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At least 73 records · Page 4Linked to original sources
PubMed1999

Construction of chromosome-specific paints for meta- and submetacentric autosomes and the sex chromosomes in the horse and their use to detect homologous chromosomal segments in the donkey.

A pilot study comparing horse and donkey karyotypes on a molecular basis was initiated using the chromosomal microdissection approach. All equine meta- and submetacentric chromosomes, viz. ECA1 to ECA13 and the X and Y chromosomes, were microdissected. The DNA was PCR amplified, non-radioactively labelled and used as probes on equine metaphase chromosomes to confirm their origin. Once tested, the paints were used as probes on donkey metaphase chromosomes to detect homologous chromosomal segments between the two species. The results not only detected conservation of whole chromosome and/or arm synteny between the two karyotypes, but also highlighted varying degrees of rearrangements. The findings also enable deduction of homology between parts of donkey and human karyotypes. In light of the molecular evidence, this study examines the accuracy of the available comparative cytogenetic data between horse and donkey.

Animals↗
PubMed1992

Gamma irradiation induced deletions in an alien chromosome segment of the wheat 'Indis' and their use in gene mapping.

Deletion mutants were produced in a translocated chromosome segment derived from Thinopyrum distichum (Thunb.) Löve. Spikes of the translocation line 'Indis' were irradiated with gamma rays at dosages of 15, 20, and 25 Gy. The irradiated spikes were pollinated with 'Inia 66' pollen and the F2 and F3 generations screened for translocation mutants, using the genes for leaf rust resistance and yellow endosperm pigmentation as markers. Finally, endopeptidase polymorphisms were utilized to select mutant translocation homozygotes within each of 29 families. An investigation of polymorphisms at the alpha-Amy-D2 and Wsp-D1 loci of chromosome arm 7DL revealed that 'Indis' did not produce an alpha-AMY-D2 product, but it did produce a novel WSP-D1 protein. The mutants were characterized for their leaf and stem rust resistances and the presence of WSP-D1 and yellow flour pigments. The stem rust resistance gene could not be accurately mapped. The linear order of the remaining loci on 7DL was centromere - leaf rust resistance - Wsp-D1 and yellow pigment. The data obtained suggested that the 'Indis' translocation has homo(eo)logy to the Lr19 translocation and homoeology to 7DL of common wheat.

Chromosome Deletion↗
PubMed1982

Transposition of a chromosomal segment bounded by redundant rRNA genes into other rRNA genes in Escherichia coli.

We have constructed several mutants of Escherichia coli which have the chromosomal segment between the directly repeated rrnB and rrnE genes deleted from the normal position and transposed into another one of the seven redundant rRNA genes. We have examples where the transposition has been into rrnC, rrnD, rrnG, and rrnH. Included in the evidence for each of these transpositions was the finding that each transposition specifically affected a different one of the seven BamHI-PstI restriction nuclease fragments known to correspond to the seven rrn genes. The transposition mutants were generally healthy, but sensitive mixed-growth experiments revealed that most of them grew somewhat more slowly than the parental control in rich medium. The maximal detrimental effect was a 4 to 5% reduction in growth rate when the transposition of the rrnB-rrnE segment was into rrnG. We have found that a rrnF gene, reported by others to be linked to malA, does not exist in our standard strain, a derivative of Cavalli Hfr. Instead of rrnF, we identified a new rrn gene, rrnH, which mapped near min 5.

Chromosome Mapping↗
PubMed1995

Fluorescent in situ hybridization and C-banding analyses of highly repetitive DNA sequences in the heterochromatin of rye (Secale montanum Guss.) and wheat incorporating S. montanum chromosome segments.

The molecular characterization of C-banded regions of Secale montanum Guss. by means of in situ hybridization was performed in order to provide new information about their chromosome structure relative to cultivated rye, Secale cereale L. Accurate identification of individual chromosomes was achieved using simultaneous and (or) successive fluorescent in situ hybridization (FISH) and C-banding. FISH identification was performed using total rye DNA, three highly repetitive rye DNA sequences (pSc119.2, pSc74, and pSc34), and the ribosomal RNA probes pTa71 (18S, 5.8S, and 26S rDNA) and pTa794 (5S rDNA). FISH was also used to identify the chromosome segment involved in two spontaneous translocation lines recovered from a 'Chinese Spring'--S. montanum wheat-rye addition line. FISH analysis revealed the exact translocation breakpoints and allowed the identification of the transferred rye segments. The value of this type of analysis is discussed.

Chromosome Banding↗
PubMed2004

QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines.

The genetic mechanism underlying six palatability properties of cooked rice and three physico-chemical traits was dissected in 66 BC(3)F(2) chromosome segment substitution lines (CSSLs), using a complete linkage map in three successive years. The CSSLs showed transgressive segregation for all traits studied. Significant correlation was detected among most palatability traits. A total of 25 QTLs for the nine traits were identified on nine chromosomes, and many QTLs affecting different quality traits were mapped in the same regions. Six QTLs--qLT-8 for luster, qTD-6 and qTD-8 for tenderness, qIVOE-6 and qIVOE-8 for integrated value of organoleptic evaluation, and qAC-8 for amylose content--were repeatedly detected across the 3 years. Phenotypic values were significantly different between the recurrent parent, cultivar Asominori, and the CSSLs harboring any of the six QTL alleles across the three environments, indicating that these six QTLs were non-environment-specific and could be used for marker-assisted selection in rice quality improvement.

Chromosome Mapping↗
PubMed2002

Generation of large homozygous chromosomal segments by mitotic recombination during lymphomagenesis in F1 hybrid mice.

The loss of heterozygosity (LOH) has been reported in numerous neoplasms in both human and animals, and has often been observed in chromosomal regions, which contain tumor-suppressor genes. We previously found frequent LOH on chromosomes 4, 12 and 19 in radiation-induced lymphomas from (BALB/cHeA x STS/A)F1 hybrid mice by allelotype analysis at polymorphic microsatellite loci. In this study, to elucidate the nature of allelic losses, we refined the loss regions on chromosomes 4, 12 and 19 of the tumors from the F1 mice and then analyzed them cytogenetically. The results represent evidence of a wide range of allelic losses owing to mitotic recombination on chromosomes 4 and 19 in the tumors, possibly reflecting functional losses of putative tumor-suppressor genes. It is suggested that the generation of these large homozygous chromosomal segments probably containing the affected genes is one of the genetic alterations responsible for tumorigenesis.

Animals↗
PubMed2001

Size of donor chromosome segments around introgressed loci and reduction of linkage drag in marker-assisted backcross programs.

This article investigates the efficiency of marker-assisted selection in reducing the length of the donor chromosome segment retained around a locus held heterozygous by backcrossing. First, the efficiency of marker-assisted selection is evaluated from the length of the donor segment in backcrossed individuals that are (double) recombinants for two markers flanking the introgressed gene on each side. Analytical expressions for the probability density function, the mean, and the variance of this length are given for any number of backcross generations, as well as numerical applications. For a given marker distance, the number of backcross generations performed has little impact on the reduction of donor segment length, except for distant markers. In practical situations, the most important parameter is the distance between the introgressed gene and the flanking markers, which should be chosen to be as closely linked as possible to the introgressed gene. Second, the minimal population sizes required to obtain double recombinants for such closely linked markers are computed and optimized in the context of a multigeneration backcross program. The results indicate that it is generally more profitable to allow for three or more successive backcross generations rather than to favor recombinations in early generations.

Chromosomes↗
PubMed1994

Fully automatic chromosome segmentation.

This paper is concerned with automatic segmentation of high resolution digitized metaphases. This includes automatic detection and rejection of interphase nuclei, stain debris, and other "noise"; automatic detection and segmentation of touching and overlapping chromosome clusters; and automatic rejection of cells which are evaluated as being incomplete, or incorrectly segmented, or where the cell is otherwise unsuitable for further analysis. In this paper, a rule-based approach is described which treats the cell as a whole rather than as a series of individual chromosomes or clusters. The rules adapt classification and segmentation parameters for each cell. Initially, different sets of parameters are chosen according to the staining method of the cells, and the goal of the segmentation. A chromosome number predictor is used to guide the adaptation of the parameters and to estimate the performance. The adaptation is iterative, and the self-adjustment will stop when either a satisfactory result is achieved or if the cell is rejected. The method was implemented on both a Sun workstation and a Cytoscan, a commercial machine for chromosome analysis. Seven hundred and thirteen cells from real data have been tested. A success rate of 90-95% has been achieved. The procedure has been implemented in an automatic aberration scoring system for routine use.

Chromosome Aberrations↗
PubMed1999

Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain.

Using genotypes from nearly 8,000 short tandem-repeat polymorphisms typed in eight of the reference families from the Centre d'Etude du Polymorphisme Humain (CEPH), we identified numerous long chromosomal segments of marker homozygosity in many CEPH individuals. These segments are likely to represent autozygosity, the result of the mating of related individuals. Confidence that the complete segment is homozygous is gained only with markers of high density. The longest segment in the eight families spanned 77 cM and included 118 homozygous markers. All individuals in family 884 showed at least one segment of homozygosity: the father and mother were homozygous in 8 and 10 segments with an average length of 13 and 16 cM, respectively, and covering a total of 105 and 160 cM, respectively. The progeny in family 884 were homozygous over 5-16 segments with average length 11 cM. The progeny in family 102 were homozygous over 4-12 segments with average length 19 cM. Of the 100 individuals in the other six families, 1 had especially long homozygous segments, and 19 had short but significant homozygous segments. Our results indicate that long homozygous segments are common in humans and that these segments could have a substantial impact on gene mapping and health.

Alleles↗
PubMed2004

Bayesian association-based fine mapping in small chromosomal segments.

A Bayesian method for fine mapping is presented, which deals with multiallelic markers (with two or more alleles), unknown phase, missing data, multiple causal variants, and both continuous and binary phenotypes. We consider small chromosomal segments spanned by a dense set of closely linked markers and putative genes only at marker points. In the phenotypic model, locus-specific indicator variables are used to control inclusion in or exclusion from marker contributions. To account for covariance between consecutive loci and to control fluctuations in association signals along a candidate region we introduce a joint prior for the indicators that depends on genetic or physical map distances. The potential of the method, including posterior estimation of trait-associated loci, their effects, linkage disequilibrium pattern due to close linkage of loci, and the age of a causal variant (time to most recent common ancestor), is illustrated with the well-known cystic fibrosis and Friedreich ataxia data sets by assuming that haplotypes were not available. In addition, simulation analysis with large genetic distances is shown. Estimation of model parameters is based on Markov chain Monte Carlo (MCMC) sampling and is implemented using WinBUGS. The model specification code is freely available for research purposes from http://www.rni.helsinki.fi/~mjs/.

Algorithms↗
PubMed1988

Definition of selectable cell surface markers for human chromosomes and chromosome segments in rodent-human hybrids.

A panel of 22 monoclonal antibodies (MAbs) recognizing 21 distinct human cell surface antigens was tested by mixed hemadsorption assays for reactivity with a large number of rodent-human somatic cell hybrids containing different subsets of the human chromosome complement. The serological typing results permit the assignment of six gene loci determining cell surface antigens to human chromosomes 3, 6, 11, 19, 20, and 22. In addition, analysis of hybrids retaining deleted copies (but no normal homologs) of specific human chromosomes provides regional assignments for 18 gene loci, located on seven different chromosomes. These findings extend and refine the genetic map for human cell surface antigens and identify new selectable markers for defined chromosome segments.

Animals↗
PubMed1998

Sporadic breast cancers exhibit loss of heterozygosity on chromosome segment 10q23 close to the Cowden disease locus.

Cowden disease, a dominantly inherited syndrome characterized by a variety of proliferative lesions and predisposition to breast and thyroid cancer, has recently been linked to the polymorphic marker D10S215 on chromosome segment 10q23. Loss of heterozygosity in prostate cancer is linked to the same marker, whereas loss of heterozygosity in glioblastoma, endometrial cancer, and other malignancies also localizes to this region. Most recently, a putative tumor suppressor gene (PTEN/MMAC1) has been identified in the region between D10S215 and an adjacent, more telomeric marker (D10S541) and was found to be altered in breast cancers, prostate cancers, and glioblastomas. We examined 22 invasive breast cancers for loss of heterozygosity in the 10q23 region and found loss in 41% (9/22). There were two distinct regions of loss, including one near the D10S541 marker, with an approximately equal frequency of deletion in each. The observed pattern of deletion is consistent with the presence of a tumor suppressor gene between D10S215 and D10S541. Most of the poorly differentiated carcinomas in the case collection showed loss of heterozygosity in the region near D10S215, suggesting that this loss correlates with a poor prognosis.

Adenocarcinoma, Mucinous↗
PubMed2003

Genome plasticity in Acinetobacter: new degradative capabilities acquired by the spontaneous amplification of large chromosomal segments.

In Acinetobacter sp. ADP1, growth on benzoate requires regulation of the cat genes by two transcriptional activators. Here, mutants were obtained from a strain lacking both activators by selecting for growth on benzoate medium. The mutants, which arose within 3 weeks at a frequency of approximately 10-8, carried amplified chromosomal regions (amplicons) encompassing the cat genes. Multiple occurrences of low-level expression of catA and the catBCIJFD operon provided sufficient transcription for growth. The amplicons of four independently isolated mutants varied in size from approximately 30-100 kbp of the normally 3.8 Mbp chromosome. Mutants had approximately 10-20 copies of an amplicon in adjacent head-to-tail orientations. At the amplicon's chromosomal endpoint, an atypical junction juxtaposed normally distant DNA regions from opposite sides of the cat genes. The sequences of these junctions revealed the precise recombination sites underlying amplification. Additionally, amplicon stability was evaluated in the absence of selective pressure. The natural competence of Acinetobacter for transformation by linear DNA has allowed the development of a powerful new model system for investigating chromosomal rearrangements and for engineering DNA amplifications for wide-ranging applications. The frequent spontaneous amplification of these large chromosomal segments demonstrated the importance of supra-operonic gene clustering in the evolution of catabolic pathways.

Acinetobacter↗
PubMed1977

Genetic control of mitochondrial malate dehydrogenases: evidence for duplicated chromosome segments.

The genetic control of the major mitochondrial isoenzymes of malate dehydrogenase (L-malate:NAD+ oxidoreductase; EC 1.1.1.37) has been investigated in Zea mays. The mitochondrial isozymes are coded at four nuclear gene loci. Two of the loci (mdh1 and mdh2) are diallelic and tightly linked. The other two loci (mdh3 and mdh4) appear to have arisen by duplication of the chromosome segment carrying mdh1 and mdh2, but are not linked to them. The segregation of such a duplicate segment can explain anomalous backcross and F2 segregation ratios.

Alleles↗
PubMed1983

Gamma delta-mediated deletions of chromosomal segments on F-prime plasmids.

Deleted derivatives of F lac+ proC+ tsx+/- purE+ plasmids ORF203 and F13 were isolated and physically characterized. Among 31 deletions, 24 were adjacent to the gamma delta element on F, four were associated with IS2 or IS3 elements normally present on F, and three displayed additional DNA rearrangements. With the genetic selection employed, the deletion endpoints in the chromosomal segment could fall anywhere within a 210 kb (5 min) region between proC and lac. The distribution of endpoints in this region was not random: the endpoints primarily occurred in an extended region near purE, and a 50 kb segment between tsx and purE was devoid of deletion endpoints. Deletion termini for mutants obtained from F13, which contains an additional 48 kb-segment interposed between gamma delta and the target region on ORF203, displayed a distribution similar to that seen for ORF203. Among simple deletions, there was no marked tendency for the chromosomal deletion endpoints to fall at IS1, IS3, or IS5 elements normally present in this chromosomal region. Point mutations and mutations caused by gamma delta or IS transposition into lac appeared in a small proportion of all plasmids studied.

Chromosome Deletion↗
PubMed1993

A multi-marker model for detecting chromosomal segments displaying QTL activity.

A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F2 progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among QTLs). Simultaneous use of several methods, including this one, should lead to better efficiency in QTL detection.

Animals↗
PubMed2003

Haplotype sharing refines the location of an imprinted quantitative trait locus with major effect on muscle mass to a 250-kb chromosome segment containing the porcine IGF2 gene.

We herein describe the fine mapping of an imprinted QTL with major effect on muscle mass that was previously assigned to distal SSC2p in the pig. The proposed approach exploits linkage disequilibrium in combination with QTL genotyping by marker-assisted segregation analysis. By identifying a haplotype shared by all "Q" chromosomes, we map the QTL to an approximately 250-kb chromosome segment containing INS and IGF2 as the only known paternally expressed genes. This considerably reinforces the candidacy of these genes, justifying their detailed analysis.

Animals↗