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 2000. 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
(2010-2016) 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 2012-13 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) + 89. 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) + 89. 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 2012-2013 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 (2013-15). 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
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 2013-2015, 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
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
Table 1: Fertility and pregnancy confirmation data summary, by breed Breed Fertility Pregnancy Herds Herds DIM Positive Ayrshire 53,943 1072 13,788 358 89 Brown 8890 535 4002 210 96 Swiss Canadienne 1445 160 335 37 89 Guernsey Heifers 2290 103 748 39 99 Holstein 2,286,143 16,061 972,779 7580 97 Jersey 51,162 2732 22,638 999 97 Milking Shorthorn 770 79 682 33 100 Ayrshire 177,978 1791 46,698 694 198 79 87 Brown 27,526 864 12,789 375 211 88 93 Swiss Canadienne 5048 188 1557 63 201 83 85 Guernsey Cows 6808 133 2287 52 241 94 97 Holstein 6,300,895 18,716 2,694,811 9609 203 85 93 Jersey 150,572 3685 72,289 1588 205 83 96 Milking Shorthorn 3347 110 2130 58 210 77 100 Table 2: Summary of Holstein pregnancy check data, by pregnancy check year (2010-2016) Year Average DIM Positive 2010 Heifers 110,309 98 2011 124,810 97 2012 132,288 97 2013 137,575 96 2014 145,572 96 2015 134,341 96 2016 1811 97 2010 Cows 315,868 208 94 2011 340,291 205 93 2012 358,374 201 93 2013 366,385 198 92 2014 395,138 197 91 2015 394,502 196 90 2016 4701 202 91 5
Table 3: Calving to First Service (CTFS) and First Service to Conception () statistics for Holsteins, by parity Parity CTFS Missing 1 0 - - - 1,573,937 17.9 33.5-1 2,323,532 88.8 33.4 1,650,433 33.9 46.2 30 2 1,637,498 87.6 32.4 1,085,458 37.7 48.1 34 3 1,001,569 87.8 32.4 623,146 38.6 48.6 38 4 537,248 88.6 32.7 311,945 40.1 49.4 42 5 256,491 89.2 33.1 140,212 41.6 50.3 45 1 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 1 2010 158,958 458.9 121.7 120,639 17.9 33.3 24 2011 166,390 450.6 128.1 129,305 18.5 33.8 22 2012 167,637 455.6 107.8 133,660 18.7 33.7 20 2013 Heifers 166,983 453.0 101.9 132,448 19.0 33.9 21 2014 168,842 449.6 100.5 79,429 18.7 33.7 53 2015 130,618 286.7 241.0 - - - 100 2016 128 246.2 246.2 - - - 100 2010 396,136 87.4 32.5 269,074 38.7 48.8 34 2011 398,718 86.2 31.8 285,136 38.1 48.2 28 2012 Cows 417,762 84.8 31.1 293,531 37.6 47.9 30 2013 408,626 84.4 30.8 284,674 37.7 47.9 30 2014 406,372 83.3 30.3 168,321 38.1 48.4 59 2015 234,507 87.3 33.3 - - - 100 2016 221 99.9 45.2 - - - 100 1 Relative to 'AFS ' for heifers or 'CTFS ' for cows 6
Table 5: Overall validation results for heifers Breed Calving (2013) Confirmed Pregnant Matched Matched 1 (2012-2013) Ayrshire 3216 3746 974 30 Brown Swiss 601 965 238 40 Canadienne 99 89 16 16 Guernsey 140 216 70 50 Holstein 150,527 264,758 79,715 53 Jersey 3703 6040 1558 42 Milking 71 186 29 41 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 1 2010 9942 9492 95 21.2 37.4 2011 10,723 10,239 95 21.4 36.1 2012 9577 9025 94 21.6 36.9 2013 10,397 9761 94 21.4 36.4 2014 45,248 44,515 98 19.9 34.2 2015 29,721 29,507 99 18.8 33.3 1 Relative to ' Matched' Table 7: Herd specific validation 1 results for Holstein heifers (parity = 0) in 2013-2015 (year of first service) Threshold for Validation Criterion 1 Recovered 2013 2014 2015 Recovered 2 Recovered 2 None 9761 7 44,515 33 29,507 22 0 9432 7 40,750 30 26,687 20 25 9005 7 39,006 29 25,510 19 50 7799 6 34,182 26 22,499 17 75 6210 5 28,695 21 18,821 14 1 Within herd: (No. of confirmed pregnancies in 2012-2013 resulted in calvings in 2013/No. of calving records in 2013)*100 2 Relative to heifer records in 2012 (133,660) 2 7
Table 8: Overall validation results for cows Breed Calving (2013) Confirmed Pregnant Matched Matched 1 (2012-2013) Ayrshire 9042 11,714 2618 29 Brown Swiss 1522 3090 652 43 Canadienne 304 327 49 16 Guernsey 303 658 113 37 Holstein 344,994 712,628 168,006 49 Jersey 10,603 19,461 4286 40 Milking 211 559 61 30 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 3 2010 100,062 36,112 36 30,067 83 43.0 51.8 2011 113,582 32,078 28 25,901 81 43.0 51.3 2012 124,231 34,209 28 27,579 81 40.9 50.2 2013 123,952 37,069 30 29,720 80 42.0 50.9 2014 238,051 122,572 51 114,868 94 37.5 47.3 2015 234,507 78,433 33 76,225 97 36.8 47.6 1 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 2013-2015 (year of first service) Threshold for Validation Criterion 1 New Correct 2013 2014 2015 New Correct 2 New Correct 2 None 29,720 10 114,868 39 76,225 26 0 28,882 10 107,141 37 69,740 24 25 27,839 9 102,623 35 66,613 23 50 24,437 8 89,168 30 57,489 20 75 17,262 6 64,426 22 41,405 14 1 Within herd: (No. of confirmed pregnancies in 2012-2013 resulted in calvings in 2013/No. of calving records in 2013)*100 2 Relative to cow records in 2012 (293,531) 8
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 1999 - - - 2 79.0 8.5 2000 178 15.1 28.4 611 34.9 48.0 2001 474 16.8 32.5 622 30.8 43.6 2002 616 15.7 32.1 815 34.4 45.5 2003 791 18.1 33.3 1208 39.5 49.1 2004 1194 19.0 35.6 1390 34.7 46.7 2005 2118 18.5 34.5 1891 36.1 48.4 2006 3986 18.7 34.7 2988 37.5 48.2 2007 7927 24.7 42.4 9456 76.9 65.3 2008 40,429 21.3 36.6 121,322 42.7 50.3 2009 54,180 19.4 34.7 149,773 39.3 48.8 2010 59,213 18.6 33.7 151,406 39.0 48.8 2011 68,885 19.1 33.9 169,171 38.6 48.3 2012 73,620 19.4 33.9 178,478 37.7 47.7 2013 76,851 19.9 34.4 180,776 38.3 48.1 2014 48,235 19.7 34.2 112,459 38.5 48.6 1 Averages and were identical for extracted from the fertility data and calculated using pregcheck data 9
Table 12: Summary of the use of pregnancy check for recovery (for years of the first service 2013-2015), by breed Breed From February 2016 extract Calculated from pregcheck data combined New heifers New cows 2013 1 2014 2015 2013 2014 2015 N 159,635 5891 165,526 129 518 307 327 1699 1082 Ayrshire Brown Swiss Cannadie nne Guernsey Holstein Jersey 29.0 41.8 31.0 42.4 29.1 41.8 22.8 34.8 N 22,278 1851 24,129 28 175 80 125 483 246 28.4 43.4 32.4 45.5 28.8 43.6 7.7 19.4 N 4338 162 4500 4 32 5 7 48 35 21.9 37.2 28.6 43.9 22.1 37.5 13.3 16.5 N 5727 354 6081 11 31 11 20 71 43 29.5 43.0 37.5 47.2 30.0 43.3 42.5 40.4 N 5,645,427 428,659 6,063,086 9759 44,516 29,506 26,678 114,820 76,229 30.9 44.7 34.3 46.6 31.2 44.9 21.3 36.3 N 130,137 10,395 140,532 258 1003 647 668 2910 2106 24.3 39.4 28.1 42.3 24.6 39.6 20.6 35.6 20.8 34.2 23.0 35.0 27.5 41.7 32.8 38.0 20.0 34.4 20.5 35.9 20.7 32.4 27.1 44.6 14.0 31.3 6.0 13.7 18.6 32.9 21.4 36.8 32.9 46.3 40.9 52.4 45.9 70.5 44.4 65.2 41.7 50.6 31.4 44.6 32.2 43.1 36.8 47.7 28.8 43.7 38.9 46.9 37.6 47.3 28.5 41.5 32.3 43.0 31.8 45.9 30 38.1 45.9 58.9 36.4 47.2 31.9 44.4 Milking Shorthorn N 2284 161 2445 6 11 1 9 41 13 1 Year of first service 17.4 32.9 10.7 30.1 17.0 32.8 0 0 30.6 50.5 0 0 22.7 60.2 10.8 25.0 11.7 25.1 10