The impact of population structure on genomic prediction in stratified populations

Key message

Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize.

Abstract

Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5 % of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65 % improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in genomic prediction.     

Helping patients travel by air.

Although safe and rapid, air travel may present problems for people with certain medical conditions. Most medical emergencies that occur during a flight are preventable by judicious screening and preparation. We provide guidelines for physicians who are consulted about the wisdom of undertaking a journey by air. Potential stresses before, during and after the flight are outlined, including decreased atmospheric pressure, low humidity, turbulence, inactivity and time changes. We recommend precautionary measures for passengers with certain medical conditions, such as recent myocardial infarction, pulmonary disorders, pneumothorax, cerebrovascular accidents and diabetes and for those who have recently had surgery. The policy regarding air travel for pregnant women varies with each airline, but for certain conditions associated with pregnancy supplemental oxygen should be ordered before the trip. The special equipment and care that most airlines offer to ill or disabled people are described.     

Sheep twin chimaeras with admixtures of red cell amino acid and potassium transport phenotypes

A pair of sheep twins each had two populations of red cells. Population 1 was positive for antigens Aa, Ma and Mb, was low-potassium type, possessed an amino acid transport system and was lysine-negative phenotype. Population 2 was negative for antigens Aa, and Mb, was high-potassium type, lacked the amino acid transport system and was lysine-positive phenotype. Population 2 disappeared from both sheep over a period of 8 years.     

Seasonality in cattle

Although cattle are basically not seasonal breeders, several physiological changes occur in response to two major climatic variables of season: ambient temperature and photoperiod. Ambient temperatures above 27°C lengthen the estrous cycle, decrease duration and intensity of estrus, decrease fertility and increase embryonic mortality. Some of these effects may be mediated via decreased secretion of luteinizing hormone and increased secretion of progesterone. Heat stress also suppresses growth rate, milk production and feed intake. In comparison with cattle exposed to less than 12 h of light per day, 14 to 16 h of light has relatively little effect on secretion of gonadotropins and fertility; however, growth rates, feed intake and milk yield are stimulated. Of all hormones measured in cattle, prolactin is the most responsive to changes in seasons, ambient temperature and photoperiod. Prolactin is greatest in summer when ambient temperatures are highest and photoperiods are longest.     

Light sensitivity of the ciliate Tetrahymena vorax induced by the fluorescent dye acridine orange

The ciliate Tetrahymena vorax is normally insensitive to light. However, after uptake of acridine orange, blue light evokes instant backward swimming. The dye accumulates mainly in posterior vacuoles, with half-maximal uptake after 1 min. Illumination for 10 s induced a depolarisation of approximately 15 mV lasting less than 2 s, followed by a sustained hyperpolarisation of approximately 20 mV. Deciliated cells displayed a similar response. The hyperpolarisation was linked to reduced membrane resistance, showed a reversal potential of approximately −55 mV and was blocked by 1 mmol l⁻¹ TEA. The rate of rise of electrically evoked Ca²⁺-spikes was reduced during the hyperpolarisation, which is compatible with elevated cytosolic Ca²⁺ concentration. This suggests that the hyperpolarisation may be caused by activation of Ca²⁺-sensitive K⁺ channels. The depolarisation was abolished in Ca²⁺-free medium, whereas the hyperpolarisation was unaffected. Illumination for 2 s, or prolonged stimulation restricted to the anterior part of the cell, induced depolarisation only. Illumination of the posterior part caused delayed hyperpolarisation with no preceding depolarisation. We conclude that the induced backward swimming is associated with Ca²⁺ influx through anterior channels, while Ca²⁺ released from intracellular stores activates K⁺ channels responsible for the delayed hyperpolarisation.     

The solubilization of the L and M antigens from sheep red cell membranes

The Lp, L1 and M antigens from sheep red cells were solubilized using the non-ionic detergent Triton X-100 in the presence of dithiothreitol. Recovery rates were improved when membranes were sonicated at 4 degrees C in the presence of the detergent; values in the range 16-25% (M) and 9-17% (Lp and L1) were achieved for recovery.     

Electron microscopic investigations of zymomonas mobilis cells grown in low and high glucose concentrations

Summary Zymomonas mobilis cells grown in the presence of low and high glucose concentrations were examined by electron microscopy. Using ultrathin sectioning and agar diffusion method, significant changes in morphology were observed. Although the fine structure resembles that of a typical gram-negative bacterium, changes in glucose concentration and phases of growth lead to large cell wall vesicle or blebs formation. The possible implications of this morphological change to glucose uptake and ethanol formation are discussed.     

Low acute hypoxic ventilatory response and hypoxic depression in acute altitude sickness

Persons with acute altitude sickness hypoventilate at high altitude compared with persons without symptoms. We hypothesized that their hypoventilation was due to low initial hypoxic ventilatory responsiveness, combined with subsequent blunting of ventilation by hypocapnia and/or prolonged hypoxia. To test this hypothesis, we compared eight subjects with histories of acute altitude sickness with four subjects who had been asymptomatic during prior altitude exposure. At a simulated altitude of 4,800 m, the eight susceptible subjects developed symptoms of altitude sickness and had lower minute ventilations and higher end-tidal PCO2's than the four asymptomatic subjects. In measurements made prior to altitude exposure, ventilatory responsiveness to acute hypoxia was reduced in symptomatic compared to asymptomatic subjects, both when measured under isocapnic and poikolocapnic (no added CO2) conditions. Diminution of the poikilocapnic relative to the isocapnic hypoxic response was similar in the two groups. Ventilation fell, and end-tidal PCO2 rose in both groups during 30 min of steady-state hypoxia relative to values observed acutely. After 4.5 h at 4,800 m, ventilation was lower than values observed acutely at the same arterial O2 saturation. The reduction in ventilation in relation to the hypoxemia present was greater in symptomatic than in asymptomatic persons. Thus the hypoventilation in symptomatic compared to asymptomatic subjects was attributable both to a lower acute hypoxic response and a subsequent greater blunting of ventilation at high altitude.