503 Selection signatures in a prolific meat sheep breed

Abstract

Abstract In sheep meat production, prolificity is one of the main factors influencing economic profitability of a farm. Belclare sheep are used for meat production and have passed through intense selection pressure to high prolificity, leading them to have large litter sizes. This study aimed to identify selection signature regions and carry out functional analyses related to reproduction traits in the Belclare breed in contrast to a group of non-prolific meat breeds. A total of 50,166 biallelic SNPs from the Illumina OvineSNP50 genotyped in the Belclare breed (n = 2,377) and four meat breeds (Beltex, n = 146; Charollais, n = 1,477; Suffolk, n = 1,231 and Texel, n = 3,330). SNP filtering and quality control were performed within each breed using PLINK v1.9. Only SNPs on autosomal chromosomes with defined positions according to the sheep (Ovis aries) genome assembly OAR3.1 were analyzed. Samples and SNPs with a call rate below 95% were discarded, as well as SNPs with MAF below 1% and deviation of Hardy-Weinberg equilibrium with P-value ≤ 10-6. Imputation of missing genotypes and haplotype phasing were performed using BEAGLE v.3.3.2. After quality control, an average of 30,249 SNPs were further analyzed. Selection signature detection was performed by Cross-Population Extended Haplotype Homozygosity (XP-EHH) and Ratio of Site-specific Extended Haplotype Homozygosity between populations (Rsb), with the REHH v.3.2.2 software in R, using 100 kb non-overlapping windows with at least two markers per window. The top 1% windows with the greatest average values were considered regions under positive selection. Gene and QTL annotation were conducted with the GALLO R package. Gene and metabolic pathways enrichment (FDR< 0.10) were performed with gprofiler2 software. A total of 67 genomic regions co-localized with 76 candidate genes and 65 QTLs were identified. The genes were enriched for 12 molecular function terms. Among the annotated genes, FSHR, INSL6, HSD17B12, and SGK1 were previously found to be related to reproduction traits. The enriched term follicle-stimulating hormone receptor activity was related to the FSHR gene. The follicle-stimulating hormone (FSH) has an important role in follicular development, and their concentrations are regulated by the FSH receptor (FSHR), which suggests that FSHR is also involved in prolificity of the ewe. The testes weight trait was detected in the reproductive QTL class, but no gene related to fertility was identified. The gene INSL6 is associated with spermatogenesis and sperm motility and, as Belclare rams are used to produce prolific replacements, it may have an important role in semen quality and prolificity, as increased semen quality might increase the chance of a successful fecundation. The identification of selection signatures highlights that the selection pressure left footprints in the Belclare breed genome related to reproduction, which may affect the litter sizes.