September 2006 - CGIL

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eported in other studies. In addition to the effects of pregnancy this drop in milk production was confounded by effect of DIM. It was noted that more than 35% of the cows were found to never become pregnant in first lactation, which was an expected result. However, 60% of the cows were recorded as not yet becoming pregnant when the test was taken. This percentage was expected to be closer to 30%. Cows coded as not becoming pregnant until after 310 days in milk had the highest level of milk production. Perhaps the owners of these cows chose not to inseminate these cows until later in lactation because they were high producers. A suggestion was made to graph the decline of milk production in terms of percentage of yield rather than by kilograms of yield so that the decrease can be compared across breeds. In addition, estimation of the interaction between stage of lactation and stage of pregnancy was recommended. 2 CONFORMATION TRAITS, i. Genetic Evaluation (Domestic) 2.1 Table showing if Fixed or Random contemporary group was included in analysis This table was given to the committee for reference, but was not discussed. 2.2 Approximate Reliability Patch for Conformation Sullivan and VanDoormaal CDN started providing Parent Averages (PA) for animals whose index or proof could not be calculated. Due to some inconsistencies between reliabilities calculated in February and those calculated in May (specifically unexpected drops in reliabilities), a review of the reliability approximation procedure used in the new type system was initiated. Researchers found no errors in the methodology, but rather an issue with how the approximation was designed. Drops in reliability from one proof run to the next, although theoretically possible, could cause problems with extension. Therefore, it was decided to modify the procedure to ensure that the PA reliability never went down. The modification (or patch) substituted the matrix of Tier and Meyer with one that accounted for knowing sire and dam were mates in the parent contribution of the approximation algorithm. In this case, the parent contributions to reliability were corrected to be a maximum of 50% (rather than 40%). Changes in reliability between the old and new approximation procedures were summarized. Changes were small for animals with either low or high reliability. Animals with originally intermediate reliability (20-60%), which would be mostly based on parent information, changed by 2 to 3 percentage points. After the patch was applied, reliabilities only increased as desired. Changes in reliabilities between procedures were smaller if old reliabilities were high. Researchers concluded that extension problems related to decreases in parent average reliabilities would have mostly applied to animals that did not have contemporaries for their first official evaluation, since their own performance record would not contribute to the reliability. Small contemporaries are less common in production evaluations. Therefore, investigation into applying a similar patch to the reliability approximation procedure for production traits was not suggested.
There was a general concern that reliabilities tend to be overestimated and that warranted further investigation. The patch was implemented in August. 2.3 Including Reclassifications after 1 st Lactation in Genetic Evaluation Sullivan, Kistemaker and Van Doormaal Prior to May <strong>2006</strong>, only first classifications in first lactation were included in calculation of bull evaluations for type and the most recent classification was included for calculation of cow indexes. Currently, all first lactation classifications (FIRST) are included for calculation of both indexes and proofs (one data set). Cow indexes were significantly inflated in the previous system, because only the most recent classification was included but compared to her contemporaries when she was first classified. Under the current system (using all first lactation classifications) some over-inflated cow indexes dropped significantly. In addition, cows that were never classified in first lactation lost their index. Bull proofs were only minimally affected. This study was conducted to investigate the inclusion of all classifications (ALL) or the cow’s most recent classification in addition to all her first lactation classifications (LATEST) for genetic evaluation. A majority of classification data was recorded in first lactation. The evaluation model included an effect of age*stage*time, an interaction for type of record (first or re-classification) in first or later lactations (4 in total), and an effect of herd-round-classifier. Correlations between bull proofs under the FIRST and LATEST methods were high for all traits. No difference in bull proofs was noted between the LATEST and ALL methods. Average changes in conformation EBV were essentially zero. Approximately half of the cow indexes and bull proofs for conformation did not change moving from the FIRST to the LATEST or ALL methods. Of those proofs or indexes that changed a majority changed by plus or minus 1. Range in change for cow indexes was slightly larger than for bull proofs. Proofs of bulls who had daughters that reclassified did not change more than proofs of bulls that did not have reclassified daughters, moving from the FIRST to the LATEST method. As the percentage of daughters reclassified increased, the reliability of the bulls proof increased more (~2.5). Differences between proofs changing from the FIRST to LATEST and FIRST to ALL methods were not large. When a high percentage of daughters were reclassified reliabilities increased more under the ALL method (to a maximum of ~5) compared to that under the LATEST method. As the number of reclassifications increased so did the reliability of the cow indexes switching to the LATEST or ALL methods. In some cases, average change in reliability of cow indexes was an increase of 30%. Cows that originally scored higher tended to have greater increases in EBV due to their reclassification in a later lactation. Cows with higher scores were the only cows reclassified multiple times in later lactations. EBVs increased the most for cows with the largest number of classifications. The average phenotype in reclassified daughters was higher compared to the rest of the population. Animals that were reclassified 6 times were more likely cows scored multiple times as being excellent. It would be interesting to compare a bull’s first proof to that once his daughters have been reclassified. All increases were assumed to be genetic. Permanent environmental variance should be substantial and were not estimated or accounted for under the proposed model. However, if a permanent environment and frequency of reclass effect was included in the model, essentially no genetic change would be realized. Under the new classification system, animals that are presented for classification but not rescored and raised can be accounted for. The possibility exists that bias was introduced because
Page 1 and 2: Participants Larry Schaeffer, CGIL
Page 3: Therefore, one can assume that phan
Page 7 and 8: 3.1.2 Analysis of Stillbirth Rates
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September 2006 - CGIL

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