Comparative Mapping Data Research Articles

Comparative Genomics: Mammalian Radiations -- Genome Maps 10

![Figure][1] Traces of evolutionary history appear in functional morphology and DNA sequences of living and extinct species. These remnants of the past can lead to insights into the relationships among extant groups of animals, the forces driving evolution, and the utility of animal models for studying human disease. We present below one evolutionary interpretation of the still-disputed hierarchy of surviving placental mammalian orders (excluding monotremes and marsupials), a synthesis of accumulated molecular and morphological inferences. The time scale is derived largely from molecular data; indicated fossil remains are much younger, raising controversies around the precise age of mammal ancestors. The tips of the phylogenetic tree depict genomes for 21 representative species from 11 orders, which are labeled on the vertical lines. These examples show genome-wide homology alignments assessed by comparative gene mapping or direct visualization of chromosome painting, in which fluorescently labeled, individual chromosomes are hybridized to chromosomes from distantly related species. Species were selected to maximize the number of orders represented and to illustrate patterns of genome conservation. The 24 human chromosomes are distinguished by 24 colors, and regions of human chromosome homology in other species are indicated by color and human chromosome number (for example, cat chromosome A1 contains gene stretches homologous to human chromosomes 5 and 13). Selected gene homologs in each species represent a subset of extensive comparative gene mapping data; thus genes listed may not reflect the extreme borders of the conserved segments. Gene orders have been determined in human, cat, pig, sheep, rat, mouse, and zebrafish; in other species the genes are listed in the order in which they appear in humans. The zebrafish map, including 25 linkage groups not yet assigned to the 25 chromosomes, is presented to illustrate the array of gene segments conserved for 450 million years. Further information and discussion of dissenting views of mammalian evolution can be found in this issue of Science and the associated web site at ![Figure][1] CREDITS Science Coordinators: Barbara R. Jasny and Pamela J. Hines Authors: Phylogenetic tree Stephen J. O'Brien, National Cancer Institute, Frederick, MD, USA; John F. Eisenberg, University of Florida, Gainesville, FL, USA; Michael Miyamoto, University of Florida, Gainesville, FL, USA; S. Blair Hedges, Pennsylvania State University, University Park, PA, USA; Sudhir Kumar, Arizona State University, Tempe, AZ, USA; Don E. Wilson, Smithsonian Institution, Washington, DC, USA. Genomic maps Stephen J. O'Brien, Marilyn Menotti-Raymond, William J. Murphy, William G. Nash, Leslie A. Lyons, Joan C. Menninger, Roscoe Stanyon, Johannes Wienberg, Neal G. Copeland, Nancy A. Jenkins, National Cancer Institute, Frederick, MD, USA; Joel Gellin, Martine Yerle, Institut National de la Recherche Agronomique, Castanet-Tolosan, France; Leif Andersson, Swedish University of Agricultural Sciences, Uppsala, Sweden; James Womack, Texas A & M University, College Station, TX, USA; Thomas Broad, AgResearch, Invermay, Mosgiel, New Zealand; John Postlethwait, University of Oregon, Eugene, OR, USA; Oleg Serov, Institute of Cytology and Genetics, Siberian Branch of the Academy of Sciences of Russia, Novosibirsk, Russia; Ernie Bailey, University of Kentucky, Lexington, KY, USA; Michael R. James, Wellcome Trust Centre for Human Genetics, Headington, UK; Takeshi K. Watanabe, Otsuka GEN Research Institute, Tokushima, Japan; Matthew J. Wakefield, Jennifer Marshall Graves, La Trobe University, Melbourne, Australia. Design and Art Direction: C. Faber Smith Graphics: Nathalie Cary Illustrations: Katharine Sutliff Production Assistance: Holly Bishop, Leslie Blizard, Inja Lin, Darcel Pugh Proofreading: Harry Jach [1]: pending:yes

Close association between sequence polymorphism in the KIT gene and the roan coat color in horses.

The roan coat color in horses is controlled by a dominant allele that is lethal in the homozygous condition. Phenotypic similarities to some pigmentation disorders in human and mouse, combined with comparative mapping data, identified KIT, encoding the mast cell growth factor receptor, as a major candidate gene for the roan locus (Rn). Rn has previously been mapped to equine linkage group (LG) II. In this study, LGII was expanded with KIT and PDGFRA (platelet-derived growth factor receptor alpha) by use of RFLP and linkage analysis. Moreover, highly significant linkage disequilibrium between Rn and a KIT TaqI RFLP, representing a synonymous substitution in exon 19, was revealed. There was a strong KIT-Rn association in most breeds. Almost the complete KIT-encoding sequence was determined by sequence analysis of RT-PCR products. Comparison of horse KIT cDNA sequences, representing three different alleles (two different rn and one Rn), revealed five sequence polymorphisms and several mRNA splice variants, but none of these proved to be specifically associated with Rn. An insertion of a partial (79 bp) LINE1-element between exons 1 and 2, leading to a frameshift, represented about 30% of KIT transcripts in the Belgian roan horse used for the sequence analysis. However, an association between this L1 splice insertion and the roan phenotype was not verified when testing additional unrelated roan and non-roan horses from different breeds. The study strengthens the hypothesis that the roan coat color is controlled by KIT, but further analyses are needed to reveal the causative mutation(s).

A successful strategy for comparative mapping with human ESTs: 65 new regional assignments in the pig.

Large-scale sequencing of cDNAs from numerous tissues is currently being performed within the framework of the Human Genome Project. These expressed sequence tags (ESTs) are then mapped on a radiation hybrid panel to produce a high-resolution map of human genes. In this report, we estimate the efficiency of mapping these ESTs in the pig. A total of 344 human ESTs from Généthon were selected for amplification in other species by Zoo-PCR: 186 of these could be reproducibly amplified by use of pig DNA and the corresponding human primer pairs. One-hundred seven of these were tested on a porcine-rodent somatic cell hybrid panel, permitting regional localizations of 65 ESTs with agarose or single-strand conformation polymorphism analysis gels. The corresponding pig PCR products were sequenced: 60 ESTs matched significantly with the expected human sequences. Fifty-one of these localizations in the pig are in agreement with the comparative mapping data between humans and pigs based on heterologous chromosome painting. Seven ESTs that were localized in an unexpected region may indicate new chromosomal correspondences. This work significantly increases the number of genes mapped on the pig genome and demonstrates that this approach can be successfully applied to improve the gene density of mammalian genomic maps in chromosomal regions of interest, such as those in which QTL (Quantative Trait Loci) have been identified.

Comparative Mapping of Mouse and Rat Chromosomes by Fluorescencein SituHybridization

Comparative fluorescencein situhybridization mapping using DNA libraries from flow-sorted mouse chromosomes and region-specific mouse BAC clones on rat chromosomes reveals chromosomal homologies between mouse (Mus musculus,MMU) and rat (Rattus norvegicus,RNO). Each of the MMU 2, 3, 4, 6, 7, 9, 12, 14, 15, 16, 18, 19, and X chromosomes paints only a single rat chromosome or chromosome segment and, thus, the chromosomes are largely conserved between the two species. In contrast, the painting probes for MMU chromosomes 1, 5, 8, 10, 11, 13, and 17 produce split hybridization signals in the rat, disclosing evolutionary chromosome rearrangements. Comparative mapping data delineate several large linkage groups on RNO 1, 2, 4, 7, and 14 that are conserved in human but diverged in the mouse. On the other hand, there are linkage groups in the mouse, i.e., on MMU 1, 8, 10, and 11, that are disrupted in both rat and human. In addition, we have hybridized probes forNap2, p57, Igf2, H19,andSh3d2cfrom MMU 7 to RNO 1q and found the orientation of the imprinting gene cluster andSh3d2cto be the same in mouse and rat. Hybridization of rat genomic DNA shows blocks of (rat-specific) repetitive sequences in the pericentromeric region of RNO chromosomes 3–5, 7–13, and 20; on the short arms of RNO chromosomes 3, 12, and 13; and on the entire Y chromosome.

Identification of two paralogous regions mapping to the short and long arms of human chromosome 2 comprising LIS1 pseudogenes

Reiner et al. (1995b) reported on the existence of a gene with a coding region virtually identical to LIS1, the gene responsible for Miller-Dieker lissencephaly. This gene, LIS2, was mapped to chromosome 2p11.2, and a related pseudogene, LIS2P, was mapped to 2q13→q14. By sequencing genomic clones that were mapped by means of 2p and 2q-only hybrids, we now demonstrate the existence of two LIS1 processed pseudogenes mapping to 2p11.2 and 2q13 (PAFAH1P1 and PAFAH1P2, respectively). The two sequences appear to lie within larger paralogous regions and share a 98.6% degree of identity. Comparative mapping data by cytogenetic analysis on great apes indicate that the duplication of the genomic region comprising the LIS1 pseudogenes occurred in humans. We also demonstrate that the cDNA sequence shown as part of the LIS2 gene and marking its chromosome 2 specificity belongs to the 3′ untranslated region of a different gene (C1orf6) that we mapped to 1q21 by FISH analysis.

Reciprocal chromosome painting shows that genomic rearrangement between rat and mouse proceeds ten times faster than between humans and cats

Reciprocal chromosome painting between mouse and rat using complete chromosome probe sets of both species permitted us to assign the chromosomal homology between these rodents. The comparative gene mapping data and chromosome painting have a better than 90% correspondence. The reciprocal painting results graphically show that mouse and rat have strikingly different karyotypes. At least 14 translocations have occurred in the 10–20 million years of evolution that separates these two species. The evolutionary rate of chromosome translocations between these two rodents appears to be up to 10 times greater than that found between humans and cats, or between humans and chimpanzees, where over the last 5–6 million years just one translocation has occurred. Outgroup comparison shows that the mouse genome has incorporated at least three times the amount of interchromosomal rearrangements compared to the rat genome. The utility of chromosome painting was also illustrated by the assignment of two new chromosome homologies between rat and mouse unsuspected by gene mapping: between mouse 11 and rat 20 and between mouse 17 and rat 6. We conclude that reciprocal chromosome painting is a powerful method, which can be used with confidence to chart the genome and predict the chromosome location of genes. Reciprocal painting combined with gene mapping data will allow the construction of large-scale comparative chromosome maps between placental mammals and perhaps other animals.

The adipocyte fatty acid-binding protein locus: characterization and association with intramuscular fat content in pigs.

The porcine A-FABP gene (FABP4) was isolated and sequenced to study the role of A-FABP in the differentiation of intramuscular fat (IMF) accretion in pigs. The coding sequence of the porcine A-FABP gene is highly conserved across human, mouse, and rat. Moreover, all the functionally important amino acids are conserved. This high similarity extends into the first 270 bp of the 5' upstream region. Within this region, a 56-bp nucleotide sequence was completely identical with the corresponding sequence in the mouse A-FABP gene, which contains the transcription factor binding sites for C/EBP and AP-1, and is implicated in the differentiation-dependent regulation of A-FABP. The A-FABP gene was assigned to porcine Chromosome (Chr) 4 by a porcine sequence-specific PCR on a cell hybrid panel, fully consistent with comparative mapping data with human and mouse. In the first intron of the porcine A-FABP gene, a microsatellite sequence was detected that was polymorphic for all six pig breeds tested. This genetic variation within the A-FABP gene was associated with differences in IMF content and possibly growth in a Duroc population, whereas no effect on backfat thickness and drip loss of the meat were detected. A considerable and significant contrast of approximately 1% IMF was observed between certain genotype classes. We conclude that the A-FABP locus is involved in the regulation of intramuscular fat accretion in Duroc pigs.

Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library.

In total, 82 ESTs were generated from 51 unique clones randomly selected from a cattle ovary cDNA library. Among these clones, 22 (42.1%) had 5' and/or 3' ends that matched with known human or other mammalian coding sequences, 18 (35.3%) matched human or other ESTs, and 11 (21.6%) represented novel transcripts with no significant match to any sequence in the databases. The relatively high frequency of ESTs with no matches in GenBank or dbEST indicates that bovine ovary may be a source of novel candidate genes for loci affecting cattle reproduction traits. Primers were designed for 11 ESTs that had human orthologs in GenBank. These ESTs were mapped to 10 bovine autosomes by PCR screening of a somatic cell hybrid panel. Among these 11 ESTs, 4 corresponded to genes previously mapped in humans and had chromosome assignments on the bovine map that were consistent with available comparative mapping data. Although the human orthologs of the remaining 7 mapped bovine ESTs have not been mapped, the human map location could be predicted on the basis of existing comparative mapping data. Because of the general utility of our approach for comparative genome analysis, we have termed it comparative mapping by annotation and sequence similarity (COMPASS). With the cost of large-scale EST sequencing becoming more affordable, and the rapid expansion of DNA databases, it is likely that COMPASS will be a preferred strategy for high throughput comparative mapping.

Internet Comparative Mapping Resources.

Databases accessible over the Internet have become an essential tool in the study of genome organization. Recent growth in the field of genomics has resulted in the study of an increasing number of organisms in addition to a flood of data from the more intensively studied organisms. Although this rapid growth in the quantity of data has greatly increased the likelihood that data useful to an individual researcher will be available, the job of finding that data in the traditional journal publication system is significantly more difficult. To increase the accessibility of these data, several databases have been established and made available via the Internet. This availability allows the rapid access of current, in-depth data not practical for journal publications, with the additional benefit of enabling searchers to extract the data based on their own criteria. Genome databases have been established on an organism-specific basis, usually with a proprietary database structure and delivery system. The largest of these databases are the Human Genome Organization's genome database at Oak Ridge National Laboratory (Oak Ridge, Tennessee) and the Mouse Genome Database at The Jackson Laboratory (Bar Harbor, Maine). Many of the species groups are now migrating to a common database platform; and several species groups including those working on pig, cattle, sheep, horse, chicken, and cat are now using the ARKdb platform developed and run at the Roslin Institute in Edinburgh, Scotland. This usage of a common system holds great promise for the integration and cross-referencing of data for these species. At the time of this writing, the status and direction of the largest genome database—the human genome database—are uncertain due to the termination of funding for its development. The database will be hosted in its current form at Oak Ridge National Laboratory with no additional development, representing a shift in the focus from geneand clone-based information to a model of annotated sequence. This shift is likely to present some difficulties for comparative mapping in the short term. Comparative mapping data are integrated into many of the species-specific databases in several ways. The basic type of comparative linkage comprises shared symbols and names and includes the use of symbols from other species as an alias. This type of linkage has many flaws, including inflexibility with regard to our evolving understanding of gene homologies and sensitivity to nomenclature changes. The more advanced comparative information is obtained from direct links by unique identifiers to entries in other databases and in some cases dedicated detailed comparative databases. The most comprehensive comparative database available as of October 1998 is the Mouse Genome Database (mammalian homology database), which lists homologies in a broad range of species as given in published journal articles (with references) and includes a powerful set of search criteria in a forms interface with tabular or graphical output. The main limitations of all current comparative mapping resources are the manual nature of establishing homology links and the typical absence of database entries that indicate the evidence for the homology. The next wave of genome database innovation will be the development of automated software agents, which will explore databases and create their own database of links between the different species databases based on a defined set of homology criteria. One of these agent systems, under development at the time of this writing at the Roslin Institute and the University of Edinburgh, will hopefully result in the efficient creation of current, robust, and well-defined homology links between species databases. Although comparative gene mapping databases are continuing to evolve, Internet-based resources have become an entrenched and vital tool for the comparative mapper. Use of this tool can only grow in importance as the data sets involved continue to expand and as more sophisticated tools are developed for their exploitation.

Baboon/human homologies examined by spectral karyotyping (SKY): a visual comparison

Baboon (Papio hamadryas) metaphase chromosomes were analyzed using spectral karyotyping (SKY), a technique combining fluorescence microscopy, CCD-imaging, and Fourier spectroscopy. Results from a comparison of SKY analyses using probes derived from human chromosomes on baboon metaphases were consistent with the majority of comparative gene mapping data between the two species. These data were also compatible with earlier studies comparing macaque and human chromosomes. Human (HSA) chromosome 2 was homologous to baboon (PHA) chromosomes 12 (HSA 2q) and 13 (HSA 2p), whereas three baboon chromosomes corresponded to two different human chromosomes: PHA 3 to HSA 7 and HSA 21, PHA 7 to HSA 14 and HSA 15, and PHA 10 to HSA 20 and HSA 22. These results support the retained synteny between the Hominidae and Cercopithecidae genomes.

A molecular cytogenetic analysis of X chromosome repatterning in the Bovidae: transpositions, inversions, and phylogenetic inference

Chromosomal homologies among the X chromosomes of species representative of eight bovid subfamilies and most of the recognized tribes were established using a combination of FISH and conventional G- and C-banding. Our analyses allowed for the delimitation of three X chromosome types represented, respectively, by cattle (Bovinae, tribe Bovini), the tragelaphines (Bovinae, tribe Tragelaphini), and a large assemblage comprising all the remaining subfamilies and their tribes (the Cephalophinae, Hippotraginae, Alcelaphinae, Antilopinae, Aepycerotinae, Peleinae, and Caprinae). The use of the bacterial artificial chromosome probe BAC 101 (which maps to Xp12 in cattle) and an Xp painting probe comprising sequences specific for the short arm of cattle Xp (Xp24→p12) allowed us to orient this region, which has moved as a conserved euchromatic block during the evolution of the bovid X chromosome. We show that the differences between the three chromosomal types are attributable to a transposition, two inversions, and heterochromatic additions/deletions. A paucity of comparative mapping data precludes the assignment of the sequences contained in cattle Xp to either the presumed conserved (XCR) or the recently added (XAR) region of the eutherian X chromosome, and the reasons for the retention of these sequences as an evolutionarily conserved unit in the intrachromosomal restructuring of the bovid X across lineages remain enigmatic.

The chicken as a model to study microchromosomes in birds: a review

The typical avian karyotype is composed of a few macrochromosomes and around 60 indistinguishable small microchromosomes. Due to its economic importance, the chicken is the avian species for which cytogenetic and genetic maps are the most developed. Based on these genome studies, it has been shown that the chicken microchromosomes are carriers of dense genetic information. Indeed, they probably bear at least 50 % of the genes and exhibit high recombination rates. Because of the presence of microchromosomes, the genetic size of the chicken genome seems higher than first estimated and could reach more than 4 000 cM for 1 200 Mb. Thus, it is worth developing the microchromosome map. From an evolutionary point of view, comparative mapping data raise many questions about the origin of microchromosomes. They could be ancestral chromosomes, from which large chromosomes formed by fusions, or conversely they could be the result of the splitting of macrochromosomes. © Inra/Elsevier, Paris

Assignment of the porcine nuclear factor I/CTF (NFI/CTF) gene to chromosome 2q12-13 by FISH.

Species: Pig (Sus scrofa domestica) Locus name: Nuclear Factor I/CTF Locus symbol: NFI/CTF Map position: 2q12-13 Method of mapping: Fluorescence in situ hybridization (FISH) Molecular reagents: An EMBL3A phage containing 40 kb of pig NF1/CTF gene [1] was biotinylated and detected by avidin-FITC. Previously identified homologs: NFIC maps to human Chromosome (Chr) 19p13 [2]. Discussion: Nuclear factor NFI/CTF is a member of a family of dimeric DNA-binding proteins. Its recognition sequence [TGG(C/ A)Ns] is present in a number of DNA viruses and in mammalian and avian genomes [see 3]. The proteins are involved in cellular transcription regulation and adenovirus transcription initiation. In the human genome, NFI-A,B,C and NFI-X genes have been identified and mapped [2,4]. NFI-C and NFI-X are located in close proximity on human Chr 19p 13, whereas NFI-A and -B genes map to lp31.2-31.3 and 9p24.1, respectively [2]. In the mouse, Nfix has been assigned to 8C1-2 [7]. Of all mammalian nuclear factor I genes isolated to date, the genomic structure of the porcine gene has been characterized in most detail [5]. Gross regional homologies between human and porcine genomes have recently been demarcated by Zoo-FISH [6,q]. These studies revealed the presence of two conserved syntenic segments between HSA19 and SSC2cen-q21 and SSC6cen-q21 [7]. Comparative gene mapping data suggest that the p and q arms of HSA 19 are each conserved as a single block in artiodactyl genomes [8]. The mapping of the porcine NFI/CTF gene to SSC2q 12-13 corroborates the conserved synteny between HSA19p and the homologous segment at SSC2cen-q21, which has also been demonstrated by a recent forward and reverse Zoo-FISH approach [9].

The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data

The Mouse Genome Database (MGD) is a comprehensive community resource of mouse genetic and biological information populated both with data from published literature and with data electronically submitted from the research community. MGD stores genetic, physical and comparative mapping data, clones/probes/PCR information, and phenotype descriptions for genes, mutations and mouse strains. Supporting software for importation, analysis, display and distribution of mouse genetic data have been developed. User support is provided through dedicated staff providing documentation, training, and response to individual user queries. MGD is accessible over the Internet at URL http://www.informatics.jax.org.

Conserved segment identification.

The quantitative study of evolution based on comparative map data is dependent on the definition and identification of conserved segments remaining after interchromosomal exchanges such as reciprocal translocation. Because of experimental error and, more important, extensive local intrachromosomal rearrangement, it is difficult to reconstruct the configuration of conserved segments produced by interchromosomal exchanges. We present a formula to evaluate possible conserved segments and an algorithm which seeks the partition of the genome into segments optimal under this evaluation. Application is made to the human-mouse comparison.

Genetic mapping of the polled/intersex locus (PIS) in goats

Sex determination in mammals is due to a complex cascade of gene regulations involving SRY and autosomal and X genes. Study of intersex cases in domestic mammals could enlighten some parts of this basic developmental pathway and therefore clarify the mechanisms of sexual differentiation in humans, especially for autosomal mutations affecting non Y-downstream sex-determining genes. Intersex condition is well documented in dairy goats. It is due to a recessive gene which is associated with the dominant autosomal gene for hornlessness, P. In the homozygous state, the P gene causes masculinization of all polled genetic females PP. The study of 13 polled intersex goats permitted to describe in detail the external morphology, anatomy of the reproductive tract, gonadal histology and chromosomal constitution. All animals exhibited two inguinally located udders. Seven of them appeared to be closer to the female phenotype on the basis of general conformation, external and internal genitalia while the other six had the general appearance and internal reproductive tract resembling males. The gonads of all animals contained seminiferous tubules lined by Sertoli cells. No germ cells were observed. The chromosome analyses of the blood and gonadal cultures prepared from each animal showed a normal female karyotype (2n = 60,XX). No Y chromosome was observed in any of the metaphase spreads. Futhermore, using PCR amplification and Southern blot, no DNA specific sequence of the Y chromosome (SRY and ZFY) was detected. A linkage analysis within 12 pedigrees segregating for the polled trait allowed the localization of the polled/intersex locus in the distal region of goat chromosome 1. According to comparative mapping data, no sex-determining gene has been described so far in the human homologous region. This genetic localization constitutes the first step towards the identification of a new autosomal sex determining gene in mammals.

Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor.

Comparative mapping data suggested that the dominant white coat color in pigs may be due to a mutation in KIT which encodes the mast/stem cell growth factor receptor. We report here that dominant white pigs lack melanocytes in the skin, as would be anticipated for a KIT mutation. We found a complete association between the dominant white mutation and a duplication of the KIT gene, or part of it, in samples of unrelated pigs representing six different breeds. The duplication was revealed by single strand conformation polymorphism (SSCP) analysis and subsequent sequence analysis showing that white pigs transmitted two nonallelic KIT sequences. Quantitative Southern blot and quantitative PCR analysis, as well as fluorescence in situ hybridization (FISH) analysis, confirmed the presence of a gene duplication in white pigs. FISH analyses showed that KIT and the very closely linked gene encoding the platelet-derived growth factor receptor (PDGFRA) are both located on the short arm of Chromosome (Chr) 8 at band 8p12. The result revealed an extremely low rate of recombination in the centromeric region of this chromosome, since the closely linked (0.5 cM) serum albumin (ALB) locus has previously been in situ mapped to the long arm (8q12). Pig Chr 8 shares extensive conserved synteny with human Chr 4, but the gene order is rearranged.

The extension coat color locus and the loci for blood group O and tyrosine aminotransferase are on pig chromosome 6.

A linkage map of pig chromosome 6 was constructed using a wild pig/Large White intercross pedigree. The map comprises 23 polymorphic loci, and the sex-average map length is approximately 170 cM. The study adds three new genes to the chromosome 6 map: the extension (E) coat color locus, and the blood group O (EAO) and tyrosine aminotransferase (TAT) loci. Segregation at the E locus determined two coat color phenotypes among the F2 animals: wild-type color (El-) and black-spotting (Ep/Ep). The E locus showed close genetic linkage to the most distal marker (S0035) on the short arm of chromosome 6. Comparative coat color genetics as well as comparative mapping strongly suggest that E in pigs encodes the melanocyte-stimulating hormone receptor, as previously shown for the corresponding coat color loci in mouse and cattle. TAT was also mapped to the distal part of 6p, whereas EAO was the most distal marker on 6q. A clear tendency for a higher recombination rate in both terminal regions was observed. A model for the evolution of pig chromosome 6, based on comparative mapping data, is presented.

Genomic Structure and Chromosomal Assignment of the Mouse Ku70 Gene

DNA-dependent protein kinase (DNA-PK) consists of three polypeptide subunits: Ku70, Ku80, and the DNA-PK catalytic subunit (DNA-PKcs). Mammalian mutants deficient in either Ku80 or DNA-PKcs function have been shown to be lacking in DNA double-strand break repair and V(D)J recombination, respectively. The precise role of the Ku70 gene in this process has not yet been determined, in part because no cell lines, animals, or human diseases involved with deficiencies in this gene have yet been identified. Both the human and the mouse Ku70 cDNAs have been cloned, and the human gene has been mapped to chromosome 22q13. The original mouse cDNA clones, however, lacked a complete 5′-region, and none of the mammalian Ku70 genomic sequences have been characterized. This report contains an analysis of the 5′-region of the mouse cDNA sequence, a characterization of the mouse Ku70 genomic structure, and fluorescencein situhybridization data that map the mouse gene to chromosome 15. The deduced amino acid sequence of the mouse gene consists of 608 amino acids compared to 609 for the human gene. The genomic sequence is 24 kb and consists of 13 exons, including an untranslated first exon. Sequences from the upstream region of exon 1 revealed four consensus GC box sequences and a strong transcription initiation site at a reasonable location. The assignment of the mouse Ku70 gene to chromosome 15 is consistent with the syntenic relationship of this gene in human (chromosome 22q13) and mouse and adds to the comparative mapping data for the genes involved in the SCID phenotype.

Comparative Genome Mapping of the Ataxia–Telangiectasia Region in Mouse, Rat, and Syrian Hamster

Chromosomal locations of theAtm(ataxia–telangiectasia (AT)-mutated) andAcat1(mitochondrial acetoacetyl-CoA thiolase) genes in mouse, rat, and Syrian hamster were determined by direct R-banding FISH. Both genes were colocalized to the C-D band of mouse chromosome 9, the proximal end of q24.1 of rat chromosome 8, and qa4–qa5 of Syrian hamster chromosome 12. The regions in the mouse and rat were homologous to human chromosome 11q. Fine genetic linkage mapping of the mouse AT region was performed using the interspecific backcross mice.Atm, Acat1,andNpat,which is a new gene isolated from the AT region, and 12 flanking microsatellite DNA markers were examined. No recombinations were found among theAtm, Npat, Acat1,andD9Mit6loci, and these loci were mapped 2.0 cM distal toD9Mit99and 1.3 cM proximal toD9Mit102.Comparison of the linkage map of mouse chromosome 9 (MMU9) and that of human chromosome 11 (HSA11) indicates that there is a chromosomal rearrangement due to an inversion betweenEts1andAtm–Npat–Acat1and that the inversion of MMU9 originated from the chromosomal breakage at the boundary betweenGria4andAtm–Npat–Acat1on HSA11. This type of inversion appeared to be conserved in the three rodent species, mouse, rat, and Syrian hamster, using additional comparative mapping data with theRckgene.