PSXII-7 Characterization of Runs of Homozygosity Islands in American Mink Using Whole-Genome Sequencing Data
Bibliographic record
Abstract
Abstract The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy to detect the variants shared among the individuals of a population, and thereby to reveal important genomic regions for complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, ROH islands, and the gene content of those candidate regions using whole-genome sequencing data of 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. After quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for subsequent analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3–1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. We identified 63 ROH islands that harbored 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2, SLC24A4, SLC24A3, PDE5A), body size/body weight (MYLK4, PRIM2, FABP2, BBS7, EYS, PHF3), immune capacity (IL2, PTP4A1, SEMA4C, CD274, JAK2, MAD2L1, CCNA2, TNIP3), and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2, LARP1B, HSPA4L, CAMK2D). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed multiple significant terms (P ≤ 0.05), among which cGMP-PKG signaling pathway, regulation of actin cytoskeleton, and calcium signaling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to an understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.
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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 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".