Estimation of genetic parameters for test day records of dairy traits in the first three lactations

Application of test-day models for the genetic evaluation of dairy populations requires the solution of large mixed model equations. The size of the (co)variance matrices required with such models can be reduced through the use of its first eigenvectors. Here, the first two eigenvectors of (co)variance matrices estimated for dairy traits in first lactation were used as covariables to jointly estimate genetic parameters of the first three lactations. These eigenvectors appear to be similar across traits and have a biological interpretation, one being related to the level of production and the other to persistency. Furthermore, they explain more than 95% of the total genetic variation. Variances and heritabilities obtained with this model were consistent with previous studies. High correlations were found among production levels in different lactations. Persistency measures were less correlated. Genetic correlations between second and third lactations were close to one, indicating that these can be considered as the same trait. Genetic correlations within lactation were high except between extreme parts of the lactation. This study shows that the use of eigenvectors can reduce the rank of (co)variance matrices for the test-day model and can provide consistent genetic parameters.     

Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information

An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation.     

The endogenous neurotransmitter, serotonin, modifies neuronal nitric oxide synthase activities

Serotonin, an important neurotransmitter, is colocalized with neuronal nitric oxide synthase (nNOS), a homodimeric enzyme which catalyzes the production of nitric oxide (NO(.-)) and/or oxygen species. As many interactions have been reported between the nitrergic and serotoninergic systems, we studied the effect of serotonin on nNOS activities. Our results reveal that nNOS is activated by serotonin as both NADPH consumption and oxyhemoglobin (OxyHb) oxidation were enhanced. The generation of L-citrulline from L-arginine (L-Arg) was not affected by serotonin in the range of 0-200 microM, suggesting an additional production of oxygen-derived species. But 5-hydroxytryptamine (5HT) induced the formation of both O and H(2)O(2) by nNOS, as evidenced by electron paramagnetic resonance (EPR) and by using specific spin traps. Overall, these results demonstrate that serotonin is able to activate nNOS, leading to the generation of reactive oxygen species (ROS) in addition to the NO(.-) production. Such a property must be considered in vivo as various nNOS-derived products mediate different signaling pathways.     

Melatonin nitrosation promoted by NO*2; comparison with the peroxynitrite reaction

N-nitroso species have recently been detected in animal tissues. Protein N-nitrosotryptophan is the best candidate for this N-nitroso pool. N-nitrosation of N-blocked trytophan derivatives like melatonin (MelH) by N2O3 or peroxynitrite (ONOOH/ONOO- ) has been observed under conditions of pH and reagent concentrations similar to in vivo conditions. We studied the reaction of NO*2 with MelH. When NO*2 was synthesized by gamma-irradiation of aqueous neutral solutions of nitrate under anaerobic conditions, detected oxidation and nitration of MelH were negligible. In the presence of additional nitrite, when NO* was also generated, formation of 1-nitrosomelatonin increased with nitrite concentration. Nitrosation is not due to N2O3 but could proceed via successive additions of NO*2 and NO*. For comparison, peroxynitrite was infused into a solution of MelH under air leading to the same products as those detected in irradiated solutions but in different proportions. In the presence of additional nitrite, the formation of nitroderivatives increased significantly while N-formylkynuramine and 1-nitrosomelatonin were maintained at similar levels. Mechanistic implications are discussed.     

Rabies diagnosis for developing countries

Background

Canine rabies is a neglected disease causing 55,000 human deaths worldwide per year, and 99% of all cases are transmitted by dog bites. In N''Djaména, the capital of Chad, rabies is endemic with an incidence of 1.71/1,000 dogs (95% C.I. 1.45–1.98). The gold standard of rabies diagnosis is the direct immunofluorescent antibody (DFA) test, requiring a fluorescent microscope. The Centers for Disease Control and Prevention (CDC, Atlanta, United States of America) developed a histochemical test using low-cost light microscopy, the direct rapid immunohistochemical test (dRIT).

Methodology/Principal Findings

We evaluated the dRIT in the Chadian National Veterinary Laboratory in N''Djaména by testing 35 fresh samples parallel with both the DFA and dRIT. Additional retests (n = 68 in Chad, n = 74 at CDC) by DFA and dRIT of stored samples enhanced the power of the evaluation. All samples were from dogs, cats, and in one case from a bat. The dRIT performed very well compared to DFA. We found a 100% agreement of the dRIT and DFA in fresh samples (n = 35). Results of retesting at CDC and in Chad depended on the condition of samples. When the sample was in good condition (fresh brain tissue), we found simple Cohen''s kappa coefficient related to the DFA diagnostic results in fresh tissue of 0.87 (95% C.I. 0.63–1) up to 1. For poor quality samples, the kappa values were between 0.13 (95% C.I. −0.15–0.40) and 0.48 (95% C.I. 0.14–0.82). For samples stored in glycerol, dRIT results were more likely to agree with DFA testing in fresh samples than the DFA retesting.

Conclusion/Significance

The dRIT is as reliable a diagnostic method as the gold standard (DFA) for fresh samples. It has an advantage of requiring only light microscopy, which is 10 times less expensive than a fluorescence microscope. Reduced cost suggests high potential for making rabies diagnosis available in other cities and rural areas of Africa for large populations for which a capacity for diagnosis will contribute to rabies control.     

Intervention by nitric oxide, NO, and its oxide derivatives particularly in mammals

Nitric oxide (NO) is a natural and stable free radical produced in soil and water by the bacteriological reduction of nitrites and nitrates and in animals by the enzyme oxidation of L-arginine. NO is biosynthesised by finely regulated enzymatic systems called NO-synthases and readily diffuses through tissues. It reacts rapidly with hemoproteins and iron-sulphur centers to form nitrosylated compounds. It oxidises more slowly to form nitrogen oxides that nitrosate thiols into thionitrite. NO is transported in these various forms and released spontaneously or through yet unclear mechanisms into most cells; it also regulates oxygen consumption at the mitochondrial respiratory chain level through interaction with cytochrome oxidase. In the cardiovascular system, NO lowers blood pressure by activating a hemoprotein, the guanylate cyclase present in muscle cells; through such interaction it acts also as a neuromediator and neuromodulator in the nervous system. However, many of NO's roles result from rapid coupling to other radicals; for example, it reacts with the superoxide anion (O2-) to form oxoperoxinitrate (ONOO-, also known as peroxynitrite). This strong oxidant of metallic centers, thiols, and antioxidants is also able to convert tyrosine to 3-nitrotyrosine and to act upon tyrosine residues contained in proteins. The biological aspects of the roles of NO are presented with particular respect to the rapid interactions of NO with hemoproteins' iron and other radicals. Concurrently, NO oxidation enables nitrosation reactions primarily of thiols but ultimately of nucleic bases. The thionitrite function (R-S-NO) thus formed and the dimerisation and nitration of tyrosine residues are protein post-translational modifications that are being investigated in animals.     

Abnormal Fossil Upper Molar of Pongo from Thailand: Quaternary Climatic Changes in Southeast Asia as a Possible Cause

We interpret an unusual left M ³ attributed to Pongo from the Late Middle Pleistocene of Thailand to be an abnormal tooth rather than a supernumerary molar. Its peculiar morphology cannot be related to classical known causes that affect the dental germ: Gemination, schizodontia, synodontia. The ontogenic mechanism that might have led to the morphology of the tooth perhaps reflects stress related to a phase of marked climatic changes during the Late Middle Pleistocene in Southeast Asia.     

Principal component and factor analytic models in international sire evaluation

Background

Interbull is a non-profit organization that provides internationally comparable breeding values for globalized dairy cattle breeding programmes. Due to different trait definitions and models for genetic evaluation between countries, each biological trait is treated as a different trait in each of the participating countries. This yields a genetic covariance matrix of dimension equal to the number of countries which typically involves high genetic correlations between countries. This gives rise to several problems such as over-parameterized models and increased sampling variances, if genetic (co)variance matrices are considered to be unstructured.

Methods

Principal component (PC) and factor analytic (FA) models allow highly parsimonious representations of the (co)variance matrix compared to the standard multi-trait model and have, therefore, attracted considerable interest for their potential to ease the burden of the estimation process for multiple-trait across country evaluation (MACE). This study evaluated the utility of PC and FA models to estimate variance components and to predict breeding values for MACE for protein yield. This was tested using a dataset comprising Holstein bull evaluations obtained in 2007 from 25 countries.

Results

In total, 19 principal components or nine factors were needed to explain the genetic variation in the test dataset. Estimates of the genetic parameters under the optimal fit were almost identical for the two approaches. Furthermore, the results were in a good agreement with those obtained from the full rank model and with those provided by Interbull. The estimation time was shortest for models fitting the optimal number of parameters and prolonged when under- or over-parameterized models were applied. Correlations between estimated breeding values (EBV) from the PC19 and PC25 were unity. With few exceptions, correlations between EBV obtained using FA and PC approaches under the optimal fit were ≥ 0.99. For both approaches, EBV correlations decreased when the optimal model and models fitting too few parameters were compared.

Conclusions

Genetic parameters from the PC and FA approaches were very similar when the optimal number of principal components or factors was fitted. Over-fitting increased estimation time and standard errors of the estimates but did not affect the estimates of genetic correlations or the predictions of breeding values, whereas fitting too few parameters affected bull rankings in different countries.     

A common reference population from four European Holstein populations increases reliability of genomic predictions

Background

Size of the reference population and reliability of phenotypes are crucial factors influencing the reliability of genomic predictions. It is therefore useful to combine closely related populations. Increased accuracies of genomic predictions depend on the number of individuals added to the reference population, the reliability of their phenotypes, and the relatedness of the populations that are combined.

Methods

This paper assesses the increase in reliability achieved when combining four Holstein reference populations of 4000 bulls each, from European breeding organizations, i.e. UNCEIA (France), VikingGenetics (Denmark, Sweden, Finland), DHV-VIT (Germany) and CRV (The Netherlands, Flanders). Each partner validated its own bulls using their national reference data and the combined data, respectively.

Results

Combining the data significantly increased the reliability of genomic predictions for bulls in all four populations. Reliabilities increased by 10%, compared to reliabilities obtained with national reference populations alone, when they were averaged over countries and the traits evaluated. For different traits and countries, the increase in reliability ranged from 2% to 19%.

Conclusions

Genomic selection programs benefit greatly from combining data from several closely related populations into a single large reference population.