ABSTRACT
Key words
INTRODUCTION
MATERIALS AND METHODS
Data Set
Trait | Mean | Incidence | Minimum | Maximum | % of censored records |
---|---|---|---|---|---|
Continuous | |||||
Interval from calving to first service | 91.8 (41.0) | — | 20 | 259 | 20.3 |
Days open | 127.8 (70.2) | — | 20 | 394 | 24.2 |
Calving interval | 419.5 (75.4) | — | 277 | 761 | — |
Categorical | |||||
Calving rate (%) | — | 49.9 | — | — | — |
Nonreturn rate at d 56 (%) | — | 33.1 | — | — | — |
Statistical Analyses
Genetic Models
where y is the vector of phenotypic records of the continuous traits (ICF, DO, and CInt) or the liabilities of the categorical traits (CR and NR56); b is the vector of systematic effects: parity and year-season of calving (a combination of the year and the season of calving in 12 categories of 5 d each; season 1 = calvings from April to September, season 2 = October to March); h, p, a, i, and e are the vectors of random effects of herd, permanent environment, animal additive genetic, inbreeding load, and residuals, respectively; f is the vector of total inbreeding of the recorded individual; c is the covariate with total inbreeding; a and i are genetic effects: a (the additive genetic effect) is expressed in all phenotypes, whereas i (the inbreeding load) is expressed in the phenotypes of the inbred descendants (
where , , and are the herd, permanent environment, and residual variances, respectively. In addition, the prior distribution of the additive genetic and inbreeding load effects was
where A is the numerator relationships matrix, and
where and are the additive genetic variance, the inbreeding load variance, and the covariance between the additive genetic and the inbreeding load effects, respectively. Finally, the prior distribution of the systematic effects (b) and the variance components was uniform within appropriate bounds.
Gibbs Sampler
- R Core Team
where σai is the covariance between the additive genetic and the inbreeding load, and and are the additive genetic and inbreeding load variances, respectively. The i2 was defined as the proportion of phenotypic variation caused by variability in the inbreeding load variance. The calculation of i2 requires the assumption of a reference point defined by the inbreeding caused by one specific ancestor. We used a continuum from F = 0.001 to F = 0.100 in sequences of 0.001 to reflect the trend associated with i2 in different scenarios to an extreme (F = 0.100) with highly inbred individuals. To estimate i2 across the continuum, we rescaled the estimates depending on the reference point of F by multiplying it by the square of the ratio between the 2 reference points (the original and the new one). Thus, the posterior estimate of the inbreeding load for ICF with a reference point of F = 0.025 and based on F = 0.100 was 30.842 = 493.471 × (0.025/0.100)2. We then calculated the corresponding h2 that reflects the change in the magnitude due to i2. The estimates of β were defined as the deviations from F. Furthermore, the reliability of the predictions of the jth inbreeding load was approximated as
where PSD(ij) is the posterior standard deviation of the jth inbreeding load, and is the posterior mean estimate of the inbreeding load variance.
RESULTS AND DISCUSSION
Mendelian Decomposition of Inbreeding
Item | Continuous traits | Categorical traits |
---|---|---|
Animals (no.) | 61,062 | 73,246 |
Sires (no.) | 2,585 | 2,859 |
Dams (no.) | 39,772 | 47,045 |
Generations from pedigree (no.) | 12 | 13 |
Fp (no.; % of total) | 178,252 | 268,525 |
>0.001 | 92,241 (51.74) | 137,837 (51.33) |
>0.01 | 5,891 (3.30) | 7,518 (2.80) |
>0.10 | 124 (0.07) | 162 (0.06) |
Maximum | 0.125 | 0.125 |
Ancestors generating inbreeding (no.) | 443 | 513 |
>10 | 153 | 188 |
>100 | 81 | 93 |
>1,000 | 27 | 29 |
>10,000 | 8 | 9 |
Genetic Parameters
Item 3 β(F = 0.10) = slope of the covariate with total inbreeding; σa2 = additive genetic variance; σi(F=0.10)2 = inbreeding load variance at a partial inbreeding coefficient of 0.10; σia(F=0.10) = covariance between the additive genetic and inbreeding load effects at a partial inbreeding coefficient of 0.10; r(a,i) = correlation between additive genetic and inbreeding load, r(a,i)=σaiσa2×σi2;σh2 = herd variance; σpe2 = permanent environment variance; σe2 = residual variance. | ICF | DO | CInt | CR | NR56 |
---|---|---|---|---|---|
β(F = 0.10) | 4.54 (−1.84; 10.79) | 8.43 (0.49; 16.45) | 0.26 (−7.30; 7.67) | −0.068 (−0.169; 0.039) | −0.087 (−0.191; 0.022) |
244.9 (177.4; 322.9) | 703.4 (546.4; 874.5) | 309.6 (229.3;402.7) | 0.021 (0.013; 0.032) | 0.019 (0.010; 0.030) | |
493.5 (149.4; 1213.1) | 629.6 (159.0; 1926.5) | 770.1 (148.3; 2303.3) | 0.123 (0.025; 0.374) | 0.146 (0.037; 0.382) | |
−103.9 (−369.3; 130.1) | −27.5 (−657.7; 529.4) | −72.8 (−448.3; 315.6) | −0.007 (−0.039; 0.027) | −0.013 (−0.005; 0.027) | |
r(a,i) | −0.281 (−0.793; 0.445) | −0.029 (−0.775; 0.734) | −0.141 (−0.751; 0.639) | −0.157 (−0.706; 0.533) | −0.238 (−0.735; 0.565) |
646.6 (584.1; 713.8) | 1,046.3 (942.6; 1,157.7) | 554.3 (495.9; 617.0) | 0.085 (0.074; 0.095) | 0.098 (0.087; 0.111) | |
447.6 (360.9; 532.9) | 1,278.9 (1,099.6; 1,457.3) | 539.0 (438.1; 638.6) | 0.054 (0.033; 0.076) | 0.042 (0.019; 0.066) | |
1,859.0 (1,793.2; 1,927.1) | 6,485.5 (6,346.8; 6,627.5) | 4,343.6 (4,255.5; 4,432.7) | 1 | 1 |

Prediction of Inbreeding Loads
Trait | Estimate of reliability | No. of individuals with reliability: | Maximum value of reliability | ||||
---|---|---|---|---|---|---|---|
Mean | SD | >0.3 | >0.4 | >0.5 | >0.7 | ||
ICF | 0.179 | 0.109 | 6,856 | 629 | 29 | 3 | 0.820 |
DO | 0.151 | 0.118 | 7,233 | 271 | 17 | 3 | 0.759 |
CInt | 0.164 | 0.111 | 6,172 | 828 | 26 | 3 | 0.857 |
CR | 0.122 | 0.099 | 3,901 | 65 | 13 | 3 | 0.770 |
NR56 | 0.132 | 0.105 | 4,222 | 74 | 14 | 4 | 0.779 |

Item | Individual ID | ||||
---|---|---|---|---|---|
12783 | 12782 | 21519 | 12530 | 11170 | |
Year of birth | 2006 | — | 1995 | — | — |
ICF (d; reliability) | −22.32 (0.79) | 8.07 (0.82) | 22.12 (0.72) | 1.18 (0.66) | 7.41 (0.63) |
DO (d; reliability) | −16.20 (0.72) | −1.46 (0.76) | 10.81 (0.73) | 4.88 (0.49) | 0.17 (0.64) |
CInt (d; reliability) | −13.12 (0.80) | 2.46 (0.86) | 12.77 (0.75) | −3.62 (0.68) | −12.86 (0.69) |
CR (%) | 0.027 (0.77) | −0.199 (0.76) | −0.013 (0.73) | −0.054 (0.67) | −0.204 (0.67) |
NR56 (%) | −0.067 (0.78) | −0.286 (0.75) | 0.106 (0.75) | −0.082 (0.70) | −0.087 (0.67) |
Sons (no.) | 251 | 403 | 1,930 | 385 | 53 |
Grandsons (no.) | 3,548 | 3,583 | 3,688 | 3,290 | 873 |
Great-grandsons (no.) | 13,762 | 8,636 | 2,917 | 8,772 | 7,167 |
F generated (no.) | 15,272 | 2,552 | 370 | 3,873 | 11,170 |
Fp | 0.00614 | 0.0077 | 0.0201 | 0.0061 | 0.0027 |
CONCLUSIONS
ACKNOWLEDGMENTS
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