Heritability Estimates for Conformation Traits Gladys Huapaya and Gerrit Kistemaker Canadian Dairy Network

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1 Heritability Estimates for Conformation s 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 current 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 correlations for the current Classification System using Ayrshire and Jersey data and to present the estimated heritabilities for all breeds. The second objective was to show the impact of using estimated heritabilities (as recommended by the DCBGC in March 2011) in the calculation of bull proofs and cow indexes. Data and Methods Holstein data and pedigrees files from the December 2010 proof run were used in this research. Ayrshire and Jersey data and pedigrees files were more recent and were from the official April 2011 proof run. 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. Records from herds with at least 35 classified records in at least 7 rounds for both the old and the current system were selected. 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) were available for 29 linear and 7 measured traits in the Holstein breed. 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. More extensive results were presented at the previous meeting. For Ayrshire, after editing 36,778 records were available for the 29 linear traits (52% from old and 48% from the current classification system). For Jersey, 19,748 records were available for the 29 linear traits (49.6 % from old and 50.4 %

2 from the current classification system). For each of these breeds this data set was used in a single analysis to estimate heritabilities for each trait. For each data set the parameters were estimated using the 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 very similar to the model used in 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. Some of the traits were added in 2005 (Ayrshire and Jersey) and as a result these traits had no data in the old system, to be able to get proofs for all bulls a related trait was used as the old data and this is indicated in the result tables. Results and Discussion Estimated heritabilities for Holstein, 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 The estimated heritability for the traits using the old data were similar to the heritabilities that are in use (estimated using similar 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 case 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 shows (Table 1 and Figure 1) that most heritabilities would go down if these new estimates are implemented. The median genetic correlations 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 correlation 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.

3 Estimated heritabilities for Ayrshire and Jersey are shown in Table 2 and 3. These tables 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 Heritabilities used for the others breeds (Table 4, Brown Swiss, Guernsey, Canadienne and Milking Shorthorn) were calculated as the average of the estimated heritabilities for Ayrshire and Jersey. Table 4 also shows 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 The estimated heritabilities in Ayrshire and Jersey follow the same tendency as in Holstein. Estimates using the old data were similar to the heritabilities that are currently used (estimated using similar data in May 2006). 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. One of the biggest changes was observed for Pin Setting in Ayrshire, heritability estimates using the old data were around 0.20 while estimates from the current data were 0.02 which is much more in line with the other breeds. The genetic correlations between the two systems ranged from 0.55 to 1.00 for Ayrshire and from 0.63 to 1.00 for Jersey when the same trait was available in the old and current systems. When a different trait was substituted the estimated correlation tended to be lower, especially for Teat Length. The impact of applying the heritabilities estimated using the current data (shown in bold in Tables 1 to 4) without changing the correlation between traits (as recommended by the DCGBC in March 2011) is shown in tables 5 and 6. Changes in bull proofs (Tables 5a to 5g) and cow indexes (Table 6a to 6g) are fairly small for most traits. Some traits have larger changes in proofs and indexes due to a larger change in the heritability. The largest change is observed in Ayrshire due to a drop in the heritability from 0.20 to Conclusion and Recommendation Estimated heritabilities using data from the old system are comparable to previous estimates but estimates for the current system are lower. Based on the DCGBC recommendation in March 2011 proofs using estimated heritabilities from the current system were submitted to the September Interbull test run. It is recommended to implement these heritabilities in the December 2011 official proof run.

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5 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 ** 0.93 (max.99) Dairy Strength ** 0.96 Rump Feet and Legs * 0.89 Mammary System Stature 0.53 M M 0.45 ** 0.98 Front End * 0.97 Chest Width ** 0.96 Body Depth * 0.97 Loin Strength ** 0.98 Pin Width 0.34 M M 0.31 ** 0.98 Pin Setting ** 0.99 Rump Angle 0.37 M M 0.39 * 0.98 Bone Quality ** 0.98 Foot Angle * 0.98 Heel Depth Set of Rear Legs ** 0.91 Rear Legs Side View * 0.96 Rear Legs Rear View (max.98) Udder Depth 0.41 M M Udder Texture ** 0.92 Median Suspensory * 0.96 Fore Attachment ** 0.98 Fore Teat Placement * 0.99 Teat Length 0.29 M Rear Attachment Height 0.23 M M Rear Attachment Width 0.20 M M Rear Teat Placement Angularity ** 0.97 M Calculated using measurement data. Old and Current heritabilities are: * significant different at 5% level and ** highly different at 1% level.

6 Table 2. Heritabilities and correlations currently used in Official Genetic Evaluations and estimates using April 2011 data from Old and Current System for the Ayrshire Breed. TRAIT Official Estimated Heritability Heritability Correlation Heritability Heritability Correlation Ayrshire Holstein Old Current Conformation Dairy Strength (DS) Rump Feet and Legs (FL) Mammary System Stature Front End DS Chest Width Body Depth DS Loin Strength Pin Width Pin Setting Rump Angle Bone Quality Foot Angle (FAN) Heel Depth FAN Set of Rear Legs Rear Legs Side View Rear Legs Rear View FL Udder Depth Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length DS Rear Attachment Height Rear Attachment Width Rear Teat Placement Angularity DS

7 Table 3. Heritabilities and correlations currently used in Official Genetic Evaluations and estimates using April 2011 data from Old and Current System for the Jersey Breed. TRAIT Official Estimated Heritability Heritability Correlation Heritability Heritability Correlation Jersey Holstein Old Current Conformation Dairy Strength (DS) Rump Feet and Legs (FL) Mammary System Stature Front End DS Chest Width Body Depth DS Loin Strength Pin Width Pin Setting Rump Angle Bone Quality Foot Angle (FAN) Heel Depth FAN Set of Rear Legs Rear Legs Side View Rear Legs Rear View FL Udder Depth Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length 0.29 M 0.50 DS Rear Attachment Height Rear Attachment Width Rear Teat Placement Angularity DS

8 Table 4. Heritabilities and correlations currently used in Official Genetic Evaluations and estimates using April 2011 data from Old and Current System for the Brown Swiss, Guernsey, Canadienne and Milking Shorthorn. TRAIT Official Estimated Heritability Heritability Correlation Heritability CB Holstein Current Conformation Dairy Strength (DS) Rump Feet and Legs (FL) Mammary System Stature Front End Chest Width Body Depth Loin Strength Pin Width Pin Setting Rump Angle Bone Quality Foot Angle (FAN) Heel Depth Set of Rear Legs Rear Legs Side View Rear Legs Rear View Udder Depth Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length Rear Attachment Height Rear Attachment Width Rear Teat Placement Angularity

9 Table 5a. Change in Holstein bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

10 Table 5b. Change in Ayrshire bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

11 Table 5c. Change in Jersey bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

12 Table 5d. Change in Brown Swiss bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) 226 Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View 226 Udder Depth (meas) Udder Texture 226 Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) 226 Rear Teat Placement Angularity

13 Table 5e. Change in Guernsey bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) 153 Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View 153 Udder Depth (meas) Udder Texture 153 Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) 153 Rear Teat Placement Angularity

14 Table 5f. Change in Canadienne bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) 44 Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View 2 42 Rear Leg Rear View 44 Udder Depth (meas) Udder Texture 44 Median Suspensory Fore Attachment 42 2 Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) 44 Rear Teat Placement 44 Angularity

15 Table 5g. Change in Milking Shorthorn bull proofs when using the new heritabilities. Change in Proof < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) 37 3 Pin Setting Rump Angle (meas) 5 35 Bone Quality 36 4 Foot Angle Heel Depth 33 7 Set of Rear Legs Rear Leg Side View Rear Leg Rear View 37 3 Udder Depth (meas) 6 34 Udder Texture Median Suspensory 35 5 Fore Attachment Fore Teat Placement 36 4 Teat Length (meas) 31 9 Rear Attachment Height(meas) Rear Attachment Width (meas) 33 7 Rear Teat Placement 37 3 Angularity

16 Table 6a. Change in Holstein cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

17 Table 6b. Change in Ayrshire cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

18 Table 6c. Change in Jersey cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

19 Table 6d. Change in Brown Swiss cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

20 Table 6e. Change in Guernsey cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity

21 Table 6f. Change in Canadienne cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) 3651 Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View 3651 Udder Depth (meas) Udder Texture 3651 Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) 3651 Rear Teat Placement Angularity

22 Table 6g. Change in Milking cow indexes when using the new heritabilities. Change in Index < Conformation Dairy Strength Rump Feet & Legs Mammary System Stature (meas) Height at Front End Chest Width Body Depth Loin Strength Pin Width (meas) Pin Setting Rump Angle (meas) Bone Quality Foot Angle Heel Depth Set of Rear Legs Rear Leg Side View Rear Leg Rear View Udder Depth (meas) Udder Texture Median Suspensory Fore Attachment Fore Teat Placement Teat Length (meas) Rear Attachment Height(meas) Rear Attachment Width (meas) Rear Teat Placement Angularity