Reciprocal Chromosome Translocations in the Domestic Pig, the Prevalence, Genetic and Genomic Factors Associated with Breakpoint Formation
Bibliographic record
Abstract
Chromosome rearrangements such as reciprocal translocations are prevalent in the domestic pig, estimated to occur in 1/200 live births, and are suspected to be the reason behind 50% of cases of hypoprolificacy. Despite there being over 200 chromosome rearrangements found in the pig, little is known about why rearrangements form in the pig genome. In order to better understand chromosome rearrangements, their breakpoints, and factors influencing their formation a routine cytogenetic screening program was created to identify carriers in Canadian swine herds. Using data from this project and others a comprehensive analysis of rearrangement breakpoints was conducted, and a GWAS and CNV analysis was performed using DNA samples from identified carrier boars. Routine cytogenetic screening of 6491 boars revealed 101 carriers of chromosome rearrangements, with a prevalence of 1.56%. Comprehensive analysis of rearrangement breakpoints in pigs revealed a non-random distribution with hotspots for rearrangement sharing a set of architectural features including a euchromatic composition, as well as higher densities of genes, simple repeats, and tRNA. A GWAS and CNV analysis of carrier boars and their parents revealed five SNP associations, four CNVR and eleven nearby genes each of which played roles in genomic stability or DNA repair. The results of this study show the high prevalence of rearrangements in pigs, as well as the effectiveness of screening efforts. In addition, genomic architectural features along with genetic and genomic variants in the pig genome may be proposed to influence chromosome breakage and promote rearrangement.
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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 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".