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1.  Genetic Loci that Regulate Ectopic Calcification in Response to Knee Trauma in LG/J by SM/J Advanced Intercross Mice 
This study reports on genetic susceptibility to ectopic calcification in the LG/J and SM/J advanced intercross mice. Using 347 mice in 98 full-sibships, destabilization of medial meniscus (DMM) was performed to induce joint injury. We performed quantitative trait locus (QTL) analysis to map ectopic calcification phenotypes to discrete genomic locations. To validate the functional significance of the selected QTL candidate genes, we compared mRNA expression between parental LG/J and SM/J inbred strains. We found that joint destabilization instigated ectopic calcifications as detected and quantified by micro-CT. Overall, we detected 20 QTLs affecting synovial and meniscus calcification phenotypes with 11 QTLs linked to synovial calcification. Functional and bioinformatic analyses of single nucleotide polymorphism identified functional classifications relevant to angiogenesis (Myo1e, Kif26b, Nprl3, Stab2, Fam105b), bone metabolism/calcification (Tle3, Tgfb2, Lipc, Nfe2l1, Ank, Fam105b), arthritis (Stab2, Tbx21, Map4k4, Hoxb9, Larp6, Col1a2, Adam10, Timp3, Nfe2l1, Trpm3), and ankylosing-spondylitis (Ank, Pon1, Il1r2, Tbkbp1) indicating that ectopic calcification involves multiple mechanisms. Furthermore, the expression of 11 candidate genes was significantly different between LG/J and SM/J. Correlation analysis showed that Aff3, Fam81a, Syn3, and Ank were correlated with synovial calcification. Taken together, our findings of multiple genetic loci suggest the involvement of multiple genes contributing to ectopic calcification.
doi:10.1002/jor.22944
PMCID: PMC5025301  PMID: 25989359
ectopic calcification; QTL analysis; gene expression; genetics; advanced intercross line; osteoarthritis
2.  Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation 
Journal of evolutionary biology  2015;28(4):973-985.
We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation.
doi:10.1111/jeb.12628
PMCID: PMC4405477  PMID: 25818173
morphospace; quantitative genetics; constraints; mammals
3.  The Genetic Basis of Baculum Size and Shape Variation in Mice 
G3: Genes|Genomes|Genetics  2016;6(5):1141-1151.
The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.
doi:10.1534/g3.116.027888
PMCID: PMC4856068  PMID: 26935419
baculum; sexual selection; shape; size
4.  Further evidence for phenotypic signatures of hybridization in descendent baboon populations 
Journal of human evolution  2014;76:54-62.
Hybridization may have played a substantial role in shaping the diversity of our evolving lineage. Although recent genomic evidence has shown that hybridization occurred between anatomically modern humans (AMHS) and Neanderthals, it remains difficult to pin down precisely where and when this gene flow took place. Investigations of the hybrid phenotype in primates and other mammals are providing models for identifying signatures of hybridization in the fossil record. However, our understanding of intra- and inter-taxon variation in hybrids is still limited. Moreover, there is little evidence from these studies that is pertinent to the question of how long hybrid skeletal traits persist in descendants, and therefore it is not clear whether observed hybrid phenotypes are evidence of recent (e.g., F1) or much earlier hybridization events. Here, we present an analysis updating a previous study of cranial variation in pedigreed olive and yellow baboons and their hybrids. Results suggest that traits previously associated with hybrids in baboons and other mammalian species are also present in this expanded data set; many of these traits are highly heritable, confirming a genetic basis for their variation in this mixed population. While F1 animals – and especially F1 males – still have the highest number of dental anomalies, these and other atypical traits persist into later hybrid generations (such as F2 and B1). Moreover, non-F1 recombinants also show extremely rare trait variations, including reduced canines and rotated teeth. However, these results must be considered in light of the possibility that some founding individuals may have themselves been unrecognized hybrids. Despite this, the data are compelling, and indicate once again that further controlled research remains to be done on primates and other mammals in order to better understand variation in the hybrid phenotype.
doi:10.1016/j.jhevol.2014.05.004
PMCID: PMC4378831  PMID: 24935168
Gene flow; Papio cynocephalus; Papio anubis; Supernumerary teeth; Cranial variation
5.  Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides 
BMC Genomics  2015;16(1):415.
Background
The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity.
Results
We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length.
Conclusions
We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1592-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1592-3
PMCID: PMC4445795  PMID: 26016481
Mouse models; Quantitative trait loci (QTL); Complex traits; Identity-by-descent (IBD); Predicted deleterious mutations; Quantitative trait gene (QTG); Quantitative trait nucleotide (QTN); Candidate loci; Whole genome sequence; Small nucleotide variant (SNV)
6.  Weak Genetic Relationship Between Trabecular Bone Morphology and Obesity in Mice 
Bone  2012;51(1):46-53.
Obesity, in addition to being associated with metabolic diseases, such as diabetes, has also been found to lower the risk of osteoporotic fractures. The relationship between obesity and bone trabecular structure is complex, involving responses to mechanical loading and the effects of adipocyte-derived hormones, both directly interacting with bone tissue and indirectly through central nervous system signaling. Here we examine the effects of sex, a high fat diet, and genetics on the trabecular density and structure of the lumbar and caudal vertebra and the proximal tibia along with body weight, fat pad weight, and serum leptin levels in a murine obesity model, the LGXSM Recombinant Inbred (RI) mouse strains. The sample included 481 mice from 16 RI strains. We found that vertebral trabecular density was higher in males while the females had higher tibial trabecular density. The high fat diet led to only slightly higher trabecular density in both sexes despite its extreme effects on obesity and serum leptin levels. Trait heritabilities are moderate to strong and genetic correlations among trabecular features are high. Most genetic variation contrasts strains with large numbers of thick, closely-spaced, highly interconnected, plate-like trabeculae with a high bone volume to total volume ratio against strains displaying small numbers of thin, widely-spaced, sparsely connected, rod-like trabeculae with a low bone volume to total volume ratio. Genetic correlations between trabecular and obesity-related traits were low and not statistically significant. We mapped trabecular properties to 20 genomic locations. Only one-quarter of these locations also had effects on obesity. In this population obesity has a relatively minor effect on trabecular bone morphology. Key Words: bone; trabecular morphology; obesity; quantitative trait loci; mice
doi:10.1016/j.bone.2012.03.031
PMCID: PMC3371175  PMID: 22503703
7.  Diet-Dependent Genetic and Genomic Imprinting Effects on Obesity in Mice 
Obesity (Silver Spring, Md.)  2010;19(1):160-170.
Although the current obesity epidemic is of environmental origin, there is substantial genetic variation in individual response to an obesogenic environment. In this study, we perform a genome-wide scan for quantitative trait loci (QTLs) affecting obesity per se, or an obese response to a high-fat diet in mice from the LG/J by SM/J Advanced Intercross (AI) Line (Wustl:LG,SM-G16). A total of 1,002 animals from 78 F16 full sibships were weaned at 3 weeks of age and half of each litter placed on high- and low-fat diets. Animals remained on the diet until 20 weeks of age when they were necropsied and the weights of the reproductive, kidney, mesenteric, and inguinal fat depots were recorded. Effects on these phenotypes, along with total fat depot weight and carcass weight at necropsy, were mapped across the genome using 1,402 autosomal single-nucleotide polymorphism (SNP) markers. Haplotypes were reconstructed and additive, dominance, and imprinting genotype scores were derived every 1 cM along the F16 map. Analysis was performed using a mixed model with additive, dominance, and imprinting genotype scores, their interactions with sex, diet, and with sex-by-diet as fixed effects and with family and its interaction with sex, diet, and sex-by-diet as random effects. We discovered 95 trait-specific QTLs mapping to 40 locations. Most QTLs had additive effects with dominance and imprinting effects occurring at two-thirds of the loci. Nearly every locus interacted with sex and/ or diet in important ways demonstrating that gene effects are primarily context dependent, changing depending on sex and/or diet.
doi:10.1038/oby.2010.141
PMCID: PMC3677968  PMID: 20539295
8.  Characterizing the Evolutionary Path(s) to Early Homo 
PLoS ONE  2014;9(12):e114307.
Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must be invoked to explain an Au. africanus—Au. sediba—Homo transition, while transitions from late australopiths to various early Homo species that exclude Au. sediba can be achieved through drift alone. Rate tests indicate that selection is largely directional, acting to rapidly differentiate these taxa. Reconstructions of patterns of directional selection needed to drive the Au. africanus—Au. sediba—Homo transition suggest that selection would have affected all regions of the skull. These results may indicate that an evolutionary path to Homo without Au. sediba is the simpler path and/or provide evidence that this pathway involved more reliance on cultural adaptations to cope with environmental change.
doi:10.1371/journal.pone.0114307
PMCID: PMC4255019  PMID: 25470780
9.  Neuroanatomic and behavioral traits for autistic disorders in age-specific restricted index selection mice 
Neuroscience  2011;189:215-222.
The pathogenesis of neurodevelopmental disorders such as autism is believed to be influenced by interactions between genetic and environmental factors, and appropriate animal models are needed to assess the influence of such factors on relevant neurodevelopmental phenotypes. A set of inbred mouse strains (Atchley strains) including A12 (E+L0) and A22 (E-L0) were generated by age-specific restricted index selection from a baseline random-bred ICR mouse population obtained from Harlan Sprague-Dawley (Atchley et al., 1997; Indianapolis, IN). As compared with the A22 strain, A12 mice had significantly increased early (P0-P10) body weight gain with minimal changes in late (P28 to P56) body weight gain. We found that these strains also differed in brain weight, brain volume, cell proliferation, and FGF-2 levels in certain brain regions. Specifically, brain weight and volume were significantly greater in A12 mice than that in A22 mice at P10 and P28. Quantitative analysis of Bromodeoxyuridine (BrdU) labeling of proliferating cells showed that the number of BrdU-positive cells in the A12 strain was significantly greater in the frontal cortex and lesser in the dentate gyrus than that in the A22 strain at P28. Western blot revealed that fibroblast growth factors-2 (FGF-2), but not brain-derived neurotrophic factor (BDNF), expression was significantly increased in the frontal cortex of A12 strain at P28. Also, A12 mice exhibited decreased intra-strain social interaction and increased repetitive stereotyped behaviors at P28. Our study suggests that A12 mice may partially mimic the anatomic and behavioral traits of patients with neurodevelopmental disorders such as autism spectrum disorders, and therefore may yield insights into the developmental mechanisms involved in their pathogenesis.
doi:10.1016/j.neuroscience.2011.05.017
PMCID: PMC3150457  PMID: 21624435
neurodevelopment; brain weight; brain volume; neurogenesis; social interaction; Autism
10.  Relationship of age and body mass index to the expression of obesity and osteoarthritis related genes in human meniscus 
Objective
Aging and obesity contribute to the initiation and progression of osteoarthritis with little information on their relation to gene expression in joint tissues, particularly the meniscus. Here, we test the hypothesis that patient age and body mass index (BMI) correlate with the expression of osteoarthritis- and obesity-related gene signatures in the meniscus.
Design
Meniscus was obtained from patients (N=68) undergoing arthroscopic partial meniscectomy. The mRNA expression of twenty-four osteoarthritis-related and four obesity-related genes in meniscus was assessed by qRT-PCR. The relationship between gene expression and patient age and BMI was analyzed using Spearman’s rank-order correlation. Hierarchical cluster dendrogram and heat maps were generated to study inter-gene associations.
Results
Age was negatively correlated (P<0.05) with the expression of MMP-1 (r=−0.447), NFκB2 (r=−0.361), NFκBIA (r=−0.312), IκBA (r=−0.308), IL-8 (r=−0.305), ADAMTS-4 (r=−0.294), APLN (r=−0.250) and IL-6 (r=−0.244). Likewise, BMI was negatively correlated with the expression of APLN (r=−0.328), ACAN (r=−0.268) and MMP-1 (r=−0.261). After adjusting for the correlation between age and BMI (r=0.310; P=0.008), the only independent effect of BMI on gene expression was for APLN (r=−0.272). However, age had an independent effect on expression on ADAMTS-4 (r=−0.253), MMP-1 (r=−0.399), IL-8 (r=−0.327), COL1A1 (r=−0.287), NFκBIA (r=−0.278), NFκB2 (r=−0.312) and IκBA (r=−0.299). The gene-correlation analysis identified four clusters of potentially relevant genes: transcription factors, matrix degrading enzymes, cytokines and chemokines, and obesity genes.
Conclusion
Age and BMI were negatively correlated with several osteoarthritis- and obesity-related genes. While the bulk of these changes appeared to be driven by age, expression of APLN was related to BMI. Inter-gene correlations implicated a common regulatory role of strongly correlated genes. Although age-related variations in gene expression are potentially more pertinent than obesity-related differences for the role of the meniscus in osteoarthritis development, further investigation into the role of APLN in meniscus and joint health is warranted.
doi:10.1038/ijo.2012.221
PMCID: PMC3751987  PMID: 23318714
Meniscus tear; gene expression; osteoarthritis; age; body mass index; obesity
11.  Genomic imprinting and parent-of-origin effects on complex traits 
Nature reviews. Genetics  2013;14(9):609-617.
Parent-of-origin effects occur when the phenotypic effect of an allele depends on whether it is inherited from an individual’s mother or father. Several phenomena can cause parent-of-origin effects, with the best characterized being parent-of-origin dependent gene expression associated with genomic imprinting. Imprinting plays a critical role in a diversity of biological processes and in certain contexts it structures epigenetic relationships between DNA sequence and phenotypic variation. The development of new mapping approaches applied to the growing abundance of genomic data has demonstrated that imprinted genes can be important contributors to complex trait variation. Therefore, to understand the genetic architecture and evolution of complex traits, including complex diseases and traits of agricultural importance, it is crucial to account for these parent-of-origin effects. Here we discuss patterns of phenotypic variation associated with imprinting, evidence supporting its role in complex trait variation, and approaches for identifying its molecular signatures.
doi:10.1038/nrg3543
PMCID: PMC3926806  PMID: 23917626
12.  The effect of dietary fat intake on hepatic gene expression in LG/J AND SM/J mice 
BMC Genomics  2014;15:99.
Background
The liver plays a major role in regulating metabolic homeostasis and is vital for nutrient metabolism. Identifying the genetic factors regulating these processes could lead to a greater understanding of how liver function responds to a high-fat diet and how that response may influence susceptibilities to obesity and metabolic syndrome. In this study we examine differences in hepatic gene expression between the LG/J and SM/J inbred mouse strains and how gene expression in these strains is affected by high-fat diet. LG/J and SM/J are known to differ in their responses to a high-fat diet for a variety of obesity- and diabetes-related traits, with the SM/J strain exhibiting a stronger phenotypic response to diet.
Results
Dietary intake had a significant effect on gene expression in both inbred lines. Genes up-regulated by a high-fat diet were involved in biological processes such as lipid and carbohydrate metabolism; protein and amino acid metabolic processes were down regulated on a high-fat diet. A total of 259 unique transcripts exhibited a significant diet-by-strain interaction. These genes tended to be associated with immune function. In addition, genes involved in biochemical processes related to non-alcoholic fatty liver disease (NAFLD) manifested different responses to diet between the two strains. For most of these genes, SM/J had a stronger response to the high-fat diet than LG/J.
Conclusions
These data show that dietary fat impacts gene expression levels in SM/J relative to LG/J, with SM/J exhibiting a stronger response. This supports previous data showing that SM/J has a stronger phenotypic response to high-fat diet. Based upon these findings, we suggest that SM/J and its cross with the LG/J strain provide a good model for examining non-alcoholic fatty liver disease and its role in metabolic syndrome.
doi:10.1186/1471-2164-15-99
PMCID: PMC4028868  PMID: 24499025
Liver; Dietary fat; Non-alcoholic fatty liver disease; NAFLD; Gene expression; Microarray; SM/J; LG/J
13.  Fine-mapping of Obesity-related Quantitative Trait Loci in an F9/10 Advanced Intercross Line 
Obesity (Silver Spring, Md.)  2009;18(7):10.1038/oby.2009.411.
Obesity develops in response to a combination of environmental effects and multiple genes of small effect. Although there has been significant progress in characterizing genes in many pathways contributing to metabolic disease, knowledge about the relationships of these genes to each other and their joint effects upon obesity lags behind. The LG, SM advanced intercross line (AIL) model of obesity has been used to characterize over 70 loci involved in fatpad weight, body weight, and organ weights. Each of these quantitative trait loci (QTLs) encompasses large regions of the genome and require fine-mapping to isolate causative sequence changes and possible mechanisms of action as indicated by the genetic architecture. In this study we fine-map QTLs first identified in the F2 and F2/3 populations in the combined F9/10 advanced intercross generations. We observed significantly narrowed QTL confidence regions, identified many single QTL that resolve into multiple QTL peaks, and identified new QTLs that may have been previously masked due to opposite gene effects at closely linked loci. We also present further characterization of the pleiotropic and epistatic interactions underlying these obesity-related traits.
doi:10.1038/oby.2009.411
PMCID: PMC3848327  PMID: 19910941
14.  Relative contribution of additive, dominance and imprinting effects to phenotypic variation in body size and growth between divergent selection lines of mice 
Evolution; international journal of organic evolution  2008;63(5):10.1111/j.1558-5646.2009.00638.x.
Epigenetic effects attributed to genomic imprinting are increasingly recognized as an important source of variation in quantitative traits. However, little is known about their relative contribution to phenotypic variation compared to those of additive and dominance effects, and almost nothing about their role in phenotypic evolution. Here we address these questions by investigating the relative contribution of additive, dominance and imprinting effects of quantitative trait loci (QTL) to variation in ‘early’ and ‘late’ body weight in an intercross of mice selected for divergent adult body weight. We identified 18 loci on 13 chromosomes; additive effects accounted for most of the phenotypic variation throughout development, and imprinting effects were always small. Genetic effects on early weight showed more dominance, less additive and, surprisingly, less imprinting variation than that of late weight. The predominance of additivity of QTL effects on body weight follows the expectation that additive effects account for the evolutionary divergence between selection lines. We hypothesize that the appearance of more imprinting effects on late body weight may be a consequence of divergent selection on adult body weight, which may have indirectly selected for alleles showing partial imprinting effects due to their associated additive effects, highlighting a potential role of genomic imprinting in the response to selection.
doi:10.1111/j.1558-5646.2009.00638.x
PMCID: PMC3846273  PMID: 19187253
15.  Molecular Insight into the Association Between Cartilage Regeneration and Ear Wound Healing in Genetic Mouse Models: Targeting New Genes in Regeneration 
G3: Genes|Genomes|Genetics  2013;3(11):1881-1891.
Tissue regeneration is a complex trait with few genetic models available. Mouse strains LG/J and MRL are exceptional healers. Using recombinant inbred strains from a large (LG/J, healer) and small (SM/J, nonhealer) intercross, we have previously shown a positive genetic correlation between ear wound healing, knee cartilage regeneration, and protection from osteoarthritis. We hypothesize that a common set of genes operates in tissue healing and articular cartilage regeneration. Taking advantage of archived histological sections from recombinant inbred strains, we analyzed expression of candidate genes through branched-chain DNA technology directly from tissue lysates. We determined broad-sense heritability of candidates, Pearson correlation of candidates with healing phenotypes, and Ward minimum variance cluster analysis for strains. A bioinformatic assessment of allelic polymorphisms within and near candidate genes was also performed. The expression of several candidates was significantly heritable among strains. Although several genes correlated with both ear wound healing and cartilage healing at a marginal level, the expression of four genes representing DNA repair (Xrcc2, Pcna) and Wnt signaling (Axin2, Wnt16) pathways was significantly positively correlated with both phenotypes. Cluster analysis accurately classified healers and nonhealers for seven out of eight strains based on gene expression. Specific sequence differences between LG/J and SM/J were identified as potential causal polymorphisms. Our study suggests a common genetic basis between tissue healing and osteoarthritis susceptibility. Mapping genetic variations causing differences in diverse healing responses in multiple tissues may reveal generic healing processes in pursuit of new therapeutic targets designed to induce or enhance regeneration and, potentially, protection from osteoarthritis.
doi:10.1534/g3.113.007302
PMCID: PMC3815053  PMID: 24002865
tissue regeneration; articular cartilage; QuantiGene Plex assay; recombinant inbred lines; osteoarthritis
16.  Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice 
Genome Biology and Evolution  2013;5(10):1926-1936.
Divergence of serially homologous elements of organisms is a common evolutionary pattern contributing to increased phenotypic complexity. Here, we study the genomic intervals affecting the variational independence of fore- and hind limb traits within an experimental mouse population. We use an advanced intercross of inbred mouse strains to map the loci associated with the degree of autonomy between fore- and hind limb long bone lengths (loci affecting the relationship between traits, relationship quantitative trait loci [rQTL]). These loci have been proposed to interact locally with the products of pleiotropic genes, thereby freeing the local trait from the variational constraint due to pleiotropic mutations. Using the known polymorphisms (single nucleotide polymorphisms [SNPs]) between the parental strains, we characterized and compared the genomic regions in which the rQTL, as well as their interaction partners (intQTL), reside. We find that these two classes of QTL intervals harbor different kinds of molecular variation. SNPs in rQTL intervals more frequently reside in limb-specific cis-regulatory regions than SNPs in intQTL intervals. The intQTL loci modified by the rQTL, in contrast, show the signature of protein-coding variation. This result is consistent with the widely accepted view that protein-coding mutations have broader pleiotropic effects than cis-regulatory polymorphisms. For both types of QTL intervals, the underlying candidate genes are enriched for genes involved in protein binding. This finding suggests that rQTL effects are caused by local interactions among the products of the causal genes harbored in rQTL and intQTL intervals. This is the first study to systematically document the population-level molecular variation underlying the evolution of character individuation.
doi:10.1093/gbe/evt144
PMCID: PMC3814202  PMID: 24065733
autonomy; pleiotropy; constraint; genetic interaction; character
17.  Heritability of Articular Cartilage Regeneration and its Association with Ear-Wound Healing 
Arthritis and Rheumatism  2012;64(7):2300-2310.
Objective
Emerging evidence suggests that genetic components contribute significantly to cartilage degeneration in osteoarthritis pathophysiology but little evidence is available on genetics of cartilage regeneration. Therefore, we investigated cartilage regeneration in genetic murine models using common inbred strains and a set of recombinant inbred lines generated from LG/J (healer of ear-wounds) and SM/J (non-healer) inbred strains.
Methods
An acute full-thickness cartilage injury was introduced through microsurgery in the trochlear groove of 8-weeks old mice (N=265). Knee joints were sagittally sectioned and stained with toluidine blue to evaluate regeneration. For ear-wound phenotype, a bilateral 2-mm through-and-through puncture was made (N=229) at 6-weeks and healing outcomes measured after 30-days. Broad-sense heritability and genetic correlations were calculated for both phenotypes.
Results
Time-course studies from recombinant inbred lines show no significant regeneration until 16-weeks post-surgery; at that time, the strains can be segregated into three categories: good, intermediate and poor healers. Heritability (H2) showed that both cartilage regeneration (H2=26%; p=0.006) and ear-wound closure (H2=53%; p<0.00001) are significantly heritable. The genetic correlations between the two healing phenotypes for common inbred strains (r=0.92) and recombinant inbred lines (r=0.86) were found to be extremely high.
Conclusion
We report that i) articular cartilage regeneration is heritable, ii) the differences between the lines being due to genetic differences and iii) a strong genetic correlation between the two phenotypes exists indicating that they plausibly share a common genetic basis. We, therefore, surmise that LG/J by SM/J intercross can be used to dissect the genetic basis of variation in cartilage regeneration.
doi:10.1002/art.34396
PMCID: PMC3360138  PMID: 22275233
articular cartilage; ear-wound; regeneration; genetics; heritability
18.  Genetic Relationships between Obesity and Osteoporosis in LGXSM Recombinant Inbred Mice 
Genetics research  2008;90(5):433-444.
Summary
Obesity and osteoporosis affect millions of Americans. While phenotypically, obesity is negatively correlated with fracture risk, research on a genetic basis for this relationship is lacking. We used males and females from 16 LGXSM recombinant inbred (RI) mouse strains to investigate the genetically-mediated relationship between obesity and osteoporosis-related traits. First, heritabilities were estimated for (1) bone morphological properties determined by microCT (femoral and radial diaphyseal bone cross-sectional area and moments of inertia, as well as proximal tibial trabecular bone volume, connectivity density, structure model index, trabecular number, trabecular thickness, and trabecular separation), (2) mechanical properties determined by bending tests (femoral and radial rigidity, yield moment, ultimate moment, fracture displacement, and post-yield displacement), and (3) effective material properties (femoral and radial modulus of elasticity and ultimate tensile strength). All femoral (H2: 43-74%) and tibial traits (H2: 31-56%) were heritable; as were eight of 10 radial traits (H2: 21-33%). Eighteen significant genetic correlations were discovered between obesity- and osteoporosis-related phenotypes. Genetic correlations indicate that gene effects associated with increased fat mass and leptin levels are also associated with larger, stronger femora. Gene effects associated with larger, stronger radii and with denser tibiae were also associated with increased fat mass but not with leptin levels. Furthermore, quantitative trait loci (QTLs) previously reported for obesity and leptin levels also had effects on bone morphology, mechanical, and material properties. Our results support the use of the LG/J x SM/J mouse intercross populations as models for normal, complex genetic variation in obesity, bone properties, and their interrelationship.
doi:10.1017/S0016672308009798
PMCID: PMC2649827  PMID: 19061533
Quantitative Genetics; obesity; osteoporosis; LGXSM mouse strains
19.  Cartilage and Bone Changes during Development of Post-Traumatic Osteoarthritis in Selected LGXSM Recombinant Inbred Mice 
Osteoarthritis and Cartilage  2012;20(6):562-571.
Introduction
Little evidence is available on the natural course of osteoarthritis development and the genes that protect and predispose individuals to it. This study was designed to compare strain-dependent development of osteoarthritis and its association with tissue regeneration in mice. Two recombinant inbred lines LGXSM-6 and LGXSM-33 generated from LG/J and SM/J intercross were used. Previous studies have indicated that LGXSM-6 can regenerate both articular cartilage and ear hole punch while LGXSM-33 cannot.
Methods
Transection of the medial meniscotibial ligament was performed on 10-week-old male mice to induce osteoarthritis. Cartilage damage was analyzed by histology and bone morphology was evaluated using micro-CT. Ear punches were performed and evaluated by measurement of residual hole diameter.
Results
Cartilage analysis showed that LGXSM-33 developed a significantly higher grade of osteoarthritis than LGXSM-6. Bone analysis showed that LGXSM-33 had substantial subchondral bone and trabecular bone thickening 8 weeks post-surgery, while LGXSM-6 showed bone loss over time. We also confirmed that LGXSM-6 can heal ear tissues significantly better than LGXSM-33.
Conclusions
Osteoarthritis was found to be negatively correlated with the degree of tissue regeneration. LGXSM-33, a poor healer of ear tissues (and articular cartilage), developed more osteoarthritis compared to LGXSM-6, which had better regenerative ability for ear tissues and articular cartilage. While these lines have different distribution of the alleles, we assume that the phenotypic differences observed here are due to genetic differences further suggesting that similar sets of physiological processes and gene variants may mediate variation in human osteoarthritis development and tissue regeneration.
doi:10.1016/j.joca.2012.01.022
PMCID: PMC3353722  PMID: 22361237
20.  Genetic loci that regulate healing and regeneration in LG/J and SM/J mice 
MRL mice display unusual healing properties. When MRL ear pinnae are hole punched, the holes close completely without scarring, with re-growth of cartilage, and reappearance of both hair follicles and sebaceous glands. Studies using (MRL/lpr x C57BL/6)F2 and backcross mice first showed that this phenomenon was genetically determined and that multiple loci contributed to this quantitative trait. The lpr mutation itself, however, was not one of them. In the present study, we examined the genetic basis of healing in the Large (LG/J) mouse strain, a parent of the MRL mouse and a strain that shows the same healing phenotype. LG/J mice were crossed with Small (SM/J) mice and the F2 population was scored for healing and their genotypes determined at >200 polymorphic markers. As we previously observed for MRL and (MRL x B6)F2 mice, the wound healing phenotype was sexually dimorphic with female mice healing more quickly and more completely than male mice. We found quantitative trait loci (QTL) on chromosomes (chr) 9, 10, 11, and 15. The heal QTL on chrs 11 and 15 were linked to differential healing primarily in male animals, whereas QTL on chrs 9 and 10 were not sexually dimorphic. A comparison of loci identified in previous crosses with those in the present report using LG/J x SM/J showed that loci on chrs 9, 11 and 15 co-localized with those seen in previous MRL crosses, whereas the locus on chr 10 was not seen before and was is contributed by SM/J.
doi:10.1007/s00335-009-9216-3
PMCID: PMC3652381  PMID: 19760323
21.  The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J x SM/J murine model 
Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci affecting serum glucose and insulin levels and response to glucose stress in an F16 Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG, SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We find that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context dependent, and that the same genomic sequence can affect traits differently depending on an individual’s sex and/or dietary environment. Our results have important implications for studies of complex traits in humans.
doi:10.1007/s00335-010-9313-3
PMCID: PMC3650899  PMID: 21210123
quantitative trait loci; imprinting; context-dependency; mouse models; diabetes
22.  Heritability of Alveolar Bone Loss from Periodontal Disease in a Baboon Population. A Pilot Study 
Journal of periodontology  2010;82(4):575-580.
Background
Reports from studies of twins, disease aggregation in families, animal models for periodontal disease, and various genetic-analysis studies have determined that genetics plays a role in the susceptibility to periodontal disease. The purpose of this pilot study was to evaluate the effect of genetics on periodontal disease by evaluating the heritability of alveolar bone loss in a captive baboon population.
Methods
A collection of baboon skulls from a pedigreed colony (for which scientists and veterinarians maintain complete genealogical and veterinary records) were obtained from the Southwest National Primate Research Center and used in this pilot study. Measurements of alveolar bone loss were performed on 390 dry baboon skulls. A periodontal probe was used to measure alveolar bone loss. Maximum likelihood methods (designed to handle complex genealogies) were used to determine the heritability of alveolar bone loss. This software utilized known pedigrees in the captive baboon sample and tested the relationship between pairwise kinship and alveolar bone loss data to determine the heritability of alveolar bone loss from periodontal disease.
Results
Genetic data were available for 347 of the 390 specimens. Using age and sex as covariates, genetic analysis indicated a heritability of 35% (standard error=20%, p=0.01). While sex was not a significant factor in periodontal disease (p=0.96), age was highly significantly associated with periodontal disease (p<0.0001).
Conclusion
In this pilot study, analysis of alveolar bone loss measurements from captive baboons indicates that bone loss increases with age and that a portion of periodontal disease risk may be due to genetic variance. These findings provide evidence that periodontal disease is heritable in captive baboons and indicate that a larger, more-detailed study is warranted.
doi:10.1902/jop.2010.100189
PMCID: PMC3575216  PMID: 21043800
periodontitis; alveolar bone; genetics; baboons
23.  Quantitative Trait Loci Affecting Liver Fat Content in Mice 
G3: Genes|Genomes|Genetics  2012;2(9):1019-1025.
Nonalcoholic fatty liver disease, a condition in which excess fat accumulates in the liver, is strongly associated with the metabolic syndrome, including obesity and other related conditions. This disease has the potential to progress from steatosis to steatohepatitis, fibrosis, and cirrhosis. The recent increase in the prevalence of the metabolic syndrome is largely driven by changes in diet and activity levels. Individual variation in the response to this obesogenic environment, however, is attributable in part to genetic variation between individuals, but very few mammalian genetic loci have been identified with effects on fat accumulation in the liver. To study the genetic basis for variation in liver fat content in response to dietary fat, liver fat proportion was determined using quantitative magnetic resonance imaging in 478 mice from 16 LG/J X SM/J recombinant inbred strains fed either a high-fat (42% kcal from fat) or low-fat (15% kcal from fat) diet. An analysis of variance confirmed that there is a genetic basis for variation in liver fat content within the population with significant effects of sex and diet. Three quantitative trail loci that contribute to liver fat content also were mapped.
doi:10.1534/g3.112.003343
PMCID: PMC3429915  PMID: 22973538
nonalcoholic fatty liver disease; NAFLD; QTL; mouse; LG/J; SM/J
24.  Evolution of pleiotropy: Epistatic interaction pattern supports a mechanistic model underlying variation in genotype-phenotype map 
The genotype-phenotype map consists of developmental and physiological mechanisms mapping genetic onto phenotypic variation. It determines the distribution of heritable phenotypic variance on which selection can act. Comparative studies of morphology as well as of gene regulatory networks show that the genotype-phenotype map itself evolves, yet little is known about the actual evolutionary mechanisms involved. The study of such mechanisms requires exploring the variation in genotype-phenotype maps at the population level, which presently is easier to quantify by statistical genetic methods rather than by regulatory network structures. We focus on the evolution of pleiotropy, a major structural aspect of the genotype-phenotype map. Pleiotropic genes affect multiple traits and underlie genetic covariance between traits, often causing evolutionary constraints. Previous quantitative genetic studies have demonstrated population-level variation in pleiotropy in the form of loci, at which genotypes differ in the genetic covariation between traits. This variation can potentially fuel evolution of the genotype-phenotype map under selection and/or drift. Here, we propose a developmental mechanism underlying population genetic variation in covariance, and test its predictions. Specifically, the mechanism predicts that the loci identified as responsible for genetic variation in pleiotropy are involved in trait-specific epistatic interactions. We test this prediction for loci affecting allometric relationships between traits in an advanced intercross between inbred mouse strains. The results consistently support the prediction. We further find a high degree of sign epistasis in these interactions, which we interpret as an indication of adaptive gene complexes within the diverged parental lines.
doi:10.1002/jez.b.21410
PMCID: PMC3112255  PMID: 21462316
25.  Hypothalamic expression of Peg3 gene is associated with maternal care differences between SM/J and LG/J mouse strains 
Brain and Behavior  2012;2(4):365-376.
Maternal care is essential in mammals, and variations in the environment provided by mothers may directly influence the viability of newborns and emotional behavior later in life. A previous study investigated genetic variations associated with maternal care in an intercross of LG/J and SM/J inbred mouse strains and identified two single-locus QTLs (quantitative trait loci). Here, we selected three candidate genes located within these QTLs intervals; Oxt on chromosome 2, and FosB and Peg3 on chromosome 7 and tested their association with maternal care. LG/J females showed impaired postpartum nest building and pup retrieval, a one-day delay in milk ejection, reduced exploratory activity, and higher anxiety-like behavior when compared to SM/J females. The nucleotide sequences of Oxt and FosB were similar between strains, as were their hypothalamic expression levels. Conversely, Peg3 nucleotide sequences showed four nonsynonymous replacement substitutions on LG/J dams, T11062G, G13744A, A13808G, and G13813A, and a 30 base pair (10 aa) in tandem repeat in the coding region with three copies in SM/J and five copies in LG/J. Maternal care impaired LG/J mothers express 37% lower Peg3 mRNA levels in the hypothalamus on the second postpartum day. We also found an association of the Peg3 repeat-variant and poor maternal care in F2 heterozygote females derived from a LG/J × SM/J intercross. These results may suggest that the maternally imprinted Peg3 gene is responsible for the single-locus QTL on chromosome 7 that has been shown to influence maternal care in these strains. Furthermore, these data provide additional support for an epigenetic regulation of maternal behavior.
doi:10.1002/brb3.58
PMCID: PMC3432959  PMID: 22950040
Chromosome; epigenetic; FosB; gene expression; gene variation; hypothalamus; imprinting; maternal behavior; Oxt; QTL

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