Identification of quantitative trait loci influencing skeletal architecture in mice: emergence of Cdh11 as a primary candidate gene regulating femoral morphology

A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles 'GGG' for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

Genetic analysis of osteoblast activity identifies Zbtb40 as a regulator of osteoblast activity and bone mass

Osteoporosis is a genetic disease characterized by progressive reductions in bone mineral density (BMD) leading to an increased risk of fracture. Over the last decade, genome-wide association studies (GWASs) have identified over 1000 associations for BMD. However, as a phenotype BMD is challenging as bone is a multicellular tissue affected by both local and systemic physiology. Here, we focused on a single component of BMD, osteoblast-mediated bone formation in mice, and identified associations influencing osteoblast activity on mouse Chromosomes (Chrs) 1, 4, and 17. The locus on Chr. 4 was in an intergenic region between Wnt4 and Zbtb40, homologous to a locus for BMD in humans. We tested both Wnt4 and Zbtb40 for a role in osteoblast activity and BMD. Knockdown of Zbtb40, but not Wnt4, in osteoblasts drastically reduced mineralization. Additionally, loss-of-function mouse models for both genes exhibited reduced BMD. Our results highlight that investigating the genetic basis of in vitro osteoblast mineralization can be used to identify genes impacting bone formation and BMD.

Genetic Dissection of Femoral and Tibial Microarchitecture

Our understanding of the genetic control of bone strength has relied mainly on estimates of bone mineral density. Here we have mapped genetic factors that influence femoral and tibial microarchitecture using high‐resolution x‐ray computed tomography (8‐μm isotropic voxels) across a family of 61 BXD strains of mice, roughly 10 isogenic cases per strain and balanced by sex. We computed heritabilities for 25 cortical and trabecular traits. Males and females have well‐matched heritabilities, ranging from 0.25 to 0.75. We mapped 16 genetic loci most of which were detected only in females. There is also a bias in favor of loci that control cortical rather than trabecular bone. To evaluate candidate genes, we combined well‐established gene ontologies with bone transcriptome data to compute bone‐enrichment scores for all protein‐coding genes. We aligned candidates with those of human genome‐wide association studies. A subset of 50 strong candidates fell into three categories: (1) experimentally validated genes already known to modulate bone function (Adamts4, Ddr2, Darc, Adam12, Fkbp10, E2f6, Adam17, Grem2, Ifi204); (2) candidates without any experimentally validated function in bone (eg, Greb1, Ifi202b), but linked to skeletal phenotypes in human cohorts; and (3) candidates that have high bone‐enrichment scores, but for which there is not yet any functional link to bone biology or skeletal system disease (including Ifi202b, Ly9, Ifi205, Mgmt, F2rl1, Iqgap2). Our results highlight contrasting genetic architecture between sexes and among major bone compartments. The alignment of murine and human data facilitates function analysis and should prove of value for preclinical testing of molecular control of bone structure. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Structural Equation Modeling and Whole-Genome Scans Uncover Chromosome Regions and Enriched Pathways for Carcass and Meat Quality in Beef

Structural equation models involving latent variables are useful tools for formulating hypothesized models defined by theoretical variables and causal links between these variables. The objectives of this study were: (1) to identify latent variables underlying carcass and meat quality traits and (2) to perform whole-genome scans for these latent variables in order to identify genomic regions and individual genes with both direct and indirect effects. A total of 726 steers from an Angus-Brahman multibreed population with records for 22 phenotypes were used. A total of 480 animals were genotyped with the GGP Bovine F-250. The single-step genomic best linear unbiased prediction method was used to estimate the amount of genetic variance explained for each latent variable by chromosome regions of 20 adjacent SNP-windows across the genome. Three types of genetic effects were considered: (1) direct effects on a single latent phenotype; (2) direct effects on two latent phenotypes simultaneously; and (3) indirect effects. The final structural model included carcass quality as an independent latent variable and meat quality as a dependent latent variable. Carcass quality was defined by quality grade, fat over the ribeye and marbling, while the meat quality was described by juiciness, tenderness and connective tissue, all of them measured through a taste panel. From 571 associated genomic regions (643 genes), each one explaining at least 0.05% of the additive variance, 159 regions (179 genes) were associated with carcass quality, 106 regions (114 genes) were associated with both carcass and meat quality, 242 regions (266 genes) were associated with meat quality, and 64 regions (84 genes) were associated with carcass quality, having an indirect effect on meat quality. Three biological mechanisms emerged from these findings: postmortem proteolysis of structural proteins and cellular compartmentalization, cellular proliferation and differentiation of adipocytes, and fat deposition.

Tomography-Based Quantification of Regional Differences in Cortical Bone Surface Remodeling and Mechano-Response

Bone has an adaptive capacity to maintain structural integrity. However, there seems to be a heterogeneous cortical (re)modeling response to loading at different regions within the same bone, which may lead to inconsistent findings since most studies analyze only one region. It remains unclear if the local mechanical environment is responsible for this heterogeneous response and whether both formation and resorption are affected. Thus, we compared the formation and resorptive response to in vivo loading and the strain environment at two commonly analyzed regions in the mouse tibia, the mid-diaphysis and proximal metaphysis. We quantified cortical surface (re)modeling by tracking changes between geometrically aligned consecutive in vivo micro-tomography images (time lapse 15 days). We investigated the local mechanical strain environment using finite element analyses. The relationship between mechanical stimuli and surface (re)modeling was examined by sub-dividing the mid-diaphysis and proximal metaphysis into 32 sub-regions. In response to loading, metaphyseal cortical bone (re)modeled predominantly at the periosteal surface, whereas diaphyseal (re)modeling was more pronounced at the endocortical surface. Furthermore, different set points and slopes of the relationship between engendered strains and remodeling response were found for the endosteal and periosteal surfaces at the metaphyseal and diaphyseal regions. Resorption was correlated with strain at the endocortical, but not the periosteal surfaces, whereas, formation correlated with strain at all surfaces, except at the metaphyseal periosteal surface. Therefore, besides mechanical stimuli, other non-mechanical factors are likely driving regional differences in adaptation. Studies investigating adaptation to loading or other treatments should consider region-specific (re)modeling differences.

Dissection of Host Susceptibility to Bacterial Infections and Its Toxins

Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies. Most of current animal models used in complex traits diseases genetic mapping have limited genetic diversity. This limitation impedes the ability to create incorporated network using genetic interactions, epigenetics, environmental factors, microbiota, and other phenotypes. A novel mouse genetic reference population for high-resolution mapping and subsequently identifying genes underlying the QTL, namely the Collaborative Cross (CC) mouse genetic reference population (GRP) was recently developed. In this chapter, we discuss a variety of approaches using CC mice for mapping genes underlying quantitative trait loci (QTL) to dissect the host response to polygenic traits, including infectious disease caused by bacterial agents and its toxins.

Increased Bone Mass in Female Mice Lacking Mast Cell Chymase

Here we addressed the potential impact of chymase, a mast-cell restricted protease, on mouse bone phenotype. We show that female mice lacking the chymase Mcpt4 acquired a persistent expansion of diaphyseal bone in comparison with wild type controls, reaching a 15% larger diaphyseal cross sectional area at 12 months of age. Mcpt4-/- mice also showed increased levels of a bone anabolic serum marker and higher periosteal bone formation rate. However, they were not protected from experimental osteoporosis, suggesting that chymase regulates normal bone homeostasis rather than the course of osteoporosis. Further, the absence of Mcpt4 resulted in age-dependent upregulation of numerous genes important for bone formation but no effects on osteoclast activity. In spite of the latter, Mcpt4-/- bones had increased cortical porosity and reduced endocortical mineralization. Mast cells were found periosteally and, notably, bone-proximal mast cells in Mcpt4-/- mice were degranulated to a larger extent than in wild type mice. Hence, chymase regulates degranulation of bone mast cells, which could affect the release of mast cell-derived factors influencing bone remodelling. Together, these findings reveal a functional impact of mast cell chymase on bone. Further studies exploring the possibility of using chymase inhibitors as a strategy to increase bone volume may be warranted.

Genetic regulation of bone strength: a review of animal model studies

Population- and family-based studies have established that fragility fracture risk is heritable; yet, the genome-wide association studies published to date have only accounted for a small fraction of the known variation for fracture risk of either the femur or the lumbar spine. Much work has been carried out using animal models toward finding genetic loci that are associated with bone strength. Studies using animal models overcome some of the issues associated with using patient data, but caution is needed when interpreting the results. In this review, we examine the types of tests that have been used for forward genetics mapping in animal models to identify loci and/or genes that regulate bone strength and discuss the limitations of these test methods. In addition, we present a summary of the quantitative trait loci that have been mapped for bone strength in mice, rats and chickens. The majority of these loci co-map with loci for bone size and/or geometry and thus likely dictate strength via modulating bone size. Differences in bone matrix composition have been demonstrated when comparing inbred strains of mice, and these matrix differences may be associated with differences in bone strength. However, additional work is needed to identify loci that act on bone strength at the materials level.

Identification of quantitative trait loci influencing inflammation-mediated alveolar bone loss: insights into polygenic inheritance of host-biofilm disequilibria in periodontitis

BACKGROUND AND OBJECTIVE

The relative contribution of genetic and environmental factors to the onset and progression of periodontitis is inconclusive. Despite the high prevalence, phenotypic heterogeneity and significant local and systemic implications of this disease, early detection and individualized therapy are problematic. Using a murine model of periodontitis in a panel of 17 recombinant inbred mice, the current study addressed the heritability of, and oral dysbiosis associated with, inflammation-mediated alveolar bone loss (iABL), the hallmark of periodontitis.

MATERIAL AND METHODS

Quantitative trait locus (QTL) genomics and quantitative PCR for over 99% of known murine oral microbiota were used.

RESULTS

It was found that iABL is a polygenic trait with 32.7% heritability. One suggestive QTL, nicknamed inflammation-mediated alveolar bone loss locus (iABLL), was identified on chromosome 2. Eleven genes involved in innate immune responses and bone metabolism, particularly related to macrophage and osteoblast function, namely Etl4, Pdss1, Cobll1, 9330158F14Rik, Xirp2, Stk39, Mettl5, Metapl1, Itga6, Pdk1 and Sp3, were found in the iABLL using cis expression QTL and nonsynonymous single nucleotide polymorphism analyses. Specific oral microbiome shifts in saliva and tongue mucosa are associated with disease in this model.

CONCLUSION

Our results indicate that complex host-biofilm interactions generate pathogenic states that extend beyond subgingival biofilms and periodontal tissues. Although no temporal relationship between the onset of iABL and microbiome changes were established, our findings suggest that host factors may be responsible for pathogenic shifts in subgingival biofilms when persistent and undisturbed.

Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle

Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to voluntary exercise, body composition, and changes in body composition as a result of exercise. Using brain tissue in a subset of the G4 (n = 244), we have also previously reported expression QTL (eQTL) colocalizing with the QTL for the higher-level phenotypes. Here, we examined the transcriptional landscape of hind limb muscle tissue via global mRNA expression profiles. Correlations revealed an ∼1,168% increase in significant relationships between muscle transcript expression levels and the same exercise and body composition phenotypes examined previously in the brain. The exercise trait most often significantly correlated with gene expression in the brain was running duration while in the muscle it was maximum running speed. This difference may indicate that time spent engaging in exercise behavior may be more influenced by central (neurobiological) mechanisms, while intensity of exercise may be largely controlled by peripheral mechanisms. Additionally, we used subsets of cis-acting eQTL, colocalizing with QTL, to identify candidate genes based on both positional and functional evidence. We discuss three plausible candidate genes (Insig2, Prcp, Sparc) and their potential regulatory role.

Gene-by-diet interactions influence calcium absorption and bone density in mice

Dietary calcium (Ca) intake is needed to attain peak bone mineral density (BMD). Habitual low Ca intake increases intestinal Ca absorption efficiency to protect bone mass, but the mechanism controlling, and the impact of genetics on, this adaptive response is not clear. We fed 11 genetically diverse inbred mouse lines a normal (0.5%) or low (0.25%) Ca diet from 4 to 12 weeks of age (n = 8 per diet per line) and studied the independent and interacting effects of diet and genetics on Ca and bone metabolism. Significant genetic variation was observed in all bone, renal, and intestinal phenotypes measured including Ca absorption. Also, adaptation of Ca absorption and bone parameters to low dietary Ca was significantly different among the lines. Ca absorption was positively correlated to femur BMD (r = 0.17, p = 0.02), and distal femur bone volume/tissue volume (BV/TV) (r = 0.34, p < 0.0001). Although Ca absorption was correlated to 1,25 dihydroxyvitamin D (1,25(OH)2 D) (r = 0.35, p < 0.0001), the adaptation of Ca absorption to low Ca intake did not correlate to diet-induced adaptation of 1,25(OH)2 D across the 11 lines. Several intestinal proteins have been proposed to mediate Ca absorption: claudins 2 and 12, voltage gated Ca channel v1.3 (Cav1.3), plasma membrane Ca ATPase 1b (PMCA1b), transient receptor potential vanilloid member 6 (TRPV6), and calbindin D9k (CaBPD9k). Only the mRNA levels for TRPV6, CaBPD9k, and PMCA1b were related to Ca absorption (r = 0.42, 0.43, and 0.21, respectively). However, a significant amount of the variation in Ca absorption is not explained by the current model and suggests that novel mechanisms remain to be determined. These observations lay the groundwork for discovery-focused initiatives to identify novel genetic factors controlling gene-by-diet interactions affecting Ca/bone metabolism.

QTL mapping in outbred populations: successes and challenges

Quantitative trait locus (QTL) mapping in animal populations has been a successful strategy for identifying genomic regions that play a role in complex diseases and traits. When conducted in an F2 intercross or backcross population, the resulting QTL is frequently large, often encompassing 30 Mb or more and containing hundreds of genes. To narrow the locus and identify candidate genes, additional strategies are needed. Congenic strains have proven useful but work less well when there are multiple tightly linked loci, frequently resulting in loss of phenotype. As an alternative, we discuss the use of highly recombinant outbred models for directly fine-mapping QTL to only a few megabases. We discuss the use of several currently available models such as the advanced intercross (AI), heterogeneous stocks (HS), the diversity outbred (DO), and commercially available outbred stocks (CO). Once a QTL has been fine-mapped, founder sequence and expression QTL mapping can be used to identify candidate genes. In this regard, the large number of alleles found in outbred stocks can be leveraged to identify causative genes and variants. We end this review by discussing some important statistical considerations when analyzing outbred populations. Fine-resolution mapping in outbred models, coupled with full genome sequence, has already led to the identification of several underlying causative genes for many complex traits and diseases. These resources will likely lead to additional successes in the coming years.

Quantitative trait loci for bone mineral density and femoral morphology in an advanced intercross population of mice

Osteoporosis, characterized by low levels of bone mineral density (BMD), is a prevalent medical condition in humans. We investigated its genetic and environmental basis by searching for quantitative trait loci (QTLs) affecting six skeletal (including three BMD) traits in a G10 advanced intercross population produced from crosses of mice from the inbred strain C57BL/6J with mice from a strain selected for high voluntary wheel running. The mice in this population were fed either a high-fat or a matched control diet throughout the study, allowing us to test for QTL by diet interactions for the skeletal traits. Our genome scan uncovered a number of QTLs, the great majority of which were different from QTLs previously found for these same traits in an earlier (G4) generation of the same intercross. Further, the confidence intervals for the skeletal trait QTLs were reduced from an average of 18.5 Mb in the G4 population to an equivalent of about 9 Mb in the G10 population. We uncovered a total of 50 QTLs representing 32 separate genomic sites affecting these traits, with a distal region on chromosome 1 harboring several QTLs with large effects on the BMD traits. One QTL was located on chromosome 5 at 4.0 Mb with a confidence interval spanning from 4.0 to 4.6 Mb. Only three protein coding genes reside in this interval, and one of these, Cyp51, is an attractive candidate as others have shown that developing Cyp51 knockout embryos exhibit shortened and bowed limbs and synotosis of the femur and tibia. Several QTLs showed significant interactions with sex, although only two QTLs interacted with diet, both affecting only mice fed the high-fat diet.

Mid-gestational gene expression profile in placenta and link to pregnancy complications

Despite the importance of placenta in mediating rapid physiological changes in pregnancy, data on temporal dynamics of placental gene expression are limited. We completed the first transcriptome profiling of human placental gene expression dynamics (GeneChips, Affymetrix®; ∼47,000 transcripts) from early to mid-gestation (n = 10; gestational weeks 5–18) and report 154 genes with significant transcriptional changes (ANOVA, FDR P<0.1). TaqMan RT-qPCR analysis (n = 43; gestational weeks 5–41) confirmed a significant (ANOVA and t-test, FDR P<0.05) mid-gestational peak of placental gene expression for BMP5, CCNG2, CDH11, FST, GATM, GPR183, ITGBL1, PLAGL1, SLC16A10 and STC1, followed by sharp decrease in mRNA levels at term (t-test, FDR P<0.05). We hypothesized that normal course of late pregnancy may be affected when genes characteristic to mid-gestation placenta remain highly expressed until term, and analyzed their expression in term placentas from normal and complicated pregnancies [preeclampsia (PE), n = 12; gestational diabetes mellitus (GDM), n = 12; small- and large-for-gestational-age newborns (SGA, LGA), n = 12+12]. STC1 (stanniocalcin 1) exhibited increased mRNA levels in all studied complications, with the most significant effect in PE- and SGA-groups (t-test, FDR P<0.05). In post-partum maternal plasma, the highest STC1 hormone levels (ELISA, n = 129) were found in women who had developed PE and delivered a SGA newborn (median 731 vs 418 pg/ml in controls; ANCOVA, P = 0.00048). Significantly higher expression (t-test, FDR P<0.05) of CCNG2 and LYPD6 accompanied with enhanced immunostaining of the protein was detected in placental sections of PE and GDM cases (n = 15). Our study demonstrates the importance of temporal dynamics of placental transcriptional regulation across three trimesters of gestation. Interestingly, many genes with high expression in mid-gestation placenta have also been implicated in adult complex disease, promoting the discussion on the role of placenta in developmental programming. The discovery of elevated maternal plasma STC1 in pregnancy complications warrants further investigations of its potential as a biomarker.

Functional genomic architecture of predisposition to voluntary exercise in mice: expression QTL in the brain

The biological basis of voluntary exercise is complex and simultaneously controlled by peripheral (ability) and central (motivation) mechanisms. The accompanying natural reward, potential addiction, and the motivation associated with exercise are hypothesized to be regulated by multiple brain regions, neurotransmitters, peptides, and hormones. We generated a large (n = 815) advanced intercross line of mice (G(4)) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped multiple quantitative trait loci (QTL) that contribute to the biological control of voluntary exercise levels, body weight, and composition, as well as changes in body weight and composition in response to short-term exercise. Currently, using a subset of the G(4) population (n = 244), we examined the transcriptional landscape relevant to neurobiological aspects of voluntary exercise by means of global mRNA expression profiles from brain tissue. We identified genome-wide expression quantitative trait loci (eQTL) regulating variation in mRNA abundance and determined the mode of gene action and the cis- and/or trans-acting nature of each eQTL. Subsets of cis-acting eQTL, colocalizing with QTL for exercise or body composition traits, were used to identify candidate genes based on both positional and functional evidence, which were further filtered by correlational and exclusion mapping analyses. Specifically, we discuss six plausible candidate genes (Insig2, Socs2, DBY, Arrdc4, Prcp, IL15) and their potential role in the regulation of voluntary activity, body composition, and their interactions. These results develop a potential initial model of the underlying functional genomic architecture of predisposition to voluntary exercise and its effects on body weight and composition within a neurophysiological framework.