Detection of genetic variants affecting cattle behaviour and their impact on milk production: a genome‐wide association study

Behaviour traits of cattle have been reported to affect important production traits, such as meat quality and milk performance as well as reproduction and health. Genetic predisposition is, together with environmental stimuli, undoubtedly involved in the development of behaviour phenotypes. Underlying molecular mechanisms affecting behaviour in general and behaviour and productions traits in particular still have to be studied in detail. Therefore, we performed a genome‐wide association study in an F₂ Charolais × German Holstein cross‐breed population to identify genetic variants that affect behaviour‐related traits assessed in an open‐field and novel‐object test and analysed their putative impact on milk performance. Of 37 201 tested single nucleotide polymorphism (SNPs), four showed a genome‐wide and 37 a chromosome‐wide significant association with behaviour traits assessed in both tests. Nine of the SNPs that were associated with behaviour traits likewise showed a nominal significant association with milk performance traits. On chromosomes 14 and 29, six SNPs were identified to be associated with exploratory behaviour and inactivity during the novel‐object test as well as with milk yield traits. Least squares means for behaviour and milk performance traits for these SNPs revealed that genotypes associated with higher inactivity and less exploratory behaviour promote higher milk yields. Whether these results are due to molecular mechanisms simultaneously affecting behaviour and milk performance or due to a behaviour predisposition, which causes indirect effects on milk performance by influencing individual reactivity, needs further investigation.     

Measurement of 7-dehydrocholesterol and cholesterol in hair can be used in the diagnosis of Smith-Lemli-Opitz syndrome

7-dehydrocholesterol (7-DHC) and cholesterol (CHOL) are biomarkers of Smith-Lemli-Opitz Syndrome (SLOS), a congenital autosomal recessive disorder characterized by elevated 7-DHC level in patients. Hair samples have been shown to have great diagnostic and research value, which has long been neglected in the SLOS field. In this study, we sought to investigate the feasibility of using hair for SLOS diagnosis. In the presence of antioxidants (2,6-ditert-butyl-4-methylphenol and triphenylphosphine), hair samples were completely pulverized and extracted by micro-pulverized extraction in alkaline solution or in n-hexane. After microwave-assisted derivatization with N,O-Bis(trimethylsilyl)trifluoroacetamide, the analytes were measured by GC-MS. We found that the limits of determination for 7-DHC and CHOL were 10 ng/mg and 8 ng/mg, respectively. In addition, good linearity was obtained in the range of 50–4000 ng/mg and 30–6000 ng/mg for 7-DHC and CHOL, respectively, which fully meets the requirement for SLOS diagnosis and related research. Finally, by applying the proposed method to real hair samples collected from 14 healthy infants and two suspected SLOS patients, we confirmed the feasibility of hair analysis as a diagnostic tool for SLOS. In conclusion, we present an optimized and validated analytical method for the simultaneous determination of two SLOS biomarkers using human hair.     

Sex ratios and sex-biased infection behaviour in the entomopathogenic nematode genus Steinernema

In experimentally infected insects, the sex ratio of first generation nematodes of five species of Steinernema was female-biased (male proportion 0.35-0.47). There was a similar female bias when the worms developed in vitro (0.37-0.44), indicating that the bias in these species is not due to a lower rate of infection by male infective juveniles (IJs). Experimental conditions influenced the proportion of males establishing in insects, indicating that male and female IJs differ in their behaviour. However, there was no evidence that males are the colonising sex in any species, contrary to what has previously been proposed. Time of emergence from the host in which the nematodes had developed influenced sex ratios in experimental infections. In three species (Steinernema longicaudum, Steinernema glaseri and Steinernema kraussei), early emerged nematodes had a higher proportion of males than those that emerged later, with the reverse trend for Steinernema carpocapsae and Steinernema feltiae. In a more detailed in vitro study of S. longicaudum, the proportion of males was similar whether or not the nematodes passed through the developmentally arrested IJ stage, indicating that the female bias is not due to failure of males to exit this stage. The sex ratio in vitro was independent of survival rate from juvenile to adult, and was female-biased even when all juveniles developed, indicating that the bias is not explained by failure of males to develop to adults. The female-biased sex ratio characteristic of Steinernema populations appears to be present from at least the early juvenile stage. We hypothesise that the observed female bias is the population optimal sex ratio, a response to cycles of local mate competition experienced by nematodes reproducing within insect hosts interspersed with periods of outbreeding with less closely related worms following dispersal.     

Confidence Intervals for the Risk Ratio in Cohort Studies under Inverse Sampling

Three simple interval estimates for the risk ratio in inverse sampling are considered. The first two interval estimates are derived on the basis of Fieller's Theorem and the delta method with the logarithmic transformation, respectively. The third interval estimate is derived on the basis of an F-test statistic proposed by BENNETT (1981) for testing equal probabilities of a disease between two comparison groups when the disease is rare. To evaluate the performance of these three methods, a Monte Carlo simulation is used to compare the actual coverage probability with the nominal confidence level for each method and to estimate the expected length of the corresponding confidence interval in a variety of situations. On the basis of the results found in the simulation, we have concluded that the method with the logarithmic transformation is either equivalent to or better than the other two methods for all situations considered here.     

Stress integrated tests and cytological analyses reveal Brassica villosa subsp. drepanensis seed quality decrease upon long-term storage

Under stress integrated germination test (SIGT), seeds undergo osmo-saline stresses, which enable to detect differences in vigour of long-term stored seeds with high germination percentage (G%). The quality of Brassica villosa subsp. drepanensis seeds stored in a genebank (at ? 20°C for 16 years) was compared with seeds at harvest by standard germination tests (GT), SIGT and cytogenetic analysis. No differences were detected in G% and mean germination time under GT. Conversely, SIGT performed with NaCl ? 0.9 MPa osmotic potential did not influence G% at harvest but reduced that of stored seeds, SIGT at ? 1.4 MPa reduced G% of both. Cytogenetic analysis showed reduction of mitotic index, appearance of chromosomal aberrations and smaller nucleoli in stored seeds compared with harvest seeds germinated in water. SIGT at ? 0.9 MPa had no effect on mitotic index, but increased chromosome aberrations and nucleoli number. SIGT at ? 1.4 MPa inhibited G% of harvest and stored seeds, reduced mitoses in harvest and completely prevented it in stored seeds. The results indicate that GT does not faithfully reflect the quality of stored seeds, with misinterpretation of their vigour, whereas SIGT and cytogenetical parameters are sensitive, reliable and inexpensive methods for early prediction of genetic erosion in germplasm banks.     

Modulation of Coordinated Activity across Cortical Layers by Plasticity of Inhibitory Synapses

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Female and male Texas cichlids (Herichthys cyanoguttatum) do not fight by the same rules

Selection usually acts differently on males and females duringintrasexual competition for resources and/or mates. Nevertheless,agonistic behavior has been examined both theoretically andempirically mostly in males. Our research questions whethermales and females follow the same rules of engagement in intrasexualcontests as predicted by the sequential assessment model (SAM).The SAM predicts negative correlations between contest intensityand duration and the magnitude of asymmetry in resource holdingpower (RHP) between the contestants, such that the most escalatedcontests are those between similarly endowed individuals. Westaged male and female intrasexual contests with varying degreesof body size asymmetry under a round robin design using themonogamous Texas cichlid fish (Herichthys cyanoguttatum) asa study case. We used Mantel's matrix analysis to compare howthe behavioral content, duration, structure, and outcome ofmale and female contests were affected by the relative bodysize of the contestants. In the case of males, relative sizein each contest predicted outcome, duration, and frequency ofconventional and escalated behaviors according to prevailingtheory. Female contest structure and outcome, however, werenot predicted by the relative size of contestants. We discussour results in terms of other asymmetries that might be importantin structuring female contests, and we propose potential approachesto study female–female aggression.     

Patterns and sources of variation in Daphnia phosphorus content in nature

It has recently been shown that Daphnia can vary in the phosphorus (P)-content of their body tissues, but the relative importance of genetic versus environmental causes for this variation is unexplored. We measured variation in P-content (as % body mass) of Daphnia from eight lakes and conducted experiments to contrast three sources of variation: interspecific variation, clonal variation and phenotypic plasticity. Daphnia P-content decreased with increasing seston C:P ratio across lakes. This relationship reflected both inter- and intraspecific variation. Daphnia parvula and D. dubia exhibited high P-content and were found in shallow lakes with low C:P seston, whereas D. pulicaria had low P-content and was found in deep, stratified lakes having high C:P seston. Populations of D. dentifera spanned this lake gradient and exhibited P-content that was negatively related to seston C:P. Evidence for phenotypic plasticity came from experiments with D. pulicaria and D. dentifera collected from a lake with P-deficient seston and fed a P-sufficient diet in the laboratory. In addition, populations of D. dentifera differed in P-content even after 7 d of feeding on P-sufficient resources, suggesting within-species clonal variation. However, mesocosm experiments revealed broad and surprisingly continuous variation in the P-content of individual clones of D. pulex (range 1.54–1.05%) and D. mendotae (1.51–1.07%) over a gradient in dietary C:P. The broad range in P-content exhibited by individual clones, acclimated for generations, suggests that variation in Daphnia P-content from laboratory experiments needs to be interpreted with caution. These results also show that phenotypic variation in response to environment can be a larger source of variation in P-content than genetic differences within or among species.     

Soil and plant tests for available sulfur in wetland rice soils

Summary Soil tests, plant performance, and plant tissue analyses were used to study the availability of sulfur to wetland rice in 30 Philippine soils. The critical concentrations of available sulfur by the calcium phosphate, lithium chloride, ammonium acetate, and hydrochloric acid extractions were 9, 25, 30, and 5 mg/kg, respectively. The critical total sulfur limits were 0.11% in the shoot at maximum tillering 0.055% in the straw at maturity, and 0.065% in the grain. The critical N:S ratio was 15 in the shoot at maximum tillering, 14 in the straw at maturity, and 26 in the grain. The critical sulfate-sulfur limit was 150 mg/kg in the shoot at maximum tillering and 100 mg/kg in the straw at maturity. The critical sulfate-sulfur/total sulfur percentage ratio was 15% in the shoot at maximum tillering and the straw at maturity. Plant performance, judged by appearance and yield of dry matter, straw, and grain, was generally poorer in the sulfur deficient soils than in the other soils. Although the calcium phosphate and ammonium acetate methods gave a better correlation between plant performance and available sulfur than the others, all four methods separated sulfur-deficient soils from non-deficient ones. The hydrochloric acid method merits further study because it is simple and versatile.     

A New Rank Test Against Ordered Alternatives in K-Sample Problems

The distribution-free test against ordered alternatives proposed by Jonckheere (1954) is based on the Kendall's rank correlation coefficient τ. A new rank test is proposed and illustrated with a numerical example. The proposed test is based on Spearman's σ and has similar functional structure as the Kruskal-Wallis test. A useful by-product is a test for departure from a trend.