Scope for the Use of Pregnancy Confirmation Data in Genetic Evaluation for Reproductive Performance

Transcription

1 Scope for the Use of Pregnancy Confirmation Data in Genetic Evaluation for Reproductive Performance J. Jamrozik and G.J. Kistemaker Canadian Dairy Network The data on cow's pregnancy diagnostics has been included in the CDN's data base since The use of the data that confirm (or exclude) pregnancy would be beneficial in defining phenotypes for some traits, that are the subject of genetic evaluation in the Canadian system for reproductive performance. This refers, in particular, to the interval from the First Service to Conception () (expressed in days), that currently is determined based only on the subsequent calving records. This is an important trait; for cows has the weight of 25 in the Daughter Fertility index. in heifers is genetically correlated with expressed in later parity cows (correlation of 0.67) which indicates the importance of heifer. Shortening the time interval in which phenotypes on are available would contribute to more timely and accurate genetic evaluation for female fertility. The objective of this project was to examine the possibility of using pregnancy check data in the genetic evaluation system for female reproductive performance. Data on individual pregnancy checks included: - Cow id, - Herd id, - Calving date, - Observation date, - Days in milk (DIM), and - Result of the examination. The codes that indicate how the pregnancy check was done (e.g. palpation, ultrasound, milk analysis, or other) are not uploaded into Vision2000 and thus are not available at CDN (R. Moore, pers. comm.). The February 2016 pregnancy check data on all Canadian dairy breeds were extracted and edited for: - year of examination (>1999). Similarly, national genetic evaluation fertility data for February 2016 was extracted and further edited for: - parity (<6), and - year of last insemination (>1999). The characteristics of both data sets (pregnancy and fertility), by breed, are in Table 1. Distribution of Holstein pregnancy check data by recent years of examination 1

2 ( ) is given in Table 2. Table 3 shows the summary of fertility data by parity (Holsteins only), with respect to Calving to First Service (CTFS) and traits. The same statistics by years of first insemination for the Holstein breed are in Table 4. Validation of pregcheck derived data using subsequent calving records Calving records in 2013 were matched with the confirmed pregnancy data from to assign for the overall, breed specific, validation. The matching procedure was preformed seperately for heifers and cows and the martching criteria were: - Cow id, - Examination date < Calving date (in the fertility data), and - Last insemination date (in the fertility data) +29 < Examination date < Last insemination (in the fertility data) Results of this validation are in Tables 5 and 8 for heifers and cows, respectively. Missing data on for was recovered by matching pregnancy check and fertility data with missing (10 last months of the data discarded) for Holsteins only. The matching criteria were: - Cow id (for heifers) or Cow id by (previous) calving date (for cows) - Last insemination (in the fertility data) +29 < Examination date < Last insemination (in the fertility data) The estimated for records with confirmed pregnancy (result of the pregnancy check = 1) was further edited as 0 < estimated < 207. Results, by year of first service, are in Tables 6 and 9 for heifers and cows, respectively. Finally, the recovery process for missing was restricted to herds that passed a minimal threshold criterion (= constant) for a validation defined as: - (Number of Confirmed Pregnancies in Resulted in Calvings in 2013/Number of Calving in 2013)*100 > constant, with the matching criterion being the same as for the breed specific validation. Only herds that passed the validation were included in the recovery process and the validation was performed seperately for heifers and cows. Four values of the constant (0, 25, 50, and 75) were tested and compared to the 'No validation' scenario, for missing in the last three years of the fertility data that were the subject of recovery ( ). Results are in Table 7 and 10 for heifers and cows, respectively. Validation of the procedure for pregcheck derived data using fertility data The method of calculating using the pregcheck data was validated using the phenotypes for included in the official fertility data for the Holstein breed. with in the ferility data were selected and then matched with the 'new' calculated using the procedure that was described earlier. All herds were included 2

3 i.e. no herd validation procedure was applied. Results, by year of the first service, are in Table 11. Finally, the precheck data based recovery method for missing in the official fertility data was applied for the Holstein breed using fertility data for year of the first service greater than 2007 and no restrictions on the data due to herd validation. Results, overall and for first insemination in , and separately for heifers and cows are in Table 12. Observations 1. Only selected herds (up to approx. 50 of Holstein herds with the reproductive traits data) have participated up till now in the pregnancy diagnostics data collection. 2. Majority of the pregnancy check data consisted of records confirming the pregnancy. CanWest DHI collects only records with confirmed pregnancy (R. Moore, pers. comm.). 3. The amount of pregnancy check data increased in time; average DIM (for cows in milk) decreased, and the proportion of cows with non-confirmed pregnancy increased with the calving year. 4. Proportion of missing records in the current Holstein fertility data increased with the parity number. Based on averages and, seemed to be different phenotypic trait across parities. 5. Proportion of missing records in Holsteins stayed approximately constant for earlier calving years (up to 2013) and then increased (up to 100 in 2015). This means that approximately 30 cows with insemination data does not have a corresponding calving records (e.g. embrio loss, pregnancy aborted, or a cow culled or transferred later during lactation). Consequently, the current trait which is used for genetic evaluation purposes is, in fact, the 'First Service to Conception Resulted in a Calving' trait. Both traits are not necessary (and probably not) equivalent, particularly in a genetic context. 6. The overall breed validation results bases on calving data were poor; only GU and HO exceeded the 50 of the overall validation success for heifers. This indicated again a strong selective participation of herds (or/and cows within a herd) in a pregnancy check data collection. 7. The matching of fertility and pregnancy check data procedure resulted in relatively good overall recovery rate across all years in Holsteins. The correct was successfully estimated for a smaller proportion of missing records. Estimated were similar in means and for different years of first service, with the exception of the last two years (2014 and 2015) when the average newly estimated was slightly shorter. Estimated average () for were also larger (~ 2 days for heifers and ~3 days for cows in milk) then estimated using the 'subsequent calving' data. 8. Recovery of with the within herd validation for Holsteins performed in a similar way for a no validation scenario and validations with different minimal validation criteria of a moderate values (up to 50). Stronger validation options (i.e. 75) resulted in a significant drop in size of the estimated data. Summary and Recommendations 1. Pregnancy diagnostic data seems to be potentially useful in recovering missing. 3

4 2. Very high proportion of positive pregnancy checks does not limit the usefulness of this data for calculation. Similarly, the use of pregcheck data for selective herds (as well as cows within herds) should not be a source of biases for the proposed procedure. 3. Current and the estimated from the pregnancy check data could be different traits. Using both as one phenotype in genetic evaluation might therefore be not straightforward. 4. Genetic parameters for reproductive traits including the newly defined should be re-estimated. 5. The present level of pregnancy check recording does not allow to take into account a proper (within herd) validation of the data for the inclusion in the early recovery process. No herd validation approach based on the calving data is recommended. 6. The procedure of estimating censored data from the pregnancy check results works well as indicated by a perfect agreement with the inseminations that could be confirmed by calving. 7. Only insemination data from 2008 and on should be used for calculating missing records with the pregcheck data. 8. in the Canadian model for reproductive performance should be redefined as 'First Service to Conception' replacing the current 'First Service to Conception confirmed by a subsequent calving' definition. 9. No immediate implementation of using pregnancy check data in the genetic evaluation system for female fertility traits is possible without testing and comparing evaluations with the new phenotypes. 4

5 Table 1: Fertility and pregnancy confirmation data summary, by breed Breed Fertility Pregnancy Herds Herds DIM Positive Ayrshire 53, , Brown Swiss Canadienne Guernsey Heifers Holstein 2,286,143 16, , Jersey 51, , Milking Shorthorn Ayrshire 177, , Brown 27, , Swiss Canadienne Guernsey Cows Holstein 6,300,895 18,716 2,694, Jersey 150, , Milking Shorthorn Table 2: Summary of Holstein pregnancy check data, by pregnancy check year ( ) Year Average DIM Positive 2010 Heifers 110, , , , , , Cows 315, , , , , ,

6 Table 3: Calving to First Service (CTFS) and First Service to Conception () statistics for Holsteins, by parity Parity CTFS Missing ,573, ,323, ,650, ,637, ,085, ,001, , , , , , Relative to 'CTFS records' Table 4: Age at First Service (AFS), Calving to First Service (CTFS) and First Service to Conception () statistics for Holsteins, by year of first service Year AFS (heifers)/ctfs (cows) Missing , , , , , , Heifers 166, , , , , , , , , Cows 417, , , , , , , Relative to 'AFS ' for heifers or 'CTFS ' for cows 6

7 Table 5: Overall validation results for heifers Breed Calving (2013) Confirmed Pregnant Matched Matched 1 ( ) Ayrshire Brown Swiss Canadienne Guernsey Holstein 150, ,758 79, Jersey Milking Shorthorn 1 Relative to 'Calving (2013)' Table 6: Recovery statistics for First Service to Conception () for Holstein heifers (parity = 0), by year of first service Year Matched Estimated with Correct Correct ,723 10, , ,248 44, ,721 29, Relative to ' Matched' Table 7: Herd specific validation 1 results for Holstein heifers (parity = 0) in (year of first service) Threshold for Validation Criterion 1 Recovered Recovered 2 Recovered 2 None , , , , , , , , , , Within herd: (No. of confirmed pregnancies in resulted in calvings in 2013/No. of calving records in 2013)*100 2 Relative to heifer records in 2012 (133,660) 2 7

8 Table 8: Overall validation results for cows Breed Calving (2013) Confirmed Pregnant Matched Matched 1 ( ) Ayrshire , Brown Swiss Canadienne Guernsey Holstein 344, , , Jersey 10,603 19, Milking Shorthorn 1 Relative to 'Calving (2013)' Table 9: Recovery statistics for First Service to Conception () for Holstein cows (parity > 0), by year of first service Year Missing 1 Matched Matched 2 Estimated with Correct Correct ,062 36, , ,582 32, , ,231 34, , ,952 37, , , , , ,507 78, , with CTFS and with missing 2 Relative to ' Missing' 3 Relative to ' Matched' Table 10: Herd specific validation 1 results for Holstein cows (parity > 0) in (year of first service) Threshold for Validation Criterion 1 New Correct New Correct 2 New Correct 2 None 29, , , , , , , , , , , , , , , Within herd: (No. of confirmed pregnancies in resulted in calvings in 2013/No. of calving records in 2013)*100 2 Relative to cow records in 2012 (293,531) 8

9 Table 11: Comparison of from the fertility data and calculated using pregnancy check data, by year of first service Year Heifers Cows Number 1 Number 1 of records of records , , , , , , , , , , , , , , Averages and were identical for extracted from the fertility data and calculated using pregcheck data 9

10 Table 12: Summary of the use of pregnancy check for recovery (for years of the first service ), by breed Breed From February 2016 extract Calculated from pregcheck data combined New heifers New cows N 159, , Ayrshire Brown Swiss Cannadie nne Guernsey Holstein Jersey N 22, , N N N 5,645, ,659 6,063, ,516 29,506 26, ,820 76, N 130,137 10, , Milking Shorthorn N Year of first service