39 research outputs found
Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness
International audienceDomestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during the formation and maintenance of modern breeds. While previous studies focused on the identification of alleles that contribute to small skeletal size, little is known about the underlying genetics controlling large size. We first performed a genome-wide association study (GWAS) using the Illumina Canine HD 170,000 single nucleotide polymorphism (SNP) array which compared 165 large-breed dogs from 19 breeds (defined as having a Standard Breed Weight (SBW) >41 kg [90 lb]) to 690 dogs from 69 small breeds (SBW â€41 kg). We identified two loci on the canine X chromosome that were strongly associated with large body size at 82â84 megabases (Mb) and 101â104 Mb. Analyses of whole genome sequencing (WGS) data from 163 dogs revealed two indels in the Insulin Receptor Substrate 4 (IRS4) gene at 82.2 Mb and two additional mutations, one SNP and one deletion of a single codon, in Immunoglobulin Superfamily member 1 gene (IGSF1) at 102.3 Mb. IRS4 and IGSF1 are members of the GH/IGF1 and thyroid pathways whose roles include determination of body size. We also found one highly associated SNP in the 5âUTR of Acyl-CoA Synthetase Long-chain family member 4 (ACSL4) at 82.9 Mb, a gene which controls the traits of muscling and back fat thickness. We show by analysis of sequencing data from 26 wolves and 959 dogs representing 102 domestic dog breeds that skeletal size and body mass in large dog breeds are strongly associated with variants within IRS4, ACSL4 and IGSF1
Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids
Identification of genes involved in genetic diseases in human and dog : from dermatology to neurology
L'espĂšce canine (Canis lupus familiaris) rassemble plus de 350 races issues d'une sĂ©lection artificielle drastique menĂ©e par l'Homme au cours des derniers siĂšcles. De ce fait, chaque race peut ĂȘtre considĂ©rĂ©e comme un isolat gĂ©nĂ©tique dĂ©veloppant chacune des affections gĂ©nĂ©tiques de maniĂšre spontanĂ©e avec parfois de fortes frĂ©quences. Ainsi, l'espĂšce canine constitue un modĂšle puissant pour identifier les gĂšnes et allĂšles responsables de ces affections homologues Ă certaines maladies gĂ©nĂ©tiques humaines. Mon premier projet a portĂ© sur la recherche des causes gĂ©nĂ©tiques de deux kĂ©ratodermies plantaires chez le terrier irlandais et le dogue de Bordeaux. En combinant plusieurs analyses d'association (GWAS : « Genome Wide Association Study ») et des techniques de sĂ©quençage NGS (Next Generation Sequencing), un nouveau gĂšne mutĂ© a Ă©tĂ© identifiĂ© pour le terrier irlandais. Concernant les dogues de Bordeaux, nous avons gĂ©notypĂ© plus de 170 000 SNPs sur plus de 200 dogues. Une analyse de liaison gĂ©nĂ©tique a permis d'identifier un locus de 20 Mb sur le chromosome 9 contenant un cluster de kĂ©ratines. En combinant les donnĂ©es cliniques et gĂ©nĂ©tiques, la kĂ©ratine 16 s'avĂ©rait le meilleur gĂšne candidat. Son sĂ©quençage complet a permis d'identifier une mutation complexe gĂ©nĂ©rant une protĂ©ine tronquĂ©e. Des analyses de PCR quantitatives ont rĂ©vĂ©lĂ© que ce gĂšne mutĂ© Ă©tait sous exprimĂ© chez les individus atteints. Ce travail nous permet donc de proposer cette race de chien comme le premier modĂšle animal spontanĂ© de kĂ©ratodermie focale non-Ă©pidermolytique (FNEPPK). En parallĂšle de ce projet, j'ai menĂ© des recherches sur les bases molĂ©culaires d'un syndrome d'automutilation acrale dĂ©crit dans plusieurs races. Cette neuropathie est homologue aux neuropathies hĂ©rĂ©ditaires sensitives et autonomes (HSANs) chez l'Homme et se caractĂ©rise par une perte de sensibilitĂ© Ă la douleur au niveau des membres. A partir d'un GWAS, j'ai pu identifier un locus de 1,5 Mb chez le chien, dont l'orthologue humain n'est pas encore dĂ©crit chez des patients HSANs. Le sĂ©quençage complet de ce locus a menĂ© Ă l'identification d'un variant situĂ© dans une rĂ©gion cis-enhancer en amont d'un gĂšne candidat. La mise en Ă©vidence d'une sous-expression du gĂšne candidat indique que ce variant rĂ©gulateur semblerait modifier l'activitĂ© de l'enhancer nous permettant de le proposer comme la mutation causale chez le chien. Cette dĂ©couverte offre donc de nouvelles perspectives de recherche pour des patients humains atteints de neuropathies hĂ©rĂ©ditaires sensitives. En combinant des approches gĂ©nĂ©tiques complĂ©mentaires sur des modĂšles spontanĂ©s de maladies bien caractĂ©risĂ©es chez le chien, j'ai pu participer Ă l'identification de trois nouveaux gĂšnes, dont deux excellents candidats pour ces maladies homologues humaines. Le troisiĂšme reprĂ©sente un vrai modĂšle spontanĂ© de kĂ©ratodermie K16, ouvrant ainsi des perspectives thĂ©rapeutiques qui bĂ©nĂ©ficieront Ă l'Homme et au chien.The dog species (Canis lupus familiaris) contains more than 350 distinct breeds resulting from human drastic selection during the last centuries. Each breed can then be considered as a genetic isolate, developing specific spontaneous genetic diseases with high frequencies. Thus, dogs constitute a powerful model to identify new genes and alleles involved in disorders homologous to human diseases. For my thesis, I worked on two main topics. The first one focused on the search of the genetic causes of two footpad keratodermas in the Irish terrier and the dogue de Bordeaux breeds. Concerning the Irish terrier, the work was conduced by Tosso Leebâs team in the University of Berne, in collaboration with the Antagene Company. Using a Genome Wide Association Study (GWAS) and Next Generation Sequencing (NGS), the mutation in a new gene has been identified in footpad hyperkeratosis in this breed. For the dogue de Bordeaux project, we genotyped more than 170 000 SNPs on over 200 dogs. We then performed a genetic linkage study with a subset of 68 dogs, including 14 affected dogs. We identified a significant locus of 20 Mb on the canine chromosome 9 containing one keratin cluster. Comparing clinical, histopathological and immunochemistry data, keratin 16 appeared as an excellent candidate. The sequencing of the gene revealed a complex mutation leading to a non-functional truncated K16 protein. Quantitative RT-PCR analyses showed a strong decrease of the level of KRT16 expression in affected footpads. These results led to propose the dogue de Bordeaux footpad hyperkeratosis as the first spontaneous model of focal non-epidermolytic palmoplantar keratoderma (FNEPPK). In parallel, I studied an acral mutilation syndrome described in several hunting dog breeds. This neuropathy corresponds to human hereditary sensory and autonomic neuropathies (HSANs) and is characterized by an insensitivity to pain only in the limb. With a classical GWAS strategy, using 24 affected and 30 unaffected dogs, we identified a 1.5 Mb locus in dogs, the human orthologous locus being still unknown in human patients. Targeted sequencing of this locus revealed one single variant localized in a cis-enhancer region closed to a strong candidate gene. A lower level of expression of the candidate gene in affected dogs seems to show a functional effect of the mutation in the enhancer activity. These results led to propose this variant as the causative mutation for this canine neuropathy, and so this canine model as an opportunity to identify a new human HSAN gene. Combining complementary genetic approaches on spontaneous models of well characterized canine diseases, I did participated to the identification of three new genes, two of which being novel excellent candidates for the homologous human diseases. The third represents a true homologous model of KRT16 human keratoderma, opening the field to the development of new treatments benefiting to both humans and dogs
Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1
International audienceNaturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy, and low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (ORâ=â8.42, CIâ=â3.12â22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for most of the disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs
Conservation of <i>IGSF1</i> mutated codons (in bold) between mammals.
<p>Conservation of <i>IGSF1</i> mutated codons (in bold) between mammals.</p
Derived allele frequencies at multiple loci involved in body weight and size variations in (A) modern dog breeds, (B) modern dog breeds without inclusion of muscled breeds, (C) only muscled breeds.
<p>The frequency of the derived allele in 5-kg weigh classes is represented on a color scale. Dogs with a SBW above 65 kg are collapsed in a single category (>65 kg) due to the lack of genotype variation in the group at these markers. Muscled breeds include the Boston Terrier (BOST), French Bulldog (FBUL), Miniature Bull Terrier (MBLT), Staffordshire Bull Terrier (STAF), Chinese Shar-pei (SHAR), Bulldog (BULD), Chow-Chow (CHOW), American Staffordshire Terrier (AMST), Boxer (BOX), Beauceron (BEAU), Bullmastiff (BULM), Bernese Mountain Dog (BMD), Rottweiler (ROTT), Leonberger (LEON), Tibetan Mastiff (TIBM), Neapolitan Mastiff (NEAM), Newfoundland (NEWF), Dogue de Bordeaux DDBX), English Mastiff (MAST) and Saint Bernard (STBD).</p
Observed genotypes for the ten most strongly associated variants identified in large dogs using WGS data.
<p>The three first columns correspond to the dog, breed, sex and standard breed weight (SBW). The next 10 columns correspond to the 10 most strongly associated variants at locus 1, identified from WGS data. The first part of the table corresponds to large dogs (SBW >41 kg). Homozygous and hemizygous genotypes for the âlarge alleleâ are colored in red, homozygous/hemizygous genotypes for the âsmall/mediumâ allele are colored in blue and heterozygous genotypes are colored in yellow. The second part of the table shows the distribution of the âlarge alleleâ in the 140 dogs with a SBW â€41 kg. Values correspond to the percentage of this control population showing each genotype by variant. The last row shows the respective p-value estimated (Wald test) for each variant.</p
Best SNP markers associated with SBW above 41 kg in dogs.
<p>Best SNP markers associated with SBW above 41 kg in dogs.</p
Conservation of <i>IRS4</i> mutated codons (in bold) between mammals.
<p>Conservation of <i>IRS4</i> mutated codons (in bold) between mammals.</p
Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology
Being manâs best friend, dogs have been bred and selected for certain morphologic traits and breed-associated behaviours. Here, Plassais et al. analyse 722 canine whole genome sequences including modern breeds, wild canids and village dogs by GWAS and search for signatures of selection