Intermarker Distances Research Articles

Population structure and genomic analyses of carcass back Length, shoulder width and leg width in purebred and crossbred German Merino sheep

In order to derive suitable breeding strategies for complex traits, it is indispensable that their genetic architecture as well as population specific parameters are thoroughly investigated. Large samples of genotyped individuals are required in order to produce reliable results and to draw adequate inferences. Whereas in cattle, pig and chicken such data are available for many populations, such datasets are rare for sheep. Except for some sheep breeding nations where genomic selection is applied to sheep, the majority of datasets of genotyped sheep come from experiments with often small sample sizes. Pooling data from different breeds and crosses is one way to increase the sample size for genomic analyses but is somehow challenging due to the multi-breed composition of the datasets. Population structure and genetic diversity has an impact on the results of genomic analyses but is often not studied in the populations in which genomic analyses are conducted. Genetically diverse populations as found in sheep often compromise the analyses and the interpretation of results. Here, we investigated the genetic diversity and population structure of purebred Merino and several Merino crossbred lambs as well as in their pooled data and conducted separate and joint genetic analyses. Linkage disequilibrium was studied in the pooled data as well as in the single datasets. Consistency of phase was calculated among crosses. Population structure assessed by principal component analysis. Variance components were estimated and genome-wide association studies were performed for three carcass traits. All investigations based on 50k genotype data. Large genetic diversity was found between and also within crosses. The populations showed low levels of linkage disequilibrium (average r² between 0.155 and 0.171 within crosses and 0.138 in the pooled dataset for inter-marker distances up to 0.059 Mbp) which decayed fast with increasing inter-marker distance which was particularly pronounced when the data were pooled. The population genetic structure of the purebred Merino sample was similar as in Merino crosses and the genetic differentiation between the different populations were small. Variance components could solely be estimated at acceptable standard errors for some of the single crosses and hence genome-wide association studies could not be performed for all crosses. Pooling data drastically reduced standard errors in variance component estimation but did only marginally improve gene mapping results in terms of power but not precision. The heritabilities estimated in the pooled dataset were 0.30, 0.18 and 0.18 for back length, shoulder width and leg width. Only one genome-wide significant SNP for shoulder width was detected. Further, across all traits and datasets, 25 SNPs were found to be putatively trait associated. Larger datasets and denser marker panels are required to utilize such datasets for gene mapping analyses at high power and precision and would improve population genetic investigations. If possible, and to avoid the application of too complex models, data pooling should rather be done by combining several populations of the same breed instead of multiple crosses.

CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map.

The arrangement of markers on the genome can be defined in either physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a genetic (or linkage) map pictures the recombination rate between pairs of markers. High-resolution genetic maps are key elements for genomic research, such as fine-mapping of quantitative trait loci, but they are also needed for creating and updating chromosome-level assemblies of whole-genome sequences. Based on published results on a large pedigree of German Holstein cattle and newly obtained results with German/Austrian Fleckvieh cattle, we aim at providing a platform that allows users to interactively explore the bovine genetic and physical map. We developed the R Shiny app CLARITY available online at https://nmelzer.shinyapps.io/clarity and as R package at https://github.com/nmelzer/CLARITY that provides access to the genetic maps built on the Illumina Bovine SNP50 genotyping array with markers ordered according to the physical coordinates of the most recent bovine genome assembly ARS-UCD1.2. The user is able to interconnect the physical and genetic map for a whole chromosome or a specific chromosomal region and can inspect a landscape of recombination hotspots. Moreover, the user can investigate which of the frequently used genetic-map functions locally fits best. We further provide auxiliary information about markers being putatively misplaced in the ARS-UCD1.2 release. The corresponding output tables and figures can be downloaded in various formats. By ongoing data integration from different breeds, the app also facilitates comparison of different genome features, providing a valuable tool for education and research purposes.

Cyclic tensile tests of Shetland pony superficial digital flexor tendons (SDFTs) with an optimized cryo-clamp combined with biplanar high-speed fluoroscopy

BackgroundLong-term cyclic tensile testing with equine palmar/plantar tendons have not yet been performed due to problems in fixing equine tendons securely and loading them cyclically. It is well established that the biomechanical response of tendons varies during cyclic loading over time. The aim of this study was to develop a clamping device that enables repetitive cyclic tensile testing of equine superficial digital flexor tendon for at least 60 loading cycles and for 5 min.ResultsA novel cryo-clamp was developed and built. Healthy and collagenase-treated pony SDFTs were mounted in the custom-made cryo-clamp for the proximal tendon end and a special clamping device for the short pastern bone (os coronale). Simultaneously with tensile testing, we used a biplanar high-speed fluoroscopy system (FluoKin) to track tendon movement. The FluoKin system was additionally validated in precision measurements. During the cyclic tensile tests of the SDFTs, the average maximal force measured was 325 N and 953 N for a length variation of 2 and 4 % respectively. The resulting stress averaged 16 MPa and 48 MPa respectively, while the modulus of elasticity was 828 MPa and 1212 MPa respectively. Length variation of the metacarpal region was, on average, 4.87 % higher after incubation with collagenase. The precision of the FluoKin tracking was 0.0377 mm, defined as the standard deviation of pairwise intermarker distances embedded in rigid bodies. The systems accuracy was 0.0287 mm, which is the difference between the machined and mean measured distance.ConclusionIn this study, a good performing clamping technique for equine tendons under repetitive cyclic loading conditions is described. The presented cryo-clamps were tested up to 50 min duration and up to the machine maximal capacity of 10 kN. With the possibility of repetitive loading a stabilization of the time-force-curve and changes of hysteresis and creep became obvious after a dozen cycles, which underlines the necessity of repetitive cyclical testing. Furthermore, biplanar high-speed fluoroscopy seems an appropriate and highly precise measurement tool for analysis of tendon behaviour under repetitive load in equine SDFTs.

Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data.

Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-by-sequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (FHOM) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of FHOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.

PSVIII-31 Genome-wide estimation of linkage disequilibrium using American mink genotyping-by-sequencing data

Abstract Linkage disequilibrium (LD) has been defined as the correlation between alleles at different loci in the genome. The LD levels can be influenced by the evolutionary processes and historical events in populations. The main objective of this study was to estimate the LD levels at different distances of American mink genome using genotyping-by-sequencing (GBS) data. A total of 285 American mink (Neovison vison) were sequenced based on GBS libraries prepared by digesting the genomic DNA with the restriction enzyme ApeKI. After quality control, 13,321 single nucleotide polymorphism (SNP) markers located on 46 Scaffolds were used to determine the extension of LD in the genome. The average r2 was computed for all syntenic SNP pairwise at inter-marker distances from 0 up to 1 Mb. The average r2 between adjacent SNPs was 0.29, ranged from 0.18 to 0.53 across all scaffolds. In addition, the average distance between adjacent markers was 51 kb. The average r2 above 0.3 was observed in less than 1 kb distances and declined with increase in distances between markers. The average r2 was estimated to be less than 0.2 for markers more than 10 kb apart. Furthermore, the average LD level was decreased to 0.08 for inter-marker distances between 0.9 and 1 Mb. The results of this study can be used to determine the optimum maker density required for obtaining enough accuracy and power in both genomic selection and genome-wide association studies.

Construction of a high-density genetic map of tree peony (Paeonia suffruticosa Andr. Moutan) using restriction site associated DNA sequencing (RADseq) approach

High-density genetic maps play a vital role in dissecting genetic components of biologically or agronomically important traits and molecular marker-assisted selection breeding, especially for a species with limited genomic information. Tree Peony (Paeonia suffruticosa Andr. Moutan DC.) is a traditional flowering plant in China, with important ornamental value, which have been spread around the world. However, less genetic and genomic information is available for the tree peony molecular studies. Here, we performed restriction site-associated DNA sequencing (RADseq) of an F1 population, derived from a traditional variety “Qing Long Wo Mo Chi (QL)” and a variety “Mo Zi Lian (MZL)”. High-density genetic maps were developed using RADseq markers for female (1471 markers) and male (793 markers) parents. They covered 965.69 and 870.21 cM, with the average marker intervals of 0.66 and 1.10 cM along the seven and five linkage groups (LGs), respectively. Furthermore, the identified markers were assigned to 1671 bins, representing the unique genetic positions in LGs, and inter-marker distances smaller than 5 cM covered 97.93% of genetic maps. This study suggests that rapid de novo construction of genetic maps in peony could be conducted through RADseq approach, which provides an important tool for further linkage mapping and genomic structure analysis, and enable development of molecular markers for molecular breeding in tree peony.

Interfraction prostate displacement during image-guided radiotherapy using intraprostatic fiducial markers and a cone-beam computed tomography system: A volumetric off-line analysis in relation to the variations of rectal and bladder volumes.

Prostate motion during the radiotherapy course is an important issue. This study investigated the inter-fraction prostate motion in controlled rectal filling condition. 10 prostate cancer patients underwent image-guided radiotherapy (IGRT) using a cone-beam computed tomography (CBCT) system, after the insertion of fiducial markers (FMs). The planning CT was the reference CT (CTref) used to estimate the reference intermarker distances, and CBCTs were used for off-line comparison with CTref. We evaluated the influence of rectal and bladder volume on prostate shifts. We calculated the required planning target volume (PTV) margins in this patient population. 120 CBCTs were analyzed. Mean prostate displacements (± SD) along the 3 axes (x, y, z) averaged over the 10 patients, were: 0.90 ± 0.84 mm in x, 0.00 ± 2.07 mm in y, -0.80 ± 1.28 mm in z. There is a statistically significant anti-correlation between prostate displacements and: bladder volume variations (P < 0.001) in the y-axis, and rectal volume variations (P < 0.05) in the z-axis. PTV margins obtained for the directions x, y and z are respectively 2.5, 5.6 and 3.9 mm. IGRT in reproducible empty rectum condition allow a high reduction of daily treatment uncertainties.

Localization accuracy of two electromagnetic tracking systems in prostate cancer radiotherapy: A comparison with fiducial marker based kilovoltage imaging

The aim of this study was to evaluate the localization accuracy of electromagnetic (EM) tracking systems RayPilot (Micropos Medical AB) and Calypso (Varian Medical Systems) in prostate cancer radiotherapy. The accuracy was assessed by comparing couch shifts obtained with the EM methods to the couch shifts determined by simultaneous fiducial marker (FM) based orthogonal kilovoltage (kV) imaging. Agreement between the methods was compared using Bland-Altman analysis. Interfractional positional stability of the FMs, RayPilot transmitters and Calypso transponders was investigated. 582 fractions from 22 RayPilot patients and 335 fractions from 26 Calypso patients were analyzed. Mean (± standard deviation (SD)) differences between RayPilot and kV imaging were 0.3 ± 2.2, −2.2 ± 2.4 and −0.0 ± 1.0 mm in anterior-posterior (AP), superior-inferior (SI) and left-right (LR) directions, respectively. Corresponding 95% limits of agreement (LOA) were ±4.3, ±4.7 and ±2.1 mm around the mean. Mean (±SD) differences between Calypso and kV imaging were −0.2 ± 0.6, 0.1 ± 0.5 and −0.1 ± 0.4 mm in AP, SI and LR directions, respectively, and corresponding LOAs were ±1.3, ±1.0 and ±0.8 mm around the mean. FMs and transponders were stable: SD of intermarker and intertransponder distances was 0.5 mm. Transmitters were unstable: mean caudal transmitter shift of 1.8 ± 2.0 mm was observed. Results indicate that the localization accuracy of the Calypso is comparable to kV imaging of fiducials and the methods could be used interchangeably. The localization accuracy of the RayPilot is affected by transmitter instability and the positioning of the patient should be verified by other setup techniques. The study is part of clinical trial NCT02319239.

Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances

BackgroundRuns of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle.MethodsROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses.ResultsIn Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR.ConclusionsOur findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.

Evaluation of gold fiducial marker manual localisation for magnetic resonance-only prostate radiotherapy

BackgroundThe use of intraprostatic gold fiducial markers (FMs) ensures highly accurate and precise image-guided radiation therapy for patients diagnosed with prostate cancer thanks to the ease of localising FMs on photon-based imaging, like Computed Tomography (CT) images. Recently, Magnetic Resonance (MR)-only radiotherapy has been proposed to simplify the workflow and reduce possible systematic uncertainties. A critical, determining factor in the accuracy of such an MR-only simulation will be accurate FM localisation using solely MR images.PurposeThe aim of this study is to evaluate the performances of manual MR-based FM localisation within a clinical environment.MethodsWe designed a study in which 5 clinically involved radiation therapy technicians (RTTs) independently localised the gold FMs implanted in 16 prostate cancer patients in two scenarios: employing a single MR sequence or a combination of sequences. Inter-observer precision and accuracy were assessed for the two scenarios for localisation in terms of 95% limit of agreement on single FMs (LoA)/ centre of mass (LoA CM) and inter-marker distances (IDs), respectively.ResultsThe number of precisely located FMs (LoA <2 mm) increased from 38/48 to 45/48 FMs when localisation was performed using multiple sequences instead of single one. When performing localisation on multiple sequences, imprecise localisation of the FMs (3/48 FMs) occurred for 1/3 implanted FMs in three different patients. In terms of precision, we obtained LoA CM within 0.25 mm in all directions over the precisely located FMs. In terms of accuracy, IDs difference of manual MR-based localisation versus CT-based localisation was on average (±1 STD) 0.6 ±0.6 mm.ConclusionsFor both the investigated scenarios, the results indicate that when FM classification was correct, the precision and accuracy are high and comparable to CT-based FM localisation. We found that use of multiple sequences led to better localisation performances compared with the use of single sequence. However, we observed that, due to the presence of calcification and motion, the risk of mislocated patient positioning is still too high to allow the sole use of manual FM localisation. Finally, strategies to possibly overcome the current challenges were proposed.

A new method to quantify liner deformation within a prosthetic socket for below knee amputees

Many amputees who wear a leg prosthesis develop significant skin wounds on their residual limb. The exact cause of these wounds is unclear as little work has studied the interface between the prosthetic device and user. Our research objective was to develop a quantitative method for assessing displacement patterns of the gel liner during walking for patients with transtibial amputation. Using a reflective marker system and a custom clear socket, evaluations were conducted with a clear transparent test socket mounted over a plaster limb model and a deformable limb model. Distances between markers placed on the limb were measured with a digital caliper and then compared with data from the motion capture system. Additionally, the rigid plaster set-up was moved in the capture volume to simulate walking and evaluate if inter-marker distances changed in comparison to static data. Dynamic displacement trials were then collected to measure changes in inter-marker distance due to vertical elongation of the gel liner. Static and dynamic inter-marker distances within day and across days confirmed the ability to accurately capture displacements using this new approach. These results encourage this novel method to be applied to a sample of amputee patients during walking to assess displacements and the distribution of the liner deformation within the socket. The ability to capture changes in deformation of the gel liner will provide new data that will enable clinicians and researchers to improve design and fit of the prosthesis so the incidence of pressure ulcers can be reduced.

A Novel Marker Based Method to Teeth Alignment in MRI

Abstract Magnetic resonance imaging (MRI) can precisely capture the anatomy of the vocal tract. However, the crowns of teeth are not visible in standard MRI scans. In this study, a marker-based teeth alignment method is presented and evaluated. Ten patients undergoing orthognathic surgery were enrolled. Supraglottal airways were imaged preoperatively using structural MRI. MRI visible markers were developed, and they were attached to maxillary teeth and corresponding locations on the dental casts. Repeated measurements of intermarker distances in MRI and in a replica model was compared using linear regression analysis. Dental cast MRI and corresponding caliper measurements did not differ significantly. In contrast, the marker locations in vivo differed somewhat from the dental cast measurements likely due to marker placement inaccuracies. The markers were clearly visible in MRI and allowed for dental models to be aligned to head and neck MRI scans.

A Study of Vicon System Positioning Performance.

Motion capture setups are used in numerous fields. Studies based on motion capture data can be found in biomechanical, sport or animal science. Clinical science studies include gait analysis as well as balance, posture and motor control. Robotic applications encompass object tracking. Today’s life applications includes entertainment or augmented reality. Still, few studies investigate the positioning performance of motion capture setups. In this paper, we study the positioning performance of one player in the optoelectronic motion capture based on markers: Vicon system. Our protocol includes evaluations of static and dynamic performances. Mean error as well as positioning variabilities are studied with calibrated ground truth setups that are not based on other motion capture modalities. We introduce a new setup that enables directly estimating the absolute positioning accuracy for dynamic experiments contrary to state-of-the art works that rely on inter-marker distances. The system performs well on static experiments with a mean absolute error of 0.15 mm and a variability lower than 0.025 mm. Our dynamic experiments were carried out at speeds found in real applications. Our work suggests that the system error is less than 2 mm. We also found that marker size and Vicon sampling rate must be carefully chosen with respect to the speed encountered in the application in order to reach optimal positioning performance that can go to 0.3 mm for our dynamic study.

Action Sport Cameras as an Instrument to Perform a 3D Underwater Motion Analysis.

Action sport cameras (ASC) are currently adopted mainly for entertainment purposes but their uninterrupted technical improvements, in correspondence of cost decreases, are going to disclose them for three-dimensional (3D) motion analysis in sport gesture study and athletic performance evaluation quantitatively. Extending this technology to sport analysis however still requires a methodologic step-forward to making ASC a metric system, encompassing ad-hoc camera setup, image processing, feature tracking, calibration and 3D reconstruction. Despite traditional laboratory analysis, such requirements become an issue when coping with both indoor and outdoor motion acquisitions of athletes. In swimming analysis for example, the camera setup and the calibration protocol are particularly demanding since land and underwater cameras are mandatory. In particular, the underwater camera calibration can be an issue affecting the reconstruction accuracy. In this paper, the aim is to evaluate the feasibility of ASC for 3D underwater analysis by focusing on camera setup and data acquisition protocols. Two GoPro Hero3+ Black (frequency: 60Hz; image resolutions: 1280×720/1920×1080 pixels) were located underwater into a swimming pool, surveying a working volume of about 6m3. A two-step custom calibration procedure, consisting in the acquisition of one static triad and one moving wand, carrying nine and one spherical passive markers, respectively, was implemented. After assessing camera parameters, a rigid bar, carrying two markers at known distance, was acquired in several positions within the working volume. The average error upon the reconstructed inter-marker distances was less than 2.5mm (1280×720) and 1.5mm (1920×1080). The results of this study demonstrate that the calibration of underwater ASC is feasible enabling quantitative kinematic measurements with accuracy comparable to traditional motion capture systems.

Extent of genome-wide linkage disequilibrium in Pinzgau cattle

The aim of this study was to describe the extent of linkage disequilibrium (LD) based on genotyping data in Pinzgau cattle population. DNA samples were obtained from 19 bulls of active Pinzgau cattle population in Slovakia. Genotyping was carried out in commercial lab using an Illumina BovineSNP50 BeadChip. The genotyping array contained 54,609 single nucleotide polymorphisms (SNPs). After quality control SNPs localized on sex chromosomes were excluded. A total of 42,248 (79.97%) SNPs were found to be polymorphic. The distribution of SNPs over entire genomes of all chromosomes was not uniform. The minor allele frequencies across autosomal loci ranged from 0.266 (BTA4) to 0.280 (BTA23) with average value 0.273±0.133. Only adjacent SNPs with distance less than 5 Mb and LD (r2) values from 0.01 to 0.99 were used in the characterization of LD extent. After filtering, the genome coordinates of 31,063 SNP markers covered all regions of autosomes on the length 2519232 kb. The spacing across genome between adjacent SNPs was in average 46.89±47.48 kb and within autosomes ranged from 43.65 kb (BTA25) to 52.59 kb (BTA5). The distribution of SNPs on different chromosomes ranged from 633 (79.13%) on BTA29 to 1123 (83.62%) on BTA14. The average LD between adjacent markers within autosomes reached values from 0.189 to 0.234 for chromosomes BTA 29 and 21, respectively. Division of r2-values over all 29 autosomes were performed according to their physical intermarker distances and averaged within the groups for analysis of distance effect on LD. The results of our study indicated the rapid decay of LD with increasing distance between markers. Further investigation will be oriented on evaluation of effective population size based on LD data. This could allow improvement of our knowledge about genetic diversity and its use for breed preservation of original phenotype supported by the current selection schemes and breeding programmes.

Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data.

BackgroundKnowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data.ResultsA total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r2 criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r2 above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations.ConclusionsA wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds.

The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers.

Evaluation of serrated intraprostatic gold coils positional stability using on-board cone beam computed tomography scans acquired throughout the radiation treatment course

PurposeTo investigate intraprostatic gold coils positional stability analyzing intermarker distance in on-board cone beam computed tomography (CBCT) scans acquired throughout the entire treatment course. Methods and materialsA total of 29 fiducial markers (FMs) were implanted in 10 patients through the transperineal approach, under ultrasound guidance. After 2 weeks from the FM implantation, all the patients underwent CT and magnetic resonance imaging under radiation therapy–planning conditions. The planning CT was the reference CT (CTref) used to calculate the initial intermarker distances. For every patient, 8 CBCTi (i varying from 1 to 8) acquired once a week during the treatment course were selected to calculate intermarker distances and compared with CTref. Reconstructed images of CBCTi were exported to the treatment planning system, and every FM was contoured. A point of interest at the center of mass of each contoured FM was created. The mean coordinates obtained for point of interest at the center of mass of FMs were used to calculate relative marker distances on CTref and CBCTi. ResultsNo patient developed postimplantation complications. A total of 224 marker distance variations (MDVs) were calculated for all 29 markers. The average directional variation of all MDVs (± standard deviation [SD]) was −0.14 ± 0.86 mm. The average absolute variations of all MDVs (± SD) were 0.71 ± 0.51 mm. The largest observed variation was 1.9 mm. All patients had not significant temporal trends in their marker distances. The SD of the MDVs was computed for each set of markers in all 10 patients. The SDs ranged between 0.4 and 1.1 mm in individual patients. The average of the mean SDs was 0.6 mm. ConclusionsThe three-dimensional definition of each fiducial marker volume, using on-board CBCT, demonstrated the stability of FMs position throughout the entire radiation therapy treatment course.

Prostate volume and implant configuration during 48 hours of temporary prostate brachytherapy: limited effect of oedema.

BackgroundIn pulsed-dose rate prostate brachytherapy the dose is delivered during 48 hours after implantation, making the treatment sensitive to oedematic effects possibly affecting dose delivery. The aim was to study changes in prostate volume during treatment by analysing catheter configurations on three subsequent scans.MethodsProstate expansion was determined for 19 patients from the change in spatial distribution of the implanted catheters, using three CT-scans: a planning CT (CT1) and two CTs after 24 and 48 hours (CT2, CT3). An additional 4 patients only received one repeat CT (after 24 hours). The mean radial distance (MRD) of all dwell positions to the geometric centre of all dwell positions used was calculated to evaluate volume changes. From three implanted markers changes in inter-marker distances were assessed. The relative shifts of all dwell positions were determined using catheter- and marker-based registrations. Wilcoxon signed-rank tests were performed to compare the results from the different time points.ResultsThe MRDs measured on the two repeat CTs were significantly different from CT1. The mean prostate volume change derived from the difference in MRD was +4.3% (range −9.3% to +15.6%) for CT1-CT2 (p < .05) and +4.4% (range −7.5% to +16.3%) for CT1-CT3 (p < .05). These values represented a mean increase of 1.2 cm3 in the first 24 hours and 1.5 cm3 in the subsequent 24 hours. There was no clear sign of prostate expansion from the change in inter-marker distance (CT1-CT2: 0.2 ± 1.8 mm; CT1-CT3: 0.6 ± 2.2 mm). Catheter configuration remained stable; shifts in catheter positions were largest in the C-C direction: 0 ± 1.8 mm for CT1-CT2 and 0 ± 1.4 mm for CT2-CT3.ConclusionsThe volume changes derived from catheter displacements were small and therefore considered clinically insignificant. Implant configuration remains stable during 2 days of treatment, confirming the safety of this technique.