A rat genetic map constructed by representational difference analysis markers with suitability for large-scale typing

The Bh (Black at Hatch) Gene that Causes Abnormal Feather Pigmentation Maps to Chromosome 1 of the Japanese Quail

Japanese quail embryos normally have longitudinal black and brown stripes formed by colored feather buds on their back whereas an autosomal dominant mutation, black at hatch (Bh), disrupts this pigmentation pattern by causing overall black and brown coating in heterozygotes and homozygotes, respectively. These phenotypes of the Bh mutant embryos suggest that the Bh locus plays an important role in the pigment pattern formation of plumage, but its genetic origin, including cloning of the responsible gene, has been insufficiently studied. In this study, we adapted genetically directed representational difference analysis with elimination of excessive clones (GDRDA-WEEC) to Bh quails and isolated two genetic markers linked to the Bh locus as DNA fragments. Cytogenetic study by fluorescence in situ hybridization (FISH) of the DNA fragments used as probes demonstrated that the marker loci were located in the same region on the long arm of chromosome 1. Close genetic linkage between the Bh and the marker loci, and the chromosomal location of the latter suggested that the Bh locus is located on the long-arm of chromosome 1 of the Japanese quail.

Mapping of porcine genetic markers generated by representational difference analysis

Representational difference analysis (RDA) was performed using pig genomic DNA from a Landrace non-selected control population and a Landrace population selected for increased loin muscle area (LMA) for five generations. Pigs used for the analysis differed phenotypically for various carcass traits and were divergent in genotype at the skeletal muscle ryanodine receptor 1 locus. Two RDA experiments were performed using BamHI and BglII. Fourteen BamHI and 37 BglII difference products were cloned and sequenced. Oligonucleotide primers were designed to amplify RDA difference products and sequence-tagged sites (STS) were developed for 16 RDA fragments (two BamHI and 14 BglII). These 16 STS were mapped using the INRA-Minnesota porcine Radiation Hybrid panel. Polymorphisms identified in nine of the STS were used to place these markers on the PiGMaP genetic linkage map. Sequence-tagged sites were localized to 11 different chromosomes including three markers on chromosome 11 and four markers on chromosome 14. Development of RDA markers increases the resolution of the pig genome maps and markers located within putative quantitative trait locus (QTL) regions can be used to refine QTL positions.

An integrated rat genome map based on genetic and cytogenetic data

In this study we combined three major rat genome maps, by adding 66 markers to the Kyoto Laboratory Animal Science map (KLAS map), and constructed an integrated map. The resultant integrated map consists of 5,682 redundant markers, spanning a genetic length of 2,028 cM. Eighty genetic markers were anchored to the cytogenetic map, fixing all the genetic maps in the physically correct orientation. This map encapsulates the progress in rat mapping studies in past years and offers useful information for QTL analysis. The map figures are available at http:/(/)www.anim.med.kyoto-u.ac.jp/.

Development of the arbitrarily primed-representational difference analysis method and chromosomal mapping of isolated high throughput rat genetic markers

Linkage mapping of quantitative trait loci requires analysis of a large number of animals. Although genetic markers isolated by representational difference analysis (RDA) and its modifications meet the needs, the number of these markers has been limited. In the present study, we established the arbitrarily primed (AP)-RDA method to isolate virtually an unlimited number of the high throughput genetic markers. A representation of the genome, an AP-amplicon, was prepared by AP-PCR with a single primer or with a combination of primers using genomic DNA of the ACI/N (ACI) or BUF/Nac (BUF) rat as a template. By subtracting the AP-amplicon of ACI from that of BUF, a total of 40 polymorphic and independent markers were isolated in seven series of AP-RDA using a single primer. Two series of AP-RDA with primer combination yielded seven additional independent markers. All of the markers gave clear positive/negative signals by hybridization of a filter where AP-amplicons from F2 rats of ACI and BUF were dot-blotted at a high density without any concentration or purification. All of the 47 independent markers were mapped to unique chromosomal positions by linkage analysis, even though some arbitrary primers had very similar sequences. The markers were also informative between other strains of rats. Simultaneous hybridization of multiple filters made it possible to genotype a large number of rats simultaneously for multiple genetic loci. The AP-RDA method promises isolation of a large number of high throughput genetic markers in any species and is expected to facilitate linkage mapping of subtle quantitative trait loci.

Linkage mapping of the Bra, Brb and Brg genes for rat protein phosphatase 2A 55 kDa B-regulatory subunit isotypes

We previously identified the rat Bra, Brb and Brg genes, which encode alpha, beta and gamma isotypes of the 55 kDa B-regulatory subunit of protein phosphatase 2A. Polymerase chain reaction-single strand conformation polymorphism analysis in the present study identified polymorphisms in Bra, Brb and Brg between the ACI and BUF, ZI and TM, and BN and WTC strains, respectively. Linkage analysis using mapping panels composed of F2 or back-crosses of these strains allowed Bra, Brb and Brg to be assigned to chromosomes 15, 18 and 14, respectively. Furthermore, it was revealed that Bra is located close to the Rb1 locus. Using polymorphism in Bra, loss of heterozygosity (LOH) was analyzed for rat mammary tumors induced in (SD x F344) F1 female rats by a food-borne carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, and a typical mammary carcinogen, 7,12-dimethylbenz[a]anthracene. No LOH was detected at the Bra locus.

Construction and characterization of a 10-fold genome equivalent rat P1-derived artificial chromosome library

A rat PAC library was constructed in the vector pPAC4 from genomic DNA isolated from female Brown Norway rats. This library consists of 215,409 clones arrayed in 614,384-well microtiter plates. An average insert size of 143 kb was estimated from 217 randomly isolated clones, thus representing approximately 10-fold genome coverage. This coverage provides a very high probability that the library contains a unique sequence in genome screening. Tests on randomly selected clones demonstrated that they are very stable, with only 4 of 130 clones showing restriction digest fragment alterations after 80 generations of serial growth. FISH analysis using 70 randomly chosen PACs revealed no significant chimeric clones. About 7% of the clones analyzed contained repetitive sequences related to centromeric regions that hybridized to some but not all centromeres. DNA plate pools and superpools were made, and high-density filters each containing an array of 8 plates in duplicate were prepared. Library screening on these superpools and appropriate filters with 10 single-locus rat markers revealed an average of 8 positive clones, in agreement with the estimated high genomic coverage of this library and representation of the rat genome. This library provides a new resource for rat genome analysis, in particular the identification of genes involved in models of multifactorial disease. The library and high-density filters are currently available to the scientific community.

Positional cloning without a genome map: using 'Targeted RFLP Subtraction' to isolate dense markers tightly linked to the regA locus of Volvox carteri

The ability to isolate genes defined by mutant phenotypes has fueled the rapid progress in understanding basic biological mechanisms and the causes of inherited diseases. Positional cloning, a commonly used method for isolating genes corresponding to mutations, is most efficiently applied to the small number of model organisms for which high resolution genetic maps exist. We demonstrate a new and generally applicable positional cloning method that obviates the need for a genetic map. The technique is based on Restriction Fragment Length Polymorphism (RFLP) Subtraction, a method that isolates RFLP markers spanning an entire genome. The new method, Targeted RFLP Subtraction (TRS), isolates markers from a specific region by combining RFLP Subtraction with a phenotypic pooling strategy. We used TRS to directly isolate dense markers tightly linked to the regA gene of the eukaryotic green alga Volvox. As a generally applicable method for saturating a small targeted region with DNA markers, TRS should facilitate gene isolation from diverse organisms and accelerate the process of physically mapping specific regions in preparation for sequence analysis.

Experimental chemical carcinogenesis in the stomach and colon

Experimental chemical carcinogenesis in the digestive tract is reviewed, mainly on the basis of information obtained in the laboratories of the National Cancer Center Research Institute. It is generally accepted that cancer is the outcome of DNA damage, resulting in mutation, loss, amplification and recombination of genes. Gastric cancer is no exception. It was shown very early that cancer of the glandular stomach can be produced in rats by administration of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), a widely used mutagen. However, this depends on the genotype. Whereas the ACI rat is susceptible to MNNG, the Buffalo rat is resistant and this is a dominantly inherited trait. Genes responsible for the sensitivity to gastric cancer induction are at present under investigation by linkage analysis of rat genome markers. With regard to cancer in humans, our finding that cooked proteinaceous foods can give rise to a series of heterocyclic amines (HCAs) is of major significance. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), one of the most abundant, causes colon cancers in male rats, whereas in females it induces breast cancers. The colon cancers induced by PhIP feature a deletion of G as represented by 5-GGGA-3-->5-GGA-3 in the Apc gene, resulting in a truncated Apc molecule. Microsatellite mutations have also been found in PhIP-induced colon tumors, as in human hereditary non-polyposis colorectal cancer cases. Similarly to the case of gastric cancer production by MNNG, there is a genetic component and F344 rats are more susceptible to PhIP colon carcinogenesis than the ACI/N strain and the gene responsible is being sought. Since carcinogenesis proceeds with accumulation of genetic alteration, often involving genomic instability, exposure to any kind of carcinogenic substances, either xeno- or autobiotics, needs to be reduced as far as possible, taking account of inconvenience at the individual and socio-economical levels.

The polymerase chain reaction: from functional genomics to high-school practical classes

After a decade of intensive use as an in vitro alternative to cloning DNA, PCR is now well established as the default method for DNA and RNA analysis. Recent developments have consolidated this position by the introduction of more robust formats, improvements in thermal cyclers and labelling and detection methods. The trend is towards increasing automation, although comparatively few diagnostic kits based on PCR are in wide use. At the same time the applications of PCR are being extended with modifications such as long, accurate PCR and arrayed oligonucleotides or expressed sequences.

A comparative genetic map of rat, mouse and human genomes

The increasing availability of molecular markers and the development of highly efficient gene mapping strategies for the mouse, rat and human genomes have generated vast quantities of information allowing for the progressive refinement of comparative maps. In this publication we report on an updated version of our rat/mouse/human comparative genetic map, based on the mouse map. Databases for mouse, rat and human gene mapping were used for the collection of homologs mapped in the species. The comparative map was constructed with a total of 1,235 mouse loci having known homologs in the rat and/or human: 16 having homologs only in the rat, 884 having only in the human and 335 both in the rat and human. The combined length of the segments conserved between the rat and mouse spans 758 cM on the mouse map. This indicates that about 47% of the mouse genome is now covered by known rat homologous regions. Five novel regions homologous for the rat and mouse were identified. This comparative genetic map should be useful for researchers working on genetic studies in the rat, mouse and human.

Isolation of genomic fragments from polymorphic regions by representational difference analysis

Representational difference analysis is an effective technique for isolating the differences between two nearly identical genomes. We have found the technique to be extremely valuable in our analyses of mouse germline mutations. We also present several technical improvements in the procedure that make it more efficient and reliable.

Rat chromosome 1: regional localization of seven genes (Slc9a3, Srd5a1, Esr, Tcp1, Grik5, Tnnt3, Jak2) and anchoring of the genetic linkage map to the cytogenetic map

Seven genes were regionally localized on rat Chromosome (Chr) 1, from 1p11 to 1q42, and two of these genes were also included in a linkage map. This mapping work integrates the genetic linkage map and the cytogenetic map, and allows us to orient the linkage map with respect to the centromere, and to deduce the approximate position of the centromere in the linkage map. These mapping data also indicate that the Slc9a3 gene, encoding the Na+/H+ exchanger 3, is an unlikely candidate for the blood pressure loci assigned to rat Chr 1. These new localizations expand comparative mapping between rat Chr 1 and mouse or human chromosomes.

Genetic mapping of genes regulating the thymus size in back-cross rats between the laboratory BUF/Mna strain and the MITE strain derived from the wild rat, Rattus norvegicus

The thymoma prone BUF/Mna (B) rat is a useful model for studying the genes responsible for thymus enlargement during the stage of young growth. Among the strains of rats, B rats have the largest thymuses at all stages of life. A locus, Ten-1, which contributes to thymus enlargement in back-cross (BC) rats between the B and WKY/NCrj (W) strains, was mapped on chromosome 1. To determine the precise location of the locus, ¿B x(B x MITE)F1¿ BC rats were generated by crossing the B strain with the inbred MITE (M) strain, which was established from captured, Japanese wild rats, and were examined by linkage study using polymerase chain reaction with 67 microsatellite markers. Linkages with thymus enlargement were found in genotypes of seven markers, BSIS, LSN, MYL2, IGF2, PBPC2, D1Mgh11, and D1MIt6, by chi2-test and Student's t-test, which confirmed the presence of the genetic locus associated with thymus enlargement, Ten-1, in this region. Paradoxically, a suppressive locus, Tsu-1, to thymus enlargement was also found on chromosome 3, showing linkages of phenotype of the small thymus with genotypes of SCN2A, CAT, D3MIt16, and D3MIt13. By analyses of MAPMAKER/EXP and MAPMAKER/QTL, Ten-1 was mapped at 4.6 cM proximal from IGF2 locus on chromosome 1 and Tsu-1 at 4.0 cM proximal from CAT locus on chromosome 3, respectively.

Physical and linkage mapping of human chromosome 17 loci to dog chromosomes 9 and 5

Genome mapping in the dog is in its early stages. Here we illustrate an approach to combined physical and linkage mapping of type 1 anchor (gene) loci in the dog using information on syntenic homology from human and mouse, an interbreed cross/backcross, and a strategy for isolation of dog genomic clones containing both gene-specific sequences and simple sequence repeat polymorphisms. Eleven gene loci from human chromosome 17q (HSA17q) were mapped to the centromeric two-thirds of dog chromosome 9 (CFA9), an acrocentric chromosome of medium size: P4HB, GALK1, TK1, GH1, MYL4, BRCA1, RARA, THRA1, MPO, NF1, and CRYBA1. Eight of these were also positioned on a linkage map spanning 38.6 cM. Based on combined fluorescence in situ hybridization and linkage mapping, the gene order on CFA9 is similar to that of the homologous genes on HSA17q and mouse chromosome 11 (MMU11), but in the dog the gene order is inverted with respect to the centromere. Canine loci, GALK1, TK1, GH1, MYL4, THRA1, and RARA constitute a closely linked group near the centromeric end of CFA9, spanning a genetic distance of only 4.7 cM. Canine NF1 and CRYBA1 lie distally, near the lower border of the Giemsa band adjacent to the distal one-third of CFA9. NF1 and CRYBA1 are loosely linked to the more centromeric group (31.2 cM). No HSA17 genes were found on the telomeric one-third of CFA9. Painting of dog chromosomes with a human whole chromosome 17 probe showed hybridization with only the proximal two-thirds of CFA9, consistent with the conclusion that the distal one-third corresponds to a segment or segments of other human chromosomes. Two loci, GLUT4 and PMP22, located on HSA17p, were mapped by FISH to dog chromosome 5 in a region also identified by the whole human chromosome 17 paint, indicating disruption of HSA17 syntenic homology at the centromere.

A linkage map of the rat genome derived from three F2 crosses

We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of microsatellite markers. The loci define 21 linkage groups corresponding to the 20 rat autosomal chromosomes and the X chromosome. The map spans a genetic length of 1998 cM. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of rat models characterized for complex phenotypes.

Establishment of methylation-sensitive-representational difference analysis and isolation of hypo- and hypermethylated genomic fragments in mouse liver tumors

Methylation of CpG sites in the genome, which is generally conserved during cell replication, is considered to play important roles in cell differentiation and carcinogenesis. However, investigations on changes in methylation status have been limited to known genes. To make a genome-wide search for differentially methylated genes, we developed a methylation-sensitive-representational difference analysis (MS-RDA) method. The representation of the genome was prepared using the methylation-sensitive restriction enzyme HpaII, and the mixture ratio of tester and driver DNAs was optimized to detect differences in methylation status of a single copy per diploid mammalian genome. By performing comparative MS-RDA of one hepatocellular carcinoma and of background liver tissue of one mouse treated with a food carcinogen (2-amino-3,4-dimethylimidazo[4,5-f] quinoline), we were able to identify (i) extensive hypomethylation of long interspersed nuclear element repetitive sequences in a number of hepatocellular carcinomas, (ii) reduction of the gene dosage of their mitochondrial DNA, and (iii) a hypermethylated DNA fragment of unknown origin. Furthermore, by adding the clones obtained in the first MS-RDA to the driver DNA [MS-RDA with elimination of excessive clones (MS-RDA-WEEC)], nine DNA fragments that could not be detected at the first MS-RDA were isolated as differentially methylated DNA fragments. MS-RDA, combined with MS-RDA-WEEC, is thus a promising approach to identify DNA fragments differentially methylated in two DNA sources.

Phylogenetics of the laboratory rat Rattus norvegicus

A genealogic tree was constructed for inbred strains of the laboratory rat, including 63 strains and 214 of their substrains. Information on genetic and biochemical marker typings of these lines was collected from the literature and from the World Wide Web. Data on 995 polymorphisms were processed into a phylogenetic distance matrix, and a tree was obtained by the Fitch-Margoliash distance matrix method. The inbred strains of the laboratory rat showed an average polymorphism for pairwise comparison of 53%. Strain BN showed the highest genetic divergence from all the other ones. Comparison with the mouse phylogenetic tree indicated that laboratory rats possess a higher diversity than inbred strains of mice not derived from wild species. These results provide a phylogenetic basis in the choice of rat strains for genetic linkage experiments.