Genomic and phenotypic analyses of antral follicle count in Aberdeen Angus cows
Bibliographic record
Abstract
Antral follicle count (AFC) was phenotypically and genetically evaluated in a Bos taurus cow population. A total of 257 Aberdeen Angus cows underwent an ovarian ultrasound evaluation and hormonal synchronization for timed artificial insemination (TAI). These animals were between 40 and 70 d postpartum with a body score condition (BSC) between 2 and 4 (average = 2.7) on a scale of 1–5. The number of antral follicles was assessed 10 d before (D-10) the beginning of TAI. Visible follicles (≥3 mm in diameter) were counted from both ovaries (right and left) to determine the number of total follicles, and animals were allocated into groups according to the number of antral follicles: low AFC was defined as ≤ 15 follicles (n = 93); intermediate AFC as < 24 follicles and >16 follicles (n = 97); and high AFC as ≥ 25 follicles (n = 67). The comparison between the average AFC and pregnancy rate was performed using the chi-square test in the Minitab® 19.2 statistical software, adopting a P-value ≤ 0.05. Hair samples of Aberdeen Angus cows were collected for genomic DNA extraction and subsequent genotyping analysis using the GGP HD array. The associations between SNP markers and phenotypic information (AFC) were determined using the GBLUP methodology. Windows explaining more than 1% of the total additive genetic variance were selected as candidates for functional prospection using QTL colocalization and enrichment analysis using a hypergeometric test. The GWAS identified seven candidate genomic windows and 54 annotated genes within them. Among these genes, DUSP1, SOX17, XKR4, PLAG1, HFM1, PPM1K, IBSP, NCAPG-LCORL, and HMGHZ were associated with biological processes that might be related to follicle count in Angus cows. Enrichment analysis of the reproduction-related traits found enriched QTLs in BTA5 (“Inhibin level”, “Insulin-like growth factor 1 level”), BTA6 (“Calving ease”, “Calf size”, “Calving index”), and BTA14 (“Insulin-like growth factor 1 level”; “Age at puberty”, “Interval to first estrus after calving”). This study brings new knowledge of the genomic background of AFC and may lead to further investigations regarding physiological explanations for different AFCs and their relationship to fertility.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".