A fast and efficient method for isolation of the BAC end

As a new developmental vector system, the bacterial artificial chromosome (BAC) has been used widely in constructing genomic libraries and in generating transgenic animals. Isolation of the BAC insert end is useful to analyze the BAC clone. Here, we describe a fast and efficient method to obtain the BAC end by ligating the BAC fragments digested with Not I and another selected restriction enzyme into universal cloning vector, followed by determining the correct clones with HindIII digestion. Further DNA sequencing analysis verified the results mentioned above.     

Genome Analysis of Lotus japonicus

Lotus japonicus , a model legume plant, was reviewed and compared with Medicago truncatula and soybean. Several mutant libraries are being analyzed, focusing on the nodulation mechanism. The first plant nodulation gene nin was cloned by Ac-transposon tagging. Soybean remains as the most studied legume, especially in relation to the disease resistance genes. However, Lotus japonicus offers several advantages for molecular genetics, and the remained lackings were recently filled up, namely 1) an appropriate crossing partner for Gifu, accession Miyakojima, was proposed for its 4% polymorphism and smooth recombining ability; 2) a genome library with long inserts, average of 140 kb, and 8.2 genome equivalents of library size, has been established; and 3) the rather low polymorphic rate between Gifu and Miyakojima can be overcome with the HEGS (High Efficiency Genome Scanning). With this infrastructure, positional cloning of the causative genes of several mutant libraries will be accomplished in a short term. Genome sizes of L. japonicus acc. Gifu and Miyakojima were determined with high accuracy, to be 494±0 MB and 512±1 MB, respectively. The feasibility of constructing a physical map of the entire genome, for functional genomics, was discussed. Received 5 September 2000/ Accepted in revised form 11 October 2000     

图位克隆技术在农作物基因分离中的应用与评价

图位克隆(Map-based cloning)作为分离基因的有效方法, 已在小基因组作物的基因分离中得到了广泛应用和发展, 而在具有大量重复DNA序列的大基因组作物中的应用仍存在挑战。基于图位克隆在基因分离中的重要性, 文章就图位克隆技术的基本内容及发展做简要概述, 着重对图位克隆技术在大基因组作物中的应用进行分析和评价, 同时对它今后可能的发展方向进行了讨论, 以期为大基因组作物基因的分离提供借鉴。     

Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population

Rice is a leading grain crop and the staple food for over half of the world population. Rice is also an ideal species for genetic and biological studies of cereal crops and other monocotyledonous plants because of its small genome and well developed genetic system. To facilitate rice genome analysis leading to physical mapping, the identification of molecular markers closely linked to economic traits, and map-based cloning, we have constructed two rice bacterial artificial chromosome (BAC) libraries from the parents of a permanent mapping population (Lemont and Teqing) consisting of 400 F9 recombinant inbred lines (RILs). Lemont (japonica) and Teqing (indica) represent the two major genomes of cultivated rice, both are leading commercial varieties and widely used germplasm in rice breeding programs. The Lemont library contains 7296 clones with an average insert size of 150 kb, which represents 2.6 rice haploid genome equivalents. The Teqing library contains 14208 clones with an average insert size of 130 kb, which represents 4.4. rice haploid genome equivalents. Three single-copy DNA probes were used to screen the libraries and at least two overlapping BAC clones were isolated with each probe from each library, ranging from 45 to 260 kb in insert size. Hybridization of BAC clones with chloroplast DNA probes and fluorescent in situ hybridization using BAC DNA as probes demonstrated that both libraries contain very few clones of chloroplast DNA origin and are likely free of chimeric clones. These data indicate that both BAC libraries should be suitable for map-based cloning of rice genes and physical mapping of the rice genome.     

新疆军垦型细毛羊基因组BAC文库的构建

选用新疆军垦型细毛羊为材料,.构建了含有190 464个克隆的BAC文库,文库平均插入片段大小为133 kb,同时文库92.5%的克隆插入片段大于100 kb,而且有部分克隆甚至大于300 kb,这将满足大多数基因筛选的要求.假定绵羊的基因组含有3x106 kb,根据文库的平均插入片段大小,计算的文库基因组覆盖率为8倍.因此,从文库筛选到目的片段的概率为98.2%.由于该文库中插入的外源片段来自新疆军垦型细毛羊的基因组,这对于研究新疆军垦型细毛羊的特殊性状的基因与其他绵羊品种和物种之间的差异,及构建其全基因组物理图谱和基因图谱地完善是非常有利的.     

野生一粒小麦BAC文库的构建和鉴定

以细菌人工染色体pECBAC1为载体,构建了野生一粒小麦(Triticum boeoticum B oiss)的基因组BAC文库.该文库共包含约17万个克隆,平均插入片段长度为104 kb,按野生一粒小麦基因组为5 600 Mb计算,文库覆盖了约3倍的该物种基因组.用大麦叶绿体psb A基因和玉米线粒体atp6基因作混合探针,检测发现该文库中含细胞器基因组同源序列的克隆数小于1% .该文库的建成,为小麦基因的克隆及基因组学研究提供了技术平台.     

野生一粒小麦BAC文库的构建和鉴定

以细菌人工染色体pECBAC1为载体 ,构建了野生一粒小麦 (TriticumboeoticumBoiss)的基因组BAC文库。该文库共包含约 17万个克隆 ,平均插入片段长度为 10 4kb ,按野生一粒小麦基因组为 5 6 0 0Mb计算 ,文库覆盖了约 3倍的该物种基因组。用大麦叶绿体psbA基因和玉米线粒体atp6基因作混合探针 ,检测发现该文库中含细胞器基因组同源序列的克隆数小于 1%。该文库的建成 ,为小麦基因的克隆及基因组学研究提供了技术平台     

A Sorghum propinquum BAC library,suitable for cloning genes associated with loss-of-function mutations during crop domestication

A large insert Sorghum propinquum BAC library has been constructed to analyze the physical organization of the sorghum genome and to facilitate positional cloning of sorghum genes and QTLs associated with the early stages of grain crop domestication. This library was established from 12 different ligations using high-molecular-weight DNA generated from either one cycle or two cycles of size selection. This library consists of 38 016 BAC clones with an estimated average insert size of 126 kb and coverage of 6.6 genome equivalents. The 6.6 genome-equivalent BAC library of S. propinquum provides a 99.7% probability of finding one or more BACs that contain genes of interest. Twenty mapped DNA probes, ten homologous and ten heterologous, were used to screen the library, and 121 positive clones were identified, 6.05 per locus or 6.37 per probe.     

一种存放大基因组文库的新方法

用野生一粒小麦为材料,以细菌人工染色体（pECBAC1)为载体构建了细菌人工染色体克隆混合池（Bacterial artificial chromosome pool）,每池100个克隆。经初步验证,池中靶克隆经12h的培养后仍稳定存活。克隆之间的竞争实验仍在进行当中。     

内蒙古草原不同基因组大小植物对氮水添加的响应

被子植物基因组大小的种间差异巨大,约为2400倍.基因组大小与植物从细胞核到个体水平的一系列性状密切相关,进而影响植物对环境变化的响应.作为水分和养分共同限制的生态系统,内蒙古草原植物群落对氮素、水分有效性变化的响应具有明显的种间差异,这种差异可能与种间基因组大小不同有关.本研究利用流式细胞术测定了内蒙古典型草原水分、氮素添加实验平台植物的基因组大小,研究了不同基因组大小植物地上净初级生产力(ANPP)和物种丰富度对水分、氮素添加及其交互作用的响应.结果表明:基因组大小显著影响了不同植物ANPP对水分的响应,小基因组植物ANPP对氮水添加响应更敏感,加水和氮水共同添加显著增加了小基因组植物ANPP,而大基因组植物ANPP对所有处理响应均不显著.加氮对大小基因组植物ANPP都无显著影响.大小基因组植物的物种丰富度对氮水添加的响应也均不显著.基因组大小影响内蒙古草原不同植物ANPP对水分增加的响应.作为植物细胞核水平上十分稳定且种间差异巨大的物种性状,将基因组大小引入生态学研究将对全球变化背景下生态系统结构与功能变化研究起到重要作用.     

大豆BAC克隆基因注释

根据来源于大豆BAC克隆库中的基因组序列,与其比对的基因或蛋白质序列可以从一些数据库中搜索,如GenBank序列数据库、EMBL数据库、PDB数据库等,然后利用NCBI的Entrz程序在数据库中搜索大豆基因类似物,获取其登录号及核苷酸序列,以及这些基因编码的氨基酸序列,通过GENSCAN等软件分析,得出的是与拟南芥等物种序列比对的结果,根据GENSCAN的预测结果,可以初步得知序列长度、基因数目及具有编码某种功能蛋白的基因存在的可能性,进而对预测出的氨基酸或核苷酸序列利用数据库NCBI中的BLAST进行序列的相似性搜索及比对分析,寻找其保守区域。最后对其功能基因进行注释。     

Through a genome, darkly: comparative analysis of plant chromosomal DNA

Plant nuclear genomes encompass a wide range of variation in size and nucleotide composition with diverse arrangements of chromosomal segments, repetitive sequences and distribution of genes. Comparative genomic analysis may be undertaken at different levels of organisation, which are reflected in this review, together with a focus on the genetic and functional significance of the observed variation. Patterns of genome organisation have been revealed which reflect the different underlying mechanisms and constraints driving change. Thus comparative issues of genome size, nucleotide sequence composition and genome heterogeneity are provided as a background to understanding the different levels of segmental and repetitive sequence duplication and distribution of genes. The extent of synteny and collinearity revealed by recent genetic and sequence comparisons is discussed, together with a consideration of problems associated with such analyses. The possible origins and mechanisms of variation in genome size and organisation are covered, including the prevalence of duplication at different levels of organisation. The likely genetic, functional and adaptive consequences of replicated loci are discussed with evidence from comparative studies. The scope for comparative analysis of epigenetic plant genome variation is considered. Finally, opportunities for applying comparative genomics to isolating genes and understanding complex crop genomes are addressed.     

植物大片段 DNA 的研究进展

植物大片段 DNA 的研究成为了基因组学研究的一个重要方面．对它的研究得益于容纳大片段 DNA 片段载体的发展．对构建植物大片段 DNA 的载体、植物大片段 DNA 的提取方法、植物大片段 DNA 的主要应用领域的最新进展进行了介绍．     

Construction of an arabidopsis BAC library and isolation of clones hybridizing with disease-resistance,gene-like sequences

A bacterial artificial chromosome (BAC) library consisting of 9,000 clones (representing a 4.5 genome equivalents) with an average DNA insert size of 60 kb was constructed from arabidopsis nuclear DNA. We have demonstrated the usefulness of this library by identifying one BAC clone that hybridizes with the arabidopsisPHYB gene and seven clones, representing four distinct classes, that hybridize to a putative disease-resistance gene. This library represents an additional resource for map-based cloning and physical mapping in arabidopsis.