Rearranged gene order between pig and human in a quantitative trait loci region on SSC3

A quantitative trait locus (QTL) for ovulation rate on chromosome 3 that peaks at 36 cM has been identified in a Meishan-White composite resource population with an additive effect of 2.2 corpora lutea. As part of an effort to identify the responsible gene(s), typing of additional genes on the INRA-University of Minnesota porcine radiation hybrid (IMpRH) map of SSC3 and comparative analysis of gene order was conducted. We placed 52 known genes and expressed sequence tags, two BAC-end sequences and one microsatellite (SB42) on a framework map that fills gaps on previous RH maps. Data were analysed for two-point and multipoint linkage with the IMpRH mapping tool and were submitted to the IMpRH database (http://imprh.toulouse.inra.fr/). Gene order was confirmed for 42 loci residing in the QTL region (spanning c. 17 Mb of human sequence) by using the high-resolution IMpRH2 panel. Carthagène (http://www.inra.fr/internet/departments/MIA/T/CarthaGene) was used to estimate multipoint marker distance and order using all public markers on SSC3 in the IMpRH database and those typed in this study. For the high-resolution map, only data for markers typed in both panels were used. Comparative analysis of human and porcine maps identified conservation of gene order for SSC3q and multiple blocks of conserved segments for SSC3p, which included six distinct segments of HSA7 and two segments of HSA16. The results of this study allow significant refinement of the SSC3p region that contains an ovulation rate QTL.     

A comparative genome approach to marker ordering

MOTIVATION: Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering. RESULTS: In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model. AVAILABILITY: The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.     

The chicken RH map: current state of progress and microchromosome mapping

The ChickRH6 radiation hybrid panel has been used to construct consensus chromosome radiation hybrid (RH) maps of the chicken genome. Markers genotyped were either from throughout the genome or targeted to specific chromosomes and a large proportion (one third) of data was the result of collaborative efforts. Altogether, 2,531 markers were genotyped, allowing the construction of RH reference maps for 20 chromosomes and linkage groups for four other chromosomes. Amongst the markers, 581 belong to the framework maps, while 1,721 are on the comprehensive maps. Around 800 markers still have to be assigned to linkage groups. Our attempt to assign the supercontigs from the chrun (virtual chromosome containing all the genome sequence that could not be attributed to a chromosome) as well as EST (Expressed Sequence Tag) contigs that do not have a BLAST hit in the genome assembly led to the construction of new maps for microchromosomes either absent or for which very little data is present in the genome assembly. RH data is presented through our ChickRH webserver (http://chickrh.toulouse.inra.fr/), which is a mapping tool as well as the official repository RH database for genotypes. It also displays the RH reference maps and comparison charts with the sequence thus highlighting the possible discrepancies. Future improvements of the RH maps include complete coverage of the sequence assigned to chromosomes, further mapping of the chrun and mapping of EST contigs absent from the assembly. This will help finish the mapping of the smallest gene-rich microchromosomes.     

Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome

Motivation: Quick and easy gene mapping by the use of a panelof cytogenetically characterized somatic cell hybrids is possible,even if some discordant experimental results arise. Results: An interactive program is proposed and is made availableon a WWW site to users of a somatic cell hybrid panel. Assignmentsto chromosomes and subchromosomal regions are based on likelihoodcalculations and Bayes' theorem, and a confidence level is provided.The method is illustrated in the case of the pig genome. Availability: The program can be accessed free of charge atURL http:/ /www. toulouse. inra.fr/lgc/lgc.html. Contact: E-mail: chevalet{at}toulouse.inra.fr     

VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data

MOTIVATION: Identifying differentially regulated genes in experiments comparing two experimental conditions is often a key step in the microarray data analysis process. Many different approaches and methodological developments have been put forward, yet the question remains open. RESULTS: Varmixt is a powerful and efficient novel methodology for this task. It is based on a flexible and realistic variance modelling strategy. It compares favourably with other popular techniques (standard t-test, SAM and Cyber-T). The relevance of the approach is demonstrated with real-world and simulated datasets. The analysis strategy was successfully applied to both a 'two-colour' cDNA microarray and an Affymetrix Genechip. Strong control of false positive and false negative rates is proven in large simulation studies. AVAILABILITY: The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html CONTACT: delmar@inapg.inra.fr SUPPLEMENTARY INFORMATION: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html.     

CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome

SUMMARY: CRH_Server is an on line Comparative and Radiation Hybrid mapping Server dedicated to canine genomics. CRH_Server allows users to compute their own RH data using the current canine RH map, and allows comparative dog/human mapping analyses. Finally, it suggests multiple options for storage and queries of the dog RH database. AVAILABILITY: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html. SUPPLEMENTARY INFORMATION: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html.     

An alternative to radiation hybrid mapping for large-scale genome analysis in barley

The presence of a monosomic gametocidal chromosome (GC) in a barley chromosome addition line of common wheat generates structural aberrations in the barley chromosome as well as in the wheat chromosomes of gametes lacking the GC. A collection of structurally aberrant barley chromosomes is analogous to a panel of radiation hybrid (RH) mapping and is valuable for high-throughput physical mapping. We developed 90 common wheat lines (GC lines) containing aberrant barley 7H chromosomes induced by a gametocidal chromosome, 2C. DNAs isolated from these GC lines provided a panel of 7H chromosomal fragments in a wheat genetic background, comparable with RH mapping panels in mammals. We used this 7H GC panel and the methodology for RH mapping to physically map PCR-based barley markers, SSRs and AFLPs, onto chromosome 7H, relying on polymorphism between the 7H chromosome and the wheat genome. We call this method GC mapping. This study describes a novel adaptation and combination of methods of inducing chromosomal rearrangements to produce physical maps of markers. The advantages of the presented method are similar to RH mapping in that non-polymorphic markers can be used and the mapping panels can be relatively easily obtained. In addition, mapping results are cumulative when using the same mapping set with new markers. The GC lines will be available from the National Bioresources Project-KOMUGI (). Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

A high-resolution radiation hybrid map of the proximal portion of mouse chromosome 5

Radiation hybrid (RH) mapping of the mouse genome provides a useful tool in the integration of existing genetic and physical maps, as well as in the ongoing effort to generate a dense map of expressed sequence tags. To facilitate functional analysis of mouse Chromosome 5, we have constructed a high-resolution RH map spanning 75 cM of the chromosome. During the course of these studies, we have developed RHBase, an RH data management program that provides data storage and an interface to several RH mapping programs and databases. We have typed 95 markers on the T31 RH panel and generated an integrated map, pooling data from several sources. The integrated RH map ranges from the most proximal marker, D5Mit331 (Chromosome Committee offset, 3 cM), to D5Mit326, 74.5 cM distal on our genetic map (Chromosome Committee offset, 80 cM), and consists of 138 markers, including 89 simple sequence length polymorphic markers, 11 sequence-tagged sites generated from BAC end sequence, and 38 gene loci, and represents average coverage of approximately one locus per 0.5 cM with some regions more densely mapped. In addition to the RH mapping of markers and genes previously localized on mouse Chromosome 5, this RH map places the alpha-4 GABA(A) receptor subunit gene (Gabra4) in the central portion of the chromosome, in the vicinity of the cluster of three other GABA(A) receptor subunit genes (Gabrg1-Gabra2-Gabrb1). Our mapping effort has also defined a new cluster of four genes in the semaphorin gene family (Sema3a, Sema3c, Sema3d, and Sema3e) and the Wolfram syndrome gene (Wfs1) in this region of the chromosome.     

Assignment of T cell receptor (TCR) alpha-chain gene (A), beta-chain gene (B), gamma-chain gene (G), and delta-chain gene (D) loci on swine chromosomes by in situ hybridization and radiation hybrid mapping

Using the cDNA sequence of porcine T-cell receptor (TCR) alpha-, beta-, gamma-, and delta-chain genes, we screened a porcine BAC library to isolate clones containing these genes. The isolated BAC clones were confirmed to carry these TCR genes by partial nucleotide sequencing. Among the clones obtained in the present screening, two clones carried both the TCR alpha-chain gene (TRA) and the TCR delta-chain gene (TRD) while one clone each carried only the sequence of either TRA or TRD. This observation demonstrated that TRA and TRD are localized in close proximity on a swine chromosome. Also two clones contained the sequence of the TCR beta-chain gene (TRB), and two clones contained the sequence of TCR gamma-chain gene (TRG). Fluorescence in situ hybridization using the above BAC clones as probes revealed that TRA and TRD, TRB, and TRG loci reside on swine chromosomes 7q15.3-->q21, 18q11.3-->q12, and 9q21-->q22, respectively. The chromosome positions of TRA and TRB are consistent with those determined by somatic cell hybrid analysis (Rettenberger et al., 1996). In addition, RH mapping of these genes was performed using the INRA-University of Minnesota RH panel DNA. The result confirmed the position of TRA and TRB reported earlier (http://imprh.toulouse.inra.fr/), and further demonstrated that TRG was located 11 cR away from genetic marker SW989 toward the marker S0019.     

The ProDom database of protein domain families.

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail (prodom@toulouse.inra.fr) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows for interactive analysis of protein homology relationships. Recent improvements to the server include: ProDom search by keyword; links to PROSITE and PDB entries; more sensitive ProDom similarity search with BLAST or WU-BLAST; alignments of query sequences with homologous ProDom domain families; and links to the SWISS-MODEL server (http: //www.expasy.ch/swissmod/SWISS-MODEL.html ) for homology based 3-D domain modelling where possible.     

SPiD: a subtilis protein interaction database.

MOTIVATION: Protein-protein interactions are a potential source of valuable clues in determining the functional role of as yet uncharacterized gene products in metabolic pathways. Graph-like structures emerging from the accumulation of interaction data make it difficult to maintain a consistent and global overview by hand. Bioinformatics tools are needed to perform this graph visualization while maintaining a link to the experimental data. RESULTS: "SPiD" is an online database for exploring networks of interacting proteins in Bacillus subtilis characterized by the two-hybrid system. Graphical displays of interaction networks are created dynamically as users interactively navigate through these networks. Third party applications can interface the database through a Common Object Request Broker Architecture (CORBA) tier. AVAILABILITY: SPiD is available through its web site at http://www-mig.versailles.inra.fr/bdsi/SPiD, and through an Interoperable Object Reference (IOR) and its associated Interface Definition Language (IDL). CONTACT: hoebeke@versailles.inra.fr     

Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design

Key message

We enhance power and accuracy of QTL mapping in multiple related families, by clustering the founders of the families on their local genomic similarity.

Abstract

MCQTL is a linkage mapping software application that allows the joint QTL mapping of multiple related families. In its current implementation, QTLs are modeled with one or two parameters for each parent that is a founder of the multi-cross design. The higher the number of parents, the higher the number of model parameters which can impact the power and the accuracy of the mapping. We propose to make use of the availability of denser and denser genotyping information on the founders to lessen the number of MCQTL parameters and thus boost the QTL discovery. We developed clusthaplo, an R package (http://cran.r-project.org/web/packages/clusthaplo/index.html), which aims to cluster haplotypes using a genomic similarity that reflects the probability of sharing the same ancestral allele. Computed in a sliding window along the genome and followed by a clustering method, the genomic similarity allows the local clustering of the parent haplotypes. Our assumption is that the haplotypes belonging to the same class transmit the same ancestral allele. So their putative QTL allelic effects can be modeled with the same parameter, leading to a parsimonious model, that is plugged in MCQTL. Intensive simulations using three maize data sets showed the significant gain in power and in accuracy of the QTL mapping with the ancestral allele model compared to the classical MCQTL model. MCQTL_LD (clusthaplo outputs plug in MCQTL) is a versatile and powerful tool for QTL mapping in multiple related families that makes use of linkage and linkage disequilibrium (web site http://carlit.toulouse.inra.fr/MCQTL/).     

Integration of the feline radiation hybrid and linkage maps

The recent development of genome mapping resources for the domestic cat provides a unique opportunity to study comparative medicine in this companion animal which can inform and benefit both veterinary and human biomedical concerns. We describe here the integration and order comparison of the feline radiation hybrid (RH) map with the feline interspecies backcross (ISB) genetic linkage map, constructed by a backcross of F₁ hybrids between domestic cat (Felis catus) and the Asian leopard cat (Prionailurus bengalensis). Of 253 microsatellite loci mapped in the ISB, 176 equivalently spaced markers were ordered among a framework of 424 Type I coding markers in the RH map. The integration of the RH and ISB maps resolves the orientation of multiple linkage groups and singleton loci from the ISB genetic map. This integrated map provides the foundation for gene mapping assessments in the domestic cat and in related species of the Felidae family. Received: 10 July 2000 / Accepted: 01 February 2001     

famoz: a software for parentage analysis using dominant,codominant and uniparentally inherited markers

famoz (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant and uniparentally inherited markers. It is written in C and TclTk languages and is available for Unix, Linux and Windows systems at http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html . Parameters and assumptions used in the calculations are few and simple. Exclusion and identity probabilities, log‐likelihoods of any genetic relationship, potential father and parent or parent pair, half‐ and full‐sibship are calculated based on real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations can be done to build statistical tests for parentage assignment.     

Recent improvements of the ProDom database of protein domain families.

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).     

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons

ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.     

AGScan: a pluggable microarray image quantification software based on the ImageJ library

Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997-2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms. AVAILABILITY: The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.     

Cross-referencing radiation hybrid data to the recombination map: lessons from mouse chromosome 18

We are building a framework map of known-order anchor markers between the mouse T31 radiation hybrid (RH) panel and the recombination map based on The Jackson Laboratory (TJL) interspecific backcross panels using the established genetic order to evaluate and strengthen the RH results. In making this map comparison, we have elucidated several problems inherent in RH mapping and minimized these by careful attention to data gathering and interpretation methods. We describe lessons and pitfalls of developing radiation hybrid maps, using the example of mouse Chromosome 18, for which we have built a framework map of microsatellite anchor loci spanning the entire chromosome at significant LOD with no gaps. Sixty-five D18Mit- simple sequence length polymorphism (SSLP) markers form a continuous linkage along the T31 RH Chromosome 18 (RH map length 1598 cR, genetic length 41 cM) with all LODs greater than 6. These markers are also placed on TJL interspecific backcrosses, and the order of the markers in the two systems is in complete agreement. We are continuing to cross-reference the RH data to TJL backcross data for the other mouse chromosomes to improve further the power of RH mapping and to integrate more precisely the extensive existing recombination mapping data for the mouse with the incoming radiation hybrid map data.     

Hydrogen-induced structural changes at the nickel site of the regulatory [NiFe] hydrogenase from Ralstonia eutropha detected by X-ray absorption spectroscopy

For the first time, the nickel site of the hydrogen sensor of Ralstonia eutropha, the regulatory [NiFe] hydrogenase (RH), was investigated by X-ray absorption spectroscopy (XAS) at the nickel K-edge. The oxidation state and the atomic structure of the Ni site were investigated in the RH in the absence (air-oxidized, RH(ox)) and presence of hydrogen (RH(+H2)). Incubation with hydrogen is found to cause remarkable changes in the spectroscopic properties. The Ni-C EPR signal, indicative of Ni(III), is detectable only in the RH(+H2) state. XANES and EXAFS spectra indicate a coordination of the Ni in the RH(ox) and RH(+H2) that pronouncedly differs from the one in standard [NiFe] hydrogenases. Also, the changes induced by exposure to H(2) are unique. A drastic modification in the XANES spectra and an upshift of the K-edge energy from 8339.8 (RH(ox)) to 8341.1 eV (RH(+H2)) is observed. The EXAFS spectra indicate a change in the Ni coordination in the RH upon exposure to H(2). One likely interpretation of the data is the detachment of one sulfur ligand in RH(+H2) and the binding of additional (O,N) or H ligands. The following Ni oxidation states and coordinations are proposed: five-coordinated Ni(II)(O,N)(2)S(3) for RH(ox) and six-coordinated Ni((III))(O,N)(3)X(1)S(2) [X being either an (O,N) or H ligand] for RH(+H2). Implications of the structural features of the Ni site of the RH in relation to its function, hydrogen sensing, are discussed.