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小麦B-box基因家族全基因组鉴定与表达分析

本站小编 Free考研考试/2021-12-26

王艳朋,, 凌磊, 张文睿, 王丹, 郭长虹,*哈尔滨师范大学生命科学与技术学院/黑龙江省分子细胞遗传与遗传育种重点实验室, 黑龙江哈尔滨 150025

Genome-wide identification and expression analysis of B-box gene family in wheat

WANG Yan-Peng,, LING Lei, ZHANG Wen-Rui, WANG Dan, GUO Chang-Hong,*Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province/College of Life Science and Technology, Harbin Normal University, Harbin 150025, Heilongjiang, China

通讯作者: * 郭长虹, E-mail:kaku3008@126.com

收稿日期:2020-09-18接受日期:2021-01-13网络出版日期:2021-08-12
基金资助:国家重点基础研究发展计划(973计划)前期研究计划项目.2011CB111500
哈尔滨师范大学研究生创新基金项目.HSDSSCX2020-08


Received:2020-09-18Accepted:2021-01-13Online:2021-08-12
Fund supported: Preliminary Research Project of the National Basic Research Program of China (973 Program).2011CB111500
Graduate innovation fund of Harbin Normal University.HSDSSCX2020-08

作者简介 About authors
E-mail:13694609045@163.com



摘要
B-box (BBX)是一类含有1个或2个B-box结构域的锌指蛋白, 在植物生长发育中起着重要作用。本研究明确小麦B-box转录因子的数量、基因结构和分类进化关系, 研究各基因成员在不同组织中的特异性表达以及对非生物胁迫的响应。从小麦全基因组中鉴定得到87个B-box基因家族成员, 所有TaBBXs蛋白均含有B-box结构域。TaBBXs编码146~489个氨基酸, 理论等电点为4.32~10.42。染色体定位分析表明, TaBBXs分布在除1A、1B和1D之外的18条小麦染色体上。通过系统发育分析将TaBBXs划分为5个亚家族, 有0~4个内含子。在同组内同一个系统进化树分支中的亚族成员具有高度相似的基因结构。qRT-PCR分析的20个TaBBXs基因, 具有不同的组织表达模式, 16个基因在叶中有较高表达, TaBBX10TaBBX39仅在叶中有较高表达, 而TaBBX74在穗中表达, TaBBX43在根中特异性表达。在不同逆境胁迫下, TaBBXs呈现不同表达模式, 11个基因在低温胁迫后上调表达, 12个基因在ABA处理后下调表达, 盐胁迫后10个基因出现上调表达, 干旱胁迫后7个基因出现下调表达, TaBBX10TaBBX39TaBBX60、TaBBX67TaBBX74基因在2种或2种以上胁迫下有显著的上调表达。
关键词: 小麦;全基因组;B-box基因家族;非生物胁迫;基因表达

Abstract
B-box (BBX) is a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The number, gene structure and phylogenetic relationship of wheat B-box transcription factors, as well as their expression specificity in different tissues and response to abiotic stress were investigated. A total of 87 members of B-box gene family were identified from wheat genome and all contained the B-box domain. TaBBXs encoded 146 to 489 amino acids and the isoelectric points ranged from 4.32 to 10.42. Chromosome mapping showed that these genes were distributed on 18 wheat chromosomes except 1A, 1B, and 1D. Based on phylogenetic analysis, TaBBXs were divided into five subfamilies, with 0-4 introns. The members of the subfamily in the same phylogenetic tree branch in the same group had highly similar gene structures. The qRT-PCR revealed that the investigated 20 genes had different expression patterns, and most genes were highly expressed in leaves, and TaBBX10 and TaBBX39 were only highly expressed in leaves, while TaBBX74 was expressed in spikes, TaBBX43 was specifically expressed in roots. These genes showed different expression patterns under different stress. 11 genes were up-regulated after low temperature stress, 13 genes were down-regulated after ABA treatment, 10 genes were up-regulated after salt stress, and 7 genes were down-regulated after drought stress. TaBBX10, TaBBX39, TaBBX60, TaBBX67, and TaBBX74 were significantly up-regulated under two or more stresses.
Keywords:wheat;genome-wide;B-box gene family;abiotic stress;gene expression


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本文引用格式
王艳朋, 凌磊, 张文睿, 王丹, 郭长虹. 小麦B-box基因家族全基因组鉴定与表达分析. 作物学报[J], 2021, 47(8): 1437-1449 DOI:10.3724/SP.J.1006.2021.01077
WANG Yan-Peng, LING Lei, ZHANG Wen-Rui, WANG Dan, GUO Chang-Hong. Genome-wide identification and expression analysis of B-box gene family in wheat. Acta Agronomica Sinica[J], 2021, 47(8): 1437-1449 DOI:10.3724/SP.J.1006.2021.01077


小麦(Triticum aestivum L.)是世界上最重要的粮食作物之一, 占谷物种植面积的30% [1,2]。其基因组十分复杂, 由A、B、D 3个亚基因组整合而形成的异源六倍体(AABBDD), 重复序列高达85%, 大小约为15 GB [3,4]。小麦在生长发育过程中面临多种环境胁迫, 其中盐、干旱、低温等非生物胁迫严重影响小麦的产量和品质[5]。植物B-box蛋白可参与逆境响应, 但目前尚未对小麦B-box基因家族进行系统分析。因此, 本研究基于小麦全基因组对B-box基因家族进行分析, 为进一步研究该基因家族成员功能提供参考, 研究结果对进一步培育或改良小麦抗性品种具有重要意义。

转录因子(transcription factors, TF)能够调节植物的生长发育, 在植物对高盐、干旱和高温等逆境的响应及应答过程中具有重要作用[6]。B-box转录因子家族是一个具有B-box结构域的锌指蛋白家族。1995年首次在拟南芥(Arabidopsis thaliana)的一个晚花突变体中鉴定得到B-box基因, 命名为CONSTANS (CO), 并证实了该基因参与植物开花和其他生命活动的调节[7]。随后的研究进一步揭示, 植物B-box转录因子在调节种子萌发[8]、开花[9]、避荫反应[10]、生物或非生物应激反应[11]、植物激素信号转导[12]等多种生命活动中发挥着重要的作用。如AtBBX19可以通过诱导ABI5抑制种子萌发[13], AtBBX31能促进UV-B辐射下的光形态发生, 增强对高剂量UV-B辐射的耐受性[14]。Gangappa等[15]指出, AtBBX25通过与HY5形成二聚体并抑制其功能, 参与植物光形态发生的负调控。最新研究表明, 苹果中的MdBBX37能够和MdMYB1和MdMYB9相互作用, 抑制这两种蛋白与目标基因的结合, 从而对花青素生物合成产生负调控作用[16]。非生物胁迫方面, AtBBX24 (最初被称为STO)参与盐胁迫的信号转导, 可以使盐敏感型的突变体酵母具有更强的耐盐能力[17,18]AtBBX5通过ABA途径参与胁迫响应, 在受到外源的ABA、盐和渗透胁迫时, 该基因上调表达[19]AtBBX18的下调表达可以使植物的耐热性增加, 过表达该基因可以降低植物的耐热性[11]MdBBX10能够增强拟南芥的耐盐耐旱性, 在大肠杆菌(E. coli)中表达的MdBBXs分别增强了细胞对盐胁迫和渗透胁迫的耐受性[20,21]。梨PuBBX24启动子显著响应ABA、光、低温、渗透以及盐胁迫处理[22]

目前B-box基因家族的研究主要集中在模式植物拟南芥、水稻和蒺藜苜蓿中, 而在小麦中尚未见报道。随着小麦基因组的公布[4], 使得对小麦B-box基因家族分析成为可能。通过生物信息学方法对全基因组中小麦B-box基因家族成员进行鉴定, 对所有家族成员的理化信息、结构功能、表达模式进行分析。利用qRT-PCR实验分析20个B-box基因在不同组织中以及非生物胁迫条件下的表达模式, 为解析B-box基因家族在小麦中的功能提供参考。

1 材料与方法

1.1 材料与处理

植物试验材料为小麦中国春(Triticum aestivum L., Chinese Spring), 将小麦种子表面用15%次氯酸钠消毒5 min, 蒸馏水冲洗3次, 消毒后的种子置于无菌培养皿中进行发芽培养24 h, 将幼芽移栽至小麦水培盒中, 种植在1/2 Hoagland营养液中, 在22℃光照16 h的温室中生长。将2周龄小麦幼苗分别用0.2 mol L-1 NaCl、20% PEG、100 μmol L-1 ABA和4℃进行胁迫处理, 以正常条件下的幼苗为对照。处理6 h后对处理组和对照组植株进行取材, 每个样品3个重复。此外, 采集在4月至7月大田中培养的小麦组织: 根、茎、叶、穗(开花前1 d)和籽粒(授粉后10 d)进行组织表达分析, 每个样品3个重复。将所有样品液氮速冻后, -80℃保存备用。

1.2 小麦B-box基因家族成员的鉴定

小麦全基因组数据、蛋白序列和注释文件从Ensembl Plants数据库中下载, 拟南芥和水稻B-box基因序列和蛋白序列下载自NCBI (https://www.ncbi.nlm.nih.gov/)。已知的拟南芥[23]、水稻[24]B-box蛋白序列为参考对小麦的蛋白序列进行本地Blast, 设置E-value参数为0.001, 得到候选的小麦B-box蛋白序列。去重复之后提交到SMART (http://smart.embl-heidelberg.de/)和NCBI的在线工具CDD (Conserved Domain Database)进行蛋白结构预测, 以确定其含有B-box所特有的B-box保守结构域。

1.3 小麦B-box蛋白理化性质及结构域预测分析

利用ExPASy网站(http://expasy.org/)对小麦B-box氨基酸序列进行等电点、分子量预测等理化性质分析。根据CDD所提供的家族成员所含结构域起始位点整理结构域氨基酸序列, 再采用weblogo (http://weblogo.berkeley.edu/)对结构域保守氨基酸位点进行可视化显示。

1.4 小麦B-box基因家族的系统进化分析

使用ClustalX软件对小麦B-box氨基酸序列进行多序列比对, 通过MEGA7.0软件构建系统发育树: 采用邻接法(Neighbor-Joining algorithm), 泊松校正(Poission correction), 成对删除(pairwise deletion), Bootstrap重复值1000次。参考拟南芥和水稻B-box基因家族的亚族分类结果对小麦B-box基因家族进行亚族分类。

1.5 小麦B-box基因结构及染色体定位分析

从小麦基因信息GFF3文件中提取TaBBXs的染色体位置和基因结构信息, 分别使用MapDraw和GSDS (http://gsds.cbi.pku.edu.cn/)工具将TaBBXs的染色体定位信息和基因结构信息(外显子、内含子等)进行可视化显示。

1.6 小麦B-box基因家族的复制事件及同源性分析

使用BLASTp、OrthoMCL、多重共线扫描工具包(MCScanX)和默认参数分析基因复制事件(E<1e-5), 如果2个同源基因被5个或更少的基因分开, 则它们被鉴定为串联重复, 如果2个基因被5个以上的基因分开或分布在不同的染色体上, 则称为片段重复。同源基因结合系统发育树进一步鉴定, 鉴定标准为: 同源序列覆盖率>75%, 同源性>75%。

1.7 小麦B-box基因家族的启动子分析

从小麦全基因组数据库中提取每个小麦B-box基因启动子区域(上游2000 bp), Plant CARE数据库(http://bioinformatics.psb.ugent.be/webtools/plantcare/)分析顺式作用元件(cis-acting element)的种类、数目及功能。

1.8 RNA提取和实时荧光定量PCR分析

采用RNAprep Pure Plant Kit试剂盒提取小麦总RNA, 将提取出的总RNA作为模板, 利用PrimeScript RT Reagent Kit with gDNA Eraser (Perfect Real Time) (RR047, TaKaKa)反转录获得cDNA。利用软件Primer 3和Primer Premier 6设计引物, 具体引物序列见表1, 其中小麦Actin为内参基因。PCR反应体系为cDNA 2 μL, 2×SYBR Premix ExTaq 10 μL, 50×ROX Reference Dye 0.4 μL, 正、反向引物各0.8 μL和ddH2O 6 μL。扩增程序为94℃ 30 s; 94℃ 5 s, 54℃ 15 s, 72℃ 31 s, 40个循环。每个处理3个生物学重复, 并使用2-ΔΔCT方法计算基因的相对表达量。用SPSS软件进行差异显著性分析, P < 0.05表示差异显著, P < 0.01表示差异极显著。

Table 1
表1
表1本试验所用引物
Table 1Primers used in this study
基因
Gene
正向引物
Forward primer (5′-3′)
反向引物
Reverse primer (5′-3′)
TaBBX01AACGGGGGAGTGTTACTTCTAGTTGGAGCAGAGGAACCGA
TaBBX06AACTCGCCAAGTCGGAGGAAGCTGCTGATACGGAGGTACA
TaBBX08TACCGCCGACGTGTTCTTTCAGAGGAGGATACGCTGTG
TaBBX10CTCGCATCGTCCTCTCCAATCTGCTGGCATGAAGGTACA
TaBBX12CACAGCGTATCGTCGTCTGAATCTCCTCGTGCTCCTCCAT
TaBBX13TCGAACAAGCCGTATCAGCAAGAAGGAGGAGCCGAGAGAC
TaBBX14AGCCGGAGGTAATCAAAGCCGAGGAGGACGACAACGATCC
TaBBX18GGGTTCTCCGGGTTCGACCCTCTAACTCTTGCTCCGGC
TaBBX35TGACATTGAAAGGCTGCGTTGACATTGAAAGGCTGCGT
TaBBX39ACCGCCGATTCCTCATCACCCAATGTCGTCTTCTCCTCCT
TaBBX43CTCCGAGTACCTCACCAAGACCAATGCTCCTGCCTCATCCA
TaBBX46CACGCGGTACATGGCACGCCGGTGCGCTTGACGAAG
TaBBX52CCGAACTGCGAGGAAGGAATAGCTGGCTGATGTGTAGGAAGT
TaBBX60GCCGAACTGTGAGGAAGGAAAGGCTGATGCGTAGGAAGTG
TaBBX62CACGACGGGCGGGTAAAGGGCTCCTTTTCAAGAACTGCG
TaBBX67GAGAAGGAAGGGAGCGAGTGGCTGGACTGGACCGTATTGT
TaBBX74GCAACCAAGAGCAGTATGTGATTGTTGACGGAATCTGTGTAAGC
TaBBX76AGGTAAGCTCATGCACCTCGCGTCTCGCTGTCGATCCTTG
TaBBX77GACGAGCCCATTCACAGCGGGCAGATGTTGGTGAGGTAGTC
TaBBX86AGGGCGGGAAGATGGACTACATGAGGAGCTGTAGGTCTGC
TaActinTACTCCCTCACAACAACCGAGAACCTCCACTGAGAACAA

新窗口打开|下载CSV

2 结果与分析

2.1 小麦基因组中B-box家族基因鉴定

参考AtBBX、OsBBX基因, 共获得87个小麦B-box基因家族成员, 根据它们在染色体上的相对位置将其命名为TaBBX1-87。预测结果显示, 大多数TaBBXs蛋白的等电点都小于7, 只有TaBBX27TaBBX28TaBBX33TaBBX34TaBBX38、TaBBX64TaBBX65七个成员在7以上; TaBBXs基因的长度有很大差距, 从441 bp (TaBBX26)到1473 (TaBBX69) bp, 分子量从15,371.44 Da (TaBBX26)到52,005.04 (TaBBX69) Da (附表1)。

Table S1
附表1
附表1B-box家族的基本信息分析
Table S1TaBBX genes information identified in the wheat genome
基因名
Gene name
基因登录号
Gene ID
染色体位点
Chromosome location
基因长度
Length (bp)
氨基酸长度
Length (aa)
等电点
Isoelectric point (pI)
分子量
Molecular weight (kD)
外显子个数
Exon number
分组
Group
结构域类型
Domain type
TaBBX01TraesCS2A02G1196002A:70102039-7010469911493825.7340010.8341BBX + CCT
TaBBX02TraesCS2A02G3489002A:587750669-5877519387652544.9527209.5222BBX
TaBBX03TraesCS2A02G3539002A:594579959-5945816719513165.5633724.5122BBX+ CCT
TaBBX04TraesCS2A02G3661002A:610710308-6107129397892624.7928237.5122BBX
TaBBX05TraesCS2A02G3885002A:635722864-6357245537772585.8227357.532BBX
TaBBX06TraesCS2B02G1403002B:106954443-10695665611643875.4440384.3241BBX + CCT
TaBBX07TraesCS2B02G3673002B:523760095-5237617427742574.8927492.8522BBX
TaBBX08TraesCS2B02G3720002B:530306217-5303078959603195.5633908.6622BBX+ CCT
TaBBX09TraesCS2B02G4066002B:575903665-5759052557952645.8227823.9932BBX
TaBBX10TraesCS2D02G1214002D:70622968-7062556711463815.7239968.9141BBX + CCT
TaBBX11TraesCS2D02G3473002D:445396017-4453975197772584.8127494.7622BBX
TaBBX12TraesCS2D02G3519002D:450234732-4502361929603195.5633936.7422BBX+ CCT
TaBBX13TraesCS2D02G3863002D:491429370-4914311717892625.8227600.8132BBX
TaBBX14TraesCS3A02G1393003A:117227850-11723021610503495.1537168.4732BBX
TaBBX15TraesCS3B02G1569003B:150154692-15015694710503495.2237477.832BBX
TaBBX16TraesCS3D02G1396003D:99748881-9975118410503495.3237482.832BBX
TaBBX17TraesCS4A02G1406004A:216145053-21614801212394125.545256.4451BBX + CCT
TaBBX18TraesCS4A02G2685004A:580733925-58073610712334105.8544829.1921BBX + CCT
TaBBX19TraesCS4B02G0457004B:32896523-3289869512364116.0444870.3321BBX + CCT
TaBBX20TraesCS4B02G1558004B:281732350-28173592111943976.0643627.831BBX + CCT
TaBBX21TraesCS4D02G0462004D:21774703-2177688612334105.8544816.2521BBX + CCT
TaBBX22TraesCS4D02G1673004D:288428472-28843259511943976.143454.5131BBX + CCT
TaBBX23TraesCS5A02G1661005A:355071283-3550728049813265.7835576.3621BBX + CCT
TaBBX24TraesCS5A02G3171005A:528110873-5281147416362115.7423146.752BBX
TaBBX25TraesCS5A02G3360005A:545058736-5450594115401795.2919206.9421BBX
TaBBX26TraesCS5A02G3361005A:545073760-5450743174411464.5715371.4421BBX
TaBBX27TraesCS5A02G3390005A:546563819-5465645237052349.2724319.8211BBX
TaBBX28TraesCS5A02G3391005A:546575974-54657657660320010.4221432.5611BBX
TaBBX29TraesCS5B02G1635005B:302753429-3027549759783255.9635477.3221BBX + CCT
TaBBX30TraesCS5B02G3177005B:501954375-5019584836362115.8523088.6652BBX
TaBBX31TraesCS5B02G3352005B:518472466-518473347468155516721.0921BBX
TaBBX32TraesCS5B02G3353005B:518481548-51848414511073686.2339645.2641BBX + CCT
TaBBX33TraesCS5B02G3374005B:520970152-5209708506992329.0224101.5611BBX
TaBBX34TraesCS5B02G3375005B:521031958-5210325726152049.6521590.8711BBX
TaBBX35TraesCS5D02G1707005D:267762539-2677642019783255.9635519.42211BBX + CCT
TaBBX36TraesCS5D02G3234005D:415613354-4156176236362115.8523084.6752BBX
TaBBX37TraesCS5D02G3410005D:429289528-42929188610833606.3338690.3541BBX + CCT
TaBBX38TraesCS5D02G3433005D:431251824-4312525437202399.0325267.9611BBX
TaBBX39TraesCS6A02G1439006A:121616223-1216198296452144.7222147.2722BBX
TaBBX40TraesCS6A02G1509006A:134947729-13494947810953645.6837982.3532BBX+ CCT
TaBBX41TraesCS6A02G2164006A:398252913-3982544257712565.1427782.3222BBX
TaBBX42TraesCS6A02G2189006A:405166583-4051681349663215.2433625.4222BBX+ CCT
TaBBX43TraesCS6A02G2393006A:449584187-4495858807112365.7725104.9632BBX
TaBBX44TraesCS6A02G2864006A:518666410-5186706509723236.6535122.4732BBX+ CCT
TaBBX45TraesCS6A02G2894006A:521451709-52145409911103695.9141051.8222BBX+ CCT
TaBBX46TraesCS6A02G2932006A:524718099-52472032612814266.8146496.9121BBX + CCT
TaBBX47TraesCS6B02G1723006B:184884215-1848866536452144.8922154.3522BBX
TaBBX48TraesCS6B02G1790006B:198984566-19898631211253745.2838846.1432BBX+ CCT
TaBBX49TraesCS6B02G2465006B:439021199-4390223767832604.9828026.5622BBX
TaBBX50TraesCS6B02G2484006B:445852206-4458539779663215.3433887.822BBX+ CCT
TaBBX51TraesCS6B02G2852006B:514117744-5141193207172386.0425141.0632BBX
TaBBX52TraesCS6B02G3154006B:563320471-56332461611733904.9642531.4142BBX+ CCT
TaBBX53TraesCS6B02G3195006B:567397520-56739949711133705.5841154.9122BBX+ CCT
TaBBX54TraesCS6B02G3234006B:572391940-57239394012874286.446597.0921BBX + CCT
TaBBX55TraesCS6D02G1331006D:100871867-1008743826452144.9722054.1922BBX
TaBBX56TraesCS6D02G1409006D:110442898-11044472110953645.6838019.4132BBX+ CCT
TaBBX57TraesCS6D02G1992006D:277099701-2771010297832605.1428221.8322BBX
TaBBX58TraesCS6D02G2020006D:284849813-2848508669543175.1733352.0822BBX+ CCT
TaBBX59TraesCS6D02G2217006D:312763126-3127648547172385.7725258.0832BBX
TaBBX60TraesCS6D02G2671006D:377220309-37722496911793924.7943027.9542BBX+ CCT
TaBBX61TraesCS6D02G2695006D:379572086-37957412511103695.540998.7222BBX+ CCT
TaBBX62TraesCS6D02G2741006D:382588127-38259014313054346.1247026.5421BBX + CCT
TaBBX63TraesCS7A02G1084007A:65969778-6597597110803595.138311.7332BBX
TaBBX64TraesCS7A02G1087007A:66173971-661744564861618.9817172.8211BBX
TaBBX65TraesCS7A02G1321007A:85159979-851607287502497.6525502.3511BBX + CCT
TaBBX66TraesCS7A02G2062007A:168812422-16881372012994325.3247132.2111BBX + CCT
TaBBX67TraesCS7A02G2113007A:174203246-17420572011583856.0642218.8722BBX+ CCT
TaBBX68TraesCS7A02G2186007A:185642724-18564814511913964.9243615.3642BBX+ CCT
TaBBX69TraesCS7A02G2635007A:261221617-26122567014734906.152005.0441BBX + CCT
TaBBX70TraesCS7A02G3834007A:558402604-5584041848522835.0429956.5932BBX
TaBBX71TraesCS7A02G4972007A:686936894-68693847911193725.9639566.5522BBX+ CCT
TaBBX72TraesCS7B02G0064007B:3684186-368942710173384.8336159.2442BBX
TaBBX73TraesCS7B02G1134007B:131376607-13137842712994325.347173.1811BBX + CCT
TaBBX74TraesCS7B02G1183007B:137793769-13779614211523836.2442114.8922BBX+ CCT
TaBBX75TraesCS7B02G1255007B:146898679-14690486610143374.3236449.1732BBX
TaBBX76TraesCS7B02G1615007B:220866464-22087045914674886.4451810.8941BBX + CCT
TaBBX77TraesCS7B02G2863007B:521577849-5215791719363115.6933195.4922BBX
TaBBX78TraesCS7B02G4006007B:667070044-66707176811193725.939407.4622BBX+ CCT
TaBBX79TraesCS7D02G1033007D:63325536-6333140310923635.0338772.2132BBX
TaBBX80TraesCS7D02G1317007D:83472836-834740587532506.0925596.3311BBX + CCT
TaBBX81TraesCS7D02G2090007D:167228163-16722982912994325.2647125.1711BBX + CCT
TaBBX82TraesCS7D02G2130007D:171311981-17131446511193726.3141073.7722BBX+ CCT
TaBBX83TraesCS7D02G2203007D:180685905-18069143411913964.9243609.3542BBX+ CCT
TaBBX84TraesCS7D02G2643007D:244952312-24495639014704896.2151903.8941BBX + CCT
TaBBX85TraesCS7D02G3799007D:492148581-4921502408582855.0230133.8132BBX
TaBBX86TraesCS7D02G4844007D:594729348-59473095011193725.8639527.5722BBX+ CCT
TaBBX87TraesCSU02G091500Un:81434193-8143711811103696.2140011.4341BBX + CCT

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2.2 小麦B-box基因家族蛋白序列及系统进化分析

TaBBXs蛋白的分子长度在146~490个氨基酸不等。在87个TaBBXs中, 23个TaBBXs包含2个B-box结构域和1个保守的CCT结构域。29个成员包含2个B-box结构域, 但没有CCT结构域。9个TaBBXs只包含1个B-box结构域, 剩下的26个包含1个B-box域和1个CCT结构域(附表1)。蛋白质序列比对显示, TaBBXs的B-box1和B-box2结构域具有相似的保守序列, TaBBXs蛋白质中的CCT结构域是高度保守的(图1)。此外, 特定位点的氨基酸残基高度保守, 暗示其保守的功能, 例如1、4、13、21和24位点的半胱氨酸残基在B-box结构域中高度保守。

图1

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图1小麦B-box基因家族的保守结构域

Fig. 1Conserved domains of B-box genes family in wheat



为了详细研究TaBBXs成员的系统发育关系和功能差异, 对87个TaBBXs蛋白质序列构建系统发育树, 包括AtBBXs和OsBBXs系统发育树(附图1)。根据Khanna等[23]的分组研究和分析, 将TaBBXs进一步划分为5个亚家族(图2), 5个亚家族成员数量分别为23、9、21、28、6。亚家族I、II和III的成员是同时包含B-box结构域和CCT结构域的TaBBXs。亚家族I成员包含1~2个B-box结构域和1个CCT结构域, 亚家族II成员包含1个B-box结构域和1个CCT结构域, 亚家族III成员包含1~2个B-box结构域和0~1个CCT结构域。小麦有两类在拟南芥中没有发现的B-box基因, 亚族I成员中有一类, 它包含1个B-box结构域(TaBBX23TaBBX29TaBBX35TaBBX65TaBBX80); 另一类是亚族III成员, 其中大多数成员具有1个B-box结构域和1个CCT结构域, 但TaBBX44TaBBX52TaBBX60TaBBX68TaBBX75拥有B-box2结构域, 这与包含2个B-box结构域的其他成员分组不同。第IV组和第V组的成员没有CCT结构域, 分别有2个和1个B-box结构域。

附图1

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附图1小麦、拟南芥和水稻B-box基因系统进化树

Fig. S1Phylogenetic tree of B-box genes in wheat, A. thaliana and Oryza sativa



图2

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图2小麦B-box基因家族进化树

Fig. 2Phylogenetic tree of B-box genes family in wheat



2.3 小麦B-box基因家族的染色体定位与基因复制

小麦B-box基因不均等地分布在小麦21条染色体中的18条上, 1A、1B、1D染色体上没有发现B-box基因, 其中的1个成员(TaBBX87)无法进一步定位到染色体(图3)。在7A染色体上分布的基因最多, 共含有9个基因; 其次是6A、6B、6D和7D染色体上分别含有8个基因; 其余染色体上均含有1~7个基因不等。有92% (80/87)的小麦B-box成员显示出重复事件, 在122个复制事件中并未发现串联重复事件, 在不同的染色体中发现了高度相似的基因, 出现了片段重复事件。如图3所示, 重复事件主要发生在染色体6A、6B和6D上, 而3A、3B和3D上则较少。此外, 我们对同源基因进行进一步聚类分析发现, 所有同源基因都处于同一进化分支中(附图2), 除TaBBX17TaBBX20TaBBX65TaBBX80基因外, 在3个部分同源染色体组(A、B、D)上都有同源位点, 如: TaBBX03、TaBBX08TaBBX12为同源基因位于同一进化分支中, 且分别位于2A、2B和2D染色体上, 表明小麦B-box基因具有大量的同源位点, 同源保留率高。

图3

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图3小麦B-box基因家族成员在染色体上的位置和基因复制

每个彩色条代表一条染色体, 基因命名是根据它们在染色体上的位置来标记的, 片段复制基因用彩色线条连接。
Fig. 3Chromosome location and gene duplications of the B-box gene family in wheat

Each colored bar represents a chromosome, gene names are labeled on the basis of their positions on the chromosomes, segmental duplication genes are linked by colored lines.


附图2

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附图2小麦B-box同源基因进化树

红色:位于2A、2B和2D染色体上的基因;黑色:位于3A、3B和3D染色体上的基因;黄色:位于4A、4B和4D染色体上的基因;棕色:位于5A、5B和5D染色体上的基因;蓝色:位于6A、6B和6D染色体上的基因;橘色:位于7A、7B和7D染色体上的基因。
Fig. S2Phylogenetic tree of B-box homoeologs genes in wheat

Red: gene on chromosome 2A, 2B and 2D; Black: gene on chromosome 3A, 3B and 3D; Yellow: gene on chromosome 4A, 4B and 4D; Brown: gene on chromosome 5A, 5B and 5D; Blue: gene on chromosome 6A, 6B and 6D; Orange: gene on chromosome 7A, 7B and 7D.


2.4 小麦B-box基因家族的基因结构分析

小麦B-box家族成员的外显子数目为1~5个, 内含子数目为0~4个(图4)。对基因结构进一步分析发现, I组的大多数成员具有1个内含子; II组中TaBBX66TaBBX73TaBBX81不含内含子, 其余基因含1个内含子; III组和IV组的成员结构较相似, 含1~4个内含子; V组中的基因结构较简单, 所有成员都不含内含子。

图4

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图4小麦B-box基因家族基因结构

Fig. 4Gene structure of B-box gene family in wheat



2.5 小麦B-box基因家族的启动子分析

从TaBBXs中鉴定出101种顺式作用元件, 其中40种在大多数成员中被检测出来。除了2种传统的启动子元件(TATA-box, CAAT-box)外, 其余38个顺式作用元件可分为4组: 14个具有光响应性, 包括MRE、G-Box、ACE、AE-box、Sp1、GT1-motif、GATA-motif、TCCC-motif、I-box、TCT-motif、GA-motif、Box I、Box 4和ATCT-motif; 8个是激素反应性的, 包括CGTCA-motif、TGACG-motif、ABRE、P-box、ERE、GARE-motif、AuxRR-core和TGA-element; 9个是胁迫响应元件: ARE、MBS、LTR、W box、GC-motif、CCAAT-box、TCA-element、WUN-motif和TC-rich repeats。第4组为其他顺式作用元件, 如: 胚乳表达所需的顺式作用元件(GCN4_motif), 与分生组织表达相关的顺式作用调控元件(CAT-box)等。下表展示了与胁迫和激素响应相关的元件(表2)。

Table 2
表2
表2预测小麦B-box家族基因启动子中顺式调控元件
Table 2Putative regulatory cis-elements in wheat B-box family gene promoters
顺式作用元件
cis-elements
基因数目
Number of genes
顺式作用元件的功能
Functions of cis-elements
CAAT-box87Common cis-acting element in promoter and enhancer regions
TATA-box87Core promoter element around -30 of transcription start
CGTCA-motif75cis-acting regulatory element involved in the MeJA-responsiveness
TGACG-motif75cis-acting regulatory element involved in the MeJA-responsiveness
ABRE84cis-acting element involved in the abscisic acid responsiveness
ARE67cis-acting regulatory element essential for the anaerobic induction
MBS49MYB binding site involved in drought-inducibility
LTR57cis-acting element involved in low-temperature responsiveness
W box51Wounding and pathogen responsiveness.
TGA-element42Auxin-responsive element
GC-motif51Enhancer-like element involved in anoxic specific inducibility
CCAAT-box24MYBHv1 binding site
TCA-element30cis-acting element involved in salicylic acid responsiveness
P-box31Gibberellin-responsive element
WUN-motif20Wound-responsive element
ERE18Ethylene-responsive element
GARE-motif23Gibberellin-responsive element
TC-rich repeats27cis-acting element involved in defense and stress responsiveness
AuxRR-core18cis-acting regulatory element involved in auxin responsiveness

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2.6 小麦B-box基因家族在不同组织和非生物胁迫及激素处理下的表达

采用qRT-PCR分析了20个小麦B-box基因在不同组织和干旱、低温、盐和ABA处理下的表达模式(图5)。20个基因在所有检测组织中均有不同程度的表达, TaBBX08、TaBBX12、TaBBX14、TaBBX43、TaBBX76在所有组织中均有表达, 大多数(16个)基因在叶中有较高的表达, 其次是在穗、根和茎中表达, 而较少在籽粒中表达。TaBBX10TaBBX39在叶中有较高表达, TaBBX74在穗中特异性表达, TaBBX43在根中特异性表达, TaBBX52TaBBX60在穗和根中表达量较高。

图5

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图5小麦B-box基因家族在不同组织中的表达分析

Fig. 5Expression profile of B-box gene family in different tissues of wheat



TaBBXs响应非生物胁迫, 但表达水平不同(图6)。在干旱胁迫下, TaBBX10TaBBX52TaBBX60TaBBX67TaBBX74TaBBX86显著上调表达; 大多数基因在低温胁迫下上调表达, TaBBX08TaBBX10TaBBX12TaBBX39TaBBX60等11个基因的表达量与对照组相比显著上调; 在盐胁迫处理下, 基因出现上调或下调表达, 其中TaBBX60、TaBBX62、TaBBX67TaBBX76等10个基因显著上调表达; 在ABA处理下, 除TaBBX14、TaBBX35TaBBX86外, 所有小麦B-box基因成员的表达水平都很低; TaBBX10TaBBX39TaBBX60、TaBBX67TaBBX74在2种或2种以上胁迫下相比对照有显著的上调表达。

图6

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图6小麦B-box基因家族在不同处理下的表达分析

A: 对照; B: 20% PEG处理6 h; C: 4℃处理6 h; D: 0.2 mol L-1 NaCl处理6 h; E: 100 μmol L-1 ABA处理6 h。*表示在0.05水平上显著; **表示在0.01水平上显著。
Fig. 6Expression profile of B-box gene family under different treatments in wheat

A: control; B: six hours of 20% PEG treatment; C: six hours of 4℃ treatment; D: six hours of 0.2 mol L-1 NaCl treatment; E: six hours of 100 μmol L-1 ABA treatment. * and ** indicate significantly different at P < 0.05 and P < 0.01, respectively.


3 讨论

B-box基因家族是锌指转录因子中的一个家族, 包含B-box和CCT结构域[23,25]。目前, B-box基因家族已经在多个物种中被鉴定出来, 比如在拟南芥[23]、水稻[24]、番茄[26]、马铃薯[27]、苹果[28,29]、梨[30]、葡萄[31]分别鉴定出32、30、29、30、64、37、24个B-box家族成员。本研究从小麦全基因组数据库中获得了87个B-box基因成员, 均高于上述物种中的成员数, 可能是因为小麦是异源六倍体, 具有3个部分同源基因组, 存在更多的同源基因(homoeologs), 高同源保留率也可以部分解释小麦B-box基因数量多的原因。

根据B-box结构域的数目和序列特征以及CCT结构域的存在特征, B-box在拟南芥中被分为5组, I组和II组中的所有成员都包含2个B-box和CCT结构域, 第III组具有1个B-box和CCT结构域, 第IV组和V组分别具有2个和1个B-box结构域[23]。在小麦中同样被分为5组, 有1个或2个B-box结构域和1个CCT结构域的53个TaBBXs被分为I组、II组和III组, 具有2个B-box结构域的28个成员为IV组, V组6个成员含有1个B-box结构域。但其中III组中有4个TaBBXs (TaBBX25、TaBBX26TaBBX31TaBBX75)不具有CCT结构域, 这与拟南芥分组不一致, 在其他物种中也发现了类似的不一致, 例如, 水稻中的OsBBX25OsBBX27属于第I组, 玉米中的ZmBBX7属于第II组, 尽管它们都缺少1个B-box结构域[25,32]。番茄中的SlBBX9SlBBX11SlBBX12以及水稻中的OsBBX7OsBBX19属于第III组, 尽管它们有2个B-box结构域[25,26]。可能是进化缺失或重复导致了分组的差异, 与之前在水稻研究中的分类相似[25]

基因结构的多样性在基因家族的进化中也起着重要的作用。本研究结果显示, 小麦B-box基因在同组内同一个系统进化树分支中的亚族成员具有高度相似的基因结构, 总体内含子数目较少, 显示出进化的保守性。V组中的一些同源基因, 如TaBBX24、TaBBX30TaBBX36显示了一个保守的基因结构, 与同组成员有所差异。这种差异可能不是偶然的突变事件, 而是植物B-box转录因子进化的一种保守模式[33]。此外, 保守序列分析发现, B-box1与B-box2相比具有更高的保守性, CCT结构域是高度保守的[32]。前人报道中, 有一种理论认为, 最初仅有的B-box2结构域在进化过程中发生复制事件随后又发生删除事件, 导致出现B-box结构域数目不同的B-box基因[32]。本研究中B-box1比B-box2具有更高的保守性, 所以可能是B-box2中发生了删除事件并产生B-box1, 与Crocco和Botto提出的进化模型一致[32]

复制事件对植物进化过程中基因家族成员的扩增至关重要[34]。植物中的基因复制主要有片段复制和串联复制[35,36]。在本研究中, 没有发现串联复制事件只发生了片段复制事件。表明片段复制事件可能是小麦B-box基因家族成员扩增的主要原因, 这与玉米、水稻等物种相类似[37]

基因表达模式可以提供相关基因功能的重要信息。在拟南芥中, B-box基因(BBX6, COL5)的过表达促进开花[38], 而过表达COL9 (BBX7)则延迟开花[39], 在小麦中与BBX6处于同一组的基因有TaBBX08TaBBX12TaBBX35TaBBX67TaBBX74TaBBX86, 其中TaBBX08TaBBX12TaBBX35基因在低温胁迫下显著上调表达。小麦开花主要受春化影响, 即小麦开花需经过长时间环境低温诱导的生理过程, 同时在TaBBX12TaBBX35启动子区发现了参与低温响应的顺式作用元件LTR (表2), 因此TaBBX12TaBBX35基因可能参与了小麦开花调控过程。在玉米中, B-box同源基因参与不同的生物学过程, 在基因表达上具有明显的组织特异性[40]; B-box基因家族成员在番茄各组织中均有不同程度的表达[26], 马铃薯B-box家族成员在不同器官中表达模式不同[27]。小麦B-box基因在不同组织中有不同的表达模式, TaBBX10TaBBX39等16个基因在叶中有较高的表达, TaBBX43TaBBX52TaBBX60TaBBX74在穗、根等组织中表达量较高, 说明小麦B-box基因在植物生长发育过程中可能发挥重要作用, 在不同发育阶段可能具有独特的功能。

非生物胁迫, 如盐、干旱、极端温度, 都会对植物的生长和发育产生负面影响[41,42]。本研究发现, 在B-box基因启动子区存在胁迫反应顺式作用元件, 如ARE、LTR、MBS和TC-rich, 与干旱、盐和低温有关。79个B-box基因都至少具有1个胁迫响应顺式作用元件, 表明它们在逆境反应中可能发挥着重要作用。在盐、低温、干旱胁迫和ABA处理下, 小麦B-box家族成员均有不同程度的诱导表达。之前的研究结果表明, 耐盐蛋白AtBBX24在拟南芥的高盐度条件下促进根的生长, 耐盐活性也在酵母细胞中触发[17], 小麦TaBBX13TaBBX14TaBBX39TaBBX43TaBBX77AtBBX24处于同一分组内, 这些基因受到盐胁迫诱导, 因此TaBBX13TaBBX14TaBBX39TaBBX43TaBBX77可能参与了盐胁迫调控。菊花CmBBX24能够提高植物的耐寒性或耐旱性[43], OsBBX25在拟南芥中过表达, 可以增强转基因植物对干旱胁迫的抗性[44], 小麦TaBBX08TaBBX12TaBBX35TaBBX67TaBBX74TaBBX86OsBBX25处于同一分组内, 干旱胁迫显著诱导TaBBX35TaBBX67TaBBX74TaBBX86的表达, 并且在TaBBX67TaBBX74基因启动子中发现含有响应干旱胁迫的顺式作用元件MBS (表2), 表明TaBBX67TaBBX74在干旱胁迫过程中可能起着重要的作用。我们还发现, TaBBX10TaBBX60在盐、低温和干旱胁迫下都上调表达, 表明这2个基因可能整合了不同的非生物胁迫信号。TaBBX01TaBBX08TaBBX13等11个基因在盐、低温和干旱胁迫下表现出不同的表达模式, 说明这些基因可能在小麦响应不同的非生物胁迫过程中发挥作用。

4 结论

本研究对小麦B-box基因家族进行了全基因组鉴定, 共筛选获得87个TaBBXs家族成员, 可分为5组。除了1A、1B和1D号染色体外, 其他的18条小麦染色体上均有TaBBXs分布, TaBBXs内含子数目0~4个。小麦B-box基因家族表达具有组织特异性, TaBBXs不同程度地响应盐、干旱和低温胁迫, 推测TaBBXs可能参与调控小麦的盐、 干旱和低温等逆境响应过程。

附表和附图 请见网络版: 1) 本刊网站http://zwxb.chinacrops.org/; 2) 中国知网http://www.cnki.net/; 3) 万方数据http://c.wanfangdata.com.cn/Periodical-zuowxb.aspx

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