转Xa21基因水稻中T-DNA整合的遗传定位

利用转抗白叶枯病基因Xa21的水稻材料,通过TAIL－PCR方法扩增T－DNA整合的侧翼序列。从中筛选属于水稻基因组DNA的T－DNA整合的侧翼序列作为探针,将外源基因整合位点定位到窄叶青／京系17DH群体构建的水稻分子连锁图谱上。共获得属于水稻基因组DNA的T－DNA侧翼序列22个,其中的19个序列在定位群体的两个亲本之间显示RFLP多态性,分别定位在水稻基因组的第3,4,5,7,9,10,11和12染色体上。带有转基因Xa21的T－DNA整合的定位为研究外源基因在不同染色体位点的位置效应和稳定遗传打下基础。     

转基因抗虫棉Bt基因插入区碱基组成分析

利用TAIL－PCR的方法克隆不同来源的转基因抗虫棉中外源基因插入区的侧翼序列并对其进行序列和结构分析,结果表明,同一个较基因的单构自交得到的不同株系中外源基因插入区的两侧DNA序列完全相同,不同的转基因抗虫棉虫的外源基因插入位置各不相同,不同来源的转基因品种外源基因插入的上游侧翼片段含有一段残留质粒片段,外源基因插入的下游侧翼片段为富含AT碱基结构,其中泗棉3号转基因抗虫品系中下游侧翼片段的AT碱基高达92％,Southern杂交结果显示这些侧翼序列为高AT含量的多拷贝序列,序列中没有发现拓扑异构酶的结合位点。     

水稻Ac×Ds后代基因组DNA中Ds侧翼序列的扩增及其Ds插入分析

采用TAIL-PCR技术从经鉴定含Ac/Ds双元件的材料中扩增Ds侧翼序列并测序, 对水稻Ac×Ds后代基因组DNA进行Ac和Ds插入的PCR分析。利用NCBI的BLAST软件, 以Ds侧翼序列为待查询序列进行GenBank在线搜索比对, 获得Ds插入相关基因的染色体定位和功能注释等信息。对扩增的93个有效Ds侧翼序列进行分析, 结果显示, 有21个水稻杂交后代中Ds插入于基因编码区, 其余72个插入在基因间序列, 其中12个插入在特定基因的上游3 kb以内的间隔区。本研究强调了提高Ds侧翼序列扩增和Ac/Ds植株筛选效率的技术关键。     

无载体主干序列的bar和cecropin B 基因表达框共转化水稻

基因枪等直接转化法可将去除质粒载体主干序列的外源基因表达框导入植物基因组,消除质粒主干序列对植物基因组的影响,同时由于转基因分子较小,比较容易实现多个基因的共转化,在植物基因工程育种上有重要的应用价值,研究了基因枪介导外源基因表达框（包括启动子、基因开放阅读框和终止子）转化水稻的影响因素和转基因的整合模式,结果表明：（1）基因枪介导外源基因表达框转化水稻的频率约在0.1%～0.5%之间,非选择标准基因与选择标记基因的共转化频率约为50%～60%,增加基因表达框DNA浓度可提高转化率。相同基因构建物对不同品质水稻的转化率不同,基因构建物的侧边序列对基因枪转化的品种差异可能具有重要影响。（2）非选择标记基因cecropin B表达框在水稻基因组内整合模式简单,仅有1～3个拷贝;筛选标记基因bar表达框却比完整质粒转化后的整合模式复杂得多,插入拷贝数在4～14个之间,线形基因表达框的游离DNA末端和CaMV 35S启动中子重组热点介导的转基因重组可能是导致bar基因表达框复杂整合的重要原因。     

无选择标记和载体骨干序列的Xa21转基因水稻的获得

利用双右边界T-DNA载体通过根癌农杆菌介导法将水稻白叶枯病广谱抗性基因Xa21导入杂交稻重要恢复系C418中。T0代共获得27个独立转基因株系,通过田间抗性鉴定与PCR分析,有17个株系的Xa21基因分子鉴定为阳性,且对白叶枯病原菌P6生理小种具有抗性。通过对17个株系的后代植株进行田间抗性鉴定,分子标记辅助选择及Southern杂交分析,结果显示4个株系的T1代植株中能分离出无潮霉素标记基因的Xa21转基因植株。无选择标记Xa21转基因株系的获得率为15%。PCR检测还表明,这些无选择标记的Xa21转基因植株不带有载体骨架序列。通过对转基因后代进一步的抗性鉴定与PCR辅助选择,获得了无选择标记和载体骨架序列的转基因Xa21纯合的抗白叶枯病水稻。     

山梨糖脱氢酶基因在大肠杆菌染色体上整合及表达

以质粒pKF3为模板,扩增出两翼与ptsG基因上下游序列同源,中间为氯霉素抗性基因的DNA片段,连至pMD18T载体,构建得到pMD18PC。以质粒pQE60SDH为模板,扩增山梨糖脱氢酶基因sdh,与pMD18PC连接,得到pMD18PCSDH。将其用PvuⅡ酶切,回收含ptsG1catsdhptsG2的目的片段,电转化至JM109/pKD46,在Red重组酶的作用下,外源DNA片段与染色体上对应区域发生同源重组,将基因ptsG敲除,替换为catsdh基因,获得整合sdh基因的JM109s。经检测JM109s具有山梨糖脱氢酶活性。以 ptsG基因上下游序列为引物,JM109s基因组DNA为模板进行PCR,扩增产物测序结果表明sdh基因染色体整合成功。     

牛β-酪蛋白5′端上游调控序列的克隆和序列分析

该文用PCR扩增了牛β－酪蛋白基因5′－端上游调控序列,并对其进行了克隆和序列分析。采集成年母牛肝,提取DNA。在牛β－酪蛋白基因外显子1和上游调控区内设计引物,扩增其上游调控序列。两条引物长均为19个核苷酸,引物间跨度为635bp。以牛肝DNA为模板,进行PCR扩增,扩增产物在2％琼脂糖凝胶上电泳,可见特异的目的条带。从凝胶中回收目的片段,克隆到pGEM－T载体中。重组质粒提取DNA,进行序列分析。测序结果与文献发表的类似序列相比,仅有4个碱基不同,同源性达99．4％。表明获得了牛β－酪蛋白基因5′－端上游调控序列的克隆。     

人地中海贫血β654基因作为外源基因用于转基因的制备方法

目的探讨人地中海贫血β654基因为外源基因用于转基因小鼠制作时,外源基因的制备方法,为进一步制作转基因小鼠打下基础。方法采用反向点杂交法确诊人地中海贫血β654纯合子DNA,以PCR法扩增获得人地中海贫血β654基因,分离纯化后,通过连接酶反应将其克隆入含βLCR调控序列的基础载体pBGT51质粒中,经PCR扩增、酶切、反向点杂交及DNA测序鉴定重组质粒,用EcoRⅤ酶切获得转基因所用的外源基因。结果将人地中海贫血β654基因作为外源基因克隆入基础载体pBGT51质粒中构建了重组质粒βBGT51,用EcoRV酶切获得含人β654基因及βLCR调控序列的6.5kb的DNA片段,制备了可用于显微注射转基因的外源基因。结论采用该方法构建的含人地中海贫血β654基因的重组质粒,可获得用于显微注射转基因的外源基因。     

云南野生稻中Xa21基因外显子Ⅱ的分离及序列分析

Xa21是已经分离克隆的一个具有广谱抗性的水稻白叶枯病抗性基因,根据已克隆的白叶枯病抗性基因Xa21外显子Ⅱ序列设计特异性引物对云南3种野生稻及其他稻种进行PCR扩增.结果表明,只有普通野生稻(景洪普通野生稻和元江普通野生稻)及长雄野生稻中扩增到了长400bp的目的片段,而疣粒野生稻和药用野生稻及栽培稻中均没有扩增到目的片段.通过序列比较发现所克隆的序列同长雄野生稻的氨基酸序列变化是随机的.     

云南野生稻中Xa21基因外显子II的分离及序列分析

Xa21是已经分离克隆的一个具有广谱抗性的水稻白叶枯病抗性基因,根据已克隆的白叶枯病抗性基因Xa21外显子II序列设计特异性引物对云南三种野生稻及其它稻种进行PCR扩增。结果表明只有普通野生稻（景洪普通野生稻和元江普通野生稻）及长雄野生稻中扩增到了长400 bp的目的片段,而疣粒野生稻和药用野生稻及栽培稻中均没有扩增到目的片段。通过序列比较发现所克隆的序列同长雄野生稻的氨基酸序列变化是随机的。     

Analysis of T-DNA-<Emphasis Type="Italic">Xa21</Emphasis> loci and bacterial blight resistance effects of the transgene <Emphasis Type="Italic">Xa21</Emphasis> in transgenic rice

The genetic loci and phenotypic effects of the transgene Xa21, a bacterial blight (BB) resistance gene cloned from rice, were investigated in transgenic rice produced through an Agrobacterium-mediated transformation system. The flanking sequences of integrated T-DNAs were isolated from Xa21 transgenic rice lines using thermal asymmetric interlaced PCR. Based on the analysis of 24 T-DNA- Xa21 flanking sequences, T-DNA loci in rice could be classified into three types: the typical T-DNA integration with the definite left and right borders, the T-DNA integration linked with the adjacent vector backbone sequences and the T-DNA integration involved in a complicated recombination in the flanking sequences. The T-DNA integration in rice was similar to that in dicotyledonous genomes but was significantly different from the integration produced through direct DNA transformation approaches. All three types of integrated transgene Xa21 could be stably inherited and expressed the BB resistance through derived generations in their respective transgenic lines. The flanking sequences of the typical T-DNA integration consisted of actual rice genomic DNA and could be used as probes to locate the transgene on the rice genetic map. A total of 15 different rice T-DNA flanking sequences were identified. They displayed restriction fragment length polymorphisms (RFLPs) between two rice varieties, ZYQ8 and JX17, and were mapped on rice chromosomes 1, 3, 4, 5, 7, 9, 10, 11 and 12, respectively, by using a double haploid population derived from a cross between ZYQ8 and JX17. The blast search and homology comparison of the rice T-DNA flanking sequences with the rice chromosome-anchored sequence database confirmed the RFLP mapping results. On the basis of genetic mapping of the T-DNA- Xa21 loci, the BB resistance effects of the transgene Xa21 at different chromosome locations were investigated using homozygous transgenic lines with only one copy of the transgene. Among the transgenic lines, no obvious position effects of the transgene Xa21 were observed. In addition, the BB resistance levels of the Xa21 transgenic plants with different transgene copy numbers and on different genetic backgrounds were also investigated. It was observed that genetic background (or genome) effects were more obvious than dosage effects and position effects on the BB resistance level of the transgenic plants.     

Generation and flanking sequence analysis of a rice T-DNA tagged population

Insertional mutagenesis provides a rapid way to clone a mutated gene. Transfer DNA (T-DNA) of Agrobacterium tumefaciens has been proven to be a successful tool for gene discovery in Arabidopsis and rice (Oryza sativa L. ssp. japonica). Here, we report the generation of 5,200 independent T-DNA tagged rice lines. The T-DNA insertion pattern in the rice genome was investigated, and an initial database was constructed based on T-DNA flanking sequences amplified from randomly selected T-DNA tagged rice lines using Thermal Asymmetric Interlaced PCR (TAIL-PCR). Of 361 T-DNA flanking sequences, 92 showed long T-DNA integration (T-DNA together with non-T-DNA). Another 55 sequences showed complex integration of T-DNA into the rice genome. Besides direct integration, filler sequences and microhomology (one to several nucleotides of homology) were observed between the T-DNA right border and other portions of the vector pCAMBIA1301 in transgenic rice. Preferential insertion of T-DNA into protein-coding regions of the rice genome was detected. Insertion sites mapped onto rice chromosomes were scattered in the genome. Some phenotypic mutants were observed in the T₁ generation of the T-DNA tagged plants. Our mutant population will be useful for studying T-DNA integration patterns and for analyzing gene function in rice.Electronic Supplementary Material Supplementary material is available in the online version of this article at .Communicated by D. Mackill     

利用Inverse PCR快速筛选单个T—DNA拷贝转基因水稻植株的方法

In order to obtain single T-DNA copy transgenic rice, we have established a quick method to estimate the T-DNA copy number in transgenic rice using inverse PCR (IPCR). IPCR was used to amplify junction fragments, i.e. plant genomic DNA sequences flanking the known T-DNA sequences, which will help to estimate the T-DNA copy number in transgenic rice. We have analyzed 20 transgenic plants of 15 transgenic lines. Most plants (12) contain one integrated T-DNA copy per genome, 3 plants contain two and 1 plant contains 3 copies. In 4 transgenic plants no T-DNA copies could be detected using this method. The IPCR results were further tested by Southern analysis and sequence analysis.     

High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences

Isolation of unknown DNA sequences flanked by known sequences is an important task in molecular biology research. Thermal asymmetric interlaced PCR (TAIL-PCR) is an effective method for this purpose. However the success rate of the original TAIL-PCR needs to be increased, and it is more desirable to obtain target products with larger sizes. Here we present a substantially improved TAIL-PCR procedure with special primer design and optimized thermal conditions. This high-efficiency TAIL-PCR (hiTAIL-PCR) combines the advantages of the TAIL-cycling and suppression-PCR, thus it can block the amplification of nontarget products and suppress small target ones, but allow efficient amplification of large target sequences. Using this method, we isolated genomic flanking sequences of T-DNA insertions from transgenic rice lines. In our tests, the success rates of the reactions were higher than 90%, and in most cases the obtained major products had sizes of 1-3 kb.     

A quick method to estimate the T-DNA copy number in transgenic plants at an early stage after transformation,using inverse PCR

Agrobacterium-mediated transformation of plants is known to result in transgenic plants with a variable number of integrated T-DNA copies [1, 2, 3, 7]. Our aim was to obtain transgenic tobacco plants containing one integrated T-DNA copy per genome. Therefore, a quick method was developed to estimate the T-DNA copy number of young transgenic plantlets within 10 weeks after transformation. Inverse polymerase chain reaction (IPCR) was used to amplify junction fragments, i.e. plant genomic DNA sequences flanking the known T-DNA sequences [5].     

T-DNA Integration Category and Mechanism in Rice Genome

T-DNA integration is a key step in the process of plant transformation, which is proven to be important for analyzing T-DNA integration mechanism. The structures of T-DNA right borders inserted into the rice (Oryza sativa L.) genome and their flanking sequences were analyzed. It was found that the integrated ends of the T-DNA right border occurred mainly on five nucleotides "TGACA" in inverse repeat (IR)sequence of 25 bp, especially on the third base "A". However, the integrated ends would sometimes lie inward of the IR sequence, which caused the IR sequence to be lost completely. Sometimes the right integrated ends appeared on the vector sequences rightward of the T-DNA right border, which made the TDNA, carrying vector sequences, integrated into the rice genome. These results seemingly suggest that the IR sequence of the right border plays an important role in the process of T-DNA integration into the rice genome, but is not an essential element. The appearance of vector sequences neighboring the T-DNA right border suggested that before being transferred into the plant cell from Agrobacterium, the entire T-DNA possibly began from the left border in synthesis and then read through at the right border. Several nucleotides in the T-DNA right border homologous with plant DNA and filler DNAs were frequently discovered in the integrated position ofT-DNA. Some small regions in the right border could match with the plant sequence, or form better matches, accompanied by the occurrence of filler DNA, through mutual twisting, and then the TDNA was integrated into plant chromosome through a partially homologous recombination mechanism. The appearance of filler DNA would facilitate T-DNA integration. The fragments flanking the T-DNA right border in transformed rice plants could derive from different parts of the inner T-DNA region; that is, disruption and recombination could occur at arbitrary positions in the entire T-DNA, in which the homologous area was comparatively easier to be disrupted. The structure of flanking sequences of T-DNA integrated in the rice chromosome presented various complexities. These complexities were probably a result of different patterns of recombination in the integrating process. Some types of possible integrating mechanism are detailed.     

Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction

Gene targeting refers to the alteration of a specific DNA sequence in an endogenous gene at its original locus in the genome by homologous recombination. Through a gene-targeting procedure with positive–negative selection, we previously reported the generation of fertile transgenic rice plants with a positive marker inserted into the Adh2 gene by using an Agrobacterium-mediated transformation vector containing the positive marker flanked by two 6-kb homologous segments for recombination. We describe here that base changes within the homologous segments in the vector could be efficiently transferred into the corresponding genomic sequences of rice recombinants. Interestingly, a few sequences from the host genome were flanked by the changed sequences derived from the vector in most of the recombinants. Because a single-stranded T-DNA molecule in Agrobacterium-mediated transformation is imported into the plant nucleus and becomes double-stranded, both single-stranded and double-stranded T-DNA intermediates can serve in gene-targeting processes. Several alternative models, including the occurrence of the mismatch correction of heteroduplex molecules formed between the genomic DNA and either a single-stranded or double-stranded T-DNA intermediate, are compared to explain the observation, and implications for the modification of endogenous genes for functional genomic analysis by gene targeting are discussed.     

水稻转基因系CX8621中Xa21的整合和表达

农杆菌介导的转基因技术在植物中已被广泛应用,而目的基因能否发挥功能受到多种因素的影响。前期,通过农杆菌介导的转化,实验室创制了无选择标记、无载体骨架残留的水稻转Xa21基因系CX8621。截止目前,CX8621已稳定遗传16代,依然保持着对水稻白叶枯病的优良抗性。在此基础上,本研究对外源基因Xa21在CX8621中的整合和表达情况进行了分析。首先,通过在转化载体p BXa21的左右边界与Xa21基因序列设计嵌套引物,确定Xa21被完整地整合到CX8621中。随后,利用改良的Tail-PCR方法体外克隆了整合位点的边界序列,明确了Xa21被整合在CX8621的2号染色体上。然后,通过RT-PCR分析了Xa21在CX8621中不同时期和不同组织的表达情况,结果表明Xa21在CX8621中能稳定表达,其表达量的变化与之前报道的抗病性反应吻合。此外,还制备了天然XA21蛋白的抗体,对CX8621不同时期、不同组织中XA21蛋白的表达量进行了检测,结果发现在种子中检测不到XA21蛋白。由此,通过对外源基因Xa21的整合和表达分析,为CX8621的转基因生物安全评价提供了部分科学依据。