Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale. Methods: Here, we analyzed high-depth genomes of 210 sheep from 20 worldwide breeds to identify the pattern and distribution of genome-wide runs of homozygosity (ROH) and detect candidate selected genes in ROH islands for agronomic and phenotypic traits. Results: Leveraging whole-genome sequencing data, we found a large number of short ROH (e.g., <1.0 Mb) in all breeds and observed the overall higher values of ROH statistics and inbreeding coefficient in European breeds than in Asian breeds and Dorper sheep. We identified some well-known candidate genes (e.g., CAMK4, HOXA gene family, ALOX12, FGF11, and MTOR) and 40 novel genes (e.g., KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, and PAX1) that are functionally associated with fecundity, body size, and wool-related traits in sheep. Based on the candidate genes, we revealed different genetic bases for the fecundity traits of European and Asian sheep. Conclusions: This study improves the resolution of ROH detection and provides new insights into genomic inbreeding and trait architecture in sheep as well as useful markers for future breeding practice.

Background: Convergent evolution offers a unique lens through which to explore the molecular underpinnings of significant phenotypic transformations. Similar selective pressures likely drove the evolution of analogous milk traits in sheep and goats. Consequently, the current study aimed to identify common selection signals for milk traits across dairy and non-dairy breeds of sheep and goats worldwide. Results: In this study, a total of 308 whole-genome sequences from diverse sheep ( n = 108) and goat ( n = 200) breeds, including both dairy and non-dairy types, across the world were utilized. The population structure and genetic diversity of dairy and non-dairy sheep and goat breeds were characterized. Species-specific genes associated with milk traits, such as POU2F1 , ABCD2 , TRNAC-GCA in sheep and PRPF6 , VPS13C , TPD52L2 , NFX1 and B4GALT1 in goats, were identified. Further gene annotation and bioinformatics analyses indicated that different biological pathways are important for milk traits in each species: fatty acid oxidation and AMP metabolic process in sheep, the U2-type spliceosomal complex and propanoate metabolism in goats. Additionally, common signatures of selection such as CLASP1 , PDS5B , ZNF831 , CCDC73 were found in sheep and goats. Haplotype and transcriptional analyses further confirmed the role of these genes in milk production and provided evidence for their analogous evolution in sheep and goats. The CLASP1 gene was identified as a target of convergent selection, representing a promising candidate for genetic improvement programs in dairy species. Conclusions: These results provide insights into the genetic basis of convergent dairy traits, offering valuable targets for improving milk production and advancing dairy sheep and goat breeding programs.

Background: Sheep (Ovis aries) exhibit significant diversity in adipose tissue deposition, which influences meat quality, environmental adaptation, and economic value. Tail fat, in particular, varies widely among breeds, yet the transcriptomic basis of this variation remains incompletely understood. This study aims to systematically compare the transcriptional profiles of five adipose depots across five sheep breeds to identify molecular mechanisms underlying fat deposition and tail phenotype divergence. Methods: We analyzed 250 publicly available RNA-seq samples from five adipose tissues (caul, subcutaneous, perirenal, intermuscular, and tail fat) of five sheep breeds (Altay, Tibetan, Merino, Wadi, Small-tailed Han). Data were processed using FastQC, STAR, and featureCounts. Differential expression analysis was performed with DESeq2, followed by GO and KEGG enrichment analyses. Breeds were grouped into three tail phenotypes: fat-tailed, short fat-tailed, and thin-tailed. Cross-tissue and phenotype-specific pathway analyses were conducted to identify key regulatory genes. Results: Transcriptional divergence was most pronounced in subcutaneous and intermuscular fat, while tail fat exhibited both conserved and phenotype-specific pathways. Fat-tailed breeds showed enrichment in mitochondrial oxidative phosphorylation and lipid biosynthesis genes (TAFAZZIN, GPAM, COQ family). Short fat-tailed breeds were characterized by extracellular matrix remodeling genes (MMP9, MMP12, MMP19). Thin-tailed sheep lacked these pro-lipogenic and structural remodeling pathways. A dual-axis model of tail fat development is proposed to explain phenotypic diversity. Conclusions: This study reveals that distinct molecular mechanisms underpin tail fat phenotypes in sheep: fat-tailed breeds prioritize metabolic efficiency, short fat-tailed breeds rely on ECM remodeling, and thin-tailed breeds lack these enhancements. The identified candidate genes may serve as potential targets for molecular breeding strategies aimed at optimizing fat deposition and adaptive traits in sheep.

Background Convergent evolution offers a unique lens through which to explore the molecular underpinnings of significant phenotypic transformations. Similar selective pressures likely drove the evolution of analogous milk traits in sheep and goats. Consequently, the current study aimed to identify common selection signals for milk traits across dairy and non-dairy breeds of sheep and goats worldwide. Results We utilized a total of 308 whole-genome sequences from diverse sheep and goat breeds, including both dairy and non-dairy types, across the world. We characterized the population structure and genetic diversity of dairy and non-dairy sheep and goat breeds. We identified species-specific genes associated with milk traits, such as POU2F1 , ABCD2 , TRNAC - GCA in sheep and PRPF6 , VPS13C , TPD52L2 , NFX1 and B4GALT1 in goats. Further gene annotation and bioinformatics analyses indicated that different biological pathways are important for milk traits in each species: fatty acid oxidation and AMP metabolic process in sheep, the U2-type spliceosomal complex and propanoate metabolism in goats. Additionally, we also found common signatures of selection such as CLASP1 , PDS5B , ZNF83 , CCDC73 in sheep and goats. Haplotype and transcriptional analyses further confirmed the role of these genes in milk production and provided evidence for their analogous evolution in sheep and goats. The gene CLASP1 was identified as a target of convergent selection, representing a promising candidate for genetic improvement programs in dairy species. Conclusions These results provide insights into the genetic basis of convergent dairy traits, offering valuable targets for improving milk production and advancing dairy sheep and goat breeding programs.