Chromosome Substitution Strains Research Articles

Confirmation of provisional quantitative trait loci for voluntary alcohol consumption: genetic analysis in chromosome substitution strains and F2 crosses derived from A/J and C57BL/6J progenitors

Earlier research utilizing AXB/BXA recombinant inbred (RI) and AcB/BcA recombinant congenic (RC) strains of mice independently mapped provisional quantitative trait loci (QTL) for voluntary alcohol consumption (VAC) to common chromosomal regions. This study was designed to confirm QTL on chromosomes 2, 3, 5, 7, and 15 in an A/J (A)xC57Bl/6J (B6) F2 cross, and a panel of B6.A chromosome substitution strains (CSS). AxB6F2 mice, CSS, and A/J and C57BL/6J progenitors were tested for VAC. Previously identified QTL regions were targeted for genotyping in the AxB6F2 mice. Among the AxB6F2 mice, significant differences in VAC were associated with loci on chromosome 2 (peak marker D2Mit367) and chromosome 3 (D3Mit189). Additionally, a significant interaction was observed between loci on chromosome 15 (D15Mit245) and chromosome 2 (D2Mit367). A survey of the CSS panel provided further evidence for VAC QTLs on chromosomes 2 and 15. In the CSS panel, lower ethanol consumption was observed in those strains carrying the A/J 2 or 15 chromosome on a B6 background. This finding is consistent with the allelic influences observed in AxB6F2 mice in this study and those reported previously in the RI and RC strains of mice. Specifically, A/J alleles were associated with decreased ethanol consumption whereas C57BL/6J alleles were associated with increased ethanol consumption. The present results confirm previously reported QTL, on chromosomes 2 and 15 for VAC in RI and RC strains. Collectively, the regions on chromosomes 2 and 15 have now been replicated in at least three independent crosses derived from the A/J and C57BL/6J progenitors. The identification of potential candidate genes for the chromosome 15 QTL is discussed in the context of an in-silico analysis.

Differences in DBA/1J and DBA/2J reveal lipid QTL genes

Recent advances in mouse genomics have revealed considerable variation in the form of single-nucleotide polymorphisms (SNPs) among common inbred strains. This has made it possible to characterize closely related strains and to identify genes that differ; such genes may be causal for quantitative phenotypes. The mouse strains DBA/1J and DBA/2J differ by just 5.6% at the SNP level. These strains exhibit differences in a number of metabolic and lipid phenotypes, such as plasma levels of triglycerides (TGs) and HDL. A cross between these strains revealed multiple quantitative trait loci (QTLs) in 294 progeny. We identified significant TG QTLs on chromosomes (Chrs) 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 16, and 19, and significant HDL QTLs on Chrs 3, 9, and 16. Some QTLs mapped to chromosomes with limited variability between the two strains, thus facilitating the identification of candidate genes. We suggest that Tshr is the QTL gene for Chr 12 TG and HDL levels and that Ihh may account for the TG QTL on Chr 1. This cross highlights the advantage of crossing closely related strains for subsequent identification of QTL genes.

Pathophysiological, Genetic and Gene Expression Features of a Novel Rodent Model of the Cardio-Metabolic Syndrome

BackgroundComplex etiology and pathogenesis of pathophysiological components of the cardio-metabolic syndrome have been demonstrated in humans and animal models.Methodology/Principal FindingsWe have generated extensive physiological, genetic and genome-wide gene expression profiles in a congenic strain of the spontaneously diabetic Goto-Kakizaki (GK) rat containing a large region (110 cM, 170 Mb) of rat chromosome 1 (RNO1), which covers diabetes and obesity quantitative trait loci (QTL), introgressed onto the genetic background of the normoglycaemic Brown Norway (BN) strain. This novel disease model, which by the length of the congenic region closely mirrors the situation of a chromosome substitution strain, exhibits a wide range of abnormalities directly relevant to components of the cardio-metabolic syndrome and diabetes complications, including hyperglycaemia, hyperinsulinaemia, enhanced insulin secretion both in vivo and in vitro, insulin resistance, hypertriglyceridemia and altered pancreatic and renal histological structures. Gene transcription data in kidney, liver, skeletal muscle and white adipose tissue indicate that a disproportionately high number (43–83%) of genes differentially expressed between congenic and BN rats map to the GK genomic interval targeted in the congenic strain, which represents less than 5% of the total length of the rat genome. Genotype analysis of single nucleotide polymorphisms (SNPs) in strains genetically related to the GK highlights clusters of conserved and strain-specific variants in RNO1 that can assist the identification of naturally occurring variants isolated in diabetic and hypertensive strains when different phenotype selection procedures were applied.ConclusionsOur results emphasize the importance of rat congenic models for defining the impact of genetic variants in well-characterised QTL regions on in vivo pathophysiological features and cis-/trans- regulation of gene expression. The congenic strain reported here provides a novel and sustainable model for investigating the pathogenesis and genetic basis of risks factors for the cardio-metabolic syndrome.

Complex genetic regulation of bone mineral density and insulin-like growth factor-I in C57BL/6J-Chr #A/J/NaJ chromosome substitution strains

Low bone mineral density (BMD) is a phenotype associated with osteoporosis and increased risk of fracture. Since 60-80% of variation in BMD is associated with genetic factors, we used the novel approach of chromosome substitution strains (CSS) to identify chromosomes that harbor genes that regulate BMD. Specifically, we evaluated 24 wk old C57BL/6J-Chr #(A/J)/NaJ CSS (n = 7 to 18) in which each chromosome in the host C57BL/6J strain is replaced by a corresponding chromosome from the donor A/J strain (19 autosomes, X, Y). We determined several A/J chromosomes contribute to body weight (BW), percent body fat (BF), whole body areal BMD (aBMD), and serum insulin-like growth factor (IGF)-I in both a positive and negative manner when compared with C57BL/6J. Specifically, C57BL/6J-Chr 5(A/J)/NaJ (B.A-5) (males) and B.A-13 (females) contributed to increased BW, whereas B.A-3, 4, 8, 9, 12, and 18 (males) and B.A-3, 4, and 11 (females) contributed to reduced BW. B.A-5 (males) and B.A-13 (females) contributed to increased BF, whereas B.A-12 (males) and B.A-3, 4, 10, and 11 (females) contributed to reduced BF. B.A-14 (females) contributed to increased aBMD and B.A-1, 2, 6, 9, 10, and 18 (males) and B.A-8, 9, and 10 (females) contributed to reduced aBMD. To determine if similar chromosomes regulate aBMD and IGF-I, we determined serum concentrations of IGF-I. B.A-14 and Y (males) and B.A-6 (females) contributed to increased IGF-I and male B.A-3 and female B.A-8 contributed to reduced IGF-I. Overall, we identified several sex-dependent and -independent chromosomes that regulate aBMD and IGF-I in adult mice.

Differential genetic regulation of motor activity and anxiety-related behaviors in mice using an automated home cage task.

Traditional behavioral tests, such as the open field test, measure an animal's responsiveness to a novel environment. However, it is generally difficult to assess whether the behavioral response obtained from these tests relates to the expression level of motor activity and/or to avoidance of anxiogenic areas. Here, an automated home cage environment for mice was designed to obtain independent measures of motor activity levels and of sheltered feeding preference during three consecutive days. Chronic treatment with the anxiolytic drug chlordiazepoxide (5 and 10 mg/kg/day) in C57BL/6J mice reduced sheltered feeding preference without altering motor activity levels. Furthermore, two distinct chromosome substitution strains, derived from C57BL/6J (host strain) and A/J (donor strain) inbred strains, expressed either increased sheltering preference in females (chromosome 15) or reduced motor activity levels in females and males (chromosome 1) when compared to C57BL/6J. Longitudinal behavioral monitoring revealed that these phenotypic differences maintained after adaptation to the home cage. Thus, by using new automated behavioral phenotyping approaches, behavior can be dissociated into distinct behavioral domains (e.g., anxiety-related and motor activity domains) with different underlying genetic origin and pharmacological responsiveness.

Resistance to diet-induced obesity in mice with a single substituted chromosome

Obesity and its comorbidities are taking an increasing toll on human health. Key pathways that were identified with single gene variants in humans and model organisms have led to improved understanding and treatment of rare cases of human obesity. However, similar progress remains elusive for the more common multifactorial cases of metabolic dysfunction and disease. A survey of mouse chromosome substitution strains (CSSs) provided insight into the complex genetic control of diet-induced obesity and related conditions. We now report a survey of 60 traits related to obesity and metabolic syndrome in mice with a single substituted chromosome as well as selected traits measured in congenic strains derived from the substituted strain. We found that each strain that was resistant to diet-induced obesity had a distinct phenotype that uniquely modeled different combinations of traits related to metabolic disease. For example, the chromosome 6 CSS remained insulin resistant in the absence of obesity, demonstrating an atypical relationship between body weight and insulin resistance. These results provide insights into the genetic control of constant components of this mouse model of diet-induced metabolic disease as well as phenotypes that vary depending on genetic background. A better understanding of these genotype-phenotype relationships may enable a more individualized diagnosis and treatment of obesity and the metabolic syndrome.

Quantitative trait locus analysis for hemostasis and thrombosis.

Susceptibility to thrombosis varies in human populations as well as many in inbred mouse strains. The objective of this study was to characterize the genetic control of thrombotic risk on three chromosomes. Previously, utilizing a tail-bleeding/rebleeding assay as a surrogate of hemostasis and thrombosis function, three mouse chromosome substitution strains (CSS) (B6-Chr5(A/J), Chr11(A/J), Chr17(A/J)) were identified (Hmtb1, Hmtb2, Hmtb3). The tail-bleeding/rebleeding assay is widely used and distinguishes mice with genetic defects in blood clot formation or dissolution. In the present study, quantitative trait locus (QTL) analysis revealed a significant locus for rebleeding (clot stability) time (time between cessation of initial bleeding and start of the second bleeding) on chromosome 5, suggestive loci for bleeding time (time between start of bleeding and cessation of bleeding) also on chromosomes 5, and two suggestive loci for clot stability on chromosome 17 and one on chromosome 11. The three CSS and the parent A/J had elevated clot stability time. There was no interaction of genes on chromosome 11 with genes on chromosome 5 or chromosome 17. On chromosome 17, twenty-three candidate genes were identified in synteny with previously identified loci for thrombotic risk on human chromosome 18. Thus, we have identified new QTLs and candidate genes not previously known to influence thrombotic risk.

Short-term selective breeding for High and Low prepulse inhibition of the acoustic startle response; pharmacological characterization and QTL mapping in the selected lines

Selective breeding offers several important advantages over using inbred strain panels in detecting genetically correlated traits to the selection phenotype. The purpose of the current study was to selectively breed for prepulse inhibition (PPI) of the acoustic startle response (ASR), to pharmacologically and behaviorally characterize the selected lines and to use the lines for quantitative trait loci (QTL) mapping. Starting with heterogeneous stock mice formed by crossing the C57BL/6J, DBA/2J, BALB/cJ and LP/J inbred strains and using a short-term selective breeding strategy, animals were selected for High and Low PPI. The selection phenotype was the 80 dB prepulse tone (15 dB above the background noise). After five generations of selection, the High and Low lines differed significantly (78.1 ± 3.1 vs. 45.2 ± 3.9 [percent inhibition], p < 0.00001). The effects of haloperidol and MK-801 on PPI were not different between the High and Low lines. However, at the highest dose tested (10 mg/kg), the High line was more sensitive than the Low line to the disruptive PPI effects of methamphetamine. The lines did not differ in terms of basal activity or methamphetamine-induced changes in locomotor activity. The High and Low lines were genotyped using a panel of 768 SNPs. Significant QTLs (LOD > 10) were detected on chromosomes 11 and 16 that appeared similar to those detected previously [Hitzemann, R., Bell, J., Rasmussen, E., McCaughran, J. Mapping the genes for the acoustic startle response (ASR) and prepulse inhibition of the ASR in the BXD recombinant inbred series: effect of high-frequency hearing loss and cochlear pathology. In: Willott JF, editor. Handbook of mouse auditory research: From behavior to molecular biology. New York: CRC Press; 2001. p. 441–455.; Petryshen, T.L., Kirby, A., Hammer, R.P. Jr, Purcell, S., O'Leary, S.B., Singer, J.B., et al. Two quantitative trait loci for prepulse inhibition of startle identified on mouse chromosome 16 using chromosome substitution strains. Genetics 2005; 171: 1895–1904.]. Overall, the current study illustrates that the heritability of PPI is sufficient for short-term selective breeding and that the lines which are developed can be used to characterize the factors associated with the regulation of PPI.

Diverse effects of stanozolol in C57BL/6J and A/J mouse strains

Although skeletal muscle is the principal target for androgenic anabolic steroids (AAS) other physiological and behavioral processes are also affected. Wide variations in response to AAS are known to exist in individuals but the genetic basis of this has hardly been explored. Female mice from the A/J and C57BL/6J strains were divided into four experimental groups: CTRL-Sham, housed in a regular mouse cage and subjected to a sham operation mimicking implantation of steroids; CTRL-AAS, mice similarly housed and implanted with a pellet containing stanozolol (release rate, 4.6 mg/kg/day); EX-Sham, sham operated mice housed in a cage with two towers which required mice to climb 1 m to obtain food or water; EX-AAS, mice similarly housed and implanted with a stanozolol pellet. The experimental treatment was initiated at 10 weeks of age and lasted for 7 weeks. Body weight was assessed periodically during the experiment (time effect), systolic blood pressure (BP) and heart rate (HR) were measured after 6 weeks of treatment, and weights of gastrocnemius (GAST), soleus, tibialis anterior (TA), extensor digitorum longus (EDL), quadriceps femoris (QF) and biceps brachii (BB) muscles, heart, liver, kidney and abdominal fat were measured after 7 weeks of treatment. AAS treatment significantly increased weight of GAST (P << 0.001), TA (P < 0.01), EDL (P < 0.01) and QF (P << 0.001) muscles in both of the strains. Several of the measured indices were differentially affected in the two strains by AAS (body weight, Time x Strain x AAS P < 0.02; BP and HR, Strain x AAS P < 0.03 and P < 0.01, respectively). These findings encourage the view that recombinant inbred strains and chromosome substitution strains derived from the A/J and C57BL/6J mice can be utilized to explore the genetic architecture of these interactions in order to elucidate the mechanism underlying both the positive and negative health-related effects of AAS.

A Quantitative Trait Locus (LSq-1) on Mouse Chromosome 7 Is Linked to the Absence of Tissue Loss After Surgical Hindlimb Ischemia

Peripheral arterial disease (PAD) caused by occlusive atherosclerosis of the lower extremity has 2 major clinical manifestations. Critical limb ischemia is characterized by rest pain and/or tissue loss and has a > or = 40% risk of death and major amputation. Intermittent claudication causes pain on walking, has no tissue loss, and has amputation plus mortality rates of 2% to 4% per year. Progression from claudication to limb ischemia is infrequent. Risk factors in most PAD patients overlap. Thus, we hypothesized that genetic variations may be linked to presence or absence of tissue loss in PAD. Hindlimb ischemia (murine model of PAD) was induced in C57BL/6, BALB/c, C57BL/6 x BALB/c (F1), F1 x BALB/c (N2), A/J, and C57BL/6J-Chr7(A/J)/NaJ chromosome substitution strains. Mice were monitored for perfusion recovery and tissue necrosis. Genome-wide scanning with polymorphic markers across the 19 murine autosomes was performed on the N2 mice. Greater tissue loss and poorer perfusion recovery occurred in BALB/c than in the C57BL/6 strain. Analysis of 105 N2 progeny identified a single quantitative trait locus on chromosome 7 that exhibited significant linkage to both tissue necrosis and extent of perfusion recovery. Using the appropriate chromosome substitution strain, we demonstrate that C57BL/6-derived chromosome 7 is required for tissue preservation. We have identified a quantitative trait locus on murine chromosome 7 (LSq-1) that is associated with the absence of tissue loss in a preclinical model of PAD and may be useful in identifying gene(s) that influence PAD in humans.

A locus on distal chromosome 10 ( ahl4) affecting age-related hearing loss in A/J mice

The ahl locus, shown to be a strain-specific Cdh23 dimorphism, contributes to age-related hearing loss in many inbred mouse strains. A/J mice begin to lose hearing by 4 weeks of age, much earlier than C57BL/6J (B6) mice, although both strains have the same Cdh23 ahl variant. Here, we use recombinant inbred strains, chromosome substitution strains, and a linkage backcross to map a locus on distal Chromosome 10, designated ahl4, that contributes to the early-onset hearing loss of A/J mice. Cochleae of 9-week-old A/J mice exhibit inner and outer hair cell loss from the basal turn through the apical turn, with outer hair cell loss at the base being severest. To quantify the progression of hair cell loss, cytocochleograms were evaluated from 0 to 20 weeks of age. A/J mice showed evidence of hair cell loss in the base of the cochlea as early as 14 days of age and the magnitude and extent of loss increased rapidly during the following 2–5 months. Hair cell loss occurred earlier and was much more severe and widespread in A/J mice than in B6 mice during the first 5 months of age. Spiral ganglion neurons, cells of the stria vascularis, and vestibular hair cell densities, however, appeared normal in 20-week-old A/J mice.

Mouse inter-subspecific consomic strains for genetic dissection of quantitative complex traits

Consomic strains, also known as chromosome substitution strains, are powerful tools for assigning polygenes that control quantitative complex traits to specific chromosomes. Here, we report generation of a full set of mouse consomic strains, in which each chromosome of the common laboratory strain C57BL/6J (B6) is replaced by its counterpart from the inbred strain MSM/Ms, which is derived from Japanese wild mouse, Mus musculus molossinus. The genome sequence of MSM/Ms is divergent from that of B6, whose genome is predominantly derived from Western European wild mouse, Mus musculus domesticus. MSM/Ms exhibits a number of quantitative complex traits markedly different from those of B6. We systematically determined phenotypes of these inter-subspecific consomic strains, focusing on complex traits related to reproduction, growth, and energy metabolism. We successfully detected more than 200 statistically significant QTLs affecting 26 traits. Furthermore, phenotyping of the consomic strains revealed that the measured values for quantitative complex traits often far exceed the range between B6 host and MSM/Ms donor strains; this may result from segregation of alleles or nonadditive interactions among multiple genes derived from the two mouse subspecies (that is, epistasis). Taken together, the results suggest that the inter-subspecific consomic strains will be very useful for identification of latent genetic components underlying quantitative complex traits.

Mouse consomic strains: Exploiting genetic divergence between Mus m. musculus and Mus m. domesticus subspecies

Consomic (chromosome substitution) strains (CSs) represent the most recent addition to the mouse genetic resources aimed to genetically analyze complex trait loci (QTLs). In this study, we report the development of a set of 28 mouse intersubspecific CSs. In each CS, we replaced a single chromosome of the C57BL/6J (B6) inbred strain (mostly Mus m. domesticus) with its homolog from the PWD/Ph inbred strain of the Mus m. musculus subspecies. These two progenitor subspecies diverged less than 1 million years ago and accumulated a large number of genetic differences that constitute a rich resource of genetic variation for QTL analyses. Altogether, the 18 consomic, nine subconsomic, and one conplastic strain covered all 19 autosomes, X and Y sex chromosomes, and mitochondrial DNA. Most CSs had significantly lower reproductive fitness compared with the progenitor strains. CSs homosomic for chromosomes 10 and 11, and the C57BL/6J-Chr X males, failed to reproduce and were substituted by less affected subconsomics carrying either a proximal, central, or distal part of the respective chromosome. A genome-wide scan of 965 DNA markers revealed 99.87% purity of the B6 genetic background. Thirty-three nonsynonymous substitutions were uncovered in the protein-coding regions of the mitochondrial DNA of the B6.PWD-mt conplastic strain. A pilot-phenotyping experiment project revealed a high number of variations among B6.PWD consomics.

Chromosomal Assignment of Quantitative Trait Loci Influencing Modified Hole Board Behavior in Laboratory Mice using Consomic Strains, with Special Reference to Anxiety-related Behavior and Mouse Chromosome 19

Male mice from a panel of chromosome substitution strains (CSS, also called consomic strains or lines)--in which a single full-length chromosome from the A/J inbred strain has been transferred onto the genetic background of the C57BL/6J inbred strain--and the parental strains were examined in the modified hole board test. This behavioral test allows to assess for a variety of different motivational systems in parallel (i.e. anxiety, risk assessment, exploration, memory, locomotion, and arousal). Such an approach is essential for behavioral characterization since the motivational system of interest is strongly influenced by other behavioral systems. Both univariate and bivariate analyses, as well as a factor analysis, were performed. The C57BL/6J and A/J mouse parental inbred strains differed in all motivational systems. The chromosome substitution strain survey indicated that nearly all mouse chromosomes (with the exception of chromosome 2) each contain at least one quantitative trait locus (QTL) that is involved in modified hole board behavior. The results agreed well with previous reports of QTLs for anxiety-related behavior using the A/J and C57BL/6J as parental strains. The present study confirmed that mouse chromosomes 5, 8, 10, 15, 18 and 19 likely contain at least one anxiety QTL. There was also evidence for a novel anxiety QTL on the Y chromosome. With respect to anxiety-related avoidance behavior towards an unprotected area, we have special interest for mouse chromosome 19. CSS-19 (C57BL/6J-Chr19(A)/NaJ) differed in avoidance behavior from the C57BL/6J, but not in locomotion. Thus pleiotropic contribution of locomotion could be excluded.

Chromosome X modulates incidence of testicular germ cell tumors in Ter mice.

Germ cell tumor development in humans has been proposed to be part of testicular dysgenesis syndrome (TDS), which manifests as undescended testes, sterility, hypospadias, and, in extreme cases, as germ cell tumors. Males of the Ter mouse strain show interesting parallels to TDS because they either lack germ cells and are sterile or develop testicular germ cell tumors. We found that these defects in Ter mice are due to mutational inactivation of the Dead-end (Dnd1) gene. Here we report that chromosome X modulates germ cell tumor development in Ter mice. We tested whether the X or the Y chromosome influences tumor incidence. We used chromosome substitution strains to generate two new mouse strains: 129-Ter/Ter that carry either a C57BL/6J (B6)-derived chromosome (Chr) X or Y. We found that Ter/Ter males with B6-Chr X, but not B6-Chr Y, showed a significant shift in propensity from testicular tumor development to sterile testes phenotype. Thus, our studies provide unambiguous evidence that genetic factors from Chr X modulate the incidence of germ cell tumors in mice with inactivated Dnd1.

Chromosomal mapping of the genetic basis of hypertension and renal disease in FHH rats

This study examined the genetic basis for hypertension and renal disease phenotypes in Fawn Hooded hypertensive (FHH) rats using chromosome substitution strains (consomic rats) in which each of the 20 autosomes as well as the X and Y chromosomes were transferred from the normal Brown Norway (BN) rat onto the FHH genetic background. Male and female rats of each of the parental and consomic strains were maintained for 2 wk on high-salt (8.0% NaCl) chow with N(G)-nitro-l-arginine methyl ester (l-NAME) in the drinking water (12.5 mg/l) to induce hypertension and renal disease. Mean arterial blood pressure (MAP) was significantly higher (by over 60 mmHg) in the male FHH compared with BN rats. Urinary protein and albumin excretion rates were increased by 15- and 40-fold, respectively, in the male FHH compared with the BN. Plasma renin activity was 10-fold higher in the FHH than the BN. Similar significant differences were observed between the female FHH and BN, but the degree of hypertension and proteinuria was of a lesser magnitude. Substitution of chromosome 20 from the BN to the FHH attenuated the development of l-NAME-induced hypertension, normalized plasma renin activity, and decreased plasma creatinine in male rats. In female rats, substitution of chromosome 15 decreased MAP and urinary protein excretion. Urinary excretion of albumin in males was decreased by substitution of chromosomes 1, 15, 16, and 18 from the BN into the FHH genetic background. The present data indicate that genes that can modify l-NAME-induced hypertension and proteinuria are on chromosomes 1, 15, 16, 18, and 20.

Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain

Chromosome substitution strains (CSS or consomic strains) are useful for mapping phenotypes to chromosomes. However, huge efforts are needed to identify the gene(s) responsible for the phenotype in the complex context of the chromosome. Here we report the identification of candidate disease genes from a CSS by using a combination of genetic and genomic approaches and by using knowledge about the germ cell tumor disease etiology. We used the CSS 129.MOLF-Chr19 chromosome substitution strain, in which males develop germ cell tumors of the testes at an extremely high rate. We were able to identify three protein-coding genes and one microRNA on chromosome 19 that have previously not been implicated to be testicular tumor susceptibility genes. Our findings suggest that changes in gene expression levels in the gonadal tissues of multiple genes from Chr 19 likely contribute to the high testicular germ cell tumor (TGCT) incidence of the 129.MOLF-Chr19 strain. Our data advance the use of CSS to identify disease susceptibility genes and demonstrate that the 129.MOLF-Chr19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development.

Reciprocal Congenic Lines of Mice Capture the Aliq1 Effect on Acute Lung Injury Survival Time

Acute lung injury (ALI) is a devastating condition resulting from diverse causes. Genetic studies of human populations indicate that ALI is a complex disease with substantial phenotypic variance, incomplete penetrance, and gene-environment interactions. To identify genes controlling ALI mortality, we previously investigated mean survival time (MST) differences between sensitive A/J (A) and resistant C57BL/6J (B) mice in ozone using quantitative trait locus (QTL) analysis. MST was significantly linked to QTLs (Aliq1-3) on chromosomes 11, 13, and 17, respectively. Additional QTL analyses of separate and combined backcross and F(2) populations supported linkage to Aliq1 and Aliq2, and established significance for previously suggestive QTLs on chromosomes 7 and 12 (named Aliq5 and Aliq6, respectively). Decreased MSTs of corresponding chromosome substitution strains (CSSs) verified the contribution of most QTL-containing chromosomes to ALI survival. Multilocus models demonstrated that three QTLs could explain the MST difference between progenitor strains, agreeing with calculated estimates for number of genes involved. Based on results of QTL genotype analysis, a double CSS (B.A-6,11) was generated that contained Aliq1 and Aliq4 chromosomes. Surprisingly, MST and pulmonary edema after exposure of B.A-6,11 mice were comparable to B mice, revealing an unpredicted loss of sensitivity compared with separate CSSs. Reciprocal congenic lines for Aliq1 captured the corresponding phenotype in both background strains and further refined the QTL interval. Together, these findings support most of the previously identified QTLs linked to ALI survival and established lines of mice to further resolve Aliq1.

The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics

Mouse genetic resources include inbred strains, recombinant inbred lines, chromosome substitution strains, heterogeneous stocks, and the Collaborative Cross (CC). These resources were generated through various breeding designs that potentially produce different genetic architectures, including the level of diversity represented, the spatial distribution of the variation, and the allele frequencies within the resource. By combining sequencing data for 16 inbred strains and the recorded history of related strains, the architecture of genetic variation in mouse resources was determined. The most commonly used resources harbor only a fraction of the genetic diversity of Mus musculus, which is not uniformly distributed thus resulting in many blind spots. Only resources that include wild-derived inbred strains from subspecies other than M. m. domesticus have no blind spots and a uniform distribution of the variation. Unlike other resources that are primarily suited for gene discovery, the CC is the only resource that can support genome-wide network analysis, which is the foundation of systems genetics. The CC captures significantly more genetic diversity with no blind spots and has a more uniform distribution of the variation than all other resources. Furthermore, the distribution of allele frequencies in the CC resembles that seen in natural populations like humans in which many variants are found at low frequencies and only a minority of variants are common. We conclude that the CC represents a dramatic improvement over existing genetic resources for mammalian systems biology applications.

Haldane, Bailey, Taylor and recombinant-inbred lines.

THAT mouse Mecca, the Jackson Laboratory, has repeatedly pioneered in bringing mouse genetics to its present state. There was George Snell's Nobel-Prize-winning work on histocompatibility, Roy Stevens' work on embryonal carcinoma, Tibby Russell's on hematopoiesis, and many others (reviewed by Paigen 2003a,b). It has also been the site of several important methodological innovations. First and most important, C. C. Little had the foresight to establish inbred lines (Crow 2002). His first line was started in 1909; by 1980, there were >300 (Paigen 2003a). Another innovation was the development of congenic strains—inbred lines with a small foreign chromosomal region introgressed by repeated backcrossing into the line (Snell 1948). A third was chromosome substitution (consomic) strains. These have a single chromosome introgressed into an inbred line (Singer et al. 2004). The fourth innovation, in many ways the cleverest, was recombinant inbred (RI) lines. These innovations each required many years of advance work before they could be utilized effectively. Such projects certainly would not fare well as grant applications today. Only in an organization with a long-time commitment, such as the Jackson Laboratory, could such projects be carried through.