Putative Loci Causing Early Embryonic Mortality in Duroc Swine
Bibliographic record
Abstract
Lethal recessive variants are usually maintained at relatively low frequencies in populations as heterozygous state. However, they can cause prenatal death of homozygous offspring which may result in smaller litter size in pigs. This study aimed to detect the putative lethal variants in the Duroc breed and estimate their harmful effects on five fertility traits: total number of born (TNB), number of born alive (BA), number alive at 24h (L24), stillborn piglets (SB), and number of mummified fetuses (MM). Imputed genotypes of 650K SNPs for 1359 Duroc boars were used in this study. Eight SNPs were detected (P < 0.01) and the most significant one (P = 1.7E-11) was located on SSC14 with 45.3 homozygous individuals expected but none observed. Haplotype analyses detected 152 haplotypes as potentially harboring recessive lethal mutations. Twenty-six of them were confirmed in the association studies as they showed significantly harmful effects on at least one fertility trait. The most important regions were located on SSC8 (Hap14), SSC9 (Hap16), SSC11 (Hap17), SSC12 (Hap18), SSC14 (Hap21) and SSC17 (Hap26) which were significant for the fertility traits in both random and designed matings. A few candidate genes identified within these five regions were described as being involved in spermatogenesis and male fertility (TEX14, SEP4 and HSF5), or displayed recessive lethality (SCD5 and PCF11) in other species. The putative loci detected in this study provide valuable information to potentially increase Duroc litter size by avoiding carrier-by-carrier matings in breeding programs. Further study of the identified candidate genes responsible for such lethal effects may lead to new insights into functions regulating pig fertility.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".