,ARF | 74.99 | 7.28 | 16.42 | 4.94 | 64.97 | 13.66 |
ZmARF12 | Zm00001d041497 | 888 | B5,ARF,AUX_IAA | 97.84 | 6.08 | 29.73 | 8.00 | 46.96 | 15.32 |
ZmARF13 | Zm00001d042267 | 822 | B6,ARF,AUX_IAA | 91.85 | 6.91 | 19.83 | 4.99 | 59.73 | 15.45 |
ZmARF14 | Zm00001d041056 | 652 | B7,ARF,AUX_IAA | 71.86 | 7.43 | 15.95 | 3.53 | 65.18 | 15.34 |
ZmARF15 | Zm00001d043922 | 708 | B3,ARF | 77.97 | 7.11 | 14.69 | 4.24 | 66.10 | 14.97 |
ZmARF16 | Zm00001d039267 | 686 | B3,ARF | 76.72 | 6.29 | 19.97 | 4.52 | 57.58 | 17.93 |
ZmARF17 | Zm00001d053819 | 914 | B7,ARF,AUX_IAA | 100.94 | 6.03 | 29.65 | 4.92 | 52.08 | 13.35 |
ZmARF18 | Zm00001d051172 | 689 | B3,ARF | 73.69 | 7.36 | 20.39 | 4.78 | 61.04 | 13.78 |
ZmARF19 | Zm00001d050781 | 511 | B7,ARF,AUX_IAA | 56.73 | 6.83 | 19.77 | 4.89 | 55.38 | 19.96 |
ZmARF20 | Zm00001d049295 | 850 | B7,ARF,AUX_IAA | 93.15 | 7.01 | 20.82 | 5.41 | 58.47 | 15.29 |
ZmARF21 | Zm00001d014507 | 716 | B3,ARF | 77.52 | 7.13 | 19.17 | 4.41 | 60.28 | 16.14 |
ZmARF22 | Zm00001d014377 | 739 | B7,ARF,AUX_IAA | 82.00 | 6.99 | 24.63 | 5.01 | 54.80 | 15.56 |
ZmARF23 | Zm00001d015243 | 1 147 | B7,ARF,AUX_IAA | 127.24 | 6.08 | 33.48 | 6.54 | 42.55 | 17.44 |
ZmARF24 | Zm00001d014013 | 644 | B3,ARF | 70.96 | 6.97 | 19.57 | 4.66 | 59.94 | 15.84 |
ZmARF25 | Zm00001d014690 | 975 | B7,ARF,AUX_IAA | 107.54 | 6.60 | 30.87 | 7.08 | 47.38 | 14.67 |
ZmARF26 | Zm00001d016838 | 677 | B7,ARF,AUX_IAA | 75.13 | 6.30 | 19.50 | 4.58 | 59.23 | 16.69 |
ZmARF27 | Zm00001d039006 | 736 | B3,ARF | 80.42 | 7.83 | 15.22 | 4.08 | 65.08 | 15.62 |
ZmARF28 | Zm00001d000358 | 700 | B3,ARF | 75.51 | 7.56 | 17.86 | 4.29 | 61.14 | 16.71 |
ZmARF29 | Zm00001d038698 | 680 | B3,ARF | 73.94 | 6.86 | 16.18 | 4.41 | 66.32 | 13.09 |
ZmARF30 | Zm00001d011953 | 728 | B7,ARF,AUX_IAA | 81.43 | 7.66 | 15.25 | 3.16 | 65.66 | 15.93 |
ZmARF31 | Zm00001d012731 | 340 | B3,ARF | 37.38 | 7.95 | 23.24 | 5.00 | 49.41 | 22.35 |
ZmARF32 | Zm00001d025871 | 588 | B3,ARF | 63.91 | 8.77 | 18.54 | 4.08 | 63.10 | 14.29 |
ZmARF33 | Zm00001d023659 | 813 | B7,ARF,AUX_IAA | 89.71 | 7.25 | 20.33 | 4.09 | 59.75 | 15.83 |
ZmARF34 | Zm00001d026687 | 462 | B3,ARF | 50.56 | 5.41 | 17.32 | 3.68 | 58.01 | 21.00 |
ZmARF35 | Zm00001d026540 | 958 | B7,ARF,AUX_IAA | 105.29 | 6.44 | 28.50 | 4.91 | 53.03 | 13.57 |
ZmARF36 | Zm00001d045026 | 1 053 | B7,ARF,AUX_IAA | 116.75 | 6.67 | 37.42 | 6.84 | 42.36 | 13.39 |
Table 1 Characteristics of ARFs gene family in maize
基因编号 Gene name | 基因ID Gene ID | 长度 Length/aa | 结构域 Domain | 分子量 Molecular weight/kDa | 等电点 pI | ɑ-螺旋 ɑ-Helix /% | β-转角 β-Turn /% | 无规则卷曲 Random coil/% | 延伸链 Extender china/% |
---|---|---|---|---|---|---|---|---|---|
ZmARF1 | Zm00001d031064 | 897 | B3,ARF,AUX_IAA | 98.37 | 6.23 | 29.21 | 8.47 | 45.82 | 16.50 |
ZmARF2 | Zm00001d032683 | 681 | B3,ARF | 74.54 | 7.92 | 18.21 | 4.41 | 61.53 | 15.86 |
ZmARF3 | Zm00001d031522 | 1 086 | B3,ARF,AUX_IAA | 120.17 | 6.25 | 27.99 | 6.91 | 45.40 | 19.71 |
ZmARF4 | Zm00001d030801 | 446 | B3,ARF | 48.73 | 8.66 | 14.35 | 3.81 | 59.64 | 22.20 |
ZmARF5 | Zm00001d030803 | 418 | B3,ARF | 46.83 | 7.07 | 18.66 | 3.59 | 57.89 | 19.86 |
ZmARF6 | Zm00001d003601 | 657 | B3,ARF,AUX_IAA | 72.95 | 6.14 | 25.27 | 4.26 | 54.64 | 15.83 |
ZmARF7 | Zm00001d001945 | 935 | B4,ARF,AUX_IAA | 102.87 | 6.12 | 26.95 | 7.17 | 50.37 | 15.51 |
ZmARF8 | Zm00001d001879 | 817 | B5,ARF,AUX_IAA | 90.99 | 6.37 | 30.11 | 6.24 | 47.12 | 16.52 |
ZmARF9 | Zm00001d003011 | 273 | B3,ARF | 29.73 | 7.58 | 17.95 | 5.86 | 56.78 | 19.41 |
ZmARF10 | Zm00001d002929 | 513 | B3,ARF | 55.45 | 6.40 | 14.81 | 3.51 | 65.50 | 16.18 |
ZmARF11 | Zm00001d043431 | 688 | B3,ARF | 74.99 | 7.28 | 16.42 | 4.94 | 64.97 | 13.66 |
ZmARF12 | Zm00001d041497 | 888 | B5,ARF,AUX_IAA | 97.84 | 6.08 | 29.73 | 8.00 | 46.96 | 15.32 |
ZmARF13 | Zm00001d042267 | 822 | B6,ARF,AUX_IAA | 91.85 | 6.91 | 19.83 | 4.99 | 59.73 | 15.45 |
ZmARF14 | Zm00001d041056 | 652 | B7,ARF,AUX_IAA | 71.86 | 7.43 | 15.95 | 3.53 | 65.18 | 15.34 |
ZmARF15 | Zm00001d043922 | 708 | B3,ARF | 77.97 | 7.11 | 14.69 | 4.24 | 66.10 | 14.97 |
ZmARF16 | Zm00001d039267 | 686 | B3,ARF | 76.72 | 6.29 | 19.97 | 4.52 | 57.58 | 17.93 |
ZmARF17 | Zm00001d053819 | 914 | B7,ARF,AUX_IAA | 100.94 | 6.03 | 29.65 | 4.92 | 52.08 | 13.35 |
ZmARF18 | Zm00001d051172 | 689 | B3,ARF | 73.69 | 7.36 | 20.39 | 4.78 | 61.04 | 13.78 |
ZmARF19 | Zm00001d050781 | 511 | B7,ARF,AUX_IAA | 56.73 | 6.83 | 19.77 | 4.89 | 55.38 | 19.96 |
ZmARF20 | Zm00001d049295 | 850 | B7,ARF,AUX_IAA | 93.15 | 7.01 | 20.82 | 5.41 | 58.47 | 15.29 |
ZmARF21 | Zm00001d014507 | 716 | B3,ARF | 77.52 | 7.13 | 19.17 | 4.41 | 60.28 | 16.14 |
ZmARF22 | Zm00001d014377 | 739 | B7,ARF,AUX_IAA | 82.00 | 6.99 | 24.63 | 5.01 | 54.80 | 15.56 |
ZmARF23 | Zm00001d015243 | 1 147 | B7,ARF,AUX_IAA | 127.24 | 6.08 | 33.48 | 6.54 | 42.55 | 17.44 |
ZmARF24 | Zm00001d014013 | 644 | B3,ARF | 70.96 | 6.97 | 19.57 | 4.66 | 59.94 | 15.84 |
ZmARF25 | Zm00001d014690 | 975 | B7,ARF,AUX_IAA | 107.54 | 6.60 | 30.87 | 7.08 | 47.38 | 14.67 |
ZmARF26 | Zm00001d016838 | 677 | B7,ARF,AUX_IAA | 75.13 | 6.30 | 19.50 | 4.58 | 59.23 | 16.69 |
ZmARF27 | Zm00001d039006 | 736 | B3,ARF | 80.42 | 7.83 | 15.22 | 4.08 | 65.08 | 15.62 |
ZmARF28 | Zm00001d000358 | 700 | B3,ARF | 75.51 | 7.56 | 17.86 | 4.29 | 61.14 | 16.71 |
ZmARF29 | Zm00001d038698 | 680 | B3,ARF | 73.94 | 6.86 | 16.18 | 4.41 | 66.32 | 13.09 |
ZmARF30 | Zm00001d011953 | 728 | B7,ARF,AUX_IAA | 81.43 | 7.66 | 15.25 | 3.16 | 65.66 | 15.93 |
ZmARF31 | Zm00001d012731 | 340 | B3,ARF | 37.38 | 7.95 | 23.24 | 5.00 | 49.41 | 22.35 |
ZmARF32 | Zm00001d025871 | 588 | B3,ARF | 63.91 | 8.77 | 18.54 | 4.08 | 63.10 | 14.29 |
ZmARF33 | Zm00001d023659 | 813 | B7,ARF,AUX_IAA | 89.71 | 7.25 | 20.33 | 4.09 | 59.75 | 15.83 |
ZmARF34 | Zm00001d026687 | 462 | B3,ARF | 50.56 | 5.41 | 17.32 | 3.68 | 58.01 | 21.00 |
ZmARF35 | Zm00001d026540 | 958 | B7,ARF,AUX_IAA | 105.29 | 6.44 | 28.50 | 4.91 | 53.03 | 13.57 |
ZmARF36 | Zm00001d045026 | 1 053 | B7,ARF,AUX_IAA | 116.75 | 6.67 | 37.42 | 6.84 | 42.36 | 13.39 |
Fig.2 ARF family protein phylogenetic tree of Arabidopsis, sorghum, rice and maize Note: At:Arabidopsis thaliana. Sb: Sorghum bicolor. Os:Oryza sativa. Zm:Zea mays.
Fig.3 Collinear analysis of protein sequences of ARF family members in Arabidopsis, sorghum, rice and maize Note: The genes connected by arcs and the same color have a collinear relationship.
顺式元件 Cis-element | 序列 Sequence | 功能 Function | 基因 Gene |
---|---|---|---|
ABRE | ACGTG | 脱落酸响应元件 | ZmARF1,ZmARF3~ZmARF17,ZmARF20~ZmARF26, ZmARF27~ZmARF36 |
ARE | AAACCA | 与厌氧诱导相关的调控元件 | ZmARF4,ZmARF5,ZmARF8,ZmARF9,ZmARF12~ZmARF21, ZmARF23,ZmARF25,ZmARF26,ZmARF29,ZmARF32, ZmARF33,ZmARF35 |
AuxRR-core | GGTCCAT | 调控生长素响应元件 | ZmARF1,ZmARF2,ZmARF7,ZmARF14,ZmARF17~ZmARF20, ZmARF22,ZmARF25,ZmARF26,ZmARF28,ZmARF35 |
CAT-box | GCCACT | 分生组织表达相关的元件 | ZmARF1~ZmARF3 |
TGACG-motif/ CGTCA-motif | TGACG/CGTCA | 茉莉酸甲酯响应元件 | ZmARF1~ZmARF13,ZmARF15~ZmARF26, ZmARF28-ZmARF32,ZmARF35,ZmARF36 |
GARE-motif | TCTGTTG | 赤霉素反应元件 | ZmARF2,ZmARF3,ZmARF8,ZmARF17,ZmARF26, ZmARF30,ZmARF31,ZmARF34-ZmARF36 |
GCN4-motif | TGAGTCA | 胚乳表达相关的元件 | ZmARF1,ZmARF4,ZmARF6,ZmARF14, ZmARF18~ZmARF20,ZmARF29,ZmARF32 |
LTR | CCGAAA | 低温响应 | ZmARF1~ZmARF3,ZmARF8,ZmARF11~ZmARF13, ZmARF18~ZmARF22,ZmARF24~ZmARF26,ZmARF28, ZmARF29,ZmARF33 |
MBS | CAACTG | 干旱诱导的MYB结合位点 | ZmARF1,ZmARF3~ZmARF7,ZmARF10~ZmARF13, ZmARF15~ZmARF20,ZmARF25,ZmARF26,ZmARF28, ZmARF30,ZmARF31,ZmARF34,ZmARF35 |
TCA-element | CCATCTTTTT | 水杨酸反应元件 | ZmARF1~ZmARF3,ZmARF5,ZmARF8,ZmARF10~ZmARF12, ZmARF14,ZmARF17,ZmARF20,ZmARF21,ZmARF24 ~ZmARF26,ZmARF28,ZmARF29,ZmARF32,ZmARF34 |
TC-rich repeats | ATTCTCTAAC | 参与防御和应激反应 | ZmARF1,ZmARF5,ZmARF7,ZmARF13,,ZmARF16, ZmARF17,ZmARF19,ZmARF29,ZmARF35 |
TGA-element | AACGAC | 生长素反应元件 | ZmARF2,ZmARF8,ZmARF16~ZmARF18,ZmARF20 ~ZmARF22,ZmARF24,ZmARF28,ZmARF30, ZmARF35 |
Table 2 Cis-element regulatory in prometer of ZmARFs gene family
顺式元件 Cis-element | 序列 Sequence | 功能 Function | 基因 Gene |
---|---|---|---|
ABRE | ACGTG | 脱落酸响应元件 | ZmARF1,ZmARF3~ZmARF17,ZmARF20~ZmARF26, ZmARF27~ZmARF36 |
ARE | AAACCA | 与厌氧诱导相关的调控元件 | ZmARF4,ZmARF5,ZmARF8,ZmARF9,ZmARF12~ZmARF21, ZmARF23,ZmARF25,ZmARF26,ZmARF29,ZmARF32, ZmARF33,ZmARF35 |
AuxRR-core | GGTCCAT | 调控生长素响应元件 | ZmARF1,ZmARF2,ZmARF7,ZmARF14,ZmARF17~ZmARF20, ZmARF22,ZmARF25,ZmARF26,ZmARF28,ZmARF35 |
CAT-box | GCCACT | 分生组织表达相关的元件 | ZmARF1~ZmARF3 |
TGACG-motif/ CGTCA-motif | TGACG/CGTCA | 茉莉酸甲酯响应元件 | ZmARF1~ZmARF13,ZmARF15~ZmARF26, ZmARF28-ZmARF32,ZmARF35,ZmARF36 |
GARE-motif | TCTGTTG | 赤霉素反应元件 | ZmARF2,ZmARF3,ZmARF8,ZmARF17,ZmARF26, ZmARF30,ZmARF31,ZmARF34-ZmARF36 |
GCN4-motif | TGAGTCA | 胚乳表达相关的元件 | ZmARF1,ZmARF4,ZmARF6,ZmARF14, ZmARF18~ZmARF20,ZmARF29,ZmARF32 |
LTR | CCGAAA | 低温响应 | ZmARF1~ZmARF3,ZmARF8,ZmARF11~ZmARF13, ZmARF18~ZmARF22,ZmARF24~ZmARF26,ZmARF28, ZmARF29,ZmARF33 |
MBS | CAACTG | 干旱诱导的MYB结合位点 | ZmARF1,ZmARF3~ZmARF7,ZmARF10~ZmARF13, ZmARF15~ZmARF20,ZmARF25,ZmARF26,ZmARF28, ZmARF30,ZmARF31,ZmARF34,ZmARF35 |
TCA-element | CCATCTTTTT | 水杨酸反应元件 | ZmARF1~ZmARF3,ZmARF5,ZmARF8,ZmARF10~ZmARF12, ZmARF14,ZmARF17,ZmARF20,ZmARF21,ZmARF24 ~ZmARF26,ZmARF28,ZmARF29,ZmARF32,ZmARF34 |
TC-rich repeats | ATTCTCTAAC | 参与防御和应激反应 | ZmARF1,ZmARF5,ZmARF7,ZmARF13,,ZmARF16, ZmARF17,ZmARF19,ZmARF29,ZmARF35 |
TGA-element | AACGAC | 生长素反应元件 | ZmARF2,ZmARF8,ZmARF16~ZmARF18,ZmARF20 ~ZmARF22,ZmARF24,ZmARF28,ZmARF30, ZmARF35 |
Fig.4 Gene Ontology of ARFs gene family in maize Note: The blue square represents the ID number of GO, and the small blue circle represents the gene number.
Fig.5 Relative expressions of ZmARFs gene in different tissues Note: R: Root. S: Stem. L: Leaf. FS: Female spikelet. T: Tassel. P: Pollen. E: Embry. EM: Endosperm.
Fig.6 Relative expressions of ZmARFs gene treated with exogenous hormones ABA, high temperature, NaCl and PEG Note:A-D: ABA treatment. E-H: High temperature. I-L: NaCl treatment. M-D: PEG treatment. Different lowercase letters indicate that the gene expression at different time points under the same treatment reaches significant difference level (P<0.05).
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