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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2517-2532.doi: 10.3724/SP.J.1006.2022.14185

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

谷子III型PRX基因家族全基因组鉴定及干旱胁迫下表达分析

马鑫磊1,2(), 许瑞琪2, 索晓曼2, 李婧实1,2, 顾鹏鹏1,2, 姚锐1,2, 林小虎1,2,*(), 高慧1,2,*()   

  1. 1河北省作物逆境生物学重点实验室, 河北秦皇岛 066004
    2河北科技师范学院农学与生物科技学院, 河北秦皇岛 066004
  • 收稿日期:2021-10-12 接受日期:2022-01-05 出版日期:2022-10-12 网络出版日期:2022-02-15
  • 通讯作者: 林小虎,高慧
  • 作者简介:第一作者联系方式: E-mail: maxinlei5966@126.com
  • 基金资助:
    国家“十三五”重点研发计划项目(2019YFD1001701-2);河北省现代农业产业技术体系创新团队(杂粮杂豆)项目(HBCT2018070404);河北省自然科学基金项目(C2019407089);河北省高等学校科学技术研究项目(QN2020154);河北省在读研究生创新能力培养资助项目(CXZZSS2021152)

Genome-wide identification of the Class III PRX gene family in foxtail millet (Setaria italica L.) and expression analysis under drought stress

MA Xin-Lei1,2(), XU Rui-Qi2, SUO Xiao-Man2, LI Jing-Shi1,2, GU Peng-Peng1,2, YAO Rui1,2, LIN Xiao-Hu1,2,*(), GAO Hui1,2,*()   

  1. 1Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao 066004, Hebei, China
    2College of Life Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, Hebei, China
  • Received:2021-10-12 Accepted:2022-01-05 Published:2022-10-12 Published online:2022-02-15
  • Contact: LIN Xiao-Hu,GAO Hui
  • Supported by:
    National Key Research and Development Program of the 13th Five-Year Plan of China(2019YFD1001701-2);Modern Agricultural Industrial Technology System Innovation Team (Grain and Soybean) Project of Hebei Province(HBCT2018070404);National Natural Science Foundation of Hebei Province(C2019407089);Science and Technology Research Project of Higher Education in Hebei Province(QN2020154);Innovation Ability Training Project of Postgraduate Students in Hebei Province(CXZZSS2021152)

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摘要：

III型过氧化物酶(Class III peroxidase, PRX)是植物中特有的过氧化物酶家族, 在植物生长发育以及非生物胁迫中发挥重要作用。谷子作为C4植物是禾本科抗逆研究的模式植物, 然而目前对于谷子中III型过氧化物酶家族基因功能鲜有报道。为探究谷子III型过氧化物酶基因家族(SitPRXs)在干旱胁迫和ABA诱导下的表达模式, 进行了全基因组表达分析。本研究利用生物信息学方法在谷子全基因组中鉴定出132个III型PRX基因家族成员, 并根据其在染色体上位置顺序依次命名为SitPRX1~SitPRX132。通过对谷子、拟南芥和水稻的系统进化分析将其分为5个亚家族, 基因结构和保守基序分析表明同一亚家族具有较高的保守性。基因复制分析显示, 17个SitPRX基因(13%)存在片段复制, 78个SitPRX基因(59%)存在串联复制, 串联复制事件在SitPRX基因扩增中起重要作用。谷子与拟南芥、水稻和玉米的物种间同源性分析显示谷子中大多数SitPRXs是在双子叶植物和单子叶植物分化后形成的。转录组分析显示, SitPRX基因家族成员在谷子幼苗、根、茎、叶以及圆锥花序中表达存在差异。启动子顺式作用元件分析显示, 79个SitPRXs含有与干旱胁迫响应相关的顺式作用元件, 进一步qRT-PCR分析显示, SitPRX12、SitPRX41、SitPRX81、SitPRX110和SitPRX126受PEG和ABA诱导表达, 表明这些基因可能通过ABA依赖的信号通路来调控和响应干旱胁迫, 可作为进一步研究III型PRX基因家族抗旱功能的候选基因。研究结果为全面解析SitPRX基因结构与生物学功能、抗旱分子机制以及分子育种提供了新信息, 以期为今后培育高效抗逆作物新品种提供思路。

关键词: III型过氧化物酶, 基因家族分析, 干旱胁迫响应, 谷子

Abstract:

Class III peroxidases (PRX) are a family of plant-specific peroxidases that play an important role in plant growth and development as well as in abiotic stresses. Foxtail millet (Setaria italica L.), as a C4 plant, is a model plant for stress resistance. However, the function of class III peroxidases family genes is rarely reported in foxtail millet. A genome-wide expression analysis was conducted to investigate the expression pattern of class III peroxidase gene family (SitPRXs) under drought stress and ABA induction. In this study, 132 members of the Class III PRX gene family were identified in the whole genome in foxtail millet by bioinformatics and named SitPRX1-SitPRX132 according to their chromosomal position. 132 members were classified into Mα, Mβ, Mγ, MIKCC, and MIKC* subfamilies by phylogenetic analysis of foxtail millet, Arabidopsis, and rice. Gene structure and conserved motif analysis indicated a high level of conservation in the same subfamily. Gene duplication analysis revealed fragmental duplication in 17 SitPRX genes (13%) and tandem duplication in 78 SitPRX genes (59%), thus tandem duplication events playing an important role in SitPRX gene amplification. Interspecies homology analysis with Arabidopsis, rice and maize revealed that most SitPRXs were formed after dicotyledonous and monocotyledonous plants diverged. Transcriptome analysis implied that members of the SitPRX gene family were differentially expressed in seedlings, roots, stems, and leaves, as well as in panicles in foxtail millet. Analysis of promoter cis-acting elements showed that 79 SitPRXs contained cis-acting elements associated with drought stress response, and further qRT-PCR analysis showed that SitPRX12, SitPRX41, SitPRX81, SitPRX110, and SitPRX126 were induced to be expressed by PEG and ABA, suggesting that these genes may be regulated through an ABA-dependent signalling pathway in response to drought stress and could be used as these genes may be candidates for further studies on the drought resistance function of the class III PRX gene family. These results of this study provide new information for the comprehensive analysis of the structure and biological functions of SitPRX genes, the molecular mechanism of drought resistance, and molecular breeding in foxtail millet, with a view of providing ideas for the breeding of new varieties of highly efficient stress-resistant crops in the future.

Key words: class III peroxidase, gene family analysis, drought stress response, Setaria italica

附表1

SitPRX基因家族qRT-PCR引物"

基因名称
Gene name		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
SitPRX9 AGCCAACGCTGGTCTGATT TTCTGTGACATCCACCCGTC
SitPRX12 GGCCAGCCCTCGTTTTCTAT TTTGCTCTGCTCCGCTGTTT
SitPRX33 ACTGCTTCGTCAGGGGTTG GTCGTCGATCACCTCGAACG
SitPRX41 GTCCGTCGCACTTGAT AAGGCTGAGACGATGATC
SitPRX49 ACTACTCCAAGACATGCCCG ACTGATCCATCACATCCCTGC
SitPRX72 TGATGCCGTTGATCTGACCG TGTGGGCACCGACTAATGTT
SitPRX81 GTGTCGTCCAGTTCTACC CTCGGCAAGCGTTGAA
SitPRX87 ACGTGATTCGTCAGTGTGCC GGATGAGCCTTTCCCAGAGT
SitPRX110 GTCGTGGTCTTATCGGGAGC TCCAGCGTCGGATCTACTGA
SitPRX126 GAGCCCGTGAAGGAGGAGTT CCTCAGATGGTCAGAACCCTTA
SitEF1a-2 TGACTGTGCTGTCCTCATCA GTTGCAGCAGCAAATCATCT

附表2

SitPRX基因家族蛋白质理化性质"

基因名称
Gene name		 序列名称
Sequence ID		 染色体
Chr.		 氨基酸
Size (aa)		 分子量
Molecular weight (kD)		 等电点
pI		 不稳定系数
Instability index		 脂肪系数
Aliphatic index
SitPRX1 Seita.1G022200 1 323 34.01297 4.65 46.44 86.19
SitPRX2 Seita.1G022300 1 320 33.99131 6.06 35.99 86.94
SitPRX3 Seita.1G022500 1 321 34.06693 6.93 35.87 94.92
SitPRX4 Seita.1G022900 1 323 32.94039 8.77 35.46 85.76
SitPRX5 Seita.1G023000 1 320 32.79593 5.16 34.89 87.69
SitPRX6 Seita.1G023100 1 325 33.59487 8.61 50.68 84.25
SitPRX7 Seita.1G079000 1 347 36.77990 8.08 43.59 83.00
SitPRX8 Seita.1G170200 1 342 36.70845 6.44 24.42 85.67
SitPRX9 Seita.1G192100 1 478 51.19841 5.18 50.25 67.80
SitPRX10 Seita.1G281400 1 331 35.85566 5.74 40.75 79.64
SitPRX11 Seita.1G380000 1 327 33.90540 7.10 43.36 83.49
SitPRX12 Seita.2G236400 2 343 37.36357 5.82 35.23 81.40
SitPRX13 Seita.2G266900 2 337 35.49031 6.00 33.43 80.53
SitPRX14 Seita.2G320200 2 357 38.91543 9.00 30.86 79.58
SitPRX15 Seita.2G371600 2 324 33.41573 9.27 41.70 84.51
SitPRX16 Seita.2G406700 2 413 44.45746 6.41 46.79 70.70
SitPRX17 Seita.2G407000 2 364 38.15130 5.98 44.02 79.95
SitPRX18 Seita.2G407100 2 372 39.60795 6.89 30.53 86.34
SitPRX19 Seita.2G407200 2 553 57.24306 7.56 78.21 59.89
SitPRX20 Seita.2G407400 2 350 37.48503 9.07 39.39 82.80
SitPRX21 Seita.2G411900 2 328 35.06796 6.33 38.71 82.77
SitPRX22 Seita.2G430900 2 317 33.14664 9.11 38.83 90.98
SitPRX23 Seita.2G431000 2 351 36.48558 6.57 35.11 94.93
SitPRX24 Seita.2G431100 2 312 33.15028 5.48 48.85 84.87
SitPRX25 Seita.2G431200 2 312 32.73764 5.67 44.13 84.55
SitPRX26 Seita.2G431300 2 318 33.09396 6.19 40.08 79.91
SitPRX27 Seita.2G431500 2 311 32.45267 6.97 39.19 87.97
SitPRX28 Seita.3G004800 3 323 33.71242 6.23 33.82 97.99
SitPRX29 Seita.3G004900 3 332 35.23111 6.89 42.79 90.33
SitPRX30 Seita.3G005100 3 348 36.75468 5.05 38.65 93.42
SitPRX31 Seita.3G005200 3 350 37.21731 5.65 42.99 91.23
SitPRX32 Seita.3G022600 3 333 35.59788 9.16 40.76 91.23
SitPRX33 Seita.3G052400 3 344 37.47289 8.51 32.37 91.10
基因名称
Gene name		 序列名称
Sequence ID		 染色体
Chr.		 氨基酸
Size (aa)		 分子量
Molecular weight (kD)		 等电点
pI		 不稳定系数
Instability index		 脂肪系数
Aliphatic index
SitPRX34 Seita.3G052500 3 328 34.69369 8.34 32.54 83.63
SitPRX35 Seita.3G052600 3 321 33.78561 6.30 32.81 80.9
SitPRX36 Seita.3G052700 3 328 34.82772 8.33 32.72 83.35
SitPRX37 Seita.3G052800 3 325 33.93987 7.51 36.99 85.97
SitPRX38 Seita.3G052900 3 333 36.42036 6.26 38.96 79.97
SitPRX39 Seita.3G053000 3 334 35.86602 9.36 37.01 85.36
SitPRX40 Seita.3G053100 3 336 36.71877 7.13 42.16 78.96
SitPRX41 Seita.3G190300 3 345 37.79519 5.54 43.42 85.10
SitPRX42 Seita.3G190400 3 326 35.42539 6.25 34.41 79.05
SitPRX43 Seita.3G234900 3 318 34.02132 5.41 42.17 87.52
SitPRX44 Seita.3G235000 3 317 34.15256 5.68 46.78 87.76
SitPRX45 Seita.3G235100 3 324 34.70026 6.65 45.38 86.51
SitPRX46 Seita.3G270300 3 337 36.09192 7.52 34.24 83.59
SitPRX47 Seita.3G347500 3 344 35.56654 8.59 39.48 88.72
SitPRX48 Seita.4G105100 4 342 36.82120 8.78 38.15 81.40
SitPRX49 Seita.4G122600 4 378 41.42903 5.03 27.18 78.23
SitPRX50 Seita.4G134900 4 364 39.37921 7.09 34.97 94.64
SitPRX51 Seita.4G135000 4 328 35.59600 8.29 28.43 91.34
SitPRX52 Seita.4G135100 4 327 35.10916 6.45 28.98 88.44
SitPRX53 Seita.4G165000 4 331 35.97672 5.20 47.40 82.90
SitPRX54 Seita.4G165100 4 330 35.90367 5.20 48.44 83.42
SitPRX55 Seita.4G165200 4 333 36.09562 5.34 47.66 76.58
SitPRX56 Seita.4G176600 4 359 38.13847 9.37 37.13 87.10
SitPRX57 Seita.4G176800 4 312 33.60469 10.58 48.94 78.37
SitPRX58 Seita.4G247300 4 339 36.26934 8.95 36.81 78.94
SitPRX59 Seita.4G247400 4 319 34.40781 6.72 39.28 79.56
SitPRX60 Seita.4G247500 4 318 34.20550 5.93 39.72 76.76
SitPRX61 Seita.4G247600 4 319 34.11854 5.24 33.72 80.00
SitPRX62 Seita.5G029700 5 347 38.28653 5.96 33.92 92.51
SitPRX63 Seita.5G029800 5 348 38.20653 6.31 34.03 93.65
SitPRX64 Seita.5G030000 5 330 34.54058 4.73 33.19 82.00
SitPRX65 Seita.5G030100 5 317 33.48703 6.30 42.21 82.65
SitPRX66 Seita.5G030300 5 335 36.55180 9.82 36.56 89.13
SitPRX67 Seita.5G046600 5 347 36.50828 9.00 38.16 84.18
SitPRX68 Seita.5G053000 5 367 39.71532 8.83 47.85 86.65
SitPRX69 Seita.5G053100 5 338 36.02722 9.03 36.04 92.43
SitPRX70 Seita.5G053200 5 338 36.38048 7.61 34.48 90.65
SitPRX71 Seita.5G053300 5 347 38.32482 7.62 39.97 88.85
SitPRX72 Seita.5G122000 5 327 35.14673 5.97 42.75 84.77
SitPRX73 Seita.5G145500 5 321 33.72513 8.87 35.40 84.98
SitPRX74 Seita.5G155100 5 359 37.33727 6.11 35.90 84.37
SitPRX75 Seita.5G155200 5 370 38.68255 5.64 41.43 87.65
SitPRX76 Seita.5G155300 5 362 38.49054 6.44 37.28 83.62
SitPRX77 Seita.5G164800 5 344 36.95184 6.69 45.91 84.24
SitPRX78 Seita.5G170000 5 322 33.87709 9.27 36.20 90.09
SitPRX79 Seita.5G191900 5 337 36.27433 8.39 45.24 88.37
SitPRX80 Seita.5G293800 5 367 39.46438 5.10 43.22 78.45
SitPRX81 Seita.5G344000 5 343 37.01494 4.79 38.86 86.21
SitPRX82 Seita.5G462500 5 357 38.14559 6.11 34.90 94.87
SitPRX83 Seita.5G463200 5 356 37.71887 8.59 45.69 84.44
基因名称
Gene name		 序列名称
Sequence ID		 染色体
Chr.		 氨基酸
Size (aa)		 分子量
Molecular weight (kD)		 等电点
pI		 不稳定系数
Instability index		 脂肪系数
Aliphatic index
SitPRX84 Seita.5G463300 6 362 39.21183 9.01 35.06 87.10
SitPRX85 Seita.6G090100 6 319 34.70663 5.30 35.00 85.92
SitPRX86 Seita.6G224300 6 334 36.59959 6.39 47.66 78.56
SitPRX87 Seita.6G239800 6 288 31.41981 7.02 35.54 84.44
SitPRX88 Seita.7G006800 7 330 35.41114 5.21 31.65 90.64
SitPRX89 Seita.7G023900 7 292 31.98142 6.67 42.64 76.95
SitPRX90 Seita.7G102200 7 342 36.98169 8.79 40.93 72.13
SitPRX91 Seita.7G128200 7 336 35.92006 9.45 44.80 85.03
SitPRX92 Seita.7G154400 7 495 50.08982 8.99 68.05 75.66
SitPRX93 Seita.7G247400 7 359 38.99986 8.75 44.15 85.32
SitPRX94 Seita.7G265300 7 320 33.99704 4.82 33.00 80.28
SitPRX95 Seita.7G271000 7 364 38.88408 6.98 41.86 80.19
SitPRX96 Seita.7G271100 7 362 38.69103 8.01 37.25 84.97
SitPRX97 Seita.7G271400 7 337 35.63451 6.92 37.98 85.19
SitPRX98 Seita.7G277800 7 331 34.16931 4.39 34.08 93.02
SitPRX99 Seita.7G283600 7 311 33.94250 7.13 45.64 78.55
SitPRX100 Seita.7G327600 7 321 33.66502 8.06 35.56 80.56
SitPRX101 Seita.7G327800 7 317 33.97633 8.32 34.29 78.52
SitPRX102 Seita.8G015100 8 331 34.92851 8.31 35.24 81.99
SitPRX103 Seita.8G015200 8 355 37.31111 8.71 40.05 80.82
SitPRX104 Seita.8G100100 8 339 35.55516 6.10 32.34 85.75
SitPRX105 Seita.8G106600 8 321 34.59168 8.90 45.52 82.99
SitPRX106 Seita.9G081300 9 324 34.07148 4.44 33.58 93.77
SitPRX107 Seita.9G081400 9 326 34.65617 5.28 36.89 84.48
SitPRX108 Seita.9G186200 9 345 37.93747 9.15 34.05 87.33
SitPRX109 Seita.9G186300 9 333 35.75638 9.36 59.24 96.37
SitPRX110 Seita.9G282900 9 327 35.40278 4.73 28.03 88.53
SitPRX111 Seita.9G298200 9 340 36.51632 4.92 38.22 86.15
SitPRX112 Seita.9G298300 9 343 36.40207 5.40 28.97 84.26
SitPRX113 Seita.9G298400 9 338 36.05723 4.52 34.97 82.28
SitPRX114 Seita.9G298500 9 342 36.79289 4.50 43.85 76.78
SitPRX115 Seita.9G316400 9 330 35.44946 8.90 37.57 89.33
SitPRX116 Seita.9G316500 9 325 34.91006 5.95 32.18 94.00
SitPRX117 Seita.9G316600 9 260 28.07594 8.94 43.80 81.04
SitPRX118 Seita.9G316700 9 329 35.34733 9.09 36.90 89.27
SitPRX119 Seita.9G342200 9 323 33.49696 7.55 34.67 83.10
SitPRX120 Seita.9G355500 9 330 34.04416 5.30 37.53 87.73
SitPRX121 Seita.9G392700 9 330 34.59363 7.06 38.68 84.88
SitPRX122 Seita.9G392800 9 343 36.74207 5.66 45.64 85.63
SitPRX123 Seita.9G393100 9 330 35.86731 9.12 42.48 82.52
SitPRX124 Seita.9G393200 9 322 34.4055 7.47 35.87 82.11
SitPRX125 Seita.9G411500 9 330 34.90751 8.08 40.40 86.48
SitPRX126 Seita.9G444200 9 250 27.32902 5.69 40.56 75.80
SitPRX127 Seita.9G477900 9 332 34.68019 5.54 31.09 91.17
SitPRX128 Seita.9G478000 9 392 42.26585 9.00 44.72 75.97
SitPRX129 Seita.9G478300 9 339 36.23680 4.83 44.50 82.18
SitPRX130 Seita.9G537300 9 498 52.30507 5.63 40.28 86.65
SitPRX131 Seita.9G562400 9 334 35.11090 5.62 42.16 81.92
SitPRX132 Seita.9G562600 9 331 34.28555 5.22 29.95 81.48

图1

拟南芥、水稻与谷子Class III PRX基因家族成员系统进化树 AtPRX: 拟南芥III型PRX基因(黄色星形); SitPRX: 谷子III型PRX基因(红色圆形); OsPRX: 水稻III型PRX基因(绿色圆形)。"

图2

SitPRX基因家族成员的基因结构和保守基序 Motif: 保守基序; UTR: 非翻译区; CDS: 编码区序列。"

图3

SitPRX基因家族成员在谷子染色体上的分布 Sit1~Sit9代表谷子1号至9号染色体。"

图4

SitPRX基因家族共线性分析"

图5

SitPRX基因家族成员与拟南芥、水稻和玉米PRX基因共线性分析 A: 谷子与拟南芥PRX基因共线性分析; B: 谷子与水稻PRX基因共线性分析; C: 谷子与玉米PRX基因共线性分析。"

图6

SitPRX基因家族成员组织表达谱 Seed为吸水3 d种子; Seedling为2周龄幼苗全株; Root为灌浆期根; Stem为灌浆期茎; Leaf 1为2周龄苗的第1片完全伸展的叶; Leaf 2为1月龄苗的第2片叶; Leaf 3为旗叶; Leaf 4为第4片叶; Panicle 1为未成熟的花序; Panicle 2为授粉期的花序; Panicle 3为灌浆期的花序。"

图7

SitPRX基因家族启动子顺式作用元件统计 Light-responsive: 光响应元件; Stress-responsive: 胁迫响应元件; Hormone-responsive: 激素响应元件。"

图8

SitPRX基因家族启动子顺式作用元件分析"

图9

SitPRX基因家族成员在干旱胁迫处理和ABA诱导下的表达模式 *表示PEG或ABA处理0.5 h、1 h、3 h与未处理(0 h)在0.05水平显著差异。"

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