Fine-structure mapping of the complex locus Odc-rs5 relative to Igk and distal loci

Odc-rs5 was previously identified as a complex locus closely linked to the Igk complex on mouse Chromosome (Chr) 6 and comprising at least five copies of a sequence related to the mRNA encoding ornithine decarboxylase (ODC) in the genomes of mice of some inbred strains and at least seven copies in others (Richards-Smith and Elliott, Mammalian Genome 2: 215, 1992). In the present study, Odc-rs5 was shown to be composed of at least seven copies of the ODC sequence in both the Odc-rs5 ^a and Odc-rs5 ^b haplotypes. Based upon the distribution of DNA restriction fragments (RFs) that had previously been associated with Odc-rs5 ^a or Odc-rs5 ^b among 42 mice of inbred laboratory strains having various haplotypes at Igk and in mice of two congenic strains [B6.PL-Ly-2 ^a, Ly-3 ^a(75NS)/Cy and B6.PL-Ly-2 ^a, Ly-3 ^a(85NS)/Cy] and a backcross-derived stock (NAK) known to be recombinant within Igk, a fine structure map of Odc-rs5 was deduced relative to Igk and more distal loci. Odc-rs5-derived RFs were located to three distinct regions within and/or distal to Igk and to a fourth site between (Ly-3, Ly-2) and Raf-1. Additionally, DNAs from 19 mice of inbred strains and random-bred stocks derived from wild progenitors trapped at various locations were analyzed and found to exhibit an unexpected variety of combinations of RFs associated with the two Odc-rs5 haplotypes most frequently observed among inbred laboratory strains of mice.     

Mouse serum amyloid P-component (SAP) levels controlled by a locus on chromosome 1

Recombinant inbred strains were used to demonstrate the existence of a major locus on chromosome 1, designated Sap, which controls the endogenous concentration of the mouse acute phase reactant, serum amyloid P-component (SAP). Levels of SAP were associated with alleles at the Ly-9 locus in two sets of RI strains: BXD (C57BL/6J × DBA/2) and BXH (C57BL/6J × C3H/HeJ). Low endogenous levels of SAP were present in the C57BL/6J progenitor strain and in most of the RI strains which inherited the Ly-9 ^ballele. High levels of SAP were present in the DBA/2J and C3H/HeJ progenitors and in most of the RI strains which inherited the Ly-9 ^aallele. In the BXD strains 91% of the genetic variation of SAP levels was accounted for by segregation at the Ly-9 locus while an additional 9% was attributed to genetic factors unlinked to Ly-9. In the BXH strains the percentage of genetic variation accounted for by Ly-9 segregation was reduced to 46%, while 54% was accounted for by other genetic factors. Because of background genetic variation it was not possible to detect any crossovers between Sap and Ly-9. However, in the BXD strains the linkage between Sap and Ly-9 appears to be quite close. The B6.C-H-25 ^ccongenic strain, which carries a segment of BALB/c chromosome 1 including the minor histocompatibility locus H-25 on a C57BL/6By background, had the same endogenous SAP level as the BALB/c donor strain.     

Allelic variants of Ly-5 in inbred and natural populations of mice

Allelic variants of Ly-5 in inbred commensal and other natural populations of mice were analyzed by patterns of restriction fragment length polymorphisms (RFLP) and Southern hybridization using an Ly-5 cDNA probe and by cell-surface staining with a panel of antibodies directed against polymorphic and nonpolymorphic Ly-5 determinants. New Ly-5 alleles were defined by RFLPs generated by both Eco RI and Bam HI restriction enzyme digests. The Mus musculus subspecies and other species within the genus Mus showed a strong correlation between allelic variants defined by restriction enzymes and serologic specificities. The data also suggest the conservation of the Ly-5 gene throughout the genus Mus.     

Assignment of the Ly-6--Ril-1--Sis--H-30--Pol-5/Xmmv-72--Ins-3--Krt-1--Int-1--Gdc-1 region to mouse chromosome 15

Previous work has demonstrated linkage between Ly-6, H-30, and a locus, Ril-1, that affects susceptibility to radiation-induced leukemia. Results of preliminary linkage analyses suggested further that the cluster might be linked to Ly-11 on the proximal portion of mouse chromosome 2. Using molecular probes to examine somatic cell lines and recombinant inbred and congenic strains of mice, we have re-evaluated these linkage relationships. A cloned genomic DNA fragment derived from a retroviral site has been used to define a novel locus, Pol-5, that is tightly linked to both H-30 and Ril-1 as shown by analysis of the B6.C-H-30 ^c congenic mouse strain. Following the segregation of the Pol-5 mouse-specific DNA fragment in a series of somatic cell hybrids carrying various combinations of mouse chromosomes on a rat or Chinese hamster background mapped Pol-5 to mouse chromosome 15. During the course of these studies, restriction fragment length polymorphisms were defined associated with several loci, including Pol-5, Ly-6, Sis, Ins-3, Krt-1, Int-1, and Gdc-1. Three of these loci, Sis, Int-1, and Gdc-1, have been previously mapped to chromosome 15 by others using somatic cell hybrids or isoenzyme analyses. Following the inheritance of these eight loci in recombinant inbred strains of mice allowed the definition of a linkage group on the chromosome with the order Ly-6-Ril-1--Sis--H-30--Pol-5--Ins-3--Krt-1--Int-1--Gdc-1. Analyses of alleles inherited as passengers in B6.C-H-30 ^c, C3H.B-Ly-6 ^b, and C57BL/6By-Eh/+ congenic mouse strains and in situ hybridization experiments support the above gene order and indicate further that the cluster is located on distal chromosome 15, with Ly-6 and Sis near Eh.Abbreviations A agouti - Abl cellular homolog of the Abelson leukemia virus oncogene - Ada adenosine deaminase - Ak-1 adenylate kinase-1 - AXB A/J × C57BL/6J recombinant inbred strain - B2m beta-2 microglobulin - BXA C57BL/6J × A/J recombinant inbred strain - BXD C57BL/6J × DBA/2J recombinant inbred strain - BXH C57BL/6J × C3H/HeJ recombinant inbred strain - CXB BALB/cBy × C57BL/6By recombinant inbred strain - DNA deoxyribonucleic acid - Eh hairy ears - Fpgs folypolyglutamyl synthetase - FXI fractionated x-irradiation - Gdc-1 glycerol phosphate dehydrogenase-1 - Il2r IL-2 receptor - Ins-3 a novel insulinlike gene - Int-1 mammary tumor integration site-1 - Itp inosine triphosphatase - Krt-1 the locus designated here includes a cluster of at least three keratin genes - LTR long terminal repeat - Ly lymphocyte - Lv-6 lymphocyte antigen-6 - Ly-11 lymphocyte antigen-11 - MIH minor histocompatibility - Myc cellular homolog of the Abelson leukemia virus oncogene; pa, pallid; - Pol-5 locus encoding retroviral polymerase-5 - RFLP restriction fragment length polymorphism - RI recombinant inbred mouse strains - Ril-1 radiation-induced leukemia susceptibility-1 locus - SDP strain distribution pattern - Sis cellular homolog of the simian sarcoma virus oncogene - SFFV spleen focus-forming virus - Tpi-1 triosephosphate isomerase-1 - Ve velvet     

Linkage of acid α-glucosidase (Gaa) and Thymidine kinase (Tk-1) to Esterase-3 (Es-3) on mouse Chromosome 11

Inheritance in recombinant inbred (RI) strains of restriction fragment length variants (RFLVs) detected by probes specific for Gaa and Tk-1 showed tight linkage of both to Es-3 on mouse Chromosome (Chr) 11. This result extends the region of homology between mouse Chr 11 and human chr 17q.     

Linkage in mice of genes controlling an immunoglobulin kappa-chain marker and the surface alloantigen Ly-3 on T lymphocytes

Evidence obtained using recombinant inbred and congenic mouse strains has shown that thePC8 locus responsible for determining a marker on a singlek chain in inbred mice is linked to theLy-2,3 locus on chromosome 6. The upper limit of the map distance between these loci is approximately three centimorgans. This finding is discussed in relation to other known light-chain variants that are associated with theLy-2,3 locus.Abbreviations used in this paper are as follows L light chains - PC phosphocholine - H8 HOPC 8 - IEF isoelectric focusing - KLH keyhole limpet hemocyanin - RI recombinant inbred     

Genetic Mapping of a Possible New Alcohol Dehydrogenase Sequence to Mouse Chromosome 3 at the Adh-1/Adh-3 Complex

Southern blot analysis of mouse genomic DNA reveals two Eco RI fragments which faintly hybridize to mouse Adh-1 cDNA and are not part of the Adh-1 gene. These fragments were isolated from agarose gels, cloned, and characterized. Sequence analysis of the 2.1-kb Eco RI fragment suggests that it is likely a pseudogene since it does not contain a long open reading frame. However, the 2.0-kb Eco RI fragment contains a coding sequence with a long open reading frame which corresponds to exon 6 of the mouse Adh-1 gene. Comparison of the coding sequence with other known ADHs suggests that the sequence has diverged sufficiently from any currently known class of ADH to be a possible distinct class. Further confirmation awaits analysis of currently available genomic clones. Using these sequences as probe, restriction fragment length polymorphisms were identified for each sequence between C57Bl/6J and DBA/2J inbred mouse strains. The strain distribution pattern for these allelic differences was determined among the B × D recombinant inbred strains. This analysis revealed that the 2.1-kb Eco RI sequence is located on chromosome 3 but at a distance from the Adh-1/Adh-3 complex as previously reported. However, the new polymorphism identified in the 2.0-kb Eco RI fragment enabled this sequence to be mapped at the Adh-1/Adh-3 complex.     

Further definition of the Ly-5 system

Ly-5 is expressed by cells of the hematopoietic branch of development. Further serological analysis of the Ly-5 system, aided by Ly-5 monoclonal antibodies and by two Ly-5 congenic mouse strains, reveals two new Ly-5 alloantigens, Ly-5. 3 and Ly-5.4. The data define three thymocyte phenotypes, Ly-5.1,3, Ly-5.2,4, and Ly-5.2,3, and three corresponding genotypes, Ly-5 ^a, Ly-5 ^b, and Ly-5 ^c, respectively. Ly-5 ^ais by far the most common allele. The Ly-5 ^callele is found only in the ST/bJ strain, a finding that accords with the presently unique pattern of restriction fragments previously observed in Southern blotting of ST/bJ DNA with an Ly-5 cDNA probe. Present serological and biochemical data favor the interpretation that the compound Ly-5 phenotype of thymocytes is attributable to two separate Ly-5 molecular isoforms that exhibit a discrete difference in protein composition, bear different Ly-5 antigens, and are produced jointly by thymocytes, unlike other Ly-5 isoforms previously shown to distinguish different hematopoietic cell lineages.     

Immunoglobulin constant kappa gene alleles in twelve strains of mice

Genomic DNA for the immunoglobulin (Ig) constant kappa Igk-C gene region was amplified by the polymerase chain reaction (PCR) method and sequenced from twelve commonly used inbred mouse strains. PCR products were used directly as templates in dideoxy-DNA-sequencing, a method which avoids the sequencing errors caused by Taq polymerase, since no cloning step is required. In restriction fragment length polymorphism (RFLP) studies the SJL mouse strain has been shown to belong to a Igk-C allogroup different from other common inbred mouse strains. The BALB/c Igk-C region was sequenced earlier, but our Igk-C sequences clarify the situation and confirm the existence of three Igk-C alleles in inbred mice (Mus musculus domesticus). Mice belonging to the kappa (Igk) haplotype e (SJL) have allele c of the Igk-C gene. The strains belonging to the kappa haplotype [a albino strain, K subline (AKR), PL and d (C58)] have allele a, and all other eight strains belonging to three different Igk haplotypes (b, c, and f) use allele b of the gene. Allele b has at least one (possibly two) nucleotide differences from allele a in the Igk-C region, but five compared to allele c. The allelic sequences also predict two allotypic kappa polypeptide chains among twelve inbred strains. Alleles a and b encode identical polypetides, but allele c (SJL) has a conserved lysine to arginine substitution in residue 142.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X67002-X67012.     

Chromosomal location of the gene encoding the murine acute-phase protein serum amyloid P-component (SAP)

A full-length cDNA clone, pmSAP3, encoding the serum P component (SAP), has been used to search for DNA fragment length variation among mouse strains previously analyzed for differences in endogenous SAP levels. Three alleles were found usingEcoRI-digested DNA. The finding of a single 5.4-kb fragment, alleled, in DNA from DBA/2J mice suggests the presence of a singleSap locus. Segregation of DNA fragment associated withSap ^b andSap ^d alleles was analyzed in three sets of recombinant inbred (RI) strains. The strain distribution pattern found for theSap alleles was identical to that of alleles ofLy-9 in 43 individual RI strains, suggesting tight linkage withLy-9 on mouse chromosome 1. In the BXD RI strains, the SDP of theSap locus, defined by the difference in the endogenous SAP level, is also identical to the SDP of the DNA fragments. We propose to redesignate theSap locus to include both the structural element defined by the DNA polymorphism and the regulatory element involved in the regulation of SAP synthesis. TheSap locus is the major genetic element contributing to the regulation of SAP production. Other genetic factors are also involved, as shown by the presence of nonparental phenotypes in the individual BXH RI strains. This study was performed through special Coordination Funds of the Science and Technology Agency of the Japanese Government and PHS Grant GM24464 to R.W.E.     

Mapping of the mouse ornithine decarboxylase-related sequence family

A family of DNA sequences homologous to the mRNA encoding ornithine decarboxylase (ODC) and comprising 12 members in the mouse genome has been analyzed genetically. The inheritance of variant DNA restriction fragments detected by ODC cDNA probes on Southern blots of DNA from inbred strain mice was determined in six sets of recombinant inbred (RI) mouse strains. The distributions of these variations among the RI strains were then compared with the RI strain distribution patterns (SDPs) of previously mapped loci. This allowed the identification of nine independent ODC-related loci, of which eight could be localized to specific regions of the mouse genome: Odc-rs1 near Lamb2 on Chromosome (Chr) 1; Odc-rs2 near Psp on Chr 2; Odc-rs5, a complex locus comprising at least 5–7 copies of the ODC sequence, associated with Igk on Chr 6; Odc-rs6 between Abpa and Tam-1 on proximal Chr 7; Odc-rs7 near Hbb on distal Chr 7; Odc-rs12 near Agt and Emv-2 on distal Chr 8; Odc-rs8 associated with the Igh complex on Chr 12; and Odc-rs9 near Otf-3f on Chr 14. The ODC-related sequence family thus comprises a set of genomically dispersed marker loci, and alleles for several of these loci can be analyzed simultaneously in DNA from mice or cell lines. DNA from mice of 70 inbred strains has been characterized for alleles at all nine Odc-rs loci.     

Localization of growth arrest-specific genes on mouse Chromosomes 1, 7, 8, 11, 13, and 16

Growth arrest in NIH3T3 cells is associated with increased expression of a variety of mRNAs, several of which have been isolated as cDNA clones. Six of these growth arrest-specific (Gas) genes were mapped by following the inheritance of DNA restriction fragment length variants (RFLVs) associated with them in panels of recombinant inbred (RI) strains of mice and in the progeny of backcrosses both between laboratory mouse strains and between a laboratory strain and Mus spretus. The six genes are unlinked. Gas-1 maps to Chromosome (Chr) 13, Gas-2 to Chr 7, Gas-3 to Chr 11, Gas-4 to Chr 16, Gas-6 to Chr 8, and Gas-10 to Chr 1.     

Susceptibility to a mouse acquired immunodeficiency syndrome is influenced by theH-2

The development of a mouse acquired immunodeficiency syndrome (MAIDS) induced following LP-BM5 MuLV infection depends on host genetic factors. Susceptible mice, such as C57BL/6J mice, develop a profound impairment of lymphoproliferative response to mitogens and hyperplasia of lymphoid organs and succumb to infection within 6 months. These changes do not occur in resistant mice, such as A/J mice. Resistance to MAIDS is a dominant trait since (C57BL/6JxA/J)F₁ hybrid mice did not develop any immune dysfunctions following infection. Genetic regulation of the trait of resistance/susceptibility to MAIDS was determined in AXB/BXA recombinant inbred (RI) mouse strains (derived from resistant A/J and susceptible C57BL/6J progenitors). Two different criteria were used to determine their resistance or susceptibility to developing MAIDS: the gross pathologic evaluation of lymphoid organs at 13–15 weeks of infection, and survival. RI mouse strains segregated into two non-overlapping groups. The first group did not develop any significant pathology, and these mouse strains were considered as resistant to MAIDS. The second group showed the virus-induced pathological changes as well as an immunological dysfunction as seen in C57BL/6J progenitor mice, and these strains were thus considered as susceptible to MAIDS. This bimodal strain distribution pattern of resistance/susceptibility to MAIDS among the RI strains suggests that this phenotype is controlled by a single gene. Linkage analysis with other allelic markers showed a strong association between resistance/susceptibility to MAIDS and theH-2 complex. Possession of theH-2 ^b haplotype derived from C57BL/6J mice was associated with susceptibility to MAIDS, while theH-2 ^a haplotype conferred resistance to the disease. This finding was confirmed by demonstrating thatH-2 ^a congenics on the susceptible C57BL/10 background were as resistant to MAIDS as A/J mice which donated theH-2 ^a locus. Gene(s) within theH-2 complex thus represent the major regulatory mechanism of resistance/susceptibility to MAIDS.     

Mouse microsatellites from a flow-sorted 4:6 Robertsonian chromosome

Twenty microsatellites were generated from a previously characterized gt10 library containing C57BL/6J mouse DNA from a flow-sorted 4:6 Robertsonian chromosome. These sequences were analyzed for size variation between different strains of mice with the polymerase chain reaction (PCR) and mapped by use of either strain distribution patterns (SDPs) in recombinant inbred (RI) strains, or intra- and interspecific backcrosses. Eighty-five percent of the sequences showed allelic variations between different inbred strains of mice and the wild mouse, Mus spretus, and 70% were variant between inbred strains. Eight (62%) of the 13 repeats that have been mapped lie on Chromosomes (Chr) 4 and 6. This approach is an effective way of generating informative markers on specific chromosomes.     

Expression of Ly-6 on activated T and B cells: Possible identity with Ala-1

The antigens Ala-1 and Ly-6 were first thought to be different on the grounds that Ala-1 was present only on activated T and B lymphocytes while Ly-6 was present only on post-thymic T lymphocytes. In this paper, it is shown that Ly-6 is expressed on activated B cells, including PFC and LPS blasts, and that after typing of several recombinant inbred lines,Ala-1 andLy-6 remain genetically inseparable. Based on available data, it is most likely that Ly-6 is in fact Ala-1, although further testing is required to confirm the absence of Ly-6 from nonactivated lymphocytes.Abbreviations used in this paper Con A concavalin A - LPS lipopolysaccharide - SRBC sheep red blood cells - PFC plaque-forming cells - RI recombinant inbred strains - B6 C57BL/6 mice     

Structural variants of the alpha-fetoprotein gene in different inbred strains of rat

Summary Two structural variants of the rat -fetoprotein (AFP) gene have been detected in different inbred strains of rats by EcoRI or HindIII restriction enzyme cleavage of cellular DNA, agarose gel electrophoresis and Southern blot hybridization using ³²P-labeled cloned rat AFP cDNA probes. The type I AFP gene variant is characteristic of the Sprague-Dawley strain, and type II is found in Buffalo rats. These variants appear to represent two different allelic forms of the rat AFP gene since they are inherited in a normal Mendelian fashion when Sprague-Dawley and Buffalo rats are crossed. The mapping results suggest that the two allelic variants differ from each other by multiple cleavage site variations (base pair substitutions) and by an insertion or deletion of DNA sequences. An extensive sequence variation appears to exist between the two forms of the rat AFP gene; we have estimated that as much as 2.7% of the nucleotides in this region vary between the two alleles.     

Genes for serum amyloid A proteins map to Chromosome 7 in the mouse

Summary Several restriction fragment length variants have been detected among inbred strains using a mouse serum amyloid A cDNA clone. Five variants were shown to segregate as a single genetic unit and were mapped to Chromosome 7 between the glucose phosphate isomerase locus (Gpi-1) and the pink eye dilution locus (p) using recombinant inbred and congenic strains. The finding that no major MspI or BclI restriction fragments were shared between digests of DNAs from a Chromosome 7 congenic strain and its inbred partner, indicate that most, and probably all, sequences detected with the probe are clustered on Chromosome 7. Aneuploid mapping was used to show that the serum amyloid A gene complex (Saa) is proximal to the Chromosome 7 breakpoint in T(7;X)1Ct, a translocation in which the middle third of Chromosome 7 is inserted into the X-chromosome. A survey of inbred strains revealed a single common Saa haplotype and eight rare haplotypes. The complex distribution of 14 different variants suggests that recombination may have played a role in haplotype evolution.This work was supported by grants GM18684 and CA33093 from the National Institute of General Medical Sciences and the National Cancer Institute, respectively.     

The Ig kappa L chain allelic groups among the Ig kappa haplotypes and Ig kappa crossover populations suggest a gene order

The Ig kappa complex locus of inbred mice found on chromosome 6 contains one constant (C kappa), five joining (J kappa), and 100 to 300 variable (V kappa) exons and spans an estimated 500 to 2000 kbp of DNA. The V kappa exons are organized into groups of highly homologous coding regions (approximately 300 bp) separated by approximately 10 kbp of intervening sequence. A group contains from 1 to 30 or more exons (exon refers to uninterrupted coding region DNA which is capable of encoding all or part of V kappa gene) that can be detected with specific DNA probes in conjunction with restriction endonuclease fragments (REF) from genomic DNA. Thirteen DNA probes specific for different V kappa exon groups and one DNA probe specific for J kappa and C kappa exons were used in conjunction with 55 inbred strains in an attempt to detect RFLP that could be used to establish Ig kappa allelic groups and Ig kappa haplotypes. Each probe detected two to four different REF patterns (allelic groups) among the panel of inbred mice examined. Size estimates of the REF were made, and each probe detected 4.2 to 107.7 kbp of DNA, including faint REF, 675.6 to 723.6 kbp of DNA could be detected within a single haplotype. Based on these allelic groups, seven haplotypes were identified among the 55 inbred strains of mice. No subline differences were detected, and the distribution of allelic groups implied common ancestry among many of the inbred strains examined. The DNA probes were also used in conjunction with recombinant inbred, congenic strains and backcross populations of mice. By using the analysis of known Ig kappa r populations, and assuming a common ancestry among the inbred strains, a gene order was predicted: Centromere-Hd-(Ig kappa-V11, Ig kappa-V24, Ig kappa-V9-26)-(Ig kappa-V1, Ig kappa-V9)-(Ig kappa-V4, Ig kappa-V8, Ig kappa-V10, Ig kappa-V12, 13, Ig kappa-V19)-(Ig kappa-V28, Rn7s-6)-Ig kappa-V23-(Ig kappa-V21, Ig kappa-J, Ig kappa-C)-(Ly2, Ly3)-wa-1.     

Genetic interaction between Non-MHC T- and B-cell alloantigens in response to rous sarcomas in chickens

Chickens of Regional Poultry Research Laboratory (RPRL) inbred line 6₃ regress sarcomas induced by Bryan high-titer Rous sarcoma virus to a greater extent than chickens of line RPRL 100, although these lines are identical for the major histocompatibility B complex. They differ, however, at three independent autosomal loci: Ly-4 and Th-1 determine the surface alloantigens of partly overlapping subsets of T lymphocytes, and Bu-1 determines a surface alloantigen of B lymphocytes. The association of genotypes at these loci with quantitative variation in their ability to regress Rous sarcomas was tested in segregating F₄ generation progeny derived from crosses of lines 100 and 6₃. The Ly-4 and Bu-1 genotypes showed association with Rous sarcoma regression, but the Th-1 genotype did not. Chickens of the Ly-4 ^a/Ly-4 ^a, Bu-1 ^b/Bu-1 ^b and Ly-4 ^b/Ly-4 ^b, Bu-1 ^a/Bu-1 ^a genotypes had a significantly higher regressor ability than the other two double homozygous genotypes. These results indicate that higher regression is associated with (1) interaction between the Ly-4 and Bu-1 loci, and (2) complementation between either the line 6 Ly-4 ^a allele and the line 100 Bu-1 ^b allele, or the line 100 Ly-4 ^b allele and the line 6 Bu-1 ^a allele.     

Mapping of mouse intracisternal A-particle proviral markers in an interspecific backcross

We present a linkage map of intracisternal A-particle (IAP) proviral loci. The IAP family consists of 2000 endogenous proviral elements that are widely dispersed in the mouse genome. The map was constructed by using an interspecific backcross and markers defined by oligonucleotide probes specific for subclasses of expressed IAP elements. In genomic DNA from C57BL/6J mouse, these probes each detected from 12 to 44 HindIII restriction fragments that represent junctions between proviral and 5-flanking DNA. The fragments have characteristic strain distribution patterns (SDPs) that are particularly polymorphic in the DNAs of C57BL/6J and Mus spretus mice used for the backcross. IAP loci were placed on the map by comparison of their distribution patterns with those of known genetic markers in the backcross. The map includes 51 IAP loci that have not been previously mapped and 23 IAP proviruses that had been previously mapped in recombinant inbred (RI) strains. Comparable map positions were obtained with the IAP markers in the interspecific backcross and the RI strains. The mapped IAP loci were widely dispersed on the X Chromosome (Chr) and all of the autosomes except Chrs 9 and 19, providing useful genetic markers for linkage studies.