Browsing by Author "Misztal, Ignacy"

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    Comparisons of Holstein, Brown Swiss, and Jersey cows for age at first calving, first calving interval, and true herd-life up to five years in seven regions of the United States
    Garcia-Peniche, Teresa Beatriz (Virginia Tech, 2004-12-10)
    The objectives of this research were to evaluate breed differences for heat-stress resistance using age at first calving and first calving interval, and to assess breed by region interactions for seven regions of the United States for survival-related traits up to five years of age in Brown Swiss, Holstein, and Jersey cows. Age at first calving and first calving interval were studied in farms with two breeds, with Holstein and Brown Swiss or Holstein and Jersey cows. The survival-related traits were analyzed in farms with one or two breeds. Seven regions within the United States were defined: Northeast, Northwest, Central north, Central, Central south, Southwest and Southeast. The fertility traits were also analyzed in seven individual states: Wisconsin, Ohio, Oregon, California, Arizona, Florida, and Texas. Brown Swiss were older than Holsteins at first calving (833 ± 2.4 d vs. 806 ± 2.0 d in regions, and 830 ± 3.1 d vs. 803 ± 2.4 d in states), but Holsteins and Brown Swiss did not differ for first calving interval. Jerseys were younger than Holsteins at first calving and had shorter first calving intervals (P < 0.01). In data from individual states, Holsteins housed with Brown Swiss were older at first calving than Holsteins housed with Jerseys (800 ± 2.7 d vs. 780 ± 2.5 d). Holsteins housed with Jerseys had slightly shorter first calving intervals than Holsteins housed with Brown Swiss, and the interaction of "type of Holstein: with season of the first calving was highly significant (P < 0.01). Region and season effects were smaller for Jerseys than for Holsteins, thus, Jerseys showed evidence of heat-stress resistance with respect to Holsteins. Management modified age at first calving in Holsteins, depending on the type of herd they were located in. Longer calving intervals might have been partly due to voluntary waiting period to breed the cows. The survival-related traits were evaluated up to five years of age. They consisted of stayability, number of completed lactations, days lived, herd-life, and total days in milk. For herds with one breed, the order for stayability to five years of age, from longer to shorter-lived breed was: Brown Swiss, Jersey and Holstein, but for the ratio of days in milk to herd-life the order was: Holstein, Jersey and Brown Swiss, and for the ratio of days in milk to days lived, it was: Jersey, and Holstein and Brown Swiss tied. This last ordering was the same for number of lactations completed by five years of age. The results for two-breed herds were similar since Brown Swiss and Jerseys had larger (Chi-square P < 0.01) probabilities of living past five years of age than Holsteins, and for days in milk and number of lactations completed, Jerseys had higher values than Holsteins (P < 0.01), but Holsteins and Brown Swiss tied in some analyses. Breed by region interaction was always significant. If all other conditions were assumed equal, Jerseys would give fastest returns by five years of age. The overall conclusion is that Jerseys performed better for the traits analyzed, all of them highly influenced by environmental conditions.
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    Modeling missing pedigree in single-step genomic BLUP
    Bradford, Heather L.; Masuda, Yutaka; VanRaden, Paul M.; Legarra, Andres; Misztal, Ignacy (2019-03)
    The objective was to compare methods of modeling missing pedigree in single-step genomic BLUP (ssGBLUP). Options for modeling missing pedigree included ignoring the missing pedigree, unknown parent groups (UPG) based on A (the numerator relationship matrix) or H (the unified pedigree and genomic relationship matrix), and metafounders. The assumptions for the distribution of estimated breeding values changed with the different models. We simulated data with heritabilities of 0.3 and 0.1 for dairy cattle populations that had more missing pedigrees for animals of lesser genetic merit. Predictions for the youngest generation and UPG solutions were compared with the true values for validation. For both traits, ssGBLUP with metafounders provided accurate and unbiased predictions for young animals while also appropriately accounting for genetic trend. Accuracy was least and bias was greatest for ssGBLUP with UPG for H for the trait with heritability of 0.3 and with UPG for A for the trait with heritability of 0.1. For the trait with heritability of 0.1 and UPG for H, the UPG accuracy (SD) was -0.49 (0.12), suggesting poor estimates of genetic trend despite having little bias for validations on young, genotyped animals. Problems with UPG estimates were likely caused by the lesser amount of information available for the lower heritability trait. Hence, UPG need to be defined differently based on the trait and amount of information. More research is needed to investigate accounting for UPG in A(22) to better account for missing pedigrees for genotyped animals.
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    Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets
    Bradford, Heather L.; Masuda, Yutaka; Cole, John B.; Misztal, Ignacy; VanRaden, Paul M. (2019-03)
    The objective of this study was to model differences in pedigree accuracy caused by selective genotyping. As genotypes are used to correct pedigree errors, some pedigree relationships are more accurate than others. These accuracy differences can be modeled with uncertain parentage models that distribute the paternal (maternal) contribution across multiple sires (dams). In our case, the parents were the parent on record and an unknown parent group to account for pedigree relationships that were not confirmed through genotypes. Pedigree accuracy was addressed through simulation and through North American Holstein data. Data were simulated to be representative of the dairy industry with heterogeneous pedigree depth, pedigree accuracy, and genotyping. Holstein data were obtained from the official evaluation for milk, fat, and protein. Two models were compared: the traditional approach, assuming accurate pedigrees, and uncertain parentage, assuming variable pedigree accuracy. The uncertain parentage model was used to add pedigree relationships for alternative parents when pedigree relationships were not certain. The uncertain parentage model included 2 possible sires (dams) when the sire (dam) could not be confirmed with genotypes. The 2 sires (dams) were the sire (dam) on record with probability 0.90 (0.95) and the unknown parent group for the birth year of the sire (dam) with probability 0.10 (0.05). An additional set of assumptions was tested in simulation to mimic an extensive dairy production system by using a sire probability of 0.75, a darn probability of 0.85, and the remainder attributed to the unknown parent groups. In the simulation, small bias differences occurred between models based on pedigree accuracy and genotype status. Rank correlations were strong between traditional and uncertain parentage models in simulation ( >= 0.99) and in Holstein ( >= 0.99). For Holsteins, the estimated breeding value differences between models were small for most animals. Thus, traditional models can continue to be used for dairy genomic prediction despite using genotypes to improve pedigree accuracy. Those genotypes can also be used to discover maternal parentage, specifically maternal grandsires and great grandsires when the dam is not known. More research is needed to understand how to use discovered maternal pedigrees in genetic prediction.