Peter Mathern

Linkage map of 10 polymorphic markers on rat chromosome 2

Analysis of F2 intercross progeny of inbred F344/N x LEW/N rats led to the assignment of 10 polymorphic PCR-typable markers to rat chromosome 2. The markers form a single linkage group covering 47.9 cM with the following order: D2N1R-D2N28-FGG (gamma fibrinogen)-PKLR (liver and RBC pyruvate kinase)-ATP1A1 (the alpha-1 polypeptide of Na+/K+ transporting ATPase)-HSD3B (hydroxy-delta-5-steroid dehydrogenase)-D2N2R-D2N91-CAMKI (calmodulin-dependent protein kinase II)-D2N35. All but two of the markers (D2N1R and D2N2R) were detected using specific PCR primers flanking dinucleotide repeats. Sequences with dinucleotide repeats associated with five genes (FGG, PKLR, ATP1A1, HSD3B, and CAMKI) were identified in GenBank, and primers were designed to flank these repeats. The PCR primer pairs for three anonymous markers (D2N28, D2N91, and D2N35) were identified by sequencing cloned LEW/N rat genomic DNA containing (CA)n.(GT)n repeats. D2N1R and D2N2R were identified by PCR amplification of genomic DNA with single, nonspecific 10-base oligonucleotide primers. All of the markers were codominant except for D2N1R, D2N2R, and CAMKI, which only amplified from F344/N homozygous and heterozygous rat DNA. The seven codominant markers were highly polymorphic in 10 other inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, and ACI/N), suggesting that they will be useful for general mapping studies among these strains. Comparative gene mapping analysis indicated that a portion of the mapped region of rat chromosome 2 exhibits synteny conservation with regions of human chromosome 1 and mouse Chromosome 3.

Linkage map of seven polymorphic markers on rat chromosome 18

A genetic linkage map of seven polymorphic markers was created with F2 intercross progeny of F344/N and LEW/N rats and assigned to rat Chromosome (Chr) 18. Five of the markers described were defined by simple sequence length polymorphisms (SSLPs) associated with five genes: transthyretin (TTR), trypsin inhibitor-like protein (TILP), β2 adrenergic receptor (ADRB2), olfactory neuron-specific G protein (OLF), and gap junction protein (GJA1). One marker was defined by a restriction fragment length polymorphism (RFLP) detected with a probe for the human colony stimulating factor 1 receptor (CSF1R) gene. The D18N1R locus was defined by an anonymous DNA fragment amplified by the randomly amplified polymorphic DNA (RAPD) technique with a single short primer. These seven DNA loci formed a single genetic linkage group 30.4 cM in length with the following order: TTR-6.8 cM-D18N1R-9.1 cM-TILP-4.3 cM-CSF1R-0 cM-ADRB2-10.2 cM-OLF-0 cM-GJA1. The five SSLP markers were highly polymorphic. In a total of 13 inbred rat strains analyzed (F344/ N, LEW/N, LOU/MN, WBB1/N, WBB2/N, MR/N, MNR/N, ACI/N, SHR/N, WKY/N, BN/SsN, BUF/N, and LER/N), three to six alleles were detected for each marker. Remarkable linkage conservation was detected between the region of rat Chr 18 mapped and a region of mouse Chr 18. However, genes associated with these markers have been mapped to three different human chromosomes (Chrs 5, 6, and 18). The markers described here should be useful for genetic mapping studies and genetic monitoring of inbred rat strains.

Map of seven polymorphic markers on rat Chromosome 14: linkage conservation with human Chromosome 4

Seven polymorphic markers identified by polymerase chain reaction (PCR) amplification, including markers for six genes—DRD1L (dopamine receptor, D1-like-2), GLUKA (glucokinase), PF4 (platelet factor 4), ALB (albumin), AFP (α-fetoprotein), and BSP (bone sialoprotein)—and one anonymous locus (D14N52), were mapped to a single 67-cM linkage group with F2 intercross progeny of F344/N and LEW/N inbred rat strains. Two of these markers, ALB and AFP, have previously been assigned to rat Chromosome (Chr) 14, allowing assignment of this entire linkage group. Five of the markers—DRD1L, PF4, ALB, AFP, and PBSP—have been physically mapped to a large region of human Chr 4 encompassing the p arm and the q arm to band q28. Homologs of two of the markers, ALB and AFP, have been mapped to Chr 5 in the mouse. Comparison of human Chr 4 with the homologous regions on Chr 14 of the rat and Chr 5 of the mouse indicated that linkage conservation with human Chr 4 extends over a greater region in the rat than in the mouse. The markers described here were found to be highly polymorphic in twelve inbred strains (F344/N, LEW/N, ACI/N, BUF/N, BN/SsN, LOU/MN, MNR/N, MR/N, SHR/N, WBB1/N, WBB2/N, and WKY/N). These polymorphic markers should be useful in genetic linkage studies of important phenotypes in rats.

A single linkage group comprising 11 polymorphic DNA markers on rat chromosome 3.

Eleven polymorphic DNA markers were mapped to rat Chromosome (Chr) 3 by linkage analysis of F2 progeny of F344/N and LEW/N rat strains. The markers, including seven genes and four anonymous loci, formed a single linkage group covering approximately 112 cM with the following order: Ptgs1 (prostaglandin G/H synthase I)-D3Arb178-Scn2a (sodium channel, type II, α-polypeptide)-D3Arb1-Cat (catalase)-Bdnf (brain-derived neurotrophic factor)-D3Arb219-D3Arb2-Sus2 (seminal vesicle secretion II protein)-Sdc4 (ryudocan/syndecan4)-Stnl (statin-like protein). Eight of these markers were analyzed for polymorphisms in 14 additional inbred rat strains. Three to five alleles were detected for each marker, suggesting that they are highly polymorphic and useful for genetic mapping studies with inbred rat strains. Chromosomal syntenic conservation among rats, mice and humans is also discussed.

Genetic map of seven polymorphic markers comprising a single linkage group on rat chromosome 5.

Seven polymorphic markers comprising a single linkage group were assigned to rat Chromosome (Chr) 5 by linkage analysis of the progeny of an F2 intercross of Fischer (F344/N) and Lewis (LEW/N) inbred rats. Three genes, α-L-fucosidase 1 (FUCA1), mitochondrial superoxide dismutase (SOD2), and glucose transporter (GLUT1), were mapped by restriction fragment length polymorphism (RFLP) analysis. Two genes, glucose transporter (GTG3) and elastase II (ELAII), one pseudogene for α tubulin (TUBAPS), and one sequence related to the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene (PFKFBP1-related sequence) were mapped by simple sequence repeat (SSR) polymorphism analysis. The loci are in the following order: SOD2, GTG3/GLUT1, FUCA1, ELAII/PFKFBP1-related sequence, and TUBAPS. This linkage group covered 68.3 cM of rat Chr 5. The SSR markers were highly polymorphic in 13 inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, ACI/N, LER/N, F344/N, and LEW/N). These markers, located on rat Chr 5, will be useful in genetic studies of inbred rats.

Genetic map of 16 polymorphic markers forming three linkage groups assigned to rat Chromosome 4

Sixteen polymorphic markers, including markers for eight new loci, forming three linkage groups, were assigned to rat Chromosome (Chr) 4 by linkage analysis of the progeny of an F2 intercross of Fischer (F344/N) and Lewis (LEW/N) inbred rats. One gene, Igk, was mapped by restriction fragment length polymorphism (RFLP) analysis. One marker for Tcrb was identified by the polymorphic insertion of a repetitive LINE element. The remaining 14 markers contained polymorphic simple sequence repeats (SSRs). Ten were identified in genes (Tgfa, Npy, Prss1, Prss2, Aldr1, Iapp, Prp, Eno2, Cacnlla1, and Il6), one was identified in a sequence related to a gene (Egr4l1), and three were identified in anonymous DNA segments. The SSR markers were highly polymorphic in 16 inbred rat strains. These markers expand the genetic map of the rat and should be useful in future genetic studies of inbred rats.

Genetic map of eight microsatellite markers comprising two linkage groups on rat chromosome 6.

Five genes and three anonymous DNA loci were mapped to rat chromosome 6 by genetic linkage and somatic cell hybrid analyses. The eight loci were all identified by PCR-based microsatellite polymorphism analysis and were characterized in 40 F2 intercross progeny of Fischer (F344/N) and Lewis (LEW/N) inbred rats for segregation analysis. These markers formed two linkage groups spanning, respectively, 58.1 cM and 4.0 cM. The first linkage group is comprised of two anonymous DNA loci and four genes with the following map order and distances: D6Cep8 (previously D3)-17.9 cM-D6Arb309-2.5 cM-Vsnl1 (neural visinin-like protein)-20.4 cM-Prkar2b (type IIb regulatory subunit of cAMP-dependent protein kinase)-8.8 cM-Fkhl1 (forkhead-like transcription factor BF-1)-8.5 cM-Rnu1c (18-3A U1 RNA). The second linkage group is comprised of one gene, Ckb (creatine kinase, brain) and one anonymous DNA locus, D6Arb54, separated by 4.0 cM. For each marker, two to eight alleles were detected in a panel of 16 inbred rat strains (ACI/N, BN/SsN, BUF/N, DA/Bk1, F344/N, LER/N, LEW/N, LOU/MN, MNR/N, MR/N, SHR/N, SR/Jr, SS/Jr, WBB1/N, WBB2/N, and WKY/N). Comparative mapping information indicated that rat chromosome 6 exhibits syntenic conservation with mouse chromosome 12. Homologs of the rat chromosome 6 loci have been identified on human chromosomes 2, 7, and 14.

Nine polymorphic markers characterized by polymerase chain reaction techniques form two linkage groups on rat chromosome 8

Five genes and four anonymous polymorphic markers, forming two linkage groups, were mapped in F2 intercross progeny of F344/N x LEW/N rats using polymerase chain reaction (PCR) techniques. Both linkage groups were assigned to rat chromosome 8 because they contained genetic loci previously mapped to this chromosome. The first group was comprised of markers for three anonymous loci and two gene loci, thymus cell antigen-1 (Thy1) and tropoelastin (Eln). The second group was comprised of markers for one anonymous locus and three gene loci, cellular retinol binding protein II (Rbp2), matrin F/G (Matr1), and acyl-peptide hydrolase (Apeh). Seven markers (identified by simple sequence repeat associated length polymorphisms) were characterized in an additional 13 inbred rat strains (ACI/N, BN/SsN, BUF/N, LER/N, LOU/MN, MNR/N, MR/N, SHR/N, SR/Jr, SS/Jr, WBB1/N, WBB2/N, and WKY/N). Two to six alleles were detected for each marker. The reported markers should facilitate genetic mapping and monitoring of inbred rat strains.

The origin of the autoimmune disease-resistant LER rat : an outcross between the Buffalo and autoimmune disease-prone Lewis inbred rat strains

The Lewis (LEW) rat strain is highly susceptible to a large number of experimentally induced inflammatory and autoimmune diseases. The Lewis resistant (LER) rat strain, which reportedly arose as a spontaneous mutation in a closed colony of LEW rats, is resistant to many of these disorders. The mechanism of resistance is not yet clear. We report the analysis of 19 simple dinucleotide repeat polymorphisms in 13 rat strains including the LEW/N and LER/N rat strains. The LEW/N and LER/N alleles were the same in only 42% of cases. For all of the other polymorphisms, the LER/N and Buffalo (BUF/N) rat strain alleles were identical. These data provide evidence that the LER strain did not arise as a spontaneous mutation in the LEW strain but is the result of an outcross between the LEW and BUF rat strains. The LER rat strain is now a recombinant inbred rat strain. This information should facilitate the genetic analysis of the loci responsible for resistance to experimental autoimmune disease in the LER rat.

Simple sequence repeat length polymorphisms mapped to rat chromosome 11.

Two genes and two anonymous DNA loci were mapped to rat chromosome 11 using F2 intercross progeny of Fischer (F344/N) and Lewis (LEW/N) inbred rats. These four loci formed a single linkage group covering 21.5 cM with the following map order: somatostatin (SST)-D11N161-D11N18-cell surface protein (MOX2). These four loci were typed by PCR-based simple sequence repeat (SSR) length polymorphism detection. For each marker four to seven different alleles were detected using a panel of 13 inbred rat strains (F344/N, LEW/N, BN/SsN, BUF/N, LER/N, MR/N, MNR/N, LOU/MN, ACI/N, WBB1/N, WBB2/N, SHR/N, WKY/N). Comparative gene mapping analysis suggests syntenic conservation between rat chromosome 11 and mouse Chromosome 16.