197 Selection signatures on the X chromosome in a prolific meat sheep breed.
Bibliographic record
Abstract
Abstract The X chromosome (ChrX) plays a key role in natural and artificial selection and animal evolution. Both natural and artificial selection leave distinct genomic footprints, known as selection signatures (SS), which can be identified on ChrX. Belclare sheep, a composite breed, have been subjected to strong selection pressure for high prolificacy and are also used for meat production, making them valuable in efficient and sustainable production systems. Our study aimed at identifying SS regions on the ChrX and conduct functional analysis related to reproduction traits in the Belclare sheep in contrast to non-prolific meat breeds. Ewes of the different sheep breeds were genotyped using the Illumina OvineSNP50. Only SNPs on the ChrX with defined positions based on the sheep (Ovis aries) genome assembly ARS-UI_Ramb_v2.0 were included. SNP filtering and quality control were conducted across all breeds, removing SNPs and samples with call rates below 90% and SNPs with minor allele frequency < 1%. After quality control, 863 SNPs were analyzed. Imputation of missing genotypes and haplotype phasing were performed using BEAGLE. Prior to SS detection, breeds were classified into two groups: prolific (Belclare, n = 2,441) and non-prolific (Beltex, n = 146; Charollais, n = 1,490; Suffolk, n = 1,237; and Texel, n = 3,378). The SS detection was performed within the prolific group using the integrated Haplotype Score (iHS) and between groups (prolific vs. non-prolific) using Cross-Population Extended Haplotype Homozygosity (XP-EHH) and the Ratio of Site-specific Extended Haplotype Homozygosity (Rsb). The SS detection was performed in 150 kb non-overlapping windows containing at least two SNPs per window using the REHH package in R. The top 10% windows with the highest scores were considered regions under positive selection in Belclare. Gene and QTL annotation was performed using the GALLO R package and functional enrichment (FDR < 0.05) was performed in gprofiler2 package in R. A total of 19 genomic regions identified by iHS co-localized with 18 candidate genes and two milk QTLs. Fifteen regions detected by XP-EHH and Rsb co-localized with 13 candidate genes and one reproduction QTL. No significant functional enrichment was observed. The milk QTLs were associated with protein and milk yield, while the reproduction QTL was associated with prolificacy. This suggests differences in selection signatures on ChrX between Belclare and the non-prolific breeds, which relate to the Belclare breed’s reproductive and maternal ability. Among the annotated genes, AKAP4, detected by iHS, is linked to flagellated sperm motility, suggesting its role as an X-linked gene influencing ram fertility. HTATSF1, detected by XP-EHH and Rsb, is reported to be linked with estrogen receptors involved in precocious puberty. The detection of SS highlights that selection pressure has left footprints on ChrX in the Belclare, particularly in regions associated with reproduction.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 |
| 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) | 0.002 | 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".