A Radiation Map of the Short Arm of Porcine Chromosome 2

In recent years, maps of mammalian genomes have been acquiring increasingly higher resolution. Integration of maps of different types has become possible. As a tool in integrating maps of mammalian genomes of different types, high-resolution mapping with radiation-induced hybrids (RH) is used. Here, we present an RH₆₀₀₀ map of the short arm of porcine chromosome 2. The map contains 15 microsatellites and five genes (for parathyroid hormone, lactate dehydrogenase A, myogenic factor, follicle-stimulating hormone beta, and calpain I). The RH panel was obtained on the basis of a hybrid cell line bearing the single porcine chromosome 2 against the background of mink chromosomes. The mean frequency of preserving markers examined in the panel was 18.3%. Integration of four genes in the panel and a comparison of gene order in homeologous regions of human and porcine chromosomes are presented.     

An Integrated Physical Map of 210 Markers Assigned to the Short Arm of Human Chromosome 11

Using a panel of patient cell lines with chromosomal breakpoints, we constructed a physical map for the short arm of human chromosome 11. We focused on 11p15, a chromosome band harboring at least 25 known genes and associated with the Beckwith-Wiedemann syndrome, several childhood tumors, and genomic imprinting. This underlines the need for a physical map for this region. We divided the short arm of chromosome 11 into 18 breakpoint regions, and a large series of new and previously described genes and markers was mapped within these intervals using fluorescence in situ hybridization. Cosmid fingerprint analysis showed that 19 of these markers were included in cosmid contigs. A detailed 10-Mb pulsed-field physical map of the region 11p15.3-pter was constructed. These three different approaches enabled the high-resolution mapping of 210 markers, including 22 known genes.     

Distribution of Nonstructural Variation between Wheat Cultivars along Chromosome Arm 6Bp: Evidence from the Linkage Map and Physical Map of the Arm

Metaphase I (MI) pairing of homologous chromosomes in wheat intercultivar hybrids (heterohomologous chromosomes) is usually reduced relative to that within the inbred parental cultivars (euhomologous chromosomes). It was proposed elsewhere that this phenomenon is caused by polymorphism in nucleotide sequences (nonstructural chromosome variation) among wheat cultivars. The distribution of this polymorphism along chromosome arm 6Bp (=6BS) of cultivars Chinese Spring and Cheyenne was investigated. A population of potentially recombinant chromosomes derived from crossing over between telosome 6Bp of Chinese Spring and Cheyenne chromosome 6B was developed in the isogenic background of Chinese Spring. The approximate length of the Chinese Spring segment present in each of these chromosomes was assessed by determining for each chromosome the interval in which crossing over occurred (utilizing the rRNA gene region, a distal C-band and the gliadin gene region as markers). The MI pairing frequencies of these chromosomes (only the complete chromosomes were used) with the normal Chinese Spring telosome 6Bp were determined. These were directly proportional to the length of the euhomologous segment. The longer the incorporated euhomologous segment the better was the MI pairing. This provided evidence that the heterohomologous chromosomes are differentiated from each other in numerous sites distributed throughout the arm.—The comparison of the physical map of arm 6Bp with the linkage map showed a remarkable distortion of the linkage map; no crossing over was detected in the proximal 68% of the arm. A population of 49 recombinant chromosomes was assayed for recombination within the rRNA gene region, but none was detected. No new length variants of the nontranscribed spacer separating the 18S and 26S rRNA genes were detected either.     

Physical Mapping of Genetic Markers on the Short Arm of Chromosome 5

The deletion of the short arm of chromosome 5 is associated with the cri-du-chat syndrome. In addition, loss of this portion of a chromosome is a common cytogenetic marker in a number of malignancies. However, to date, no genes associated with these disorders have been identified. Physical maps are the first step in isolating causative genes, and genes involved in autosomal recessive disorders are now routinely mapped through the identification of linked markers. Extensive genetic maps based upon polymorphic short tandem repeats (STRs) have provided researchers with a large number of markers to which such disorders can be genetically mapped. However, the physical locations of many of these STRs have not been determined. Toward the goal of integrating the human genetic maps with the physical maps, a 5p somatic cell hybrid deletion mapping panel that was derived from patients with 5p deletions or translocations was used to physically map 47 STRs that have been used to construct genetic maps of 5p. These data will be useful in the localization of disease genes that map to 5p and may be involved in the etiology of the cri-du-chat syndrome.     

A Primary Genetic Linkage Map of 14 Polymorphic Loci for the Short Arm of Human Chromosome 8

A genetic linkage map of markers for the short arm of human chromosome 8 has been constructed with 14 polymorphic DNA markers on the basis of genotypes obtained in 40 CEPH reference families. This unbroken map spans 45 cM in males and 79 cM in females. The 14 markers include three genes, MSR, LPL, and NEFL, and one anonymous DNA segment that were previously assigned to chromosome 8. The other 10 marker had been isolated from a chromosome 8-specific cosmid library and physically localized to chromosomal bands by fluorescence in situ hybridization. The order of loci determined by genetic linkage was consistent with their physical locations. This map will facilitate efficient linkage studies of human genetic diseases that may be segregating on chromosome 8p and will provide anchor points for development of high-resolution maps for this chromosomal region.     

Physical and Genetic Map of the Pasteurella multocida A:1 Chromosome

A physical and genetic map of the Pasteurella multocida A:1 genome was generated by using the restriction enzymes ApaI, CeuI, and NotI. The positions of 23 restriction sites and 32 genes, including 5 rrn operons, were localized on the 2.35-Mbp single circular chromosome. This report presents the first genetic and physical map for this genus.     

水稻第六染色体长臂亚端粒区遗传图与物理图的整合

生物染色体亚闰区域在物种翰经过程中是高度活跃的。为了认识水稻染色体亚端粒区域的组织结构,用水稻第六染色体长臂亚端料区的ＲＦＬＰ标记Ｇ３４２和Ｒ１１６７作探针筛选ＢＡＣ文库,以得到的阳笥ＢＡＣ克隆为起点进行染色体眇地,构建了覆盖这２个分子标记区约５００ｋｂ的ＢＡＣ跨叠克隆群,将这一区域的跗图和物理图进行了整合。对１４个ＢＡＣ克隆插入末端进行了亚克隆,鉴定的７个亚克隆 端为单考贝或抵考贝序列,其中５个     

人X染色体长臂(Xq)和短臂(Xp)基因组学比较分析

X染色体发生X染色体失活 ,但是Xp基因有 30 %表现为逃逸 ,而Xq仅不到 3%。为了研究X染色体基因失活和表达逃逸发生和维持的分子机制 ,比较了Xq和XpDNA序列的RNA模拟结合强度。X染色体的核苷酸序列被分为 5 0kb一段 ,对每一段DNA做 7碱基 (7nt)字符串组合分析 (共有 4 7=16 384种组合 ) ,记录每段 5 0kbDNA中每种 7nt字符串的频率。选择生发中心B细胞中的 12 0个高表达基因 ,计算这些基因的内含子 7nt字符串的出现频率 ,称为intron 7nt,以此作为RNAs(RNA群 ,模拟细胞中RNA在小片段的总和 )。已知一段DNA序列的 7nt频率值和intron 7nt,即可以计算该DNA段与intron 7nt的结合强度。每段 5 0kbDNA与intron 7nt的结合强度取决于该DNA段与intron 7nt互补核苷酸的频率 ,互补的核苷酸序列越多 ,结合强度就越大。DNA段与intron 7nt的模拟结合强度称为RNA结合强度 ,试图模拟该段DNA可以结合的RNA小片段的总量。之所以采用 7nt字符串组合分析是考虑到连续 7个核苷酸互补则可以形成相对稳定的结合。研究发现 :1)Xp各DNA段的RNA结合强度均值显著大于Xq (P <0 0 0 1) ;2 )Xp上高结合RNA的DNA段数目显著高于Xq (P <0 0 0 1) ;3)RNA高结合DNA段形成的簇与X染色体基因表达逃逸区关联。有证据表明 ,RNA可以通过改变染色质     

3B染色体短臂小麦赤霉病抗性主效QTL的分析

采用区间作图和复合区间作图方法对重组自交系群体宁894037／Alondram、望水白／Alondra和苏麦3号／A1ondra进行了抗赤霉病QTL分析,结果表明,用在田间和温室的赤霉病抗性鉴定资料,在3个赤霉病抗源宁894037、望水白和苏麦3号的3B染色体短臂上均检测到主效QTL的存在。宁894037主效QTL位于标记BARCl33与Xgwm493之间的5．0cM的区间内,最高可解释42．8％的赤霉病抗性;望水白的主效QTL位于标记BARCl47与Xgwm493之间11．5cM的区间内,最高可解释15．1％的赤霉病抗性;苏麦3号的主效QTL位于Xgwm533a与Xgwm493之间13．0cM的区间内,最高可解释10．6％的赤霉病抗性。与赤霉病抗性主效QTL紧密连锁的标记均为SSR标记,可直接用于分子辅助育种。     

A Fine Physical Map of Arabidopsis thaliana Chromosome 5: Construction of a Sequence-ready Contig Map

A fine physical map of Arabidopsis thaliana chromosome 5 wasconstructed by ordering the clones from YAC, P1, TAC and BAClibraries of the genome using the sequences of a variety ofgenetic and EST markers and terminal sequences of clones. Themarkers used were 88 genetic markers, 13 EST markers, 87 YACend probes, 100 YAC subclone end probes, and 390 end probesof P1, TAC and BAC clones. The entire genome of chromosome 5,except for the centromeric and telomeric regions, was coveredby two large contigs 11.6 Mb and 14.2 Mb long separated by thecentromeric region. The minimum tiling path of the chromosomewas constituted by a total of 430 P1, TAC and BAC clones. Themap information is available at the Web site http://www.kazusa.or.jp/arabi/.     

Location of F1 ATPase-like Genes on the Physical Map of the Bacillus subtilis 168 Chromosome

A water-soluble polysaccharide, FI, extracted from the mycelium of Granoderma tsugae, was fractionated and purified by ion-exchange chromatography, gel filtration, and affinity chromatography. Sixteen polysaccharides obtained were examined for antitumor effects on Sarcoma 180 in mice.

The three active polysaccharides obtained were as follows:

FI₀-a: A glycan-protein complex containing 9.3% protein, and having a hetero-glyco-chain of mannose and xylose.

FI₀-b-α: Molecular weight 10,000, glucan-protein complex containing 25.8% protein. The inhibition ratio was 61.8% against the solid cancer Sarcoma 180/mice; the survival ratio was more than 194% of the control group (100).

FA-1-b-α: Molcular weight 16,000, a complex of glycan: protein = 42:58 w/w, consisting of glucose as a main component, and associated with arabinose, mannose, xylose, and galactose. This had a tumor inhibition ratio of 56% and a survival ratio of more than 182%.

Comparison of active glycan with the fruiting body and mycelium: Among water-soluble polysaccharides of fruiting body, FI₀-a and FA-1, with antitumor activity, were both glucogalactan-protein complexes of molecular weight 10,000, but that of mycelium was a homoglucan protein complex in FI₀-b-α and heteroglucan protein in both FA-l-a and FA-l-b-α. The heteroglucan had a low tumor inhibition ratio, but caused a high survival ratio in mice.     

Allele Deletion Mapping of the Short Arm of Human Chromosome 3 in Renal Carcinoma

Allelic deletions along the short arm of human chromosome 3 were mapped in 57 pairs of DNA samples from tumor and normal tissue of renal carcinoma patients in order to locate potential tumor suppressor genes. Twenty highly polymorphic microsatellite markers were used for deletion mapping. Allelic deletions were found in most of the samples (91%). Extended terminal deletions (56%) prevailed over shorter internal and multiple deletions and dominated (65%) in the most aggressive histopathological kidney cancer subtype, clear-cell carcinoma. Frequency analysis of loss of heterozygosity allowed detection of the human chromosome 3 regions most essential for renal carcinomas: the region adjacent to the gene VHL(3p26–p25), the region of homozygous deletions AP20 (3p22–p21.33), and a new region between markers D3S2420 and D3S2409 (3p21.31, 2.2 Mbp).     

Combined Physical and Genetic Map of the Pseudomonas putida KT2440 Chromosome

A combined physical and genetic map of the Pseudomonas putida KT2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (PFGE) and Southern hybridization. Circular genome size was estimated at 6.0 Mb by adding the sizes of 19 SwaI, 9 PmeI, 6 PacI, and 6 I-CeuI fragments. A complete physical map was achieved by combining the results of (i) analysis of PFGE of the DNA fragments resulting from digestion of the whole genome with PmeI, SwaI, I-CeuI, and PacI as well as double digestion with combinations of these enzymes and (ii) Southern hybridization analysis of the whole wild-type genome digested with different enzymes and hybridized against a series of probes obtained as cloned genes from different pseudomonads of rRNA group I and Escherichia coli, as P. putida DNA obtained by PCR amplification based on sequences deposited at the GenBank database, and by labeling of macrorestriction fragments of the P. putida genome eluted from agarose gels. As an alternative, 10 random mini-Tn5-Km mutants of P. putida KT2440 were used as a source of DNA, and the band carrying the mini-Tn5 in each mutant was identified after PFGE of a series of complete chromosomal digestions and hybridization with the kanamycin resistance gene of the mini-Tn5 as a probe. We established a circular genome map with an average resolution of 160 kb. Among the 63 genes located on the genetic map were key markers such as oriC, 6 rrn loci (rnnA to -F), recA, ftsZ, rpoS, rpoD, rpoN, and gyrB; auxotrophic markers; and catabolic genes for the metabolism of aromatic compounds. The genetic map of P. putida KT2440 was compared to those of Pseudomonas aeruginosa PAO1 and Pseudomonas fluorescens SBW25. The chromosomal backbone revealed some similarity in gene clustering among the three pseudomonads but differences in physical organization, probably as a result of intraspecific rearrangements.     

Integration of the Physical and Genetic Linkage Map for Human Chromosome 13

We have used a panel of somatic cell hybrids containing different rearrangements of human chromosome 13 to integrate genetic and physical maps of this chromosome. The positions of 17 translocation/deletion breakpoints on human chromosome 13 have been determined relative to the microsatellite markers on the genetic linkage map compiled by Généthon. Because markers on maps from several other Consortium groups have also been analyzed using many of the same hybrids, it was possible to relate these with the Généthon map. The position of all of the chromosome breakpoints have been placed, wherever possible, between two adjacent markers on the genetic linkage maps using PCR analysis for the presence/absence of the markers in the somatic cell hybrids. The positions of the breakpoints have already been determined cytogenetically, and some of these breakpoints are located at landmark positions on the chromosome. The relative density of markers along the chromosome differs between independently derived maps, and, based on the known locations of certain breakpoints in the physical map, inconsistencies in the genetic maps have been identified.     

Mapping of Dbr1 and Ypk1 Suggests a Major Revision of the Genetic Map of the Left Arm of Saccharomyces Cerevisiae Chromosome Xi

The Saccharomyces cerevisiae dbr1 mutation has been mapped on the left arm of chromosome XI. XIL is a chromosome arm that was until now rather sparsely populated with accurately mapped markers. On the basis of physical data, the overall order of markers is inverted relative to the existing genetic map of XI. We present tetrad analyses using a variety of markers on XI that indicate that the existing genetic map of XIL should be inverted, at least for the strains in which our mapping was carried out, and probably for other S. cerevisiae strains.