A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations

Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed ( G _{VR ‐O} ) or the base population ( G _{VR ‐B} ) allele frequencies and (ii) identity by descent using linkage analysis ( G _{IBD ‐L} ). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. G _{IBD ‐L} displayed the lowest sampling error and the highest correlation with true genome‐shared values. G _{VR ‐B} approximated G _{IBD ‐L} 's correlation and had lower error than G _{VR ‐O} . Accuracy of GEBV for selection candidates was significantly higher when G _{IBD ‐L} was used and identical between G _{VR ‐O} and G _{VR ‐B} . In real data, G _{IBD ‐L} 's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.     

Selecting a healthy diet score: lessons from a study of diet and health in early old age (the Boyd Orr cohort)

OBJECTIVES: To describe the selection and modification of an appropriate diet score to assess diet quality in early old age. DESIGN AND SETTING: Cross-sectional analyses of the Boyd Orr cohort - a long-term follow-up of men and women whose families took part in a survey of diet and health in pre-war Britain. Dietary data were obtained from a 113-item food-frequency questionnaire. A nine-item Healthy Diet Indicator (HDI) developed by Huijbregts and colleagues was identified from the literature and modified because some dietary variables were unavailable and to accord more closely with recommendations of the UK Committee on Medical Aspects of Food Policy. SUBJECTS: In total, 1475 traced, surviving cohort members aged 60 years and over. RESULTS: Modification resulted in a 12-item Healthy Diet Score (HDS). We found that about half the variation in the HDS was explained by variation in the HDI (r=0.71). There was, however, little misclassification of subjects (<10%) into extreme thirds of the distribution by the HDS compared with the HDI. Items of the score most strongly correlated with overall score were saturated fat (r=-0.57), red meat (r=-0.46), dietary fibre (r=0.58), fruit and vegetables (r=0.54) and percentage energy from carbohydrates (r=0.51). Modifying existing items had greater impact on agreement between HDI and HDS than the addition of new items. CONCLUSIONS: The selection and modification of diet scores is more complicated than often assumed. Furthermore, modest changes to an existing score can produce a score that is different from the original, and although it was not possible to test this issue, it may no longer predict subsequent health experience.     

Incidence of Unilateral Fertilizations after Low Dose Deep Intrauterine Insemination in Spontaneously Ovulating Sows under Field Conditions

A new procedure for non-surgical deep intrauterine insemination (DUI) in unrestrained sows hormonally induced to ovulate, has been reported. In comparison with standard artificial insemination (AI), with this procedure, the sperm numbers inseminated can be reduced 20-fold without reducing the reproductive performance of these hormonally treated sows. The present study evaluated, using two experiments, the reproductive performance applying 20-fold different sperm numbers per AI dose using DUI or standard AI in spontaneously ovulating sows, under field conditions. In experiment 1, AI was applied to crossbred sows at 12, 24 and 36 h after onset of spontaneous oestrus using one of the following two regimes: (i) DUI (treatment) with 0.15 x 10(9) fresh boar spermatozoa in 5 ml of Beltsville thawing solution (BTS) extender (n = 95), and (ii) standard cervical AI (control) with 2.85 x 10(9) fresh spermatozoa in 95 ml of BTS extender (n = 95). The farrowing rates of the two groups of sows were statistically similar (NS). However, a decrease (p < 0.002) in litter size and the total number of pigs born alive was observed in sows inseminated with the DUI procedure. In experiment 2, 42 post-weaned oestrus sows were inseminated following the same design described for experiment 1 during spontaneous oestrus. On day 6 after onset of oestrus, the proximal segment of the uterine horns of the sows were flushed under surgery to retrieve eventual embryos and evaluate the success of fertilization per cornua (e.g. occurrence of effective uni- vs bilateral sperm transport rendering uni- or bilateral, complete or partial fertilization). Retrieved embryos were assessed for cleavage and number of accessory spermatozoa. Although identical overall pregnancy rates were achieved in both insemination groups, the percentage of sows with partial bilateral fertilization and unilateral fertilization was markedly higher (p < 0.05) in the DUI group (35%) compared with the control (standard AI) group (5%), with a consequent lower (p < 0.001) percentage of viable early embryos after DUI. The number of accessory spermatozoa in the zona pellucida of the embryos was highly variable, but higher (p < 0.001) in control animals than in DUI-AI. No accessory spermatozoa were found in oocytes retrieved from sows depicting unilateral fertilization. In conclusion, DUI in spontaneously ovulating sows with 0.15 x 10(9) spermatozoa renders similar farrowing rates but a lower litter size compared with use of standard AI with a 20-fold higher sperm dose. The lower litter size ought to be related to a decreased distribution of spermatozoa after DUI leading to a higher incidence of partial bilateral and unilateral fertilization.     

Meningoencephalomyelitis in a foal due to Salmonella agona infection

CASE HISTORY: A neonatal Thoroughbred foal was presented with rib fractures and left forelimb lameness secondary to dystocia.

CLINICAL FINDINGS: The foal developed a head tilt, seizures and watery diarrhoea during hospitalisation and died at 7 days of age. Histological examination of the brain and spinal cord revealed a suppurative meningoencephalomyelitis with vasculitis, and numerous intralesional, gram-negative bacilli. Similar microscopic lesions were noted in the lungs, renal medullary interstitium, and umbilicus. Bacilli in the brain, spinal cord and umbilicus were identified immunohistochemically as Salmonella group B. Salmonella agona was isolated in pure culture from the brain, lung, liver, kidney, and intestine.

CONCLUSION: This is the first report of meningoencephalomyelitis and septicaemia due to Salmonella infection in an equine neonate.     

Biogeochemical evidence for dinoflagellate ancestors in the early cambrian

Dinoflagellates are single-celled organisms that reflect the ecological conditions in modern oceans and lakes. Ultrastructural data and molecular phylogeny suggest that they originated in the Neoproterozoic, yet dinoflagellate ancestors are classified only to the Middle Triassic ( approximately 240 million years ago). Examination of dinoflagellate-specific biological markers (dinosteranes and 4alpha-methyl-24-ethylcholestane) in concentrated microfossils with known morphology identified ancient dinoflagellate ancestors from the Early Cambrian ( approximately 520 million years ago).     

Modulation of diversity by grazing and mowing in native tallgrass prairie

Species diversity has declined in ecosystems worldwide as a result of habitat fragmentation, eutrophication, and land-use change. If such decline is to be halted ecological mechanisms that restore or maintain biodiversity are needed. Two long-term field experiments were performed in native grassland to assess the effects of fire, nitrogen addition, and grazing or mowing on plant species diversity. In one experiment, richness declined on burned and fertilized treatments, whereas mowing maintained diversity under these conditions. In the second experiment, loss of species diversity due to frequent burning was reversed by bison, a keystone herbivore in North American grasslands. Thus, mowing or the reestablishment of grazing in anthropogenically stressed grasslands enhanced biodiversity.     

Neptune's eccentricity and the nature of the kuiper belt

The small eccentricity of Neptune may be a direct consequence of apsidal wave interaction with the trans-Neptune population of debris called the Kuiper belt. The Kuiper belt is subject to resonant perturbations from Neptune, so that the transport of angular momentum by density waves can result in orbital evolution of Neptune as well as changes in the structure of the Kuiper belt. In particular, for a belt eroded out to the vicinity of Neptune's 2:1 resonance at about 48 astronomical units, Neptune's eccentricity can damp to its current value over the age of the solar system if the belt contains slightly more than an earth mass of material out to about 75 astronomical units.