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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (11): 2991-3006.doi: 10.3724/SP.J.1006.2023.34027

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜BnKNOX基因家族的鉴定与分析

陈吴钧(), 刘江栋, 蒋凯旋, 王幼平, 蒋金金()   

  1. 扬州大学生物科学与技术学院, 江苏扬州 225009
  • 收稿日期:2023-02-10 接受日期:2023-04-17 出版日期:2023-11-12 网络出版日期:2023-04-24
  • 通讯作者: 蒋金金, E-mail: jjjiang@yzu.edu.cn
  • 作者简介:E-mail: chenwujun0921@163.com
  • 基金资助:
    国家自然科学基金项目(32272055);国家自然科学基金项目(31972963);江苏省研究生实践创新计划项目(SJCX21_1602);江苏省“青蓝工程”项目资助。

Identification and analysis of BnKNOX gene family in Brassica napus

CHEN Wu-Jun(), LIU Jiang-Dong, JIANG Kai-Xuan, WANG You-Ping, JIANG Jin-Jin()   

  1. College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2023-02-10 Accepted:2023-04-17 Published:2023-11-12 Published online:2023-04-24
  • Supported by:
    National Natural Science Foundation of China(32272055);National Natural Science Foundation of China(31972963);Graduate Training Program for Innovation and Entrepreneurship(SJCX21_1602);Qinglan Project of Jiangsu Province.

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摘要：

植物特异的KNOTTED-LIKE HOMEOBOX (KNOX)蛋白属于转录调控因子家族, 该家族在植物生长发育过程和各种胁迫应答中发挥着重要的作用。KNOX蛋白中存在4个保守的结构域: TALE (three amino acid loop extension)类型的HD (homeodomain)、ELK结构域, 以及2个亚结构域KNOX1和KNOX2。目前, 甘蓝型油菜的BnKNOX基因家族还未有系统的研究报道。本研究通过生物信息学分析鉴定获得甘蓝型油菜的36个BnKNOX家族成员。通过序列比对和系统发育树分析, 将其分为3个亚家族(I、II和M类)。进化分析表明, 全基因组复制(whole genome duplication, WGD)和片段复制(segmental duplication)是BnKNOX基因家族扩张的主要动力。基于甘蓝型油菜不同发育时期组织/器官的RNA-seq分析发现, 该基因家族的BnKNAT25/26/29/30在胚乳和种子发育过程中特异表达, 而BnKNAT31/32/34在成熟种子中高表达。通过BnKNOX家族的顺式作用元件分析和非生物胁迫条件下的表达模式分析, 本文鉴定获得17个响应干旱和渗透胁迫的BnKNOX成员。

关键词: 甘蓝型油菜, KNOX, 基因家族, 表达模式, 非生物胁迫

Abstract:

The plant specific KNOTTED-LIKE HOMEOBOX (KNOX) protein is a transcription factor family that plays an important role in plant growth and development, as well as responses to various stresses. KNOX proteins contain four conserved domains [a three amino acid loop extension (TALE) type homeodomain (HD), ELK domain, and two subdomains (KNOX1 and KNOX2)]. At present, the comprehensive study of BnKNOX genes in Brassica napus has not been reported yet. In this study, 36 BnKNOX family members were identified in B. napus genome via bioinformatic analyses, which were classified into three sub-families (I, II, and M-type) based on sequence alignment and phylogenetic analyses. Evolutionary analysis showed that the whole genome duplication (WGD) and segmental duplication were the main driving forces for the expansion of BnKNOX gene family. Based on the RNA-seq data of developing tissues and organs of B. napus, BnKNAT25/26/29/30 were specifically expressed in endosperm and developing seeds, while BnKNAT31/32/34 were highly expressed in mature seeds. We analyzed the cis-acting elements and expression pattern of BnKNOXs under various abiotic stresses, and identified 17 BnKNOX members that might be involved in drought and osmotic stress responses.

Key words: Brassica napus, KNOX, gene family, expression pattern, abiotic stress

表1

本研究中用到的qPCR引物"

基因名称
Gene name		 正向引物序列
Forward primer sequence (5'-3')		 反向引物序列
Reverse primer sequence (5'-3')
BnKNAT1 AGCCATCCACAATACTCAAGAA CGCCGTAATTTTATCAACCACT
BnKNAT2 AGATTAGCATGTTGTGTCAGGA ATCCACTGTACTTCTTCAGCAA
BnKNAT3 ACCTGAGGTGGTCGATAAAATT AAGAAACGACCCACATGAATTG
BnKNAT4 CGAAAATCGCTTCTCATCCTTT CGTTTCGATCTTGTTCAGGAAA
BnKNAT5 TTCTTCGGAGAGTCTTATGTCG GAATCTCTTCCAACACATACGC
BnKNAT11 CTCTCATCCACTATACGAGCAG AGTGGTCAAGCTCCTTATCATC
BnKNAT12 GTGACGCCATGGAAAACATTAC CTGCTCGTATAGTGGATGAGAG
BnKNAT13 CACTATACGAACGGCTTTTGTC GTCCATAGTAGAGTACTTGGCC
BnKNAT18 GATGGAATGTACGGCTTTCATC AGTCGGAAGGAAACATCAGATT
BnKNAT19 GAAAGCTACCAAGAGAAGCAAG CAAAAGGCATATTCTCGGACTG
BnKNAT20 CCTTCTGATTACCAAACCTTGC TACAAAGGATGACAAGCGATCT
BnKNAT22 GTCTCTCTCGGTATCATCAAGG CCTTGCGAGATCCGACTTATAT
BnKNAT23 ATGTGACTACTCAGATAAGCCG GGATACGAAGGATGACAAGCTA
BnKNAT24 TGACACAATGACAATGGAGGTA ATCTTCGCATATTTGTTTCCCG
BnKNAT25 TACCATGTGCGAGCAATTATTG GCTGTTCTTTGAAGCTACACAA
BnKNAT33 TAAGGGAGTTGAAGGAAGCAAT TAGCACCGAATATAGCTGTCAG
BnSTM2 GTAGTAATGGACGCAACACATC GTGCAACGTTCCTAAGTATTCC

图1

甘蓝型油菜BnKNOX蛋白结构域的分布和组成 A: BnKNOX蛋白结构示意图; B: KNOX1结构域; C: KNOX2结构域; D: ELK结构域; E: HD结构域。"

表2

甘蓝型油菜BnKNOX蛋白家族的基本信息"

基因号
Gene ID		 基因名
Gene name		 拟南芥号
Arabidopsis thaliana locus		 蛋白长度
Protein length (AA)		 分子量
Molecular weight (kD)		 等电点Isoelectric point (pI) 亚细胞定位
Localization
BnaA03g23610D BnKNAT1 AT4G08150.1 402 46.36 5.82 细胞核Nucleus
BnaC03g28030D BnKNAT2 AT4G08150.1 193 23.07 7.55 细胞核Nucleus
BnaCnng59830D BnKNAT3 AT4G08150.1 349 40.19 5.89 细胞核Nucleus
BnaA02g14950D BnKNAT4 AT1G70510.1 327 36.94 4.81 细胞核Nucleus
BnaC02g19900D BnKNAT5 AT1G70510.1 327 36.90 4.80 细胞核Nucleus
BnaA02g32110D BnKNAT6 AT5G25220.1 420 46.29 5.40 细胞核Nucleus
BnaA06g27560D BnKNAT7 AT5G25220.1 299 33.43 5.82 细胞核Nucleus
BnaC02g40790D BnKNAT8 AT5G25220.1 404 44.84 5.44 细胞核Nucleus
BnaC07g29530D BnKNAT9 AT5G25220.1 444 48.91 5.11 细胞核Nucleus
BnaA02g00810D BnKNAT10 AT5G11060.1 393 44.28 5.65 细胞核Nucleus
BnaA03g03190D BnKNAT11 AT5G11060.1 386 43.15 5.67 细胞核Nucleus
BnaC03g04580D BnKNAT12 AT5G11060.1 302 33.77 5.99 细胞核Nucleus
BnaCnng20070D BnKNAT13 AT5G11060.1 393 44.23 5.62 细胞核Nucleus
BnaA01g04870D BnKNAT14 AT4G32040.1 374 41.91 5.56 细胞核Nucleus
BnaA03g51900D BnKNAT15 AT4G32040.1 382 43.18 5.48 细胞核Nucleus
BnaC01g06410D BnKNAT16 AT4G32040.1 374 41.86 5.71 细胞核Nucleus
BnaC07g43650D BnKNAT17 AT4G32040.1 400 45.35 5.37 细胞核Nucleus
BnaA08g20500D BnKNAT18 AT1G23380.1 208 22.92 4.49 细胞核Nucleus
BnaA08g20510D BnKNAT19 AT1G23380.1 121 14.03 8.25 细胞核Nucleus
BnaA09g31100D BnKNAT20 AT1G23380.1 235 26.11 4.41 细胞核Nucleus
BnaAnng30720D BnKNAT21 AT1G23380.1 204 23.26 5.96 细胞核Nucleus
BnaC05g18670D BnKNAT22 AT1G23380.1 221 24.45 4.35 细胞核Nucleus
BnaC08g06320D BnKNAT23 AT1G23380.1 314 35.23 5.10 细胞核Nucleus
BnaCnng70390D BnKNAT24 AT1G23380.2 205 23.48 6.22 细胞核Nucleus
BnaA09g12980D BnKNAT25 AT1G62990.1 293 33.02 5.62 细胞核Nucleus
BnaA09g52990D BnKNAT26 AT1G62990.1 294 33.10 5.85 细胞核Nucleus
BnaC04g20090D BnKNAT27 AT1G62990.1 104 11.46 4.90 细胞核Nucleus
BnaC04g20110D BnKNAT28 AT1G62990.1 222 25.73 7.84 细胞核Nucleus
BnaC09g12900D BnKNAT29 AT1G62990.1 102 11.09 5.15 细胞核Nucleus
BnaCnng51440D BnKNAT30 AT1G62990.1 294 33.09 5.78 细胞核Nucleus
BnaA06g09570D BnKNAT31 AT1G14760.2 141 16.25 4.57 细胞核Nucleus
BnaA09g45470D BnKNAT32 AT1G14760.2 135 15.31 4.36 细胞核Nucleus
BnaC05g10940D BnKNAT33 AT1G14760.2 137 15.70 4.95 细胞核Nucleus
BnaC08g39310D BnKNAT34 AT1G14760.2 135 15.25 4.37 细胞核Nucleus
BnaA09g13310D BnSTM1 AT1G62360.1 383 43.11 5.82 细胞核Nucleus
BnaC09g13580D BnSTM2 AT1G62360.1 383 43.20 5.92 细胞核Nucleus

图2

甘蓝型油菜、拟南芥、甘蓝和白菜型油菜中KNOX蛋白的系统进化分析"

图3

甘蓝型油菜BnKNOX基因家族的基因结构和保守基序分析 A: BnKNOX蛋白的系统进化分析; B: BnKNOX蛋白的保守基序分析, Motif 1~15为不同颜色代表的基序组成; C: BnKNOX基因结构。UTR: 非翻译区; CDS: 编码区。"

图4

BnKNOX基因的染色体分布及组内共线性分析"

附表1

甘蓝型油菜BnKNOX基因的复制类型"

基因号
Gene ID		 基因名称
Gene name		 复制方式
Duplication type
BnaA03g23610D BnKNAT1 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC03g28030D BnKNAT2 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng59830D BnKNAT3 分散复制Dispersed duplication
BnaA02g14950D BnKNAT4 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC02g19900D BnKNAT5 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA02g32110D BnKNAT6 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA06g27560D BnKNAT7 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC02g40790D BnKNAT8 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC07g29530D BnKNAT9 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA02g00810D BnKNAT10 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA03g03190D BnKNAT11 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC03g04580D BnKNAT12 分散复制Dispersed duplication
BnaCnng20070D BnKNAT13 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA01g04870D BnKNAT14 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA03g51900D BnKNAT15 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC01g06410D BnKNAT16 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC07g43650D BnKNAT17 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA08g20500D BnKNAT18 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA08g20510D BnKNAT19 分散复制Dispersed duplication
BnaA09g31100D BnKNAT20 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaAnng30720D BnKNAT21 分散复制Dispersed duplication
BnaC05g18670D BnKNAT22 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC08g06320D BnKNAT23 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng70390D BnKNAT24 分散复制Dispersed duplication
BnaA09g12980D BnKNAT25 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g52990D BnKNAT26 分散复制Dispersed duplication
BnaC04g20090D BnKNAT27 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC04g20110D BnKNAT28 分散复制Dispersed duplication
BnaC09g12900D BnKNAT29 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaCnng51440D BnKNAT30 分散复制Dispersed duplication
BnaA06g09570D BnKNAT31 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g45470D BnKNAT32 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC05g10940D BnKNAT33 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC08g39310D BnKNAT34 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaA09g13310D BnSTM1 全基因组复制或片段复制Whole genome duplication or segmental duplication
BnaC09g13580D BnSTM2 全基因组复制或片段复制Whole genome duplication or segmental duplication

图5

甘蓝型油菜与拟南芥、白菜型油菜和甘蓝KNOX基因的共线性关系"

图6

BnKNOX基因在甘蓝型油菜不同组织和发育阶段的表达模式"

附表2

甘蓝型油菜BnKNOX基因在不同组织和发育阶段的RNA-seq数据(FPKM)"

基因号
Gene ID		 基因名称Gene name 叶片Leaf 子叶Cotyledon 下胚轴Hypocotyl 根
Root		 茎尖分生组织SAM 茎Stem 花苞Bud 花Flower 胚乳Endosperm 授粉后14 d角果Silique-14 DAP 授粉后21 d种子Seed-21 DAP 授粉后28 d种子Seed-28 DAP 授粉后35 d种子Seed-35 DAP 授粉后42 d种子Seed-42 DAP 授粉后50 d种子Seed-50 DAP
BnaA03g23610D BnKNAT1 0.016 0.010 38.382 1.843 3.479 29.144 1.896 2.620 0.005 0.915 0.118 0.771 0.135 0.038 0.000
BnaC03g28030D BnKNAT2 0.016 0.200 45.299 2.049 5.101 51.947 2.567 3.286 0 1.399 0.370 1.185 0.139 0.023 0.018
BnaCnng59830D BnKNAT3 0 0.027 14.658 0.836 1.934 13.746 0.691 0.851 0 0.425 0.207 0.656 0.041 0 0
BnaA02g14950D BnKNAT4 0.018 0.364 6.640 2.548 1.230 3.904 0.957 0.890 0 0.746 0.133 1.078 0.471 0.998 1.078
BnaC02g19900D BnKNAT5 0.191 0.507 8.285 2.451 4.376 9.119 1.963 1.544 0 1.744 0.438 0.989 0.543 1.121 0.927
BnaA02g32110D BnKNAT6 2.760 10.350 5.929 1.369 4.090 2.329 5.397 8.268 0.830 9.239 2.211 1.630 0.838 1.501 1.715
BnaA06g27560D BnKNAT7 15.294 66.703 14.521 5.061 45.785 7.394 21.312 27.772 8.066 26.798 13.314 8.149 3.248 5.073 2.501
BnaC02g40790D BnKNAT8 3.086 21.930 18.387 3.817 7.507 2.332 3.834 2.333 0.439 8.187 1.745 0.699 0.251 0.962 2.632
BnaC07g29530D BnKNAT9 21.780 35.189 8.946 10.544 48.375 8.729 24.791 30.841 4.942 31.374 18.312 7.426 3.727 4.128 4.535
BnaA02g00810D BnKNAT10 6.884 8.202 1.289 0.033 16.883 1.866 7.954 5.470 1.157 11.089 1.673 3.216 0.577 0.097 0.089
BnaA03g03190D BnKNAT11 10.194 2.581 0.646 0.135 10.561 2.062 1.017 2.510 0.125 4.394 0.372 1.823 0.454 0.072 0.116
BnaC03g04580D BnKNAT12 5.192 8.137 1.622 0.472 8.129 1.447 1.784 3.371 0.372 4.989 0.574 2.097 0.444 0.066 0.033
BnaCnng20070D BnKNAT13 2.811 0 0 0 7.802 0.882 6.550 7.581 1.448 6.022 0.836 1.446 0.447 0.018 0.012
BnaA01g04870D BnKNAT14 1.749 8.448 14.776 12.178 2.868 2.952 1.899 0.651 0 5.498 3.699 1.433 4.451 2.595 2.046
BnaA03g51900D BnKNAT15 7.624 34.107 35.739 56.554 10.255 4.506 3.373 3.358 6.662 8.299 7.237 6.074 3.798 4.120 3.453
BnaC01g06410D BnKNAT16 0.679 3.106 4.643 2.947 1.017 0.940 0.692 0.080 0 1.220 0.530 0.904 2.461 0.995 0.785
BnaC07g43650D BnKNAT17 6.761 15.548 31.413 34.109 9.369 6.851 4.481 4.621 8.137 10.765 14.927 9.026 6.043 3.595 1.987
BnaA08g20500D BnKNAT18 0.006 0 9.688 1.984 1.673 6.009 2.118 2.704 0.010 0.095 0.146 0.285 0.210 0.177 0.385
BnaA08g20510D BnKNAT19 0.006 0 9.688 1.984 1.673 6.009 2.118 2.704 0.010 0.095 0.146 0.285 0.210 0.177 0.385
BnaA09g31100D BnKNAT20 0.019 0 2.196 0.385 1.311 1.625 0.478 0.229 0.128 0.197 0.315 0.377 0.110 0.062 0.106
BnaAnng30720D BnKNAT21 0.011 0.043 2.302 0.614 0.684 1.250 0.441 0.244 0.181 0.336 0.693 0.312 0.022 0.264 0.088
BnaC05g18670D BnKNAT22 0.023 0.022 1.390 0.582 0.768 1.340 0.687 0.474 0.002 0.078 0.044 0.126 0.039 0.060 0.031
BnaC08g06320D BnKNAT23 0.023 0.357 23.487 2.001 5.116 12.296 2.922 4.588 0 0.213 0.162 1.089 1.002 0.716 2.628
BnaCnng70390D BnKNAT24 0.045 0.032 1.723 1.409 1.276 2.123 1.039 0.811 0.019 0.079 0.118 0.275 0.113 0.074 0.044
BnaA09g12980D BnKNAT25 1.334 0.865 5.515 5.768 1.228 3.900 7.155 4.796 11.808 11.919 24.940 13.193 8.877 5.448 0.014
BnaA09g52990D BnKNAT26 1.294 0.096 0.444 0.534 0.549 17.354 12.259 5.379 22.756 21.863 50.558 28.156 24.423 7.101 0.053
BnaC04g20090D BnKNAT27 0.070 0.037 0.121 0.116 0.296 1.135 0.391 0.107 0.512 0.472 2.355 0.660 0.797 0.168 0.016
BnaC04g20110D BnKNAT28 0 0 0 0 0 0.079 0.023 0 0 0 0 0 0 0 0
BnaC09g12900D BnKNAT29 2.546 0.378 1.021 0.379 1.235 3.922 4.268 7.819 7.158 14.842 16.892 9.738 6.075 3.079 0.032
BnaCnng51440D BnKNAT30 1.390 0.146 0.978 0.900 1.741 13.686 10.700 5.352 21.985 16.103 37.943 19.860 17.638 5.264 0.017
BnaA06g09570D BnKNAT31 0 0 0 0.060 1.292 0 4.234 2.614 0 0.083 0.862 0 0 0.188 1.526
BnaA09g45470D BnKNAT32 0 0 0 0.688 1.327 0 0 0 0 0.034 0.398 0.348 0.080 1.149 3.517
BnaC05g10940D BnKNAT33 0 0 0 0 0.966 0.024 7.893 4.128 0 0 0.172 0.370 0.055 0.080 0.089
BnaC08g39310D BnKNAT34 0 0 0 0.245 1.902 0 0.021 0 0.067 0.114 3.166 0.137 0.063 0.239 1.408
BnaA09g13310D BnSTM1 0.020 0 0.735 1.191 5.619 66.414 8.814 11.525 0 2.708 0.166 0.286 0.160 0.022 0.027
BnaC09g13580D BnSTM2 0.010 0 6.015 0.037 8.231 85.818 12.789 16.183 0 2.980 0.284 0.485 0.133 0.051 0.074

图7

BnKNOX基因的启动子顺式作用元件分析"

图8

干旱胁迫下甘蓝型油菜叶片中BnKNOX的表达模式"

图9

渗透胁迫下甘蓝型油菜叶片中BnKNOX的表达模式"

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