Heritability Estimates for Conformation Traits in the Holstein Breed Gladys Huapaya and Gerrit Kistemaker Canadian Dairy Network Introduction The classification system used in Canada has received a major revision in 2005; however, the heritabilities that are used in routine genetic evaluations were estimated in May 2006 using classification records recorded prior to this change. At the moment more than 5 years of data from the new system is available which is enough data to estimate the heritability. The routine genetic evaluation for type traits uses a two trait model where data prior to the change in August 2005 is used as one trait and data after August 2005 is assumed to be a different but highly correlated trait. The objective of this study was to estimate the heritabilities and correlation for the current Classification System using Holstein data. Data and Methods Holstein data and pedigrees files from the December 2010 proof run were used in this study. Classification records for animals calving at less than 21 months of age or over 42 months were removed, and only first classification records from 1999 and later were used. Only records from herds with at least 35 classified records in at least 7 rounds for both the old and the current system were selected to ensure sufficient connections between both data sets. After data edits 646,780 records from the old classification system (rounds 61 to 71) and 618,030 records from the current classification system (rounds 72 to 80) remained. Twenty independent data samples were created by randomly selecting herds until each data sample contained approximately 40,000 classifications records. On average 51% of the records were from the old classification system and the remaining 49% of the records were from the current classification system. Parameters were estimated using Variance Components Estimation (VCE) software package. For each trait the following model was used: Y=Age*Stage*Time + Herd*Round*Classifier + Animal +e This model is the same to the current genetic evaluation system for type. Each trait was analyzed separately and data from the old and current classification system were treated as genetically correlated traits.
Results and Discussion Estimated heritabilities, averaged across 20 samples, are shown in Table 1. This table also includes the heritability values that are currently used in the routine genetic evaluations ( Official ) which were estimated using data from the old classification system in May 2006. Table 1. Heritabilities and correlations currently used in Official Genetic Evaluations and estimates using December 2010 data from Old and Current System for the Holstein Breed. TRAIT Official Estimated Heritability Correlation Heritability Old Heritability Current Correlation Conformation 0.26 0.98 0.27 0.21 ** 0.93 (max.99) Dairy Strength 0.36 0.95 0.35 0.24 ** 0.96 Rump 0.23 0.98 0.24 0.23 0.95 Feet and Legs 0.15 0.98 0.16 0.12 * 0.89 Mammary System 0.25 0.98 0.25 0.24 0.95 Stature 0.53 M 1.00 0.52 M 0.45 ** 0.98 Front End 0.26 1.00 0.26 0.24 * 0.97 Chest Width 0.22 1.00 0.22 0.18 ** 0.96 Body Depth 0.32 1.00 0.32 0.29 * 0.97 Loin Strength 0.25 1.00 0.26 0.19 ** 0.98 Pin Width 0.34 M 1.00 0.34 M 0.31 ** 0.98 Pin Setting 0.09 1.00 0.09 0.07 ** 0.99 Rump Angle 0.37 M 1.00 0.41 M 0.39 * 0.98 Bone Quality 0.30 1.00 0.31 0.26 ** 0.98 Foot Angle 0.11 1.00 0.10 0.09 * 0.98 Heel Depth 0.08 1.00 0.08 0.07 0.93 Set of Rear Legs 0.05 1.00 0.05 0.04 ** 0.91 Rear Legs Side View 0.24 1.00 0.23 0.20 * 0.96 Rear Legs Rear View 0.12 1.00 0.12 0.11 0.93 (max.98) Udder Depth 0.41 M 1.00 0.42 M 0.42 0.99 Udder Texture 0.14 1.00 0.16 0.14 ** 0.92 Median Suspensory 0.14 1.00 0.15 0.17 * 0.96 Fore Attachment 0.28 1.00 0.28 0.24 ** 0.98 Fore Teat Placement 0.31 1.00 0.32 0.30 * 0.99 Teat Length 0.29 M 0.95 0.29 0.30 0.95 Rear Attachment Height 0.23 M 1.00 0.23 M 0.23 0.95 Rear Attachment Width 0.20 M 1.00 0.19 M 0.20 0.95 Rear Teat Placement 0.29 1.00 0.30 0.29 0.99 Angularity 0.26 1.00 0.26 0.17 ** 0.97 M Calculated using measurement data. Old and Current heritabilities are: * significant different at 5% level and ** highly different at 1% level.
The estimated heritability for the traits using the Old data were similar to the heritabilities that are currently used (estimated using Old data in May 2006). Comparison of the heritability estimates from the old and the current system shows that for the majority of the traits the heritabilities using records from the current classification system were lower than estimates using data from the old classification system. For 13 traits the differences were significant at the 1% level and an additional 9 trait were significantly different at the 5% level, in all these cases the heritability was lower when using records from the current system. Comparing heritability estimates for the current classification system (estimated using the two trait model) to those used in official routine genetic evaluations (table 1 and figure 1) shows that most heritabilities decreased. The median genetic correlation between the two systems ranged from 0.89 to 0.99 depending on the trait. For most traits the range of estimates (since there were 20 replicates) included 1 indicating that it is possible that the actual genetic correlation between the two systems is 1. The two exceptions were Conformation (the maximum was 0.99) and Rear leg rear view (maximum was 0.98) indicating that for these traits the correlation is less than 1. Conclusion and Recommendation The data available from the current classification system has accumulated for over 5 years (since August 2005) and contain numerous dam-daughter pairs with records. Estimated heritabilities from this research show that estimates using records from the old system are comparable to previous estimates but estimates for the current system are lower. Therefore, it is recommended to implement the heritabilities estimated using current data. Estimation of heritabilities for the other breeds is ongoing. Impact on proofs In order to evaluate the impact of the recommendation on bull proofs and cow indexes the estimated heritabilities (using current data) were used together with the April 2010 pedigree and data file to calculate proofs and indexes and results were compared to the official proofs. Due to the decrease in heritability of Conformation the estimated reliability decreased by 2 to 3 points in bull proofs (Table 2) and around 4 points for cow indexes (Table 3). As a result 58 bulls lost their official domestic proof, most of these bulls were foreign proven so these bulls would receive a MACE proof instead. Changes in proofs and indexes for the major type traits are shown in Tables 2 and 3. The largest change in proofs was observed for Dairy Strength which is expected since this is the
trait with the largest change in Heritability. In nearly all cases bull proofs remained the same or changed by 1 point but in a few cases changes of 2 points were observed. Changes in cow proofs indexes were larger than for bull proofs but for most traits hardly any cow indexes changed by more than 2 points. The exception were Dairy Strength, Stature and Angularity (which had a large change in heritability) which had a wider distribution of changes. Table 2. Impact of using the estimated heritabilities on bull proofs and reliability. Change in Reliability and Proof Trait -5-4 -3-2 -1 0 1 Reliability 1 260 3082 3588 681 380 Conformation 484 7017 491 Dairy Strength 2 1088 6087 815 Rump 303 7355 334 Feet and Leg 920 6428 644 Mammary System 411 7313 268 Table 3. Impact of using the estimated heritabilities on cow indexes and reliability. Change in Reliability and Index Trait -6-5 -4-3 -2-1 0 1 2 3 4 5 Reliability 202 25201 489217 1590427 320222 1366 14 Conformation 1120 378543 1655839 388421 2726 Dairy Strength 4 152 7763 128306 630478 989347 548081 113253 8939 321 5 Rump 46840 2222740 157069 Feet and Leg 864 369164 1734486 321362 773 Mammary System 55629 2157730 213275 15