| Literature DB >> 21931517 |
Makram J Geha1, Jeffrey F Keown, L Dale Van Vleck.
Abstract
Milk yield records (305d, 2X, actual milk yield) of 123,639 registered first lactation Holstein cows were used to compare linear regression (y = β(0) + β(1)X + e), quadratic regression, (y = β(0) + β(1)X + β(2)X(2) + e) cubic regression (y = β(0) + β(1)X + β(2)X(2) + β(3)X(3) +e) and fixed factor models, with cubic-spline interpolation models, for estimating the effects of inbreeding on milk yield. Ten animal models, all with herd-year-season of calving as fixed effect, were compared using the Akaike corrected-Information Criterion (AICc). The cubic-spline interpolation model with seven knots had the lowest AICc, whereas for all those labeled as "traditional", AICc was higher than the best model. Results from fitting inbreeding using a cubic-spline with seven knots were compared to results from fitting inbreeding as a linear covariate or as a fixed factor with seven levels. Estimates of inbreeding effects were not significantly different between the cubic-spline model and the fixed factor model, but were significantly different from the linear regression model. Milk yield decreased significantly at inbreeding levels greater than 9%. Variance component estimates were similar for the three models. Ranking of the top 100 sires with daughter records remained unaffected by the model used.Entities:
Keywords: Akaike’s information criterion; cubic-spline interpolation; inbreeding; milk yield
Year: 2011 PMID: 21931517 PMCID: PMC3168185 DOI: 10.1590/S1415-47572011000300013
Source DB: PubMed Journal: Genet Mol Biol ISSN: 1415-4757 Impact factor: 1.771
Figure 1Unadjusted average 305 d milk yield (kg) with values within 1 standard deviation by inbreeding coefficient (%F).
Classification of inbreeding into seven levels, and the number of cows per category.
| Inbreeding levels | Numberof cows |
|---|---|
| 0% | 794 |
| 0–3.125% | 16308 |
| 3.125–6.250% | 81805 |
| 6.250–12.500% | 23832 |
| 12.500–18.750% | 780 |
| 18.750–25.000% | 36 |
| > 25.000% | 84 |
Position of knots at inbreeding levels (%F) for the five cubic-spline models.
| Number of knots | Position of knots |
|---|---|
| 3 | 0, 12.500, 25.000 |
| 4 | 0, 6.250, 12.500, 25.000 |
| 5 | 0, 3.125, 6.250, 12.500, 25.000 |
| 6 | 0, 3.125, 6.250, 12.50, 18.750, 25.000 |
| 7 | 0, 3.125, 6.250, 12.50, 18.750, 25.000, 37.500 |
Estimates of residual variance, logarithm of the likelihood and AICc for each model, with differences in AICc from the cubic-spline model with seven knots.
| Model | LogL (−865,000) | AICc (1,742,500) | Difference in AICc | |
|---|---|---|---|---|
| Cubic-spline with 7 knots | 125.515 | −122.913 | 15.995 | 0 |
| Cubic-spline with 4 knots | 125.519 | −126.458 | 16.473 | 0.479 |
| Cubic-spline with 5 knots | 125.520 | −126.425 | 18.612 | 2.618 |
| Cubic-spline with 6 knots | 125.521 | −126.393 | 20.751 | 4.756 |
| Linear, quadratic and cubic regression | 125.524 | −128.920 | 21.398 | 5.404 |
| Linear and quadratic regression | 125.532 | −133.385 | 28.124 | 12.130 |
| Cubic-spline with 3 knots | 125.534 | −134.370 | 30.094 | 14.100 |
| Linear regression | 125.539 | −137.357 | 33.865 | 17.870 |
| Fixed factor 7 | 125.546 | −138.180 | 50.934 | 34.940 |
| Saturated (fixed factor 32 levels) | 125.509 | −118.383 | 66.441 | 50.447 |
Figure 2Estimated 305 d milk yields (kg) by inbreeding level (%F) from the cubic-spline model adjusted for herd-year-season effects.
t statistics for testing significance in the reduction of 305 d milk yield (kg) between different inbreeding levels and 0% inbreeding from the cubic-spline interpolation model with seven knots.
| %F | 305d milk yield reduction per cow (kg) | t-value | %F | 305d milk yield reduction per cow (kg) | t-value |
|---|---|---|---|---|---|
| 0.00 | 0.00 | 0.00 | 20.00 | −332.00 | −3.46[ |
| 1.00 | 13.00 | 0.75 | 21.00 | −276.00 | −2.47[ |
| 2.00 | 22.00 | 0.72 | 23.00 | −170.00 | −1.12 |
| 3.00 | 25.00 | 0.64 | 25.00 | −146.00 | −0.84 |
| 4.00 | 21.00 | 0.49 | 26.00 | −191.00 | −1.11 |
| 5.00 | 10.00 | 0.20 | 27.00 | −275.00 | −1.68 |
| 6.00 | −9.00 | −0.27 | 28.00 | −394.00 | −2.56[ |
| 7.00 | −32.00 | −0.91 | 29.00 | −546.00 | −3.50[ |
| 8.00 | −61.00 | −1.64 | 30.00 | −727.00 | −4.04[ |
| 9.00 | −95.00 | −2.38[ | 31.00 | −933.00 | −4.10[ |
| 10.00 | −132.00 | −3.05[ | 32.00 | −1162.00 | −3.95[ |
| 11.00 | −172.00 | −3.70[ | 34.00 | −1673.00 | −3.61[ |
| 12.00 | −216.00 | −4.40[ | 36.00 | −2231.00 | −3.38[ |
| 13.00 | −262.00 | −5.18[ | 40.00 | −3390.00 | −3.13[ |
| 14.00 | −308.00 | −5.85[ | |||
| 15.00 | −349.00 | −6.12[ | |||
| 16.00 | −381.00 | −5.98[ | |||
| 17.00 | −399.00 | −5.60[ | |||
| 18.00 | −399.00 | −5.08[ | |||
| 19.00 | −377.00 | −4.39[ |
Significant reduction in milk yield from the estimated milk yield at 0% inbreeding (p < 0.05).
Estimated annual milk yield loss (kg) at different inbreeding levels for the fixed factor model with seven levels.
| Inbreeding levels | Milk yield loss (kg) |
|---|---|
| 0+–3.125% | 5.92 ± 18.85 |
| 3.125+–6.25% | 78.64 ± 21.15 |
| 6.25+–12.5% | 386.10 ± 52.45 |
| 12.5+–18.75% | 366.17 ± 208.70 |
| 18.75+–25% | 479.75 ± 148.62 |
| > 25% | 2863.37 ± 1291.89 |
Estimates of variance components (kg/100)2 and heritability for the three models.
| Model | Heritability | ||
|---|---|---|---|
| Linear regression | 59.50 ± 2.24 | 187.40 ± 0.98 | 0.31 ± 0.01 |
| Fixed factor with seven levels | 58.90 ± 2.23 | 187.20 ± 0.98 | 0.31 ± 0.01 |
| Cubic-spline with seven knots | 58.97 ± 2.24 | 187.20 ± 0.98 | 0.31 ± 0.01 |