PSXIV-18 Genome-wide association study to identify genomic regions and single nucleotide polymorphisms functionally associated with bull fertility.
Bibliographic record
Abstract
Many beef producers select their animals for production traits such as carcass weight or tenderness; however, this may result in a loss of highly reproductive traits. In order to keep up with the production and demand of beef products, the proportion of calves born needs to increase accordingly. The most effective and cost-efficient way to achieve this is by researching the potentials to improve bull fertility, as it is known to play an important role in increasing herd size. Contrary to cow fertility traits, many fertility related traits in bulls (such as semen volume, motility, and scrotal circumference (SC)) are moderately to highly heritable (ranging from 0.29 to 0.78) and therefore are significantly influenced by genetics. We performed a genome-wide association study (GWAS) to identify genomic regions and single nucleotide polymorphisms (SNPs) significantly associated with SC in crossbred beef bulls and candidate genes related to bull fertility. The population in our study included 267 purebred and crossbreed beef bulls that had been previously genotyped with the Affymetrix GeneChip® Bovine Genome High Density Array. Bulls were 139 months of age on average, and had an average SC of 36.64 cm. Genotype quality control was performed, resulting in a final marker set of 421,354 SNPs distributed across the 29 Bos taurus autosomes. Preliminary results showed two SNPs significantly associated with SC, AX-20927056 and AX-20927088, both of which were located on chromosome 16. Furthermore, a haplotype-based GWAS identified two haplotype blocks significantly associated with SC on chromosomes 3 and 4, which are located in ZSCAN20 and KCND2 respectively. Both of these genes are involved in regulating sex and reproduction processes and therefore are candidate genes influencing SC. Further analysis will identify if there is a correlation with other bull fertility traits such as motility measurements.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.006 | 0.001 |
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".