植物碱基编辑方法与流程

本发明涉及植物基因工程领域。具体而言，本发明涉及一种植物碱基编辑方法。更具体而言，本发明涉及一种通过向导rna指导的crispr-腺嘌呤脱氨酶融合蛋白对植物(例如作物植物)基因组中的靶序列进行高效a到g的碱基编辑方法，以及通过所述方法产生的植物及其后代。
背景技术：
：：高效的作物改良的前提是能够获得新的遗传突变，这些突变可以容易地引入现代栽培种中。遗传研究，尤其是基于全基因组相关的研究表明，单核苷酸的改变是构成作物性状差异的主要原因。单碱基的变异会导致氨基酸替换,从而导致优良等位基因和优异性状的进化。在基因组编辑出现前，定向诱导基因组局部突变(tilling)可以作为用于产生作物改良中迫切需要的突变的方法。然而，tilling筛选耗时耗力，并且所鉴别的点突变经常受数目和种类的限制。基因组编辑技术，特别是基于crispr/cas9系统的基因组编辑技术可以通过同源重组(hr)介导的dna修复途径来实现在基因组位点中引入特定碱基的替换。但目前，该方法的成功使用受到很大限制，主要是由于在植物中hr介导的双链断链修复发生的频率很低。另外，有效的提供足量的dna修复模板也是目前的一大难关。这些问题使得目前在植物中通过hr的方式高效而简单地实现定点突变成为一大挑战。目前，通过使用cas9与胞嘧啶脱氨酶的融合蛋白，已经在植物中实现了c至t的碱基编辑。然而本领域仍然迫切需要对植物基因组进行a至g点突变的方法。发明简述在第一方面，本发明提供一种用于对植物基因组中的靶序列进行碱基编辑的系统，其包含以下i)至v)中至少一项：i)碱基编辑融合蛋白，和向导rna；ii)包含编码碱基编辑融合蛋白的核苷酸序列的表达构建体，和向导rna；iii)碱基编辑融合蛋白，和包含编码向导rna的核苷酸序列的表达构建体；iv)包含编码碱基编辑融合蛋白的核苷酸序列的表达构建体，和包含编码向导rna的核苷酸序列的表达构建体；v)包含编码碱基编辑融合蛋白的核苷酸序列和编码向导rna的核苷酸序列的表达构建体；其中所述碱基编辑融合蛋白包含核酸酶失活的crispr效应蛋白(如cas9和cpf1等)和dna依赖型腺嘌呤脱氨酶，所述向导rna能够将所述碱基编辑融合蛋白靶向植物基因组中的靶序列，从而所述碱基编辑融合蛋白导致所述靶序列中的一或多个a被g取代。在第二方面，本发明提供一种产生经遗传修饰的植物的方法，包括将本发明的用于对植物基因组中的靶序列进行碱基编辑的系统导入植物，由此所述向导rna将所述碱基编辑融合蛋白靶向所述植物基因组中的靶序列，从而所述碱基编辑融合蛋白导致所述靶序列中的一或多个a被g取代。在第三方面，本发明提供经遗传修饰的植物或其后代，其中所述植物通过本发明的方法获得。在第四方面，本发明一种植物育种方法，包括将通过本发明的方法获得的经遗传修饰的第一植物与不含有所述遗传修饰的第二植物杂交，从而将所述遗传修饰导入第二植物。附图描述图1、适合植物细胞编辑的腺嘌呤碱基编辑构建体。图2、腺嘌呤碱基编辑系统在植物原生质体中实现外源gfp基因的碱基编辑。图3、腺嘌呤碱基编辑系统对植物内源基因的碱基编辑。图4、不同腺嘌呤碱基编辑构建系统对植物内源基因的碱基编辑。图5、pabe-1到pabe-7构建体及其基因编辑结果。图6、pabe-2和pabe-7对水稻内源基因的编辑。图7、三种sgrna形式的结构示意图，其中水稻u3启动子、小麦u6启动子、sgrnascaffold、esgrnascaffold和trna序列分别用蓝色、紫色、红色、绿色和棕色表示；转录起始位点用黄色高亮表示；箭头指示trna的rnasez裂解位点；下划线表示bsai限制性位点，可以使用退火的寡核苷酸将引导序列插入两个bsai位点之间。图8、不同sgrna形式对基因编辑的影响。图9、植物abe对于水稻基因组位点的产物纯度，其中在10个代表性水稻基因组dna位点检测了产物分布和插入缺失突变频率，样品来自用pabe-7和相应的天然sgrna、esgrna和trna-sgrna处理的水稻原生质体；在每个位置使用总共48,616-111,697个测序读段。图10、植物abe对于小麦基因组位点的产物纯度，其中在3个代表性小麦基因组dna位点检测了产物分布和插入缺失突变频率，样品来自用pabe-7和相应的天然sgrna、esgrna和trna-sgrna处理的水稻原生质体；在每个位置使用总共28,110-28,4527个测序读段。图11、sgrna形式对插入缺失突变的影响。图12、spacer序列长度对a到g碱基编辑的影响。图13、spacer序列长度对插入缺失突变的影响。图14、使用pabe-7产生具有a到g取代的水稻植物。图15、使用pabe-7产生具有a到g取代的小麦植物。图16、通过碱基编辑产生具有除草剂抗性的水稻。发明详述一、定义在本发明中，除非另有说明，否则本文中使用的科学和技术名词具有本领域技术人员所通常理解的含义。并且，本文中所用的蛋白质和核酸化学、分子生物学、细胞和组织培养、微生物学、免疫学相关术语和实验室操作步骤均为相应领域内广泛使用的术语和常规步骤。例如，本发明中使用的标准重组dna和分子克隆技术为本领域技术人员熟知，并且在如下文献中有更全面的描述：sambrook，j.，fritsch，e.f.和maniatis，t.，molecularcloning：alaboratorymanual；coldspringharborlaboratorypress：coldspringharbor，1989(下文称为“sambrook”)。同时，为了更好地理解本发明，下面提供相关术语的定义和解释。如本文所用，术语“crispr效应蛋白”通常指在天然存在的crispr系统中存在的核酸酶，以及其修饰形式、其变体、其催化活性片段等。该术语涵盖基于crispr系统的能够在细胞内实现基因靶向(例如基因编辑、基因靶向调控等)的任何效应蛋白。“crispr效应蛋白”的实例包括cas9核酸酶或其变体。所述cas9核酸酶可以是来自不同物种的cas9核酸酶，例如来自化脓链球菌(s.pyogenes)的spcas9或衍生自金黄色葡萄球菌(s.aureus)的sacas9。“cas9核酸酶”和“cas9”在本文中可互换使用，指的是包括cas9蛋白或其片段(例如包含cas9的活性dna切割结构域和/或cas9的grna结合结构域的蛋白)的rna指导的核酸酶。cas9是crispr/cas(成簇的规律间隔的短回文重复序列及其相关系统)基因组编辑系统的组分，能在向导rna的指导下靶向并切割dna靶序列形成dna双链断裂(dsb)。“crispr效应蛋白”的实例还可以包括cpf1核酸酶或其变体例如高特异性变体。所述cpf1核酸酶可以是来自不同物种的cpf1核酸酶，例如来自francisellanovicidau112、acidaminococcussp.bv3l6和lachnospiraceaebacteriumnd2006的cpf1核酸酶。如本文所用，“grna”和“向导rna”可互换使用，指的是能够与crispr效应蛋白形成复合物并由于与靶序列具有一定互补性而能够将所述复合物靶向靶序列的rna分子。例如，在基于cas9的基因编辑系统中，grna通常由部分互补形成复合物的crrna和tracrrna分子构成，其中crrna包含与靶序列具有足够互补性以便与该靶序列杂交并且指导crispr复合物(cas9+crrna+tracrrna)与该靶序列序列特异性地结合的序列。然而，本领域已知可以设计单向导rna(sgrna)，其同时包含crrna和tracrrna的特征。而在基于cpf1的基因组编辑系统中，grna通常仅由成熟crrna分子构成，其中crrna包含的序列与靶序列具有足够相同性以便与靶序列的互补序列杂交并且指导复合物(cpf1+crrna)与该靶序列序列特异性结合。基于所使用的crispr效应蛋白和待编辑的靶序列设计合适的grna序列属于本领域技术人员的能力范围内。“腺嘌呤脱氨酶”是指能够催化腺苷或脱氧腺苷(a)形成肌苷(i)的腺嘌呤脱氨酶。“基因组”在用于植物细胞时不仅涵盖存在于细胞核中的染色体dna，而且还包括存在于细胞的亚细胞组分(如线粒体、质体)中的细胞器dna。如本文所使用的，术语“植物”包括整个植物和任何后代、植物的细胞、组织、或部分。术语“植物部分”包括植物的任何部分，包括，例如但不限于：种子(包括成熟种子、没有种皮的未成熟胚、和不成熟的种子)；植物插条(plantcutting)；植物细胞；植物细胞培养物；植物器官(例如，花粉、胚、花、果实、芽、叶、根、茎，和相关外植体)。植物组织或植物器官可以是种子、愈伤组织、或者任何其他被组织成结构或功能单元的植物细胞群体。植物细胞或组织培养物能够再生出具有该细胞或组织所来源的植物的生理学和形态学特征的植物，并能够再生出与该植物具有基本上相同基因型的植物。与此相反，一些植物细胞不能够再生产生植物。植物细胞或组织培养物中的可再生细胞可以是胚、原生质体、分生细胞、愈伤组织、花粉、叶、花药、根、根尖、丝、花、果仁、穗、穗轴、壳、或茎。植物部分包括可收获的部分和可用于繁殖后代植物的部分。可用于繁殖的植物部分包括，例如但不限于：种子；果实；插条；苗；块茎；和砧木。植物的可收获部分可以是植物的任何有用部分，包括，例如但不限于：花；花粉；苗；块茎；叶；茎；果实；种子；和根。植物细胞是植物的结构和生理单元。如本文所使用的，植物细胞包括原生质体和具有部分细胞壁的原生质体。植物细胞可以处于分离的单个细胞或细胞聚集体的形式(例如，松散愈伤组织和培养的细胞)，并且可以是更高级组织单元(例如，植物组织、植物器官、和植物)的一部分。因此，植物细胞可以是原生质体、产生配子的细胞，或者能够再生成完整植物的细胞或细胞的集合。因此，在本文的实施方案中，包含多个植物细胞并能够再生成为整株植物的种子被认为是一种“植物部分”。如本文所使用的，术语“原生质体”是指细胞壁被完全或部分地除去、其脂双层膜裸露的植物细胞。典型地，原生质体是没有细胞壁的分离植物细胞，其具有再生成细胞培养物或整株植物的潜力。植物“后代”包括植物的任何后续世代。“经遗传修饰的植物”包括在其基因组内包含外源多核苷酸或修饰的基因或表达调控序列的植物。例如外源多核苷酸能够稳定地整合进基因组中，并遗传连续的世代。外源多核苷酸可单独地或作为重组dna构建体的部分整合进基因组中。修饰的基因或表达调控序列为在植物基因组中所述序列包含单个或多个脱氧核苷酸取代、缺失和添加。例如，通过本发明获得的经遗传修饰的植物可以相对于野生型植物(相应的未经所述遗传修饰的植物)包含一个或多个a至g的取代。针对序列而言的“外源”意指来自外来物种的序列，或者如果来自相同物种，则指通过蓄意的人为干预而从其天然形式发生了组成和/或基因座的显著改变的序列。“多核苷酸”、“核酸序列”、“核苷酸序列”或“核酸片段”可互换使用并且是单链或双链rna或dna聚合物，任选地可含有合成的、非天然的或改变的核苷酸碱基。核苷酸通过如下它们的单个字母名称来指代：“a”为腺苷或脱氧腺苷(分别对应rna或dna)，“c”表示胞苷或脱氧胞苷，“g”表示鸟苷或脱氧鸟苷，“u”表示尿苷，“t”表示脱氧胸苷，“r”表示嘌呤(a或g)，“y”表示嘧啶(c或t)，“k”表示g或t，“h”表示a或c或t，“i”表示肌苷，并且“n”表示任何核苷酸。“多肽”、“肽”、和“蛋白质”在本发明中可互换使用，指氨基酸残基的聚合物。该术语适用于其中一个或多个氨基酸残基是相应的天然存在的氨基酸的人工化学类似物的氨基酸聚合物，以及适用于天然存在的氨基酸聚合物。术语“多肽”、“肽”、“氨基酸序列”和“蛋白质”还可包括修饰形式，包括但不限于糖基化、脂质连接、硫酸盐化、谷氨酸残基的γ羧化、羟化和adp-核糖基化。如本发明所用，“表达构建体”是指适于感兴趣的核苷酸序列在植物中表达的载体如重组载体。“表达”指功能产物的产生。例如，核苷酸序列的表达可指核苷酸序列的转录(如转录生成mrna或功能rna)和/或rna翻译成前体或成熟蛋白质。本发明的“表达构建体”可以是线性的核酸片段、环状质粒、病毒载体，或者，在一些实施方式中，可以是能够翻译的rna(如mrna)。本发明的“表达构建体”可包含不同来源的调控序列和感兴趣的核苷酸序列，或相同来源但以不同于通常天然存在的方式排列的调控序列和感兴趣的核苷酸序列。“调控序列”和“调控元件”可互换使用，指位于编码序列的上游(5'非编码序列)、中间或下游(3'非编码序列)，并且影响相关编码序列的转录、rna加工或稳定性或者翻译的核苷酸序列。植物表达调控元件指的是能够在植物中控制感兴趣的核苷酸序列转录、rna加工或稳定性或者翻译的核苷酸序列。调控序列可包括但不限于启动子、翻译前导序列、内含子和多腺苷酸化识别序列。“启动子”指能够控制另一核酸片段转录的核酸片段。在本发明的一些实施方案中，启动子是能够控制植物细胞中基因转录的启动子，无论其是否来源于植物细胞。启动子可以是组成型启动子或组织特异性启动子或发育调控启动子或诱导型启动子。“组成型启动子”指一般将引起基因在多数细胞类型中在多数情况下表达的启动子。“组织特异性启动子”和“组织优选启动子”可互换使用，并且指主要但非必须专一地在一种组织或器官中表达，而且也可在一种特定细胞或细胞型中表达的启动子。“发育调控启动子”指其活性由发育事件决定的启动子。“诱导型启动子”响应内源性或外源性刺激(环境、激素、化学信号等)而选择性表达可操纵连接的dna序列。如本文中所用，术语“可操作地连接”指调控元件(例如但不限于，启动子序列、转录终止序列等)与核酸序列(例如，编码序列或开放读码框)连接，使得核苷酸序列的转录被所述转录调控元件控制和调节。用于将调控元件区域可操作地连接于核酸分子的技术为本领域已知的。将核酸分子(例如质粒、线性核酸片段、rna等)或蛋白质“导入”植物是指用所述核酸或蛋白质转化植物细胞，使得所述核酸或蛋白质在植物细胞中能够发挥功能。本发明所用的“转化”包括稳定转化和瞬时转化。“稳定转化”指将外源核苷酸序列导入植物基因组中，导致外源基因稳定遗传。一旦稳定转化，外源核酸序列稳定地整合进所述植物和其任何连续世代的基因组中。“瞬时转化”指将核酸分子或蛋白质导入植物细胞中，执行功能而没有外源基因稳定遗传。瞬时转化中，外源核酸序列不整合进植物基因组中。“性状”指植物或特定植物材料或细胞的生理的、形态的、生化的或物理的特征。在一些实施方式中，这些特征可以是肉眼可见的，比如种子、植株的大小等；可用生物化学技术测定的指标，如种子或叶片中蛋白、淀粉或油份的含量等；可观察的代谢或生理过程，如测定对水分胁迫、特定盐、糖或氮浓度的抗性；可检测的基因表达水平；或可观察渗透胁迫的抗性或产量等农艺性状。在一些实施方式中，性状还包括植物对除草剂的抗性。“农艺性状”是可测量的指标参数，包括但不限于：叶片绿色、籽粒产量、生长速率、总生物量或积累速率、成熟时的鲜重、成熟时的干重、果实产量、种子产量、植物总氮含量、果实氮含量、种子氮含量、植物营养组织氮含量、植物总游离氨基酸含量、果实游离氨基酸含量、种子游离氨基酸含量、植物营养组织游离氨基酸含量、植物总蛋白含量、果实蛋白含量、种子蛋白含量、植物营养组织蛋白质含量、抗旱性、氮的吸收、根的倒伏、收获指数、茎的倒伏、株高、穗高、穗长、抗病性、抗寒性、抗盐性和分蘖数等。二、植物腺嘌呤碱基编辑系统本发明提供了一种用于对植物基因组中的靶序列进行碱基编辑的系统，其包含以下i)至v)中至少一项：i)碱基编辑融合蛋白，和向导rna；ii)包含编码碱基编辑融合蛋白的核苷酸序列的表达构建体，和向导rna；iii)碱基编辑融合蛋白，和包含编码向导rna的核苷酸序列的表达构建体；iv)包含编码碱基编辑融合蛋白的核苷酸序列的表达构建体，和包含编码向导rna的核苷酸序列的表达构建体；v)包含编码碱基编辑融合蛋白的核苷酸序列和编码向导rna的核苷酸序列的表达构建体；其中所述碱基编辑融合蛋白包含核酸酶失活的crispr效应蛋白(如cas9和cpf1等)和dna依赖型腺嘌呤脱氨酶，所述向导rna能够将所述碱基编辑融合蛋白靶向植物基因组中的靶序列，从而所述碱基编辑融合蛋白导致所述靶序列中的一或多个a被g取代。如本发明所用，“核酸酶失活的crispr效应蛋白”是指crispr效应蛋白的双链核酸切割活性缺失，然而还保留grna指导的dna靶向能力。缺失双链核酸切割活性的crispr效应蛋白也涵盖切口酶(nickase)，其在双链核酸分子形成切口(nick)，但不完全切断双链核酸。在一些实施方案中，所述核酸酶失活的crispr效应蛋白是核酸酶失活的cas9。cas9核酸酶的dna切割结构域已知包含两个亚结构域：hnh核酸酶亚结构域和ruvc亚结构域。hnh亚结构域切割与grna互补的链，而ruvc亚结构域切割非互补的链。在这些亚结构域中的突变可以使cas9的核酸酶活性失活，形成“核酸酶失活的cas9”。所述核酸酶失活的cas9仍然保留grna指导的dna结合能力。因此，原则上，当与另外的蛋白融合时，核酸酶失活的cas9可以简单地通过与合适的向导rna共表达而将所述另外的蛋白靶向几乎任何dna序列。天然存在的腺嘌呤脱氨酶同常以rna为底物，通过脱氨作用将单链rna上的腺苷转变成肌苷(i)。最近，通过定向进化的方法，已经基于大肠杆菌的trna腺嘌呤脱氨酶tada获得了能够以单链dna为底物，将单链dna上的脱氧鸟苷转变为肌苷(i)的dna依赖型腺嘌呤脱氨酶。参见nicloem.gaudelli等人，doi：10.1038/nature24644，2017。然而，这样的dna依赖型腺嘌呤脱氨酶能否在植物中发挥作用是未知的，且难以预期。本发明人令人惊奇地发现，将核酸酶失活的crispr效应蛋白如(核酸酶失活的cas9)与dna依赖型腺嘌呤脱氨酶融合，在向导rna的指导下，融合蛋白可以靶向植物基因组中的靶序列，由于crispr效应蛋白的核酸酶活性缺失，dna双链不被切割，而融合蛋白中的dna依赖型腺嘌呤脱氨酶能够将crispr效应蛋白-向导rna-dna复合物形成中产生的单链dna的腺苷脱氨转换成肌苷(i)，由于dna聚合酶会将肌苷(i)当做鸟嘌呤(g)处理，因此通过碱基错配修复可以实现a至g的取代。在本发明的一些实施方案中，所述dna依赖型腺嘌呤脱氨酶是大肠杆菌trna腺嘌呤脱氨酶tada(ectada)的变体，特别是可以接受单链dna作为底物的变体，所述变体相对于野生型ectada包含一或多组选自以下的突变：1)a106v和d108n；2)d147y和e155v；3)l84f、h123y和i156f；4)a142n；5)h36l、r51l、s146c和k157n；6)p48s/t/a；7)a142n；8)w23l/r；9)r152h/p。在本发明一优选实施方式中，所述dna依赖型腺嘌呤脱氨酶相对于野生型ectada包含以下突变：w23r、h36l、r51l、s146c、k157n、a106v、d108n、p48a、l84f、h123y、i156f、d147y、e155v、r152p。野生型ectada氨基酸序列如seqidno:1所示。优选的ectada衍生的dna依赖型腺嘌呤脱氨酶氨基酸序列如seqidno:2所示。本发明所述核酸酶失活的cas9可以衍生自不同物种的cas9，例如，衍生自化脓链球菌(s.pyogenes)cas9(spcas9)，或衍生自金黄色葡萄球菌(s.aureus)cas9(sacas9)。同时突变cas9的hnh核酸酶亚结构域和ruvc亚结构域(例如，包含突变d10a和h840a)使cas9的核酸酶失去活性，成为核酸酶死亡cas9(dcas9)。突变失活其中一个亚结构域可以使得cas9具有切口酶活性，即获得cas9切口酶(ncas9)，例如，仅具有突变d10a的ncas9。因此，在本发明的一些实施方案中，本发明所述核酸酶失活的cas9相对于野生型cas9包含氨基酸取代d10a和/或h840a。在本发明的一些优选的实施方案中，本发明所述核酸酶失活的cas9具有切口酶活性。不受任何理论限制，据认为真核生物的错配修复通过dna链上的切口(nick)来指导该链错配碱基的移除和修复。dna依赖型腺嘌呤脱氨酶作用形成的i:t错配可能被修复为a:t。通过在包含未编辑的t的一条链上引入切口，将能够优先地将i:t错配修复为期望的c:g。因此，优选地，所述核酸酶失活的cas9是cas9切口酶，其保留cas9的hnh亚结构域的切割活性，而ruvc亚结构域的切割活性失活。例如，所述核酸酶失活的cas9相对于野生型cas9包含氨基酸取代d10a。在本发明的一些具体实施方式中，所述核酸酶失活的cas9还可以包含额外的突变。例如核酸酶失活的spcas9还可以包含vqr或vrer突变以及sacas9还可以包含kkh突变(kimetal.nat.biotechnol.35,371–376.)。在本发明的一些具体实施方式中，所述核酸酶失活的spcas9包含seqidno:3所示的氨基酸序列。在本发明的一些实施方案中，所述dna依赖型腺嘌呤脱氨酶被融合至所述核酸酶失活的crispr效应蛋白(如核酸酶失活的cas9)的n末端。在一些优选实施方案中，所述dna依赖型腺嘌呤脱氨酶的n端融合有对应的野生型腺嘌呤脱氨酶。预期dna依赖型腺嘌呤脱氨酶与野生型腺嘌呤脱氨酶形成异二聚体可以显著提高融合蛋白a至g的编辑活性。在本发明的一些实施方案中，所述dna依赖型腺嘌呤脱氨酶和所述核酸酶失活的crispr效应蛋白(如核酸酶失活的cas9)或所述对应的野生型腺嘌呤脱氨酶通过接头融合。所述接头可以是长1-50个(例如1、2、3、4、5、6、7、8、9、10、11、12、13、14、15、16、17、18、19、20个或20-25个、25-50个)或更多个氨基酸、无二级以上结构的非功能性氨基酸序列。例如，所述接头可以是柔性接头，例如ggggs、gs、gap、(ggggs)x3、ggs和(ggs)x7等。优选地，所述接头长32个氨基酸。在一些优选的实施方案中，所述接头的氨基酸序列为：sggssggssgsetpgtsesatpessggssggs。在本发明的一些实施方案中，本发明的碱基编辑融合蛋白还包含核定位序列(nls)。一般而言，所述碱基编辑融合蛋白中的一个或多个nls应具有足够的强度，以便在植物细胞的核中驱动所述碱基编辑融合蛋白以可实现其碱基编辑功能的量积聚。一般而言，核定位活性的强度由所述碱基编辑融合蛋白中nls的数目、位置、所使用的一个或多个特定的nls、或这些因素的组合决定。在本发明的一些实施方案中，本发明的碱基编辑融合蛋白的nls可以位于n端和/或c端。在本发明的一些实施方案中，本发明的碱基编辑融合蛋白的nls可以位于所述腺嘌呤脱氨酶与所述核酸酶失活的crispr效应蛋白之间。在本发明的一些实施方案中，本发明的碱基编辑融合蛋白的nls可以位于所述dna依赖型腺嘌呤脱氨酶与所述核酸酶失活的crispr效应蛋白之间。在一些实施方案中，所述碱基编辑融合蛋白包含约1、2、3、4、5、6、7、8、9、10个或更多个nls。在一些实施方案中，所述碱基编辑融合蛋白包含在或接近于n端的约1、2、3、4、5、6、7、8、9、10个或更多个nls。在一些实施方案中，所述碱基编辑融合蛋白包含在或接近于c端约1、2、3、4、5、6、7、8、9、10个或更多个nls。在一些实施方案中，所述碱基编辑融合蛋白包含这些的组合，如包含在n端的一个或多个nls以及在c端的一个或多个nls。当存在多于一个nls时，每一个可以被选择为不依赖于其他nls。在本发明的一些优选实施方式中，所述碱基编辑融合蛋白包含至少2个nls，例如所述至少2个nls位于c端。在一些优选的实施方案中，所述nls位于所述碱基编辑融合蛋白的c末端。在一些优选的实施方案中，所述碱基编辑融合蛋白包含至少3个nls。在更优选的实施方案中，所述碱基编辑融合蛋白在c末端包含至少3个nls。在一些优选的实施方案中，所述碱基编辑融合蛋白在n端和/或在所述腺嘌呤脱氨酶与所述核酸酶失活的crispr效应蛋白之间不包含nls。一般而言，nls由暴露于蛋白表面上的带正电的赖氨酸或精氨酸的一个或多个短序列组成，但其他类型的nls也是已知的。nls的非限制性实例包括：kkrkv(核苷酸序列5’-aagaagagaaaggtc-3’)、pkkkrkv(核苷酸序列5’-cccaagaagaagaggaaggtg-3’或ccaaagaagaagaggaaggtt)，或sggspkkkrkv(核苷酸序列5’-tcgggggggagcccaaagaagaagcggaaggtg-3’)。在本发明的一些实施方式中，所述碱基编辑融合蛋白的n端包含pkkkrkv所示的氨基酸序列的nls。在本发明的一些实施方式中，所述碱基编辑融合蛋白的c端包含krpaatkkagqakkkk所示的氨基酸序列的nls。在本发明的一些实施方式中，所述碱基编辑融合蛋白的c端包含pkkkrkv所示的氨基酸序列的nls效率更高。此外，根据所需要编辑的dna位置，本发明的碱基编辑融合蛋白还可以包括其他的定位序列，例如细胞质定位序列、叶绿体定位序列、线粒体定位序列等。在本发明的另一些具体实施方式中，所述碱基编辑融合蛋白包含seqidno:4所示的氨基酸序列。在本发明的另一些具体实施方式中，所述碱基编辑融合蛋白包含seqidno:5所示的氨基酸序列。在本发明的另一些具体实施方式中，所述碱基编辑融合蛋白包含seqidno:18-25之一所示的氨基酸序列。在本发明的另一些具体实施方式中，所述碱基编辑融合蛋白包含seqidno:33-39之一所示的氨基酸序列。在本发明的另一些优选实施方式中，所述碱基编辑融合蛋白包含seqidno:33-35、38和39之一所示的氨基酸序列。在优选的实施方案中，所述碱基编辑融合蛋白包含seqidno:39所示的氨基酸序列。为了在植物中获得有效表达，在本发明的一些实施方式中，所述编码碱基编辑融合蛋白的核苷酸序列针对待进行碱基编辑的植物进行密码子优化。密码子优化是指通过用在宿主细胞的基因中更频繁地或者最频繁地使用的密码子代替天然序列的至少一个密码子(例如约或多于约1、2、3、4、5、10、15、20、25、50个或更多个密码子同时维持该天然氨基酸序列而修饰核酸序列以便增强在感兴趣宿主细胞中的表达的方法。不同的物种对于特定氨基酸的某些密码子展示出特定的偏好。密码子偏好性(在生物之间的密码子使用的差异)经常与信使rna(mrna)的翻译效率相关，而该翻译效率则被认为依赖于被翻译的密码子的性质和特定的转运rna(trna)分子的可用性。细胞内选定的trna的优势一般反映了最频繁用于肽合成的密码子。因此，可以将基因定制为基于密码子优化在给定生物中的最佳基因表达。密码子利用率表可以容易地获得，例如在www.kazusa.orjp/codon/上可获得的密码子使用数据库(“codonusagedatabase”)中，并且这些表可以通过不同的方式调整适用。参见，nakamuray.等，“codonusagetabulatedfromtheinternationaldnasequencedatabases:statusfortheyear2000.nucl.acidsres.，28:292(2000)。在本发明一些具体实施方式中，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:6。在本发明另一些具体实施方式中，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:7。在本发明另一些具体实施方式中，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:10-17之一。在本发明另一些具体实施方式中，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:26-32之一。在本发明另一些优选实施方式中，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:26-28、31和32之一。优选地，经密码子优化的所述编码碱基编辑融合蛋白的核苷酸序列示于seqidno:32。在本发明一些实施方式中，所述向导rna是单向导rna(sgrna)。根据给定的靶序列构建合适的sgrna的方法是本领域已知的。例如，可参见文献：wang,y.etal.simultaneouseditingofthreehomoeoallelesinhexaploidbreadwheatconfersheritableresistancetopowderymildew.nat.biotechnol.32,947-951(2014)；shan,q.etal.targetedgenomemodificationofcropplantsusingacrispr-cassystem.nat.biotechnol.31,686-688(2013)；liang,z.etal.targetedmutagenesisinzeamaysusingtalensandthecrispr/cassystem.jgenetgenomics.41,63–68(2014)。在本发明一些具体实施方式中，sgrna的序列包括以下的scaffold序列：gttttagagctagaaatagcaagttaaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgc(seqidno:138，对应于实施例sgrna)或gtttaagagctatgctggaaacagcatagcaagtttaaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcggtgc(seqidno:139，对应于实施例esgrna)，其中sgrna中靶序列(或spacer序列)在上述scaffold序列的5’端。在优选的实施方案中，所述碱基编辑融合蛋白包含seqidno:39所示的氨基酸序列，所述向导rna是包含由seqidno:139所示的scaffold序列的单向导rna。在本发明一些实施方式中，所述编码碱基编辑融合蛋白的核苷酸序列和/或所述编码向导rna的核苷酸序列与植物表达调控元件如启动子可操作地连接。本发明可使用的启动子的实例包括但不限于：花椰菜花叶病毒35s启动子(odelletal.(1985)nature313:810-812)、玉米ubi-1启动子、小麦u6启动子、水稻u3启动子、玉米u3启动子、水稻肌动蛋白启动子、trppro5启动子(美国专利申请no.10/377,318；2005年3月16日提请)、pemu启动子(lastetal.(1991)theor.appl.genet.81:581-588)、mas启动子(veltenetal.(1984)emboj.3:2723-2730)、玉米h3组蛋白启动子(lepetitetal.(1992)mol.gen.genet.231:276-285和atanassovaetal.(1992)plantj.2(3):291-300)和欧洲油菜(brassicanapus)als3(pct申请wo97/41228)启动子。可用于本发明的启动子还包含mooreetal.(2006)plantj.45(4):651-683中综述的常用组织特异性启动子。在本发明可使用的sgrna的精确rna的获得借助于trna的自身切割产生(zhangetal.(2017)genomebiology,2017,18:191)。三、产生经遗传修饰的植物的方法在另一方面，本发明提供了一种产生经遗传修饰的植物的方法，包括将本发明的用于对植物基因组中的靶序列进行碱基编辑的系统导入植物，由此所述向导rna将所述碱基编辑融合蛋白靶向所述植物基因组中的靶序列，导致所述靶序列中的一或多个a被g取代。可以被cas9和向导rna复合物识别并靶向的靶序列的设计属于本领域普通技术人员的技能范围。一般而言，靶序列是与向导rna中包含的大约20个核苷酸的引导序列互补的序列，且3’末端紧邻前间区序列邻近基序(protospaceradjacentmotif)(pam)ngg。例如，在本发明的一些实施方案中，所述靶序列具有以下结构：5’-nx-ngg-3’，其中n独立地选自a、g、c和t；x为14≤x≤30的整数；nx表示x个连续的核苷酸，ngg为pam序列。在本发明的一些优选的实施方案中，x为20。在一些实施方案中，碱基编辑的窗口位于靶序列的位置4-8。也就是说，本发明的系统可以使靶序列从5’末端起的第4-8位范围内的一或多个a被g取代。在本发明所述方法的一些实施方案中，还包括筛选具有期望的核苷酸取代的植物。可以通过t7ei、pcr/re或测序方法检测植物中的核苷酸取代，例如可参见shan,q.,wang,y.,li,j.&gao,c.genomeeditinginriceandwheatusingthecrispr/cassystem.nat.protoc.9,2395-2410(2014)。在本发明的方法中，所述碱基编辑系统可以本领域技术人员熟知的各种方法导入植物。可用于将本发明的碱基编辑系统导入植物的方法包括但不限于：基因枪法、peg介导的原生质体转化、土壤农杆菌介导的转化、植物病毒介导的转化、花粉管通道法和子房注射法。优选地，通过瞬时转化将所述碱基编辑系统导入植物。在本发明的方法中，只需在植物细胞中导入或产生所述碱基编辑融合蛋白和向导rna即可实现对靶序列的修饰，并且所述修饰可以稳定遗传，无需将所述碱基编辑系统稳定转化植物。这样避免了稳定存在的碱基编辑系统的潜在脱靶作用，也避免外源核苷酸序列在植物基因组中的整合，从而具有更高生物安全性。在一些优选实施方式中，所述导入在不存在选择压力下进行，从而避免外源核苷酸序列在植物基因组中的整合。在一些实施方式中，所述导入包括将本发明的碱基编辑系统转化至分离的植物细胞或组织，然后使所述经转化的植物细胞或组织再生为完整植物。优选地，在不存在选择压力下进行所述再生，也即是，在组织培养过程中不使用任何针对表达载体上携带的选择基因的选择剂。不使用选择剂可以提高植物的再生效率，获得不含外源核苷酸序列的经修饰的植物。在另一些实施方式中，可以将本发明的碱基编辑系统转化至完整植物上的特定部位，例如叶片、茎尖、花粉管、幼穗或下胚轴。这特别适合于难以进行组织培养再生的植物的转化。在本发明的一些实施方式中，直接将体外表达的蛋白质和/或体外转录的rna分子转化至所述植物。所述蛋白质和/或rna分子能够在植物细胞中实现碱基编辑，随后被细胞降解，避免了外源核苷酸序列在植物基因组中的整合。因此，在一些实施方式中，使用本发明的方法对植物进行遗传修饰和育种可以获得无外源dna整合的植物，即非转基因(transgene-free)的经修饰的植物。此外，本发明的碱基编辑系统在植物中进行碱基编辑时具有高特异性(低脱靶率)，这也提高了生物安全性。可以通过本发明的方法进行碱基编辑的植物包括单子叶植物和双子叶植物。例如，所述植物可以是作物植物，例如小麦、水稻、玉米、大豆、向日葵、高粱、油菜、苜蓿、棉花、大麦、粟、甘蔗、番茄、烟草、木薯或马铃薯。在本发明的一些实施方式中，其中所述靶序列与植物性状如农艺性状相关，由此所述碱基编辑导致所述植物相对于野生型植物具有改变的性状。在本发明中，待进行修饰的靶序列可以位于基因组的任何位置，例如位于功能基因如蛋白编码基因内，或者例如可以位于基因表达调控区如启动子区或增强子区，从而实现对所述基因功能修饰或对基因表达的修饰。相应地，在本发明的一些实施方式中，所述a至g的取代导致靶蛋白中的氨基酸取代。在本发明的另一些实施方式中，所述a至g的取代导致靶基因的表达发生变化。在一些具体实施方式中，通过本发明的方法进行修饰的基因可以是抗除草剂基因乙酰乳酸合酶(als)和乙酰辅酶a羧化酶(acc)基因。对抗除草剂基因als和acc的关键氨基酸位点进行a到g的突变，可以使植物获得除草剂抗性。在一些实施方案中，对acc基因进行修饰。在一些实施方案中，对水稻acc基因进行修饰，经修饰的acc基因所编码的acc蛋白具有c2186r突变。在本发明的一些实施方式中，所述方法还包括获得所述经遗传修饰的植物的后代。在另一方面，本发明还提供了经遗传修饰的植物或其后代或其部分，其中所述植物通过本发明上述的方法获得。在一些实施方式中，所述经遗传修饰的植物或其后代或其部分是非转基因的。在另一方面，本发明还提供了一种植物育种方法，包括将通过本发明上述的方法获得的经遗传修饰的第一植物与不含有所述遗传修饰的第二植物杂交，从而将所述遗传修饰导入第二植物。实施例构建ncas9-abe表达载体abe、xten、ncas9(d10a)序列针对植物进行密码子优化并订购自genscript(nanjing)。使用引物对hindiii-f(具有hindiii限制位点)和ecori(具有ecori限制位点)扩增全长ncas9-abe片段。pcr产物用hindiii和ecori消化，然后插入至这两种酶消化的pjit163-gfp载体(该载体序列示于seqidno：8)以产生融合表达载体pn/dcas9-pbe。构建sgrna表达载体根据之前描述(wang,y.etal.simultaneouseditingofthreehomoeoallelesinhexaploidbreadwheatconfersheritableresistancetopowderymildew.nat.biotechnol.32,947-951,2014；shan,q.etal.targetedgenomemodificationofcropplantsusingacrispr-cassystem.nat.biotechnol.31,686-688,2013；和liang,z.etal.targetedmutagenesisinzeamaysusingtalensandthecrispr/cassystem.jgenetgenomics.41,63–68,2014)基于ptau6-sgrna(addgeneid53062)或posu3-sgrna(addgeneid53063)或pzmu3-sgrna(addgeneid5306)或osu3/tau6-trna-sgrna(zhangetal.2017.genomebiology.doi:10.1186/s13059-017-1325-9)构建sgrna表达载体：ptau3-mgfpp-sgrna、posu3-mgfp-sgrna、pzmu3-mgfp-sgrna、posu3-dep1-t6-sgrna、posu3-dep1-t7-sgrna、posu3-acc-t3-sgrna、posu3-nrt1.1-t1-sgrna.gfp表达载体pubi-mgfp，该载体序列示于seqidno：9。原生质体测定在本研究中使用小麦bobwhite品种、水稻日本晴品种。如下所述进行原生质体转化。平均转化效率为55-70％。每种质粒用10μg通过peg介导方法进行转化，48小时后，收集原生质体，提取dna用于t7ei和pcr-re测定。小麦原生质体制备及转化1)取小麦(玉米)幼嫩的叶片，将其中间部分切成0.5-1mm的丝，放入0.6m的mannitol溶液中避光处理10分钟，再用滤网过滤，将其放入50ml酶液中20-25℃避光，10rmp缓慢摇晃消化5小时。2)加10mlw5稀释酶解产物，用75μm尼龙滤膜过滤酶解液于圆底离心管中(50ml)。3)23℃，100g，离心3min，弃上清。4)用w510ml轻轻悬起，冰上放置30min使原生质体逐渐沉降，弃上清。5)加适量mmg悬浮，至于冰上，待转化。6)2ml离心管中加10-20μg质粒，200μl原生质体(大约4×105细胞)，220μl新配的peg溶液，混匀，室温避光放置10-20分钟诱导转化。7)诱导转化结束后缓慢加880μlw5溶液，轻轻颠倒混匀，100g水平离心3min，吸弃上清。8)加2mlw5溶液重悬，转移到六孔板中，室温(或25℃)暗处培养。若用于提取原生质体基因组dna，需培养48h。水稻原生质体制备及转化：1)选取幼苗叶鞘部分分离原生质体，用锋利刀片切成大约0.5mm宽。2)切开后立刻转移到0.6mmannitol溶液中，避光放置10min。3)过滤掉mannitol溶液，转移到酶解液中，避光抽真空30min。4)避光酶解5-6h，同时缓慢摇动(脱色摇床，速度10)。5)酶解结束后，加入等体积的w5，水平摇动10sec，释放原生质体。6)使用40μm尼龙膜过滤原生质体到50ml圆底离心管，再加w5溶液冲洗。7)250g水平离心3min沉淀原生质体，吸弃上清。8)加10mlw5重悬原生质体，250g离心3min，弃上清。9)加适量mmg溶液重悬原生质体浓度为2×106/ml。注：以上所有步骤在室温进行。10)2ml离心管中加10-20μg质粒，200μl原生质体(大约4×105细胞)，220μl新配的peg溶液，混匀，室温避光放置10-20分钟诱导转化。11)诱导转化结束后缓慢加880μlw5溶液，轻轻颠倒混匀，250g水平离心3min，吸弃上清。12)加2mlwi溶液重悬，转移到六孔板中，室温(或25℃)暗处培养，若用于提取原生质体基因组dna，需培养48h。pcr/re检测：1)提取植物基因组dna。2)合成基因特异引物，扩增含有靶位点的片段，长度为350-1000bp之间：10×easytaqbuffer5μldntp(2.5mm)4μl正向引物(10μm)2μl正向引物(10μm)2μleasytaq0.5μldna2μlddh2o至50μl3)一般反应条件是：94℃变性5min；94℃变性30s，58℃复性30s，72℃延伸30s，扩增30至35个循环；72℃保温5min；12℃保温。取5μlpcr产物电泳检测。4)限制性内切酶酶切pcr产物，一般的酶切体系如下：5)37℃，酶切2-3h。1.2％琼脂糖凝胶电泳检测。6)回收纯化pcr产物中未切开的突变条带，进行ta克隆。反应体系如下：peasy-tvector1μl回收的未切开的pcr产物4μl7)22℃连接10min，转化e.coli感受态细胞，涂lb固体平板(amp100、iptg和x-gal)，培养12-16h，挑选白色菌落鉴定阳性克隆，送测序。农杆菌介导的水稻愈伤组织转化用ph-pabe-7-esgrna或ph-pabe-7-sgrna二元载体通过电穿孔转化根癌农杆菌(agrobacteriumtumefaciens)菌株agl1。根据shanq等(shanqetal.,rapidandefficientgenemodificationinriceandbrachypodiumusingtalens.molplant2013,6:1365-1368)描述的方法对水稻(中华11)愈伤组织进行农杆菌介导的转化，并使用潮霉素选择转基因植物。用基因枪将dna构建体导入小麦未成熟的胚细胞通过基因枪轰击将pabe-7和ptau6-esgrna质粒dna同时导入未成熟的小麦胚，并根据之前的描述(zhangy,liangz,zongy,wangy,liuj,chenk,qiujl,gaoc:efficientandtransgene-freegenomeeditinginwheatthroughtransientexpressionofcrispr/cas9dnaorrna.natcommun2016,7:12617)再生植物而不用选择剂。测序不同的sgrna表达载体分别与abe以及pwcas9转化至小麦、水稻原生质体48小时-60小时后，收集原生质体，提取dna进行测序。在第一轮pcr中，靶区域使用位点特异性引物进行扩增。在二轮pcr中，将正向和反向标签添加至pcr产物末端进行文库构建。合并等量不同pcr产物。样品然后在beijinggenomicsinstitute使用illuminahigh-seq4000测序，或者在megagenomics(中国北京)使用illuminanextseq500平台对样品进行测序。实施例1.abe系统在植物原生质体中对gfp的碱基编辑发明人首先构建了适合植物细胞编辑的abe(腺嘌呤碱基编辑)系统，包括spncas9-abe(seqidno:4、seqidno:6)、spncas9-vqr-abe(seqidno:10、seqidno:18)、spncas9-vrer-abe(seqidno:11、seqidno:19)、sancas9-abe(seqidno:12、seqidno:20)、sancas9-kkh-abe(seqidno:13、seqidno:21)、spncas9-abe-1(seqidno:5、seqidno:7)、spncas9-vqr-abe-1(seqidno:14、22)、spncas9-vrer-abe-1(seqidno:15、seqidno:23)、sancas9-abe-1(seqidno:16、seqidno:24)、sancas9-kkh-abe-1(seqidno:17、seqidno:25)，各个系统均针对植物中的表达进行了密码子优化。各个碱基编辑融合蛋白的氨基酸序列和核苷酸序列见所附序列表。各构建体结构如图1所示。发明人然后利用原生质体瞬时表达体系和gfp报告系统检测abe系统在植物细胞中的工作情况。首先，构建ubi启动子驱动的失活gfp表达载体(ubi-mgfp)，其中将gfp的第70位的氨基酸密码子(cag)突变为终止密码子(tag)，使gfp失去活性。将该载体与上述abe系统共转化植物原生质体。如果abe系统将终止密码子(tag)突变为(cag)，则会使mgfp恢复为野生型，使其发出绿色荧光。实验原理如图2a所示。实验结果如图2b所示。阴性对照ubi-mgfp载体单独转化原生质体细胞无绿色荧光，阳性对照ubi-gfp单独转化原生质体细胞有绿色荧光。当ubi-mgfp载体与针对mgfp的abe系统共转化时，产生了绿色荧光。而当ubi-mgfp载体与针对不相关基因dep1的abe系统共转化时，没有产生绿色荧光。可见，abe系统可以在植物原生质体中实现a至g的碱基编辑。实施例2.abe对植物内源基因的编辑选取水稻osdep1，oscdc48，osacc以及osnrt1.1b基因为研究对象，靶序列见图3b下划线部分。在突变位点处选取酶切位点用于pcr/re检测。酶切和测序结果表明在靶位点处具有a到g的突变(图3和图4)。实施例3.abe结构对基因编辑的影响在本实施例中，构建了7种abe融合蛋白。这7种融合蛋白命名为pabe-1到pabe-7，其区别在于腺嘌呤脱氨酶的位置以及nls的数目和位置。7种融合蛋白的结构示于图5a，其序列如seqidno:33-39所示，其基于谷物而进行密码子优化的编码序列如seqidno:26-32所示。首先，通过如实施例1所述的将突变体gfp恢复为野生型gfp的实验，测试了上述pabe融合蛋白的编辑效率。结果显示，用这7种融合蛋白中的5种(pabe-1、pabe-2、pabe-3、pabe-6和pabe-7)处理的细胞显示了稳定的gfp荧光(图5b)。流式细胞仪分析显示，发荧光的细胞百分比为0.1％-32.8％(图5c)。在ncas9的c末端具有3个拷贝的nls(pabe-7)处理产生表达gfp的细胞的产率最高，显著高于pabe-2和其它pabe构建体(图5b、c)。nls仅在c端的pabe效率高于n段有nls的pabe。实施例4.pabe-2和pabe-7对植物内源基因的编辑为进一步比较pabe-2和pabe-7的编辑效率，在本实施例中，靶向16个水稻内源基因组位点进行了测试。具体靶位点和序列如表1所示。表1.sgrna的靶位点和序列。发现植物abe修饰了下划线标记的a/t碱基。各靶序列中的pam结构域以粗体字显示。通过测序(每基因座100,000-220,000读段)评估原生质体中各基因的a到g碱基编辑。如图6所示，pabe-7的碱基编辑效率更高，与pabe-2相比，在各位点的a/t到c/g转化平均升高大约1.1倍。总的来说，这些结果证明，植物abe系统能够在水稻中诱导a到g的转化，并且在ncas9的c末端存在3个nls使编辑效率最大化。实施例5.sgrna对编辑效率的影响为鉴定对于pabe-7活性最佳的sgrna形式，本实施例在大范围的内源性基因座中测试了多种sgrna修饰。发明人分别在表1中的10个水稻内源性基因组靶位点和3个小麦内源性基因组靶位点比较了三种sgrna形式(天然sgrna、esgrna和trna-sgrna)的碱基编辑活性。将靶向这些内源基因的前间区序列分别克隆到3种sgrna结构中(如图7所示)，并与pabe-7共转化。野生型cas9(wtcas9)用作对照以产生缺失和/或插入突变(indel)。每种pabe-7与sgrna表达系统的组合都在全部13个靶位点观察到了a到g的转化，在前间区序列内的位置4-8具有有效的编辑频率(图8a)。图8a还显示，在三种sgrna构建体中，esgrna在大部分测试中显示最高的碱基编辑效率，在水稻和小麦中，范围都是0.1-7.5％。13个位点的esgrna平均效率比天然sgrna高约2倍，比trna-sgrna高约3倍(图8b)。在上述研究中，只观察到了a到g的转化，而没有任何证据显示在任何水稻和小麦的基因组靶基因座有不想要的编辑(<0.02％)(图9、10)，并且插入缺失突变的频率(<0.1％)比wtcas9(3.3-31.6％)低得多(图11)。综上所述，pabe-7碱基编辑构建体与esgrna一起可以高效地诱导a到g的取代，并且在水稻和小麦中的多个基因座具有高精确度。实施例6.spacer序列对编辑的影响本实施例通过靶向osev和osod(如表1所示)测试了esgrna的spacer序列长度对碱基编辑效率的影响。结果如图12所示，常规的20-nt的spacer序列显示最高的a到g转化效率。在这两个位点，与具有常规的20-nt的spacer序列的esgrna(<4.5％)相比，spacer序列长度为14-nt至19-nt的esgrna显示基本上下降的或检测不到的a到g碱基编辑活性(<0.9％)。另外，在这两个位点，在使用wtcas9的对照中，spacer序列长度为14-nt至19-nt的esgrna的插入缺失突变频率(0.3-12.6％)比spacer序列长度为20-nt的esgrna低得多(图13)。这些结果提示，具有20-nt的spacer序列的esgrna对植物abe系统是至关重要的，对缩短长度没有耐受性。实施例7.产生具有a到g取代的水稻和小麦在本实施例中，通过农杆菌介导的转基因，用pabe-7靶向6个水稻基因组基因座(osacc-t1、osals-t1、oscdc48-t3、osdep1-t1、osdep1-t2和osnrt1.1b-t1，如表1、2所示)，并再生水稻突变体植物。载体结构如图14a所示。a到g的取代效率为15.8％-59.1％。对于osacc-t1、osdep1-t1、osdep1-t2和osnrt1.1b-t1分别鉴定到1、6、1和13个突变体纯系。重要的是，对比实验显示，用esgrna时，pabe-7的转化频率在各位点平均比用天然sgrna高1.7倍(如表2所示)。这与使用原生质体所观察到的结果一致(图8a、b)。在所有6个靶位点，有效的脱氨基窗(位置4到8)与原生质体结果一致。另外，转基因水稻植物在靶位点都不含有任何插入缺失突变或不想要的编辑(图14b-g)。表2.pabe-7在t0水稻和小麦植物中诱导的突变频率a水稻突变株系的数量和小麦突变植物的数量。b基于带有观察到的突变的t0株系(水稻)或植物(小麦)的数量与所分析的t0转基因水稻株系和经轰击的小麦的未成熟的胚的总数的比。在本实施例中，还通过基因枪转基因，使用植物abe系统靶向tadep1和tagw2基因产生碱基编辑的小麦植物。通过t7e1和sanger测序，从460个经轰击的未成熟的胚再生得到了5株a8到g8杂合的tadep1突变植物(如表2和图15a所示)，其中4株是tadep1-a的杂合突变体(tadep1-aabbdd)，1株是tadep1-b的杂合突变体(tadep1-aabbdd)。对于tagw2靶位点，鉴定到2株杂合突变体，都在tagw2-b的位置5具有a到g的取代(tagw2-aabbdd)(如表2所示)。在所有突变植物的靶区域中也都没有观察到插入缺失突变。此外，用特异于pabe-7和ptau6-esgrna的6组引物(如表3所示)进行pcr筛选确定，5个tadep1突变体中的3个和2个tagw2突变体不携带转基因载体(如图16所示)。表3.pcr引物综上所述，这些结果表明，植物abe系统在水稻和小麦中以高度特意和精确的方式，有效地诱导了特定位点突变，而没有引起其他基因组修饰。并且，本发明的植物abe系统进行基因组修饰时没有将外源dna序列(如转基因载体)整合到植物基因组。实施例8.在水稻中诱导除草剂抗性在本实施例中，分析了在靶位点osacc-t1进行修饰的水稻的除草剂抗性。该修饰靶向水稻中acc基因，经修饰的水稻acc携带突变c2186r，对应于黑草acc的突变c2088r。对160个ph-pabe-7-esgrna转化的株系进行检测，显示其中33个株系在靶区域具有至少一个t到c的取代(突变效率20.6，如表2所示)。这些突变株系中的1个含有纯合的取代(t4t7到c4c7)，而另外32个含有杂合取代，其中20个具有双碱基取代(t4t7到c4c7)，10个具有t4到c4的单碱基取代，还有2个含有在等位基因之一具有提供想要的c2186r氨基酸取代的单碱基取代(t7到c7；t0-7和t0-13)。结果如图14b、17和表2所示。此外，在所有的突变株系中，都没有在潜在的脱靶区域检测到突变(如表4所示)。表4.对于osacc-t1内源性基因组基因座的潜在的脱靶位点分析a潜在脱靶位点(14个)中的错配碱基以小写字母表示。pam继续以加粗字体表示。进一步，发明人测试了t0-13株系的除草剂抗性。在补充有0.086ppm的吡氟氯禾灵-r-甲酯的再生培养基上生长一周后，突变体植物具有正常表型，没有损伤的症状，而野生型(wt)植物显示严重萎缩且枯萎的叶(如图17所示)。上述结果表明，使用基因组编辑工具产生了acc携带c2186r取代的除草剂抗性水稻。上述结果还表明，本发明的基因组编辑系统在植物中脱靶率低，可以进行精确的碱基编辑。序列表<110>中国科学院遗传与发育生物学研究所<120>植物碱基编辑方法<130>149131<150>201711393160.7<151>2017-12-21<150>201810402244.0<151>2018-04-28<160>39<170>patentinversion3.5<210>1<211>166<212>prt<213>escherichiacoli<400>1sergluvalglupheserhisglutyrtrpmetarghisalaleuthr151015leualalysargalatrpaspgluarggluvalprovalglyalaval202530leuvalhisasnasnargvalileglygluglytrpasnargproile354045glyarghisaspprothralahisalagluilemetalaleuarggln505560glyglyleuvalmetglnasntyrargleuileaspalathrleutyr65707580valthrleugluprocysvalmetcysalaglyalametilehisser859095argileglyargvalvalpheglyalaargaspalalysthrglyala100105110alaglyserleumetaspvalleuhishisproglymetasnhisarg115120125valgluilethrgluglyileleualaaspglucysalaalaleuleu130135140seraspphepheargmetargargglngluilelysalaglnlyslys145150155160alaglnserserthrasp165<210>2<211>166<212>prt<213>artificialsequence<220><223>mu-ectada(7.10)<400>2sergluvalglupheserhisglutyrtrpmetarghisalaleuthr151015leualalysargalaargaspgluarggluvalprovalglyalaval202530leuvalleuasnasnargvalileglygluglytrpasnargalaile354045glyleuhisaspprothralahisalagluilemetalaleuarggln505560glyglyleuvalmetglnasntyrargleuileaspalathrleutyr65707580valthrphegluprocysvalmetcysalaglyalametilehisser859095argileglyargvalvalpheglyvalargasnalalysthrglyala100105110alaglyserleumetaspvalleuhistyrproglymetasnhisarg115120125valgluilethrgluglyileleualaaspglucysalaalaleuleu130135140cystyrphepheargmetproargglnvalpheasnalaglnlyslys145150155160alaglnserserthrasp165<210>3<211>1367<212>prt<213>artificialsequence<220><223>spncas9<400>3asplyslystyrserileglyleualaileglythrasnservalgly151015trpalavalilethraspglutyrlysvalproserlyslysphelys202530valleuglyasnthrasparghisserilelyslysasnleuilegly354045alaleuleupheaspserglygluthralaglualathrargleulys505560argthralaargargargtyrthrargarglysasnargilecystyr65707580leuglngluilepheserasnglumetalalysvalaspaspserphe859095phehisargleuglugluserpheleuvalglugluasplyslyshis100105110gluarghisproilepheglyasnilevalaspgluvalalatyrhis115120125glulystyrprothriletyrhisleuarglyslysleuvalaspser130135140thrasplysalaaspleuargleuiletyrleualaleualahismet145150155160ilelyspheargglyhispheleuilegluglyaspleuasnproasp165170175asnseraspvalasplysleupheileglnleuvalglnthrtyrasn180185190glnleupheglugluasnproileasnalaserglyvalaspalalys195200205alaileleuseralaargleuserlysserargargleugluasnleu210215220ilealaglnleuproglyglulyslysasngly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