Aaron Rendahl

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Genome‐wide association analysis of osteochondrosis of the tibiotarsal joint in Norwegian Standardbred trotters

Osteochondrosis (OC), a disturbance in the process of endochondral ossification, is by far the most important equine developmental orthopaedic disease and is also common in other domestic animals and humans. The purpose of this study was to identify quantitative trait loci (QTL) associated with osteochondrosis dissecans (OCD) at the intermediate ridge of the distal tibia in Norwegian Standardbred (SB) using the Illumina Equine SNP50 BeadChip whole-genome single-nucleotide polymorphism (SNP) assay. Radiographic data and blood samples were obtained from 464 SB yearlings. Based on the radiographic examination, 162 horses were selected for genotyping; 80 of these were cases with an OCD at the intermediate ridge of the distal tibia, and 82 were controls without any developmental lesions in the joints examined. Genotyped horses descended from 22 sires, and the number of horses in each half-sib group ranged from 3 to 14. The population structure necessitated statistical correction for stratification. When conducting a case-control genome-wide association study (GWAS), mixed-model analyses displayed regions on chromosomes (Equus callabus chromosome - ECA) 5, 10, 27 and 28 that showed moderate evidence of association (P ≤ 5 × 10(-5); this P-value is uncorrected i.e. not adjusted for multiple comparisons) with OCD in the tibiotarsal joint. Two SNPs on ECA10 represent the most significant hits (uncorrected P=1.19 × 10(-5) in the mixed-model). In the basic association (chi-square) test, these SNPs achieved statistical significance with the Bonferroni correction (P=0.038) and were close in the permuted logistic regression test (P=0.054). Putative QTL on ECA 5, 10, 27 and 28 represent interesting areas for future research, validation studies and fine mapping of candidate regions. Results presented here represent the first GWAS of OC in horses using the recently released Illumina Equine SNP50 BeadChip.

Metabolomics Reveals the Origins of Antimicrobial Plant Resins Collected by Honey Bees

The deposition of antimicrobial plant resins in honey bee, Apis mellifera, nests has important physiological benefits. Resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or the benefits of specific resins to bees. We used metabolomic methods as a type of environmental forensics to track individual resin forager behavior through comparisons of global resin metabolite patterns. The resin from the corbiculae of a single bee was sufficient to identify that resins botanical source without prior knowledge of resin composition. Bees from our apiary discriminately foraged for resin from eastern cottonwood (Populus deltoides), and balsam poplar (P. balsamifera) among many available, even closely related, resinous plants. Cottonwood and balsam poplar resin composition did not show significant seasonal or regional changes in composition. Metabolomic analysis of resin from 6 North American Populus spp. and 5 hybrids revealed peaks characteristic to taxonomic nodes within Populus, while antimicrobial analysis revealed that resin from different species varied in inhibition of the bee bacterial pathogen, Paenibacillus larvae. We conclude that honey bees make discrete choices among many resinous plant species, even among closely related species. Bees also maintained fidelity to a single source during a foraging trip. Furthermore, the differential inhibition of P. larvae by Populus spp., thought to be preferential for resin collection in temperate regions, suggests that resins from closely related plant species many have different benefits to bees.

Species-specific interaction of seminal plasma on sperm–neutrophil binding

Bovine semen is naturally deposited in the vagina and spermatozoa migrate through the cervix into the uterus leaving the bulk of seminal plasma (SP) behind. In equine, both spermatozoa and SP are deposited directly in the uterus and SP reduces sperm binding to neutrophils and prevents the formation of DNA-based neutrophil extracellular traps (NETs). We investigated the role of bovine SP on sperm-neutrophil binding using the four most common bovine semen extenders. Contrary to equine, bovine spermatozoa removed from SP had low binding to neutrophils for up to 3h, but as little as 10% SP increased sperm-neutrophil binding and NETs formation over time. Similar results were obtained with neutrophils isolated from peripheral blood or from the uterus. Scanning electron microscopy showed that the binding can be mediated by NETs or by direct attachment of the cell membranes for both species. The increased binding with SP reduced the number of free spermatozoa indicating that sperm transport to the site of fertilization (and thus fertility) may be hindered. Surprisingly, egg yolk negated the role of bovine SP on sperm-neutrophil binding compared to all the other semen extenders, but did not alter equine sperm binding to neutrophils. Current artificial insemination in bovine relies heavily on egg yolk extender and introduces variable amounts of SP into the uterus, which naturally remains in the vagina. Our results indicate a need to re-evaluate the composition of semen extenders and the semen processing procedures in relation to sperm transport, longevity and fertilizing ability.

Experimental Support for Multiple Locus Complementary Sex Determination in the Parasitoid Cotesia vestalis

Despite its fundamental role in development, sex determination is highly diverse among animals. Approximately 20% of all animals are haplodiploid, with haploid males and diploid females. Haplodiploid species exhibit diverse but poorly understood mechanisms of sex determination. Some hymenopteran insect species exhibit single-locus complementary sex determination (sl-CSD), where heterozygosity at a polymorphic sex locus initiates female development. Diploid males are homozygous at the sex locus and represent a genetic load because they are inviable or sterile. Inbreeding depression associated with CSD is therefore expected to select for other modes of sex determination resulting in fewer or no diploid males. Here, we investigate an alternative, heretofore hypothetical, mode of sex determination: multiple-locus CSD (ml-CSD). Under ml-CSD, diploid males are predicted to develop only from zygotes that are homozygous at all sex loci. We show that inbreeding for eight generations in the parasitoid wasp Cotesia vestalis leads to increasing proportions of diploid males, a pattern that is consistent with ml-CSD but not sl-CSD. The proportion of diploid males (0.27 ± 0.036) produced in the first generation of inbreeding (mother–son cross) suggests that two loci are likely involved. We also modeled diploid male production under CSD with three linked loci. Our data visually resemble CSD with linked loci because diploid male production in the second generation was lower than that in the first. To our knowledge, our data provide the first experimental support for ml-CSD.

Measuring the turnover rates of Arabidopsis proteins using deuterium oxide: an auxin signaling case study

Rapid environmental responses in plants rely on endogenous signaling mechanisms, which in many cases are mediated by changes in protein turnover rates. It is therefore necessary to develop methods for measuring protein dynamics that monitor large sets of plant proteins to begin to apply a systems biology approach to the study of plant behavior. The use of stable isotope labeling strategies that are adaptable to proteomic methods is particularly attractive for this purpose. Here, we explore one example of such methods that is particularly suitable for plants at the seedling stage, where measurement of amino acid and protein turnover rates is accomplished using a heavy water labeling strategy. The method is backed by microarray evaluation to define its feasibility for specific experimental approaches, and the CULLIN-ASSOCIATED AND NEDDYLATION DISSOCIATED 1 (CAND1) and TRANSPORT INHIBITOR RESPONSE 1 (TIR1) proteins are used to illustrate the potential utility in understanding hormonal signaling regulation. These studies provide insight not only into the potential utility of the method, but also address possible areas of concern regarding the use of heavy water labeling during plant growth. These considerations suggest a prescription for specific experimental designs that minimize interference resulting from the induction of treatment-specific gene expression in the results obtained.

Genetic risk factors for insidious equine recurrent uveitis in Appaloosa horses

Appaloosa horses are predisposed to equine recurrent uveitis (ERU), an immune-mediated disease characterized by recurring inflammation of the uveal tract in the eye, which is the leading cause of blindness in horses. Nine genetic markers from the ECA1 region responsible for the spotted coat color of Appaloosa horses, and 13 microsatellites spanning the equine major histocompatibility complex (ELA) on ECA20, were evaluated for association with ERU in a group of 53 Appaloosa ERU cases and 43 healthy Appaloosa controls. Three markers were significantly associated (corrected P-value <0.05): a SNP within intron 11 of the TRPM1 gene on ECA1, an ELA class I microsatellite located near the boundary of the ELA class III and class II regions and an ELA class II microsatellite located in intron 1 of the DRA gene. Association between these three genetic markers and the ERU phenotype was confirmed in a second population of 24 insidious ERU Appaloosa cases and 16 Appaloosa controls. The relative odds of being an ERU case for each allele of these three markers were estimated by fitting a logistic mixed model with each of the associated markers independently and with all three markers simultaneously. The risk model using these markers classified ~80% of ERU cases and 75% of controls in the second population as moderate or high risk, and low risk respectively. Future studies to refine the associations at ECA1 and ELA loci and identify functional variants could uncover alleles conferring susceptibility to ERU in Appaloosa horses.

Frequency of urinary tract infection in dogs with inflammatory skin disorders treated with ciclosporin alone or in combination with glucocorticoid therapy: a retrospective study.

BACKGROUND Few studies have investigated the frequency of urinary tract infection (UTI) in dogs receiving long-term ciclosporin therapy. HYPOTHESIS/OBJECTIVES The goal of the study was to investigate the frequency of UTI in dogs receiving ciclosporin with or without glucocorticoids. A secondary goal was to determine whether bacteriuria, pyuria and urine specific gravity were good predictors of UTI, and if ciclosporin dose, concurrent ketoconazole therapy, sex or duration of therapy affected the frequency of UTI. Animals -  Eighty-seven dogs with various inflammatory skin disorders and 59 control dogs with inflammatory skin conditions that had not received glucocorticoids or ciclosporin for 6 months were enrolled. METHODS This study was retrospective. The first urine culture from dogs receiving ciclosporin was compared with control dogs using Fishers exact test. A logistic mixed model was used to test for association between a positive bacterial culture and duration of treatment, dose of ciclosporin, concurrent ketoconazole therapy and sex. The sensitivities and specificities for bacteriuria, pyuria and urine specific gravity were determined. RESULTS Twenty-six of 87 (30%) ciclosporin-treated dogs had at least one positive culture. Compared with 3% positive control samples, 15% were positive in treated dogs (P=0.027). The sensitivity and specificity were, respectively, 64.1 and 98.1% for bacteriuria, 74.4 and 70.9% for pyuria, and 56.4 and 65.3% for urine specific gravity. All other analysed parameters were not significantly different. CONCLUSIONS AND CLINICAL IMPORTANCE The results suggest that routine urine cultures and assessment of bacteriuria by cystocentesis should be part of the monitoring for dogs on long-term ciclosporin with and without glucocorticoids.

Genome-wide association study implicates testis-sperm specific FKBP6 as a susceptibility locus for impaired acrosome reaction in stallions.

Impaired acrosomal reaction (IAR) of sperm causes male subfertility in humans and animals. Despite compelling evidence about the genetic control over acrosome biogenesis and function, the genomics of IAR is as yet poorly understood, providing no molecular tools for diagnostics. Here we conducted Equine SNP50 Beadchip genotyping and GWAS using 7 IAR–affected and 37 control Thoroughbred stallions. A significant (P<6.75E-08) genotype–phenotype association was found in horse chromosome 13 in FK506 binding protein 6 (FKBP6). The gene belongs to the immunophilins FKBP family known to be involved in meiosis, calcium homeostasis, clathrin-coated vesicles, and membrane fusions. Direct sequencing of FKBP6 exons in cases and controls identified SNPs g.11040315G>A and g.11040379C>A (p.166H>N) in exon 4 that were significantly associated with the IAR phenotype both in the GWAS cohort (n = 44) and in a large multi-breed cohort of 265 horses. All IAR stallions were homozygous for the A-alleles, while this genotype was found only in 2% of controls. The equine FKBP6 was exclusively expressed in testis and sperm and had 5 different transcripts, of which 4 were novel. The expression of this gene in AC/AG heterozygous controls was monoallelic, and we observed a tendency for FKBP6 up-regulation in IAR stallions compared to controls. Because exon 4 SNPs had no effect on the protein structure, it is likely that FKBP6 relates to the IAR phenotype via regulatory or modifying functions. In conclusion, FKBP6 was considered a susceptibility gene of incomplete penetrance for IAR in stallions and a candidate gene for male subfertility in mammals. FKBP6 genotyping is recommended for the detection of IAR–susceptible individuals among potential breeding stallions. Successful use of sperm as a source of DNA and RNA propagates non-invasive sample procurement for fertility genomics in animals and humans.

Estimation of body weight and development of a body weight score for adult equids using morphometric measurements

Excessive BW has become a major health issue in the equine (Equus caballus) industry. The objectives were to determine if the addition of neck circumference and height improved existing BW estimation equations, to develop an equation for estimation of ideal BW, and to develop a method for assessing the likelihood of being overweight in adult equids. Six hundred and twenty-nine adult horses and ponies who met the following criteria were measured and weighed at 2 horse shows in September 2011 in Minnesota: age ≥ 3 yr, height ≥ 112 cm, and nonpregnant. Personnel assessed BCS on a scale of 1 to 9 and measured wither height at the third thoracic vertebra, body length from the point of shoulder to the point of the buttock, neck and girth circumference, and weight using a portable livestock scale. Individuals were grouped into breed types on the basis of existing knowledge and were confirmed with multivariate ANOVA analysis of morphometric measurements. Equations for estimated and ideal BW were developed using linear regression modeling. For estimated BW, the model was fit using all individuals and all morphometric measurements. For ideal BW, the model was fit using individuals with a BCS of 5; breed type, height, and body length were considered as these measurements are not affected by adiposity. A BW score to assess the likelihood of being overweight was developed by fitting a proportional odds logistic regression model on BCS using the difference between ideal and estimated BW, the neck to height ratio, and the girth to height ratio as predictors; this score was then standardized using the data from individuals with a BCS of 5. Breed types included Arabian, stock, and pony. Mean (± SD) BCS was 5.6 ± 0.9. BW (kg) was estimated by taking [girth (cm)(1.48)6 × length (cm)(0.554) × height (cm)(0.599) × neck (cm)(0.173)]/3,596, 3,606, and 3,441 for Arabians, ponies, and stock horses, respectively (R(2) = 0.92; mean-squared error (MSE) = 22 kg). Ideal BW (kg) was estimated by taking [length (cm) × 2.8] + [height (cm) × 4.2] - 611, 606, and 577 for Arabians, ponies, and stock horses, respectively (R(2) = 0.86; MSE = 24). Equids with a BCS of ≥ 7 had a greater likelihood of being overweight, and the model suggested cutoffs at the 48th and 83rd percentiles for underweight and overweight individuals, respectively. Morphometric measurements were successfully used to develop equid BW-related equations.