药用野生稻基因组文库构建与大片段DNA转化
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摘要
野生稻是重要的遗传资源，是栽培稻遗传改良和重要基因克隆的基础。野生稻在其漫长的进化历程中，形成了极其丰富的遗传多样性，具有多种在栽培稻中没有或已消失的优良性状，如抗病、抗虫、抗逆、细胞质雄性不育、高蛋白质含量等等。药用野生稻(Oryza officinalis)是原产我国的3种特有的珍稀野生稻种质资源之一。其优良特性表现在：有很强的抗虫能力，高抗褐飞虱、白背飞虱，对叶蝉、螟虫、稻蓟马等也有很好的抗性；对白叶枯病、稻瘟病等有强的抗性。此外，药用野生稻米粒中的蛋白质含量在12％以上。我国是水稻生产大国，也是野生稻资源最为丰富的国家之一。但利用杂交、回交等常规手段转移野生稻有利基因遇到很多困难，存在很多问题，效率也非常低。因此，我们需要开拓新的途径来研究和利用野生稻优良基因。
植物遗传转化不仅是遗传改良的重要手段，而且是研究基因和基因组功能必不可少的技术环节。从不同途径克隆的基因都需要通过转化来验证及进行功能分析。但常规的克隆转化载体一般只能转化5～20kb的DNA片段，对超过50kb的片段就无能为力了。因此，用YAC、PAC和BAC等基因组文库
进行目的基因筛选，在获得大片段(大于50Kb)的侯选克隆后，通常要进行
亚克隆，然后对每个亚克隆逐一转化进行基因功能互补实验;不仅工作量大，
而且有遗漏目的基因的危险。而BmAC这种双功能载体，既可用于大片段文
库的构建，还可直接对克隆的片段进行转化，侯选克隆的插入片段(基因)
通过农杆菌的介导直接导入宿主，并通过表达分析其功能，这样就可减小或
消除亚克隆的危险性。此外，大片段DNA转化技术在转移基因簇(Gene
clusters)、多基因(Multi一genes)、数量性状座位(QTL)，代谢工程(pathway
engineering)，基因的图位克隆(M叩一based cloning)，消除基因的位点依赖性
表达(site一dependent gene expression)，提高转基因效率等方面都有重要意义。
所以说，大片段DNA转化既是植物转化的发展趋势，也是植物转化的现实
要求。
为了更好地研究和克隆药用野生稻中有利基因，我们利用新一代可转化
的细菌人工染色体即双元细菌人工染色体(BIBAC)载体构建了第一个药用
野生稻基因组文库。该文库包括55296个克隆贮存在144个384孔的微量培
养板中。随机检测的140个BmAC克隆中，插入片段大小分布于15~235Kb
之间，平均为7lKb。用来源于小麦的4个叶绿体基因和玉米的4个线粒体基
因对文库进行筛选，结果表明，大约有0.61%的克隆含叶绿体基因组DNA的
同源序列，有0.04%的克隆含有线粒体基因组DNA的同源序列。除去4.8%
的不含插入片段的克隆，0.61%的含叶绿体DNA和0.04%含线粒体DNA的
克隆，按平均插入体积71Kb及药用野生稻基因组大小为697Mb计算，该文
库相当于5.3倍药用野生稻基因组，理论上筛选到任一药用野生稻基因或
DNA序列的概率为99.5%。克隆稳定性实验表明，BIBAC克隆在细菌及农杆
菌中都能稳定存在。用与褐飞虱抗性基因QbPZ紧密连锁的两个RFLp标记
R288和C82O筛选文库，分别得到7个和8个阳性克隆。分析结果表明该文
库具有较高的质量，适合于野生稻基因的分离、克隆以及基因组相关的研究。
通过比较不同的受体材料，不同的预培养、共培养条件，不同的去除农
杆菌及选择阳性愈伤的方式等对转化效率的影响，建立了适合水稻BmAC
系统的转化体系。该体系的技术要点包括:以H1493为转化受体;以含毒性
辅助质粒PCH32的 LBA4404菌株(HP4404)为侵染菌株;前培养的培养基
pHS .6;以N6A代替AAM悬浮农杆菌;侵染菌液浓度为oD600二1 .0:共培
养温度为24oC;采用过渡(Resting)培养除去农杆菌;采用二步法进行选择
等。基于GUS、PCR检测，Southem分析的结果表明，BIBAC载体所携带的
下DNA及标记基因己整合到转化植株的基因组中。这个体系的建立为在水稻
中利用BmAC系统进行大片段DNA转化奠定基础。
在构建野生稻BIBAC基因组文库及建立水稻BIBAC系统转化体系的基
础上，从文库中挑选一个120Kb的BIBAC克隆(114G9)，采用优化的转化
体系，在水稻中实现了大片段DNA的转化。实验结果表明，通过BIBAC系
统利用农杆菌介导水稻大片段DNA转化，以H1493为受体材料，以带有毒
性辅助质粒pCH咒的农杆菌菌株LBA4404为转化菌株所获得的转化效率最
高。通过GUS试验，PCR检测，Southern分析和荧光原位杂交(FISH)定
位，证实BmAC载体上T-DNA及其所携带的120Kb的大片段已被转移到水
稻基因组中。实验结果还表明，利用BIBAC系统进行的大片段转化与农杆菌
介导的普通的双元载体转化之间的最大区别是大片段转化需要额外的毒性基
因vi州3/virE的参与;而且在转化机制(如插入拷贝数)上存在差异。
这套系统的建立将为野生稻优良基因的发掘和利用提供新的技术手段，
也可能为野生稻基因克隆、基因功能分析，多基因转化及基因组相关研究开
拓途径。
The wild germplasm is a valuable gene pool that can be used to broaden the genetic background of modern crops. Because of the massive international exchange of germplasm and repeated use of the limited number of productive parental materials in breeding programs, new varieties are usually derived from crosses among genetically related modern varieties. The genetic diversity in improved rice has narrowed, limiting the further increase in yield potential of newly developed varieties. There is thus an urgent need to explore and utilize the wild Oryza germplasm to meet various challenges affecting rice production.
O. officinalis well ex watt, a species with a diploid CC genome, occurs wildly in the South and Southeast Asia. O. officinalis has been intensively studied.
Some of these genes including resistance to brown planthopper (BPH), white backed planthooper (WBPH) and bacterial blight (BB) have been transferred from O. officinalis into several rice breeding lines by interspecific hybridization and backcrossing.
The bacterial artificial chromosome (BAC) cloning system has provided a powerful tool for physical mapping, map-based cloning and genome sequencing in genome research. While BAC vectors are designed for cloning large fragment of DNA, they are not engineered for transformation of the cloned DNA back into plant genomes. A new generation of vector (termed binary-BAC or BIBAC) has been designed that is capable of replicating in both Escherichia coli and Agrobacterium tumefaciens and is able to deliver a large insert of DNA directly into the plant genome via Agrobacterium-mediated transformation. BIBAC libraries not only can be used as large-insert DNA libraries in genome research, but also facilitate gene discovery and functional studies by direct transformation of BIBACs carrying the genes, gene clusters (e.g., genes of disease resistance) or QTL of interest, into plant. While the BIBAC is proved as a useful system for transfer of large DNA fragments into the plant genome in dicotyledon, the construction of BIBAC library and the transfer of large insert DNA have not yet been reported in monocotyledonous plants.
DNA transfer to plants has been accomplished by many methods, including Agrobacterium-mediated transformation, biolistic transformation (particle bombardment), and microinjection. Whereas plant transformation with DNA fragments up to circa 20 kb is routine, success in stable plant transformation with DNA fragments larger than 50 kb is limited. The technologies of cloning and transferring of large DNA fragments in plants are important for high-efficiency identification of new genes and study of gene functions. A reliable system for transforming large fragments of DNA into plant make it feasible to introduce a natural gene cluster or a series of previously unlinked foreign genes into a single locus. Thus, several diseases and/or pest resistance genes or genes encoding the enzymes of metabolic pathways can be simultaneously introduced in only
transformation step. Large insert transformation would make it feasible to study the expression of plant genes or gene clusters in their native genomic context and might eliminate site-dependent gene expression, which can be serious problem in plant transformation experiments.
To develop the resource for transferring and identifying valuable genes and carrying out genome-related research in O. officinalis, we constructed the first genomic library of wild rice using a new generation of vector BIBAC2. The library consists of 55,296 clones and stored in 144 384-well plates. A random sampling of 140 clones indicated an average insert size of 71 Kb at range of 15-235 Kb and 4.8% empty vectors. Four wheat chloroplast probes and four maize mitochondrial probes were hybridized separately to the library, showing that contamination with organellar DNAs is very low (0.61% and 0.04%, respectively). The BIBAC library provides 5.3 haploid genome equivalents, implying a 99.5% probability of recovering any specific sequence of interest. A stability test indicated that the
植物遗传转化不仅是遗传改良的重要手段，而且是研究基因和基因组功能必不可少的技术环节。从不同途径克隆的基因都需要通过转化来验证及进行功能分析。但常规的克隆转化载体一般只能转化5～20kb的DNA片段，对超过50kb的片段就无能为力了。因此，用YAC、PAC和BAC等基因组文库
进行目的基因筛选，在获得大片段(大于50Kb)的侯选克隆后，通常要进行
亚克隆，然后对每个亚克隆逐一转化进行基因功能互补实验;不仅工作量大，
而且有遗漏目的基因的危险。而BmAC这种双功能载体，既可用于大片段文
库的构建，还可直接对克隆的片段进行转化，侯选克隆的插入片段(基因)
通过农杆菌的介导直接导入宿主，并通过表达分析其功能，这样就可减小或
消除亚克隆的危险性。此外，大片段DNA转化技术在转移基因簇(Gene
clusters)、多基因(Multi一genes)、数量性状座位(QTL)，代谢工程(pathway
engineering)，基因的图位克隆(M叩一based cloning)，消除基因的位点依赖性
表达(site一dependent gene expression)，提高转基因效率等方面都有重要意义。
所以说，大片段DNA转化既是植物转化的发展趋势，也是植物转化的现实
要求。
为了更好地研究和克隆药用野生稻中有利基因，我们利用新一代可转化
的细菌人工染色体即双元细菌人工染色体(BIBAC)载体构建了第一个药用
野生稻基因组文库。该文库包括55296个克隆贮存在144个384孔的微量培
养板中。随机检测的140个BmAC克隆中，插入片段大小分布于15~235Kb
之间，平均为7lKb。用来源于小麦的4个叶绿体基因和玉米的4个线粒体基
因对文库进行筛选，结果表明，大约有0.61%的克隆含叶绿体基因组DNA的
同源序列，有0.04%的克隆含有线粒体基因组DNA的同源序列。除去4.8%
的不含插入片段的克隆，0.61%的含叶绿体DNA和0.04%含线粒体DNA的
克隆，按平均插入体积71Kb及药用野生稻基因组大小为697Mb计算，该文
库相当于5.3倍药用野生稻基因组，理论上筛选到任一药用野生稻基因或
DNA序列的概率为99.5%。克隆稳定性实验表明，BIBAC克隆在细菌及农杆
菌中都能稳定存在。用与褐飞虱抗性基因QbPZ紧密连锁的两个RFLp标记
R288和C82O筛选文库，分别得到7个和8个阳性克隆。分析结果表明该文
库具有较高的质量，适合于野生稻基因的分离、克隆以及基因组相关的研究。
通过比较不同的受体材料，不同的预培养、共培养条件，不同的去除农
杆菌及选择阳性愈伤的方式等对转化效率的影响，建立了适合水稻BmAC
系统的转化体系。该体系的技术要点包括:以H1493为转化受体;以含毒性
辅助质粒PCH32的 LBA4404菌株(HP4404)为侵染菌株;前培养的培养基
pHS .6;以N6A代替AAM悬浮农杆菌;侵染菌液浓度为oD600二1 .0:共培
养温度为24oC;采用过渡(Resting)培养除去农杆菌;采用二步法进行选择
等。基于GUS、PCR检测，Southem分析的结果表明，BIBAC载体所携带的
下DNA及标记基因己整合到转化植株的基因组中。这个体系的建立为在水稻
中利用BmAC系统进行大片段DNA转化奠定基础。
在构建野生稻BIBAC基因组文库及建立水稻BIBAC系统转化体系的基
础上，从文库中挑选一个120Kb的BIBAC克隆(114G9)，采用优化的转化
体系，在水稻中实现了大片段DNA的转化。实验结果表明，通过BIBAC系
统利用农杆菌介导水稻大片段DNA转化，以H1493为受体材料，以带有毒
性辅助质粒pCH咒的农杆菌菌株LBA4404为转化菌株所获得的转化效率最
高。通过GUS试验，PCR检测，Southern分析和荧光原位杂交(FISH)定
位，证实BmAC载体上T-DNA及其所携带的120Kb的大片段已被转移到水
稻基因组中。实验结果还表明，利用BIBAC系统进行的大片段转化与农杆菌
介导的普通的双元载体转化之间的最大区别是大片段转化需要额外的毒性基
因vi州3/virE的参与;而且在转化机制(如插入拷贝数)上存在差异。
这套系统的建立将为野生稻优良基因的发掘和利用提供新的技术手段，
也可能为野生稻基因克隆、基因功能分析，多基因转化及基因组相关研究开
拓途径。
The wild germplasm is a valuable gene pool that can be used to broaden the genetic background of modern crops. Because of the massive international exchange of germplasm and repeated use of the limited number of productive parental materials in breeding programs, new varieties are usually derived from crosses among genetically related modern varieties. The genetic diversity in improved rice has narrowed, limiting the further increase in yield potential of newly developed varieties. There is thus an urgent need to explore and utilize the wild Oryza germplasm to meet various challenges affecting rice production.
O. officinalis well ex watt, a species with a diploid CC genome, occurs wildly in the South and Southeast Asia. O. officinalis has been intensively studied.
Some of these genes including resistance to brown planthopper (BPH), white backed planthooper (WBPH) and bacterial blight (BB) have been transferred from O. officinalis into several rice breeding lines by interspecific hybridization and backcrossing.
The bacterial artificial chromosome (BAC) cloning system has provided a powerful tool for physical mapping, map-based cloning and genome sequencing in genome research. While BAC vectors are designed for cloning large fragment of DNA, they are not engineered for transformation of the cloned DNA back into plant genomes. A new generation of vector (termed binary-BAC or BIBAC) has been designed that is capable of replicating in both Escherichia coli and Agrobacterium tumefaciens and is able to deliver a large insert of DNA directly into the plant genome via Agrobacterium-mediated transformation. BIBAC libraries not only can be used as large-insert DNA libraries in genome research, but also facilitate gene discovery and functional studies by direct transformation of BIBACs carrying the genes, gene clusters (e.g., genes of disease resistance) or QTL of interest, into plant. While the BIBAC is proved as a useful system for transfer of large DNA fragments into the plant genome in dicotyledon, the construction of BIBAC library and the transfer of large insert DNA have not yet been reported in monocotyledonous plants.
DNA transfer to plants has been accomplished by many methods, including Agrobacterium-mediated transformation, biolistic transformation (particle bombardment), and microinjection. Whereas plant transformation with DNA fragments up to circa 20 kb is routine, success in stable plant transformation with DNA fragments larger than 50 kb is limited. The technologies of cloning and transferring of large DNA fragments in plants are important for high-efficiency identification of new genes and study of gene functions. A reliable system for transforming large fragments of DNA into plant make it feasible to introduce a natural gene cluster or a series of previously unlinked foreign genes into a single locus. Thus, several diseases and/or pest resistance genes or genes encoding the enzymes of metabolic pathways can be simultaneously introduced in only
transformation step. Large insert transformation would make it feasible to study the expression of plant genes or gene clusters in their native genomic context and might eliminate site-dependent gene expression, which can be serious problem in plant transformation experiments.
To develop the resource for transferring and identifying valuable genes and carrying out genome-related research in O. officinalis, we constructed the first genomic library of wild rice using a new generation of vector BIBAC2. The library consists of 55,296 clones and stored in 144 384-well plates. A random sampling of 140 clones indicated an average insert size of 71 Kb at range of 15-235 Kb and 4.8% empty vectors. Four wheat chloroplast probes and four maize mitochondrial probes were hybridized separately to the library, showing that contamination with organellar DNAs is very low (0.61% and 0.04%, respectively). The BIBAC library provides 5.3 haploid genome equivalents, implying a 99.5% probability of recovering any specific sequence of interest. A stability test indicated that the
引文
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