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PubMed1996

The dysmorphic human-mouse homology database (DHMHD): an interactive World-Wide Web resource for gene mapping.

Genetic mapping and the examination of "candidate genes" for isolating loci associated with clinical syndromes can be greatly accelerated if there is information about where in the genome a particular locus might be situated. Such clues can come from homology to mouse mutants that have been mapped and knowledge of homology between mouse and human chromosomal segments. Further clues can come from chromosome aberrations giving a similar phenotype. However, these clues are often scattered widely in published reports, and even if they are collected together in catalogues or databases there is no rapid way of moving from one data type to another. The Dysmorphic Human and Mouse Homology Database (DHMHD) is designed to ease this data transition. DHMHD comprises detailed information from four separate sources and enables cross referencing through phenotypic and chromosome homology. The DHMHD system is a prototype which is now available online through the World-Wide Web.

Animals↗
PubMed2004

Ethnicity and human genetic linkage maps.

Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined--for the first time, to our knowledge--racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, and Blood Institute-funded Family Blood Pressure Program, the largest sample used for map construction to date. Although the maps for the different groups are generally similar, we did find regional and genomewide differences across ethnic groups, including a longer genomewide map for African Americans than for other populations. Some of this variation was explained by genotyping artifacts--namely, null alleles (i.e., alleles with null phenotypes) at a number of loci--and by ethnic differences in null-allele frequencies. In particular, null alleles appear to be the likely explanation for the excess map length in African Americans. We also found that nonrandom missing data biases map results. However, we found regions on chromosome 8p and telomeric segments with significant ethnic differences and a suggestive interval on chromosome 12q that were not due to genotype artifacts. The difference on chromosome 8p is likely due to a polymorphic inversion in the region. The results of our investigation have implications for inferences of possible genetic influences on human recombination as well as for future linkage studies, especially those involving populations of nonwhite ethnicity.

Black or African American↗
PubMed2025

High-resolution, genotype-free mapping of genetic variation with CRI-SPA-Map.

Genetic variation within species shapes phenotypes, but identifying the specific genes and variants that cause phenotypic differences is costly and challenging. Here, we introduce CRI-SPA-Map, a genetic mapping strategy combining CRISPR-Cas9 genome engineering, selective ploidy ablation (SPA), and high-throughput phenotyping for precise genetic mapping with or without genotyping in the yeast Saccharomyces cerevisiae. In CRI-SPA-Map, a donor strain carrying SPA machinery is mated to a genetically different recipient strain harboring a genome-integrated selectable cassette. In the resulting diploid, CRISPR-Cas9 cuts the cassette for replacement with DNA from the homologous donor chromosome. Donor chromosomes are then removed using SPA to yield haploid recombinant strains. To establish CRI-SPA-Map, we mated a W303 SPA strain to 92 strains from the BY4742 yeast knockout collection that carry gene deletion cassettes on the left arm of chromosome XIV and created 1,451 recombinant isolates. Whole-genome sequencing verified that deletion cassette replacement introduced short donor DNA tracts of variable length, resulting in a finely recombined mapping population. Using only the known location of the gene deletions, which marks where donor DNA is introduced, we identified a 6.5 kb-region shaping yeast growth. Further dissection of this region pinpointed two causal variants in two genes, MKT1 and SAL1. Engineering these variants alone and in combination revealed gene-by-environment interactions at both genes, as well as epistatic interactions between them that were in turn dependent on the environment. CRI-SPA-Map is a cost-effective strategy for creating high-resolution recombinant panels of yeast strains for identifying the genetic basis of phenotypic variation.

Journal Article↗
PubMed2002

Mapping unexplored genomes: a genetic linkage map of the Hawaiian cricket Laupala.

As with many organisms of evolutionary interest, the Hawaiian cricket Laupala genome is not well characterized genetically. Mapping such an unexplored genome therefore presents challenges not often faced in model genetic organisms and not well covered in the literature. We discuss the evolutionary merits of Laupala as a model for speciation studies involving prezygotic change, our choice of marker system for detecting genetic variation, and the initial genetic expectations pertaining to the construction of any unknown genomic map in general and to the Laupala linkage map construction in particular. We used the technique of amplified fragment length polymorphism (AFLP) to develop a linkage map of Laupala. We utilized both EcoRI/MseI- and EcoRI/PstI-digested genomic DNA to generate AFLP bands and identified 309 markers that segregated among F(2) interspecific hybrid individuals. The map is composed of 231 markers distributed over 11 and 7 species-specific autosomal groups together with a number of putative X chromosome linkage groups. The integration of codominant markers enabled the identification of five homologous linkage groups corresponding to five of the seven autosomal chromosomal pairs found in Laupala.

Animals↗
PubMed2002

Comparison between Poncirus and Citrus genetic linkage maps.

Five genetic linkage maps were constructed for the parents of three progenies: Citrus aurantium (A) x Poncirus trifoliata var. Flying Dragon (Pa), C. volkameriana (V) x P. trifoliata var. Rubidoux (Pv) and a self-pollination of P. trifoliata var. Flying Dragon (Pp). The number of polymorphic markers assayed ranged from 48 for Pa to 120 for A according to the heterozygosity of each parental. As our focus was on genome comparison, most of the markers were newly generated simple sequence repeats. Inter-retrotransposon amplified polymorphisms based on four retrotransposon sequences isolated from Citrus spp were also used to saturate the maps. These polymorphisms were much more frequent in A (53) than in Pa (15) and randomly distributed throughout both genomes. Since comparative genomics and quantitative trait locus analysis applicability depends on the reliability of marker ordering, the causes of variation in marker order were investigated. Around 25% of the markers showed gametal segregation distortions. Segregation distortions were also observed at the zygotic level towards a reduction in the observed frequency of homozygotes from that expected in linkage groups 5 and 7. The presence of balanced lethal factors or gametal incompatibility genes in those genomic regions would explain a zygotic advantage of heterozygotes at these specific regions. Four differences in genomic organization were observed; three are putative translocations and affect homeologous linkage groups 3, 7 and 11, where highly distorted markers are found. Other causes of variation in marker order are also discussed: the introduction of new markers in the map, lowering the LOD score and the mapping software. These results represent the first comparative mapping analysis among Citrus and Poncirus species.

Chromosome Mapping↗
PubMed2003

[MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

English Abstract↗
PubMed2003

Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach.

Comparative genetic mapping in interspecific pedigrees presents a powerful approach to study genetic differentiation, genome evolution and reproductive isolation in diverging species. We used this approach for genetic analysis of an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and Eucalyptus globulus (Labill.). This wide interspecific cross is characterized by hybrid inviability and hybrid abnormality. Approximately 20% of loci in the genome of the F(1) hybrid are expected to be hemizygous due to a difference in genome size between E. grandis (640 Mbp) and E. globulus (530 Mbp). We investigated the extent of colinearity between the two genomes and the distribution of hemizygous loci in the F(1) hybrid using high-throughput, semi-automated AFLP marker analysis. Two pseudo-backcross families (backcrosses of an F(1) individual to non-parental individuals of the parental species) were each genotyped with more than 800 AFLP markers. This allowed construction of de novo comparative genetic linkage maps of the F(1) hybrid and the two backcross parents. All shared AFLP marker loci in the three single-tree parental maps were found to be colinear and little evidence was found for gross chromosomal rearrangements. Our results suggest that hemizygous AFLP loci are dispersed throughout the E. grandis chromosomes of the F(1) hybrid.

Chromosome Mapping↗
PubMed2002

A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci.

A genetic map for the model legume Lotus japonicus has been developed. The F(2) mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa et al. 2002(this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.

Chromosome Mapping↗
PubMed1991

Progress towards completing the human linkage map.

Genetic linkage maps order polymorphic loci (markers) along a chromosome and provide a measure of distance that is an inherently statistical measure of the frequency of meiotic recombination and has no simple relationship to DNA length in Mb. Few accurate and dense maps now exist. Maps with markers spaced every 2 cM providing accurate estimates of distance should be available in the next few years, however.

Alleles↗
PubMed1991

A genetic linkage map of human chromosome 5 with 60 RFLP loci.

A genetic map of human chromosome 5 that contains 60 restriction fragment length polymorphism (RFLP) loci in one linkage group has been constructed. Segregation data using these markers and 40 large multigenerational families supplied by the Centre d'Etude du Polymorphisme Humain have been collected. Linkage analyses were performed with the program package CRI-MAP; using odds greater than 1000:1, 30 RFLP loci could be placed on the map. This genetic map spans 289 cM sex-equal, 353 cM in females, and 244 cM in males. While the relative rate of recombination for female meioses is nearly twice that of males over much of the chromosome, several instances of statistically significant excess male recombination were observed. The order of probes on the genetic map has been confirmed by their physical order as determined by somatic cell hybrid lines containing deletions of normal chromosome 5. There is concordance between the physical positions of markers and their genetic positions. Our most distal probes on the genetic map are cytologically localized to the most distal portions of the chromosome. This suggests that our genetic map spans most of chromosome 5.

Blotting, Southern↗
PubMed2006

Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map.

An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).

Chromosome Mapping↗
PubMed1997

Murine albino-deletion complex: high-resolution microsatellite map and genetically anchored YAC framework map.

The murine albino-deletion complex developed as part of the Oak Ridge specific-locus test covers 6-11 cM of chromosome 7. This complex has proven to be a valuable resource for localizing traits to a small target region for positional cloning. In this study, we mapped the endpoints of deletions in this complex using all of the available Mit simple-sequence length polymorphism (SSLP) markers. Concurrently, this mapping has determined the map order of nearly all of the SSLP markers, most of which were previously unresolved. The SSLP-based deletion map was confirmed and genetic distances were determined using the European Collaborative Interspecific Backcross panel of nearly a thousand mice. The average SSLP marker resolution is 0.3-0.4 cM, comparable to the cloning capacity of yeast artificial chromosomes (YACs). The SSLP markers were then used to construct a genetically anchored YAC framework map that further confirms the deletion map. We find that the largest deleted region distal to Tyr is about two to three times larger than the largest proximal deletion region, and the original C3H/101 regions flanking the deletions (moved to an St2A cch/cch background) are smaller than anticipated, which we suggest may result from increased recombination rates immediately flanking the deleted regions.

Animals↗
PubMed1994

Mapping factors controlling genetic expression.

A methodology relying on two-dimensional (2D) electrophoresis and genetic mapping is proposed to dissect the genetic architecture of the quantitative control of gene products. Seventy-two anonymous polypeptide spots resolved using silver-stained high-resolution 2D gels of maize coleoptile extracts were automatically quantified for every individual of an F2 progeny between distant lines. A complete genetic linkage map, including 70 RFLP and 39 protein markers, allowed us to map Mendelian factors underlying quantitative variation for 42 polypeptides. One to 5 unlinked chromosomal regions were found to affect single polypeptides, 27% of which resulted in more than a doubling of the polypeptide spot intensity. Dominance was observed for half of the factors, with high amount dominant over low amount in most cases, which is consistent with the observation that the relative abundance of proteins in F1 hybrids is in average deviated to the high parental values. Epistatic interactions were shown to be involved in the control of 14% of the proteins. These features contrast sharply with the observations from 20 agromorphological traits measured in the same progeny, where limited substitution and dominance effects, and no epistatic interaction, were found.

Alleles↗
PubMed1987

Isolation and characterization of Salmonella typhimurium glyoxylate shunt mutants.

Growth of Salmonella typhimurium on acetate as a sole carbon source requires expression of the glyoxylate shunt; however, the genes for the glyoxylate shunt enzymes have not been previously identified in S. typhimurium. In this study, we isolated transposon insertions in the genes for the two unique enzymes of this pathway, aceA (isocitrate lyase) and aceB (malate synthase). The aceA and aceB genes were located at 89.5 min on the S. typhimurium genetic map. Genetic linkage to nearby loci indicated that the relative gene order is purDJ metA aceB aceA. Transposon insertions in aceB were polar on aceA, suggesting that the genes form an operon transcribed from aceB to aceA. Transcriptional regulation of the aceBA operon was studied by constructing mini-Mu d(lac Kan) operon fusions. Analysis of these fusions indicated that expression of the aceBA operon is regulated at the level of transcription; the aceBA genes were induced when acetate was present and repressing carbon sources were absent. Although glucose represses expression of the aceBA operon, repression does not seem to be mediated solely by cyclic AMP-cyclic AMP receptor protein complex. Mutants with altered regulation of the aceBA operon were isolated.

Acetates↗
PubMed1997

Use of microgenomic technology for analysis of alterations in DNA copy number and gene expression in malignant melanoma.

Chromosome abnormalities in human malignancies have identified the genomic location of several important growth-regulatory genes, including cellular oncogenes and tumour suppressor genes. Melanomas are characterized by recurring chromosome alterations, and it is important to identify those genes whose altered expression may be causally related to melanocytic transformation. This short report presents an overview of strategies used which combine the materials and technologies of the Human Genome Project with clinically directed studies of melanoma biology. The Human Genome Project combines various technologies, including cytogenetic, physical mapping, genetic mapping and DNA sequencing, in order to identify all of the human genes, but especially the 4000 estimated to contribute to human disease. This report focuses first on advances in genome technology that provide information on chromosome rearrangements and DNA copy number changes. This includes a discussion of chromosome microdissection as well as the microexcision of tissue specimens to gain insights into chromosome regions altered in association with melanocyte transformation. Next, there is a brief discussion of the generation and characterization of subtracted cDNA sublibraries which allow the identification of genes uniquely expressed in association with the transformed phenotype of human melanoma cells. Finally, we briefly discuss the feasibility of using a recently developed system for parallel examination of multiple genes based upon robotic printing of cDNAs on glass slides, and simultaneous two-colour fluorescence hybridization to study the expression patterns of cDNAs for their association with melanoma tumour suppression. The combination of these varied molecular technologies may provide insights into previously unrecognized genes involved causally in the pathobiology of this important neoplasm, and may provide new targets for clinical intervention.

Chromosome Mapping↗
PubMed1994

A PCR-based genetic linkage map of human chromosome 16.

A high-resolution cytogenetic-based physical map and a genetic linkage map of human chromosome 16 have been developed based on 79 PCR-typable genetic markers and 2 Southern-based RFLP markers. The PCR-based markers were previously characterized polymorphic (AC)n repeats. Two approaches have led to the characterization of 47 highly informative genetic markers spread along chromosome 16, some of which are closely linked to disease loci. In addition, 22 markers (D16S401-423) previously genetically mapped were also physically mapped. Ten markers characterized by other laboratories were physically mapped and genotyped on the CEPH families. These 32 markers were incorporated into the PCR-based map. Seventy-two markers have heterozygosities > 0.50 and 51 of these markers > 0.70. By multipoint linkage analysis a framework genetic map and a comprehensive genetic map were constructed. The length of the sex-averaged framework genetic map is 152.1 cM. The average distance and the median distance between markers on this map are 3.2 and 2.7 cM, respectively, and the largest gap is 15.9 cM. These maps were anchored to the high-resolution cytogenetic map (on average 1.5 Mb per interval). Together these integrated genetic and physical maps of human chromosome 16 provide the basis for the localization and ultimately the isolation of disease genes that map to this chromosome.

Animals↗
PubMed1993

Localization of seed protein genes on flow-sorted field bean chromosomes.

Chromosomes from reconstructed field bean (Vicia faba L.) karyotypes were flow-sorted and the DNA was used for the physical localization of seed storage and nonstorage (USP) protein genes using PCR with sequence specific primers. The data were confirmed and refined by using DNA of microisolated chromosomes of other karyotypes as the target for PCR. The specificity of the PCR products was proved by restrictase digestion into fragments of predicted length or by reamplification using 'nested' primers. The genes are located within defined regions of chromosome I (USP = unknown seed protein genes), II (vicilin genes, legumin B3 genes), III (legumin B4 genes), IV (pseudogenes psi 1) and V (legumin A genes and pseudogenes psi 1). Except for the pseudogene derived from the sequence of legumin B4 gene, all members of each gene family are located in one chromosome region exclusively. This approach proved to be useful for localizing genes that cannot be mapped genetically (due to the lack of allelic variants) and might be applied to integrate physical and genetic maps.

Base Sequence↗
PubMed1983

Marker rescue from bleomycin-treated Chlamydomonas reinhardi.

A new method has been developed for gene transfer in eukaryotic cells. Chlamydomonas reinhardi, a unicellular eukaryotic alga, was treated with a lethal dose of bleomycin, an agent that induces chromosome breakage. Bleomycin-treated cells were mated with untreated cells, and the mixture was plated onto selective agar medium. The progeny that arose contained the genetic markers from the untreated parent plus a subset of the genetic markers from the bleomycin-treated parent. Those markers derived from the untreated parent were stable, whereas those recovered from the bleomycin-treated parent were often unstable. Markers closely linked in the bleomycin-treated parent were usually rescued or lost together, whereas distantly linked or unlinked markers were rescued or lost independently. These results suggest that bleomycin treatment of C. reinhardi leads to the formation of chromosome fragments, and fusion of bleomycin-treated cells to untreated cells results in the rescue of some of these fragments. This procedure provides a new means of gene transfer that may be useful for genetic mapping, genetic engineering and for the study of genetic organization.

Bleomycin↗