中国美利奴细毛羊BAC文库的三维PCR筛选

本研究利用中国美利奴细毛羊全基因组BAC文库,构建了可供快速筛选的两级水平的混合池,一级混合池和二级混合池(Primary pools and secondary pools).一级混合池基于每一384-well盘而构建,由盘、行,列三维混合池组成,二级混合池基于整个BAC文库而构建.设计了一种基于PCR技术的快速筛选方法,先筛选二级混合池m再根据结果筛选相应的一级混合池.利用此方法只需一步共66个PCR反应即可从BAC丈库中7.4万个克隆中筛选出1个阳性克隆,或三步100个以内的PCR反应筛选出多个阳性克隆.以绵羊基因组多态性分子标记BF94-1为引物,用一步共66个PCR反应成功筛选到1个阳性克隆373D13.     

棉花BAC文库快速筛选法

目的:构建棉花细菌人工染色体(Bacterial Artificial Chromosome,BAC)文库的快速筛选法,以期从BAC文库中大量、快速、高效筛选出特定BAC克隆,为从事基因组测序、分离和分析特定基因、构建物理图谱及基因图位克隆等生物学技术研究奠定基础。方法:构建了整板、行、列的三维混合池,以菌液PCR为基础,从BAC文库中筛选出含有特定DNA片段的BAC单克隆。结果:从BAC文库的3 456个克隆中,共筛选出16个阳性单克隆,涉及13条染色体、11个SSR标记。结论:该文构建的棉花BAC文库筛选体系,筛选快速、准确,适合从BAC文库中大量筛选BAC单克隆。结合当前的多种BAC文库筛选方法进行探讨,根据不同的实验目的选择更合适的筛选方法和操作步骤。     

东方田鼠部分BAC文库的微卫星筛选

目的 从东方田鼠的部分BAC文库中筛选微卫星.方法 应用非放射性的菌落杂交方法和磁珠富集法从东方田鼠的BAC文库中筛选高质量的微卫星标记.结果 以地高辛标记的寡聚核苷酸(CA)20为探针,通过菌落杂交法从136个东方田鼠BAC克隆中筛选出杂交信号最强的20个阳性克隆.再将这20个阳性克隆分别通过链霉亲和素磁珠法构建亚克隆文库,从中选取400个经PCR鉴定为阳性的亚克隆进一步测序分析,共得到220个微卫星序列,阳性率55％.选取重复次数高,侧翼序列完整的微卫星序列设计74对引物,共有35对引物能扩增出清晰的条带,其中16对引物具有多态性.结论 成功且高效地从阳性BAC克隆中筛选出微卫星序列,这些微卫星和阳性BAC克隆可用于后续的定位研究.     

一种使用混合PCR筛选技术高效延伸水稻BAC—重叠群的方法

使用“克隆连克隆 (clonebyclone)”战略进行水稻基因组测序需要依赖于构建好的基因组物理图。工作着眼于水稻籼稻广陆矮 4号 (OryzasativaindicaGuangLuAi4)第四号染色体长臂上 5 6 .1～ 6 8cM的区域 ,采用PCR方法筛选BAC全库来延伸重叠群 ,构建物理图。通过参照特异遗传探针定位的BAC克隆 (seedBAC)末端序列设计了 14对引物 ,按特定规则分成 3组 ,分别以代表水稻BAC库 (共 2 2 36 8个BAC )的 2 33个BACpool为模板进行PCR反应 ,一共获得了 6 5个阳性BAC克隆 ,通过末端测序、酶切杂交等方法确定了其中 2 9个BAC克隆作为有效延伸的克隆 ,延伸了 8个重叠群。通过酶切杂交、末端测序等方法还获知阳性BAC的延伸方向、延伸长度以及与seedBAC之间的重叠长度。8个重叠群总的延伸长度达到5 10kb。与实验室原用于作物理图的其他方法如指纹图、点杂交等相比 ,该方法有高效率、高灵敏度、专一性好、可重复使用等优点。创新之处在于通过引物的合理分组和PCR实验条件的改进降低了假阳性和假阴性率     

筛选和定位含水稻端粒相关序列的BAC克隆

根据水稻的端粒重复序列 ,设计了 2个引物 :(TTTAGGG) ₃ 和 (CCC TAAA) ₃ CCC ,利用单引物在水稻总DNA中进行PCR扩增 ,分别得到Tas1和Tas2 .这 2个片段在定位亲本间均无多态性 .Tas1的原位杂交表明该序列位于 2对染色体端部 .以Tas1为探针在所构建的水稻基因组BAC文库中筛选到 1个克隆 ,South ern杂交证明此克隆也包含序列Tas2 ,取该克隆中的单拷贝序列利用ZYQ/JX1 7DH群体将其定位在第 6号染色体的端部 .并对Tas1和Tas2在此克隆中的排列进行了初步研究     

温敏核不育水稻5460S细菌人工染色体文库的构建和鉴定

为了构建温敏核不育 (TGMS)基因区域的精细物理图谱并最终分离TGMS基因 ,以温敏核不育水稻 5 46 0S为材料 ,摸索优化了构建植物细菌人工染色体 (BAC)文库的方法 ,构建了一个高质量的BAC文库 .该文库由 1 95 84个克隆构成 ,插入片段平均长度为 1 1 0kb ,相当于水稻单倍体基因组大小的 5倍 ;以分子量分别为 1 40和2 5 0kb的 2个大BAC克隆进行稳定性传代实验 ,经 1 0 0代传代后其插入的DNA片段仍然稳定存在 ;以线粒体和叶绿体基因为探针筛选BAC文库 ,未检验出叶绿体和线粒体DNA的污染 ;以和tms1基因连锁的 3个分子标记作为探针对BAC文库进行了筛选 ,每个探针至少可获得一个阳性克隆 ,利用热不对称性交错PCR(Tail PCR)法成功分离了阳性克隆的左右末端序列 .     

甘蓝型油菜A基因组候选BAC克隆的筛选及其插入片段大小分析

选择甘蓝型油菜A基因组10个连锁群上特有的85个SSR分子标记,合成其引物序列,采用四维PCR法筛选甘蓝型油菜-新疆野生油菜二体异附加系BAC文库,成功筛选到甘蓝型油菜A基因组39个BAC克隆,其插入片段介于50～300 kb之间,平均为120 kb。甘蓝型油菜A基因组10个连锁群BAC克隆的获得,对后续开展甘蓝型油菜A基因组染色体识别、基因染色体定位、遗传距离与物理距离间关系分析等均具有重要价值。     

玉米转录因子ABP9基因的BAC克隆鉴定及染色体定位

为得到玉米转录因子ABP9的准确基因组序列及其旁侧基因组序列,应用PCR法对玉米自交系齐319 BAC文库中含有ABP9基因的单克隆进行筛选,得到了19个一级阳性混池,从中选择BAC-103、BAC-159进一步筛选获得了4个阳性单克隆。以其中1个阳性单克隆BAC-103-C3为模板进行全序列测定,比对分析后将ABP9基因初定位于玉米自交系Mo17基因组的3号染色体上。另以玉米自交系齐319、自交系Mo17萌发种子的根尖染色体滴片为材料,以绿色荧光标记的ABP9基因ORF区质粒DNA为探针进行荧光原位杂交,确认在这2个自交系中ABP9基因定位于3号染色体上。ABP9基因组序列的获得及其染色体定位为该基因分子标记的开发及应用于分子育种奠定了基础。     

云南药用野生稻BIBAC文库混合克隆池制备及筛选

在已构建完成的云南药用野生稻BIBAC( binary bacterial artificial chomosome)文库的基础上,将文库制备成一、二、三级混合克隆池,各级混合池的数量分别为3 360、140和14个.根据Xa21抗病基因序列设计1对特异引物,利用4步PCR法对文库混合克隆池进行逐级筛选,初步确定了3个抗病基因阳性克隆.为今后以PCR法高效利用云南药用野生稻BIBAC文库挖掘其优异基因奠定了良好的基础.     

利用染色体区段混合BAC探针鉴定食管癌细胞中的染色体畸变

染色体畸变是恶性肿瘤细胞的重要遗传学特征, 文章旨在应用BAC DNA克隆鉴定食管癌细胞中的染色体臂和染色体区段的畸变。针对染色体各区段选取5~10个1 Mb BAC DNA, 分别混合制备成特定染色体区段的BAC DNA混合克隆, 然后将染色体臂上覆盖所有区段的上述混合克隆进一步混合制备成特定染色体臂BAC DNA混合克隆。利用简并寡核苷酸引物聚合酶链反应(Degenerate oligonucleotide primed PCR, DOP-PCR)标记染色体臂探针, 利用切口平移法(Nick translation)标记染色体区段探针, 并对食管癌细胞中期染色体进行荧光原位杂交(Fluorescence in situ hybridization, FISH)分析。正常人外周血淋巴细胞中期染色体FISH结果显示, 上述方法标记的探针具有较高的特异性。进一步利用染色体臂混合探针, 确定了多个食管癌细胞中的染色体重排所涉及的特定染色体臂; 利用染色体区段混合探针, 鉴定出KYSE140的t(1q;7q)衍生染色体中1q上的断点范围位于1q32-q41。文章成功建立了1 Mb BAC DNA混合克隆探针标记技术, 并鉴定出多个食管癌细胞中的染色体臂和染色体区段畸变, 不仅为利用M-FISH技术鉴定肿瘤细胞中的染色体畸变提供了更为准确的方法, 而且还可能进一步将该法推广应用于恶性血液病的核型分析以及产前诊断。     

An ordered BAC contig map of the equine major histocompatibility complex

A physical map of ordered bacterial artificial chromosome (BAC) clones was constructed to determine the genetic organization of the horse major histocompatibility complex. Human, cattle, pig, mouse, and rat MHC gene sequences were compared to identify highly conserved regions which served as source templates for the design of overgo primers. Thirty-five overgo probes were designed from 24 genes and used for hybridization screening of the equine USDA CHORI 241 BAC library. Two hundred thirty-eight BAC clones were assembled into two contigs spanning the horse MHC region. The first contig contains the MHC class II region and was reduced to a minimum tiling path of nine BAC clones that span approximately 800 kb and contain at least 20 genes. A minimum tiling path of a second contig containing the class III/I region is comprised of 14 BAC clones that span approximately 1.6 Mb and contain at least 34 genes. Fluorescence in situ hybridization (FISH) using representative clones from each of the three regions of the MHC localized the contigs onto ECA20q21 and oriented the regions relative to one another and the centromere. Dual-colored FISH revealed that the class I region is proximal to the centromere, the class II region is distal, and the class III region is located between class I and II. These data indicate that the equine MHC is a single gene-dense region similar in structure and organization to the human MHC and is not disrupted as in ruminants and pigs.     

Human BAC library: construction and rapid screening

We have constructed a human genomic bacterial artificial chromosome (BAC) library using high molecular weight DNA from a pre-pro-B cell line, FLEB14-14, with a normal male diploid karyotype. This BAC library consists of 96 000 clones with an average DNA insert size of 110 kb, covering the human genome approximately 3 times. The library can be screened by three different methods. (1) Probe hybridization to 31 high-density replica (HDR) filters: each filter contains 3072 BAC clones which were gridded in a 6×6 pattern. (2) Probe hybridization to two Southern blot filters to which 31 HindIII digests of the pooled 3072 BAC clones were loaded. This identifies a particular HDR filter for which further probe hybridization is performed to identify a particular clone(s). (3) Two-step polymerase chain reaction (PCR). First, PCR is applied to DNA samples prepared from ten superpools of 9600 BAC clones each to identify a particular superpool and the second PCR is applied to 40 unique DNA samples prepared from the four-dimensionally assigned BAC clones of the particular superpool. We present typical examples of the library screening using these three methods. The two-step PCR screening is particularly powerful since it allows us to isolate a desired BAC clone(s) within a day or so. The theoretical consideration of the advantage of this method is presented. Furthermore, we have adapted Vectorette method to our BAC library for the isolation of terminal sequences of the BAC DNA insert to facilitate contig formation by BAC walking.     

BAC contig development by fingerprint analysis in soybean.

We constructed a soybean bacterial artificial chromosome (BAC) library suitable for map-based cloning and physical mapping in soybean. This library consists of approximately 40 000 clones (4-5 genome equivalents) stored individually in 384-well microtiter dishes. A random sampling of 224 clones yielded an average insert size of 150 kb, giving a 98% probability of recovering any specific sequence. We screened the library for seven single or very low copy genie or genomic sequences using the polymerase chain reaction (PCR) and found between one and seven BACs for each of the seven sequences. When testing the library with a portion of the soybean psbA chloroplast gene, we found less than 1% chloroplast DNA representation. We also screened the library for eight different classes of disease resistance gene analogs (RGAs) and identified BACs containing all RGAs except class 8. We arranged nine of the class 1 RGA BACs and six of the class 3 RGA BACs into individual contigs based on fingerprint patterns observed after Southern probing of restriction digests of the member BACs with a class-specific sequence. This resulted in the partial localization of the different multigene family sequences without precise definition of their exact positions. Using PCR-based end rescue techniques and RFLP mapping of BAC ends, we mapped individual BACs of each contig onto linkage group J of the soybean public map. The class 1 contig mapped to the region on linkage group J that contains several disease resistance genes. The class 1 contig extended approximately 400 kb. The arrangement of the BACs within this contig has been confirmed using PCR. One end of the class 1 contig core BAC mapped to two positions on linkage group J and cosegregated with two class 1 RGA loci, suggesting that this segment is within an area of regional duplication.     

A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb

ABSTRACT: BACKGROUND: The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of the ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution. RESULTS: A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by the DNA fingerprinting, BAC-end sequencing, and the sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826. CONCLUSIONS: We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants.     

A BAC clone-based physical map of ovine major histocompatibility complex

An ovine bacterial artificial chromosome (BAC) library containing 190,000 BAC clones was constructed and subsequently screened to construct a BAC-based physical map for the ovine major histocompatibility complex (MHC). Two hundred thirty-three BAC clones were selected by 84 overgo probes designed on human, mouse, and swine MHC sequence homologies. Ninety-four clones were ordered by DNA fingerprinting to form contigs I, II, and III that correspond to ovine MHC class I-class III, class IIa, and class IIb. The minimum tiling paths of contigs I, II, and III are 15, 4, and 4 BAC clones, spanning approximately 1900, 400, and 300 kb, respectively. The order and orientation of most BAC clones in each contig were confirmed by BAC-end sequencing. An open gap exists between class IIa and class III. This work helps to provide a foundation for detailed study of ovine MHC genes and of evolution of MHCs in mammals.     

Construction and characterization of an ovine BAC contig spanning the callipyge locus

We describe the construction of an ovine BAC contig spanning a 4.6 centimorgan (cM) chromosome segment known to contain the callipyge (CLPG) locus. The contig comprises 21 ovine BAC clones jointly covering approximately 900 kilobases (Kb). Two gaps in the BAC contig, spanning 10 and 7.5 Kb, respectively, were bridged by long range PCR. The corresponding chromosome region was shown to be characterized by an unusually low Kb to cM ratio (164 Kb/cM) and a high density of Not1 sites (1:126 Kb) possibly reflecting a high gene density in the corresponding chromosome region. Equivalent amplification of 64 sequence tagged sites spanning the corresponding region from homozygous +/+ and CLPG/CLPG individuals disproves the hypothesis of a major deletion causing the CLPG mutation.     

Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes.