Selection signatures on the autosomes and the X chromosome in the prolific Belclare sheep breed

Sheep ( Ovis aries ) is a poly-ovulatory species, with litter size varying considerably within and among breeds. Litter size reflects ewe prolificacy, and prolific breeds represent valuable genetic resources for the sheep industry. Belclare is a composite sheep breed developed primarily for reproductive performance and used for meat production. Artificial selection for beneficial alleles related to reproductive traits can create detectable genomic patterns known as selection signatures (SS). This study aimed to detect selection signatures on autosomes and the X chromosome in Belclare sheep and annotate candidate regions associated with reproductive traits. A total of 8,421 ewes genotyped with the OvineSNP50 BeadChip were analyzed. Breeds were classified into two groups: prolific (Belclare) and less prolific (Beltex, Charollais, Suffolk, and Texel). Inter-population selection signatures were detected using Cross-Population Extended Haplotype Homozygosity (XP-EHH) and Fixation Index (FST) in 100-kb non-overlapping windows across autosomes (top 1%) and the X chromosome (top 10%). Overlapping signals formed regions ranging from 200-400 kb. Using XP-EHH, regions of 400 kb were detected on OAR3 and OAR5, while one shared SS between XP-EHH and F ST was identified on OARX. The genes within these regions were associated with reproductive traits in both ewes and rams. X-linked genes, including TAF7L, ATP1B4 , and ZMYND12 , were associated with sperm motility. Genes involved in ovarian processes, including follicular development, ovulation, and early pregnancy, such as MID1IP1, IL1RAPL2 , and EDN2 , were also identified within the SS regions. Overall, the SS detected in Belclare elucidated the genetic basis underlying its prolificacy relative to less prolific breeds.