Genomic prediction of dry matter intake in dairy cattle from an international data set consisting of research herds in Europe, North America, and Australasia
Bibliographic record
Abstract
With the aim of increasing the accuracy of genomic estimated breeding values for dry matter intake (DMI) in Holstein-Friesian dairy cattle, data from 10 research herds in Europe, North America, and Australasia were combined. The DMI records were available on 10,701 parity 1 to 5 records from 6,953 cows, as well as on 1,784 growing heifers. Predicted DMI at 70 d in milk was used as the phenotype for the lactating animals, and the average DMI measured during a 60- to 70-d test period at approximately 200 d of age was used as the phenotype for the growing heifers. After editing, there were 583,375 genetic markers obtained from either actual high-density single nucleotide polymorphism (SNP) genotypes or imputed from 54,001 marker SNP genotypes. Genetic correlations between the populations were estimated using genomic REML. The accuracy of genomic prediction was evaluated for the following scenarios: (1) within-country only, by fixing the correlations among populations to zero, (2) using near-unity correlations among populations and assuming the same trait in each population, and (3) a sharing data scenario using estimated genetic correlations among populations. For these 3 scenarios, the data set was divided into 10 sub-populations stratified by progeny group of sires; 9 of these sub-populations were used (in turn) for the genomic prediction and the tenth was used for calculation of the accuracy (correlation adjusted for heritability). A fourth scenario to quantify the benefit for countries that do not record DMI was investigated (i.e., having an entire country as the validation population and excluding this country in the development of the genomic predictions). The optimal scenario, which was sharing data, resulted in a mean prediction accuracy of 0.44, ranging from 0.37 (Denmark) to 0.54 (the Netherlands). Assuming near-unity among-country genetic correlations, the mean accuracy of prediction dropped to 0.40, and the mean within-country accuracy was 0.30. If no records were available in a country, the accuracy based on the other populations ranged from 0.23 to 0.53 for the milking cows, but were only 0.03 and 0.19 for Australian and New Zealand heifers, respectively; the overall mean prediction accuracy was 0.37. Therefore, there is a benefit in collaboration, because phenotypic information for DMI from other countries can be used to augment the accuracy of genomic evaluations of individual countries.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".