Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high‐copy Mutator lines of maize

High‐copy transposons have been effectively exploited as mutagens in a variety of organisms. However, their utility for phenotype‐driven forward genetics has been hampered by the difficulty of identifying the specific insertions responsible for phenotypes of interest. We describe a new method that can substantially increase the throughput of linking a disrupted gene to a known phenotype in high‐copy Mutator (Mu) transposon lines in maize. The approach uses the Illumina platform to obtain sequences flanking Mu elements in pooled, bar‐coded DNA samples. Insertion sites are compared among individuals of suitable genotype to identify those that are linked to the mutation of interest. DNA is prepared for sequencing by mechanical shearing, adapter ligation, and selection of DNA fragments harboring Mu flanking sequences by hybridization to a biotinylated oligonucleotide corresponding to the Mu terminal inverted repeat. This method yields dense clusters of sequence reads that tile approximately 400 bp flanking each side of each heritable insertion. The utility of the approach is demonstrated by identifying the causal insertions in four genes whose disruption blocks chloroplast biogenesis at various steps: thylakoid protein targeting (cpSecE), chloroplast gene expression (polynucleotide phosphorylase and PTAC12), and prosthetic group attachment (HCF208/CCB2). This method adds to the tools available for phenotype‐driven Mu tagging in maize, and could be adapted for use with other high‐copy transposons. A by‐product of the approach is the identification of numerous heritable insertions that are unrelated to the targeted phenotype, which can contribute to community insertion resources.     

植物抗病相关基因分离策略

近年来植物基因克隆技术已经取得了很大进展。文章对分离植物抗病相关基因的一系列策略及其研究进展进行了综述,并对这些技术的异同,各自的优缺点,以及它们在植物中的应用现状及前景作了评述。     

转座子Tn917插入位点侧翼序列的扩增

为了克隆到生防菌株的抗病基因,以一株对灰葡萄孢菌表现很高拮抗活性的蜡样芽孢杆菌B-02菌株为材料,利用转座子标签技术得到拮抗性消失的突变体,进而利用TAIL-PCR技术扩增出Tn917插入位点两侧的未知序列,利用生物信息学分析扩增序列,为进一步研究该基因片段与菌株拮抗性之间的关系奠定了基础。     

基因克隆技术的研究进展

为能快速而准确地克隆目的基因,综述了一些基因克隆常用技术,包括差异表达基因分离技术、转座子标签技术、图位克隆技术、同源序列技术、表达序列标签技术的原理、应用及应用潜力,并对其作了简要的评价.这些技术有利有弊,应根据不同的实验目的和水平来选择相应的技术.     

Molecular analysis of high-copy insertion sites in maize

High-copy transposon mutagenesis is an effective tool for creating gene disruptions in maize. In order to molecularly define transposon-induced disruptions on a genome-wide scale, we optimized TAIL-PCR to amplify genomic DNA flanking maize Robertson’s Mutator insertions. Sample sequencing from 43 Mutator stocks and the W22 inbred line identified 676 non-redundant insertions, and only a small fraction of the flanking sequences showed significant similarity to maize repetitive sequences. We further designed and tested 79 arbitrary primers to identify 12 primers that amplify all Mutator insertions within a DNA sample at 3.1-fold redundancy. Importantly, the products are of sufficient size to use as substrates or probes for hybridization-based identification of gene disruptions. Our adaptation simplifies previously published TAIL-PCR protocols and should be transferable to other high-copy insertional mutagens.     

T-DNA标签在植物基因克隆和功能分析中的应用

在植物功能基因组学的研究中,插入突变已成为迅速识别和研究标签基因的一个有效遗传工具.本文介绍了T-DNA标签的概念及应用前提,详细论述了T-DNA标签在大规模植物基因功能分析中的应用以及使用启动子和增强子诱捕技术分离时空特异性启动子和表达基因,另外还分析了利用其特殊形式激活标签进行基因克隆和功能分析的优越性,并展望了T-DNA标签的应用前景.     

植物抗病基因克隆的研究进展

本从抗病基因克隆技术,抗病基因的产物和结构,抗病基因介导的抗病信号传导以及抗病基因进化等方面入手,综述了近几年来植物抗病基因克隆的研究进展,并对转座子标签法和定位克隆法做了较为详细的阐述。     

Transposon mutagenesis of nuclear photosynthetic genes in Zea mays

The discovery of a new maize (Zea mays L.) transposon system, Mutator, and the cloning of the 1.4 kilobase transposon, Mul, have made feasible the isolation of nuclear photosynthetic genes which are recognized only by their mutant phenotype. Mutant maize plants which express a high chlorophyll fluorescent (hcf) phenotype due to a defect in the electron transport or photophosphorylation apparatus have been isolated following mutagenesis with an active Mutator stock. The affected genes and their products in these mutants are inaccessible to classical methods of analysis. However, mutagenesis with the Mutator transposon makes it possible to isolate these genes.Although the PSII-deficient mutant hcf3 has been thoroughly studied by classical photo-biological methods, the nature of the lesion which results in the observed phenotype has not been established. A Mutator-induced allele of hcf3 has been isolated. A fragment of genomic DNA has been identified which is homologous to Mul and co-segregates with the mutant phenotype. This fragment is expected to contain a portion of the hcf3 locus which will be used to clone the normal gene. Direct study of the gene can provide insight into the nature and function of its polypeptide product.This approach can be used to study any photosynthetic gene which has been interrupted by a transposon. The isolation of more than 100 different chemically-induced hcf mutants, most of which can not be fully characterized using classical means, indicates the wealth of information which can be obtained using a transposon tagging technique.     

乔丹基因:在团藻中发现的跳跃基因

Ｄａｖｉｄ Ｋｉｒｋ 和 Ｓｔｅｐｈｅｎ Ｍ ｉｌｌｅｒ 最近用一种特殊的转座子 乔丹基因作为标记克隆了两个控制团藻发育的重要基因：ｇｌｓ Ａ 基因和 ｒｅｇ Ａ 基因⒚他们的这一工作可能为遗传学研究开辟了一条新的道路⒚     

利用转座标签mTn-lacZ/leu2插入突变发酵性丝孢酵母2.1368-Leu?筛选高效产油突变株

为提高微生物油脂产率,降低其生产成本,以转座标签mTn-lacZ/leu2插入突变发酵性丝孢酵母2.1368-Leu?筛选高效产油突变株。利用LacZ显色反应、脂肪酸合成酶抑制剂Cerulenin和磷酸香草醛反应,最终在玉米秸秆糖化液中筛选出一株高效产油突变株2.1368-Leu?-7。结果表明其油脂含量为38.30％,比对照的29.33％高了8.97％,而其产油率为8.35％,比对照的6.92％提高了20.63％;在玉米秸秆糖化液中的糖利用率为77％,每100 g玉米秸秆可转化油脂8.32 g。可为未来生物柴油产业提供了廉价原料。     

插入玉米Ds转座因子的水稻转化群体及其分子分析

转座子标签法是一种利用转座因子插入高等植物基因组中造成基因突变,然后通过分离转座因子插入的旁邻顺序,进而克隆出突变基因的策略。这种策略在高等植物功能基因组学的研究中是十分有用的。为此目的,将玉米的Ds因子及bar基因连接至载体pCAMBIA1300的T-DNA区域中,构建成重组Ti质粒pDsBar1300。pDsBar1300中T-DNA区域中的潮霉素抗性基因可在转化过程中用作水稻转化植株的选择标记。插入在Ds因子中的bar基因可追踪转化后代的Ds因子。pDsBar1300通过根瘤农杆茵介导引入水稻品种中花11号的幼胚组织。从各转化愈伤组织中获得了1400株独立的Ds水稻转化植株。通过PPT抗性检测和PCR分析证明了水稻转化植株中Ds因子的整合。Southernblot分析了转化植株基因组中Ds因子的插入拷贝数,其中单拷贝插入比率约占70％。这些插有Ds因子的水稻转化植株,当引入自主型的Ac因子反式活化Ds因子后,可使Ds因子跳跃到不同位点上,就可得到更多的突变植株。     

Phenotypic analysis and molecular cloning of discolored-1 (dsc1), a maize gene required for early kernel development

Recessive mutations in the maize dsc1 locus prevent normal kernel development. Solidification of the endosperm in homozygous dsc1– mutant kernels was undetectable 12 days after pollination, at which time the tissue was apparently completely solidified in wild-type kernels. At later times endosperm did solidify in homozygous dsc1– mutant kernels, but there was a marked reduction in the volume of the tissue. Embryo growth in homozygous dsc1– kernels was delayed compared to wild-type kernels, but proceeded to an apparently normal stage 1 in which the scutellum, coleoptile, and shoot apex were clearly defined. Embryo growth then ceased and the embryonic tissues degraded. Late in kernel development no tissue distinctions were obvious in dsc1– mutant embryos. Immature mutant embryos germinated when transplanted from kernels to tissue culture medium prior to embryonic degeneration, but only coleoptile proliferation was observed. The dsc1 gene was isolated by transposon tagging. Analysis of the two different dsc1– mutations confirmed that transposon insertion into the cloned genomic locus was responsible for the observed phenotype. Dsc1 mRNA was detected specifically in kernels 5–7 days after pollination. These data indicate Dsc1 function is required for progression of embryo development beyond a specific stage, and also is required for endosperm development.     

T-DNA and transposon tagging in aspen

Abstract: We have investigated the somatic activity of the maize Activator (Ac) element in haploid and diploid aspen with the objective of developing an efficient transposon-based system for gene isolation in the model tree species Populus. It was shown that Ac is reinserted, frequently into or near coding regions in aspen, and therefore can be used for gene tagging studies. A number of phenotypic variants were also found following transformation of constructs harbouring the rolC gene. Comparative analyses of T-DNA flanking regions of variants and wild type lines indicate that T-DNA insertion has occurred in or near coding regions. However, the frequency of T-DNA insertion into genes is about one half of the frequency of Ac insertion hitting coding sequences. The results obtained give a proof-of-concept for transposon tagging in a tree system. Given the long generation cycles in tree species, gene tagging strategies are practical only to obtain dominant gain-of-function mutants that do not require selfing or test crossing. In order to obtain recessive loss-of-function mutants, we have regenerated haploid lines from immature pollen. These lines were successfully transformed with a construct containing the rolC transgene from Agrobacterium rhizogenes and Ac element from maize. The results indicate that Ac is also active in haploid aspen and hence can be used in general for gene tagging in trees.     

插入含Ds因子的T-DNA产生的水稻脆秆突变株的遗传和分子分析

在构建由农杆菌介导的玉米Ds转座因子插入的水稻转化群体中,得到了一个茎秆等组织发生脆性突变的株系。理化指标定量测定表明,脆性株系的载荷强度和纤维素含量都比正常植株低很多,可溶性糖含量略有减少。对这个突变株的分子检测结果表明Ds因子在脆性株系中为单位点插入。检测了自前3代（T1,T2,T3)植株中T-DNA(Ds)插入与脆性表型的共分离关系。初步结果表明这个突变是T－DNA（Ds)的插入造成的,这个突变基因可能与水稻纤维素合成有关。     

转座子标签法在构建G-细菌突变体库中的应用

应用转座子标签法以水稻黄单胞菌 (Xoo)为研究对象 ,构建了Xoo的突变体库 ,为革兰氏阴性细菌突变体库的建立 ,验证了一个较新的方法和思路。经分子生物学检测 ,此方法简便易得、高效稳定 ,可以定向突变 ,为研究G-细菌的各项功能提供了良好的素材 ,加快了研究进程。     

Mutational analysis of loxP sites for efficient Cre-mediated insertion into genomic DNA

The Cre/loxP system has been used in transgenic models primarily to excise DNA flanked by loxP sites for gene deletion. However, the insertion reaction is more difficult to control since the excision event is kinetically favored. Mutant loxP sites favoring integration were identified using a novel, bacterial screening system. Utilizing lambda integrase, mutant loxP sites were placed at the E. coli attB site and the excision-insertion ratios of incoming DNA plasmids carrying a second, complementary mutant loxP site were determined. Comparison of 50 mutant loxP sites combinations to the native loxP site revealed that mutations to the inner 6 bp of the Cre binding domain severely inhibited recombination, while those in the outer 8 bps were more tolerated. The most efficient loxP combinations resulted in 1421-fold and 1529-fold increases in relative integration rates over wild-type loxP sites. These loxP mutants could be exploited for site-directed "tag and insert" recombination experiments.     

玉米Ac双因子转座标签系统的构建及其转化烟草后代的遗传分析

用使质粒pKU3所携带的玉米Ac因子的5'末端和中间编码转座酶的基因片段分别发生缺失的方法构建成质粒pKU3（△B）和pKU3（△H）。质粒所携带缺失的Ac因子单独存在时都无自主转座能力,但当Ac（△H）和Ac（△B）共存于一个细胞时,由于Ac（△B）产生转座酶的互补作用促使Ac（△H）恢复转座能力,而当Ac（△B）和Ac（△H）因子被分离后即获得Ac（△H）因子的稳定插入突变株,它可克服因突变不稳定而给用转座因子标签法分离基因所造成的困难。将双因子系统导入烟草原生质体并获得再生植株,从而选得卡那霉素抗性植株,显示Ac（△H）因子已经从原质粒上的NPTⅡ前导顺序中切离。Sortharnblot和PCR分析表明：Ac（△H）和Ac（△B）因子已经整合在转化烟草的基因组并能遗传至F1和F2代植株中;有些植株后代中已检测不到Ac（△B）因子的存在,说明它们的Ac（△B）因子已与Ac（△H）因子相分离;各转化植株中Ac（△H）因子在基因组中的插入拷贝数从一个到几个不等;初步显示Ac（△H）因子多数插入或转座在基因组的结构基因中。     

转座子随机插入鉴定肠炎沙门氏菌生物膜形成相关基因

[目的]生物膜在沙门氏菌的致病性和引起沙门氏菌食物中毒等方面起着重要作用,本研究为了鉴定影响沙门氏菌生物膜形成的基因.[方法]利用结晶紫染色定量法对74株鸡源的肠炎、鸡白痢和鸡伤寒沙门氏菌进行生物膜测定,选择生物膜生长较好的肠炎沙门氏菌C050041,采用转座子随机插入法构建突变株库.[结果]84%的鸡源沙门氏菌菌株可在塑料表面形成生物膜;通过转座子插入获得1924个突变株,筛选的生物膜降低突变株经生长曲线测定、测序和序列比对及Southern blot分析鉴定出15个插入基因,它们分别为metE、ompR、rpoS、,和G、rfaJ、rfaK、rfaP、rfbH、rhlE、spiA、steB、tpx、ybdN和2个未知功能的基因.[结论]我们鉴定出了多个影响生物膜形成的新基因,这些基因的发现为进一步研究沙门氏菌生物膜形成的调控机制,研制减毒沙门氏菌疫苗奠定了基础.     

Germinal virus vector WDV (wheat dwarf virus)-mediated multiple insertions of a maize transposon,Ds (dissociation), in rice

Wheat dwarf virus (WDV) is a monocot-infecting geminivirus that replicates in infected tissue as double-stranded DIMA. We evaluated whether the WDV vector system bearingDs could be used as an effective insertional mutagen in rice. Molecular data showed thatDs was excised from WDV vectors once the WDV-carryingDs (WDV::Ds) and the genomicAc vector were co-introduced into rice calli. Mature TO and T1 transgenic plants were analyzed for the distribution and inheritance ofDs inserts. Southern analysis indicated that theDs elements excised from WDV vectors were stably inserted into genomes. The number of transposedDs ranged from zero to three copies, among independent transformants. Meanwhile, untransposedDs (WDV::Ds) were present in multiple-copies in genomes. Southern analysis of the selfed progeny of T0 plants demonstrated that most WDV::Ds were co-segregated among siblings. This indicated that these elements were integrated into the same single loci. However, a fewDs were found to segregate independently from the majority ofDs. In this report, we discuss the efficiency of WDV vectors in generating multicopyDs in rice genomes.