Ac/Ds标签系统与水稻功能基因组学

自2002年水稻基因组测序完成后,水稻功能基因组学研究正在成为水稻研究的重要内容.构建突变体库是研究功能基因组学的一条重要而有效的途径.利用外源的Ac/Ds (Activator/Dissociation)标签系统是构建插入突变体库较为理想的方法,经过多年发展完善,其在水稻中已有广泛的应用,但仍面临着一些需要解决的实际问题.文章对Ac/Ds标签系统的转座行为及其构建突变体库的问题和优点进行了综述,总结了近年来Ac/Ds标签系统在水稻中的研究进展,分析了利用Ac/Ds标签系统进行功能基因组学研究所面临的挑战.     

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。     

Reverse Genetic Approaches for Functional Genomics of Rice

T-DNA and transposable elements e.g., Ds and Tos17, are used to generate a large number of insertional mutant lines in rice. Some carry the GUS or GFP reporter for gene trap or enhancer trap. These reporter systems are valuable for identifying tissue- or organ-preferential genes. Activation tagging lines have also been generated for screening mutants and isolating mutagenized genes. To utilize these resources more efficiently, tagged lines have been produced for reverse genetic approaches. DNA pools of the T-DNA tagged lines and Tos17 lines have been prepared for PCR screening of insertional mutants in a given gene. Tag end sequences (TES) of the inserts have also been produced. TES databases are beneficial for analyzing the function of a large number of rice genes.     

植物功能基因组研究方法及进展

随着植物功能基因组研究的深入,T-DNA标签、转座子标签、反义RNA技术、基因敲除、基因陷阱和TILLING技术等多种研究方法获得了建立,并随着植物功能基因组学的不断发展而进一步完善.综述了各类研究方法的原理,并对这些方法的优缺点进行了比较与分析.     

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.     

Ds因子在烟草染色体插入位点旁邻顺序的克隆

用ＮｅｓｔｅｄＰＣＲ 方法从含Ｄｓ 因子的转基因烟草ＤＮＡ 中克隆了Ｄｓ 因子在烟草染色体插入位点的９ 个旁邻ＤＮＡ 片段,以这些片段作探针,和野生型烟草的ＤＮＡ 进行Ｓｏｕｔｈｅｒｎ 杂交,以检测这些片段在烟草基因组中的拷贝数,结果表明它们都属于烟草染色体上的低拷贝ＤＮＡ。另外,对这些ＤＮＡ 片段进行核苷酸序列测定,并将它们的顺序与Ｇｅｎｂａｎｋ 数据库中已有的核苷酸序列相比较,其中长度为１２８ 核苷酸的片段１ 和荷兰芹的４ＣＬ２ 基因的一个区段有５７ ．８ ％ 同源性,而另一长度为１６９ 核苷酸的片段３ 和百合中的反转座子的一个区段有６０ ．９ ％ 的同源性。这都表明Ｄｓ 因子在异源植物烟草中插入染色体单拷贝基因的机率很高,这对转座子标签法克隆基因是非常有利的。     

Large-scale T-DNA mutagenesis in Arabidopsis for functional genomic analysis

In planta Agrobacterium-mediated transformation combined with a soil-based herbicide selection for transgenic plants was used to recover large numbers of transgenic Arabidopsis plants for functional genomic studies. A tissue-culture-free system for generating transgenic plants was achieved by infiltrating Arabidopsis plants with Agrobacterium tumefaciens harboring a binary T-DNA vector containing the phosphinothricin acetyltransferase gene from Streptomyces hygroscopicus, and by selecting transgenic Arabidopsis growing in soil by foliar application of the herbicide Finale (phosphinothricin). Analysis of herbicide-resistant plants indicated that all were transgenic and that the T-DNA transformation process occurred late during flower development, resulting in a preponderance of independently derived T-DNA insertions. T-DNA insertions were usually integrated in a concatenated, rearranged form, and using linkage analysis, we estimated that T1 plants carried between one and five T-DNA loci. Using pooling strategies, both DNA and seed pools were generated from about 38,000 Arabidopsis plants representing over 115,000 independent T-DNA insertions. We show the utility of these transgenic lines for identifying insertion mutations using gene sequence and PCR-based screening. Electronic Publication     

Multi-functional T-DNA/Ds tomato lines designed for gene cloning and molecular and physical dissection of the tomato genome

In order to make the tomato genome more accessible for molecular analysis and gene cloning, we have produced 405 individual tomato (Lycopersicon esculentum) lines containing a characterized copy of pJasm13, a multifunctional T-DNA/modifiedDs transposon element construct. Both the T-DNA and the Ds element in pJasm13 harbor a set of selectable marker genes to monitor excision and reintegration of Ds and additionally, target sequences for rare cutting restriction enzymes (I-PpoI, SfiI, NotI) and for site-specific recombinases (Cre, FLP, R). Blast analysis of flanking genomic sequences of 174 T-DNA inserts revealed homology to transcribed genes in 69 (40%), of which about half are known or putatively identified as genes and ESTs. The map position of 140 individual inserts was determined on the molecular genetic map of tomato. These inserts are distributed over the 12 chromosomes of tomato, allowing targeted and non-targeted transposon tagging, marking of closely linked genes of interest and induction of chromosomal rearrangements including translocations or creation of saturation-deletions or inversions within defined regions linked to the T-DNA insertion site. The different features of pJasm13 were successfully tested in tomato and Arabidopsis thaliana, thus providing a new tool for molecular/genetic dissection studies, including molecular and physical mapping, mutation analysis and cloning strategies in tomato and potentially, in other plants as well.Equal contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this workEqual contributors to this work     

植物转座子及其在番茄功能基因组的应用

转座子作为插入突变原或分子标签被广泛应用于基因的分离和克隆,已成为发现新基因和基因功能分析的有效工具。该文综述了植物转座子及其在基因分离中的研究进展,并讨论其在番茄功能基因遗传资源、功能基因组分离等研究中的应用。     

Selection of independent Ds transposon insertions in somatic tissue of potato by protoplast regeneration

Potato is an autotetraploid crop plant that is not very amenable to the deployment of transposon tagging for gene cloning and gene identification. After diploidisation it is possible to get potato genotypes that grow well, but they are self-incompatible. This prevents the production of selfed progeny that are normally used in gene tagging approaches to select for parental lines with the target gene to be tagged in a homozygous stage. We describe here an alternative selection method for directed transposon tagging for a gene of interest in a heterozygous background. Diploid potato plants with a Ds transposon linked to the desired gene of interest (the Phytophthora infestans R1 resistance locus) in a heterozygous stage were used for the development of this directed transposon tagging strategy. After crossing to a diploid Ac transposon-containing genotype, 22 ’interesting’ seedlings (R1Ds/r–; Ac/–) were selected that showed active Ds transposition as displayed by DNA blot hybridisation, empty donor site PCR and sequencing. Protoplast isolation and the use of the hygromycin gene as a cell-specific selection marker of Ds excision enabled the direct selection of Ds excision sectors in these highly chimaeric seedlings. This somatic selection of Ds transpositions and the regeneration through protoplasts resulted in the development of a large population of almost 2000 hygromycin-resistant plants. Southern blot analysis confirmed the insertion of Ds at independent positions in the genome. Every selected plant displayed independent Ds excisions and re-insertions due to the expression of the Ac transposase throughout development. This population, which is developed from seedlings with the desired R1 gene in a heterozygous stage, is directly useful for searching for transposon-tagged R1 mutants. In general, this approach for selecting for somatic transpositions is particularly suitable for the molecular isolation of genes in a heterozygous crop like potato. Received: 29 November 1999 / Accepted: 30 December 1999     

Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome

Induction of knockout mutations by T-DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T-DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T-DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T-DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T-DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T-DNA insertions in 3'- and 5'-regulatory regions of genes, corresponding to 300 bp intervals 3' downstream of stop and 5' upstream of ATG codons, was 1.7-2.3-fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5'-regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T-DNA tags induced knockout mutations in Arabidopsis.     

Mapping Ds insertions in barley using a sequence-based approach

A transposon tagging system, based upon maize Ac/Ds elements, was developed in barley (Hordeum vulgare subsp. vulgare). The long-term objective of this project is to identify a set of lines with Ds insertions dispersed throughout the genome as a comprehensive tool for gene discovery and reverse genetics. AcTPase and Ds-bar elements were introduced into immature embryos of Golden Promise by biolistic transformation. Subsequent transposition and segregation of Ds away from AcTPase and the original site of integration resulted in new lines, each containing a stabilized Ds element in a new location. The sequence of the genomic DNA flanking the Ds elements was obtained by inverse PCR and TAIL-PCR. Using a sequence-based mapping strategy, we determined the genome locations of the Ds insertions in 19 independent lines using primarily restriction digest-based assays of PCR-amplified single nucleotide polymorphisms and PCR-based assays of insertions or deletions.The proncipal strategy was to identify and map sequence polymorphisms in the regions corresponding to the flanking DNA using the Oregon Wolfe Barley mapping population. The mapping results obtained by the sequence-based approach were confirmed by RFLP analyses in four of the lines. In addition, cloned DNA sequences corresponding to the flanking DNA were used to assign map locations to Morex-derived genomic BAC library inserts, thus integrating genetic and physical maps of barley. BLAST search results indicate that the majority of the transposed Ds elements are found within predicted or known coding sequences. Transposon tagging in barley using Ac/Ds thus promises to provide a useful tool for studies on the functional genomics of the Triticeae.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by M.-A. GrandbastienThe first three authors contributed equally to this work     

基因组信息的整合与植物功能基因组学研究的策略

近年来,随着许多植物基因组测序和可利用序列的增加,相继建立了一些基于靶基因诱变的“反向”遗传学研究策略,如T—DNA诱变、基因敲除、基因沉默和超表达分析等。同时,DNA微阵列和基因芯片技术的发展使得快速、定量检测植物发育不同时期和不同组织器官的基因转录时空变化成为现实。作图技术的改进和来自不同物种基因组信息的整合也正在加速图谱克隆程序的简化和发展。因此,随着生物基因组测序工作日益增多,整合不同类群植物基因组的信息和资源,在植物功能基因组学研究中的重要性日趋显著。     

基因打靶技术在植物基因功能研究中的应用

水稻、拟南芥等模式植物基因组测序计划的完成,验证预测基因的功能成为植物功能基因组学的重要内容,基因打靶(gene targeting)技术在哺乳动物中的成功应用为该技术在植物上展现了广阔的应用前景。现对植物基因打靶技术的影响因素、基因打靶在植物中的应用现状作一介绍。     

嗜热四膜虫——具有发展潜力的功能基因组学研究模型

在真核生物的分子生物学和遗传学研究方面,纤毛类原生动物嗜热四膜虫(Tetrahymenathermophila)已经被证明是一种有价值的生物学模型。通过对它的研究,人们发现并且掌握了核酶的分子机制、RNA的自我拼接、端粒的结构和功能、DNA序列重组等机理。这种原生动物的基因组功能分别由两个细胞核执行,即二倍体的小核与生殖过程有关,而多倍体的大核决定细胞的基因转录,并为转化基因的表达提供了强有力的手段。     

肠道病毒71型的功能基因组学研究进展

肠道病毒71型（enterovirus type 71,EV71）感染通常引起婴幼儿手足口病（hand,foot and mouth disease,HFMD）,但少数可引起无菌性脑膜炎（asepic meningitis）、脑炎（encephalitis）和类脊髓灰质炎的麻痹性疾病（poliomyelitis-like paralysis）等严重的神经系统疾病。功能基因组学研究对于探讨EV71的感染及复制过程、药物及疫苗的研制具有重大意义。该文就EV71的基因组结构及其功能的研究进展作简要的概述。     

Progress in TILLING as a tool for functional genomics and improvement of crops

Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes(TILLING), which combines traditional chemical mutagenesis with high‐throughput genome‐wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or evenallohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small‐scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2(or M3) plants.     

High-efficiency transformation of the diploid strawberry (Fragaria vesca) for functional genomics

Fragaria vesca L., a diploid (2n=2x=14) relative of the commercial octoploid strawberry, is an attractive model for functional genomics research in Rosaceae. Its small genome size, short reproductive cycle, and facile vegetative and seed propagation make F. vesca a promising candidate for forward and reverse genetics experiments. However, the lack of a high-efficiency transformation protocol required for systematic production of thousands of T-DNA insertional mutant lines and high-throughput gene validation is a major bottleneck. We describe a new transformation procedure that uses leaf explants from newly unfolded trifoliate leaves obtained from stock plants 6–7 weeks after seed germination, co-cultivation with Agrobacterium strain GV3101, and stringent selection on MS medium containing 4 mg l⁻¹ hygromycin. Using this protocol we achieved 100% transformation efficiency for 6 of 14 F. vesca accessions tested. Accession PI 551572 was determined to be the best candidate for a model in F. vesca functional genomics research, as it showed the greatest propensity for callus formation, transformation, shoot regeneration, ex vitro establishment, and plant growth, requiring only 14–15 weeks to complete its life cycle in different seasons in the greenhouse.     

Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus

Nitrogen-fixing root nodules develop on legumes as a result of an interaction between host plants and soil bacteria collectively referred to as rhizobia. The organogenic process resulting in nodule development is triggered by the bacterial microsymbiont, but genetically controlled by the host plant genome. Using T-DNA insertion as a tool to identify novel plant genes that regulate nodule ontogeny, we have identified two putatively tagged symbiotic loci, Ljsym8 and Ljsym13, in the diploid legume Lotus japonicus. The sym8 mutants are arrested during infection by the bacteria early in the developmental process. The sym13 mutants are arrested in the final stages of infection, and ineffective nodules are formed. These two plant mutant lines were identified in progeny from 1112 primary transformants obtained after Agrobacterium tumefaciens T-DNA-mediated transformation of L. japonicus and subsequent screening for defects in the symbiosis with Mesorhizobium loti. Additional nontagged mutants arrested at different developmental stages were also identified and genetic complementation tests assigned all the mutations to 16 monogenic symbiotic loci segregating recessive mutant alleles. In the screen reported here independent symbiotic loci thus appeared with a frequency of ∼1.5%, suggesting that a relatively large set of genes is required for the symbiotic interaction. Received: 12 May 1998 / Accepted: 24 June 1998