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Pleiotropic patterns of quantitative trait loci for 70 murine skeletal traits. Genetics 2008; 178:2275-88. [PMID: 18430949 DOI: 10.1534/genetics.107.084434] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Quantitative trait locus (QTL) studies of a skeletal trait or a few related skeletal components are becoming commonplace, but as yet there has been no investigation of pleiotropic patterns throughout the skeleton. We present a comprehensive survey of pleiotropic patterns affecting mouse skeletal morphology in an intercross of LG/J and SM/J inbred strains (N = 1040), using QTL analysis on 70 skeletal traits. We identify 798 single-trait QTL, coalescing to 105 loci that affect on average 7-8 traits each. The number of traits affected per locus ranges from only 1 trait to 30 traits. Individual traits average 11 QTL each, ranging from 4 to 20. Skeletal traits are affected by many, small-effect loci. Significant additive genotypic values average 0.23 standard deviation (SD) units. Fifty percent of loci show codominance with heterozygotes having intermediate phenotypic values. When dominance does occur, the LG/J allele tends to be dominant to the SM/J allele (30% vs. 8%). Over- and underdominance are relatively rare (12%). Approximately one-fifth of QTL are sex specific, including many for pelvic traits. Evaluating the pleiotropic relationships of skeletal traits is important in understanding the role of genetic variation in the growth and development of the skeleton.
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52
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Watanabe A, Toyota T, Owada Y, Hayashi T, Iwayama Y, Matsumata M, Ishitsuka Y, Nakaya A, Maekawa M, Ohnishi T, Arai R, Sakurai K, Yamada K, Kondo H, Hashimoto K, Osumi N, Yoshikawa T. Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype. PLoS Biol 2007; 5:e297. [PMID: 18001149 PMCID: PMC2071943 DOI: 10.1371/journal.pbio.0050297] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 09/19/2007] [Indexed: 01/11/2023] Open
Abstract
Deficits in prepulse inhibition (PPI) are a biological marker for schizophrenia. To unravel the mechanisms that control PPI, we performed quantitative trait loci (QTL) analysis on 1,010 F2 mice derived by crossing C57BL/6 (B6) animals that show high PPI with C3H/He (C3) animals that show low PPI. We detected six major loci for PPI, six for the acoustic startle response, and four for latency to response peak, some of which were sex-dependent. A promising candidate on the Chromosome 10-QTL was Fabp7 (fatty acid binding protein 7, brain), a gene with functional links to the N-methyl-D-aspartic acid (NMDA) receptor and expression in astrocytes. Fabp7-deficient mice showed decreased PPI and a shortened startle response latency, typical of the QTL's proposed effects. A quantitative complementation test supported Fabp7 as a potential PPI-QTL gene, particularly in male mice. Disruption of Fabp7 attenuated neurogenesis in vivo. Human FABP7 showed altered expression in schizophrenic brains and genetic association with schizophrenia, which were both evident in males when samples were divided by sex. These results suggest that FABP7 plays a novel and crucial role, linking the NMDA, neurodevelopmental, and glial theories of schizophrenia pathology and the PPI endophenotype, with larger or overt effects in males. We also discuss the results from the perspective of fetal programming.
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Affiliation(s)
- Akiko Watanabe
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Yuji Owada
- Histology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Takeshi Hayashi
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Ibaragi, Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Miho Matsumata
- Division of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yuichi Ishitsuka
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Akihiro Nakaya
- Department of Computational Biology, University of Tokyo, Tokyo, Japan
| | - Motoko Maekawa
- Division of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Tetsuo Ohnishi
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Ryoichi Arai
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Katsuyasu Sakurai
- Division of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazuo Yamada
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
| | - Hisatake Kondo
- Histology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, Japan
| | - Noriko Osumi
- Division of Developmental Neuroscience, Center for Translational and Advanced Animal Research, Tohoku University Graduate School of Medicine, Miyagi, Japan
- CREST, Japan Science and Technology Agency (JST), Saitama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan
- CREST, Japan Science and Technology Agency (JST), Saitama, Japan
- * To whom correspondence should be addressed. E-mail:
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53
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Sillanpää MJ, Hoti F. Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data. Genetics 2007; 177:2361-77. [PMID: 18073434 PMCID: PMC2219510 DOI: 10.1534/genetics.107.081299] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 10/05/2007] [Indexed: 02/04/2023] Open
Abstract
A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the log-normal survival time or censored/selected traits. A great benefit of the approach is that it enables the utilization of multiple-QTL models, is easy to incorporate into different data designs (experimental and outbred populations), and can potentially be extended to epistatic models. In inbred lines, the method exploits the fact that the parental mating type and the linkage phases (haplotypes) are known by definition. In outbred populations, two-generation data are needed, for example, selected offspring and one of the parents (the sires) in breeding material. The idea is to statistically (computationally) generate a fully complementary, maximally dissimilar, observation for each offspring in the sample. Bayesian data augmentation is then used to sample the space of possible trait values for the pseudoobservations. The benefits of the approach are illustrated using simulated data sets and a real data set on the survival of F(2) mice following infection with Listeria monocytogenes.
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Affiliation(s)
- Mikko J Sillanpää
- Department of Mathematics and Statistics, University of Helsinki, Finland.
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54
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Cepica S, Bartenschlager H, Geldermann H. Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map. Anim Genet 2007; 38:634-8. [PMID: 17931399 DOI: 10.1111/j.1365-2052.2007.01661.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.
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Affiliation(s)
- S Cepica
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic.
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55
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Davidson CE, Li Q, Churchill GA, Osborne LR, McDermid HE. Modifier locus for exencephaly inCecr2mutant mice is syntenic to the 10q25.3 region associated with neural tube defects in humans. Physiol Genomics 2007; 31:244-51. [PMID: 17623803 DOI: 10.1152/physiolgenomics.00062.2007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neural tube defects (NTDs), the second most common birth defect in humans, are multifactorial with complex genetic and environmental causes, although the genetic factors are almost completely unknown. In mice, >100 single gene mutations cause NTDs; however, the penetrance in many of these single gene mutant lines is highly dependent on the genetic background. We previously reported that a homozygous Cecr2 mutation on a BALB/c background causes exencephaly at a frequency of 74% compared with 0% on an FVB/N background. We now report that a major genetic modifier on chromosome 19, mapped using whole genome linkage analysis, increases the relative risk of exencephaly by 3.74 times in homozygous BALB embryos vs. BALB/FVB heterozygotes. Scanning electron microscopy revealed that the modifier does not affect the location of neural tube closure site 2, a known murine susceptibility factor for exencephaly. Crossing the Sp ( Splotch) mutation in the Pax3 gene onto the FVB/N background for two generations indicated that this resistant strain also decreases the penetrance of spina bifida. The chromosome 19 modifier region corresponds to a linkage region on human chromosome 10q25.3 mapped in a whole genome scan of human NTD families. Since the FVB/N genetic background affects susceptibility to both exencephaly and spina bifida, the human homolog of the chromosome 19 modifier locus may be a better candidate for human NTD susceptibility factors than genes that when mutated actually cause NTDs in mice.
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Affiliation(s)
- Courtney E Davidson
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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56
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Shaw KL, Parsons YM, Lesnick SC. QTL analysis of a rapidly evolving speciation phenotype in the Hawaiian cricket Laupala. Mol Ecol 2007; 16:2879-92. [PMID: 17614904 DOI: 10.1111/j.1365-294x.2007.03321.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In mate recognition systems, the functional necessity to coordinate traits involved in sexual communication should result in reduced pairing potential for new variants outside the distribution of common reproductive signals. Yet, many closely related, sexual species differ in mate recognition traits, suggesting that directional selection influences the divergence of mate recognition systems. Species of the endemic Hawaiian cricket genus Laupala are morphologically and ecologically cryptic, although both male calling song and female acoustic preference have diverged rapidly between closely related species. These mate recognition phenotypes are therefore often likely to be speciation phenotypes, i.e. traits whose divergence contributes, directly or indirectly, to a reduction of gene flow during speciation, given their frequent participation in early lineage divergence. We conducted a replicated, quantitative trait loci (QTL) mapping study of the genetic basis of differences in male calling song between two closely related species, Laupala paranigra and Laupala kohalensis, allowing us to examine the genetic basis of traits involved in rapid speciation. We found statistical support for eight QTL in one replicate, with at least four of these QTL mapping to the same regions in a second replicate. QTL effects ranged between 3.0% and 10.7% of the difference in pulse rate between L. paranigra and L. kohalensis, and are thus of moderate to small effect. All QTL identified show directional effects consistent with the hypothesis of directional selection. Thus, we conclude that rapid speciation can occur under the influence of many genes of moderate to small effect. This study implicates the role of directional selection in the divergence of mate recognition traits and speciation the Hawaiian cricket genus Laupala.
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Affiliation(s)
- Kerry L Shaw
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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Prows DR, Hafertepen AP, Winterberg AV, Gibbons WJ, Liu C, Nick TG. Genetic analysis of hyperoxic acute lung injury survival in reciprocal intercross mice. Physiol Genomics 2007; 30:271-81. [PMID: 17488888 DOI: 10.1152/physiolgenomics.00038.2007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute lung injury (ALI) and its most severe presentation, acute respiratory distress syndrome, represent a full spectrum of a complex and devastating illness, with associated mortality that still hovers around 30-40%. Even supplemental O2, a routine and necessary therapy for such patients, paradoxically causes lung injury. The detrimental effects of O2 have established hyperoxic ALI (HALI) as a conventional model to study neonatal and adult forms of respiratory distress syndromes in experimental animals. To confront the high ALI mortality problem quite differently, we recently identified a mouse model (sensitive C57BL/6J and resistant 129X1/SvJ mice) to assess the genetic complexity of HALI and to identify genes affecting strain survival differences. Segregation analysis of 840 F2 mice generated from all four possible intercrosses between C57BL/6J and 129X1/SvJ mice demonstrated that survival time is a quantitative trait with decreased penetrance, and significant sex, cross, and parent-of-origin effects. Quantitative trait locus (QTL) analyses of the total F2 population identified three highly significant (named Shali1, Shali2 and Shali3, for Survival to hyperoxic acute lung injury) and one significant (Shali4) linkage. Analysis of F2 subpopulations further identified a male-specific QTL (Shali5). QTL allelic comparisons supported cross and sex effects and were consistent with imprinting. Genome-wide pairwise analysis predicted additive gene-gene interactions between the QTLs and also revealed a significant epistatic interaction with an otherwise unlinked region. QTL results confirmed that both parental strains contribute dominant resistance alleles to their offspring to determine individual HALI susceptibility.
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Affiliation(s)
- Daniel R Prows
- Department of Pediatrics, University of Cincinnati College of Medicine, Children's Hospital Medical Center, Cincinnati, Ohio, USA
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58
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Lightfoot JT, Turner MJ, Knab AK, Jedlicka AE, Oshimura T, Marzec J, Gladwell W, Leamy LJ, Kleeberger SR. Quantitative trait loci associated with maximal exercise endurance in mice. J Appl Physiol (1985) 2007; 103:105-10. [PMID: 17412788 DOI: 10.1152/japplphysiol.01328.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The role of genetics in the determination of maximal exercise endurance is unclear. Six- to nine-week-old F2 mice (n = 99; 60 female, 39 male), derived from an intercross of two inbred strains that had previously been phenotyped as having high maximal exercise endurance (Balb/cJ) and low maximal exercise endurance (DBA/2J), were treadmill tested to estimate exercise endurance. Selective genotyping of the F2 cohort (n = 12 high exercise endurance; n = 12 low exercise endurance) identified a significant quantitative trait locus (QTL) on chromosome X (53.7 cM, DXMit121) in the entire cohort and a suggestive QTL on chromosome 8 (36.1 cM, D8Mit359) in the female mice. Fine mapping with the entire F2 cohort and additional informative markers confirmed and narrowed the QTLs. The chromosome 8 QTL (EE8(F)) is homologous with two suggestive human QTLs and one significant rat QTL previously linked with exercise endurance. No effect of sex (P = 0.33) or body weight (P = 0.79) on exercise endurance was found in the F2 cohort. These data indicate that genetic factors in distinct chromosomal regions may affect maximal exercise endurance in the inbred mouse. Whereas multiple genes are located in the identified QTL that could functionally affect exercise endurance, this study serves as a foundation for further investigations delineating the identity of genetic factors influencing maximum exercise endurance.
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Affiliation(s)
- J Timothy Lightfoot
- Department of Kinesiology, University of North Carolina-Charlotte, Charlotte, North Carolina 28223, USA.
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59
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Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, von Smith R, Yi N. R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics 2007; 23:641-3. [PMID: 17237038 PMCID: PMC4995770 DOI: 10.1093/bioinformatics/btm011] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED R/qtlbim is an extensible, interactive environment for the Bayesian Interval Mapping of QTL, built on top of R/qtl (Broman et al., 2003), providing Bayesian analysis of multiple interacting quantitative trait loci (QTL) models for continuous, binary and ordinal traits in experimental crosses. It includes several efficient Markov chain Monte Carlo (MCMC) algorithms for evaluating the posterior of genetic architectures, i.e. the number and locations of QTL, their main and epistatic effects and gene-environment interactions. R/qtlbim provides extensive informative graphical and numerical summaries, and model selection and convergence diagnostics of the MCMC output, illustrated through the vignette, example and demo capabilities of R (R Development Core Team 2006). AVAILABILITY The package is freely available from cran.r-project.org.
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Affiliation(s)
- Brian S. Yandell
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA
| | - Tapan Mehta
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samprit Banerjee
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Daniel Shriner
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ramprasad Venkataraman
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jee Young Moon
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA
| | - W. Whipple Neely
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA
| | - Hao Wu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205 USA
| | - Randy von Smith
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Nengjun Yi
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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