Strain distribution pattern for SSLP markers in the SWXJ recombinant inbred strain set: Chromosomes 1 to 6

We typed 147 simple sequence length polymorphisms in the SWXJ recombinant inbred (RI) strain set spanning Chromosomes (Chrs) 1–6. The strain distribution pattern for these loci was combined with data from 18 previously typed loci for SWXJ, resulting in new chromosome maps for this RI set, with an average density of 3.5 cM between loci. This is the first systematic effort to develop a more highly resolved genetic map for the SWXJ RI set and thereby improves the usefulness of this genetic tool for mapping genes underlying both simple and complex genetic disorders.     

Strain distribution pattern in AXB and BXA recombinant inbred strains for loci on murine Chromosomes 10, 13, 17, and 18

Strain distribution patterns (SDPs) of selected loci previously mapped to murine Chromosomes (Chrs) 10, 13, 17, and 18 are reported for the AXB, BXA recombinant inbred (RI) strain set derived from the progenitor strains A/J (A) and C57BL/6J (B). The loci included the simple sequence length polymorphisms (D10Nds1, D10Mit2, D10Mit10, D10Mit14, D13Mit3, D13Nds1, D13Mit10, D13Mit13, D13Mit7, D13Mit11, D17Mit18, D17Mit10, D17Mit20, D17Mit3, D17Mit2, D18Mit17, D18Mit9, and D18Mit4), the restriction fragment length polymorphisms Pdea and Csfmr, and the biochemical marker AS-1. These loci were chosen because they map to genomic regions that had few or no genetic markers in the AXB, BXA RI set. Several of these loci also were typed in backcross progeny of matings of the (AXB)F₁ to strain A or B. The strain distribution patterns for chromosomes 10, 13, 17, and 18 are reported, and the gene order and map distances determined from the backcross data. The addition of these markers to the AXB, BXA RI strain set increases the genomic region over which linkage for new markers can be detected.     

Improved strain distribution patterns of SMXA recombinant inbred strains by microsatellite markers.

To develop SMXA recombinant inbred (RI) strains as more valuable genetic resources, 302 microsatellite (Mit) loci were added to the strain distribution patterns (SDP) reported previously. The improved SDP were constructed in a total of 1085 loci containing 484 Mit markers, 571 restriction landmark genomic scanning (RLGS) spot markers and 30 others. This substantially improved SDP can be freely accessed on our homepage (http://www.med.nagoya-u.ac.jp/sisetu/SDP.htm).     

Typing recombinant inbred mouse strains for microsatellite markers on Chromosomes 10, 16, 18, 19, and X

A total of 57 different microsatellite variants have been typed in one or more of five different sets of recombinant inbred (RI) mouse strains. The present report concentrates on markers for Chromosomes (Chrs) 10, 16, 18, 19 and X. These markers extend the regions swept in these RI strains, provide reference markers for integrating RI and conventional maps, and provide additional estimates of genetic distances. Multilocus maps, based on maximum likelihood analysis of present and previously published RI SDPs on five chromosomes, are presented. Unexpectedly, three microsatellite markers, previously assigned to Chr 10, detected polymorphic fragments mapping to other chromosomes.     

Enzyme markers in inbred rat strains: Genetics of new markers and strain profiles

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.     

Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana using recombinant inbred lines

A new collection of 129 Arabidopsis thaliana RFLP markers has been established based upon DNA fragments cloned in the pUC119 plasmid vector and insert end sequences of P1 clones. Dominant/null alleles affecting low-copy number sequences account for nine of the mapped polymorphisms, suggesting that deletions are not rare in A. thaliana . Recombinant inbred (RI) lines were used for mapping these marker loci. RI line-based mapping allows integration of this set of markers with markers previously reported as well as with any markers mapped in the future using this replenishable mapping resource. These markers are useful for map-based gene isolation and genome physical mapping in A. thaliana as well as studies of chromosome colinearity (synteny) with related species.     

The SMXA: a new set of recombinant inbred strain of mice consisting of 26 substrains and their genetic profile

A new set of recombinant inbred (RI) strain SMXA consisting of 26 substrains was established between SM/J and A/J. The history of the SMXA RI strains and their genetic prolife covering 158 genetic marker loci are reported. From the strain distribution pattern among SMXA RI strains, the chromosomal location of salivary and tear protein genes Spel-r, Spel-s, Spe2, and Tpe1 were newly determined.     

Strain distribution patterns for genetic markers in the LSXSS recombinant-inbred series

We present the strain distribution patterns (SDPs) of 118 SSLP markers and three pigmentation genes that have been characterized in 27 strains from the LSXSS RI series. This coarse map provides a resource for linkage studies of phenotypes that are heritable in the LSXSS RI series. The LSXSS recombinant inbred (RI) strains were derived from the Long-Sleep (LS) and Short-Sleep (SS) selected lines of mice that were selected for differential sensitivity to ethanol but are also differentially sensitive to a variety of other alcohols, barbiturates, sedative hypnotics, and general anesthetics. Since the parents were not inbred, two atypical factors are present in these SDPs. First, more than two alleles are frequently found in these RIs, and second, some alleles can be uniquely associated with one or the other parent while other alleles may be found in both parental lines. To validate the markers found in the parental line, we genotyped all parental mice from one generation of both the LS and SS lines, thus leading to a set of marker SDPs that are useful for further phenotypic association and identification of provisional QTLs. Received: 15 November 1995 / Accepted: 6 February 1996     

Initial characterization of STS markers in the LSXSS series of recombinant inbred strains

We are mapping quantitative trait loci (QTLs) that influence ethanol-induced anesthesia (sleep time) in the Long-sleep (LS) and Short-sleep (SS) slected lines of mice. Fifty microsatellite-STS markers were initially screened for simple-sequence length polymorphisms between the LS and SS lines. Nineteen markers were polymorphic. Eleven markers unequivocally differentiated the LS and SS lines and were used to establish strain distribution patterns for the LSXSS series of recombinant inbred strains. Five markers each accounted for at least 5% of sleep-time genetic variance among the RI strains. Linkage of provisional QTLs detected among RIs will be confirmed or disproved in a large F₂ population. This ongoing QTL-mapping project eventually will result in a strain distribution pattern for the LSXSS RI series with an average marker spacing of 5 centimorgans.     

Using molecular markers to map multiple quantitative trait loci: models for backcross,recombinant inbred,and doubled haploid progeny

Summary To maximize parameter estimation efficiency and statistical power and to estimate epistasis, the parameters of multiple quantitative trait loci (QTLs) must be simultaneously estimated. If multiple QTL affect a trait, then estimates of means of QTL genotypes from individual locus models are statistically biased. In this paper, I describe methods for estimating means of QTL genotypes and recombination frequencies between marker and quantitative trait loci using multilocus backcross, doubled haploid, recombinant inbred, and testcross progeny models. Expected values of marker genotype means were defined using no double or multiple crossover frequencies and flanking markers for linked and unlinked quantitative trait loci. The expected values for a particular model comprise a system of nonlinear equations that can be solved using an interative algorithm, e.g., the Gauss-Newton algorithm. The solutions are maximum likelihood estimates when the errors are normally distributed. A linear model for estimating the parameters of unlinked quantitative trait loci was found by transforming the nonlinear model. Recombination frequency estimators were defined using this linear model. Certain means of linked QTLs are less efficiently estimated than means of unlinked QTLs.     

Expression of murine leukemia viruses in the highly lymphomatous BXH-2 recombinant inbred mouse strain

Among 12 recombinant inbred strains of mice derived from crossing two strains, C57BL/6J and C3H/HeJ, which have a low incidence of neoplastic disease, one strain (BXH-2) has been found to have a high incidence of lymphoma, of non-T-cell origin, at an early age. The BXH-2 strain carries the Fv-1b allele and spontaneously expresses a B-tropic murine leukemia virus beginning at as early as 10 days of gestation and continuing throughout their life. No significant differences in ecotropic virus titers were observed at any age tested (16 to 17 days of gestation through 7 months), whereas xenotropic virus was first detected in lymphoid tissues of 2-month-old mice and virus titers increased with age. Dual tropic virus(es), which induced cytopathic changes on mink lung cells, was isolated from BXH-2 lymphomatous tissues. Unlike AKR mink lung focus-forming virus (N-tropic recombinant), BXH-2 dual tropic virus is B tropic and induces cytopathic changes in mouse fibroblast cultures as well. The BXH-2 mouse provides a model system for studying the role of replication-competent viruses in spontaneously occurring leukemias of non-T-cell lineage and neurological disease.     

Trichinella spiralis: Characterization and strain distribution of rapid expulsion in inbred mice

Appropriately immunized mice display a response that is biologically equivalent to rat rapid expulsion. Only two inbred strains ($\text{NFR}\text{N}\text{and}\text{NFS}\text{N}$ derived from NIH Swiss mice) have been shown to respond in this manner. Mice of the $\text{Balb}\text{c}$, CBA, $\text{A}\text{He}$, C₃H, SJL, or C₅₇Bl strains are “nonresponders” which require approximately twice as much intestinal exposure (in days) to Trichinella spiralis to elicit a response half as effective. Genetically, the responder is dominant, autosomal, and does not appear to be linked to the MHC. The characteristics of mouse and rat rapid expulsion of T. spiralis are not identical but share these features: initial rejection within 24 hr of challenge; a rejection efficiency >90%, from 1 to 5 weeks after the primary; induction of response does not require exposure to the complete infection; rapid expulsion is immunologically specific for preadults; adult worms are resistant. While a genetic basis for responsiveness exists in mice there is, as yet, no evidence for genetic control in rats. In both mice and rats, rapid expulsion is distinguished from the intestinal hyperreactivity associated with rejection of the primary infection by the kinetics and amplitude of the rejection of transplanted adult worms.     

A note on the effect of within-strain sample sizes on QTL mapping in recombinant inbred strain studies

This note explores the effect of within-strain sample sizes on the correlations between a phenotype and a molecular-genetic marker in a battery of inbred strains. It is shown that the maximum correlation possible between a molecular marker and a behavioral or neuronal phenotype equals the additive-genetic correlation. How close the strain correlation will approach the additive-genetic correlation depends only on heritability and within-strain sample sizes. The equations derived can be used to optimize designs of studies attempting to localize Quantitative Trait Loci utilizing Recombinant Inbred Strains, provided information about the heritability of the character under study is available.     

Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

A diversity array technology (DArT) marker platform was developed for the cotton genome, to evaluate the use of DArT markers compared with AFLP markers in mapping and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium L. that already contained ~5000 loci, which coalesced into 26 chromosomes, to anchor newly developed DArT and AFLP markers with the aim of further improving utility and map resolution. Our results indicated that the percentage of polymorphic DArT markers that could be genetically mapped (78.15%) was much higher than that of AFLP markers (22.28%). Sequence analysis of DArT markers indicated that a majority matched known expressed sequence tag (EST) sequences from tetraploid and diploid Gossypium species. A total of 794 Arabidopsis genes were homologous with various DArT marker sequences. Chromosomes 5(A), 7(A), 19(D), 23(D), and 24(D) had more Arabidopsis syntenic DArT markers than the other chromosomes. Anchoring DArT markers from the reference map to a recombinant inbred line (RIL) map indicated that DArT markers will speed the building of maps in de novo RIL populations.