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Simultaneous and quantitative assessment of skin functional characteristics in different modalities will facilitate diagnosis and therapy in many clinical applications such as wound healing. However, many existing clinical practices and multimodal imaging systems are subjective, qualitative, sequential for multimodal data collection, and need co-registration between different modalities. To overcome these limitations, we developed a multimodal imaging system for quantitative, non-invasive, and simultaneous imaging of cutaneous tissue oxygenation and blood perfusion parameters. The imaging system integrated multispectral and laser speckle imaging technologies into one experimental setup. A Labview interface was developed for equipment control, synchronization, and image acquisition. Advanced algorithms based on a wide gap second derivative reflectometry and laser speckle contrast analysis (LASCA) were developed for accurate reconstruction of tissue oxygenation and blood perfusion respectively. Quantitative calibration experiments and a new style of skinsimulating phantom were designed to verify the accuracy and reliability of the imaging system. The experimental results were compared with a Moor tissue oxygenation and perfusion monitor. For In vivo testing, a post-occlusion reactive hyperemia (PORH) procedure in human subject and an ongoing wound healing monitoring experiment using dorsal skinfold chamber models were conducted to validate the usability of our system for dynamic detection of oxygenation and perfusion parameters. In this study, we have not only setup an advanced multimodal imaging system for cutaneous tissue oxygenation and perfusion parameters but also elucidated its potential for wound healing assessment in clinical practice.

Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ∼6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.

Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel.Contact: pjb39@cornell.edu

Fatty acid binding protein 4 (FABP4), which is expressed in adipose tissue, interacts with peroxisome proliferator-activated receptors and binds to hormone-sensitive lipase and therefore, plays an important role in lipid metabolism and homeostasis in adipocytes. The objective of this study was to investigate associations of the bovine FABP4 gene with fat deposition. Both cDNA and genomic DNA sequences of the bovine gene were retrieved from the public databases and aligned to determine its genomic organization. Primers targeting two regions of the FABP4 gene were designed: from nucleotides 5433-6106 and from nucleotides 7417-7868 (AAFC01136716). Direct sequencing of polymerase chain reaction (PCR) products on two DNA pools from high- and low-marbling animals revealed two single nucleotide polymorphisms (SNPs): AAFC01136716.1:g.7516G>C and g.7713G>C. The former SNP, detected by PCR-restriction fragment length polymorphism using restriction enzyme MspA1I, was genotyped on 246 F2 animals in a Waygu x Limousin F2 reference population. Statistical analysis showed that the FABP4 genotype significantly affected marbling score (P = 0.0398) and subcutaneous fat depth (P = 0.0246). The FABP4 gene falls into a suggestive/significant quantitative trait loci interval for beef marbling that was previously reported on bovine chromosome 14 in three other populations.

As the consequence of complex interactions between different parts of an organ, shape can be used as a predictor of structural–functional relationships implicated in changing environments. Despite such importance, however, it is no surprise that little is known about the genetic detail involved in shape variation, because no approach is currently available for mapping quantitative trait loci (QTLs) that control shape. Here, we address this problem by developing a statistical model that integrates the principle of shape analysis into a mixture-model-based likelihood formulated for QTL mapping. One state-of-the-art approach for shape analysis is to identify and analyze the polar coordinates of anatomical landmarks on a shape measured in terms of radii from the centroid to the contour at regular intervals. A procrustes analysis is used to align shapes to filter out position, scale and rotation effects on shape variation. To the end, the accurate and quantitative representation of a shape is produced with aligned radius-centroid-contour (RCC) curves, that is, a function of radial angle at the centroid. The high dimensionality of the RCC data, crucial for a comprehensive description of the geometric feature of a shape, is reduced by principal component (PC) analysis, and the resulting PC axes are treated as phenotypic traits, allowing specific QTLs for global and local shape variability to be mapped, respectively. The usefulness and utilization of the new model for shape mapping in practice are validated by analyzing a mapping data collected from a natural population of poplar, Populus szechuanica var tibetica, and identifying several QTLs for leaf shape in this species. The model provides a powerful tool to compute which genes determine biological shape in plants, animals and humans.

To compare the long-term outcome of tibial plateau leveling osteotomy (TPLO) and extracapsular repair (ECR) for treatment of a ruptured cranial cruciate ligament (RCCL).Prospective clinical trial.Normal adult dogs (control, n = 79); dogs with unilateral CCL disease (n = 38).Dogs had TPLO (n = 15) or ECR (n = 23) for treatment of RCCL. Force plate gait analysis was performed for the control group at one time point and for treatment groups at serial points: preoperatively, 2 weeks, 8 weeks, 6 and 12 months postoperatively. Symmetry indices (SIs) were calculated between operated and unoperated pelvic limb for ground reaction forces (GRFs), including peak vertical force (PVF), contact time (CT), and vertical impulse (VI). GRFs of the treatment groups and control group were compared using a general linear model and Kaplan-Meier survival analysis.At 8 weeks, for PVF and VI, the TPLO group had more symmetric limb loading than the ECR group at the walk and trot. SIs of the TPLO group were not different from the control group by 6 months to 1 year postoperatively. SIs for the ECR group were less symmetrical than the control group at all time periods. Using survival analysis, median time to normal function was no different at the walk between groups, but was shorter for the TPLO group for VI and PVF.Dogs achieved normal limb loading faster after TPLO than ECR. TPLO resulted in operated limb function that was indistinguishable from the control population by 1 year postoperatively.

Lead zirconate titanate specimens, at composition Zr 48.9±1.0 /Ti 51.1±1.0 , of grain sizes ranging from 0.5 to 15 μm were prepared by hot pressing. The fracture toughness showed a 40% increase in the fine-grained specimens. Poling produced anisotropy in the fracture toughness. A tensor representation for the fracture toughness, now a function of the crack plane normal and the poling direction, is developed. The maximum and minimum values in the toughness tensor are shown to be related to the unpoled toughness by a simple phenomenological relationship. We also find that the piezoelectric coefficient, d 33 , shows a slight increase for the fine-grained specimens, which is in conflict with the general view that smaller-grained materials can sustain vanishingly small values of spontaneous polarization.

This study was conducted to evaluate the in vitro immunomodulatory effects of supercritical CO(2)Ligustrum lucidum extract (LLE) on the immune cells of piglets. The results showed that the LLE enhanced the proliferative activity of piglet blood lymphocytes and up-regulated the CD4(+) CD8(+) and CD4(+) CD8(-) cell populations. The LLE also regulated the expression of Th1- and Th2-related cytokines; elevated the levels of IL-2, IFN-γ and TNF-α, which were produced by Th1 lymphocytes; and decreased the levels of IL-4 and IL-10, which were produced by Th2 lymphocytes. Furthermore, the LLE stimulated the NO secretion of lymphocytes. These results indicated that LLE might have potential immunomodulatory effects on the immune system of piglets and provided scientific and experimental foundations for the development of a new kind of LLE immune adjuvant in the pig production.

Recent studies have shown that, in numerous species, systemically administered bone marrow-derived mesenchymal stem cells undergo site-specific differentiation. This suggests that osteoblasts, by means of cytokine secretion, may promote dental pulp stem cells (DPSCs) to undergo osteogenesis. The objective of this study was to assess the potential synergistic interaction effect of osteoblasts on DPSCs for promotion of osteogenesis. Stem cells, derived from dental pulp of healthy human donors, were co-cultured with calvaria osteoblasts using a culture insert system. The proliferation rate, calcium deposition, osteogenic-related gene expression of induced DPSCs, including Runx-2, bone sialoprotein, osteocalcin and collagen-1, were assayed using MTT, Alizarin Red S staining and reverse transcriptase polymerase chain reaction, respectively. Co-cultured DPSCs had the highest rate of proliferation compared with those cultured in absence of osteoblasts. The morphology and ultrastructure of DPSCs in the co-cultures showed improvement, with co-cultured DPSCs becoming more osteoblast-like as compared with DPSCs cultured alone, and the mineralization potential of co-cultured DPSCs was enhanced compared with DPSCs cultured alone. Furthermore, osteogenic-related genes were significantly over-expressed in co-cultured DPSCs after osteogenic induction. The results demonstrate that DPSCs successfully differentiate towards osteoblasts and that the paracrine interaction of osteoblasts is likely to contribute to DPSC differentiation. It is believed that this study demonstrates certain useful applications for DPSCs in bone tissue engineering.

BackgroundCanine hip dysplasia (HD) is a common polygenic trait characterized by hip malformation that results in osteoarthritis (OA). The condition in dogs is very similar to developmental dysplasia of the human hip which also leads to OA.Methodology/principal findingsA total of 721 dogs, including both an association and linkage population, were genotyped. The association population included 8 pure breeds (Labrador retriever, Greyhounds, German Shepherd, Newfoundland, Golden retriever, Rottweiler, Border Collie and Bernese Mountain Dog). The linkage population included Labrador retrievers, Greyhounds, and their crosses. Of these, 366 dogs were genotyped at ∼22,000 single nucleotide polymorphism (SNP) loci and a targeted screen across 8 chromosomes with ∼3,300 SNPs was performed on 551 dogs (196 dogs were common to both sets). A mixed linear model approach was used to perform an association study on this combined association and linkage population. The study identified 4 susceptibility SNPs associated with HD and 2 SNPs associated with hip OA.Conclusion/significanceThe identified SNPs included those near known genes (PTPRD, PARD3B, and COL15A1) reported to be associated with, or expressed in, OA in humans. This suggested that the canine model could provide a unique opportunity to identify genes underlying natural HD and hip OA, which are common and debilitating conditions in both dogs and humans.

Lead zirconate titanate specimens, at composition Zr 48.9±1.0 /Ti 51.1±1.0 , of grain sizes ranging from 0.5 to 15 μm were prepared by hot pressing. The fracture toughness showed a 40% increase in the fine-grained specimens. Poling produced anisotropy in the fracture toughness. A tensor representation for the fracture toughness, now a function of the crack plane normal and the poling direction, is developed. The maximum and minimum values in the toughness tensor are shown to be related to the unpoled toughness by a simple phenomenological relationship. We also find that the piezoelectric coefficient, d 33 , shows a slight increase for the fine-grained specimens, which is in conflict with the general view that smaller-grained materials can sustain vanishingly small values of spontaneous polarization.

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

Mixed linear model (MLM) methods have proven useful in controlling for population structure and relatedness within genome-wide association studies. However, MLM-based methods can be computationally challenging for large datasets. We report a compression approach, called ‘compressed MLM’, that decreases the effective sample size of such datasets by clustering individuals into groups. We also present a complementary approach, ‘population parameters previously determined’ (P3D), that eliminates the need to re-compute variance components. We applied these two methods both independently and combined in selected genetic association datasets from human, dog and maize. The joint implementation of these two methods markedly reduced computing time and either maintained or improved statistical power. We used simulations to demonstrate the usefulness in controlling for substructure in genetic association datasets for a range of species and genetic architectures. We have made these methods available within an implementation of the software program TASSEL.

Background Canine Hip Dysplasia (CHD) is a common inherited disease that affects dog wellbeing and causes a heavy financial and emotional burden to dog owners and breeders due to secondary hip osteoarthritis. The Orthopedic Foundation for Animals (OFA) initiated a program in the 1960's to radiograph hip and elbow joints and release the OFA scores to the public for breeding dogs against CHD. Over last four decades, more than one million radiographic scores have been released. Methodology/Principal Findings The pedigrees in the OFA database consisted of 258,851 Labrador retrievers, the major breed scored by the OFA (25% of total records). Of these, 154,352 dogs had an OFA hip score reported between 1970 and 2007. The rest of the dogs (104,499) were the ancestors of the 154,352 dogs to link the pedigree relationships. The OFA hip score is based on a 7-point scale with the best ranked as 1 (excellent) and the worst hip dysplasia as 7. A mixed linear model was used to estimate the effects of age, sex, and test year period and to predict the breeding value for each dog. Additive genetic and residual variances were estimated using the average information restricted maximum likelihood procedure. The analysis also provided an inbreeding coefficient for each dog. The hip scores averaged 1.93 (±SD = 0.59) and the heritability was 0.21. A steady genetic improvement has accrued over the four decades. The breeding values decreased (improved) linearly. By the end of 2005, the total genetic improvement was 0.1 units, which is equivalent to 17% of the total phenotypic standard deviation. Conclusion/Significance A steady genetic improvement has been achieved through the selection based on the raw phenotype released by the OFA. As the heritability of the hip score was on the low end (0.21) of reported ranges, we propose that selection based on breeding values will result in more rapid genetic improvement than breeding based on phenotypic selection alone.

Understanding the genetic basis of nitrogen and carbon metabolism will accelerate the development of plant varieties with high yield and improved nitrogen use efficiency. A robotized platform was used to measure the activities of 10 enzymes from carbon and nitrogen metabolism in the maize (Zea mays) intermated B73 × Mo17 mapping population, which provides almost a 4-fold increase in genetic map distance compared with conventional mapping populations. Seedling/juvenile biomass was included to identify its genetic factors and relationships with enzyme activities. All 10 enzymes showed heritable variation in activity. There were strong positive correlations between activities of different enzymes, indicating that they are coregulated. Negative correlations were detected between biomass and the activity of six enzymes. In total, 73 significant quantitative trait loci (QTL) were found that influence the activity of these 10 enzymes and eight QTL that influence biomass. While some QTL were shared by different enzymes or biomass, we critically evaluated the probability that this may be fortuitous. All enzyme activity QTL were in trans to the known genomic locations of structural genes, except for single cis-QTL for nitrate reductase, Glu dehydrogenase, and shikimate dehydrogenase; the low frequency and low additive magnitude compared with trans-QTL indicate that cis-regulation is relatively unimportant versus trans-regulation. Two-gene epistatic interactions were identified for eight enzymes and for biomass, with three epistatic QTL being shared by two other traits; however, epistasis explained on average only 2.8% of the genetic variance. Overall, this study identifies more QTL at a higher resolution than previous studies of genetic variation in metabolism.

The toxicity caused by Aluminum (Al) is one of the most limiting factors for crop growth and development on acid soils. In sorghum, allelic variation at the AltSB locus accounts for nearly 80% of the phenotypic variation for the trait in some mapping populations, even though other loci controlling Al tolerance do exist. Our previous positional cloning effort led to the identification of a gene belonging to the multidrug and toxic compound extrusion (MATE) family that underlies the AltSB locus. Attempting to identify the molecular determinants of allelic effects at AltSB, we completely sequenced a 24.6kbp region defined by high resolution mapping of AltSB in the parents of a sorghum RIL population, SC283 (Al tolerant) and BR007 (Al sensitive). Six candidates regions containing polymorphisms were subsequently selected for association studies. These candidates regions were genotyped or sequenced in 254 sorghum accessions comprising our association panel. Association tests were performed using a mixed linear model that accounts for multiple levels of relatedness for appropriate Type I error control. Highly significant associations were detected for traits related to Al inhibition of root growth in nutrient solution. An important role in Al tolerance is possibly played by a polymorphism located in the second intron of the AltSB gene, which had a major contribution to an overall Al tolerance index created by principal component analysis. However, this polymorphism is in strong linkage disequilibrium with others in the region, which prevented us to definite the causative nature of the associated loci. Highly associated SNPs are being used to develop tag markers for marker-assisted selection, which can be used for allele mining in diverse sorghum germplasm. (Texte intégral)

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

To study the chemical constituents of the bee-collected rape pollen.The compounds were isolated by column chromatography on silica gel; Sephadex LH-20 and C18. Their structures were elucidated on the basis of spectral analysis.Nine compounds were isolated from the bee-collected rape pollen and the structures of them were kaemferol-3-O-beta-D-glucosyl-(2--1)-beta-D-glucoside (1), kaemferol-3,4'-di-O-beta-D-glucoside (2), quercetin-3-O-beta-D-glucosyl-(2--1)-beta-D-glucoside (3), nicotinic acid (4), nicotinamide (5), trans-p-coumaric acid-4-O-beta-D-glucopyranoside (6), kaemferol (7), beta-sitosterol (8) and 5-hydroxymethylfurfural (9).Compounds 1-6 were isolated from the bee-collected rape pollen for the first time.

The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, association mapping (also known as linkage disequilibrium mapping) is increasingly being adopted as the mapping method of choice. Association mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage mapping. We emphasize here that linkage and association mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and association mapping to increase statistical power and mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of association mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation.

Objective—To estimate heritabilities and genetic correlations among 4 traits of hip joints (distraction index [DI], dorsolateral subluxation [DLS] score, Norberg angle [NA], and extended–hip joint radiograph [EHR] score) and to derive the breeding values for these traits in dogs. Animals—2,716 dogs of 17 breeds (1,551 dogs in which at least 1 hip joint trait was measured). Procedures—The NA was measured, and an EHR score was assigned. Hip joint radiographs were obtained from some dogs to allow calculation of the DI and DLS score. Heritabilities, genetic correlations, and breeding values among the DI, DLS score, NA, and EHR score were calculated by use of a set of multiple-trait, derivative-free, restricted maximum likelihood computer programs. Results—Among 2,716 dogs, 1,411 (52%) had an estimated inbreeding coefficient of 0%; the remaining dogs had a mean inbreeding coefficient of 6.21%. Estimated heritabilities were 0.61, 0.54, 0.73, and 0.76 for the DI, DLS score, NA, and EHR score, respectively. The EHR score was highly genetically correlated with the NA (r = −0.89) and was moderately genetically correlated with the DI (r = 0.69) and DLS score (r = −0.70). The NA was moderately genetically correlated with the DI (r = −0.69) and DLS score (r = 0.58). Genetic correlation between the DI and DLS score was high (r = −0.91). Conclusions and Clinical Relevance—Establishment of a selection index that makes use of breeding values jointly estimated from the DI, DLS score, NA, and EHR score should enhance breeding programs to reduce the incidence of hip dysplasia in dogs.

Hip dysplasia is a common inherited trait of dogs that results in secondary osteoarthritis. In this article the methods used to uncover the mutations contributing to this condition are reviewed, beginning with hip phenotyping. Coarse, genome-wide, microsatellite-based screens of pedigrees of greyhounds and dysplastic Labrador retrievers were used to identify linked quantitative trait loci (QTL). Fine-mapping across two chromosomes (CFA11 and 29) was employed using single nucleotide polymorphism (SNP) genotyping. Power analyses and preferential selection of dogs for ongoing SNP-based genotyping is described with the aim of refining the QTL intervals to 1-2 megabases on these and several additional chromosomes prior to candidate gene screening. The review considers how a mutation or a genetic marker such as a SNP or haplotype of SNPs might be combined with pedigree and phenotype information to create a 'breeding value' that could improve the accuracy of predicting a dog's hip conformation.

5 pages, 5 figures.-- Supporting information (Materials and Methods, Suppl. figs S1-S75, tabs S1-S5, refs., 88 page PDF file) available at: http://www.sciencemag.org/cgi/content/full/sci;325/5941/714/DC1, Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis., This work was supported by U.S. NSF Plant Genome Program (DBI-9872631, DBI-0321467, DBI-0820619 to E.S.B., M.M.G. (98,03), J.B.H. (03,08), M.D.M. (03,08), S.K. (03,08), D.W. (03); DBI-0604923 to T.R.R.; U.S. Department of Agriculture–Agricultural Research Service (to E.S.B., J.B.H., M.D.M.), and Spanish Ministry for Education and Science (AP-2004-6033, fellowship to M.C.R.).

Objective—To identify quantitative trait loci (QTL) associated with osteoarthritis (OA) of hip joints of dogs by use of a whole-genome microsatellite scan. Animals—116 founder, backcross, F1, and F2 dogs from a crossbred pedigree. Procedures—Necropsy scores and an optimized set of 342 microsatellite markers were used for interval mapping by means of a combined backcross and F2 design module from an online statistical program. Breed and sex were included in the model as fixed effects. Age of dog at necropsy and body weight at 8 months of age were also included in the model as covariates. The chromosomal location at which the highest F score was obtained was considered the best estimate of a QTL position. Chromosome-wide significance thresholds were determined empirically from 10,000 permutations of marker genotypes. Results—4 chromosomes contained putative QTL for OA of hip joints in dogs at the 5% chromosome-wide significance threshold: chromosomes 5, 18, 23, and 31. Conclusions and Clinical Relevance—Osteoarthritis of canine hip joints is a complex disease to which many genes and environmental factors contribute. Identification of contributing QTL is a strategy to elucidate the genetic mechanisms that underlie this disease. Refinement of the putative QTL and subsequent candidate gene studies are needed to identify the genes involved in the disease process.

Objective—To evaluate the quantitative inheritance of secondary hip joint osteoarthritis in a canine pedigree. Animals—137 Labrador Retrievers, Greyhounds, and mixed-breed dogs. Procedures—Necropsy scores ranging from 0 to 4 were obtained for each hip joint. Seven unaffected Greyhounds with normal hip joint conformation were also used for genetic modeling, but were not euthanized. Sixty-six male and 71 female dogs were allocated to 2 groups (≤ 12 months of age and > 12 months of age). Statistical models were developed to establish the inheritance pattern of hip joint osteoarthritis that developed secondary to hip dysplasia. Results—62 dogs had evidence of osteoarthritis in a hip joint, and 75 had no evidence of osteoarthritis. After sex was adjusted for, the necropsy score was found to be inherited additively but without dominance. Each Labrador Retriever allele increased the necropsy score by 0.7 to 0.9 points, compared with the Greyhound allele, and male sex increased the necropsy score 0.74 over female sex. Approximately 10% of the variation in necropsy score was attributable to the litter of puppies' origin. Conclusions and Clinical Relevance—Because secondary hip joint osteoarthritis is inherited additively, selection pressure could be applied to reduce its incidence. Similar statistical models can be used in linkage and association mapping to detect the genes in the underlying quantitative trait loci that contribute to hip joint osteoarthritis.

Canine hip dysplasia is a common developmental inherited trait characterized by hip laxity, subluxation or incongruity of the femoral head and acetabulum in affected hips. The inheritance pattern is complex and the mutations contributing to trait expression are unknown. In the study reported here, 240 microsatellite markers distributed in 38 autosomes and the X chromosome were genotyped on 152 dogs from three generations of a crossbred pedigree based on trait-free Greyhound and dysplastic Labrador Retriever founders. Interval mapping was undertaken to map the QTL underlying the quantitative dysplastic traits of maximum passive hip laxity (the distraction index), the dorsolateral subluxation score, and the Norberg angle. Permutation testing was used to derive the chromosome-wide level of significance at p < 0.05 for each QTL. Chromosomes 4, 9, 10, 11 (p < 0.01), 16, 20, 22, 25, 29 (p < 0.01), 30, 35, and 37 harbor putative QTL for one or more traits. Successful detection of QTL was due to the crossbreed pedigree, multiple-trait measurements, control of environmental background, and marked advancement in canine mapping tools.

Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.

Background Equine recurrent laryngeal neuropathy (RLN) is a bilateral mononeuropathy with an unknown pathogenesis that significantly affects performance in Thoroughbreds. A genetic contribution to the pathogenesis of RLN is suggested by the higher prevalence of the condition in offspring of RLN-affected than unaffected stallions. To better understand RLN pathogenesis and its genetic basis, we performed a genome-wide association (GWAS) of 282 RLN-affected and 268 control Thoroughbreds. Results We found a significant association of RLN with the LCORL/NCAPG locus on ECA3 previously shown to affect body size in horses. Using height at the withers of 505 of these horses, we confirmed the strong association of this locus with body size, and demonstrated a significant phenotypic and genetic correlation between height and RLN grade in this cohort. Secondary genetic associations for RLN on ECA18 and X did not correlate with withers height in our cohort, but did contain candidate genes likely influencing muscle physiology and growth: myostatin (MSTN) and integral membrane protein 2A (ITM2A). Conclusions This linkage between body size and RLN suggests that selective breeding to reduce RLN prevalence would likely reduce adult size in this population. However, our results do not preclude the possibility of modifier loci that attenuate RLN risk without reducing size or performance, or that the RLN risk allele is distinct but tightly linked to the body size locus on ECA3. This study is both the largest body size GWAS and the largest RLN GWAS within Thoroughbred horses to date, and suggests that improved understanding of the relationship between genetics, equine growth rate, and RLN prevalence may significantly advance our understanding and management of this disease.