Comparison of parametric, orthogonal, and spline functions to model individual lactation curves for milk yield in Canadian Holsteins

Test day records for milk yield of 57,390 first lactation Canadian Holsteins were analyzed with a linear model that included the fixed effects of herd-test date and days in milk (DIM) interval nested within age and calving season. Residuals from this model were analyzed as a new variable and fitted with a five parameter model, fourth-order Legendre polynomials, with linear, quadratic and cubic spline models with three knots. The fit of the models was rather poor, with about 30%-40% of the curves showing an adjusted R-square lower than 0.20 across all models. Results underline a great difficulty in modelling individual deviations around the mean curve for milk yield. However, the Ali and Schaeffer (5 parameter) model and the fourth-order Legendre polynomials were able to detect two basic shapes of individual deviations among the mean curve. Quadratic and, especially, cubic spline functions had better fitting performances but a poor predictive ability due to their great flexibility that results in an abrupt change of the estimated curve when data are missing. Parametric and orthogonal polynomials seem to be robust and affordable under this standpoint

Fit of different functions to the individual deviations in random regression test day models for milk yield in dairy cattle

The shape of individual deviations of milk yield for dairy cattle from the fixed part of a random regression test day model (RRTDM) was investigated. Data were 53,217 TD records for milk yield of 6,229 first lactation Canadian Holsteins in Ontario. Data were fitted with a model that included the fixed effects of herd-testdate, DIM interval nested within age and season of calving. Residuals of the model were then fitted with the following functions: Ali and Schaeffer 5 parameter model, fourth-order Legendre Polynomials, and cubic spline with three, four or five knots. Result confirm the great variability of shape that can be found when individual lactation are modeled. Cubic splines gave better fitting pe4rformances although together with a marked tendency to yield aberrant estimates at the edge of the lactation trajectory

Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

Background The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. Methods Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. Results In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. Conclusions Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available

Mediterranean River Buffalo CSN1S1 gene: search for polymorphisms and association studies.

The aim of the present work was to study the variability at CSN1S1 locus of the Italian Mediterranean river buffalo and to investigate possible allele effects on milk yield and its composition. Effects of parity, calving season and month of production were also evaluated. Three SNPs were detected. The first mutation, located at position 89 of 17th exon (c.628C>T), is responsible for the amino acid change (p.Ser178Leu). The other two polymorphisms, detected at the positions 144 (c.882G>A) and 239 (c.977A>G) of 19th exon respectively, are silent (3’ UTR). Associations between the CSN1S1 genotypes and milk production traits were investigated using 4,122 test day records of 503 lactations from 175 buffalo cows. Milk yield, fat and protein percentages were analyzed using a mixed linear model. A significant association between the c.628C>T SNP and the protein percentage was found. In particular, the CC genotype showed an average value of about 0.04% higher than the CT and TT genotypes. The allele substitution effect of the cytosine into the thymine was -0.014, with a quite low (0.3%) protein percentage (PP) contribution on total phenotypic variance. A large dominance effect was detected. Furthermore, a characterization of the CSN1S1 transcripts and a method based on MboI-ACRS-PCR for a rapid genotyping of c.628C>T were provided

BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous cattle breeds

Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local cattle breeds. Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local cattle breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian cattle breeds (Agerolese, Bar\ue0-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d\u2019Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, Sardo-Modicana and Ottonese-Varzese) and two cosmopolitan breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several breeds were detected in the frame of the project, whereas for some breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multi-dimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian cattle breeds

The ALICE Zero Degree Calorimeters

In the ALICE experiment at Cern LHC, a set of hadron calorimeters will be used to determine the centrality of the Pb-Pb collision. The spectator protons and neutrons, will be separated from the ion beams, using the separator magnet (D1) of the LHC beam optics and respectively detected by a proton (ZP) and a neutron (ZN) "Zero-degree Calorimeter" (ZDC). The detectors will be placed in front of the separator D2 magnet, 115 meters away from the beam intersection point. The ZDCs are quartz-fiber spaghetti calorimeters that exploit the Cherenkov light produced by the shower particles in silica optical fibers.This technique offers the advantages of high radiation hardness (up to several Grad), fast response and reduced lateral dimension of the detectable shower. In addition, quartz-fiber calorimeters are intrinsically insensitive to radio-activation background, which produces particles below the Cherenkov threshold.The ALICE ZDC should have an energy resolution comparable with the intrinsic energy fluctuations, which range from about 20 0.000000or central events to about 5 0.000000or peripheral ones, according to simulations that use HIJING as event generator. The fiber-to-absorber filling ratio must be chosen as a good compromise between the required energy resolution and the fiber cost.The design of the proposed calorimeter will be discussed, together with the expected performances. Whenever possible, the simulated results will be compared with the experimental ones, obtained with the built prototypes and with the NA50 ZDC, which can be considered as a working prototype for the ALICE neutron calorimeter

Centrality Behaviour of J/ψ\psi Production in Na50

The J/$\psi$ production in 158 A GeV Pb-Pb interactions is studied, in the dimuon decay channel, as a function of centrality, as measured with the electromagnetic or with the very forward calorimeters. After a first sharp variation at mid centrality, both patterns continue to fall down and exhibit a curvature change at high centrality values. This trend excludes any conventional hadronic model and is in agreement with a deconfined quark-gluon phase scenario. We report also preliminary results on the measured charged multiplicity, as given by a dedicated detector.Comment: 5 pages, 7 figures (in eps) talk given at XXXI International Symposium on Multiparticle Dynamics, Sep. 1-7, 2001, Datong China URL http://ismd31.ccnu.edu.cn

A new measurement of J/psi suppression in Pb-Pb collisions at 158 GeV per nucleon

We present a new measurement of J/psi production in Pb-Pb collisions at 158 GeV/nucleon, from the data sample collected in year 2000 by the NA50 Collaboration, under improved experimental conditions with respect to previous years. With the target system placed in vacuum, the setup was better adapted to study, in particular, the most peripheral nuclear collisions with unprecedented accuracy. The analysis of this data sample shows that the (J/psi)/Drell-Yan cross-sections ratio measured in the most peripheral Pb-Pb interactions is in good agreement with the nuclear absorption pattern extrapolated from the studies of proton-nucleus collisions. Furthermore, this new measurement confirms our previous observation that the (J/psi)/Drell-Yan cross-sections ratio departs from the normal nuclear absorption pattern for semi-central Pb-Pb collisions and that this ratio persistently decreases up to the most central collisions.Comment: 19 pages, 10 figures. Submitted to Eur. Phys. J.