Selection signatures associated with the number of lambs per lambing in Baluchi ewes

The number of lambs per lambing is one of the most important reproductive traits in sheep. Many studies have reported that genetic mechanisms play an important role in the variation of litter size in sheep. Selection for higher litter size in sheep has led to a variation of this trait within and across different breeds. Natural and artificial selection related to adaptation and economic traits, such as litter size, results in changes at the genomic level which leads to the appearance of selection signatures. Detection of these regions provides an opportunity for a better understanding of genetic mechanisms underlying the phenotypic variation of litter size in sheep. Several tests including the linkage disequilibrium-based approach, site frequency spectrum, and population differentiation-based approach have been developed to explore the footprints of selection in the genome. This study aimed to identify selection signatures in Baluchi sheep to investigate the genes annotated in these regions as well as the biological pathways involved. For this purpose, XP-EHH and FST analyses were conducted using the genome-wide single nucleotide polymorphisms (SNPs).

In this study, data from 96 Baluchi ewes genotyped using Illumina Ovine SNP50K BeadChip were used to identify genomic regions under selection associated with litter size in sheep. Phenotypic and pedigree data were collected at the Abbasabad Sheep Breeding Station. Based on records on different litters, ewes were divided into two groups: the case (two lambs per litter) and control (one lamb per litter).Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. To identify the signatures of selection, two statistical methods of FST and XP-EHH were used under FST and EHH software packages, respectively. We also calculated unbiased estimates of FST. Because the results were strongly correlated with the FST results, unbiased estimates have not been reported. In our study, all the SNPs ranking above 0.1 percentile of the distribution of test statistics were selected as candidates for the signature of selection. Gene ontology analysis for identified genes was performed using DAVID online database.

We used the FST and XP-EHH statistics to identify genomic regions that have been under positive selection associated with litter size in Baluchi sheep. Using FST approach, we identified 14 genomic regions on chromosomes 1 and 2 (two regions per chromosome), 3, 7, 9, 14, 18, 22, 23 (one region per chromosome), and X chromosome (three regions). Also, XP-EHH analysis identified nine genomic regions on chromosomes 2, 12, 13, and 22 (one region per chromosome), 7 (three regions), and X (two regions). Some of the genes located in identified regions under selection were associated with the number of lambs per lambing (ACVR1 and TGIF1), ovarian and follicle growth (DDX24), and fertility (FOXH1). Bone morphogenetic proteins are critical regulators of chondrogenesis during development which transduce their signals through three type I receptors namely BMPR1A, BMPR1B, and ACVR1/ALK2. TGIF1 is highly expressed in sheep ovaries suggesting that TGIF1 plays an important role in ewe reproduction. Also, TGF-β/SMAD signaling is critical in reproductive processes such as follicular activation, ovarian follicle development, and oocyte maturation. It has been evidenced that Ddx24 is highly expressed in sheep uterus affecting the development of ovaries and follicles. Foxh1 was first introduced as a transcriptional partner for Smad proteins and has been reported to play an important role in embryonic development. Results of gene ontology analysis identified two biological pathways namely defense response and cell motility which play an important role in the ovulation rate and the number of lambs per lambing. Reproductive activity and immune defenses can be mutually constraining, with increased reproductive activity limiting immune function and immune system activation leading to decreased reproductive function.

The results of this study identified candidate genes involved in the regulation of litter size in sheep suggesting that ACVR1 and TGIF1 genes can be considered as candidate genes related to the number of lambs per litter in sheep breeding programs to improve reproductive performance.