A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species

Background

With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods.

Results

For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations.

Conclusions

All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0087-7) contains supplementary material, which is available to authorized users.     

Direct measurement of oxygen consumption rate on the nematode Caenorhabditis elegans by using an optical technique

It is well known that aging and longevity strongly correlate with energy metabolism. The nematode Caenorhabditis elegans is widely used as an ultimate model of experimental animals. Thus, we developed a novel tool, which is constructed from an optical detector, using an indirect method that can measure simply the energy metabolism of C. elegans. If we measure the oxygen consumption rate using this optical tool, we can easily evaluate the activity of mitochondria as an index in the aging process. However, a direct measurement of the oxygen consumption rate of C. elegans exposed in air is thought to be impossible because of the high concentration of atmospheric oxygen and the small size of the animals. We demonstrate here that we can directly detect the oxygen consumption with a small number of animals (相似文献   

Differences in penetration routes and establishment rates of four entomopathogenic nematode species into four white grub species

We compared the penetration of the entomopathogenic nematodes Steinernema scarabaei (AMK001 strain), S. glaseri (NC1 strain), Heterorhabditis zealandica (X1 strain), and H. bacteriophora (GPS11 strain) into third-instars of the scarabs Popillia japonica, Anomala orientalis, Cyclocephala borealis, and Rhizotrogus majalis. When larvae were exposed to nematodes for 6-72 h larval mortality and nematode establishment rate and occasionally speed of kill often showed the same pattern within nematode-white grub combinations. But no two nematodes or white grub species had the same pattern for these observations for all white grub or nematode species, respectively. Mortality, establishment, and speed of kill followed a similar pattern for H. zealandica, S. glaseri, and S. scarabaei, but there was no clear relationship for H. bacteriophora. Significant nematode establishment was only observed after at least 48 h exposure in most nematode-white grub combinations. Faster establishment was observed only for H. zealandica in A. orientalis and R. majalis (after 24 h) and for S. scarabaei in P. japonica and R. majalis (after 12 h). Nematode establishment after 72 h in the different scarab species was generally low for S. glaseri (<1.5%) and H. bacteriophora (<3%), higher for H. zealandica (2-5%), and the highest for S. scarabaei (1-14%). However, in another experiment establishment was generally higher after 96h exposure. Nematode penetration sites were determined by comparing nematode establishment in larvae with mouth, anus, mouth+anus, or none sealed with glue. The trends for each nematode species were very similar in the different white grub species. H. zealandica and H. bacteriophora showed excellent cuticular penetration ability but may also penetrate through mouth and/or anus. S. glaseri also penetrated through the cuticle but lower establishment in larvae with mouth or mouth+anus sealed suggested that the mouth is an important penetration site. S. scarabaei showed a preference for the mouth as a penetration site, but it showed some cuticular penetration ability and may also use the anus as a penetration site. The methodology used cannot exclude that cuticular penetration also included penetration through the spiracles. To fully understand the effect of nematode and white grub species on nematode virulence, future studies will have to compare host immune response to the penetrating IJs and the role of the symbiotic bacteria in these interactions.     

A comparison of nematode-capturing efficiencies of fiveDactylella species at four temperatures

Conclusions The data and observations presented indicate that the factors controlling the nematode-capturing efficiency of predaceous fungi are complex. There seems to be little correlation between the ability to capture nematodes and the optimum growth rate of the capturing fungus, but there may be some relation between the motility of a nematode and the ease with which it may be captured. Since soil contains many fungi and nematodes competing for nutrients in fairly restricted spheres such as soil particles, bits of organic matter, or the rhizospheres of growing plants, the influence of a nematode-supporting fungus such asPenicillium digitatum on a predaceous fungus may be greater than the direct effect of some nematode upon the predaceous fungus or vice versa.     

A study on enzymatic reaction using a liquid emulsion membrane technique

An enzymatic reaction using a liquid emulsion membrane technique was studied to investigate the effects of some experimental variables on the stability of liquid membrane, enzyme deactivation, and transport of substrates and products. The hydrolysis of L-phenylalanine methyl ester by alpha-chymotrypsin was selected as a model reaction system. First, a transport mechanism for the substrates and products across the membrane was qualitatively identified. Second, it was found that the pH of the internal phase was one of the most important variables to determine the enzyme activity in a liquid membrane. Third, the effect of membrane phase which consists of surfactant, carrier, and organic solvent on the emulsion stability was investigated. It was found that the properties of the organic solvents greatly affect the emulsion stability. For an optimum condition, it was possible to reuse the emulsion which consists of membrane phase and internal phase without further separation. It was finally concluded that the enzyme in a liquid membrane retained 60% of its native activity in spite of vigorous mixing during the emulsification step.     

Galactose-1-phosphate uridyltransferase of lemurs: A comparison of four species

Erythrocyte galactose-1-phosphate uridyltransferase (Gal-1-PUT) was studied in four species of lemurs. Electrophoretic phenotypes of Lemur fulvusand Lemur macacowere indistinguishable and different from the phenotypes of Lemur cattaand Lemur variegatus,which were different from each other. Enzymatic activity of hemolysates was species specific, with that of Lemur variegatusabout twice that of either Lemur fulvusor Lemur macacoand almost three times that of Lemur catta.Only minor interspecific differences were demonstrated in pH optima and k_m for galactose-1-phosphate; however, thermal stability varied considerably with phenotype. Antibody inhibition studies indicated that differences in enzyme activity of hemolysates from these species are probably due to differences in enzyme concentration.     

Cognitive representation in transitive inference: A comparison of four corvid species

During operant transitive inference experiments, subjects are trained on adjacent stimulus pairs in an implicit linear hierarchy in which responses to higher ranked stimuli are rewarded. Two contrasting forms of cognitive representation are often used to explain resulting choice behavior. Associative representation is based on memory for the reward history of each stimulus. Relational representation depends on memory for the context in which stimuli have been presented. Natural history characteristics that require accurate configural memory, such as social complexity or reliance on cached food, should tend to promote greater use of relational representation. To test this hypothesis, four corvid species with contrasting natural histories were trained on the transitive inference task: pinyon jays, Gymnorhinus cyanocephalus; Clark's nutcrackers, Nucifraga columbiana; azure-winged magpies, Cyanopica cyanus; and western scrub jays, Aphelocoma californica. A simplified computer model of associative representation displayed a characteristic pattern of accuracy as a function of position in the hierarchy. Analysis of the deviation of each subject's performance from this predicted pattern yielded an index of reliance on relational representation. Regression of index scores against rankings of social complexity and caching reliance indicated that both traits were significantly and independently associated with greater use of relational representation.     

A new nematode trapping species of Dactylaria

Summary The paper deals with the isolation of a new predacious fungusDactylaria dasguptaiiShome &Shome from Indian soil. The fungus has been studied both in culture and soil. The predatory, morphological and reproductive characters of the new species accompanied by latin diagnosis has been described with illustrative diagrams.     

Rapid renaturation of denatured and aggregated proteins using liquid paraffin as a pseudolipid bilayer membrane

A means of rapidly renaturing denatured protein was devised and evaluated. Three liquids were laminarly layered in a centrifuge tube, in which two solutions sandwiched liquid paraffin so as to form a pseudolipid bilayer. Denatured and aggregted protein placed on the upper surface of liquid paraffin was renatured as it passed through liquid-paraffin layer into the renaturation buffer during the centrifugation. The aggregated and denatured protein selectively passed through the liquid-paraffin layer, whereas other solutions, such as chaotropic agents or organic solvent, could not. This means that a rapid dilution condition favorable for protein renaturation was realized in a small scale. Aggregated and denatured BSA and ribonuclease A were renatured and resolubilized as they passed through the liquid-paraffin layer into an appropriate renaturation buffer solution. This method was also applied to the rapid heme reconstitution of myoglobin from Feprotoporphyrin IX to Zn-protoporphyrin IX. (c) 1994 John Wiley & Sons, Inc.     

Response of liquid flow resistance to soil drying in seedlings of four deciduous angiosperms

Summary Soil-leaf resistance to liquid water flow (R) in moist and drying soil was compared in three-month-old seedlings of two drought tolerant (white [Quercus alba L.], post oak [Q. stellata Wangenh.]) and two drought sensitive forest species (sugar maple [Acer saccharum Marsh.], black walnut [Juglans nigra L.]). At high soil moisture (_s–0.3 MPa), R was higher in J. nigra than in the other species, and as soil water was depleted R increased most in this species. In contrast, the lowest resistance at all levels of soil moisture was observed in Q. stellata. At _s of –1.5 MPa, R of drought-sensitive J. nigra and A. saccharum was about twice as high as that of the two drought-tolerant Quercus species. The difference in R between the two Quercus species was much smaller than that between this pair and the other two species. These differences among species in flow resistance may be attributable to: 1) variation in the balance between root surface area and leaf area, 2) variation in the inherent absorption capacity of the root systems and in xylem water conducting systems or 3) differences in root permeability, shrinkage and mortality in severely stressed seedlings. As the soil dried, seedlings of all species exhibited pronounced reductions in transpiration rate, which prevented development of large water potential gradients between leaves and the soil. Reduction in transpiration in J. nigra was especially pronounced, resulting in a decrease in the soil-to-leaf water potential gradient in dry soil despite high flow resistance. The observed differences among species in flow resistance are correlated with natural distribution patterns.     

Pattern of evolutionarily distinct species among four classes of animals and their conservation status: a comparison using evolutionary distinctiveness scores

The percentage of species with high evolutionary distinctiveness (ED) scores in four different classes was related to conservation concern. We considered the number of species belonging to the upper level of the distribution of ED scores, and the overall distribution of ED scores in each category of concern assigned by IUCN. Generalized linear and mixed models were used to explore the relationship between variables, separately for each animal class. Overall values of ED score were higher for Squamates, Rhynchocephalia and amphibians than mammals and birds. However, the frequency distribution of ED scores was similar among classes, with a leptokurtotic distribution. Amphibians, reptiles, birds and mammals showed a markedly right skewed distribution, with a similar proportion of species in each equal category of the distribution. In all classes, the number of species with the highest ED score (positioned in the upper 20% of the frequency distribution of the variable) was very small ranging between 0.01 and 0.05%. ED score was slightly but negatively correlated with IUCN conservation status in amphibians, but unrelated in the other three classes. The bird population trend was unrelated to ED score of bird species in both USA and Europe. Also, the population’s trend for selected mammal species was unrelated to the ED score of those species. Our results provide more evidence that distribution shape of ED of animal forms is uniform among classes, with only very few species characterized by highest ED scores in each group. Surprisingly, ED score and IUCN conservation status were unrelated in the four classes examined. Finally, our study underlines that declining animals are not necessarily the most evolutionarily distinct species.     

洗胃法与剖胃法在四种蛙食性分析中的对比

在动物的食性研究中,剖胃法因要杀死动物,会产生一系列的生态学影响和伦理学问题,在国际上招致了越来越多的反对,而在我国仍广泛使用。尽管洗胃法已用于食性研究,它的效果却从来没有研究过。我们应用洗胃法研究了浙江宁波郭巨镇四种蛙(黑斑蛙、泽蛙、金线蛙和中华蟾蜍)的食性,并与剖胃法所获得的食性结果进行比较。结果显示:尽管洗胃法在四种蛙胃内食物量的总洗出率(在94.50%以上)和食物个体数的洗出率上(均大于93.46%)略低于剖胃法,但胃内未洗出的与洗出的平均食物个体大小间无差异(所有P>0.3061),两种方法获得的四种蛙的平均食物量和食物个体数也无差异(对食物量所有P>0.8680,对食物个体数所有P>0.7923)。结果表明,洗胃法是比较精确的,在动物的食性研究中,应广泛地推广洗胃法,摒弃剖胃法     

Influence of the aeration rate on the yields of the biocontrol nematode Heterorhabditis megidis in monoxenic liquid cultures

The entomopathogenic nematode–bacterium complex Heterorhabditis megidis–Photorhabdus luminescens was cultured in 10-l internal loop bioreactors with marine impellers at aeration rates of 0.3 vvm and 0.7 vvm. Process parameters like impeller velocity and oxygen saturation were controlled at equal set points. The bacterial density was assessed at 24 h. Nematode dauer juveniles (DJ) were then inoculated and the development to adults after 8 days and final DJ yields after 16 days were recorded. The bacterial population density and the nematode inoculum development was variable and was not influenced by the aeration rate. A significant effect on the yield was recorded at the highest aeration rate. This result was confirmed by a direct comparison in two 5-l internal loop glass bioreactors at 0.3 vvm and 1.0 vvm, which were inoculated with nematode and bacterium pre-cultures from the same flask culture. Possible reasons for the positive correlation between aeration rate and DJ yield are discussed. Received: 27 September 1999 / Received revision: 21 January 2000 / Accepted: 23 January 2000     

Allozyme comparison of four littorinid species morphologically similar to Littorina sitkana

Eight species of the genus Littorina were hitherto recognised in the north-western region of the Pacific Ocean: L. sitkana, L. brevicula, L. mandshurica, L. squalida, L. aleutica, L. naticoides, L. kasatka and L. subrotundata. Using allozyme electrophoresis it has been demonstrated that, in the Kurile Islands, three of these species (L. sitkana, L. subrotundata and L. kasatka) co-occur, together with a fourth, still undescribed species (L. sp.). These four species were compared at 16 loci coding for 13 enzymes. All species were easily distinguished by diagnostic enzyme markers. The mean genetic distances and ranges between species pairs are: L. sitkana and L. sp. D = 0.622 (0.561–0.741), L. sitkana and L. subrotundata D=0.981 (0.821–1.110), L. subrotundata and L. sp. D=0.975 (0.955–0.995). The genetic distance between L. kasatka and each of the other three species was greater than 1 (range 1.123–2.087). These data suggest that L. sitkana, L. subrotundata and L. sp could be members of a species complex; according to current classifications these three belong to the subgenus Neritrema. However, the genetic distance between L. kasatka and L. sitkana is much greater than between L. sitkana and other Neritrema species, and thus supports the classification of L. kasatka in the subgenus Littorina.     

Monoxenic liquid culture of the entomopathogenic nematode Steinernema carpocapsae using a culture medium containing whey kinetics and modeling

The submerged culture of the entomopathogenic nematode Steinernema carpocapsae and its symbiotic bacterium, Xenorhabdus nematophila, was carried out in orbitally agitated bottles using a culture medium containing whey (in grams per litre: 500 whey, 20 yeast extract, 10 dried egg yolk-food grade, 3 sodium chloride, 37 corn oil-food grade). Maximum total viable nematode concentrations of 198,333ml(-1) were achieved within fermentations of 24 days with 64% of the nematode population within the infective juvenile stage (IJ) (126,666ml(-1)) at the end. The kinetics of the bioprocess was well modelled using the four-parameter Sigmoidal model and the corresponding maximum specific rates of nematode production (0.47 day(-1)), carbohydrates consumption (0.0008g(carbohydrates)g(nematodes)(-1)day(-1)) and nitrogen consumption (4.44g(nitrogen)g(nematodes)(-1)day(-1)) are first proposed. Besides, X. nematophila appears to have the capacity of lactose hydrolysis.     

A chemical and physical comparison of ferritin subunit species fractionated by high-performance liquid chromatography

Selected chemical and physical properties were measured for different forms of ferritin subunits which had been separated by reverse-phase high-performance liquid chromatography. Ferritin subunits from porcine spleen behaved, on sodium dodecyl sulfatepolyacrylamide gel electrophoresis, as though they were ~ M_r 2000 larger than equine spleen ferritin, whereas no difference in size was observed by gel chromatography in 6 m guanidinium chloride. All subunit species exhibited similar isoelectric focusing properties. In contrast to previous reports, no carbohydrate could be found associated with any of the isolated subunit species. Thus, the aberrant behavior of the porcine ferritin subunits between the two empirical molecular weight estimation methods appears to be the result of factor(s) other than protein intrinsic charge or covalently attached carbohydrate.     

The colorimetric estimation of protein by the Lowry technique using a liquid scintillation counter

A comparison has been made of the use of the spectrophotometer and liquid scintillation counter for the colorimetric quantification of protein. The attenuation of photon detection from sealed miniature ¹⁴C radioactive standards enabled protein quantification over a concentration range far in excess of that achievable by the use of a spectrophotometer. Accuracy of quantification was high over the entire range of protein concentration. The ability of the technique to provide quick and accurate protein estimations is discussed.     

A comparison of the predatory impacts of an invasive and native crab species using a functional response approach

The European green crab (Carcinus maenas) is invasive on the West coast of North America, but the ecological consequences of this invasion remain poorly understood. Comparative functional response analysis has arisen as a method of elucidating ecological consequences of invasive species by comparing the impact of these species to native analogues. Through comparative functional response experiments of green crabs and native red rock crabs (Cancer productus) we found that green crab predation increased asymptotically (Type II functional response) when fed increasing densities of Pacific oysters (Magallana gigas), while red rock crab predation displayed a sigmoidal (Type III) response. At high oyster densities red rock crabs consume more Pacific oysters than green crabs do, due to their reduced handling time, though green crabs consume more Pacific oysters relative to their size than red rock crabs. However, compared to red rock crabs, green crabs consume more oysters at low prey densities, which implies that they have a larger, potentially destabilizing impact on low densities of Pacific oysters. As green crabs continue to spread across the West coast of North America, Pacific oysters will face increased predation pressure. Our results show the advantage of using functional response analysis to compare density dependent predation between an invasive species and a native species to predict the ecological consequences of invasions.