Sheep (*Ovis aries*) are crucial livestock, providing meat, wool, skin, and milk since the Neolithic. Genome-assisted breeding requires characterizing genome-wide sequence variation and identifying phenotype-associated functional variants. Domestication and subsequent selection's impact on genomic variation has been investigated, associating several quantitative trait loci (QTLs) and functional genes with phenotypic traits. However, most studies focused on few phenotypes and limited molecular markers and breeds. Whole-genome resequencing has identified genomic variants involved in domestication and improvement in various plants and animals, including cattle and sheep. This study uses the completed sheep reference genome to compare genomes from phenotypically diverse landraces and improved breeds with their wild ancestors, aiming to identify genomic variants associated with important morphological and agronomic traits and to provide a valuable genomic resource for future molecular-guided breeding.

Previous research has explored the genetic basis of phenotypic traits in sheep, identifying several QTLs and candidate genes associated with various characteristics. However, these studies often focused on a limited number of phenotypes and breeds, and employed a limited number of molecular markers. Recent advances in whole-genome sequencing technology have allowed for more comprehensive studies of genetic variation in livestock species, including sheep. Studies utilizing whole-genome resequencing have successfully identified genomic variants associated with domestication and improved traits in other species, providing a framework for similar investigations in sheep. However, a comprehensive analysis incorporating a diverse range of sheep breeds and a high-depth whole-genome sequencing approach has been lacking. This study aims to fill this gap by providing a high-resolution map of genetic variation and its association with important traits.

The study involved deep resequencing of 248 sheep samples: 16 Asiatic mouflon (*O. orientalis*), 172 sheep from 36 landraces, and 60 sheep from six improved breeds. Sequencing generated 137.0 billion 150-bp paired-end reads, resulting in an average depth of 25.7x per individual. Reads were mapped to the *O. aries* reference genome. SNPs, INDELs, CNVs, and SVs were identified and filtered. Population structure and demographic history were analyzed using phylogenetic trees, PCA, ADMIXTURE, and PSMC. Selective sweeps were identified using XP-CLR, π ratio, iHS, and HKA tests for both SNPs and CNVs. GWAS were performed for litter size, horn number, and nipple number. Gene expression and western blot analyses were conducted to validate the role of *PDGFD* in tail fat deposition. Detailed methodology is given in the supplementary information.

The study identified 28.36 million SNPs, 4.80 million INDELs, 13,551 CNVs, and 28,973 SVs. Domestic breeds showed lower genomic diversity than wild ancestors. Phylogenetic analysis revealed four subgroups of domestic sheep: European, Middle Eastern, Asian, and two African lineages. Linkage disequilibrium was higher in domestic breeds. XP-CLR and π ratio analyses identified 144 putative selective regions associated with domestication. Candidate genes involved in milk and meat production were enriched. Analysis of CNVs revealed 137 candidate selected regions associated with domestication. Functional analysis of genes showed enrichment in metabolic and biosynthesis processes. Global Fst analysis among domestic breeds identified 205 putatively selected genomic regions. *PAPPA2* showed a strong selective signature related to fat deposition. The study found *PDGFD* associated with tail configuration. Transcriptome, RT-PCR, qPCR, and western blot analyses confirmed *PDGFD*’s negative correlation with tail fat deposition. GWAS for litter size, horn number, and nipple number identified significant association signals, some overlapping with selective sweeps. Several novel candidate genes were identified for these traits.

This study's high-depth whole-genome sequencing of diverse sheep populations provides valuable insights into the genetic architecture of morphological and agronomic traits. The lower genomic diversity in domestic breeds compared to wild ancestors indicates a loss of variation during and after domestication. The identification of candidate genes associated with domestication and breed-specific traits, including *PDGFD*’s role in tail fat deposition, offers new avenues for improving sheep breeding. The integration of selective sweep analysis and GWAS enhances the accuracy of identifying causal genes. The findings improve our understanding of sheep domestication and breed formation, providing a genomic resource for future genetic studies and improved breeding strategies. The identification of novel candidate genes associated with various traits opens new avenues for genetic improvement programs.

This study provides a comprehensive analysis of the sheep genome, identifying numerous SNPs, INDELs, CNVs, and SVs associated with morphological and agronomic traits. The findings highlight the genetic basis of sheep domestication and breed formation, emphasizing the role of both SNPs and structural variants. The identification of *PDGFD* as a key regulator of tail fat deposition is a significant contribution. The integration of selective sweep analysis and GWAS provides powerful tools for future studies. Future research could focus on functional validation of candidate genes and the development of novel breeding strategies based on these findings.

The study's sample size, although large, might not fully represent the global diversity of sheep breeds. The reliance on existing reference genomes may introduce biases in variant calling and annotation. Functional validation of all candidate genes was not possible within the scope of this study, requiring future experimental work to confirm the findings. Further research is needed to fully understand the complex interactions between genes and the environment that shape phenotypic traits.