QTL analysis of measures of mouse home-cage activity using B6/MSM consomic strains

The activity of mice in their home cage is influenced greatly by the cycle of light and dark. In addition, home-cage activity shows remarkable time-dependent changes that result in a prominent temporal pattern. The wild-derived mouse strain MSM/Ms (MSM) exhibits higher total activity in the home cage than does C57BL/6 (B6), a commonly used laboratory strain. In addition, there is a clear strain difference in the temporal pattern of home-cage activity. This study aimed to clarify the genetic basis of strain differences in the temporal pattern of home-cage activity between MSM and B6. Through the comparison of temporal patterns of home-cage activity between B6 and MSM, the pattern can be classified into five temporal components: (1) resting phase, (2) anticipation phase, (3) 1st phase, (4) 2nd phase, and (5) 3rd phase. To identify quantitative trait loci (QTLs) involved in these temporal components, we used consomic strains established from crosses between B6 and MSM. Five consomic strains, for Chrs 2T (telomere), 3, 4, 13, and 14, showed significantly higher total activity than B6. In contrast, the consomic strains of Chrs 6C (centromere), 7T, 9, 11, and 15 were less active than B6. This indicates that multigenic factors regulate the total activity. Further analysis showed an impact of QTLs on the temporal components of home-cage activity. The present data showed that each temporal component was regulated by different combinations of multigenic factors, with some overlap. These temporal component-related QTLs are important to understand fully the genetic mechanisms that underlie home-cage activity.     

Interval mapping and congenic strains for a blood pressure QTL on rat Chromosome 13

The renin locus (Ren) on rat Chromosome (Chr) 13 had previously been shown to cosegregate with blood pressure in crosses involving Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats. In the present work, interval mapping of blood pressure on Chr 13 with a large F₂ (S × R), n = 233, population yielded a maximum LOD = 4.2 for linkage to blood pressure, but the quantitative trait locus (QTL) was only poorly localized to a large 35-centiMorgan (cM) segment of Chr 13. In the linkage analysis, the S-rat QTL allele (S) was associated with higher, and the R-rat QTL allele (R) with lower blood pressure, the difference between homozygotes being about 20 mm Hg. A congenic strain was made by introgressing the R-rat Ren allele into the recipient S strain. This congenic strain showed a 24 mm Hg reduction (P = 0.004) in blood pressure compared with S rats for rats fed 2% NaCl diet for 24 days; this difference was confirmed by two other independent tests. Two congenic substrains were derived from the first congenic strain with shorter R Chr 13 segments on the S background. Comparisons among these congenic strains showed that a blood pressure QTL was in the 24-cM chromosomal segment between Syt2 and D13M1Mit108. This segment does not include the renin locus, which is thus excluded from being the gene on rat Chr 13 responsible for genetic differences in blood pressure detected by linkage analysis. Received: 20 December 1996 / Accepted: 7 April 1997     

High-resolution mapping of the blood pressure QTL on chromosome 7 using Dahl rat congenic strains

It was previously shown using Dahl salt-sensitive (S) and salt-resistant (R) rats that a blood pressure quantitative trait locus (QTL) was present on rat chromosome 7. In the present work, this QTL was localized to a region less than 0.54 cM in size on the linkage map using a series of congenic strains. This region was contained in a single yeast artificial chromosome that was 220 kb long. This small segment still contained the primary candidate locus Cyp11b1 (11beta-hydroxylase), but the adjacent candidate genes Cyp11b2 (aldosterone synthase) and Cyp11b3 were ruled out. It is concluded that 11beta-hydroxylase, through its known genetic variants altering the production of 18-hydroxy-11-deoxy corticosterone, is very likely to account for the blood pressure QTL on chromosome 7 in the Dahl rat model of hypertension. This QTL accounts for about 23 mm Hg under the condition of 2% NaCl diet for 24 days.     

Interval-specific congenic strains (ISCS): An experimental design for mapping a QTL into a 1-centimorgan interval

A general experimental design that allows mapping of a quantitative trait locus (QTL) into a 1-cM interval is presented. The design consists of a series of strains, termed ``interval-specific congenic strains (ISCS)'. Each ISCS is recombinant at a specific 1-cM sub-interval out of an ordered set of sub-intervals, which together comprise a wider interval, to which a QTL was previously mapped. It is shown that a specific and previously detected QTL of moderate or even small effect can be accurately mapped into a 1-cM interval in a program involving a total of no more than 1000 individuals. Consequently, ISCS can serve as the ultimate genetic mapping procedure before the application of physical mapping tools for positional cloning of a QTL. Received: 2 August 1996 / Accepted: 28 October 1996     

QTL analyses of spontaneous activity by using mouse strains from Mishima battery

We reported previously that spontaneous activity in the home cage is highly variable among the Mishima battery of mouse strains. In that study, NJL and KJR were found to be hyperactive strains in contrast to BLG2, which showed one of the lowest activity levels. To unravel the genetic loci involved in this behavioral phenotype, we conducted QTL analyses on backcross populations of crosses between either NJL or KJR and BLG2 strains. In the backcross of NJL to BLG2, no single locus was associated with increased spontaneous activity. In the backcross of KJR to BLG2, linkage analysis showed that a locus on the most telomeric region of Chromosome (Chr) 3 was involved in the spontaneous activity, thus named Loco1. Further linkage analysis using selected progeny carrying the allele from KJR at the Loco1 locus suggested the presence of another locus, Loco2, on Chr 17. An analysis showed that Loco1 and Loco2 interacted epistatically.     

Localization of a blood pressure QTL to a 2.4-cM interval on rat chromosome 9 using congenic strains

A blood pressure (BP) quantitative trait locus (QTL) was previously found on rat chromosome 9 using Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats. A congenic strain, S.R(chr9), constructed by introgressing an R chromosomal segment into the S background, previously proved the existence of a BP QTL in a large 34.2-cM segment of chromosome 9. In the current work congenic substrains were constructed from the progenitor congenic strain, S.R(chr9). BP and heart weight comparisons between these congenic substrains and their S control localized the BP QTL to a 4.6-cM interval. Two solute carrier (Na(+)/H(+) exchanger) genes, Nhe2 and Nhe4, were excluded as candidates based on their map locations. A second iteration of congenic substrains was used to localize the QTL further to a 2.4-cM interval. Another solute carrier (Cl(-)/HCO3- exchanger) gene, Ae3, is in this reduced interval and was sequenced for both S and R strains, but no coding sequence variations were found. Ae3 mRNA was not differentially expressed in the kidney of congenic compared to S rats. Although the identity of the QTL remains unknown its map location has been reduced from an interval of 34.2 to 2.4 cM.     

A Fisher scoring algorithm for the weighted regression method of QTL mapping

An improved weighted least square (LS) method for quantitative trait loci (QTL) mapping using the estimating equation (EE) algorithm was developed recently. The method is more efficient than both the LS and the weighted LS methods and slightly less efficient than the mixture model maximum likelihood (ML) method. The iteration process of the EE algorithm is implicit. We developed a Fisher-scoring algorithm for the weighted LS method. The iteration process is explicit and easy to program. In addition, the method automatically provides an approximate variance-covariance matrix for the estimated QTL parameters as a by-product of the iteration process. As a consequence, a W-test statistic can be used for testing the significance of QTL. To compare the Fisher scoring algorithm with the expectation maximization (EM)-based ML method, we also developed a slightly simplified method to compute the variance-covariance matrix of the estimated parameters under the EM algorithm.     

Detection of Mls-antigens in various mouse strains using a new method

Mice of strains CBA and BALB/c, when injected with lymphocytes from theH-2-compatible Mls-antigen-incompatible strains C3H and DBA/2, respectively, develop a reduced lymphocyte reactivity against cells of the injected strains as measured in the mixed lymphocyte culture (MLC). The mechanism of the development of a depression of the MLC response against Mlsantigens is unknown. In this investigation we have tested the MLC response of lymphocytes from CBA mice preinjected with C3H lymphocytes against cells from 12 different strains. It was observed that the response decreased against cells from strains C3H, AKR, and A/Sn. Infusion of CBA mice with AKR lymphocytes decreased their MLC response against the same three strains. In contrast, infusion of CBA mice with A/Sn lymphocytes reduced their MLC responses against strains C3H, DBA/2, and the congenic strains A/Sn, A.SW, A.CA, and A.BY. BALB/c mice which were infused with DBA/2 lymphocytes developed reduced responses against DBA/2, C3H, and AKR. On the basis of these results we propose that mice of our strains C3H and AKR possess a common Mls-antigen which is strongly stimulatory, and that DBA/2 mice possess a second Mls-antigen which is also strongly stimulatory. The congenic strains A/Sn, A.SW, A.CA, and A.BY, which have differentH-2 complexes, possess a third Mls-antigen which is less stimulatory. The Mls-antigens of the strains listed above seem to exhibit extensive immunological crossreactivity.     

A comparison of regression interval mapping and multiple interval mapping for linked QTL

Regression interval mapping and multiple interval mapping are compared with regard to mapping linked quantitative trait loci (QTL) in inbred-line cross experiments. For that purpose, a simulation study was performed using genetic models with two linked QTL. Data were simulated for F(2) populations of different sizes and with all QTL and marker alleles fixed for alternative alleles in the parental lines. The criteria for comparison are power of QTL identification and the accuracy of the QTL position and effect estimates. Further, the estimates of the relative QTL variance are assessed. There are distinct differences in the QTL position estimates between the two methods. Multiple interval mapping tends to be more powerful as compared to regression interval mapping. Multiple interval mapping further leads to more accurate QTL position and QTL effect estimates. The superiority increased with wider marker intervals and larger population sizes. If QTL are in repulsion, the differences between the two methods are very pronounced. For both methods, the reduction of the marker interval size from 10 to 5 cM increases power and greatly improves QTL parameter estimates. This contrasts with findings in the literature for single QTL scenarios, where a marker density of 10 cM is generally considered as sufficient. The use of standard (asymptotic) statistical theory for the computation of the standard errors of the QTL position and effect estimates proves to give much too optimistic standard errors for regression interval mapping as well as for multiple interval mapping.     

QTL mapping for genetic determinants of lipoprotein cholesterol levels in combined crosses of inbred mouse strains

To identify additional loci that influence lipoprotein cholesterol levels, we performed quantitative trait locus (QTL) mapping in offspring of PERA/EiJxI/LnJ and PERA/EiJxDBA/2J intercrosses and in a combined data set from both crosses after 8 weeks of consumption of a high fat-diet. Most QTLs identified were concordant with homologous chromosomal regions that were associated with lipoprotein levels in human studies. We detected significant new loci for HDL cholesterol levels on chromosome (Chr) 5 (Hdlq34) and for non-HDL cholesterol levels on Chrs 15 (Nhdlq9) and 16 (Nhdlq10). In addition, the analysis of combined data sets identified a QTL for HDL cholesterol on Chr 17 that was shared between both crosses; lower HDL cholesterol levels were conferred by strain PERA. This QTL colocalized with a shared QTL for cholesterol gallstone formation detected in the same crosses. Haplotype analysis narrowed this QTL, and sequencing of the candidate genes Abcg5 and Abcg8 confirmed shared alleles in strains I/LnJ and DBA/2J that differed from the alleles in strain PERA/EiJ. In conclusion, our analysis furthers the knowledge of genetic determinants of lipoprotein cholesterol levels in inbred mice and substantiates the hypothesis that polymorphisms of Abcg5/Abcg8 contribute to individual variation in both plasma HDL cholesterol levels and susceptibility to cholesterol gallstone formation.     

Genome-wide analysis of maize cytoplasmic male sterility-S based on QTL mapping

Three types of sterile cytoplasm in cytoplasmic-male-sterility (CMS) maize, T, C and S, can be identified according to their fertility-restoration and mitochondrial DNA RFLP patterns. CMS-S, which is the least stable among the three types of CMS, is controlled by sterile cytoplasm interactions with certain nuclear-encoded factors. We constructed a high-resolution map of loci associated with male-restoration of CMS-S in BC1 populations of maize. The map covers 1730.29 cM, including 32 RFLP, 51 SSR 62 RAPD and 21 AFLP markers. Genome-wide QTL analysis detected 6 QTLs with significant effects on male fertility as assessed by their starch-filled pollen ratios. Four QTLs out of six were located between the SSR markers MSbnlg1633-Mrasg20, MSbnlg1662-Msume1126, MSume1230-MSumc1525, and RAPD marker MraopQ07-2-MraopK06-2 on chromosome 2. Two other minor loci were mapped between MraopK16-1-Mraopi4-1, on chromosome 9, and between Msuncbnlg1139-MraopR10-2, on chromosome 6. The Rf3 nuclear restoring gene was precisely located on the chromosome 2, 2.29 cM to the left of umc1525 and 8.9 cM to the right of umc1230. The results provide important markers for marker-assisted selection of stable CMS-S maize.     

Genetic analysis of rice CMS-WA fertility restoration based on QTL mapping

 The inheritance of fertility restoration of rice cytoplasmic male sterility of the wild abortive type was studied by means of QTL mapping. The two segregating populations examined showed high frequencies of highly sterile and highly fertile progenies, but a low frequency of partially sterile and partially fertile progenies. The distributions suggested that fertility restoration was mainly controlled by major genes. Based on a linkage map constructed with 57 RFLP and 61 AFLP markers on a B₁F₁ population, composite interval mapping (CIM) revealed that the fertility was restored by the additive effects of two restorer loci located on chromosome 10. One QTL, tightly linked to RFLP marker C1361 in the middle of the long arm of chromosome 10, explained 71.5% of the phenotypic variance. The second QTL was located between RFLP markers R2309 and RG257 on the short arm and explained 27.3% of the phenotypic variance. Similar results were obtained using the simple interval mapping (SIM) methods. Recived: 8 January 1998/Accepted: 22 April 1998     

Quantitative trait locus (QTL) isogenic recombinant analysis: a method for high-resolution mapping of QTL within a single population

In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.     

Limitations of a two-step moment method for mapping linked multiple QTL

As an alternative to multiple-interval mapping a two-step moment method was recently proposed to map linked multiple quantitative trait loci (QTLs). The advantage of this moment method was supposed to be its simplicity and computational efficiency, especially in detecting closely linked QTLs within a marker bracket, but also in mapping QTLs in different marker intervals. Using simulations it is shown that the two-step moment method may give poor results compared with multiple-interval mapping, irrespective of whether the QTLs are in the same or in different marker intervals, especially if linked QTLs are in repulsion. The criteria of comparison are number of identified QTLs, likelihood ratio test statistics, means and empirical standard errors of the QTL position and QTL effects estimates, and the accuracy of the residual variance estimates. Further, the joint conditional probabilities of QTL genotypes for two putative QTLs within a marker interval were derived and compared with the unmodified approach ignoring the non-independence of the conditional probabilities.     

Gene expression profiles of a mouse congenic strain carrying an obesity susceptibility QTL under obesigenic diets

Genetic factors are strongly involved in the development of obesity, likely through the interactions of susceptibility genes with obesigenic environments, such as high-fat, high-sucrose (HFS) diets. Previously, we have established a mouse congenic strain on C57BL/6 J background, carrying an obesity quantitative trait locus (QTL), tabw2, derived from obese diabetic TALLYHO/JngJ mice. The tabw2 congenic mice exhibit increased adiposity and hyperleptinemia, which becomes exacerbated upon feeding HFS diets. In this study, we conducted genome-wide gene expression profiling to evaluate differentially expressed genes between tabw2 and control mice fed HFS diets, which may lead to identification of candidate genes as well as insights into the mechanisms underlying obesity mediated by tabw2. Both tabw2 congenic mice and control mice were fed HFS diets for 10 weeks beginning at 4 weeks of age, and total RNA was isolated from liver and adipose tissue. Whole-genome microarray analysis was performed and verified by real-time quantitative RT–PCR. At False Discovery Rate adjusted P < 0.05, 1026 genes were up-regulated and 308 down-regulated in liver, whereas 393 were up-regulated and 187 down-regulated in adipose tissue in tabw2 congenic mice compared to controls. Within the tabw2 QTL interval, 70 genes exhibited differential expression in either liver or adipose tissue. A comprehensive pathway analysis revealed a number of biological pathways that may be perturbed in the diet-induced obesity mediated by tabw2.     

Localization of Idd11 using NOD congenic mouse strains: elimination of Slc9a1 as a candidate gene

 Type 1 diabetes is a multigenic autoimmune disease, the genetic basis for which is perhaps best characterized in the nonobese diabetic (NOD) mouse model. We previously located a NOD diabetes susceptibility locus, designated Idd11, on mouse Chromosome (Chr) 4 by analyzing diabetic backcross mice produced after crossing NOD/Lt with the nondiabetic resistant strain C57BL/6 (B6) strain. In order to confirm Idd11 and further refine its location, three NOD congenic mouse strains with different B6 derived intervals within Chr 4 were generated. Two of the congenic strains had a significant decrease in the cumulative incidence of diabetes compared with NOD/Lt control mice. The third NOD congenic strain, containing a B6 interval surrounding the Slc9a1 locus, was not protected against diabetes. These results define a new distal boundary for Idd11 and eliminate the Slc9a1 gene as a candidate. The Idd11 locus has now been definitively mapped to a 13cM interval on mouse Chr 4. Received: 15 May 1999 / Revised: 25 September 1999     

Prepulse inhibition （PPI） of tactile startle response in recombinant congenic strains of mice： QTL mapping and comparison with acoustic PPI

Prepulse inhibition (PPI) of the startle response is a psychophysiological measure of sensorimotor gating believed to be cross-modal between different sensory systems.We analyzed the tactile startle response (TSR) and PPI of TSR (tPPD,using light as a prepulse stimulus,in the mouse strains A/J and C57BL/6J and 36 recombinant congenic strains derived from them.Parental strains were significantly different for TSR,but were comparable for tPPI.Among the congenic strains,variation for TSR was significant in both genetic backgrounds,but that of tPPI was significant only for the C57BL/6J background.Provisional mapping for loci modulating TSR and tPPI was carded out.Using mapping data from our previous study on acoustic startle responses (ASR) and PPI of ASR (aPPI),no common markers for aPPI and tPPI were identified.However,some markers were significantly associated with both ASR and TSIL at least in one genetic background.These results indicate cross-modal genetic regulation for the startle response but not for PPI,in these mouse strains.