Background: Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat phenotypes are pivotal in facilitating the preservation and utilization of these genetic resources. However, the total genetic diversity within a species can’t be captured by the reference genome of a single individual. The pan-genome is a collection of all the DNA sequences that occur in a species, and it is expected to capture the total genomic diversity of the specific species. Results: We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals, including 723 domestic goats and 90 samples from their wild relatives, which presented a broad regional and global representation. In total, 146 Mb sequences and 974 genes were identified as absent from the reference genome (ARS1.2; GCF_001704415.2). We identified 3,190 novel single nucleotide polymorphisms (SNPs) using the pan-genome analysis. These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives. Presence/absence variation (PAV) analysis revealed gene loss and intense negative selection during domestication and improvement. Conclusions: Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations. It reveals the changes in genomic architecture during goat domestication and improvement, such as gene loss. This improves our understanding of the evolutionary and breeding history of goats.

Background: Cashmere, valued for its exceptional softness and warmth, is a major focus in goat breeding due to its high economic importance. However, the molecular mechanisms underlying cashmere production remain largely unknown, hindering efforts to optimize yield and quality. Additionally, domestic goats exhibit remarkable adaptability to diverse climates, ranging from arid northern regions to humid southern areas, yet the genetic basis for these adaptations is poorly understood. Exploring the genetic factors driving cashmere production and climatic adaptation could provide crucial insights into trait evolution and support the development of breeding strategies for improved productivity and resilience. Methods: We utilized whole-genome resequencing data from 157 samples representing 14 goat populations to analyze the genetic diversity between cashmere and non-cashmere breeds. Additionally, we conducted the tests of selective sweeps (i.e., pairwise F_ST, θπ and XP-EHH) for cashmere traits and genome–environment association analysis (i.e., XtX statistic), respectively. Results: We identified strong selective signatures in previous reports (e.g., AKT3, FOXP1, FGF5, TGFBR3) and novel genes (e.g., ZEB1, ZNRF3, MAPK8IP3, MAPK8IP2, AXIN1) associated with cashmere traits. Further gene annotation and KEGG analyses showed that these genes were identified to be the most probable genes accounting for the cashmere traits. Also, we detected some genes such as PDGFRB, PRDM8, SLC26A2, SCAMP1, EPHX1, CDC25A, and POLK that played critical roles in the adaptation of goats to local climate variation. Conclusions: Collectively, our results provide novel insights into the genetic mechanisms underlying the cashmere traits and climatic adaptation, and also identified new genetic markers for genetic improvement in goats.

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.

The reference genome plays a crucial role in uncovering genomic variations, which increase our understanding of the molecular mechanisms influencing biological traits. However, most of the sheep reference genomes derive from a single individual, which couldn't adequately represent the genetic diversity of sheep. The map-to-pan strategy was used to construct the sheep pan-genome based on 801 samples with short read whole genome sequencing data including 724 domestic individuals from 151 sheep populations/breeds and 77 wild individuals from seven genus Ovis species, and a total of 195 Mb of nonreference sequences were assembled that absent from the ARS-UI_Ramb_v2.0 reference. MAKER2 pipeline, integrating ab initio gene prediction, RNA-Seq, and protein homology was used to annotate the nonreference sequences. As a result, a total of additional 2678 genes were predicted in the nonreference sequences. We also identified 13,317 novel single nucleotide polymorphisms (SNPs) by mapping the sequences that could not be aligned to ARS1-UI_Ramb_v2.0 to the nonreference sequences. Population genetic analysis, including principal component analysis (PCA), phylogenetic tree, and ADMIXTURE based on the novel SNPs revealed a clear phylogenetic relationship of the world's domestic sheep, as well as their close wild relatives. Additionally, pangenome-wide presence and absence variations (PAVs) analysis exhibited a decreasing trend in gene number from wildto domestic populations. Several genes, including GZMH, NFE2L3, GPR146 and CALHM6 with significant changes of presence frequencies during the evolutionary history of sheep were identified by PAV selection analysis. Functional annotation revealed that these genes were primarily associated with immune responses. Our results highlight the implications of the sheep pan-genome in identifying previously unknown genetic variations.These findings broaden our knowledge about the genetic diversity in sheep genomes, and provide insight into the domestication and breeding history of sheep.

Background: The ovary is a central female reproductive organ responsible for producing oocytes and secreting steroid hormones. To investigate the molecular similarities and potential evolutionary origins of the ovary across vertebrates, we integrated publicly available single-cell and single-nucleus transcriptomic data from nine species, including oviparous animals (fish and chicken) and viviparous mammals (mouse, rat, sheep, goat, yak, monkey, and human). Results: We generated a multi-species ovarian atlas comprising 186,748 cells and identified nine cell types. Cross-species comparative analysis identified conserved and species-specific features in granulosa cells (GCs) and stromal cells (SCs), including gene expression patterns, signaling pathways, and cell–cell communication networks. For example, proliferation-associated genes such as CKAP5 , MCM3 , and GINS1 were shared across vertebrates in GC-3, highlighting the evolutionary conservation of the molecular machinery underlying granulosa cell division. A comparison of granulosa cell subtypes further revealed species-specific gene co-expression patterns in oviparous and viviparous species, indicating adaptations for their different reproductive strategies. Stromal cells showed strong evolutionary conservation, as core extracellular matrix genes (e.g., COL6A1 , FSTL1 , ACTN1 ) were co-expressed across species in SC-1. Moreover, the conserved ligand-receptor pairs such as COL4A1-CD44, COL1A1-SDC4, LAMB1-ITGA6-ITGB1, and VEGFA-NRP2 constituted fundamental signaling axes of follicle development, while interactions such as PPIA-BSG in mouse and MDK-NCL in human were higher in these species compared with others, reflecting species-specific ovarian cell communication during evolution. Conclusions: These findings provide comprehensive insights into the molecular evolution and cellular diversity of the ovary, offering a valuable resource for understanding ovarian biology and evolutionary mechanisms.

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.