J. Dairy Sci. 90:482-492
© American Dairy Science Association, 2007.
Within-Herd Heritability Estimated with DaughterParent Regression for Yield and Somatic Cell Score
C. D. Dechow*,1 and
H. D. Norman
* Department of Dairy and Animal Science, The Pennsylvania State University, University Park 16802
Animal Improvement Programs Laboratory, ARS, USDA, Beltsville, MD 20705-2350
1 Corresponding author: cdechow{at}psu.edu
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ABSTRACT
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Estimates of heritability within herd (hWH2 ) that were generated with daughterdam regression, daughtersire regression, and REML were compared, and effects of adjusting lactation records for within-herd heritability on genetic evaluations were evaluated. Holstein records for milk, fat, and protein yields and somatic cell score (SCS) from the USDA national database represented herds in the US Northeast, Southeast, Midwest, and West. Four data subsets (457 to 499 herds) were randomly selected, and a large-herd subset included the 15 largest herds from the West and 10 largest herds from other regions. Subset heritabilities for yield and SCS were estimated assuming a regression model that included fixed covariates for effects of dam yield or SCS, sire predicted transmitting ability (PTA) for yield or SCS, herd-year-season of calving, and age within parity. Dam records and sire PTA were nested within herd as random covariates to generate within-herd heritability estimates that were regressed toward mean hWH2 for the random subset. Heritabilities were estimated with REML using sire models (REMLSIRE), sirematernal grandsire models (REMLMGS), and animal models (REMLANIM) for each herd individually in the large-herd subset. Phenotypic variance for each herd was estimated from herd residual variance after adjusting for effects of year-season and age within parity. Deviations from herd-year-season mean were standardized to constant genetic variance across herds, and records were weighted according to estimated error variance to accommodate hWH2 when estimating breeding values. Mean hWH2 tended to be higher with daughterdam regression (0.35 for milk yield) than with daughtersire regression (0.24 for milk yield). Heritability estimates varied widely across herds (0.04 to 0.67 for milk yield estimated with daughterdam regression), and hWH2 deviated from subset means more for large herds than for small herds. Correlation with REMLANIM hWH2 was 0.68 for daughterdam and was 0.45 for daughtersire hWH2 for milk yield. The correlation between daughtersire hWH2 and REMLMGS was greater than the correlation between daughterdam hWH2 and REMLMGS. Data adjustments had a minimal impact on breeding value bias. Within-herd heritability can be estimated rapidly using regression techniques with moderate accuracy, but adjusting lactation records for hWH2 resulted in only a small improvement in the accuracy of genetic evaluations.
Key Words: heritability daughterdam regression daughtersire regression
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INTRODUCTION
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Genetic evaluations for most traits assume that heritability is constant across herds within a breed. However, management and environmental factors that vary across herds could result in different heritabilities. In addition, the accuracy of records that contribute to genetic evaluations varies across herds. Inaccurate parent identification reduces heritability estimates and PTA accuracy (Gelderman et al., 1986; Banos et al., 2001). Herd characteristics that may not directly influence data accuracy, such as larger herd size or higher maximum monthly temperature, also were associated with lower heritability estimates in an across-country study (Zwald et al., 2003). The herd characteristics that have received the most attention for their relationship to heritability are mean yield and yield variance. Heritability estimates typically increase as mean herd yield and herd phenotypic variance increase (Lofgren et al., 1985; Vinson, 1987; Van Tassell et al., 1999).
Herd-year heritability for yield is assumed to increase when the standard deviation (SD) for phenotype increases (Wiggans and VanRaden, 1991) and is constrained to range from 0.25 to 0.35 in the US genetic evaluation of Holsteins (Van Tassell et al., 1999). Within-herd heritability is accounted for by standardizing yield to a constant genetic SD prior to generating EBV and weighted by the ratio of base error variance to herd error variance while generating EBV (Wiggans and VanRaden, 1991). Final type scores are standardized to a constant phenotypic variance to account for reduced variance as the herd mean type score increases, but herd heritability is not assumed to vary (Weigel and Lawlor, 1994).
Efforts to standardize records to constant genetic or phenotypic variance have resulted in improvements in the accuracy of sire PTA (Wiggans and VanRaden, 1991; Powell et al., 1994; van der Werf et al., 1994; Weigel and Lawlor, 1994). The use of direct estimates of within-herd heritability (hWH2) may be more precise than heritability inferred from herd variance. Estimating a separate heritability for a large number of herds on a routine basis using REML is not feasible, and heritability estimates are not accurate for small data sets (Falconer and Mackay, 1996). Alternatively, regression techniques could be used that are computationally feasible. Within-herd heritability could be regressed toward the mean for small herds that lack sufficient data to estimate hWH2 accurately. Daughterdam regression and paternal half-sibling correlations can be used to derive heritability (Falconer and Mackay, 1996), and both are based on sources of pedigree information that are recorded to some extent in nearly all herds.
Most herds have too few paternal half-siblings to estimate heritability directly from half-sibling correlations. Regressions on sire PTA, which are generated primarily with half-sibling records, give some indication of genetic variation and could be used to infer herd heritability. In a comparison of grazing and confinement herds in the United States, genetic variance in the grazing herds was estimated to be 62 to 87% lower than in confinement herds (Kearney et al., 2004). Regression of mature-equivalent (ME) milk on sire PTA for milk was correspondingly lower in grazing herds (0.78) than in the confinement herds (0.99).
The objectives of this study were 1) to estimate hWH2 rapidly and accurately using regression techniques, 2) to evaluate hWH2 differences and factors that contribute to those differences, and 3) to evaluate the effect on genetic evaluation accuracy when using hWH2 to standardize records across herds to constant genetic variance and to weight records according to estimated error variance.
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MATERIALS AND METHODS
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Data
Mature-equivalent milk, fat, and protein yields and mean SCS records from first- through fifth-parity Holstein cows that had calved between January 1997 and June 2004 were obtained from the USDA national lactation database for selected states that represented 4 regions: West (California), Midwest (Wisconsin), Northeast (New York and Pennsylvania), and Southeast (Alabama, Arkansas, Florida, Georgia, Louisiana, Mississippi, North Carolina, Oklahoma, South Carolina, Tennessee, and Texas). Four data subsets were created to provide replication across multiple samples and to analyze a large number of herds within computational limits. The 4 subsets were created by randomly selecting herds across regions. A fifth subset was created by selecting the largest herds from the 4 original subsets: the 10 largest herds from the Northeast, Southeast, and Midwest regions and the 15 largest herds from the West. Herd size in the large-herd subset ranged from 1,076 lactation records from 671 cows to 19,856 lactation records from 9,497 cows.
All cows were required to have either a dam from the same herd or a sire with an official genetic evaluation. Dams were required to be from the same herd because heritability estimates were intended to reflect hWH2 and not the general population heritability. A minimum of 4,500 kg of ME milk was required, and records from second and later parities were retained only if a first-parity record was available. Contemporary groups were similar to those used in national genetic evaluations. Herd-year-seasons of calving were 6 bimonthly calving seasons. For herd-year-seasons with <5 cows, seasons were expanded to 4-mo intervals. Herd-year was substituted for herd-year-season if <5 cows were in the herd-year-season after expanding the season length; herd-years with <5 cows were excluded. Of the original records across subsets, 24% were removed because of additional data edits.
The numbers of records, cows, daughterdam pairs, sires, and herds for each data subset are shown in Table 1
. Data subsets ranged from 206,766 to 290,544 records. Percentages of cows with a dam record from the same herd ranged from 55 to 59% (large-herd subset). The mean number of records by region ranged from 51,469 (Midwest) to 72,306 (West).
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Table 1. Overall numbers of records, cows, daughterdam pairs, sires, and herds and regional numbers of records by data subset
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REML Estimates for hWH2
Restricted maximum likelihood heritability estimates were generated for the 45 large herds by using sire models (REMLSIRE), sirematernal grandsire models (REMLMGS), and animal models (REMLANIM). Heritability estimates were generated for each herd individually, resulting in 135 individual herd analyses (45 from each model) for each trait. Heritability for each herd was estimated by AS-REML (Gilmour et al., 2002) with the following model:
 | [1] |
where y is a vector of ME milk, fat, or protein yields or SCS, X is the incidence matrix for fixed effects, B is a vector of fixed effects (age within parity and year-season of calving), Z is the incidence matrix for additive pedigree (animal, sire, or sire + MGS), u is a vector of random pedigree effects, W is the incidence matrix for permanent environmental effects, p is a vector of random permanent environmental effects, and e is a vector of random residuals.
DaughterDam and DaughterSire Estimates for hWH2
The hWH2 for milk, fat, and protein yields and SCS were estimated with daughterdam and daughtersire regressions. Dam records were the residuals from the following model:
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where y is ME milk, fat, or protein yield or SCS for parity i of cow in year-season j; bi is the coefficient for fixed regression on age nested within parity (A), H is a fixed effect of year-season, and e is the effect of the random residual. The analysis was applied to each herd individually, which was computationally feasible and easily accommodated with the MIXED procedure of SAS (SAS Institute, 2000). Daughter ME milk, fat, and protein yields and SCS were then regressed on the corresponding dam record. Daughterdam and daughtersire regressions were conducted simultaneously. This procedure required no missing values to make use of all available dam records when sire PTA was missing, or to make use of sire PTA when dam records were missing. Sire PTA and dam records were averaged for each herd-year-season and included for cows with missing values.
Regression models to estimate hWH2 included fixed regression coefficients to estimate mean heritability for each data subset. An additional random coefficient nested within herd allowed the calculation of hWH2 estimates that were regressed toward the subset mean. The model for estimating heritabilities in AS-REML (Gilmour et al., 2002) was
 | [3] |
where y is ME milk, fat, or protein yield or SCS for parity i of cow in herd l, herd-year k, and herd-year-season j; bi is a coefficient for fixed regression on age (A) nested within parity i; H is a fixed effect of herd-year-season; b2 is a coefficient for fixed regression on dam record (D); b3 is a coefficient for fixed regression on sire PTA (S); b4 is a coefficient for fixed regression on the interaction between sire PTA and herd-year SD for yield or SCS; b1l is a coefficient for random regression on dam record nested within herd (F); b2l is a coefficient for random regression on sire PTA nested within herd (G); and e is an effect of the random residual. An analysis of milk yield without regression on fixed effects [b2D, b3S, and b4(S x SDk)] was also performed to determine the effect of deviating from an overall fixed regression coefficient.
Herd phenotypic variance estimates (and herd-year SD) were derived using residual variance for each herd from model [2]. Residual variances from current, previous, and subsequent herd-years and mean residual variance for the data subset were weighted according to the procedures of Wiggans and VanRaden (1991) to estimate herd-year phenotypic variance that was regressed toward the subset mean with the following formula:
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where
HY2 is the phenotypic variance estimate for the current herd-year,
2S is the average residual variance (eij) from model [2] for j herd-year seasons in the current year,
2HY is eij in the current year,
2HY1 is eij for the previous year,
2HY+1 is eij in the subsequent year, NHY are the degrees of freedom for the current year, NHY1 are the degrees of freedom for the previous year, and NHY+1 are the degrees of freedom for the subsequent year. The degrees of freedom were assumed to be the number of records minus 1. Weights derived from the inverse of standard errors could replace degrees of freedom, but that approach was not examined in this study.
The hWH2 from the daughterdam regression was 2(b2 + bll). To estimate hWH2 from the daughtersire regression, the additive genetic SD for the herd was first assumed to be
where SDUS is the genetic SD assumed for USDA-DHIA Holstein genetic evaluations (755 kg for ME milk). Thus, a herd with
was assumed to have twice the genetic SD of the general population. The hWH2 from daughtersire regression was herd additive genetic variance divided by
HY2. Because
HY2 was used in the analysis of daughtersire regressions, hWH2 heritability could vary each year for daughtersire regression. Midparent hWH2 was the mean of hWH2 from daughterdam and daughtersire regressions.
The relationship between hWH2 and herd parameters that could be indicators of hWH2 was assessed with a multiple regression model in the GLM procedure of SAS (SAS Institute, 2000) with hWH2 as the dependent variable. Independent variables included region (California, Northeast, Southeast, Wisconsin), average number of first-lactation animals calving per year within region, percentage of cows identified by a registration number, average age at first calving, herd average yield or SCS, and herd phenotypic SD of yield or SCS.
Data Adjustment
Animal-model EBV were generated with BLUPF90 (Misztal, 2004) with and without adjustment for hWH2 with methods similar to those of Wiggans and VanRaden (1991). The model to estimate breeding values was similar to model [1]. The only difference was that EBV were generated with records from all herds in a subset, so year-season was replaced with herd-year-season and only animal was considered as a pedigree effect.
Records were standardized to constant genetic variance prior to estimation of breeding values, whereas error variance differences among herds were accommodated by weighting records simultaneously with estimation of breeding values. Genetic and permanent environmental variances were identical to those used in national genetic evaluations, which are based on assumed heritabilities of 0.30 and repeatabilities 0.55 for yield traits (Van Tassell et al., 1999) and 0.10 and 0.35, respectively, for SCS (Schutz, 1994). Estimates of hWH2 for yield were constrained to a range between 0.10 and 0.50 before adjusting for hWH2. Heritability constraints were made to prevent overextrapolation and because negative weights would have been obtained if herd heritability had been allowed to be greater than the assumed repeatability.
Daughter milk, fat, and protein yields and SCS were deviated from herd-year-season means for those traits. Resulting deviations were multiplied by the ratio of SDUS to herd additive genetic SD. Changes in error variance were accommodated by weighting records with the ratio of error variance for national genetic evaluations to estimated error variance after adjusting for herd additive genetic SD (Wiggans and VanRaden, 1991).
Tests of Data Adjustments
Methods derived by van der Werf et al. (1994) and Reverter et al. (1994) to detect bias in genetic parameter estimates were adapted to determine the effect of data adjustments. The methods rely on comparisons of EBV in subsequent genetic evaluations. For each data subset, EBV were first generated only with records from cows calving in 2000 and earlier (EBV2000) and second with the complete data subset (EBV2004). Data adjustments for EBV2000 were based on hWH2 generated with records from calvings in 2000 and earlier. The EBV from sires that entered a young sire program between July 1995 and July 1997 were selected to evaluate the effects of data adjustments. Sires were required to have 1) daughters that calved in multiple herds by 2000 or earlier, 2) daughters in at least one additional herd after 2000, 3) a reliability for EBV2000 of at least 50% for yield or 35% for SCS, and 4) a reliability for EBV2004 of at least 80% for yield or 60% for SCS. The EBV2000 for sires that entered AI in this time period would be derived from first-crop daughters, whereas EBV2004 would include second-crop daughters. The effect of data adjustments on bias attributable to factors such as preferential treatment of daughters sired by elite proven bulls can then be detected.
The EBV2004 were regressed on EBV2000, and fluctuations in EBV were compared across subsequent genetic evaluations to determine the effects of data adjustments. van der Werf et al. (1994) obtained an observed genetic variance based on EBV fluctuation with the following formula:
where
a2 is observed genetic variance based on fluctuations in genetic evaluations, EBV2004i is EBV2004 for sire i, EBV2000i is EBV2000 for sire i,
ri 2 is the change in reliability from EBV2000 to EBV2004 for sire i, and n is the number of sires. The ratio of
a2 to the genetic variance used to derive EBV indicates whether fluctuations were larger than expected relative to the amount of information gained in subsequent evaluations, whereas regression of EBV2004 on EBV2000 would be expected to be 1 in the absence of any bias (Reverter et al., 1994). The significance of differences in fluctuations was determined by comparing
a2 before and after data adjustments with a 2-tailed paired t-test.
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RESULTS
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Large Herd hWH2
Means and correlations among daughterdam hWH2, daughtersire hWH2, midparent hWH2, REMLSIRE hWH2, REMLMGS hWH2, and REMLANIM hWH2 for milk yield are shown in Table 2
for the large-herd subset. Mean hWH2 was highest when estimated with daughterdam regression (0.32) and lowest when estimated with REMLSIRE (0.19). Heritability estimates ranged from 0.04 to 0.45 for daughterdam hWH2, 0.01 to 0.64 for daughtersire hWH2, and 0.04 to 0.36 for REMLANIM hWH2. The hWH2 estimated with REMLANIM had standard errors ranging from 0.02 to 0.08. Daughtersire hWH2 could change by year within herd because the estimation of daughtersire hWH2 was dependent on herd-year SD. The intraclass correlation for daughtersire hWH2 ranged from 0.91 (fat yield) and 0.95 (milk yield), indicating that daughtersire hWH2 varied little across years within the same herd. Thus, daughtersire hWH2 were averaged across years for each herd when generating the correlations shown in Table 2
and in subsequent tables. Correlations among heritability estimates ranged from 0.31 between daughterdam and REMLSIRE hWH2 to 0.94 between REMLSIRE and REMLMGS hWH2.
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Table 2. Mean within-herd h2 (diagonal) for milk yield for daughterdam and daughtersire regressions, midparent,1 REMLSIRE,2 REMLMGS,3 and REMLANIM4 and correlations (above diagonal) among h2 for 45 large herds
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Average hWH2 for fat and protein yields and SCS followed trends similar to those for milk yield (Table 3
). Mean hWH2 for fat yield (0.33) and for SCS (0.21) were highest when estimated with daughterdam regression and highest for protein yield (0.30) with daughtersire regression. Mean hWH2 was lowest for protein (0.19) and fat (0.16) yields when estimated with REMLSIRE and lowest for SCS (0.03) with daughtersire regression.
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Table 3. Mean within-herd h2 for fat yield, protein yield, and SCS for daughterdam and daughtersire regressions, midparent,1 REMLSIRE,2 REMLMGS,3 and REMLANIM4 for 45 large herds
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Correlations among daughterdam, daughtersire, and midparent hWH2 with REML heritability estimates are given in Table 4
. Daughterdam hWH2 was most strongly correlated with REMLANIM (range 0.50 to 0.68), whereas daughtersire hWH2 was most strongly correlated with REMLMGS (range 0.27 to 0.67). For all traits, correlations of daughtersire hWH2 with REMLSIRE and REMLMGS were greater than correlations between daughterdam hWH2 and REMLSIRE or REMLMGS. Daughterdam hWH2 was also more strongly correlated with REMLANIM hWH2 than was daughtersire hWH2 for each trait. Correlations among REML hWH2 for SCS with daughterdam and daughtersire hWH2 were generally not significantly different from 0.
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Table 4. Correlations of within-herd h2 estimated with sire models, sirematernal grandsire (MGS) models, and animal models, with within-herd h2 estimated with daughterdam regressions (DDam), daughtersire regressions (DSire), and midparent average (Mid),1 for 45 large herds for milk, fat, and protein yields and SCS
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Correlations among hWH2 for yield traits and SCS (Table 5
) were positive for midparent and REMLANIM hWH2. Correlations for midparent hWH2 ranged from 0.41 between milk yield and SCS to 0.91 between milk and protein yields. Correlations for REMLANIM hWH2 tended to be smaller and ranged from 0.05 between milk yield and SCS to 0.89 between milk and protein yields. Correlations between daughterdam and daughtersire hWH2 for the same trait (not shown) also were positive and ranged from 0.23 for SCS to 0.46 for fat yield.
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Table 5. Correlations among milk, fat, and protein yields and SCS for midparent1 (above diagonal) and REMLANIM2 (below diagonal) within-herd h2 for 45 large herds
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Mean hWH2 Across All Herds
Estimates of hWH2 for yield traits and SCS were averaged for the 1,939 herds in the randomly selected data subsets (Table 6
). Results varied minimally across subsets, so only averages across subsets are reported. Mean all-herd hWH2 ranged from 0.24 (daughtersire hWH2 for milk yield) to 0.40 (daughterdam hWH2 for fat yield). The hWH2 for SCS appeared to be overestimated by the daughterdam regression (all-herd hWH2 = 0.24) and underestimated by the daughtersire regression (all-herd hWH2 = 0.06), but midparent hWH2 (all-herd hWH2 = 0.14) was closer to the h2 of 0.10 assumed for national evaluations (Schutz, 1994). Daughterdam hWH2 were considerably higher than daughtersire hWH2 for milk and fat yields and SCS, whereas daughtersire hWH2 was nearly the same for protein yield.
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Table 6. Mean within-herd h2 for milk, fat, and protein yields and SCS estimated with daughterdam and daughtersire regressions for 1,939 herds
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Treating heritability within herd as a random effect constrained hWH2 between 0 and 1 for milk yield and effectively regressed hWH2 toward the subset average. The daughtersire hWH2 was 0 for some herds in all data subsets and was as high as 0.93, whereas the range (0.04 to 0.67) was smaller for daughterdam hWH2. Heritability estimates generally stayed between 0 and 1 for fat and protein yields and SCS as well. Of 1,939 herds, 2 had a daughterdam hWH2 of <0 for 1 trait and 6 herds had a daughtersire hWH2 of >1 for 1 trait. The hWH2 estimation procedures of model 3 also resulted in heritability estimates that increasingly deviated from mean heritability as herd size increased. Variation in hWH2 for different herd sizes is shown in Figure 1
for daughterdam hWH2. Variance for hWH2 and the interquartile range increased as herd size increased. Medium-sized herds (251 to 500 records) had a larger range than herds with >1,000 records to estimate hWH2, but variance was greatest for herds with >1,000 records available.

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Figure 1. Box plot of daughterdam h2 estimates for milk yield by the total number of lactation records per herd (herd size) used to estimate hWH2. Median values are represented by the horizontal center line, the top and bottom of the shaded boxes represent the interquartile range, the vertical bars represent extreme values that are within 1.5 times the interquartile range, and the asterisks represent extreme values outside that range.
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Variation in milk yield hWH2 for different herd sizes with no fixed regression on dam milk yield is displayed in Figure 2
. The correlation of heritability estimates generated with and without b2D (from model [3]) was 0.75, and the range of hWH2 was greater (0.48 to 1.14) when b2D was removed. Heritability estimates for larger herds were similar with and without fixed regressions, but heritability was more variable for small herds. Heritability estimates were less than 0 for 15% of herds when b2D was removed. Heritability estimates for 3% of herds without b3S (from model [3]) and 0.5% herds without b4(Sb x SDk) were greater than 1. Removal of b4(S x SDk) deflated hWH2 for small herds with high phenotypic variance. Because b2lGl is treated as a random effect, the coefficient for small herds was regressed toward the subset average more severely than were coefficients for larger herds. This created a genetic SD estimate that is only marginally higher than the subset mean genetic SD. When combined with a high phenotypic variance estimate, the result is an underestimated hWH2. The reverse is true for small herds with low phenotypic variance, and the effect was a correlation of 0.45 between daughtersire hWH2 herd genetic SD without the interaction of b4(S x SDk) for milk yield, compared with 0.54 with the interaction.

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Figure 2. Box plot of daughterdam h2 estimates with no fixed regression coefficient for milk yield by the total number of lactation records per herd (herd size) used to estimate hWH2. Median values are represented by the horizontal center line, the top and bottom of the shaded boxes represent the interquartile range, the vertical bars represent extreme values that are within 1.5 times the interquartile range, and the asterisks represent extreme values outside that range.
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Correlations between daughterdam and daughtersire hWH2 for each trait are shown in Table 7
, as well as daughterdam and daughtersire correlations among traits. Correlations between daughterdam and daughtersire hWH2 ranged from 0.05 for milk yield to 0.13 for fat yield. For daughterdam hWH2, the correlation between SCS and milk yield was 0.08 compared with a correlation of 0.81 between milk and protein yields. Correlations were similar for daughtersire hWH2 and ranged from 0.02 between milk yield and SCS to 0.75 between milk and protein yields.
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Table 7. Correlations between daughterdam and daughtersire h2 (diagonal) and correlations among daughterdam h2 (above diagonal) and among daughtersire h2 (below diagonal) for yield traits and SCS for 1,939 herds
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Data Adjustments
The ratios of observed genetic variance to assumed true genetic variance for milk, fat, and protein yield and SCS are given in Table 8
. Low ratios are preferred, and ratios greater than 1.0 indicate that more fluctuation was observed than expected. The EBV were pooled across subsets to generate a sufficient sample size. Ratios were based on EBV for 64 sires for milk, fat, and protein yield, and 59 sires for SCS. The effect of adjusting for hWH2 on observed genetic variance was inconsistent across traits. Observed genetic variance was inflated for milk yield when no adjustment was made for hWH2 and was significantly less after adjusting for daughterdam (P = 0.04) and midparent (P = 0.02)
2WH . There was little impact on fluctuations in EBV for fat yield and fluctuations increased after adjusting for hWH2 for protein yield, but not significantly (P > 0.05). Fluctuations for SCS were generally less than expected except with midparent hWH 2 adjustments.
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Table 8. Ratio of genetic variance estimated from fluctuations in subsequent genetic evaluations to assumed true genetic variance ( 2a/ 2a) and the regression (b) of subsequent breeding values on previous breeding values before and after adjustment for within-herd h2 from daughterdam and daughtersire regressions, and midparent1
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Coefficients for the regression of EBV2004 on EBV2000 are also displayed in Table 8
. Regression coefficients were less than 1.0 in all cases, indicating some level of bias in the evaluations even when adjusted for hWH2. Adjusting for daughtersire hWH2 indicated the least bias in evaluations. Adjusting for daughterdam hWH2 decreased regression coefficients for all traits compared with no data adjustment. Significance tests are not provided for regression coefficients because of the inability to obtain the error variance of regression coefficients (Reverter et al., 1994).
The relationships between herd factors and midparent hWH2 are shown in Table 9
. All factors were significant (P < 0.05) and are arranged in order of the factor associated the largest proportion of variance based on type III mean square estimates (SD of milk yield) to lowest variance (region). The variance for percentage of cows identified with a registration number is based on linear + quadratic regression coefficients. Regression coefficients indicate that greater herd phenotypic SD, higher average milk yields, a higher percentage of registered cows, and an earlier age at first calving are associated with higher hWH2 . Midparent and daughtersire hWH2 were lower from herds in California, and larger herd size (represented by more first-lactation cows) was associated with lower hWH2 in California. Daughterdam hWH2 tended to be less strongly related to herd SD and herd average, and more strongly related to the percentage of registered cows than were midparent or daughtersire hWH2. Trends for fat yield, protein yield, and SCS were similar, except that herd average SCS was not significantly associated with hWH 2.
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Table 9. Type III mean square estimates ( 2), values for herds in the 10th and 90th percentiles, and predicted change in within-herd heritability ( hWH2) from the 10th to 90th percentile for the following independent variables: herd-standard deviation of mature-equivalent milk yield (milk SD), region (California, Northeast, Southeast, Wisconsin), average number of first-lactation animals calving per year (heifers, n) nested within region, herd average mature-equivalent milk yield (milk average), percentage of cows identified by a registration number (PCTHOL), and average age at first calving
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DISCUSSION
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A heritability estimated with daughterdam regression for 400 daughterdam pairs would have a standard error of approximately 0.10 (Falconer and Mackay, 1996). Therefore, accurate heritability estimates are difficult to obtain for a large proportion of US dairy herds, and methods that constrain hWH2 for smaller herds and allow hWH2 to deviate for larger herds would be preferred. Generating hWH2 with no fixed regression coefficients resulted in a significant increase in the number of herds with heritability estimates greater than 1 or less than 0. However, methods with fixed regression coefficients successfully constrained hWH2 for small herds while allowing hWH2 from large herds to deviate from sample means. Including sire PTA and herd SD interactions was necessary to derive genetic variance estimates from daughtersire regression. Including an interaction between sire PTA and herd SD assumes that a genotypeenvironment interaction exists and that the response to selection will be less in herds with low phenotypic variance. Reduced selection response in herds with low phenotypic variances has been documented (Kearney et al., 2004). The genetic variance estimate will still be accurate, provided there is minimal reranking of bulls across environments. Within-herd h2 was regressed toward the subset mean in the current study, whereas hWH2 is indirectly regressed toward regional averages (by regressing herd phenotypic SD toward the regional phenotypic SD average) in the current procedures for national genetic evaluations in the United States (Wiggans and VanRaden, 1991).
Within-herd h2 could be regressed toward herd parameters that influence hWH2 . Herd average and SD, region of the country or state, percentage of registered cows, herd size, and average age at first calving were all significantly associated with hWH2 . Herds with greater phenotypic variance had higher heritability, which is consistent with other studies (Van Tassell et al., 1999). The heritability of yield has previously been estimated to be lower in California than in New York or Wisconsin, and heritability estimates are higher when estimated with registered daughters (Carabaño et al., 1990; Dimov et al., 1995). Larger herd size was associated with reduced heritability in some regions, which is consistent with results from Zwald et al. (2003). Although these herd parameters give some indication of hWH2 , the total variance explained by the multiple regression model was 31% (R2 = 0.31), indicating that the majority of variance in hWH2 was not accounted for by the factors analyzed.
Daughterdam hWH2 generally were higher than daughtersire hWH2. For SCS, daughterdam hWH2 were approximately twice as high (0.24) as the parameters used for national genetic evaluations (Schutz, 1994) and 4 times greater than daughtersire hWH2 . Daughterdam hWH2 for milk yield were higher than previously reported heritability estimates from paternal half-sibling correlations (Van Vleck and Bradford, 1965; Van Vleck and Bradford, 1966). Environmental effects common to daughters and dams likely inflate daughterdam hWH2 , as would any maternal or cytoplasmic effects (Van Vleck and Bradford, 1965). The relative ranking among herds for daughterdam hWH2 would be accurate if common environmental and maternal effects were similar across herds.
Lower daughtersire hWH2 could also indicate that sire misidentification is more common than dam misidentification. Sire misidentification would have a minimal impact on daughterdam hWH2 , and presumably influence hWH2 from REMLSIRE and REMLMGS more severely than REMLANIM. Daughterdam hWH2 was not as strongly correlated with hWH 2 generated from REMLSIRE and REMLMGS. Conversely, daughtersire hWH2 was more strongly correlated with hWH 2 generated by REMLMGS than hWH2 generated with REMLANIM.
Because of an interaction between genotype and environment, daughtersire hWH 2 would be biased downward more severely than would daughterdam hWH 2 . Both dam and daughter were required to be from the same herd, which would limit the effect of a genotypeenvironment interaction on hWH 2 estimates. Sire PTA are generated across herds, and regression on sire PTA would be depressed if a genotypeenvironment interaction existed. Variance of the sireherd interaction can be combined with additive genetic variance to estimate mean hWH 2 across herds (Notter et al., 1992). The herdsire interaction was estimated to be approximately 2% of phenotypic variance for milk yield in Holsteins (Dimov et al., 1995), which indicates that daughtersire hWH 2 could be appreciably depressed by the presence of a genotypeenvironment interaction.
The effect of data adjustment on EBV fluctuations was inconsistent and only daughtersire hWH 2 adjustments increased regression coefficients of EBV2004 on EBV2000. Some possible negative impacts of adjusting for hWH 2 should be considered. Daughterdam regression could expand the influence of preferential treatment. Preferential treatment within certain cow families is likely to increase daughterdam hWH 2 , and genetic evaluations that adjust for daughterdam hWH 2 would weight those records even more heavily. In addition, the method used to generate daughtersire hWH 2 has partwhole influences. Records are weighted more heavily in herds in which daughter yield is highly correlated with past sire evaluations, which could create a stronger relationship between daughter performance and sire evaluations in future evaluations and inflate future daughtersire hWH2. Alternative uses for hWH2 might avoid such issues and should be investigated. Reliability could be adjusted to reflect the impact of hWH2. Progeny-test herds with low hWH may be candidates for DNA parentage verification or removal from progeny-test programs.
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CONCLUSIONS
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Estimates for hWH 2 can be generated using the regression of daughter records on dam records and the regression of daughter records on sire PTA with moderate accuracy. Daughterdam hWH 2 were a stronger indicator of heritability estimated with an animal model, whereas daughtersire hWH 2 were stronger indicators of heritability estimated with sire and sireMGS models. Both daughterdam and daughtersire methods demonstrate that significant differences exist among herds for heritability. Those differences could result from variability in recordkeeping (especially more accurate pedigrees), genotypeenvironment interaction, or other identifiable herd factors, including the percentage of registered cows, herd size, herd average yield or SCS, herd standard deviations for yield and SCS, average age at first calving, and region of the country. Heritability differences among herds could substantially alter the accuracy of EBV depending on the average hWH 2 of the herds in which a bulls daughters are located.
Data adjustments generally did not reduce fluctuations in subsequent genetic evaluations and only daughtersire hWH 2 improved regressions of subsequent EBV. For the methods that were investigated, the effect of preferential treatment on hWH 2 is not clear, or whether partwhole influences from past genetic evaluations would artificially inflate hWH 2 for some herds. Other methods of incorporating hWH 2 into genetic evaluations, such as adjusting reliability estimates based on hWH 2 , that would avoid effects of preferential treatment and partwhole relationships should be investigated.
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ACKNOWLEDGEMENTS
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The authors appreciate funding from the Agricultural Research Service, USDA. The cooperation of AgriTech Analytics (Visalia, CA), AgSource Cooperative Services (Verona, WI), Dairy Records Management Systems (Raleigh, NC), DHI Computing Services (Provo, UT), and Texas DHIA (College Station, TX) in supplying yield data through the National Genetic Improvement Program was invaluable. The assistance of S. M. Hubbard, Animal Improvement Programs Laboratory (Beltsville, MD), and 2 anonymous reviewers in manuscript preparation is appreciated.
Received for publication December 30, 2005.
Accepted for publication August 9, 2006.
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