The canine homeobox gene MSX2: sequence, chromosome assignment and genetic analysis in dogs of different breeds

Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology

Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10⁻⁸) for cranial base width at 14q21.1 and 20q12, intercanthal width at 1p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.

There is a great deal of evidence that genes influence facial appearance. This is perhaps most apparent when we look at our own families, since we are more likely to share facial features in common with our close relatives than with unrelated individuals. Nevertheless, little is known about how variation in specific regions of the genome relates to the kinds of distinguishing facial characteristics that give us our unique identities, e.g., the size and shape of our nose or how far apart our eyes are spaced. In this paper, we investigate this question by examining the association between genetic variants across the whole genome and a set of measurements designed to capture key aspects of facial form. We found evidence of genetic associations involving measures of eye, nose, and facial breadth. In several cases, implicated regions contained genes known to play roles in embryonic face formation or in syndromes in which the face is affected. Our ability to connect specific genetic variants to ubiquitous facial traits can inform our understanding of normal and abnormal craniofacial development, provide potential predictive models of evolutionary changes in human facial features, and improve our ability to create forensic facial reconstructions from DNA.

Heritability of Face Shape in Twins: A Preliminary Study using 3D Stereophotogrammetry and Geometric Morphometrics

INTRODUCTION

Previous research suggests that aspects of facial surface morphology are heritable. Traditionally, heritability studies have used a limited set of linear distances to quantify facial morphology and often employ statistical methods poorly designed to deal with biological shape. In this preliminary report, we use a combination of 3D photogrammetry and landmark-based morphometrics to explore which aspects of face shape show the strongest evidence of heritability in a sample of twins.

METHODS

3D surface images were obtained from 21 twin pairs (10 monozygotic, 11 same-sex dizygotic). Thirteen 3D landmarks were collected from each facial surface and their coordinates subjected to geometric morphometric analysis. This involved superimposing the individual landmark configurations and then subjecting the resulting shape coordinates to a principal components analysis. The resulting PC scores were then used to calculate rough narrow-sense heritability estimates.

RESULTS

Three principal components displayed evidence of moderate to high heritability and were associated with variation in the breadth of orbital and nasal structures, upper lip height and projection, and the vertical and forward projection of the root of the nose due to variation in the position of nasion.

CONCLUSIONS

Aspects of facial shape, primarily related to variation in length and breadth of central midfacial structures, were shown to demonstrate evidence of strong heritability. An improved understanding of which facial features are under strong genetic control is an important step in the identification of specific genes that underlie normal facial variation.

Variation of BMP3 contributes to dog breed skull diversity

Since the beginnings of domestication, the craniofacial architecture of the domestic dog has morphed and radiated to human whims. By beginning to define the genetic underpinnings of breed skull shapes, we can elucidate mechanisms of morphological diversification while presenting a framework for understanding human cephalic disorders. Using intrabreed association mapping with museum specimen measurements, we show that skull shape is regulated by at least five quantitative trait loci (QTLs). Our detailed analysis using whole-genome sequencing uncovers a missense mutation in BMP3. Validation studies in zebrafish show that Bmp3 function in cranial development is ancient. Our study reveals the causal variant for a canine QTL contributing to a major morphologic trait.

As a result of selective breeding practices, modern dogs display a multitude of head shapes. Breeds such as the Pug and Bulldog popularize one of these morphologies, termed “brachycephaly.” A short, upward-pointing snout, a massive and rounded head, and an underbite typify brachycephalic breeds. Here, we have coupled the phenotypes collected from museum skulls with the genotypes collected from dogs and identified five regions of the dog genome that are associated with canine brachycephaly. Fine mapping at one of these regions revealed a causal mutation in the gene BMP3. Bmp3's role in regulating cranial development is evolutionarily ancient, as zebrafish require its function to generate a normal craniofacial morphology. Our data begin to expose the genetic mechanisms unknowingly employed by breeders to create and diversify the cranial shape of dogs.

Characterisation of the genomic canine Fgf8 locus and screen for genetic variants in 4 dogs with different face types

We are investigating the genetic basis of morphological differences in skull shape between domestic dogs of different breeds using a candidate gene approach to identify genes involved in the genetic regulation. One such candidate is Fgf8. Fgf8 is a signalling molecule important in the embryonic development and patterning of the craniofacial region. Mice conditional null for the expression of Fgf8 after E9.5 have a short foreface and a wide skull (Trumpp et al. 1999). Using a combination of bioinformatics and PCR cloning, we have characterised the genomic loci of the canine Fgf8 gene. Like the mouse homologue, it is composed of six exons and we also predict that like the mouse, there are eight alternative isoforms that are generated by alternative splicing events. We have identified a short 200 bp sequence upstream of the Fgf8 gene that is highly conserved between species and have predicted putative transcription factor binding sites using the Transfac database. Genetic analysis of 4 dogs with different skull types identified genetic variation. None of the variants however, were predicted to have any functional significance.

Inheritance of sutural pattern at the pterion in rhesus monkey skulls

Five of the bones that characteristically comprise the cranial vault articulate on the lateral aspect of the skull at or near the cephalometric landmark referred to as the pterion. The pattern of articulation in the sutures associated with these bones varies among and within primate species and has been used as a criterion for classification in taxonomic studies, as well as in archeological and forensic studies. Within species, the sutural patterns found within the region of the pterion have remarkable consistency, which lead to the hypothesis that these patterns have a genetic basis. Sutural pattern variations were investigated at the pterion in 422 skulls from 66 rhesus monkey families with known genealogies from the long-standing colony on Cayo Santiago. Four specific types of articulation patterns were recorded. The results demonstrated that the most common suture pattern at the pterion of Cayo Santiago rhesus monkeys (86%; similar to that seen in some other anthropoid species but not humans and some apes) was characterized by an articulation between the temporal bone and parietal bone. Articulation between the sphenoid and parietal bones (type SP) accounted for 14% of the specimens and was concentrated in a dozen families. Mothers with the SP phenotype had a high incidence of offspring with SP phenotypes. Most non-SP mothers having SP offspring had siblings or family members from previous generations with the SP type. This is the first study to examine variation in sutural patterns at the pterion in pedigrees. Variation of sutural patterns shows familial aggregation, suggesting that this variation is heritable. Future work will be focused on defining the inheritance patterns of variation at the pterion, with the ultimate objective of identifying the specific genes involved and their mechanism of action.

The canine genome

The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.

Molecular origins of rapid and continuous morphological evolution

Mutations in cis-regulatory sequences have been implicated as being the predominant source of variation in morphological evolution. We offer a hypothesis that gene-associated tandem repeat expansions and contractions are a major source of phenotypic variation in evolution. Here, we describe a comparative genomic study of repetitive elements in developmental genes of 92 breeds of dogs. We find evidence for selection for divergence at coding repeat loci in the form of both elevated purity and extensive length polymorphism among different breeds. Variations in the number of repeats in the coding regions of the Alx-4 (aristaless-like 4) and Runx-2 (runt-related transcription factor 2) genes were quantitatively associated with significant differences in limb and skull morphology. We identified similar repeat length variation in the coding repeats of Runx-2, Twist, and Dlx-2 in several other species. The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution.

A strong correlation exists between the distribution of retinal ganglion cells and nose length in the dog

The domestic dog, CANIS LUPUS FAMILIARIS, is a subspecies of the gray wolf, CANIS LUPUS, with almost identical mitochondrial DNA. The dog is the most diverse species on earth, with skull length varying between 7 and 28 cm whereas the wolf skull is around 30 cm long. However, eye size in dogs does not appear to vary as much. For example, small dogs such as the chihuahua appear to have very large eyes in proportion to the skull. Our aim was to examine eye size and retinal cell numbers and distribution to determine whether the dog eye exhibits as much variation as the skull. We found a correlation between eye radius and skull dimensions. However, the most surprising finding was that the distribution of ganglion cells in the eye varied tremendously from a horizontally aligned visual streak of fairly even density across the retina (as seen in the wolf) to a strong area centralis with virtually no streak (for example, as observed in a pug from the current series). This variation in ganglion cell density within a single species is quite unique. Intriguingly, the ratio of peak ganglion cell density in the area centralis to visual streak was highly negatively correlated with skull length (r = -0.795, n = 22) and positively correlated with cephalic index (r = 0.687, n = 22). The orientation of eyelid aperture was also correlated with cephalic index (r = 0.648, n = 22). Therefore, the genetic manipulation of selective breeding, which has produced an abnormal shortening of the skull and eyelids with less lateral apertures, has also produced a considerably more pronounced area centralis in the dog.

MSX2 expression in the apical ectoderm ridge is regulated by an MSX2 and Dlx5 binding site

The apical ectodermal ridge (AER) is a specialized ectodermal region essential for limb outgrowth. Msx2 expression patterns in limb development strongly suggest an important role for Msx2 in the AER. Our previous studies identified a 348-bp fragment of the chicken Msx2 gene with AER enhancer activity. In this study, the functions of four potential homeodomain binding TAAT sites in this enhancer were studied using transgenic mice and in vitro protein-DNA interactions. Transgenic studies indicate that the four TAAT sites are not redundant and that only the B-TAAT site is critical for AER enhancer activity. The expression patterns of Msx2 and Dlx5 genes in the AER suggest that they might be involved in the regulation of Msx2. In support of this hypothesis, we found that Msx2 and Dlx5 can bind to the B-TAAT site as well as to a fragment containing the D- and E-TAAT sites in the Msx2 AER enhancer sequences. (c)2002 Elsevier Science (USA).