An outbreak of lymphomas in commercial broiler breeder chickens vaccinated with a fowlpox vaccine contaminated with reticuloendotheliosis virus

Gross and microscopic examinations of affected tissues from chickens of two commercial broiler breeder flocks aged 27 and 31 weeks revealed lesions of visceral lymphomas with bursal involvement in some chickens. Reticuloendotheliosis virus (REV), but not avian leukosis virus (ALV), was isolated from blood of affected chickens. Furthermore, DNA extracted from tumours tested positive for REV, but not for ALV or Marek's disease virus by polymerase chain reaction (PCR) test. Attempts to determine the source of REV infection included testing a commercial fowlpox (FP) vaccine used to immunize flocks at 7 days of age. Chicken-embryo fibroblasts inoculated with the FP vaccine tested positive for REV by PCR and immunofluorescent tests. REV was also isolated from plasma of pathogen-free chickens experimentally inoculated with FP vaccine at hatch; two of eight (25%) inoculated chickens developed lymphomas by 34 weeks of age. Antigenic characterization of REV isolated from commercial broiler breeder chickens and from FP vaccine, using monoclonal antibodies, revealed that both isolates belong to subtype 3 of REV. The data represent the first report of an outbreak of REV-induced lymphomas in commercial chickens. The data also indicate that the source of REV infection is an REV-contaminated commercial FP vaccine.

Assessment of magnification of digital pelvic radiographs in total hip arthroplasty using templating software

INTRODUCTION

Templating of pelvic radiographs traditionally involved using implant-company provided acetates which assumed a magnification of 115-120%. With the introduction of digital imaging, many departments are becoming filmless. Templating software has been designed to allow on-screen templating of digital images. Knowledge of the true magnification of the image is required for accurate measurement.

PATIENTS AND METHODS

Fifty consecutive postoperative pelvic radiographs were analysed using templating software. The implanted component was measured using an assumed magnification factor of 115%. The template image was then reset to the known component size, and the magnification factor was adjusted until the template covered the true component.

RESULTS

An assumed magnification factor of 115% oversized the acetabular component by a mean of 6 mm (three component sizes) in all 50 components. The mean true magnification in our department was 127%.

CONCLUSIONS

Validation of the true magnification produced by a radiology department using templating software is a simple and reproducible technique. It is recommended to all departments using digital images and templating software. Assumption of a magnification factor of 115% risks oversizing components by 6 mm.

Minimal access surgery for total hip arthroplasty - current beliefs and activity profile in the UK

INTRODUCTION

There is a strong drive from patients, industry and the media to perform total hip arthroplasty (THA) through a minimal access incision. Currently in the UK, the exact definition and uptake of this procedure is not known.

PATIENTS AND METHODS

A postal questionnaire was sent to all consultant orthopaedic surgeons in the UK registered with the British Orthopaedic Association.

RESULTS

Of those performing THA, 23% have performed minimal access hip surgery (MAS). Of users, 63% perform less than 20 cases per year, 62% use the mini-posterior approach, and 12% intend to perform MAS in the future. There is an association with specialisation. The mean and mode scar sizes for MAS were 9.9 cm and 10 cm, respectively.

CONCLUSIONS

MAS is increasing in popularity but is currently performed in small numbers by those with a specialist interest in hip arthroplasty. Because no long-term results have been published regarding this procedure, it will be important to ensure that standards of implantation are not jeopardised and training remains critical. Cases should be registered with the National Joint Registry using the current definition of scar size less than 10 cm.

Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo)

The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

Candidate gene expression analysis of toxin-induced dilated cardiomyopathy in the turkey (Meleagris gallopavo)

Dilated cardiomyopathy (DCM), a heart disease, affects many vertebrates including humans and poultry. The disease can be either idiopathic (IDCM) or toxin-induced (TIDCM). Although genetic and other studies of IDCM are extensive, the specific etiology of TIDCM is still unknown. In this study, we compared mRNA levels of cardiac troponin T (cTnT) and phospholamban (PLN) in turkeys affected and unaffected by TIDCM. Cardiac TnT and PLN were chosen because their altered expression has been observed in IDCM-affected birds. A total of 72 birds, 44 affected and 28 unaffected with TIDCM, were used. Differences in the mRNA levels of cTnT and PLN between affected and unaffected turkeys were significant only for cTnT. The sequence of the turkey PLN showed significant similarity at the nucleotide level to the reference chicken sequence and to those of other species. In addition to implicating cTnT in TIDCM, the present work describes a partial turkey PLN coding sequence that could be useful for future studies.

An outbreak of wound infection in cardiac surgery patients caused by Enterobacter cloacae arising from cardioplegia ice

This paper describes an outbreak of postoperative sternal wound infections. A cardiac surgeon noted a cluster of serious infections leading to wound dehiscence, despite the fact that none of his colleagues had noticed a rise in infection rates. The infections were predominantly with Enterobacter cloacae, and molecular typing and serotyping showed these isolates to be indistinguishable. Observation of the surgeon's practice revealed nothing untoward, and there were no infections among his patients operated on in another hospital. There appeared to be no significant difference between the modes of operation of the different surgeons. The operating theatres were screened to exclude an environmental source, with samples cultured on CHROMagar Orientation, a selective/differential medium designed for urine samples. Further questioning revealed one difference between the practices of the different surgeons; this surgeon used semi-frozen Hartmann's solution to achieve cardioplegia. The freezer used for this was swabbed and yielded E. cloacae, indistinguishable from the clinical isolates. It is hypothesized that this organism contaminated the freezer, and that the contamination was passed on to the ice/slush solution, thus infecting the patients. There have been no more cases since the freezer was replaced, a rigorous cleaning schedule instituted, and steps taken to reduce the possibility of any further contamination.

Mutation analysis of the aggrecan gene in chickens with tibial dyschondroplasia

Expression studies suggest that the incidence and severity of tibial dyschondroplasia (TD) in chickens, Gallus gallus, may be affected by the aggrecan gene, AGC 1. Here, results are described of a scan for single nucleotide polymorphisms (SNP) in AGC1 in genetic lines divergently selected for TD incidence in chickens. A total of 3,048 bp of DNA sequence obtained from amplicons produced by 4 primer-pairs designed from the GenBank AGC1 cDNA sequence were scanned for SNP. Among the 18 SNP detected and validated, only 2 were nonsynonymous. Allelic frequency differences between TD-affected and nonaffected birds were not statistically significant for all the SNP. The current results do not support an association of Gallus gallus AGC1 variation at the DNA level with the incidence of TD in chickens. The genomic resources described, however, including the SNP, could be useful in further evaluating AGC1 in other populations for association with TD or other skeletal abnormalities.

Thirty-two millimetre heads and accelerated polyethylene wear in total hip arthroplasty

In total hip arthroplasty 32 mm heads are often used as the greater diameter is thought to contribute to improved stability. However, greater head diameter can also lead to greater volumetric wear. We compared polyethylene wear between patients with 32 mm heads and those with smaller heads. All patients who had Harris Galante1 metal-backed, uncemented cups inserted between 1986 and 1996 at our institute were annually reviewed clinically and radiographically. Accelerated polyethylene wear was noted between the fifth and seventh postoperative year in 17 out of 165 total hip replacements with 32 mm heads, but only in 21 out of 961 total hip arthroplasties with smaller femoral heads. In all 17 THRs, accelerated wear was also associated with thin polyethylene (<6 mm). This paper highlights a potentially serious problem. When 32 mm metal heads are used with uncemented cups and polyethylene liners, there is a risk of accelerated acetabular wear in patients with thin polyethylene.

A regular period for Saturn's magnetic field that may track its internal rotation

The rotation rate of a planet is one of its fundamental properties. Saturn's rotation, however, is difficult to determine because there is no solid surface from which to time it, and the alternative 'clock'--the magnetic field--is nearly symmetrically aligned with the rotation axis. Radio emissions, thought to provide a proxy measure of the rotation of the magnetic field, have yielded estimates of the rotation period between 10 h 39 min 22 s and 10 h 45 min 45 s (refs 8-10). Because the period determined from radio measurements exhibits large time variations, even on timescales of months, it has been uncertain whether the radio-emission periodicity coincides with the inner rotation rate of the planet. Here we report magnetic field measurements that revealed a time-stationary magnetic signal with a period of 10 h 47 min 6 s +/- 40 s. The signal appears to be stable in period, amplitude and phase over 14 months of observations, pointing to a close connection with the conductive region inside the planet, although its interpretation as the 'true' inner rotation period is still uncertain.

The crescent sign: dissociation of the polyethylene liner from a modular acetabular component in total hip arthroplasty

OBJECTIVE

To study whether there was a common pattern of clinical symptoms, signs and radiographic features for the dissociation of the polyethylene liner from an acetabular component and to postulate reasons for these features.

DESIGN AND PATIENTS

Retrospective study of notes and radiographs of cases of revision hip arthroplasty for polyethylene liner dissociation of the cementless Harris-Galante I porous-coated acetabular component (Zimmer Inc, Warsaw, IN) at the Avon Orthopaedic Centre, Bristol, UK and St. Mary's Hospital, Bristol, UK between 1995 and 2004. Patients were contacted to confirm preoperative symptoms.

RESULTS

Nine cases of late polyethylene liner dissociation of this prosthesis have been revised in these institutions. All patients presented with a reduction in mobility, groin pain and limp. Eight patients reported an audible noise on hip movement. In all cases, radiographs showed radiolucency medial to the femoral neck in association with an eccentrically placed femoral head showing contact with the acetabular metal shell, which we have termed the "crescent sign."

CONCLUSIONS

There is a typical clinical presentation in this study. The diagnosis can be made from a single anteroposterior pelvic radiograph without the need for previous films for comparison, or the need for arthrography. Clinicians should look specifically for the crescent sign when an eccentrically placed femoral head has been noted, in order to differentiate the more unusual diagnosis of dissociation from that of polyethylene wear. Early revision surgery can prevent damage to the femoral head and metal acetabular shell, thus reducing the complexity of revision surgery.

Free energy of solvation of simple ions: Molecular-dynamics study of solvation of Cl− and Na+ in the ice/water interface

Molecular-dynamics simulations of Cl(-) and Na(+) ions are performed to calculate ionic solvation free energies in both bulk simple point-charge/extended water and ice 1 h at several different temperatures, and at the basal ice 1 h/water interface. For the interface we calculate the free energy of "transfer" of the ions across the ice/water interface. For the ions in bulk water in the NPT ensemble at 298 K and 1 atm, results are found to be in good agreement with experiments, and with other simulation results. Simulations performed in the NVT ensemble are shown to give equivalent solvation free energies, and this ensemble is used for the interfacial simulations. Solvation free energies of Cl(-) and Na(+) ions in ice at 150 K are found to be approximately 30 and approximately 20 kcal mol(-1), respectively, less favorable than for water at room temperature. Near the melting point of the model the solvation of the ions in water is the same (within statistical error) as that measured at room temperature, and in the ice is equivalent and approximately 10 kcal mol(-1) less favorable than the liquid. The free energy of transfer for each ion across ice/water interface is calculated and is in good agreement with the bulk observations for the Cl(-) ion. However, for the model of Na(+) the long-range electrostatic contribution to the free energy was more negative in the ice than the liquid, in contrast with the results observed in the bulk calculations.

Potentially toxic metals in ombrotrophic peat along a 400 km English-Scottish transect

Four samples of ombrotrophic peat were collected from each of 10 upland locations in a transect from the southern Pennines to the Highland Boundary Fault, a total distance of ca. 400 km. Bulk compositions and other properties were determined. Total contents of Al and heavy metals (Ni, Cu, Zn, Cd, Pb) were determined following digestion with hydrofluoric acid, and concentrations of metals extractable with dilute nitric acid were also measured. Supernatants obtained from aqueous extractions of the peat samples were analysed for pH, major cations and anions, dissolved organic carbon and dissolved metals, and concentrations of free metal ions (Al(3+), Ni(2+), etc.) were estimated by applying a chemical speciation model. Both total and HNO(3)-extractable metal concentrations varied along the transect, the highest values being found at locations close to industrial and former mining areas. The HNO(3)-extractable soil metal contents of Ni, Cu and Cd were appreciably lower than lowest-observed-effect-concentrations (LOEC) for toxicity towards microorganisms in acid, organic rich soils. However, the contents of Zn at two locations, and of Pb at five locations exceeded LOECs, suggesting that they may be exerting toxic effects in the peats. Soil solution concentrations of free heavy metal ions (Cu(2+), Zn(2+), Cd(2+), Pb(2+)) were substantially lower than LOECs for toxicity towards vascular plants, whereas concentrations of Al(3+) were near to toxic levels at two locations.

Cassini Magnetometer Observations During Saturn Orbit Insertion

Cassini's successful orbit insertion has provided the first examination of Saturn's magnetosphere in 23 years, revealing a dynamic plasma and magnetic environment on short and long time scales. There has been no noticeable change in the internal magnetic field, either in its strength or its near-alignment with the rotation axis. However, the external magnetic field is different compared with past spacecraft observations. The current sheet within the magnetosphere is thinner and more extended, and we observed small diamagnetic cavities and ion cyclotron waves of types that were not reported before.

Kinematic geometry of osteotomies

This paper presents a novel method for defining an osteotomy that can be used to represent all types of osteotomy procedures. In essence, we model an osteotomy as a lower-pair mechanical joint to derive the kinematic geometry of the osteotomy. This method was implemented using a commercially available animation software suite in order to simulate a variety of osteotomy procedures. Two osteotomy procedures are presented for a femoral malunion in order to demonstrate the advantages of our kinematic model in developing optimal osteotomy plans. The benefits of this kinematic model include the ability to evaluate the effects of various kinds of osteotomy and the elimination of potentially error-prone radiographic assessment of deformities.

A reverse perfusion pattern during Technetium-99m stress myocardial perfusion imaging does not predict flow limiting coronary artery disease

BACKGROUND

A reverse redistribution pattern during myocardial perfusion imaging is most widely described using thallium (Tl-201), when stress images exhibit greater perfusion than rest. Technetium (Tc-99 m) radiopharmaceuticals may also yield a reverse perfusion (RP) pattern, but its significance is uncertain. This study tested the hypothesis that RP correlates with the presence and location of flow limiting coronary stenosis(es).

METHOD

We reviewed 842 consecutive Tc-99 m tetrofosmin SPECT stress studies performed at a cardiothoracic centre over a 15 month period. 69 (8.2%) demonstrated RP. Thirty-three patients (age 32-79 mean 56, 17 female) had undergone cardiac catheterisation within 12 months of the scan. Correlation was sought between the presence and location of angiographic stenoses and RP pattern.

RESULTS

10/33 (30.3%) had significant (>60%) coronary stenosis(es); 5 single-vessel, 2 two-vessel and 3 three-vessel disease (3VD). Stenosis location correlated poorly with the RP territory (LAD/Anterior 5/17, RCA/Inferior 1/10, Cx/lateral 0/4 (p = 0.57)). Of the 6 patients with a lesion in the RP territory, 3 had 3VD; 2 of these had a simultaneous reversible defect. All 5 patients with previous myocardial infarction had a simultaneous fixed defect. However only 3/12 with co-existent reversible defects had significant disease.

CONCLUSION

The reverse perfusion pattern is a poor predictor of flow limiting coronary disease, and does not correlate with stenosis location in those with significant lesions. Such patients should not undergo invasive investigation purely on the basis of this result.

Trochlear resurfacing for extensor mechanism instability following patellectomy

Patellectomy may in some cases result in persistent pain, weakness and instability of the knee. We report on three patients who had extensor tendon instability and were treated by trochlear resurfacing and extensor tendon realignment. All three cases achieved pain relief and an impressive improvement in knee function.

Preliminary linkage map of the turkey (Meleagris gallopavo) based on microsatellite markers

The turkey is an agriculturally important species for which, until now, there is no published genetic linkage map based on microsatellite markers--still the markers most used in the chicken and other farm animals. In order to increase the number of markers on a turkey genetic linkage map we decided to map new microsatellite sequences obtained from a GT-enriched turkey genomic library. In different chicken populations more than 35-55% of microsatellites are polymorphic. In the turkey populations tested here, 43% of all turkey primers tested were found to be polymorphic, in both commercial and wild type turkeys. Twenty linkage groups (including the Z chromosome) containing 74 markers have been established, along with 37 other unassigned markers. This map will lay the foundations for further genetic mapping and the identification of genes and quantitative trait loci in this economically important species. Genome comparisons, based on genetic maps, with related species such as the chicken would then also be possible. All primer information, polymerase chain reaction (PCR) conditions, allele sizes and genetic linkage maps can be viewed at http://roslin.thearkdb.org/. The DNA is also available on request through the Roslin Institute.

The Sun and Heliosphere at Solar Maximum

Recent Ulysses observations from the Sun's equator to the poles reveal fundamental properties of the three-dimensional heliosphere at the maximum in solar activity. The heliospheric magnetic field originates from a magnetic dipole oriented nearly perpendicular to, instead of nearly parallel to, the Sun's rotation axis. Magnetic fields, solar wind, and energetic charged particles from low-latitude sources reach all latitudes, including the polar caps. The very fast high-latitude wind and polar coronal holes disappear and reappear together. Solar wind speed continues to be inversely correlated with coronal temperature. The cosmic ray flux is reduced symmetrically at all latitudes.

Predicting the release of metals from ombrotrophic peat due to drought-induced acidification

Ombrotrophic peats in northern England and Scotland, close to industrial areas, have substantial contents of potentially toxic metals (Al, Ni, Cu, Zn, Cd and Pb) and of pollutant sulphur, all derived from atmospheric deposition. The peat sulphur, ordinarily in reduced form, may be converted to sulphuric acid under drought conditions, due to the entry of oxygen into the peats. The consequent lowering of soil solution pH is predicted to cause the release of metals held on ligand sites of the peat organic matter. The purpose of the present study was to explore, by simulation modelling, the extent of the metal response. Chemical variables (elemental composition, pH, metal contents) were measured for samples of ombrotrophic peats from three locations. Water extracts of the peats, and samples of local surface water, were also analysed, for pH, dissolved organic carbon (DOC) and metals. Metal release from peats due to acidification was demonstrated experimentally, and could be accounted for reasonably well using a speciation code (WHAM/Model VI). These data, together with information on metal and S deposition, and meteorology, were used to construct a simple description of peat hydrochemistry, based on WHAM/Model VI, that takes into account ion-binding by humic substances (assumed to be the "active" constituents of the peat with respect to ion-binding). The model was used to simulate steady state situations that approximated the observed soil pH, metal pools and dissolved metal concentrations. Then, drought conditions were imposed, to generate increased concentrations of H2SO4, in line with those observed during the drought of 1995. The model calculations suggest that the pH will decrease from the initial steady state value of 4.3 to 3.3-3.6 during rewetting periods following droughts, depending upon assumptions about the amount of potentially mobile soil S. The pH decreases will be accompanied by increases in concentrations of dissolved metals (Mg, Al, Ca, Ni, Cu, Zn, Cd, Pb) of an order of magnitude or more, depending upon assumptions about the replenishment of soil metal pools by deposition. In the most realistic scenario for present conditions, the severity of pH depressions will gradually decline due to the relatively slow depletion of the soil S pool by droughts. However, the magnitudes of heavy metal pulses will decline quite rapidly (over two or three droughts) because current and future metal deposition is unable to compensate for leaching losses from the soil pools.

Femoral impaction grafting in revision hip arthroplasty with irradiated bone

We evaluated the results of femoral impaction grafting with the Exeter stem (Stryker Howmedica Osteonics, Newbury, UK) and irradiated bone-graft. We followed 57 hips for an average of 27 months. Endo-Klinik grading showed 8 grade 1, 22 grade 2, and 27 grade 3 hips. Radiographic analysis revealed cortical repair in 34% and graft incorporation in 39% but no evidence of trabecular remodeling. Moderate subsidence (5-10 mm) occurred in 7 patients (12.5%), and massive subsidence (>10 mm) occurred in 4 patients (7%). Complications included 6 dislocations, 3 periprosthetic fractures, and 2 stem revisions. Impaction grafting with the Exeter system produces satisfactory results for most patients, but a few hips perform poorly, and the reasons for this are unclear. We have concerns about irradiated bone-graft because the characteristic changes of graft remodeling are not seen.

Concentration of immnoglobulin G in plasma varies among 6C.7 recombinant congenic strains of chickens

Chicken Lines 63 and 72 were inbred during selection for resistance or susceptibility to viral-induced tumors. A sandwich ELISA assay was adapted to define the milligrams per milliliter of Ig-gamma (IgG) in plasma from chickens of Lines 63 and 72, as well as 19 recombinant congenic strains (RCS). Each RCS resulted from a 7(2) x 6(3) F(1) and two backcross matings using 63 as the recurrent female line. The IgG levels in the RCS were evaluated after four to seven generations of sib-matings, when each RCS was becoming inbred and fixed for a different 12.5% of the 72 genome. In three generations approximately 24-wk-old chickens of Line 72 had higher levels of plasma IgG than chickens of Line 63 (P < 0.05). None of the RCS had repeatable IgG levels comparable to Line 7(2). However, in the last two generations, two of the 18 RCS had higher IgG levels than nine with low IgG levels (P < 0.05). There was no correlation between an IgG level of a RCS and resistance to Marek's disease. It was concluded that selected RCS may be useful for identifying genes that determine differences in IgG levels, as well as for understanding the relationship between genes, IgG levels, and other traits that differ between Lines 63 and 72.

Comparative DNA sequence analysis of genetic variation in the African grey parrot, Psittacus erythacus

Comparative genome analysis promises to provide an insight into avian species that have been very little studied. To test the feasibility of this approach, we investigated the use of heterologous primers to generate single nucleotide polymorphisms (SNP) in the African grey parrot, Psittacus erythacus, using primers specific for chicken and turkey DNA fragments. Three of the primers were specific for three expressed sequence tagged sites in the turkey and the fourth for a chicken proteoglycan core protein-like DNA sequence. A total of about 2200 bp of the parrot genome was evaluated for DNA sequence variation. Seven SNPs were identified and confirmed by Mendelian segregation. The frequency distribution of the most common nucleotide at each SNP locus in an unrelated group of parrots ranged from 0.84 to 0.97. The percent similarity of each parrot sequence to the reference sequence was inconsistent and ranged from zero to 100%. The primers as well as the nucleotide variants described represent valuable resources for genetic analysis in the parrot.

Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides

Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey.

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.