scholarly journals A High-Density Integrated Genetic Linkage and Radiation Hybrid Map of the Laboratory Rat

1999 ◽  
Vol 9 (6) ◽  
pp. AP1-AP8 ◽  
Author(s):  
Robert G. Steen ◽  
Anne E. Kwitek-Black ◽  
Christopher Glenn ◽  
Jo Gullings-Handley ◽  
William Van Etten ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Web Sites ◽  
Radiation Hybrid ◽  
Genetic Linkage ◽  
Large Scale ◽  
Inbred Strains ◽  
Genetic Maps ◽  
Sequence Length ◽  
Link Type ◽  
Laboratory Rat

The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F2 intercrosses (SHRSP × BN and FHH × ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod ≥ 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). [Bihoreau et al. (1997); James and Tanigami, RHdb (http://www.ebi.ac.uk/RHdb/index.html); Wilder (http://www.nih.gov/niams/scientific/ratgbase); Serikawa et al. (1992); RATMAP server (http://ratmap.gen.gu.se)] RH maps (v. 2.0) have been posted on our web sites at http://goliath.ifrc.mcw.edu/LGR/index.htmlor http://curatools.curagen.com/ratmap. Both web sites provide an RH mapping server where investigators can localize their own RH vectors relative to this map. The raw data have been deposited in the RHdb database. Taken together, these maps provide the basic tools for rat genomics. The RH map provides the means to rapidly localize genetic markers, genes, and ESTs within the rat genome. These maps provide the basic tools for rat genomics. They will facilitate studies of multifactorial disease and functional genomics, allow construction of physical maps, and provide a scaffold for both directed and large-scale sequencing efforts and comparative genomics in this important experimental organism.

A cytogenetically based physical map of chromosome 1B in common wheat

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 548-554 ◽  
Author(s):  
R. S. Kota ◽  
K. S. Gill ◽  
B. S. Gill ◽  
T. R. Endo
Keyword(s):  
Genetic Markers ◽  
Common Wheat ◽  
Hexaploid Wheat ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Physical Map ◽  
Wheat Chromosome ◽  
Homozygous Deletion ◽  
Genetic Maps ◽  
Rflp Markers

We have constructed a cytogenetically based physical map of chromosome 1B in common wheat by utilizing a total of 18 homozygous deletion stocks. It was possible to divide chromosome 1B into 17 subregions. Nineteen genetic markers are physically mapped to nine subregions of chromosome 1B. Comparison of the cytological map of chromosome 1B with an RFLP-based genetic linkage map of Triticum tauschii revealed that the linear order of the genetic markers was maintained between chromosome 1B of hexaploid wheat and 1D of T. tauschii. Striking differences were observed between the physical and genetic maps in relation to the relative distances between the genetic markers. The genetic markers clustered in the middle of the genetic map were physically located in the distal regions of both arms of chromosome 1B. It is unclear whether the increased recombination in the distal regions of chromosome 1B is due to specific regions of increased recombination or a more broadly distributed increase in recombination in the distal regions of Triticeae chromosomes.Key words: common wheat, chromosome 1B, homozygous deletion lines, physical map, RFLP markers.

A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms

Development ◽  
1996 ◽  
Vol 123 (1) ◽  
pp. 451-460 ◽  
Author(s):  
E.W. Knapik ◽  
A. Goodman ◽  
O.S. Atkinson ◽  
C.T. Roberts ◽  
M. Shiozawa ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Markers ◽  
Genetic Linkage ◽  
Positional Cloning ◽  
Genetic Linkage Map ◽  
Physical Map ◽  
Sequence Length ◽  
Mapping Tool ◽  
Length Polymorphisms ◽  
Simple Sequence

The ultimate informativeness of the zebrafish mutations described in this issue will rest in part on the ability to clone these genes. However, the genetic infrastructure required for the positional cloning in zebrafish is still in its infancy. Here we report a reference cross panel of DNA, consisting of 520 F2 progeny (1040 meioses) that has been anchored to a zebrafish genetic linkage map by 102 simple sequence length polymorphisms. This reference cross DNA provides: (1) a panel of DNA from the cross that was used to construct the genetic linkage map, upon which polymorphic gene(s) and genetic markers can be mapped; (2) a fine order mapping tool, with a maximum resolution of 0.1 cM; and (3) a foundation for the development of a physical map (an ordered array of clones each containing a known portion of the genome). This reference cross DNA will serve as a resource enabling investigators to relate genes or genetic markers directly to a single genetic linkage map and avoid the problem of integrating different maps with different genetic markers, as must be currently done when using randomly amplified polymorphic DNA markers, or as has occurred with human genetic linkage maps.

Rat Phenome Project: The untapped potential of existing rat strains

2005 ◽  
Vol 98 (1) ◽  
pp. 371-379 ◽  
Author(s):  
Tomoji Mashimo ◽  
Birger Voigt ◽  
Takashi Kuramoto ◽  
Tadao Serikawa
Keyword(s):  
High Throughput Screening ◽  
Large Scale ◽  
Inbred Strains ◽  
Human Diseases ◽  
Renal Diseases ◽  
Sequence Length ◽  
Rat Strains ◽  
Phenotypic Data ◽  
Hematological Disorders ◽  
Specific Pathogen

The National Bio Resource Project for the Rat in Japan collects, preserves, and distributes rat strains. More than 250 inbred strains have been deposited thus far into the National Bio Resource Project for the Rat and are maintained as specific pathogen-free rats or cryopreserved embryos. We are now comprehensively characterizing deposited strains as part of the Rat Phenome Project to reevaluate their value as models of human diseases. Phenotypic data are being collected for 7 categories and 109 parameters: functional observational battery (neurobehavior), behavior studies, blood pressure, biochemical blood tests, hematology, urology, and anatomy. Furthermore, genotypes are being determined for 370 simple sequence-length polymorphism markers distributed through the whole rat genome. Here, we report these large-scale, high-throughput screening data that have already been collected for 54 rat strains. This comprehensive, original phenotypic data can be systematically viewed by “strain ranking” for each parameter. This allows investigators to explore the relationship between several rat strains, to identify new rat models, and to select the most suitable strains for specific experiments. The discovery of several potential models for human diseases, such as hypertension, hypotension, renal diseases, hyperlipemia, hematological disorders, and neurological disorders, illustrates the potential of many existing rat strains. All deposited strains and obtained data are freely available for any interested researcher worldwide at http://www.anim.med.kyoto-u.ac.jp/nbr .

INCONSISTENCIES BETWEEN MAPS OF HUMAN CHROMOSOME 22 CORRELATE WITH INCREASED FREQUENCY OF DISEASE-RELATED LOCI

2002 ◽  
Vol 10 (04) ◽  
pp. 303-317 ◽  
Author(s):  
CLAUDE CHELALA ◽  
MARIE-DOMINIQUE DEVIGNES ◽  
SANDRINE IMBEAUD ◽  
RIMA ZOOROB ◽  
CHARLES AUFFRAY ◽  
...  
Keyword(s):  
Human Chromosome ◽  
Radiation Hybrid ◽  
Initial Phase ◽  
Genetic Linkage ◽  
Significant Positive Correlation ◽  
Genetic Maps ◽  
Chromosome 22 ◽  
Positive Correlation ◽  
Disease Related Genes ◽  
Disease Associated Genes

The relationships between genetic or radiation hybrid (RH) and sequence maps of chromosome 22 have been reconsidered based on the sequence map. Integrated maps have been constructed by retaining only common markers between genetic or RH maps and the sequence map. Local inversions of markers have been detected. Ratios between either genetic or RH distances and sequence-based distances have been calculated for each map interval. Hot zones for recombination or radiation breakage have been delineated by merging together intervals displaying high distance ratios and located close to each other for sequence-constrained RH maps, and for female and male genetic maps. A statistically significant positive correlation was found between the distribution of disease-related genes and the hot zones for recombination or radiation breakage on both female genetic and Stanford-G3 RH maps. This observation indicates that investigation of chromosomal regions displaying inconsistencies between RH or genetic linkage and sequence-based maps can accelerate the initial phase of identification of disease-associated genes.

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

Mapping global water projects: improving access to donor investment information on the web

Water Policy ◽  
2003 ◽  
Vol 5 (3) ◽  
pp. 203-212
Author(s):  
J. Lisa Jorgensona
Keyword(s):  
Water Resources ◽  
Web Sites ◽  
Large Scale ◽  
Technical Assistance ◽  
Water Withdrawal ◽  
Small Scale ◽  
Water Projects ◽  
Essential Information ◽  
Water Project ◽  
The Web

This paper discusses a series of discusses how web sites now report international water project information, and maps the combined donor investment in more than 6000 water projects, active since 1995. The maps show donor investment:  • has addressed water scarcity,  • has improved access to improvised water resources,  • correlates with growth in GDP,  • appears to show a correlation with growth in net private capital flow,  • does NOT appear to correlate with growth in GNI. Evaluation indicates problems in the combined water project portfolios for major donor organizations: •difficulties in grouping projects over differing Sector classifications, food security, or agriculture/irrigation is the most difficult.  • inability to map donor projects at the country or river basin level because 60% of the donor projects include no location data (town, province, watershed) in the title or abstracts available on the web sites.  • no means to identify donor projects with utilization of water resources from training or technical assistance.  • no information of the source of water (river, aquifer, rainwater catchment).  • an identifiable quantity of water (withdrawal amounts, or increased water efficiency) is not provided.  • differentiation between large scale verses small scale projects. Recommendation: Major donors need to look at how the web harvests and combines their information, and look at ways to agree on a standard template for project titles to include more essential information. The Japanese (JICA) and the Asian Development Bank provide good models.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

scholarly journals Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Deborah O. Dele-Oni ◽  
Karen E. Christianson ◽  
Shawn B. Egri ◽  
Alvaro Sebastian Vaca Jacome ◽  
Katherine C. DeRuff ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Model ◽  
Cellular Responses ◽  
Proteomic Profiling ◽  
Reduced Representation ◽  
Link Type ◽  
Original Dataset ◽  
Quality Control Metrics ◽  
Biological Insight ◽  
Chromatin Profiling

AbstractWhile gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles of multiple perturbations across diverse cellular backgrounds in the reduced-representation phosphoproteome (P100) and chromatin space (Global Chromatin Profiling, GCP). Here, we expand our original dataset to include profiles from a new set of cardiotoxic compounds and from astrocytes, an additional neural cell model, totaling 5300 proteomic signatures. We describe filtering criteria and quality control metrics used to assess and validate the technical quality and reproducibility of our data. To demonstrate the power of the library, we present two case studies where data is queried using the concept of “connectivity” to obtain biological insight. All data presented in this study have been deposited to the ProteomeXchange Consortium with identifiers PXD017458 (P100) and PXD017459 (GCP) and can be queried at https://clue.io/proteomics.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals Large-Scale Adaptive Hitchhiking Upon High Recombination inDrosophila simulans

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 895-900 ◽  
Author(s):  
Humberto Quesada ◽  
Ursula E M Ramírez ◽  
Julio Rozas ◽  
Montserrat Aguadé
Keyword(s):  
Genetic Linkage ◽  
Large Scale ◽  
Intermediate Frequency ◽  
Core Region ◽  
Adaptive Mutation ◽  
Nucleotide Variation ◽  
Extended Haplotype ◽  
Major Haplotype ◽  
Pattern Of Variation

AbstractNatural selection is expected to leave a characteristic footprint on neighboring nucleotide variation through the effects of genetic linkage. The size of the region affected is proportional to the strength of selection and greatly reduced with the recombinational distance from the selected site. Thus, the genomic footprint of selection is generally believed to be restricted to a small DNA stretch in normal and highly recombining regions. Here, we study the effect of selection on linked polymorphism (hitchhiking effect) by surveying nucleotide variation across a highly recombining ∼88-kb genomic fragment in an African population of Drosophila simulans. We find a core region of up to 38 kb with a major haplotype at intermediate frequency. The extended haplotype structure that gradually vanishes until disappearing is unusual for a highly recombining region. Both the presence in the structured genomic domain of a single major haplotype depleted of variability and the detected spatial pattern of variation along the ∼88-kb fragment are incompatible with neutral predictions in a panmictic population. A major role of demographic effects could also be discarded. The observed pattern of variation clearly provides evidence that directional selection has acted recently on this region, sweeping out variation around a strongly adaptive mutation. Our findings suggest a major role of positive selection in shaping DNA variability even in highly recombining regions.

Sign in / Sign up

Export Citation Format

Share Document