Filippo Miglior

Genetic parameters for producer-recorded health data in Canadian Holstein cattle

Health traits are of paramount importance for economic dairy production. Improvement in liability to diseases has been made with better management practices, but genetic aspects of health traits have received less attention. Dairy producers in Canada have been recording eight health traits (mastitis (MAST), lameness (LAME), cystic ovarian disease (COD), left displaced abomasum (LDA), ketosis (KET), metritis (MET), milk fever (MF) and retained placenta (RP)) since April 2007. Genetic analyses of these traits were carried out in this study for the Holstein breed. Edits on herd distributions of recorded diseases were applied to the data to ensure a sufficient quality of recording. Traits were analysed either individually (MAST, LAME, COD) or were grouped according to biological similarities (LDA and KET, and MET, MF and RP) and analysed with multiple-trait models. Data included 46 104 cases of any of the above diseases. Incidence ranged from 2.3% for MF to 9.7% for MAST. MET and KET also had an incidence below 4.0%. Variance components were estimated using four different sire threshold models. The differences between models resulted from the inclusion of days at risk (DAR) and a cow effect, in addition to herd, parity and sire effects. Models were compared using mean squared error statistic. Mean squared error favoured, in general, the sire and cow within sire model with regression on DAR included. Heritabilities on the liability scale were between 0.02 (MET) and 0.21 (LDA). There was a moderate, positive genetic correlation between LDA and KET (0.58), and between MET and RP (0.79).

Detection of QTL for milk protein percentage in Italian Friesian cattle by AFLP markers and selective genotyping

We targeted quantitative trait loci (QTL) for milk protein percentage (P%) in two Italian Holstein granddaughter design families using selective genotyping in combination with high throughput amplified fragment length polymorphism (AFLP) markers. A total of 64 extreme high and low sires in respect to estimated breeding value (EBV) for P% (EBVP%) were genotyped with 25 AFLP primer combinations that revealed 305 and 291 polymorphisms in the two families. Association between markers and EBVP% was investigated by a linear model only on bands having paternal origin (105 and 96 AFLP bands in family D and S, respectively). Although no marker was significantly associated with the target trait after correction for multiple comparisons, 17 AFLP markers, significant without correction for multiple tests, were considered suggestive of the presence of a QTL. Eleven of these were successfully located on six Bos taurus (BTA) chromosomes by radiation hybrid or in-silico mapping. Ten of these mapped in the immediate neighbourhood (less than 10 cM) of already described QTL for P%. Suggestive association was verified in four regions by microsatellites analysis: one on BTA 10; one on BTA 28; and two on BTA 18. Microsatellites identified significant effects by single marker and interval mapping analyses on BTA 10 and BTA 28, while they were only suggestive of the presence of QTL on BTA 18. In summary, our results firstly indicate that AFLP markers may be used to seek QTL exploiting a selective genotyping approach in GDD, a wide used experimental design in cattle; secondly, propose two approaches for AFLP mapping, namely in-silico mapping exploiting most updated release from the bovine whole genome sequencing project, and physical mapping exploiting a panel of Bovine/Hamster Radiation Hybrids; and thirdly, provide new information on QTLs for an economic important trait in a never investigated Holstein cattle population. AFLP in combination with selective genotyping can be a useful strategy for QTL searching in minor livestock species, sometimes having large economic impact in marginal areas, where more informative markers are still poorly developed.

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

Abstract 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.

Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations

The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS.

The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle

Johnes disease (or paratuberculosis), caused by Mycobacterium avium ssp. paratuberculosis (MAP) infection, is a globally prevalent disease with severe economic and welfare implications. With no effective treatment available, understanding the role of genetics influencing host infection status is essential to develop selection strategies to breed for increased resistance to MAP infection. The main objectives of this study were to estimate genetic parameters for the MAP-specific antibody response using milk ELISA scores in Canadian Holstein cattle as an indicator of resistance to Johnes disease, and to unravel genomic regions and candidate genes significantly associated with MAP infection. After data editing, 168,987 milk ELISA records from 2,306 herds, obtained from CanWest Dairy Herd Improvement, were used for further analyses. Variance and heritability estimates for MAP infection status were determined using univariate linear animal models under 3 scenarios: (a) SCEN1: the complete data set (all herds); (b) SCEN2: herds with at least one suspect or test-positive animal (ELISA optical density ≥0.07); and (c) SCEN3: herds with at least one test-positive animal (ELISA optical density ≥0.11). Heritability estimates were calculated as 0.066, 0.064, and 0.063 for SCEN1, SCEN2, and SCEN3, respectively. The correlations between estimated breeding values for resistance to MAP infection and other economically important traits, when significant, were favorable and of low magnitude. Genome-wide association analyses identified important genomic regions on Bos taurus autosome (BTA)1, BTA7, BTA9, BTA14, BTA15, BTA17, BTA19, and BTA25 showing significant association with MAP infection status. These regions included 2 single nucleotide polymorphisms located 2 kb upstream of positional candidate genes CD86 and WNT9B, which play key roles in host immune response and tissue homeostasis. This study revealed the genetic architecture of MAP infection in Canadian Holstein cattle as measured by milk ELISA scores by estimating genetic parameters along with the identification of genomic regions potentially influencing MAP infection status. These findings will be of significant value toward implementing genetic and genomic evaluations for resistance to MAP infection in Holstein cattle.

Phenotypic investigation of fine milk components in bovine milk and their prediction using mid-infrared spectroscopy

This study aimed to examine the phenotypic variation observed in fine milk components, the use of mid-infrared (MIR) spectroscopy to predict these components, and the correlations with other milk p...