Genome Scan for Locus Involved in Mandibular Prognathism in Pedigrees from China

Background

It is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped.

Methodology

In order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP) markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM). Multipoint parametric and non-parametric (model-free) linkage analyses were used for the pedigrees.

Principal Finding

The most statistically significant linkage results were with markers on chromosome 4 (LOD  = 3.166 and NPL = 3.65 with rs 875864, 4p16.1, 8.38 cM). Candidate genes within the 4p16.1 include EVC, EVC2.

Conclusion

We detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism.     

Selection signatures in Shetland ponies

Shetland ponies were selected for numerous traits including small stature, strength, hardiness and longevity. Despite the different selection criteria, Shetland ponies are well known for their small stature. We performed a selection signature analysis including genome‐wide SNPs of 75 Shetland ponies and 76 large‐sized horses. Based upon this dataset, we identified a selection signature on equine chromosome (ECA) 1 between 103.8 Mb and 108.5 Mb. A total of 33 annotated genes are located within this interval including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb. These two genes are well known to have a major impact on body height in numerous species including humans. Homozygosity mapping in the Shetland ponies identified a region with increased homozygosity between 107.4 Mb and 108.5 Mb. None of the annotated genes in this region have so far been associated with height. Thus, we cannot exclude the possibility that the identified selection signature on ECA1 is associated with some trait other than height, for which Shetland ponies were selected.     

Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses

During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The "splashed white" pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white horses are deaf. We analyzed a Quarter Horse family segregating for the splashed white coat color. Genome-wide linkage analysis in 31 horses gave a positive LOD score of 1.6 in a region on chromosome 6 containing the PAX3 gene. However, the linkage data were not in agreement with a monogenic inheritance of a single fully penetrant mutation. We sequenced the PAX3 gene and identified a missense mutation in some, but not all, splashed white Quarter Horses. Genome-wide association analysis indicated a potential second signal near MITF. We therefore sequenced the MITF gene and found a 10 bp insertion in the melanocyte-specific promoter. The MITF promoter variant was present in some splashed white Quarter Horses from the studied family, but also in splashed white horses from other horse breeds. Finally, we identified two additional non-synonymous mutations in the MITF gene in unrelated horses with white spotting phenotypes. Thus, several independent mutations in MITF and PAX3 together with known variants in the EDNRB and KIT genes explain a large proportion of horses with the more extreme white spotting phenotypes.     

Comparative human-horse sequence analysis of the CYP3A subfamily gene cluster

Cytochrome P450 enzymes (CYP450s) represent a superfamily of haem-thiolate proteins. CYP450s are most abundant in the liver, a major site of drug metabolism, and play key roles in the metabolism of a variety of substrates, including drugs and environmental contaminants. Interaction of two or more different drugs with the same enzyme can account for adverse effects and failure of therapy. Human CYP3A4 metabolizes about 50% of all known drugs, but little is known about the orthologous CYP450s in horses. We report here the genomic organization of the equine CYP3A gene cluster as well as a comparative analysis with the human CYP3A gene cluster. The equine CYP450 genes of the 3A family are located on ECA 13 between 6.97-7.53 Mb, in a region syntenic to HSA 7 99.05-99.35 Mb. Seven potential, closely linked equine CYP3A genes were found, in contrast to only four genes in the human genome. RNA was isolated from an equine liver sample, and the approximately 1.5-kb coding sequence of six CYP3A genes could be amplified by RT-PCR. Sequencing of the RT-PCR products revealed numerous hitherto unknown single nucleotide polymorphisms (SNPs) in these six CYP3A genes, and one 6-bp deletion compared to the reference sequence (EquCab2.0). The presence of the variants was confirmed in a sample of genomic DNA from the same horse. In conclusion, orthologous genes for the CYP3A family exist in horses, but their number differs from those of the human CYP3A gene family. CYP450 genes of the same family show high homology within and between mammalian species, but can be highly polymorphic.     

Size and shape of the mandibular condyle in primates

The relationships between the size of the articular surface of the mandibular condyle and masticatory muscle size, tooth size, diet, and biomechanical variables associated with mastication were studied by taking 12 measurements on skulls of 253 adult female anthropoid primates, including three to ten specimens from each of 32 species. In regressions of condylar length, width, or area against body weight, logarithmic transformations substantially improve the fit of the equations compared with untransformed data. There is a strong relationship between condylar measurements and body weight, with all correlations being .94 or higher. The slopes of the allometric regressions of length, width, and area of the condylar head indicate slight positive allometry with body size. Folivorous primates have smaller condyles than frugivorous primates, and colobines have smaller condyles than cebids, cercopithecines, or hominoids. When colobines are eliminated, the differences between frugivores and folivores are not significant. However, the two species with the relatively largest condyles are Pongo pygmaeus and Cercocebus torquatus, suggesting that there may be a relationship between unusually large condylar dimensions and the ability to crack hard nuts between the teeth. Cranial features having strong positive correlations with condylar dimensions include facial prognathism, maxillary incisor size, maxillary postcanine area, mandibular ramus breadth, and temporal fossa area. These data are interpreted as indicating that relatively large condyles are associated with relatively large masticatory muscles, relatively inefficient mandibular biomechanics, and a large dentition. These relationships support the growing evidence that the temporomandibular joint is a stress-bearing joint in normal function.     

An equine chromosome 3 inversion is associated with the tobiano spotting pattern in German horse breeds

The tobiano white-spotting pattern is one of several known depigmentation phenotypes in horses and is desired by many horse breeders and owners. The tobiano spotting phenotype is inherited as an autosomal dominant trait. Horses that are heterozygous or homozygous for the tobiano allele ( To ) are phenotypically indistinguishable. A SNP associated with To had previously been identified in intron 13 of the equine KIT gene and was used for an indirect gene test. The test was useful in several horse breeds. However, genotyping this sequence variant in the Lewitzer horse breed revealed that 14% of horses with the tobiano pattern did not show the polymorphism in intron 13 and consequently the test was not useful to identify putative homozygotes for To within this breed. Speculations were raised that an independent mutation might cause the tobiano spotting pattern in this breed. Recently, the putative causative mutation for To was described as a large chromosomal inversion on equine chromosome 3. One of the inversion breakpoints is approximately 70 kb downstream of the KIT gene and probably disrupts a regulatory element of the KIT gene. We obtained genotypes for the intron 13 SNP and the chromosomal inversion for 204 tobiano spotted horses and 24 control animals of several breeds. The genotyping data confirmed that the chromosomal inversion was perfectly associated with the To allele in all investigated horses. Therefore, the new test is suitable to discriminate heterozygous To/+ and homozygous To/To horses in the investigated breeds.     

Systematic screening and expression analysis of the head organizer genes in Xenopus embryos.

We describe here a systematic screen of an anterior endomesoderm (AEM) cDNA library to isolate novel genes which are expressed in the head organizer region. After removing clones which hybridized to labeled cDNA probes synthesized with total RNA from a trunk region of tailbud embryos, the 5' ends of 1039 randomly picked cDNA clones were sequenced to make expressed sequence tags (ESTs), which formed 754 tentative unique clusters. Those clusters were compared against public databases and classified according to similarities found to other genes and gene products. Of them, 151 clusters were identified as known Xenopus genes, including eight organizer-specific ones (5.3%). Gene expression pattern screening was performed for 198 unique clones, which were selected because they either have no known function or are predicted to be developmental regulators in other species. The screen revealed nine possible organizer-specific clones (4.5%), four of which appeared to be expressed in the head organizer region. Detailed expression analysis from gastrula to neurula stages showed that these four genes named crescent, P7E4 (homologous to human hypothetical genes), P8F7 (an unclassified gene), and P17F11 (homologous to human and Arabidopsis hypothetical genes) demarcate spatiotemporally distinct subregions of the AEM corresponding to the head organizer region. These results indicate that our screening strategy is effective in isolating novel region-specific genes.     

Maxillary advancement for mandibular prognathism: indications and rationale

The surgical correction of mandibular prognathism has traditionally involved posterior repositioning of the mandibular body. This treatment approach corrects the skeletal disproportion at the expense of reducing facial skeletal volume and can unpredictably result in inadequately supported soft tissues with loss of skeletal definition. In an effort to avoid these sequelae of mandibular reduction, 18 patients diagnosed as having mandibular prognathism were treated with maxillary advancement surgery at the Le Fort I level. Mean patient SNB angle was 85.2 degrees, as compared with a normal 79 +/- 3 degrees. Maxillae were documented to be in normal position relative to both cranial base and Frankfort horizontal. The mean maxillary advancement was 6.9 mm, with a range of 4.5 to 8.8 mm. All patients required genioplasty to reduce vertical chin height and/or to laterally shift the chin. At the time of follow-up (mean 16.2 months), all patients retained cephalometric data suggestive of enlarged mandibles and excessive anterior facial divergence. However, maxillomandibular harmony and facial convexity had been restored without sacrificing skeletal volume. Treatment results demonstrated these faces to be skeletally well proportioned despite lower face protrusion that was beyond "normal." Postoperative appearances were characterized by a well-supported soft-tissue envelope and a highlighted skeletal foundation, creating angular, well-defined lower faces. These findings support the credibility of maxillary advancement as the procedure of choice in selected individuals with mandibular prognathism. Indications and an aesthetic rationale for this surgical approach are presented.     

Nasal shape,prognathism and adaptation in man

The association between nasal shape, prognathism and the shape of the maxillary dental arch has been examined within samples of Negro and European skulls. Prognathism tends to be accompanied by an increasingly broad and short nose. Particularly high correlations exist between nasal height and the length of the cranial base and between nasal breadth and the distance which separates the upper canine teeth. Regression analysis has yielded quantitative estimates of the effect on a given dimension of variation in one or more of the others. It seems probable that both nasal shape and the maxillary dental arch-prognathism complex may be subject to direct selection by environmental stress. The morphological association between these complexes suggests that a part of the interpopulation variation in prognathism may be a secondary effect of selection acting on the nose. Similarly, selection acting on the dental arch or maxilla could produce secondary changes in the nasal index (i.e. a non-adaptive component of nasal variation).     

Genetics of swayback in American Saddlebred horses

Extreme lordosis, also called swayback, lowback or softback, can occur as a congenital trait or as a degenerative trait associated with ageing. In this study, the hereditary aspect of congenital swayback was investigated using whole genome association studies of 20 affected and 20 unaffected American Saddlebred (ASB) Horses for 48,165 single-nucleotide polymorphisms (SNPs). A statistically significant association was identified on ECA20 (corrected P=0.017) for SNP BIEC2-532523. Of the 20 affected horses, 17 were homozygous for this SNP when compared to seven homozygotes among the unaffected horses, suggesting a major gene with a recessive mode of inheritance. The result was confirmed by testing an additional 13 affected horses and 166 unaffected horses using 35 SNPs in this region of ECA20 (corrected P=0.036). Combined results for 33 affected horses and 287 non-affected horses allowed identification of a region of homozygosity defined by four SNPs in the region. Based on the haplotype defined by these SNPs, 80% of the 33 affected horses were homozygous, 21% heterozygous and 9% did not possess the haplotype. Among the non-affected horses, 15% were homozygous, 47% heterozygous and 38% did not possess the haplotype. The differences between the two groups were highly significant (P<0.00001). The region defined by this haplotype includes 53 known and predicted genes. Exons from three candidate genes, TRERF1, RUNX2 and CNPY3 were sequenced without finding distinguishing SNPs. The mutation responsible for swayback may lie in other genes or in regulatory regions outside exons. This information can be used by breeders to reduce the occurrence of swayback among their livestock. This condition may serve as a model for investigation of congenital skeletal deformities in other species.     

Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species F_IT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.     

Timing of Wingless signalling distinguishes maxillary and antennal identities in Drosophila melanogaster

The Drosophila adult head mostly derives from the composite eye-antenna imaginal disc. The antennal disc gives rise to two adult olfactory organs: the antennae and maxillary palps. Here, we have analysed the regional specification of the maxillary palp within the antennal disc. We found that a maxillary field, defined by expression of the Hox gene Deformed, is established at about the same time as the eye and antennal fields during the L2 larval stage. The genetic program leading to maxillary regionalisation and identity is very similar to the antennal one, but is distinguished primarily by delayed prepupal expression of the ventral morphogen Wingless (Wg). We find that precociously expressing Wg in the larval maxillary field suffices to transform it towards antennal identity, whereas overexpressing Wg later in prepupae does not. These results thus indicate that temporal regulation of Wg is decisive to distinguishing maxillary and antennal organs. Wg normally acts upstream of the antennal selector spineless (ss) in maxillary development. However, mis-expression of Ss can prematurely activate wg via a positive-feedback loop leading to a maxillary-to-antenna transformation. We characterised: (1) the action of Wg through ss selector function in distinguishing maxillary from antenna; and (2) its direct contribution to identity choice.     

Novel patterns of homeotic protein accumulation in the head of the Drosophila embryo

Antibodies that specifically recognize proteins encoded by the homeotic genes: Sex combs reduced, Deformed, labial and proboscipedia, were used to follow the distribution of these gene products during embryogenesis. The position of engrailed-expressing cells was used as a reference and staining conditions were established that could distinguish, among cells expressing engrailed, one of the homeotic proteins or both. Our observations demonstrate two important facts about establishing identity in the head segments. First, in contrast to the overlapping pattern of homeotic gene expression in the trunk segments, we observe a non-overlapping pattern in the head for those homeotic proteins required during embryogenesis. In contrast, the spatial accumulation of the protein product of the non-vital proboscipedia locus overlaps partially with the distribution of the Deformed and Sex combs reduced proteins in the maxillary and labial segments, respectively. Second, two of the proteins, Sex combs reduced and Deformed, have different dorsal and ventral patterns of accumulation. Dorsally, these proteins are expressed in segmental domains while, within the ventral region, a parasegmental register is observed. The boundary where this change in pattern occurs coincides with the junction between the ventral neurogenic region and the dorsal epidermis. After contraction of the germ band, when the nerve cord has completely separated from the epidermis, the parasegmental pattern is observed only within the ventral nerve cord while a segmental register is maintained throughout the epidermis.     

A comparative study of facial growth in Homo and Macaca

Sections were prepared throughout all areas of the various facial bones in young, growing Rhesus monkeys. The detailed distribution of resorptive and depository surfaces and the distribution of endosteal and periosteal bone tissue types were determined. From this information, the sequence of remodeling changes associated with the growth of the facial skeleton was then interpreted. This study is a sequal to previous reports in which growth and remodeling processes in the human face were described using similar procedures. In the present report, growth changes in the monkey and human facial skeleton are compared and contrasted. The general plan of facial growth is similar in both species, but major differences exist in the area of the muzzle. The maxillary arch in the monkey is entirely depository in nature, and it grows in a forward and downward direction as the maxillary tuberosity simultaneously grows backward. In the human, the forward part of the maxillary arch is resorptive in character. This contrasting growth factor results in a downward but not forward movement of this area. The result is decreased prognathism. Other differences in growth pattern exist in the forehead, malar, chin, and orbit. The developmental and phylogenetic basis for the upright human face is discussed and evaluated.     

扁颅鼩鼱 (Sorex roboratus) 在中国分布的证实

正扁颅鼩鼱(Sorex roboratus)隶属于食虫目(INSECTIVORA)鼩鼱科(Soricidae)鼩鼱属(Sorex),又称阿尔泰鼩鼱或西伯利亚鼩鼱,从前称S.vir,但是S.roboratus有优先权(Hoffmann,1985)。Wilson和Reeder(2005)认为其分布区域从俄罗斯东部的鄂毕河到乌苏里江,南部到阿尔泰山脉、蒙古北部和krai滨海边疆区。Hoffmann(1987)把扁颅鼩鼱作为可能分布于中国的两个鼩鼱类物种之一列于文中,王应祥(2003)在《中     

A preliminary molecular phylogenetic assessment of the lichen moths (Lepidoptera: Erebidae: Arctiinae: Lithosiini) with comments on palatability and chemical sequestration

The lichen moth tribe Lithosiini is best known for its hypothesized larval feeding behaviour, lichenivory. The larvae of some species have been found to be capable of sequestering polyphenolics, and the adults of some species are unpalatable to vertebrate predators. However, the chemical basis for the defence is unknown. Here we reconstruct a phylogenetic hypothesis using likelihood methods (maximum likelihood, Bayesian inference) for 65 species of Lithosiini representing 37 genera and seven outgroup species using 2806 bp of sequence data obtained from two mitochondrial gene fragments (COI barcoding region, CytB), and two nuclear gene fragments (RpS5 and ribosomal gene region 28S). Lithosiine species representing four of the seven subtribes and unplaced taxa are included in the analysis. The deeper relationships within the tribe are not strongly supported, and the monophyly of three of the four subtribes is not supported. The placement of the fourth subtribe, Acsalina, is weakly supported. We also conduct a survey of the secondary metabolites present within adults of five species. The species are examined for the presence of lichen polyphenolics and plant secondary metabolites sequestered by arctiines. Seven lichen polyphenolics are identified in the taxa examined, but no plant secondary metabolites are found using either analytical method. The results of this study and prior reports in the literature of chemical sequestration and unpalatability are plotted onto the resulting Bayesian inference phylogeny to examine the evolution of chemical defence within Lithosiini. Species that sequester lichen polyphenolics and unpalatable species occur in each of the major clades recovered in the analysis.