Equine trait mapping

Assigning function to genes is essential for a better understanding of biological systems. To date, approximately half of the genes in the vertebrate genome have known function. Domestic animals are a rich source for trait mapping and in this thesis we have mapped three distinct equine phenotypes. The result provides increased knowledge regarding gene function and importantly, practical implications for horse welfare. In paper I and IV, we confirm that Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is inherited as an incompletely dominant trait (p= 2.2x10-16). By first identifying a 208 kb identity-by decent (IBD) region and subsequently excluding polymorphic sites identified through Illumina sequencing, we conclude that the gene PMEL causes these defects in horse. Our findings, together with functional analyses recently published, support that the cause of MCOA syndrome is a missense mutation (Arg625Cys) near the transmembrane region of PMEL that results in altered biochemical properties. In paper II we show that variants in the MHC-II region influence the susceptibility to equine Insect Bite Hypersensitivity with the same marker risk allele identified in two distinct populations, OR 4.19 (p= 2.3x10-5) and 1.48 (p= 0.04) for Icelandic horses and Exmoor ponies respectively. In addition, homozygosity across the MHC-II region confers a higher risk of developing disease, OR= 2.67 (p= 1.3x10-3). Finally, in paper III we utilize the EquineSNP50 BeadChip to identify the first Gait locus in horse. A highly significant SNP (EMP2= 2.0x10-4) was identified to be consistent with a recessive mode of inheritance for the lateral gait pace in Icelandic horses, and confirmed in an independent sample set (p= 2.4x10-14). Illumina sequencing of an established IBD region identified a nonsense mutation in the gene DMRT3. A clearly dichotomous distribution in a panel of gaited and non-gaited breeds revealed that the DMRT3 mutation is permissive for a variety of alternate gaits. The mutation also has a favorable effect in harness racing horses. Functional characterization of the truncated protein demonstrated correct localization and an intact DNA binding profile. mRNA expression in a small population of commissural neurons from the spinal cord was confirmed in mutant and wild type horses. Further, a DMRT3 null mouse displayed a change in spinal cord circuit signaling and locomotion. These findings reveal a new molecule involved in the regulation of limb movement

Multiple congenital ocular anomalies in Icelandic horses

<p>Abstract</p> <p>Background</p> <p>Multiple congenital ocular anomalies (MCOA) syndrome is a hereditary congenital eye defect that was first described in Silver colored Rocky Mountain horses. The mutation causing this disease is located within a defined chromosomal interval, which also contains the gene and mutation that is associated with the Silver coat color (<it>PMEL17</it>, exon 11). Horses that are homozygous for the disease-causing allele have multiple defects (MCOA-phenotype), whilst the heterozygous horses predominantly have cysts of the iris, ciliary body or retina (Cyst-phenotype). It has been argued that these ocular defects are caused by a recent mutation that is restricted to horses that are related to the Rocky Mountain Horse breed. For that reason we have examined another horse breed, the Icelandic horse, which is historically quite divergent from Rocky Mountain horses.</p> <p>Results</p> <p>We examined 24 Icelandic horses and established that the MCOA syndrome is present in this breed. Four of these horses were categorised as having the MCOA-phenotype and were genotyped as being homozygous for the <it>PMEL17 </it>mutation. The most common clinical signs included megaloglobus, iris stromal hypoplasia, abnormal pectinate ligaments, iridociliary cysts occasionally extending into the peripheral retina and cataracts. The cysts and pectinate ligament abnormalities were observed in the temporal quadrant of the eyes. Fourteen horses were heterozygous for the <it>PMEL17 </it>mutation and were characterized as having the Cyst-phenotype with cysts and occasionally curvilinear streaks in the peripheral retina. Three additional horses were genotyped as <it>PMEL17 </it>heterozygotes, but in these horses we were unable to detect cysts or other forms of anomalies.</p> <p>One eye of a severely vision-impaired 18 month-old stallion, homozygous for the <it>PMEL17 </it>mutation was examined by light microscopy. Redundant duplication of non-pigmented ciliary body epithelium, sometimes forming cysts bulging into the posterior chamber and localized areas of atrophy in the peripheral retina were seen.</p> <p>Conclusions</p> <p>The MCOA syndrome is segregating with the <it>PMEL17 </it>mutation in the Icelandic Horse population. This needs to be taken into consideration in breeding decisions and highlights the fact that MCOA syndrome is present in a breed that are more ancient and not closely related to the Rocky Mountain Horse breed.</p

Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6

<p>Abstract</p> <p>Background</p> <p>Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome consists of a diverse set of abnormalities predominantly localized to the frontal part of the eye. The disease is in agreement with a codominant mode of inheritance in our horse material. Animals presumed to be heterozygous for the mutant allele have cysts originating from the temporal ciliary body, peripheral retina and/or iris. In contrast, animals predicted to be homozygous for the disease-causing allele possess a wide range of multiple abnormalities, including iridociliary and/or peripheral retinal cysts, iridocorneal angle abnormalities, cornea globosa, iris hypoplasia and congenital cataracts. MCOA is most common in the Rocky Mountain horse breed where it occurs at a high frequency among Silver colored horses. The Silver coat color is associated with mutations in <it>PMEL17 </it>that resides on ECA6q23. To map the <it>MCOA </it>locus we analyzed 11 genetic markers on ECA6q and herein describe a chromosome interval for the <it>MCOA </it>locus.</p> <p>Results</p> <p>We performed linkage analysis within 17 paternal half-sib families of the Rocky Mountain horse breed. More than half of the 131 offspring had the Cyst phenotype and about one third had MCOA. Segregation data were obtained by genotyping 10 microsatellite markers most of which are positioned on ECA6q22-23, as well as the missense mutation for the Silver phenotype in <it>PMEL17</it>. Significant linkage was found between the <it>MCOA </it>locus and eight of the genetic markers, where marker <it>UPP5 </it>(Theta = 0, z = 12.3), <it>PMEL17ex11 </it>(Theta = 0, z = 19.0) and <it>UPP6 </it>(Theta = 0, z = 17.5) showed complete linkage with the <it>MCOA </it>locus. DNA sequencing of <it>PMEL17 </it>in affected and healthy control individuals did not reveal any additional mutations than the two mutations associated with the Silver coat color.</p> <p>Conclusion</p> <p>The <it>MCOA </it>locus can with high confidence be positioned within a 4.9 megabase (Mb) interval on ECA6q. The genotype data on <it>UPP5</it>, <it>PMEL17ex11 </it>and <it>UPP6 </it>strongly support the hypothesis that horses with the Cyst phenotype are heterozygous for the mutant allele and that horses with the MCOA phenotype are homozygous for the mutant allele.</p

Association of Parental Obesity and Diabetes Mellitus With Circulating Adipokines in Nonobese Nondiabetic Offspring

BACKGROUND: Adipokines are implicated in the development of obesity-related traits. We hypothesized that nonobese participants without diabetes mellitus (DM) whose parents were obese or had DM would have altered circulating adipokines compared with those without parental history of these conditions. METHODS AND RESULTS: Participants in the community-based Framingham Third Generation cohort who were not obese (body mass index \u3c 30) and not diabetic with both parents in the Framingham Offspring cohort were included in this analysis (n=2034, mean age 40 years, 54% women). Circulating concentrations of fetuin A, RBP4 (retinol binding protein 4), FABP4 (fatty acid binding protein 4), leptin, LEP-R (leptin receptor), and adiponectin were assayed. Parental DM was defined as occurring before age 60 years, and obesity was defined as body mass index \u3e /=30 before age 60 years. General estimating equations were used to compare concentrations of adipokines among participants with 0, 1, or 2 parents affected by obesity or DM (separate analyses for each), adjusting for known correlates of adipokines. Overall, 44% had at least 1 parent who was obese and 15% had parents with DM. Parental obesity was associated with higher serum levels of FABP4 and LEP-R in their offspring (P=0.02 for both). Parental DM was associated with lower adiponectin but higher RBP4 concentrations in offspring (P \u3c /=0.02 for both). CONCLUSIONS: In our community-based sample, a parental history of DM or obesity was associated with an altered adipokine profile in nonobese nondiabetic offspring. Additional studies are warranted to evaluate whether such preclinical biomarker alterations presage future risk of disease

Mutations in \u3ci\u3eDMRT3\u3c/i\u3e Affect Locomotion in Horses and Spinal Circuit Function in Mice

Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement. These networks produce left–right alternation of limbs as well as coordinated activation of flexor and extensor muscles. Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favorable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation

Charged Pion Production in 2 to 8 AGeV Central Au+Au Collisions

Momentum spectra of charged pions over nearly full rapidity coverage from target to beam rapidity have been measured in the 0-5% most central Au+Au collisions in the beam energy range from 2 to 8 AGeV by the E895 Experiment. Using a thermal parameterization to fit the transverse mass spectra, rapidity density distributions are extracted. The observed spectra are compared with predictions from the RQMD v2.3 cascade model and also to a thermal model including longitudinal flow. The total 4$\pi$ yields of the charged pions are used to infer an initial state entropy produced in the collisions.Comment: 13 pgs, 19 figs, accepted by Phys. Rev. C. Data tables available at http://nuclear.ucdavis.edu/~e895/published_spectra.htm

Natriuretic peptides and integrated risk assessment for cardiovascular disease. an individual-participant-data meta-analysis

BACKGROUND: Guidelines for primary prevention of cardiovascular diseases focus on prediction of coronary heart disease and stroke. We assessed whether or not measurement of N-terminal-pro-B-type natriuretic peptide (NT-proBNP) concentration could enable a more integrated approach than at present by predicting heart failure and enhancing coronary heart disease and stroke risk assessment. METHODS: In this individual-participant-data meta-analysis, we generated and harmonised individual-participant data from relevant prospective studies via both de-novo NT-proBNP concentration measurement of stored samples and collection of data from studies identified through a systematic search of the literature (PubMed, Scientific Citation Index Expanded, and Embase) for articles published up to Sept 4, 2014, using search terms related to natriuretic peptide family members and the primary outcomes, with no language restrictions. We calculated risk ratios and measures of risk discrimination and reclassification across predicted 10 year risk categories (ie, <5%, 5% to <7·5%, and ≥7·5%), adding assessment of NT-proBNP concentration to that of conventional risk factors (ie, age, sex, smoking status, systolic blood pressure, history of diabetes, and total and HDL cholesterol concentrations). Primary outcomes were the combination of coronary heart disease and stroke, and the combination of coronary heart disease, stroke, and heart failure. FINDINGS: We recorded 5500 coronary heart disease, 4002 stroke, and 2212 heart failure outcomes among 95 617 participants without a history of cardiovascular disease in 40 prospective studies. Risk ratios (for a comparison of the top third vs bottom third of NT-proBNP concentrations, adjusted for conventional risk factors) were 1·76 (95% CI 1·56-1·98) for the combination of coronary heart disease and stroke and 2·00 (1·77-2·26) for the combination of coronary heart disease, stroke, and heart failure. Addition of information about NT-proBNP concentration to a model containing conventional risk factors was associated with a C-index increase of 0·012 (0·010-0·014) and a net reclassification improvement of 0·027 (0·019-0·036) for the combination of coronary heart disease and stroke and a C-index increase of 0·019 (0·016-0·022) and a net reclassification improvement of 0·028 (0·019-0·038) for the combination of coronary heart disease, stroke, and heart failure. INTERPRETATION: In people without baseline cardiovascular disease, NT-proBNP concentration assessment strongly predicted first-onset heart failure and augmented coronary heart disease and stroke prediction, suggesting that NT-proBNP concentration assessment could be used to integrate heart failure into cardiovascular disease primary prevention

Targeted analysis of four breeds narrows equine Multiple Congenital Ocular Anomalies locus to 208 kilobases

The syndrome Multiple Congenital Ocular Anomalies (MCOA) is the collective name ascribed to heritable congenital eye defects in horses. Individuals homozygous for the disease allele (MCOA phenotype) have a wide range of eye anomalies, while heterozygous horses (Cyst phenotype) predominantly have cysts that originate from the temporal ciliary body, iris, and/or peripheral retina. MCOA syndrome is highly prevalent in the Rocky Mountain Horse but the disease is not limited to this breed. Affected horses most often have a Silver coat color; however, a pleiotropic link between these phenotypes is yet to be proven. Locating and possibly isolating these traits would provide invaluable knowledge to scientists and breeders. This would favor maintenance of a desirable coat color while addressing the health concerns of the affected breeds, and would also provide insight into the genetic basis of the disease. Identical-by-descent mapping was used to narrow the previous 4.6-Mb region to a 264-kb interval for the MCOA locus. One haplotype common to four breeds showed complete association to the disease (Cyst phenotype, n = 246; MCOA phenotype, n = 83). Candidate genes from the interval, SMARCC2 and IKZF4, were screened for polymorphisms and genotyped, and segregation analysis allowed the MCOA syndrome region to be shortened to 208 kb. This interval also harbors PMEL17, the gene causative for Silver coat color. However, by shortening the MCOA locus by a factor of 20, 176 other genes have been unlinked from the disease and only 15 genes remain

The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations

Insect bite hypersensitivity (IBH) is a chronic allergic dermatitis common in horses. Affected horses mainly react against antigens present in the saliva from the biting midges, Culicoides ssp, and occasionally black flies, Simulium ssp. Because of this insect dependency, the disease is clearly seasonal and prevalence varies between geographical locations. For two distinct horse breeds, we genotyped four microsatellite markers positioned within the MHC class II region and sequenced the highly polymorphic exons two from DRA and DRB3, respectively. Initially, 94 IBH-affected and 93 unaffected Swedish born Icelandic horses were tested for genetic association. These horses had previously been genotyped on the Illumina Equine SNP50 BeadChip, which made it possible to ensure that our study did not suffer from the effects of stratification. The second population consisted of 106 unaffected and 80 IBH-affected Exmoor ponies. We show that variants in the MHC class II region are associated with disease susceptibility (praw = 2.34 × 10−5), with the same allele (COR112:274) associated in two separate populations. In addition, we combined microsatellite and sequencing data in order to investigate the pattern of homozygosity and show that homozygosity across the entire MHC class II region is associated with a higher risk of developing IBH (p = 0.0013). To our knowledge this is the first time in any atopic dermatitis suffering species, including man, where the same risk allele has been identified in two distinct populations